Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-19 11:11:37 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for gmapR on merida1


To the developers/maintainers of the gmapR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gmapR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 791/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gmapR 1.37.0  (landing page)
Michael Lawrence
Snapshot Date: 2022-01-18 13:55:18 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/gmapR
git_branch: master
git_last_commit: 4fda1cc
git_last_commit_date: 2021-10-26 12:03:53 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64... NOT SUPPORTED ...
palomino3Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: gmapR
Version: 1.37.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gmapR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gmapR_1.37.0.tar.gz
StartedAt: 2022-01-19 01:22:56 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 01:33:26 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 629.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: gmapR.Rcheck
Warnings: 5

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gmapR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gmapR_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/gmapR.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gmapR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gmapR’ version ‘1.37.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... WARNING
Found the following files with non-portable file names:
  src/gmap/config/lt~obsolete.m4
  src/gstruct/config/lt~obsolete.m4
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gmapR’ can be installed ... WARNING
Found the following significant warnings:
  WARNING: You don't seem to have gsnap specified.
  access.c:59:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  access.c:79:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  pair.c:2419:24: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
  pair.c:4651:17: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
  stage2.c:1329:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
  stage2.c:1812:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
  gmap.c:3244:28: warning: incompatible pointer types passing 'Diagpool_T' (aka 'struct Diagpool_T *') to parameter of type 'Cellpool_T' (aka 'struct Cellpool_T *') [-Wincompatible-pointer-types]
  gmap.c:3244:37: warning: incompatible pointer types passing 'Cellpool_T' (aka 'struct Cellpool_T *') to parameter of type 'Diagpool_T' (aka 'struct Diagpool_T *') [-Wincompatible-pointer-types]
  sarray-read.c:302:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
  sarray-read.c:368:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
  sarray-read.c:434:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
  sarray-read.c:526:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
  sarray-read.c:653:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
  sarray-read.c:2170:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types]
  sarray-read.c:2442:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2442:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2456:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2499:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2499:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2513:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2643:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2643:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2656:36: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2699:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2699:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2712:12: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:2752:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types]
  sarray-read.c:3024:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:3024:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:3038:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:3082:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:3082:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:3096:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:3217:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:3217:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:3231:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:3274:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:3274:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
  sarray-read.c:3288:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
See ‘/Users/biocbuild/bbs-3.15-bioc/meat/gmapR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 73.5Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    extdata   5.5Mb
    usr      65.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘AnnotationDbi’
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘S4Vectors:::labeledLine’
  ‘S4Vectors:::new_SimpleList_from_list’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
checkTallyConsistency: no visible binding for global variable
  ‘count.plus’
checkTallyConsistency: no visible binding for global variable
  ‘count.minus’
checkTallyConsistency: no visible binding for global variable
  ‘count.plus.ref’
checkTallyConsistency: no visible binding for global variable
  ‘count.minus.ref’
fieldNames: no visible global function definition for
  ‘R_iit_fieldNames’
newGmapAlignerParam: ... may be used in an incorrect context:
  ‘list(...)’
open.IITFile: no visible binding for global variable ‘R_iit_read’
open.IITFile: no visible global function definition for ‘resource’
typeNames: no visible global function definition for ‘R_iit_typeNames’
variantSummary: no visible binding for global variable ‘count.total’
variantSummary: no visible binding for global variable ‘count.ref’
variantSummary: no visible binding for global variable ‘count’
import,IITFile-ANY-ANY: no visible global function definition for
  ‘checkArgFormat’
import,IITFile-ANY-ANY: no visible binding for global variable
  ‘R_iit_read’
snps<-,GmapSnpDirectory-character-VCF: no visible global function
  definition for ‘rowData’
Undefined global functions or variables:
  R_iit_fieldNames R_iit_read R_iit_typeNames checkArgFormat count
  count.minus count.minus.ref count.plus count.plus.ref count.ref
  count.total resource rowData
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘GmapParam’ ‘gmap’
Undocumented S4 classes:
  ‘GmapParam’ ‘GmapAlignerParam’
Undocumented S4 methods:
  generic '[[<-' and siglist 'GmapSnpDirectory,ANY,ANY,ANY'
  generic 'as.character' and siglist 'GmapGenomeDirectory'
  generic 'bamPaths' and siglist 'GmapAlignerOutput'
  generic 'gmap' and siglist 'ANY,GmapParam'
  generic 'gmap' and siglist 'FastaFile,GmapParam'
  generic 'gmap' and siglist 'character,GmapParam'
  generic 'path' and siglist 'GmapAlignerOutput'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/libs/gmapR.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘gmapR_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/gmapR.Rcheck/00check.log’
for details.



Installation output

gmapR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gmapR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘gmapR’ ...
** using staged installation
** libs
** arch - 
cd gstruct/; \
        CFLAGS="-g -O3" \
	./configure --enable-static --disable-shared \
	            --prefix=/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr --includedir=/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include/gstruct \
	            --libdir=/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib \
	            --with-samtools-lib=/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/samtools \
		    --disable-maintainer-mode \
                    --disable-binaries
checking package version... 2017-01-01
checking whether to enable maintainer-specific portions of Makefiles... no
loading default site script ./config.site
checking CFLAGS... -g -O3
checking build system type... x86_64-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
checking target system type... x86_64-apple-darwin18.7.0
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking whether make supports nested variables... yes
checking dependency style of gcc... gcc3
checking bindir... /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin
checking whether to link statically... not specified so disabled by default
checking for a working version of perl... /usr/bin/perl
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin18.7.0 file names to x86_64-apple-darwin18.7.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin18.7.0 file names to toolchain format... func_convert_file_noop
checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for X... libraries /usr/X11/lib, headers 
checking whether -R must be followed by a space... neither works
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for qsub... no
checking gmap program directory... 
checking for get-genome... false
checking for iit_store... false
checking for iit_get... false
checking for gmap_build... false
checking for gmap... false
checking for gsnap... false
checking for sam_sort... false
checking for uniqscan... false
checking for rint in -lm... yes
checking for pthreads feature... not specified so enabled by default
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
checking for cc_r... gcc
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for working volatile... yes
checking for size_t... yes
checking for off_t... yes
checking for caddr_t... yes
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of off_t... 8
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for working mmap with MAP_FIXED... yes
checking for working mmap with MAP_VARIABLE... no
checking for MAP_FILE in mmap... yes
checking for MAP_VARIABLE in mmap... no
checking for MAP_SHARED in mmap... yes
checking for MAP_PRIVATE in mmap... yes
checking for MAP_FAILED in mmap... yes
checking for MADV_DONTNEED in madvise... yes
checking for MADV_WILLNEED in madvise... yes
checking for MADV_RANDOM in madvise... yes
checking for MADV_SEQUENTIAL in madvise... yes
checking for ceil... yes
checking for floor... yes
checking for index... yes
checking for log... yes
checking for madvise... yes
checking for memcpy... yes
checking for memmove... yes
checking for memset... yes
checking for munmap... yes
checking for pow... yes
checking for rint... yes
checking for stat64... yes
checking for strtoul... yes
checking for sysconf... yes
checking for sysctl... yes
checking for sigaction... yes
checking for struct stat64... yes
checking for pagesize via sysconf... yes
checking for pagesize via sysctl... yes
checking whether fopen accepts "b" mode... yes
checking whether fopen accepts "t" mode... yes
checking for builtin popcount/clz/ctz features... not specified so enabled by default
./configure: line 16917: ACX_BUILTIN_POPCOUNT: command not found
checking for bsr instruction in assembly... yes
checking whether sse2 is enabled... not specified so enabled by default
checking compiler is defective and requires an immediate in sse2 shift commands... no
checking whether ssse3 is enabled... not specified so enabled by default
checking whether sse4.1 is enabled... not specified so enabled by default
checking whether sse4.2 is enabled... not specified so enabled by default
checking whether avx is enabled... not specified so enabled by default
checking whether avx2 is enabled... not specified so enabled by default
checking whether simd is enabled... not specified so enabled by default
checking for x86 cpuid 0x00000001 output... 306e4:2200800:7fbee3ff:bfebfbff
checking whether mmx is enabled and supported by CPU... yes
checking whether sse is enabled and supported by CPU... yes
checking whether sse2 is enabled and supported by CPU... yes
checking whether sse3 is enabled and supported by CPU... yes
checking whether ssse3 is enabled and supported by CPU... yes
checking whether sse4.1 is enabled and supported by CPU... yes
checking whether sse4.2 is enabled and supported by CPU... yes
checking whether avx is enabled and supported by CPU... yes
checking for x86-AVX xgetbv 0x00000000 output... 7:0
checking whether avx is supported by operating system... yes
checking whether popcnt is enabled and supported by CPU... yes
checking for x86 cpuid 0x80000001 output... 0:0:1:2c100800
checking whether lzcnt is enabled and supported by CPU... no
checking for x86 cpuid 0x00000007 output... 0:0:0:0
checking whether avx2 is enabled and supported by CPU... no
checking whether bmi1 is enabled and supported by CPU... no
checking whether bmi2 is enabled and supported by CPU... no
checking whether C compiler accepts -mmmx... yes
checking for mmintrin.h header file... yes
checking whether C compiler accepts -msse... yes
checking for xmmintrin.h header file... yes
checking whether C compiler accepts -msse2... yes
checking for emmintrin.h header file... yes
checking whether C compiler accepts -msse3... yes
checking for pmmintrin.h header file... yes
checking whether C compiler accepts -mssse3... yes
checking for tmmintrin.h header file... yes
checking whether C compiler accepts -msse4.1... yes
checking for smmintrin.h header file... yes
checking whether C compiler accepts -msse4.2... yes
checking for nmmintrin.h header file... yes
checking whether C compiler accepts -mavx... yes
checking for immintrin.h header file... yes
checking gmapdb... /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share
checking whether to make binaries... disabled
checking for zlib support... enabled
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen in -lz... yes
checking for gzeof in -lz... yes
checking for gzgetc in -lz... yes
checking for gzgets in -lz... yes
checking for gzclose in -lz... yes
checking if zlib package is complete... working
checking for gzbuffer in -lz... yes
checking for samtools program... checking for samtools library... provided by --with-samtools-lib
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating lib/gstruct-1.0.pc
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING:

WARNING: You don't seem to have gsnap specified.

checking Standard compiler and flags to be used... gcc -g -O3
checking Standard linker flags to be used... 
checking pthread compiler flags to be used... -D_THREAD_SAFE 
checking popcnt compiler flags to be used... 
checking SIMD features available on computer...  mmx sse sse2 sse3 ssse3 sse4.1 sse4.2 avx
checking SIMD compiler flags to be used...  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c:83:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
KHASH_MAP_INIT_INT64(cache, cache_t)
^
samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
        KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_clear_##name(kh_##name##_t *h)                                            \
                   ^
<scratch space>:44:1: note: expanded from here
kh_clear_cache
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kstring.c -o samtools/kstring.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_aux.c -o samtools/bam_aux.o
samtools/bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, int)
^
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_clear_##name(kh_##name##_t *h)                                            \
                   ^
<scratch space>:85:1: note: expanded from here
kh_clear_s
^
samtools/bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function]
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)                           \
                   ^
<scratch space>:99:1: note: expanded from here
kh_del_s
^
samtools/bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function]
KHASH_MAP_INIT_STR(r2l, str_p)
^
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
        SCOPE kh_##name##_t *kh_init_##name() {                                                         \
                             ^
<scratch space>:106:1: note: expanded from here
kh_init_r2l
^
samtools/bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function]
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_destroy_##name(kh_##name##_t *h)                                          \
                   ^
<scratch space>:111:1: note: expanded from here
kh_destroy_r2l
^
samtools/bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function]
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_clear_##name(kh_##name##_t *h)                                            \
                   ^
<scratch space>:114:1: note: expanded from here
kh_clear_r2l
^
samtools/bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function]
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
        SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key)        \
                      ^
<scratch space>:117:1: note: expanded from here
kh_get_r2l
^
samtools/bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function]
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
        SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
                      ^
<scratch space>:123:1: note: expanded from here
kh_put_r2l
^
samtools/bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function]
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)                           \
                   ^
<scratch space>:128:1: note: expanded from here
kh_del_r2l
^
8 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam.c -o samtools/bam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_import.c -o samtools/bam_import.o
samtools/bam_import.c:20:1: warning: unused function 'kh_clear_ref' [-Wunused-function]
KHASH_MAP_INIT_STR(ref, uint64_t)
^
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_clear_##name(kh_##name##_t *h)                                            \
                   ^
<scratch space>:552:1: note: expanded from here
kh_clear_ref
^
samtools/bam_import.c:20:1: warning: unused function 'kh_get_ref' [-Wunused-function]
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
        SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key)        \
                      ^
<scratch space>:555:1: note: expanded from here
kh_get_ref
^
samtools/bam_import.c:20:1: warning: unused function 'kh_del_ref' [-Wunused-function]
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)                           \
                   ^
<scratch space>:566:1: note: expanded from here
kh_del_ref
^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam.c -o samtools/sam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c:64:1: warning: unused function 'kh_clear_i' [-Wunused-function]
KHASH_MAP_INIT_INT(i, bam_binlist_t)
^
samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
        KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_clear_##name(kh_##name##_t *h)                                            \
                   ^
<scratch space>:105:1: note: expanded from here
kh_clear_i
^
samtools/bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function]
samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
        KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)                           \
                   ^
<scratch space>:119:1: note: expanded from here
kh_del_i
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_pileup.c -o samtools/bam_pileup.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_md.c -o samtools/bam_md.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/razf.c -o samtools/razf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/faidx.c -o samtools/faidx.o
samtools/faidx.c:14:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, faidx1_t)
^
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_clear_##name(kh_##name##_t *h)                                            \
                   ^
<scratch space>:540:1: note: expanded from here
kh_clear_s
^
samtools/faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function]
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)                           \
                   ^
<scratch space>:554:1: note: expanded from here
kh_del_s
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/knetfile.c -o samtools/knetfile.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_sort.c -o samtools/bam_sort.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam_header.c -o samtools/sam_header.o
samtools/sam_header.c:10:1: warning: unused function 'kh_clear_str' [-Wunused-function]
KHASH_MAP_INIT_STR(str, const char *)
^
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_clear_##name(kh_##name##_t *h)                                            \
                   ^
<scratch space>:540:1: note: expanded from here
kh_clear_str
^
samtools/sam_header.c:10:1: warning: unused function 'kh_del_str' [-Wunused-function]
samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)                           \
                   ^
<scratch space>:554:1: note: expanded from here
kh_del_str
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_reheader.c -o samtools/bam_reheader.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kprobaln.c -o samtools/kprobaln.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/samtools_patch.c -o samtools/samtools_patch.o
ar -crus samtools/libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools/samtools_patch.o
cd gstruct; \
	make install
Making install in src
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c -o libgstruct_1.0_la-except.lo `test -f 'except.c' || echo './'`except.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c except.c -o libgstruct_1.0_la-except.o
mv -f .deps/libgstruct_1.0_la-except.Tpo .deps/libgstruct_1.0_la-except.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c -o libgstruct_1.0_la-assert.lo `test -f 'assert.c' || echo './'`assert.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c assert.c -o libgstruct_1.0_la-assert.o
mv -f .deps/libgstruct_1.0_la-assert.Tpo .deps/libgstruct_1.0_la-assert.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c -o libgstruct_1.0_la-mem.lo `test -f 'mem.c' || echo './'`mem.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c mem.c -o libgstruct_1.0_la-mem.o
mv -f .deps/libgstruct_1.0_la-mem.Tpo .deps/libgstruct_1.0_la-mem.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c -o libgstruct_1.0_la-intlist.lo `test -f 'intlist.c' || echo './'`intlist.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c intlist.c -o libgstruct_1.0_la-intlist.o
mv -f .deps/libgstruct_1.0_la-intlist.Tpo .deps/libgstruct_1.0_la-intlist.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c -o libgstruct_1.0_la-list.lo `test -f 'list.c' || echo './'`list.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c list.c -o libgstruct_1.0_la-list.o
mv -f .deps/libgstruct_1.0_la-list.Tpo .deps/libgstruct_1.0_la-list.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c -o libgstruct_1.0_la-littleendian.lo `test -f 'littleendian.c' || echo './'`littleendian.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c littleendian.c -o libgstruct_1.0_la-littleendian.o
mv -f .deps/libgstruct_1.0_la-littleendian.Tpo .deps/libgstruct_1.0_la-littleendian.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c -o libgstruct_1.0_la-bigendian.lo `test -f 'bigendian.c' || echo './'`bigendian.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c bigendian.c -o libgstruct_1.0_la-bigendian.o
mv -f .deps/libgstruct_1.0_la-bigendian.Tpo .deps/libgstruct_1.0_la-bigendian.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c -o libgstruct_1.0_la-interval.lo `test -f 'interval.c' || echo './'`interval.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c interval.c -o libgstruct_1.0_la-interval.o
mv -f .deps/libgstruct_1.0_la-interval.Tpo .deps/libgstruct_1.0_la-interval.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c -o libgstruct_1.0_la-uintlist.lo `test -f 'uintlist.c' || echo './'`uintlist.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c uintlist.c -o libgstruct_1.0_la-uintlist.o
mv -f .deps/libgstruct_1.0_la-uintlist.Tpo .deps/libgstruct_1.0_la-uintlist.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c -o libgstruct_1.0_la-stopwatch.lo `test -f 'stopwatch.c' || echo './'`stopwatch.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c stopwatch.c -o libgstruct_1.0_la-stopwatch.o
mv -f .deps/libgstruct_1.0_la-stopwatch.Tpo .deps/libgstruct_1.0_la-stopwatch.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c -o libgstruct_1.0_la-access.lo `test -f 'access.c' || echo './'`access.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c access.c -o libgstruct_1.0_la-access.o
access.c:59:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:79:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
2 warnings generated.
mv -f .deps/libgstruct_1.0_la-access.Tpo .deps/libgstruct_1.0_la-access.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c -o libgstruct_1.0_la-iit-read.lo `test -f 'iit-read.c' || echo './'`iit-read.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c iit-read.c -o libgstruct_1.0_la-iit-read.o
iit-read.c:1611:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                     ^~~~~~
iit-read.c:1611:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                            ^~~~~~~~
iit-read.c:1638:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:1638:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:1650:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:1650:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:1672:21: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,divno,offset,filesize);
                           ^~~~~~
iit-read.c:1672:28: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,divno,offset,filesize);
                                  ^~~~~~~~
iit-read.c:1693:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                     ^~~~~~
iit-read.c:1693:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                            ^~~~~~~~
iit-read.c:1742:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:1742:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:1779:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                     ^~~~~~
iit-read.c:1779:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                            ^~~~~~~~
iit-read.c:1834:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                     ^~~~~~
iit-read.c:1834:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                            ^~~~~~~~
iit-read.c:2344:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                     ^~~~~~
iit-read.c:2344:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                            ^~~~~~~~
iit-read.c:2360:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:2360:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:2372:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                         ^~~~~~
iit-read.c:2372:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                                ^~~~~~~~
iit-read.c:2381:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                         ^~~~~~
iit-read.c:2381:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                                ^~~~~~~~
iit-read.c:2408:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:2408:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:2429:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                     ^~~~~~
iit-read.c:2429:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                            ^~~~~~~~
iit-read.c:2446:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:2446:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:2466:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:2466:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:2495:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:2495:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:2608:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                     ^~~~~~
iit-read.c:2608:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                            ^~~~~~~~
iit-read.c:2626:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:2626:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:2643:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                         ^~~~~~
iit-read.c:2643:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                                ^~~~~~~~
iit-read.c:2652:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                         ^~~~~~
iit-read.c:2652:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                                ^~~~~~~~
iit-read.c:2681:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:2681:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:2702:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                     ^~~~~~
iit-read.c:2702:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                            ^~~~~~~~
iit-read.c:2719:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:2719:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:2744:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:2744:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:2770:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:2770:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:2823:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:2823:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:3010:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                     ^~~~~~
iit-read.c:3010:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                            ^~~~~~~~
iit-read.c:3026:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:3026:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:3043:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                         ^~~~~~
iit-read.c:3043:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                                ^~~~~~~~
iit-read.c:3052:12: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                         ^~~~~~
iit-read.c:3052:19: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filename,offset,filesize);
                                ^~~~~~~~
iit-read.c:3081:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:3081:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:3107:15: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                     ^~~~~~
iit-read.c:3107:22: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            filename,offset,filesize);
                            ^~~~~~~~
iit-read.c:3124:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:3124:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:3149:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:3149:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:3175:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:3175:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
iit-read.c:3220:17: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                       ^~~~~~
iit-read.c:3220:24: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filename,offset,filesize);
                              ^~~~~~~~
74 warnings generated.
mv -f .deps/libgstruct_1.0_la-iit-read.Tpo .deps/libgstruct_1.0_la-iit-read.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c -o libgstruct_1.0_la-chrom.lo `test -f 'chrom.c' || echo './'`chrom.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c chrom.c -o libgstruct_1.0_la-chrom.o
mv -f .deps/libgstruct_1.0_la-chrom.Tpo .deps/libgstruct_1.0_la-chrom.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c -o libgstruct_1.0_la-genomicpos.lo `test -f 'genomicpos.c' || echo './'`genomicpos.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c genomicpos.c -o libgstruct_1.0_la-genomicpos.o
mv -f .deps/libgstruct_1.0_la-genomicpos.Tpo .deps/libgstruct_1.0_la-genomicpos.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c -o libgstruct_1.0_la-md5.lo `test -f 'md5.c' || echo './'`md5.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c md5.c -o libgstruct_1.0_la-md5.o
mv -f .deps/libgstruct_1.0_la-md5.Tpo .deps/libgstruct_1.0_la-md5.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c -o libgstruct_1.0_la-sequence.lo `test -f 'sequence.c' || echo './'`sequence.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c sequence.c -o libgstruct_1.0_la-sequence.o
mv -f .deps/libgstruct_1.0_la-sequence.Tpo .deps/libgstruct_1.0_la-sequence.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c -o libgstruct_1.0_la-genome.lo `test -f 'genome.c' || echo './'`genome.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c genome.c -o libgstruct_1.0_la-genome.o
mv -f .deps/libgstruct_1.0_la-genome.Tpo .deps/libgstruct_1.0_la-genome.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c -o libgstruct_1.0_la-uinttable.lo `test -f 'uinttable.c' || echo './'`uinttable.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c uinttable.c -o libgstruct_1.0_la-uinttable.o
mv -f .deps/libgstruct_1.0_la-uinttable.Tpo .deps/libgstruct_1.0_la-uinttable.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c -o libgstruct_1.0_la-table.lo `test -f 'table.c' || echo './'`table.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c table.c -o libgstruct_1.0_la-table.o
mv -f .deps/libgstruct_1.0_la-table.Tpo .deps/libgstruct_1.0_la-table.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c -o libgstruct_1.0_la-chrnum.lo `test -f 'chrnum.c' || echo './'`chrnum.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c chrnum.c -o libgstruct_1.0_la-chrnum.o
mv -f .deps/libgstruct_1.0_la-chrnum.Tpo .deps/libgstruct_1.0_la-chrnum.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c -o libgstruct_1.0_la-bamread.lo `test -f 'bamread.c' || echo './'`bamread.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c bamread.c -o libgstruct_1.0_la-bamread.o
mv -f .deps/libgstruct_1.0_la-bamread.Tpo .deps/libgstruct_1.0_la-bamread.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c -o libgstruct_1.0_la-samread.lo `test -f 'samread.c' || echo './'`samread.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c samread.c -o libgstruct_1.0_la-samread.o
mv -f .deps/libgstruct_1.0_la-samread.Tpo .deps/libgstruct_1.0_la-samread.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c -o libgstruct_1.0_la-parserange.lo `test -f 'parserange.c' || echo './'`parserange.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c parserange.c -o libgstruct_1.0_la-parserange.o
mv -f .deps/libgstruct_1.0_la-parserange.Tpo .deps/libgstruct_1.0_la-parserange.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c -o libgstruct_1.0_la-tableuint.lo `test -f 'tableuint.c' || echo './'`tableuint.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c tableuint.c -o libgstruct_1.0_la-tableuint.o
mv -f .deps/libgstruct_1.0_la-tableuint.Tpo .deps/libgstruct_1.0_la-tableuint.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c -o libgstruct_1.0_la-iit-write.lo `test -f 'iit-write.c' || echo './'`iit-write.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c iit-write.c -o libgstruct_1.0_la-iit-write.o
mv -f .deps/libgstruct_1.0_la-iit-write.Tpo .deps/libgstruct_1.0_la-iit-write.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c -o libgstruct_1.0_la-ucharlist.lo `test -f 'ucharlist.c' || echo './'`ucharlist.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c ucharlist.c -o libgstruct_1.0_la-ucharlist.o
mv -f .deps/libgstruct_1.0_la-ucharlist.Tpo .deps/libgstruct_1.0_la-ucharlist.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c -o libgstruct_1.0_la-matchpool.lo `test -f 'matchpool.c' || echo './'`matchpool.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c matchpool.c -o libgstruct_1.0_la-matchpool.o
mv -f .deps/libgstruct_1.0_la-matchpool.Tpo .deps/libgstruct_1.0_la-matchpool.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c -o libgstruct_1.0_la-mismatchpool.lo `test -f 'mismatchpool.c' || echo './'`mismatchpool.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c mismatchpool.c -o libgstruct_1.0_la-mismatchpool.o
mv -f .deps/libgstruct_1.0_la-mismatchpool.Tpo .deps/libgstruct_1.0_la-mismatchpool.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c -o libgstruct_1.0_la-tally.lo `test -f 'tally.c' || echo './'`tally.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c tally.c -o libgstruct_1.0_la-tally.o
mv -f .deps/libgstruct_1.0_la-tally.Tpo .deps/libgstruct_1.0_la-tally.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c -o libgstruct_1.0_la-translation.lo `test -f 'translation.c' || echo './'`translation.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c translation.c -o libgstruct_1.0_la-translation.o
mv -f .deps/libgstruct_1.0_la-translation.Tpo .deps/libgstruct_1.0_la-translation.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c -o libgstruct_1.0_la-expr.lo `test -f 'expr.c' || echo './'`expr.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c expr.c -o libgstruct_1.0_la-expr.o
mv -f .deps/libgstruct_1.0_la-expr.Tpo .deps/libgstruct_1.0_la-expr.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c -o libgstruct_1.0_la-bamtally.lo `test -f 'bamtally.c' || echo './'`bamtally.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c bamtally.c -o libgstruct_1.0_la-bamtally.o
mv -f .deps/libgstruct_1.0_la-bamtally.Tpo .deps/libgstruct_1.0_la-bamtally.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c -o libgstruct_1.0_la-datadir.lo `test -f 'datadir.c' || echo './'`datadir.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c datadir.c -o libgstruct_1.0_la-datadir.o
mv -f .deps/libgstruct_1.0_la-datadir.Tpo .deps/libgstruct_1.0_la-datadir.Plo
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -I. -fPIC -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3   -D_THREAD_SAFE  -version-info 1:0:0  -o libgstruct-1.0.la -rpath /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib libgstruct_1.0_la-except.lo libgstruct_1.0_la-assert.lo libgstruct_1.0_la-mem.lo libgstruct_1.0_la-intlist.lo libgstruct_1.0_la-list.lo libgstruct_1.0_la-littleendian.lo libgstruct_1.0_la-bigendian.lo libgstruct_1.0_la-interval.lo libgstruct_1.0_la-uintlist.lo libgstruct_1.0_la-stopwatch.lo libgstruct_1.0_la-access.lo libgstruct_1.0_la-iit-read.lo libgstruct_1.0_la-chrom.lo libgstruct_1.0_la-genomicpos.lo libgstruct_1.0_la-md5.lo libgstruct_1.0_la-sequence.lo libgstruct_1.0_la-genome.lo libgstruct_1.0_la-uinttable.lo libgstruct_1.0_la-table.lo libgstruct_1.0_la-chrnum.lo libgstruct_1.0_la-bamread.lo libgstruct_1.0_la-samread.lo libgstruct_1.0_la-parserange.lo libgstruct_1.0_la-tableuint.lo libgstruct_1.0_la-iit-write.lo libgstruct_1.0_la-ucharlist.lo libgstruct_1.0_la-matchpool.lo libgstruct_1.0_la-mismatchpool.lo libgstruct_1.0_la-tally.lo libgstruct_1.0_la-translation.lo libgstruct_1.0_la-expr.lo libgstruct_1.0_la-bamtally.lo libgstruct_1.0_la-datadir.lo  -lz -lm 
libtool: link: ar cru .libs/libgstruct-1.0.a  libgstruct_1.0_la-except.o libgstruct_1.0_la-assert.o libgstruct_1.0_la-mem.o libgstruct_1.0_la-intlist.o libgstruct_1.0_la-list.o libgstruct_1.0_la-littleendian.o libgstruct_1.0_la-bigendian.o libgstruct_1.0_la-interval.o libgstruct_1.0_la-uintlist.o libgstruct_1.0_la-stopwatch.o libgstruct_1.0_la-access.o libgstruct_1.0_la-iit-read.o libgstruct_1.0_la-chrom.o libgstruct_1.0_la-genomicpos.o libgstruct_1.0_la-md5.o libgstruct_1.0_la-sequence.o libgstruct_1.0_la-genome.o libgstruct_1.0_la-uinttable.o libgstruct_1.0_la-table.o libgstruct_1.0_la-chrnum.o libgstruct_1.0_la-bamread.o libgstruct_1.0_la-samread.o libgstruct_1.0_la-parserange.o libgstruct_1.0_la-tableuint.o libgstruct_1.0_la-iit-write.o libgstruct_1.0_la-ucharlist.o libgstruct_1.0_la-matchpool.o libgstruct_1.0_la-mismatchpool.o libgstruct_1.0_la-tally.o libgstruct_1.0_la-translation.o libgstruct_1.0_la-expr.o libgstruct_1.0_la-bamtally.o libgstruct_1.0_la-datadir.o
libtool: link: ranlib .libs/libgstruct-1.0.a
libtool: link: ( cd ".libs" && rm -f "libgstruct-1.0.la" && ln -s "../libgstruct-1.0.la" "libgstruct-1.0.la" )
 ../config/install-sh -c -d '/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib'
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libgstruct-1.0.la '/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib'
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.la
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: install: ranlib /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
 ../config/install-sh -c -d '/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include/gstruct'
 /usr/bin/install -c -m 644 config.h fopen.h bool.h types.h except.h assert.h mem.h intlistdef.h intlist.h listdef.h list.h littleendian.h bigendian.h interval.h uintlist.h stopwatch.h access.h iitdef.h iit-read.h chrom.h genomicpos.h md5.h complement.h sequence.h genome.h uinttable.h table.h chrnum.h bamread.h samread.h parserange.h dynprog.h dynprog_nogap.h dynprog_simd.h dynprog_cigar.h dynprog_single.h tableuint.h iit-write.h ucharlist.h matchdef.h '/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include/gstruct'
 /usr/bin/install -c -m 644 matchpool.h mismatchdef.h mismatchpool.h tally.h translation.h bamtally.h datadir.h '/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include/gstruct'
 ../config/install-sh -c -d '/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig'
 /usr/bin/install -c -m 644 ../lib/gstruct-1.0.pc '/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -c bamreader.c -o bamreader.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -c bamtally.c -o bamtally.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -c iit.c -o iit.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -c variantsummary.c -o variantsummary.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -c genome.c -o genome.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_gmapR.c -o R_init_gmapR.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L/usr/local/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
cd gmap/; \
	 ./configure --with-gmapdb= --prefix=/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr \
	            --libdir=/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/lib --disable-maintainer-mode
checking package version... 2013-11-01
checking whether to enable maintainer-specific portions of Makefiles... no
checking CONFIG_SITE... ./config.site
loading script ./config.site
checking CFLAGS... not set by user so using default -O3
checking build system type... x86_64-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
checking target system type... x86_64-apple-darwin18.7.0
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking whether make supports nested variables... yes
checking dependency style of gcc... gcc3
checking bindir... /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin
checking for a working version of perl... /usr/bin/perl
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-apple-darwin18.7.0 file names to x86_64-apple-darwin18.7.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin18.7.0 file names to toolchain format... func_convert_file_noop
checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for rint in -lm... yes
checking for pthreads feature... not specified so enabled by default
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
checking for cc_r... gcc
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for working volatile... yes
checking for size_t... yes
checking for off_t... yes
checking for caddr_t... yes
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of off_t... 8
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether mmap is enabled... not specified so enabled by default
checking for working mmap with MAP_FIXED... yes
checking for working mmap with MAP_VARIABLE... no
checking for MAP_FILE in mmap... yes
checking for MAP_VARIABLE in mmap... no
checking for MAP_SHARED in mmap... yes
checking for MAP_PRIVATE in mmap... yes
checking for MAP_FAILED in mmap... yes
checking for MADV_DONTNEED in madvise... yes
checking for MADV_WILLNEED in madvise... yes
checking for MADV_RANDOM in madvise... yes
checking for MADV_SEQUENTIAL in madvise... yes
checking for ceil... yes
checking for floor... yes
checking for index... yes
checking for log... yes
checking for madvise... yes
checking for memcpy... yes
checking for memmove... yes
checking for memset... yes
checking for munmap... yes
checking for pow... yes
checking for rint... yes
checking for stat64... yes
checking for strtoul... yes
checking for sysconf... yes
checking for sysctl... yes
checking for sigaction... yes
checking for struct stat64... yes
checking for pagesize via sysconf... yes
checking for pagesize via sysctl... yes
checking whether fopen accepts "b" mode... yes
checking whether fopen accepts "t" mode... yes
checking for popcnt feature... not specified so enabled by default
checking for __builtin_popcount... yes
checking for __builtin_clz... yes
checking for __builtin_ctz... yes
checking for bsr instruction in assembly... yes
checking whether sse2 is enabled... not specified so enabled by default
checking whether user has declared a defective SSE2 compiler... no
checking whether sse4.1 is enabled... not specified so enabled by default
checking whether simd is enabled... not specified so enabled by default
checking for x86 cpuid 0x00000001 output... 306e4:2200800:7fbee3ff:bfebfbff
checking whether mmx is enabled and supported... yes
checking whether sse is enabled and supported... yes
checking whether sse2 is enabled and supported... yes
checking whether sse3 is enabled and supported... yes
checking whether ssse3 is enabled and supported... yes
checking whether sse4.1 is enabled and supported... yes
checking whether sse4.2 is enabled and supported... yes
checking whether avx is enabled and supported... yes
checking whether C compiler accepts -mmmx... yes
checking whether C compiler accepts -msse... yes
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -msse3... yes
checking whether C compiler accepts -mssse3... yes
checking whether C compiler accepts -msse4.1... yes
checking whether C compiler accepts -msse4.2... yes
checking whether C compiler accepts -mavx... yes
checking gmapdb... /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share
checking MAX_READLENGTH... 250
checking for zlib support... enabled
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen in -lz... yes
checking for gzeof in -lz... yes
checking for gzgetc in -lz... yes
checking for gzgets in -lz... yes
checking for gzclose in -lz... yes
checking if zlib package is complete... working
checking for gzbuffer in -lz... yes
checking for bzlib support... enabled
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking for BZ2_bzReadOpen in -lbz2... yes
checking for BZ2_bzRead in -lbz2... yes
checking for BZ2_bzReadClose in -lbz2... yes
checking if bzlib package is complete... working
checking for goby library... disabled
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating util/Makefile
config.status: creating util/gmap_compress.pl
config.status: creating util/gmap_uncompress.pl
config.status: creating util/gmap_process.pl
config.status: creating util/gmap_setup.pl
config.status: creating util/gmap_build.pl
config.status: creating util/gmap_reassemble.pl
config.status: creating util/md_coords.pl
config.status: creating util/fa_coords.pl
config.status: creating util/psl_splicesites.pl
config.status: creating util/psl_introns.pl
config.status: creating util/psl_genes.pl
config.status: creating util/gtf_splicesites.pl
config.status: creating util/gtf_introns.pl
config.status: creating util/gtf_genes.pl
config.status: creating util/gff3_splicesites.pl
config.status: creating util/gff3_introns.pl
config.status: creating util/gff3_genes.pl
config.status: creating util/dbsnp_iit.pl
config.status: creating util/gvf_iit.pl
config.status: creating util/vcf_iit.pl
config.status: creating tests/Makefile
config.status: creating tests/align.test
config.status: creating tests/coords1.test
config.status: creating tests/setup1.test
config.status: creating tests/iit.test
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
cd gmap; \
	make install
Making install in src
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-except.o -MD -MP -MF .deps/gmap-except.Tpo -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gmap-except.Tpo .deps/gmap-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-assert.o -MD -MP -MF .deps/gmap-assert.Tpo -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gmap-assert.Tpo .deps/gmap-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-mem.o -MD -MP -MF .deps/gmap-mem.Tpo -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gmap-mem.Tpo .deps/gmap-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intlist.o -MD -MP -MF .deps/gmap-intlist.Tpo -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gmap-intlist.Tpo .deps/gmap-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-list.o -MD -MP -MF .deps/gmap-list.Tpo -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gmap-list.Tpo .deps/gmap-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-littleendian.o -MD -MP -MF .deps/gmap-littleendian.Tpo -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/gmap-littleendian.Tpo .deps/gmap-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bigendian.o -MD -MP -MF .deps/gmap-bigendian.Tpo -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/gmap-bigendian.Tpo .deps/gmap-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-univinterval.o -MD -MP -MF .deps/gmap-univinterval.Tpo -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %u
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %u
2 warnings generated.
mv -f .deps/gmap-univinterval.Tpo .deps/gmap-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-interval.o -MD -MP -MF .deps/gmap-interval.Tpo -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gmap-interval.Tpo .deps/gmap-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uintlist.o -MD -MP -MF .deps/gmap-uintlist.Tpo -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gmap-uintlist.Tpo .deps/gmap-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stopwatch.o -MD -MP -MF .deps/gmap-stopwatch.Tpo -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gmap-stopwatch.Tpo .deps/gmap-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-access.o -MD -MP -MF .deps/gmap-access.Tpo -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/gmap-access.Tpo .deps/gmap-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read-univ.o -MD -MP -MF .deps/gmap-iit-read-univ.Tpo -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %u
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %u
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %u
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %u
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %u
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %u
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %u
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %u
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %u
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %u
10 warnings generated.
mv -f .deps/gmap-iit-read-univ.Tpo .deps/gmap-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read.o -MD -MP -MF .deps/gmap-iit-read.Tpo -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/gmap-iit-read.Tpo .deps/gmap-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-md5.o -MD -MP -MF .deps/gmap-md5.Tpo -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gmap-md5.Tpo .deps/gmap-md5.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bzip2.o -MD -MP -MF .deps/gmap-bzip2.Tpo -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/gmap-bzip2.Tpo .deps/gmap-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-sequence.o -MD -MP -MF .deps/gmap-sequence.Tpo -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gmap-sequence.Tpo .deps/gmap-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-reader.o -MD -MP -MF .deps/gmap-reader.Tpo -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/gmap-reader.Tpo .deps/gmap-reader.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genomicpos.o -MD -MP -MF .deps/gmap-genomicpos.Tpo -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gmap-genomicpos.Tpo .deps/gmap-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress.o -MD -MP -MF .deps/gmap-compress.Tpo -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gmap-compress.Tpo .deps/gmap-compress.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress-write.o -MD -MP -MF .deps/gmap-compress-write.Tpo -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
                                                                     ~~~              ^~~~~~~~~~
                                                                     %u
compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
3 warnings generated.
mv -f .deps/gmap-compress-write.Tpo .deps/gmap-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gbuffer.o -MD -MP -MF .deps/gmap-gbuffer.Tpo -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
mv -f .deps/gmap-gbuffer.Tpo .deps/gmap-gbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome.o -MD -MP -MF .deps/gmap-genome.Tpo -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %u
genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %u
genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %u
genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %u
4 warnings generated.
mv -f .deps/gmap-genome.Tpo .deps/gmap-genome.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_hr.o -MD -MP -MF .deps/gmap-genome_hr.Tpo -c -o gmap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gmap-genome_hr.Tpo .deps/gmap-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_sites.o -MD -MP -MF .deps/gmap-genome_sites.Tpo -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
mv -f .deps/gmap-genome_sites.Tpo .deps/gmap-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome-write.o -MD -MP -MF .deps/gmap-genome-write.Tpo -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
genome-write.c:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
                  accession,startposition,endposition,fileroot);
                            ^~~~~~~~~~~~~
genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
                  accession,startposition,endposition,fileroot);
                                          ^~~~~~~~~~~
genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                            ^~~~~~~~~~~~~~~~
genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                                             ^~~~~~~~~~~~~~
genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
                  accession,startposition,endposition,fileroot);
                            ^~~~~~~~~~~~~
genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
                  accession,startposition,endposition,fileroot);
                                          ^~~~~~~~~~~
genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                            ^~~~~~~~~~~~~~~~
genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                                             ^~~~~~~~~~~~~~
genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                          ~~~                         ^~~~~~~~~~~~~~~~
                                                          %u
genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                               ~~~                                     ^~~~~~~~~~~~~~
                                                               %u
genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                                      ~~~                                             ^~~~~~~~~~~~~~~~~
                                                                      %u
genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                                           ~~~                                                          ^~~~~~~~~~~~~~~
                                                                           %u
genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
                  accession,startposition,endposition,fileroot);
                            ^~~~~~~~~~~~~
genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
                  accession,startposition,endposition,fileroot);
                                          ^~~~~~~~~~~
genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                            ^~~~~~~~~~~~~~~~
genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                                             ^~~~~~~~~~~~~~
genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
  fprintf(stderr,"Genome length is %lu nt\n",genomelength);
                                   ~~~       ^~~~~~~~~~~~
                                   %u
17 warnings generated.
mv -f .deps/gmap-genome-write.Tpo .deps/gmap-genome-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bitpack64-read.o -MD -MP -MF .deps/gmap-bitpack64-read.Tpo -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/gmap-bitpack64-read.Tpo .deps/gmap-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb.o -MD -MP -MF .deps/gmap-indexdb.Tpo -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                     ^~~~~~~~
indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
            ^~~
indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
                                    ^~~~~~
indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
7 warnings generated.
mv -f .deps/gmap-indexdb.Tpo .deps/gmap-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb_hr.o -MD -MP -MF .deps/gmap-indexdb_hr.Tpo -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
mv -f .deps/gmap-indexdb_hr.Tpo .deps/gmap-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligo.o -MD -MP -MF .deps/gmap-oligo.Tpo -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/gmap-oligo.Tpo .deps/gmap-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-block.o -MD -MP -MF .deps/gmap-block.Tpo -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c
mv -f .deps/gmap-block.Tpo .deps/gmap-block.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrom.o -MD -MP -MF .deps/gmap-chrom.Tpo -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gmap-chrom.Tpo .deps/gmap-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-segmentpos.o -MD -MP -MF .deps/gmap-segmentpos.Tpo -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
mv -f .deps/gmap-segmentpos.Tpo .deps/gmap-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrnum.o -MD -MP -MF .deps/gmap-chrnum.Tpo -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/gmap-chrnum.Tpo .deps/gmap-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrsubset.o -MD -MP -MF .deps/gmap-chrsubset.Tpo -c -o gmap-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c
mv -f .deps/gmap-chrsubset.Tpo .deps/gmap-chrsubset.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uinttable.o -MD -MP -MF .deps/gmap-uinttable.Tpo -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c
mv -f .deps/gmap-uinttable.Tpo .deps/gmap-uinttable.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gregion.o -MD -MP -MF .deps/gmap-gregion.Tpo -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c
mv -f .deps/gmap-gregion.Tpo .deps/gmap-gregion.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-match.o -MD -MP -MF .deps/gmap-match.Tpo -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c
mv -f .deps/gmap-match.Tpo .deps/gmap-match.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-matchpool.o -MD -MP -MF .deps/gmap-matchpool.Tpo -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c
mv -f .deps/gmap-matchpool.Tpo .deps/gmap-matchpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagnostic.o -MD -MP -MF .deps/gmap-diagnostic.Tpo -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c
mv -f .deps/gmap-diagnostic.Tpo .deps/gmap-diagnostic.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage1.o -MD -MP -MF .deps/gmap-stage1.Tpo -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c
mv -f .deps/gmap-stage1.Tpo .deps/gmap-stage1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diag.o -MD -MP -MF .deps/gmap-diag.Tpo -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/gmap-diag.Tpo .deps/gmap-diag.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagpool.o -MD -MP -MF .deps/gmap-diagpool.Tpo -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/gmap-diagpool.Tpo .deps/gmap-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cmet.o -MD -MP -MF .deps/gmap-cmet.Tpo -c -o gmap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/gmap-cmet.Tpo .deps/gmap-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-atoi.o -MD -MP -MF .deps/gmap-atoi.Tpo -c -o gmap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/gmap-atoi.Tpo .deps/gmap-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-orderstat.o -MD -MP -MF .deps/gmap-orderstat.Tpo -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/gmap-orderstat.Tpo .deps/gmap-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligoindex_hr.o -MD -MP -MF .deps/gmap-oligoindex_hr.Tpo -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/gmap-oligoindex_hr.Tpo .deps/gmap-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intron.o -MD -MP -MF .deps/gmap-intron.Tpo -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/gmap-intron.Tpo .deps/gmap-intron.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent.o -MD -MP -MF .deps/gmap-maxent.Tpo -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/gmap-maxent.Tpo .deps/gmap-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent_hr.o -MD -MP -MF .deps/gmap-maxent_hr.Tpo -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/gmap-maxent_hr.Tpo .deps/gmap-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pair.o -MD -MP -MF .deps/gmap-pair.Tpo -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c
pair.c:2419:24: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^
pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^
pair.c:4651:17: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^
pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^~~
2 warnings generated.
mv -f .deps/gmap-pair.Tpo .deps/gmap-pair.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pairpool.o -MD -MP -MF .deps/gmap-pairpool.Tpo -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/gmap-pairpool.Tpo .deps/gmap-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cellpool.o -MD -MP -MF .deps/gmap-cellpool.Tpo -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/gmap-cellpool.Tpo .deps/gmap-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage2.o -MD -MP -MF .deps/gmap-stage2.Tpo -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
stage2.c:1329:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
stage2.c:1812:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
2 warnings generated.
mv -f .deps/gmap-stage2.Tpo .deps/gmap-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-doublelist.o -MD -MP -MF .deps/gmap-doublelist.Tpo -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/gmap-doublelist.Tpo .deps/gmap-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-smooth.o -MD -MP -MF .deps/gmap-smooth.Tpo -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/gmap-smooth.Tpo .deps/gmap-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicestringpool.o -MD -MP -MF .deps/gmap-splicestringpool.Tpo -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/gmap-splicestringpool.Tpo .deps/gmap-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie_build.o -MD -MP -MF .deps/gmap-splicetrie_build.Tpo -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
mv -f .deps/gmap-splicetrie_build.Tpo .deps/gmap-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie.o -MD -MP -MF .deps/gmap-splicetrie.Tpo -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/gmap-splicetrie.Tpo .deps/gmap-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-boyer-moore.o -MD -MP -MF .deps/gmap-boyer-moore.Tpo -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/gmap-boyer-moore.Tpo .deps/gmap-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-dynprog.o -MD -MP -MF .deps/gmap-dynprog.Tpo -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/gmap-dynprog.Tpo .deps/gmap-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-translation.o -MD -MP -MF .deps/gmap-translation.Tpo -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/gmap-translation.Tpo .deps/gmap-translation.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pbinom.o -MD -MP -MF .deps/gmap-pbinom.Tpo -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/gmap-pbinom.Tpo .deps/gmap-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-changepoint.o -MD -MP -MF .deps/gmap-changepoint.Tpo -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/gmap-changepoint.Tpo .deps/gmap-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage3.o -MD -MP -MF .deps/gmap-stage3.Tpo -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/gmap-stage3.Tpo .deps/gmap-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-request.o -MD -MP -MF .deps/gmap-request.Tpo -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c
mv -f .deps/gmap-request.Tpo .deps/gmap-request.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-result.o -MD -MP -MF .deps/gmap-result.Tpo -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c
mv -f .deps/gmap-result.Tpo .deps/gmap-result.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-inbuffer.o -MD -MP -MF .deps/gmap-inbuffer.Tpo -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
mv -f .deps/gmap-inbuffer.Tpo .deps/gmap-inbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-samheader.o -MD -MP -MF .deps/gmap-samheader.Tpo -c -o gmap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
mv -f .deps/gmap-samheader.Tpo .deps/gmap-samheader.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-outbuffer.o -MD -MP -MF .deps/gmap-outbuffer.Tpo -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
mv -f .deps/gmap-outbuffer.Tpo .deps/gmap-outbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chimera.o -MD -MP -MF .deps/gmap-chimera.Tpo -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/gmap-chimera.Tpo .deps/gmap-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-datadir.o -MD -MP -MF .deps/gmap-datadir.Tpo -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gmap-datadir.Tpo .deps/gmap-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt.o -MD -MP -MF .deps/gmap-getopt.Tpo -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gmap-getopt.Tpo .deps/gmap-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt1.o -MD -MP -MF .deps/gmap-getopt1.Tpo -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gmap-getopt1.Tpo .deps/gmap-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gmap.o -MD -MP -MF .deps/gmap-gmap.Tpo -c -o gmap-gmap.o `test -f 'gmap.c' || echo './'`gmap.c
gmap.c:3244:28: warning: incompatible pointer types passing 'Diagpool_T' (aka 'struct Diagpool_T *') to parameter of type 'Cellpool_T' (aka 'struct Cellpool_T *') [-Wincompatible-pointer-types]
                                                  matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
                                                                     ^~~~~~~~
gmap.c:2672:61: note: passing argument to parameter 'cellpool' here
                          Matchpool_T matchpool, Pairpool_T pairpool, Cellpool_T cellpool,
                                                                                 ^
gmap.c:3244:37: warning: incompatible pointer types passing 'Cellpool_T' (aka 'struct Cellpool_T *') to parameter of type 'Diagpool_T' (aka 'struct Diagpool_T *') [-Wincompatible-pointer-types]
                                                  matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
                                                                              ^~~~~~~~
gmap.c:2673:17: note: passing argument to parameter 'diagpool' here
                          Diagpool_T diagpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) {
                                     ^
2 warnings generated.
mv -f .deps/gmap-gmap.Tpo .deps/gmap-gmap.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3    -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o  -lz -lbz2 -lm 
libtool: link: gcc -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o  -lz -lbz2 -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-except.o -MD -MP -MF .deps/gmapl-except.Tpo -c -o gmapl-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gmapl-except.Tpo .deps/gmapl-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-assert.o -MD -MP -MF .deps/gmapl-assert.Tpo -c -o gmapl-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gmapl-assert.Tpo .deps/gmapl-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-mem.o -MD -MP -MF .deps/gmapl-mem.Tpo -c -o gmapl-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gmapl-mem.Tpo .deps/gmapl-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-intlist.o -MD -MP -MF .deps/gmapl-intlist.Tpo -c -o gmapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gmapl-intlist.Tpo .deps/gmapl-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-list.o -MD -MP -MF .deps/gmapl-list.Tpo -c -o gmapl-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gmapl-list.Tpo .deps/gmapl-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-littleendian.o -MD -MP -MF .deps/gmapl-littleendian.Tpo -c -o gmapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/gmapl-littleendian.Tpo .deps/gmapl-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bigendian.o -MD -MP -MF .deps/gmapl-bigendian.Tpo -c -o gmapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/gmapl-bigendian.Tpo .deps/gmapl-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-univinterval.o -MD -MP -MF .deps/gmapl-univinterval.Tpo -c -o gmapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %llu
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %llu
2 warnings generated.
mv -f .deps/gmapl-univinterval.Tpo .deps/gmapl-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-interval.o -MD -MP -MF .deps/gmapl-interval.Tpo -c -o gmapl-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gmapl-interval.Tpo .deps/gmapl-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-uintlist.o -MD -MP -MF .deps/gmapl-uintlist.Tpo -c -o gmapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gmapl-uintlist.Tpo .deps/gmapl-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stopwatch.o -MD -MP -MF .deps/gmapl-stopwatch.Tpo -c -o gmapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gmapl-stopwatch.Tpo .deps/gmapl-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-access.o -MD -MP -MF .deps/gmapl-access.Tpo -c -o gmapl-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/gmapl-access.Tpo .deps/gmapl-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-iit-read-univ.o -MD -MP -MF .deps/gmapl-iit-read-univ.Tpo -c -o gmapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %llu
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %llu
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %llu
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %llu
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %llu
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %llu
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %llu
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %llu
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %llu
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %llu
10 warnings generated.
mv -f .deps/gmapl-iit-read-univ.Tpo .deps/gmapl-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-iit-read.o -MD -MP -MF .deps/gmapl-iit-read.Tpo -c -o gmapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/gmapl-iit-read.Tpo .deps/gmapl-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-md5.o -MD -MP -MF .deps/gmapl-md5.Tpo -c -o gmapl-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gmapl-md5.Tpo .deps/gmapl-md5.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bzip2.o -MD -MP -MF .deps/gmapl-bzip2.Tpo -c -o gmapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/gmapl-bzip2.Tpo .deps/gmapl-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-sequence.o -MD -MP -MF .deps/gmapl-sequence.Tpo -c -o gmapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gmapl-sequence.Tpo .deps/gmapl-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-reader.o -MD -MP -MF .deps/gmapl-reader.Tpo -c -o gmapl-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/gmapl-reader.Tpo .deps/gmapl-reader.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genomicpos.o -MD -MP -MF .deps/gmapl-genomicpos.Tpo -c -o gmapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gmapl-genomicpos.Tpo .deps/gmapl-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-compress.o -MD -MP -MF .deps/gmapl-compress.Tpo -c -o gmapl-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gmapl-compress.Tpo .deps/gmapl-compress.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-compress-write.o -MD -MP -MF .deps/gmapl-compress-write.Tpo -c -o gmapl-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
                                                                     ~~~              ^~~~~~~~~~
                                                                     %llu
compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
3 warnings generated.
mv -f .deps/gmapl-compress-write.Tpo .deps/gmapl-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gbuffer.o -MD -MP -MF .deps/gmapl-gbuffer.Tpo -c -o gmapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
mv -f .deps/gmapl-gbuffer.Tpo .deps/gmapl-gbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome.o -MD -MP -MF .deps/gmapl-genome.Tpo -c -o gmapl-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
4 warnings generated.
mv -f .deps/gmapl-genome.Tpo .deps/gmapl-genome.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome_hr.o -MD -MP -MF .deps/gmapl-genome_hr.Tpo -c -o gmapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gmapl-genome_hr.Tpo .deps/gmapl-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome_sites.o -MD -MP -MF .deps/gmapl-genome_sites.Tpo -c -o gmapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
genome_sites.c:24729:17: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  printf("%u\t",startblock/3*32U);
          ~~    ^~~~~~~~~~~~~~~~
          %llu
genome_sites.c:24744:19: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    printf("%u\t",ptr/3*32U);
            ~~    ^~~~~~~~~
            %llu
genome_sites.c:24751:17: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  printf("%u\t",(endblock+3)/3*32U);
          ~~    ^~~~~~~~~~~~~~~~~~
          %llu
3 warnings generated.
mv -f .deps/gmapl-genome_sites.Tpo .deps/gmapl-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome-write.o -MD -MP -MF .deps/gmapl-genome-write.Tpo -c -o gmapl-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
genome-write.c:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                            ^~~~~~~~~~~~~
genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                                          ^~~~~~~~~~~
genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                            ^~~~~~~~~~~~~~~~
genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                                             ^~~~~~~~~~~~~~
genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                            ^~~~~~~~~~~~~
genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                                          ^~~~~~~~~~~
genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                            ^~~~~~~~~~~~~~~~
genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                                             ^~~~~~~~~~~~~~
genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                          ~~~                         ^~~~~~~~~~~~~~~~
                                                          %llu
genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                               ~~~                                     ^~~~~~~~~~~~~~
                                                               %llu
genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                                      ~~~                                             ^~~~~~~~~~~~~~~~~
                                                                      %llu
genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                                           ~~~                                                          ^~~~~~~~~~~~~~~
                                                                           %llu
genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                            ^~~~~~~~~~~~~
genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                                          ^~~~~~~~~~~
genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                            ^~~~~~~~~~~~~~~~
genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                                             ^~~~~~~~~~~~~~
genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  fprintf(stderr,"Genome length is %lu nt\n",genomelength);
                                   ~~~       ^~~~~~~~~~~~
                                   %llu
17 warnings generated.
mv -f .deps/gmapl-genome-write.Tpo .deps/gmapl-genome-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bitpack64-read.o -MD -MP -MF .deps/gmapl-bitpack64-read.Tpo -c -o gmapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/gmapl-bitpack64-read.Tpo .deps/gmapl-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-indexdb.o -MD -MP -MF .deps/gmapl-indexdb.Tpo -c -o gmapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                     ^~~~~~~~
indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
            ^~~
indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
                                    ^~~~~~
indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
7 warnings generated.
mv -f .deps/gmapl-indexdb.Tpo .deps/gmapl-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-indexdb_hr.o -MD -MP -MF .deps/gmapl-indexdb_hr.Tpo -c -o gmapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c:1008:43: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
      printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm);
                             ~~           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
                             %llu
indexdb_hr.c:1232:45: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("#%d--%d:%u  ",i,batch->nentries,batch->position);
                    ~~                      ^~~~~~~~~~~~~~~
                    %llu
2 warnings generated.
mv -f .deps/gmapl-indexdb_hr.Tpo .deps/gmapl-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-oligo.o -MD -MP -MF .deps/gmapl-oligo.Tpo -c -o gmapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/gmapl-oligo.Tpo .deps/gmapl-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-block.o -MD -MP -MF .deps/gmapl-block.Tpo -c -o gmapl-block.o `test -f 'block.c' || echo './'`block.c
mv -f .deps/gmapl-block.Tpo .deps/gmapl-block.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrom.o -MD -MP -MF .deps/gmapl-chrom.Tpo -c -o gmapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gmapl-chrom.Tpo .deps/gmapl-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-segmentpos.o -MD -MP -MF .deps/gmapl-segmentpos.Tpo -c -o gmapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
segmentpos.c:90:41: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length);
                  ~~                    ^~~~~~~~~~~~~~~~~~~~~~~
                  %llu
1 warning generated.
mv -f .deps/gmapl-segmentpos.Tpo .deps/gmapl-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrnum.o -MD -MP -MF .deps/gmapl-chrnum.Tpo -c -o gmapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/gmapl-chrnum.Tpo .deps/gmapl-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrsubset.o -MD -MP -MF .deps/gmapl-chrsubset.Tpo -c -o gmapl-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c
mv -f .deps/gmapl-chrsubset.Tpo .deps/gmapl-chrsubset.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-uinttable.o -MD -MP -MF .deps/gmapl-uinttable.Tpo -c -o gmapl-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c
mv -f .deps/gmapl-uinttable.Tpo .deps/gmapl-uinttable.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gregion.o -MD -MP -MF .deps/gmapl-gregion.Tpo -c -o gmapl-gregion.o `test -f 'gregion.c' || echo './'`gregion.c
mv -f .deps/gmapl-gregion.Tpo .deps/gmapl-gregion.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-match.o -MD -MP -MF .deps/gmapl-match.Tpo -c -o gmapl-match.o `test -f 'match.c' || echo './'`match.c
mv -f .deps/gmapl-match.Tpo .deps/gmapl-match.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-matchpool.o -MD -MP -MF .deps/gmapl-matchpool.Tpo -c -o gmapl-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c
mv -f .deps/gmapl-matchpool.Tpo .deps/gmapl-matchpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diagnostic.o -MD -MP -MF .deps/gmapl-diagnostic.Tpo -c -o gmapl-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c
mv -f .deps/gmapl-diagnostic.Tpo .deps/gmapl-diagnostic.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage1.o -MD -MP -MF .deps/gmapl-stage1.Tpo -c -o gmapl-stage1.o `test -f 'stage1.c' || echo './'`stage1.c
mv -f .deps/gmapl-stage1.Tpo .deps/gmapl-stage1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diag.o -MD -MP -MF .deps/gmapl-diag.Tpo -c -o gmapl-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/gmapl-diag.Tpo .deps/gmapl-diag.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diagpool.o -MD -MP -MF .deps/gmapl-diagpool.Tpo -c -o gmapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/gmapl-diagpool.Tpo .deps/gmapl-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-cmet.o -MD -MP -MF .deps/gmapl-cmet.Tpo -c -o gmapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/gmapl-cmet.Tpo .deps/gmapl-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-atoi.o -MD -MP -MF .deps/gmapl-atoi.Tpo -c -o gmapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/gmapl-atoi.Tpo .deps/gmapl-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-orderstat.o -MD -MP -MF .deps/gmapl-orderstat.Tpo -c -o gmapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/gmapl-orderstat.Tpo .deps/gmapl-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-oligoindex_hr.o -MD -MP -MF .deps/gmapl-oligoindex_hr.Tpo -c -o gmapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/gmapl-oligoindex_hr.Tpo .deps/gmapl-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-intron.o -MD -MP -MF .deps/gmapl-intron.Tpo -c -o gmapl-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/gmapl-intron.Tpo .deps/gmapl-intron.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-maxent.o -MD -MP -MF .deps/gmapl-maxent.Tpo -c -o gmapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/gmapl-maxent.Tpo .deps/gmapl-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-maxent_hr.o -MD -MP -MF .deps/gmapl-maxent_hr.Tpo -c -o gmapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/gmapl-maxent_hr.Tpo .deps/gmapl-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pair.o -MD -MP -MF .deps/gmapl-pair.Tpo -c -o gmapl-pair.o `test -f 'pair.c' || echo './'`pair.c
pair.c:546:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:573:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:600:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:607:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:1273:3: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                chroffset + this->genomepos + ONEBASEDP,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pair.c:1278:3: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                chroffset + this->genomepos + ONEBASEDP,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pair.c:1790:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                        ~~     ^~~~~~~~~~~~~~~~~~~~~~~~~~
                        %llu
pair.c:1790:52: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                           ~~                             ^~~~~~~~~~~~~~~~~~~~~~~~
                           %llu
pair.c:1799:27: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                         ~~      ^~~~~~~~~~~~~~~~~~~~~~~~~~
                         %llu
pair.c:1799:54: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                            ~~                              ^~~~~~~~~~~~~~~~~~~~~~~~
                            %llu
pair.c:1913:26: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                  ~~     ^~~~~~~~~~~~~~~~~~~~~~~~~~
                  %llu
pair.c:1913:53: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                     ~~                             ^~~~~~~~~~~~~~~~~~~~~~~~
                     %llu
pair.c:1922:28: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                   ~~      ^~~~~~~~~~~~~~~~~~~~~~~~~~
                   %llu
pair.c:1922:55: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                      ~~                              ^~~~~~~~~~~~~~~~~~~~~~~~
                      %llu
pair.c:2419:24: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^
pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^
pair.c:4651:17: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^
pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^~~
pair.c:6986:24: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP);
               ~~      ^~~~~~~~~~~~~~~~~~~~~
               %llu
pair.c:6986:51: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP);
                   ~~                             ^~~~~~~~~~~~~~~~~~~~~
                   %llu
18 warnings generated.
mv -f .deps/gmapl-pair.Tpo .deps/gmapl-pair.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pairpool.o -MD -MP -MF .deps/gmapl-pairpool.Tpo -c -o gmapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/gmapl-pairpool.Tpo .deps/gmapl-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-cellpool.o -MD -MP -MF .deps/gmapl-cellpool.Tpo -c -o gmapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/gmapl-cellpool.Tpo .deps/gmapl-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage2.o -MD -MP -MF .deps/gmapl-stage2.Tpo -c -o gmapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
stage2.c:1329:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
stage2.c:1812:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
2 warnings generated.
mv -f .deps/gmapl-stage2.Tpo .deps/gmapl-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-doublelist.o -MD -MP -MF .deps/gmapl-doublelist.Tpo -c -o gmapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/gmapl-doublelist.Tpo .deps/gmapl-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-smooth.o -MD -MP -MF .deps/gmapl-smooth.Tpo -c -o gmapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/gmapl-smooth.Tpo .deps/gmapl-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicestringpool.o -MD -MP -MF .deps/gmapl-splicestringpool.Tpo -c -o gmapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/gmapl-splicestringpool.Tpo .deps/gmapl-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicetrie_build.o -MD -MP -MF .deps/gmapl-splicetrie_build.Tpo -c -o gmapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
splicetrie_build.c:132:31: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%d %u",(int) leaf,position);
               ~~             ^~~~~~~~
               %llu
splicetrie_build.c:146:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
      printf("%d %u",(int) leaf,position);
                 ~~             ^~~~~~~~
                 %llu
2 warnings generated.
mv -f .deps/gmapl-splicetrie_build.Tpo .deps/gmapl-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicetrie.o -MD -MP -MF .deps/gmapl-splicetrie.Tpo -c -o gmapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/gmapl-splicetrie.Tpo .deps/gmapl-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-boyer-moore.o -MD -MP -MF .deps/gmapl-boyer-moore.Tpo -c -o gmapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/gmapl-boyer-moore.Tpo .deps/gmapl-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-dynprog.o -MD -MP -MF .deps/gmapl-dynprog.Tpo -c -o gmapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/gmapl-dynprog.Tpo .deps/gmapl-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-translation.o -MD -MP -MF .deps/gmapl-translation.Tpo -c -o gmapl-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/gmapl-translation.Tpo .deps/gmapl-translation.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pbinom.o -MD -MP -MF .deps/gmapl-pbinom.Tpo -c -o gmapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/gmapl-pbinom.Tpo .deps/gmapl-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-changepoint.o -MD -MP -MF .deps/gmapl-changepoint.Tpo -c -o gmapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/gmapl-changepoint.Tpo .deps/gmapl-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage3.o -MD -MP -MF .deps/gmapl-stage3.Tpo -c -o gmapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/gmapl-stage3.Tpo .deps/gmapl-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-request.o -MD -MP -MF .deps/gmapl-request.Tpo -c -o gmapl-request.o `test -f 'request.c' || echo './'`request.c
mv -f .deps/gmapl-request.Tpo .deps/gmapl-request.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-result.o -MD -MP -MF .deps/gmapl-result.Tpo -c -o gmapl-result.o `test -f 'result.c' || echo './'`result.c
mv -f .deps/gmapl-result.Tpo .deps/gmapl-result.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-inbuffer.o -MD -MP -MF .deps/gmapl-inbuffer.Tpo -c -o gmapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
mv -f .deps/gmapl-inbuffer.Tpo .deps/gmapl-inbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-samheader.o -MD -MP -MF .deps/gmapl-samheader.Tpo -c -o gmapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
mv -f .deps/gmapl-samheader.Tpo .deps/gmapl-samheader.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-outbuffer.o -MD -MP -MF .deps/gmapl-outbuffer.Tpo -c -o gmapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
mv -f .deps/gmapl-outbuffer.Tpo .deps/gmapl-outbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chimera.o -MD -MP -MF .deps/gmapl-chimera.Tpo -c -o gmapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/gmapl-chimera.Tpo .deps/gmapl-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-datadir.o -MD -MP -MF .deps/gmapl-datadir.Tpo -c -o gmapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gmapl-datadir.Tpo .deps/gmapl-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-getopt.o -MD -MP -MF .deps/gmapl-getopt.Tpo -c -o gmapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gmapl-getopt.Tpo .deps/gmapl-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-getopt1.o -MD -MP -MF .deps/gmapl-getopt1.Tpo -c -o gmapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gmapl-getopt1.Tpo .deps/gmapl-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gmap.o -MD -MP -MF .deps/gmapl-gmap.Tpo -c -o gmapl-gmap.o `test -f 'gmap.c' || echo './'`gmap.c
gmap.c:3244:28: warning: incompatible pointer types passing 'Diagpool_T' (aka 'struct Diagpool_T *') to parameter of type 'Cellpool_T' (aka 'struct Cellpool_T *') [-Wincompatible-pointer-types]
                                                  matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
                                                                     ^~~~~~~~
gmap.c:2672:61: note: passing argument to parameter 'cellpool' here
                          Matchpool_T matchpool, Pairpool_T pairpool, Cellpool_T cellpool,
                                                                                 ^
gmap.c:3244:37: warning: incompatible pointer types passing 'Cellpool_T' (aka 'struct Cellpool_T *') to parameter of type 'Diagpool_T' (aka 'struct Diagpool_T *') [-Wincompatible-pointer-types]
                                                  matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
                                                                              ^~~~~~~~
gmap.c:2673:17: note: passing argument to parameter 'diagpool' here
                          Diagpool_T diagpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) {
                                     ^
2 warnings generated.
mv -f .deps/gmapl-gmap.Tpo .deps/gmapl-gmap.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3    -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o  -lz -lbz2 -lm 
libtool: link: gcc -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o  -lz -lbz2 -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-except.o -MD -MP -MF .deps/get_genome-except.Tpo -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/get_genome-except.Tpo .deps/get_genome-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-assert.o -MD -MP -MF .deps/get_genome-assert.Tpo -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/get_genome-assert.Tpo .deps/get_genome-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-mem.o -MD -MP -MF .deps/get_genome-mem.Tpo -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/get_genome-mem.Tpo .deps/get_genome-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-intlist.o -MD -MP -MF .deps/get_genome-intlist.Tpo -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/get_genome-intlist.Tpo .deps/get_genome-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-list.o -MD -MP -MF .deps/get_genome-list.Tpo -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/get_genome-list.Tpo .deps/get_genome-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-littleendian.o -MD -MP -MF .deps/get_genome-littleendian.Tpo -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/get_genome-littleendian.Tpo .deps/get_genome-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-bigendian.o -MD -MP -MF .deps/get_genome-bigendian.Tpo -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/get_genome-bigendian.Tpo .deps/get_genome-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-univinterval.o -MD -MP -MF .deps/get_genome-univinterval.Tpo -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %llu
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %llu
2 warnings generated.
mv -f .deps/get_genome-univinterval.Tpo .deps/get_genome-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-interval.o -MD -MP -MF .deps/get_genome-interval.Tpo -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/get_genome-interval.Tpo .deps/get_genome-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-uintlist.o -MD -MP -MF .deps/get_genome-uintlist.Tpo -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/get_genome-uintlist.Tpo .deps/get_genome-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-stopwatch.o -MD -MP -MF .deps/get_genome-stopwatch.Tpo -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/get_genome-stopwatch.Tpo .deps/get_genome-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-access.o -MD -MP -MF .deps/get_genome-access.Tpo -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-iit-read-univ.o -MD -MP -MF .deps/get_genome-iit-read-univ.Tpo -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %llu
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %llu
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %llu
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %llu
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %llu
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %llu
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %llu
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %llu
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %llu
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %llu
10 warnings generated.
mv -f .deps/get_genome-iit-read-univ.Tpo .deps/get_genome-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-iit-read.o -MD -MP -MF .deps/get_genome-iit-read.Tpo -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-md5.o -MD -MP -MF .deps/get_genome-md5.Tpo -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/get_genome-md5.Tpo .deps/get_genome-md5.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-bzip2.o -MD -MP -MF .deps/get_genome-bzip2.Tpo -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/get_genome-bzip2.Tpo .deps/get_genome-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-sequence.o -MD -MP -MF .deps/get_genome-sequence.Tpo -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/get_genome-sequence.Tpo .deps/get_genome-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-genome.o -MD -MP -MF .deps/get_genome-genome.Tpo -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
4 warnings generated.
mv -f .deps/get_genome-genome.Tpo .deps/get_genome-genome.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-genomicpos.o -MD -MP -MF .deps/get_genome-genomicpos.Tpo -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/get_genome-genomicpos.Tpo .deps/get_genome-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrom.o -MD -MP -MF .deps/get_genome-chrom.Tpo -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/get_genome-chrom.Tpo .deps/get_genome-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrnum.o -MD -MP -MF .deps/get_genome-chrnum.Tpo -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/get_genome-chrnum.Tpo .deps/get_genome-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrsubset.o -MD -MP -MF .deps/get_genome-chrsubset.Tpo -c -o get_genome-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c
mv -f .deps/get_genome-chrsubset.Tpo .deps/get_genome-chrsubset.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-datadir.o -MD -MP -MF .deps/get_genome-datadir.Tpo -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/get_genome-datadir.Tpo .deps/get_genome-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-parserange.o -MD -MP -MF .deps/get_genome-parserange.Tpo -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
parserange.c:187:8: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
              Univinterval_low(interval),left,*genomicstart);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~
parserange.c:187:35: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
              Univinterval_low(interval),left,*genomicstart);
                                         ^~~~
parserange.c:187:40: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
              Univinterval_low(interval),left,*genomicstart);
                                              ^~~~~~~~~~~~~
3 warnings generated.
mv -f .deps/get_genome-parserange.Tpo .deps/get_genome-parserange.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-getopt.o -MD -MP -MF .deps/get_genome-getopt.Tpo -c -o get_genome-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/get_genome-getopt.Tpo .deps/get_genome-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-getopt1.o -MD -MP -MF .deps/get_genome-getopt1.Tpo -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/get_genome-getopt1.Tpo .deps/get_genome-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-get-genome.o -MD -MP -MF .deps/get_genome-get-genome.Tpo -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c
get-genome.c:194:23: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
  printf("%lu%s%lu\t",left+1,SEPARATOR,left+length);
          ~~~         ^~~~~~
          %llu
get-genome.c:194:40: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
  printf("%lu%s%lu\t",left+1,SEPARATOR,left+length);
               ~~~                     ^~~~~~~~~~~
               %llu
get-genome.c:410:41: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf(" %s:%lu%s%lu\n",dbversion,genomicstart+genomiclength,SEPARATOR,genomicstart+1U);
                  ~~~                   ^~~~~~~~~~~~~~~~~~~~~~~~~~
                  %llu
get-genome.c:410:78: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf(" %s:%lu%s%lu\n",dbversion,genomicstart+genomiclength,SEPARATOR,genomicstart+1U);
                       ~~~                                                   ^~~~~~~~~~~~~~~
                       %llu
get-genome.c:428:41: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf(" %s:%lu%s%lu\n",dbversion,genomicstart+1U,SEPARATOR,genomicstart+genomiclength);
                  ~~~                   ^~~~~~~~~~~~~~~
                  %llu
get-genome.c:428:67: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf(" %s:%lu%s%lu\n",dbversion,genomicstart+1U,SEPARATOR,genomicstart+genomiclength);
                       ~~~                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~
                       %llu
6 warnings generated.
mv -f .deps/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3    -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o  -lz -lbz2 -lm 
libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o  -lz -lbz2 -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-except.o -MD -MP -MF .deps/gmapindex-except.Tpo -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gmapindex-except.Tpo .deps/gmapindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-assert.o -MD -MP -MF .deps/gmapindex-assert.Tpo -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gmapindex-assert.Tpo .deps/gmapindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-mem.o -MD -MP -MF .deps/gmapindex-mem.Tpo -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gmapindex-mem.Tpo .deps/gmapindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-intlist.o -MD -MP -MF .deps/gmapindex-intlist.Tpo -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gmapindex-intlist.Tpo .deps/gmapindex-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-list.o -MD -MP -MF .deps/gmapindex-list.Tpo -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gmapindex-list.Tpo .deps/gmapindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-littleendian.o -MD -MP -MF .deps/gmapindex-littleendian.Tpo -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/gmapindex-littleendian.Tpo .deps/gmapindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-bigendian.o -MD -MP -MF .deps/gmapindex-bigendian.Tpo -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/gmapindex-bigendian.Tpo .deps/gmapindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-univinterval.o -MD -MP -MF .deps/gmapindex-univinterval.Tpo -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %llu
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %llu
2 warnings generated.
mv -f .deps/gmapindex-univinterval.Tpo .deps/gmapindex-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-interval.o -MD -MP -MF .deps/gmapindex-interval.Tpo -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gmapindex-interval.Tpo .deps/gmapindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-uintlist.o -MD -MP -MF .deps/gmapindex-uintlist.Tpo -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gmapindex-uintlist.Tpo .deps/gmapindex-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-stopwatch.o -MD -MP -MF .deps/gmapindex-stopwatch.Tpo -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gmapindex-stopwatch.Tpo .deps/gmapindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-access.o -MD -MP -MF .deps/gmapindex-access.Tpo -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-iit-read-univ.o -MD -MP -MF .deps/gmapindex-iit-read-univ.Tpo -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %llu
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %llu
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %llu
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %llu
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %llu
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %llu
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %llu
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %llu
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %llu
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %llu
10 warnings generated.
mv -f .deps/gmapindex-iit-read-univ.Tpo .deps/gmapindex-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-iit-write-univ.o -MD -MP -MF .deps/gmapindex-iit-write-univ.Tpo -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c
mv -f .deps/gmapindex-iit-write-univ.Tpo .deps/gmapindex-iit-write-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-iit-read.o -MD -MP -MF .deps/gmapindex-iit-read.Tpo -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/gmapindex-iit-read.Tpo .deps/gmapindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-md5.o -MD -MP -MF .deps/gmapindex-md5.Tpo -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gmapindex-md5.Tpo .deps/gmapindex-md5.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-bzip2.o -MD -MP -MF .deps/gmapindex-bzip2.Tpo -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/gmapindex-bzip2.Tpo .deps/gmapindex-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-sequence.o -MD -MP -MF .deps/gmapindex-sequence.Tpo -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gmapindex-sequence.Tpo .deps/gmapindex-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-genome.o -MD -MP -MF .deps/gmapindex-genome.Tpo -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
4 warnings generated.
mv -f .deps/gmapindex-genome.Tpo .deps/gmapindex-genome.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-genomicpos.o -MD -MP -MF .deps/gmapindex-genomicpos.Tpo -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gmapindex-genomicpos.Tpo .deps/gmapindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-compress-write.o -MD -MP -MF .deps/gmapindex-compress-write.Tpo -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
                                                                     ~~~              ^~~~~~~~~~
                                                                     %llu
compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
3 warnings generated.
mv -f .deps/gmapindex-compress-write.Tpo .deps/gmapindex-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-genome-write.o -MD -MP -MF .deps/gmapindex-genome-write.Tpo -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
genome-write.c:253:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                            ^~~~~~~~~~~~~
genome-write.c:253:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                                          ^~~~~~~~~~~
genome-write.c:256:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                            ^~~~~~~~~~~~~~~~
genome-write.c:256:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                                             ^~~~~~~~~~~~~~
genome-write.c:430:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                            ^~~~~~~~~~~~~
genome-write.c:430:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                                          ^~~~~~~~~~~
genome-write.c:433:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                            ^~~~~~~~~~~~~~~~
genome-write.c:433:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                                             ^~~~~~~~~~~~~~
genome-write.c:595:87: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                          ~~~                         ^~~~~~~~~~~~~~~~
                                                          %llu
genome-write.c:595:104: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                               ~~~                                     ^~~~~~~~~~~~~~
                                                               %llu
genome-write.c:595:119: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                                      ~~~                                             ^~~~~~~~~~~~~~~~~
                                                                      %llu
genome-write.c:595:137: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                                                                           ~~~                                                          ^~~~~~~~~~~~~~~
                                                                           %llu
genome-write.c:643:15: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                            ^~~~~~~~~~~~~
genome-write.c:643:29: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                  accession,startposition,endposition,fileroot);
                                          ^~~~~~~~~~~
genome-write.c:646:15: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                            ^~~~~~~~~~~~~~~~
genome-write.c:646:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                  accession,startposition+1U,endposition+1U,fileroot);
                                             ^~~~~~~~~~~~~~
genome-write.c:787:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  fprintf(stderr,"Genome length is %lu nt\n",genomelength);
                                   ~~~       ^~~~~~~~~~~~
                                   %llu
17 warnings generated.
mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-compress.o -MD -MP -MF .deps/gmapindex-compress.Tpo -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gmapindex-compress.Tpo .deps/gmapindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-genome_hr.o -MD -MP -MF .deps/gmapindex-genome_hr.Tpo -c -o gmapindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gmapindex-genome_hr.Tpo .deps/gmapindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-bitpack64-read.o -MD -MP -MF .deps/gmapindex-bitpack64-read.Tpo -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/gmapindex-bitpack64-read.Tpo .deps/gmapindex-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-bitpack64-write.o -MD -MP -MF .deps/gmapindex-bitpack64-write.Tpo -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
mv -f .deps/gmapindex-bitpack64-write.Tpo .deps/gmapindex-bitpack64-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-indexdb.o -MD -MP -MF .deps/gmapindex-indexdb.Tpo -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                     ^~~~~~~~
indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
            ^~~
indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
                                    ^~~~~~
indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
7 warnings generated.
mv -f .deps/gmapindex-indexdb.Tpo .deps/gmapindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-indexdb-write.o -MD -MP -MF .deps/gmapindex-indexdb-write.Tpo -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb-write.c:2495:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                ^~~~~~
indexdb-write.c:2495:10: warning: format specifies type 'int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                       ^
indexdb-write.c:2495:12: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                         ^~~~~~~~
indexdb-write.c:2727:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
              oligok,offsetscomp[gammaptrs[p-1]],cum);
              ^~~~~~
indexdb-write.c:2738:8: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
              oligok-1UL,offsets[oligok-1],cum);
              ^~~~~~~~~~
indexdb-write.c:2761:3: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                oligok-1UL,offsets[oligok-1],cum);
                ^~~~~~~~~~
indexdb-write.c:2788:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
            oligok,offsetscomp[gammaptrs[p-1]],cum);
            ^~~~~~
indexdb-write.c:2799:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
            oligok,offsets[oligok],*ptr);
            ^~~~~~
indexdb-write.c:2888:59: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T));
                             ~~~                          ^~~~~~~~~~~~~~
                             %llu
indexdb-write.c:2895:101: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part);
                                       ~~~                                                          ^~~~~~~~~~~~~~
                                       %llu
indexdb-write.c:2972:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3094:79: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]);
                              ~~~                                             ^~~~~~~~~~~~
                              %llu
indexdb-write.c:3127:101: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                              ~~~                                                                   ^~~~~~~~~~~~~~
                              %llu
indexdb-write.c:3171:102: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                              ~~~                                                                    ^~~~~~~~~~~~~~
                              %llu
indexdb-write.c:3234:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
    fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT4),offset);
                                                           ~~~                      ^~~~~~
                                                           %lld
indexdb-write.c:3246:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
    fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT8),offset);
                                                           ~~~                      ^~~~~~
                                                           %lld
indexdb-write.c:3371:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3601:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3796:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3823:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3838:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                  positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                          ^~~~~~~~
indexdb-write.c:3865:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3892:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3907:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                  positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                          ^~~~~~~~
24 warnings generated.
mv -f .deps/gmapindex-indexdb-write.Tpo .deps/gmapindex-indexdb-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-table.o -MD -MP -MF .deps/gmapindex-table.Tpo -c -o gmapindex-table.o `test -f 'table.c' || echo './'`table.c
table.c:283:18: warning: passing 'const void **' to parameter of type 'void **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
      (*keyfree)(&p->key);
                 ^~~~~~~
1 warning generated.
mv -f .deps/gmapindex-table.Tpo .deps/gmapindex-table.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-tableuint.o -MD -MP -MF .deps/gmapindex-tableuint.Tpo -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c
mv -f .deps/gmapindex-tableuint.Tpo .deps/gmapindex-tableuint.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-tableuint8.o -MD -MP -MF .deps/gmapindex-tableuint8.Tpo -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo './'`tableuint8.c
mv -f .deps/gmapindex-tableuint8.Tpo .deps/gmapindex-tableuint8.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-chrom.o -MD -MP -MF .deps/gmapindex-chrom.Tpo -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gmapindex-chrom.Tpo .deps/gmapindex-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-segmentpos.o -MD -MP -MF .deps/gmapindex-segmentpos.Tpo -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
segmentpos.c:90:41: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length);
                  ~~                    ^~~~~~~~~~~~~~~~~~~~~~~
                  %llu
1 warning generated.
mv -f .deps/gmapindex-segmentpos.Tpo .deps/gmapindex-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-saca-k.o -MD -MP -MF .deps/gmapindex-saca-k.Tpo -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo './'`saca-k.c
mv -f .deps/gmapindex-saca-k.Tpo .deps/gmapindex-saca-k.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-sarray-write.o -MD -MP -MF .deps/gmapindex-sarray-write.Tpo -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo './'`sarray-write.c
mv -f .deps/gmapindex-sarray-write.Tpo .deps/gmapindex-sarray-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-gmapindex.o -MD -MP -MF .deps/gmapindex-gmapindex.Tpo -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo './'`gmapindex.c
gmapindex.c:305:64: warning: format specifies type 'unsigned long *' but the argument has type 'Univcoord_T *' (aka 'unsigned long long *') [-Wformat]
  nitems = sscanf(Buffer,"%s %s %lu",accession_p,chrpos_string,&universal_coord);
                                ~~~                            ^~~~~~~~~~~~~~~~
                                %llu
gmapindex.c:510:19: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
              chr_string,chroffset+1,chroffset+1+chrlength-1);
                         ^~~~~~~~~~~
gmapindex.c:510:31: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
              chr_string,chroffset+1,chroffset+1+chrlength-1);
                                     ^~~~~~~~~~~~~~~~~~~~~~~
gmapindex.c:521:17: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
            chr_string,chroffset+1,chroffset+chrlength,chrlength);
                       ^~~~~~~~~~~
gmapindex.c:521:29: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
            chr_string,chroffset+1,chroffset+chrlength,chrlength);
                                   ^~~~~~~~~~~~~~~~~~~
gmapindex.c:696:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
              accessions[i],universalpos2+1U,universalpos1,
                            ^~~~~~~~~~~~~~~~
gmapindex.c:696:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
              accessions[i],universalpos2+1U,universalpos1,
                                             ^~~~~~~~~~~~~
gmapindex.c:701:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
              accessions[i],universalpos1+1U,universalpos2,
                            ^~~~~~~~~~~~~~~~
gmapindex.c:701:39: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
              accessions[i],universalpos1+1U,universalpos2,
                                             ^~~~~~~~~~~~~
gmapindex.c:1061:54: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"Total genomic length = %lu bp\n",totalnts);
                                           ~~~       ^~~~~~~~
                                           %llu
10 warnings generated.
mv -f .deps/gmapindex-gmapindex.Tpo .deps/gmapindex-gmapindex.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3    -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-genome_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-sarray-write.o gmapindex-gmapindex.o  -lz -lbz2 -lm 
libtool: link: gcc -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-genome_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-sarray-write.o gmapindex-gmapindex.o  -lz -lbz2 -lm
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-except.o -MD -MP -MF .deps/iit_store-except.Tpo -c -o iit_store-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/iit_store-except.Tpo .deps/iit_store-except.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-assert.o -MD -MP -MF .deps/iit_store-assert.Tpo -c -o iit_store-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/iit_store-assert.Tpo .deps/iit_store-assert.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-mem.o -MD -MP -MF .deps/iit_store-mem.Tpo -c -o iit_store-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/iit_store-mem.Tpo .deps/iit_store-mem.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-intlist.o -MD -MP -MF .deps/iit_store-intlist.Tpo -c -o iit_store-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/iit_store-intlist.Tpo .deps/iit_store-intlist.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-list.o -MD -MP -MF .deps/iit_store-list.Tpo -c -o iit_store-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/iit_store-list.Tpo .deps/iit_store-list.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-littleendian.o -MD -MP -MF .deps/iit_store-littleendian.Tpo -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/iit_store-littleendian.Tpo .deps/iit_store-littleendian.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-bigendian.o -MD -MP -MF .deps/iit_store-bigendian.Tpo -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/iit_store-bigendian.Tpo .deps/iit_store-bigendian.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-univinterval.o -MD -MP -MF .deps/iit_store-univinterval.Tpo -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %llu
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %llu
2 warnings generated.
mv -f .deps/iit_store-univinterval.Tpo .deps/iit_store-univinterval.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-interval.o -MD -MP -MF .deps/iit_store-interval.Tpo -c -o iit_store-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/iit_store-interval.Tpo .deps/iit_store-interval.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-uintlist.o -MD -MP -MF .deps/iit_store-uintlist.Tpo -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/iit_store-uintlist.Tpo .deps/iit_store-uintlist.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-stopwatch.o -MD -MP -MF .deps/iit_store-stopwatch.Tpo -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/iit_store-stopwatch.Tpo .deps/iit_store-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-access.o -MD -MP -MF .deps/iit_store-access.Tpo -c -o iit_store-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/iit_store-access.Tpo .deps/iit_store-access.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-iit-write-univ.o -MD -MP -MF .deps/iit_store-iit-write-univ.Tpo -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c
mv -f .deps/iit_store-iit-write-univ.Tpo .deps/iit_store-iit-write-univ.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-iit-write.o -MD -MP -MF .deps/iit_store-iit-write.Tpo -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c
mv -f .deps/iit_store-iit-write.Tpo .deps/iit_store-iit-write.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-tableint.o -MD -MP -MF .deps/iit_store-tableint.Tpo -c -o iit_store-tableint.o `test -f 'tableint.c' || echo './'`tableint.c
mv -f .deps/iit_store-tableint.Tpo .deps/iit_store-tableint.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-table.o -MD -MP -MF .deps/iit_store-table.Tpo -c -o iit_store-table.o `test -f 'table.c' || echo './'`table.c
table.c:283:18: warning: passing 'const void **' to parameter of type 'void **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
      (*keyfree)(&p->key);
                 ^~~~~~~
1 warning generated.
mv -f .deps/iit_store-table.Tpo .deps/iit_store-table.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-chrom.o -MD -MP -MF .deps/iit_store-chrom.Tpo -c -o iit_store-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/iit_store-chrom.Tpo .deps/iit_store-chrom.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-getopt.o -MD -MP -MF .deps/iit_store-getopt.Tpo -c -o iit_store-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/iit_store-getopt.Tpo .deps/iit_store-getopt.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-getopt1.o -MD -MP -MF .deps/iit_store-getopt1.Tpo -c -o iit_store-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/iit_store-getopt1.Tpo .deps/iit_store-getopt1.Po
gcc -DHAVE_CONFIG_H -I.      -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_store-iit_store.o -MD -MP -MF .deps/iit_store-iit_store.Tpo -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo './'`iit_store.c
iit_store.c:371:51: warning: format specifies type 'unsigned long *' but the argument has type 'Univcoord_T *' (aka 'unsigned long long *') [-Wformat]
  nscanned = sscanf(header,">%s %lu %lu\n",Buffer,&(*start),&(*end));
                                ~~~               ^~~~~~~~~
                                %llu
iit_store.c:371:61: warning: format specifies type 'unsigned long *' but the argument has type 'Univcoord_T *' (aka 'unsigned long long *') [-Wformat]
  nscanned = sscanf(header,">%s %lu %lu\n",Buffer,&(*start),&(*end));
                                    ~~~                     ^~~~~~~
                                    %llu
iit_store.c:596:46: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  fprintf(stderr,"Maximum coordinate: %lu\n",*max_coordinate);
                                      ~~~    ^~~~~~~~~~~~~~~
                                      %llu
iit_store.c:597:62: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  fprintf(stderr,"Total label length: %lu + %d separators\n",*label_totallength,nentries);
                                      ~~~                    ^~~~~~~~~~~~~~~~~~
                                      %llu
iit_store.c:598:67: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  fprintf(stderr,"Total annotation length: %lu + %d separators\n",*annot_totallength,nentries);
                                           ~~~                    ^~~~~~~~~~~~~~~~~~
                                           %llu
5 warnings generated.
mv -f .deps/iit_store-iit_store.Tpo .deps/iit_store-iit_store.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc   -D_THREAD_SAFE  -DUTILITYP=1 -O3    -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o  -lm 
libtool: link: gcc -D_THREAD_SAFE -DUTILITYP=1 -O3 -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o  -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-except.o -MD -MP -MF .deps/iit_get-except.Tpo -c -o iit_get-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/iit_get-except.Tpo .deps/iit_get-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-assert.o -MD -MP -MF .deps/iit_get-assert.Tpo -c -o iit_get-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/iit_get-assert.Tpo .deps/iit_get-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-mem.o -MD -MP -MF .deps/iit_get-mem.Tpo -c -o iit_get-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/iit_get-mem.Tpo .deps/iit_get-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-intlist.o -MD -MP -MF .deps/iit_get-intlist.Tpo -c -o iit_get-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/iit_get-intlist.Tpo .deps/iit_get-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-list.o -MD -MP -MF .deps/iit_get-list.Tpo -c -o iit_get-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/iit_get-list.Tpo .deps/iit_get-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-littleendian.o -MD -MP -MF .deps/iit_get-littleendian.Tpo -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/iit_get-littleendian.Tpo .deps/iit_get-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-bigendian.o -MD -MP -MF .deps/iit_get-bigendian.Tpo -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/iit_get-bigendian.Tpo .deps/iit_get-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-univinterval.o -MD -MP -MF .deps/iit_get-univinterval.Tpo -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %llu
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %llu
2 warnings generated.
mv -f .deps/iit_get-univinterval.Tpo .deps/iit_get-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-interval.o -MD -MP -MF .deps/iit_get-interval.Tpo -c -o iit_get-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/iit_get-interval.Tpo .deps/iit_get-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-uintlist.o -MD -MP -MF .deps/iit_get-uintlist.Tpo -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/iit_get-uintlist.Tpo .deps/iit_get-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-stopwatch.o -MD -MP -MF .deps/iit_get-stopwatch.Tpo -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/iit_get-stopwatch.Tpo .deps/iit_get-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-access.o -MD -MP -MF .deps/iit_get-access.Tpo -c -o iit_get-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/iit_get-access.Tpo .deps/iit_get-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-iit-read-univ.o -MD -MP -MF .deps/iit_get-iit-read-univ.Tpo -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %llu
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %llu
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %llu
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %llu
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %llu
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %llu
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %llu
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %llu
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %llu
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %llu
10 warnings generated.
mv -f .deps/iit_get-iit-read-univ.Tpo .deps/iit_get-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-iit-read.o -MD -MP -MF .deps/iit_get-iit-read.Tpo -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/iit_get-iit-read.Tpo .deps/iit_get-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-parserange.o -MD -MP -MF .deps/iit_get-parserange.Tpo -c -o iit_get-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
parserange.c:187:8: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
              Univinterval_low(interval),left,*genomicstart);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~
parserange.c:187:35: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
              Univinterval_low(interval),left,*genomicstart);
                                         ^~~~
parserange.c:187:40: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
              Univinterval_low(interval),left,*genomicstart);
                                              ^~~~~~~~~~~~~
3 warnings generated.
mv -f .deps/iit_get-parserange.Tpo .deps/iit_get-parserange.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-getopt.o -MD -MP -MF .deps/iit_get-getopt.Tpo -c -o iit_get-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/iit_get-getopt.Tpo .deps/iit_get-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-getopt1.o -MD -MP -MF .deps/iit_get-getopt1.Tpo -c -o iit_get-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/iit_get-getopt1.Tpo .deps/iit_get-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_get-iit_get.o -MD -MP -MF .deps/iit_get-iit_get.Tpo -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo './'`iit_get.c
iit_get.c:619:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu",Univinterval_low(interval),Univinterval_high(interval));
            ~~~       ^~~~~~~~~~~~~~~~~~~~~~~~~~
            %llu
iit_get.c:619:50: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu",Univinterval_low(interval),Univinterval_high(interval));
                 ~~~                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~
                 %llu
2 warnings generated.
mv -f .deps/iit_get-iit_get.Tpo .deps/iit_get-iit_get.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -DUTILITYP=1 -O3    -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o  -lm 
libtool: link: gcc -D_THREAD_SAFE -DUTILITYP=1 -O3 -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o  -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-except.o -MD -MP -MF .deps/iit_dump-except.Tpo -c -o iit_dump-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/iit_dump-except.Tpo .deps/iit_dump-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-assert.o -MD -MP -MF .deps/iit_dump-assert.Tpo -c -o iit_dump-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/iit_dump-assert.Tpo .deps/iit_dump-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-mem.o -MD -MP -MF .deps/iit_dump-mem.Tpo -c -o iit_dump-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/iit_dump-mem.Tpo .deps/iit_dump-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-littleendian.o -MD -MP -MF .deps/iit_dump-littleendian.Tpo -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/iit_dump-littleendian.Tpo .deps/iit_dump-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-bigendian.o -MD -MP -MF .deps/iit_dump-bigendian.Tpo -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/iit_dump-bigendian.Tpo .deps/iit_dump-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-intlist.o -MD -MP -MF .deps/iit_dump-intlist.Tpo -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/iit_dump-intlist.Tpo .deps/iit_dump-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-list.o -MD -MP -MF .deps/iit_dump-list.Tpo -c -o iit_dump-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/iit_dump-list.Tpo .deps/iit_dump-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-univinterval.o -MD -MP -MF .deps/iit_dump-univinterval.Tpo -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %llu
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %llu
2 warnings generated.
mv -f .deps/iit_dump-univinterval.Tpo .deps/iit_dump-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-interval.o -MD -MP -MF .deps/iit_dump-interval.Tpo -c -o iit_dump-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/iit_dump-interval.Tpo .deps/iit_dump-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-uintlist.o -MD -MP -MF .deps/iit_dump-uintlist.Tpo -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/iit_dump-uintlist.Tpo .deps/iit_dump-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-stopwatch.o -MD -MP -MF .deps/iit_dump-stopwatch.Tpo -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/iit_dump-stopwatch.Tpo .deps/iit_dump-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-access.o -MD -MP -MF .deps/iit_dump-access.Tpo -c -o iit_dump-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/iit_dump-access.Tpo .deps/iit_dump-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-iit-read-univ.o -MD -MP -MF .deps/iit_dump-iit-read-univ.Tpo -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %llu
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %llu
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %llu
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %llu
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %llu
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %llu
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %llu
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %llu
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %llu
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %llu
10 warnings generated.
mv -f .deps/iit_dump-iit-read-univ.Tpo .deps/iit_dump-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-iit-read.o -MD -MP -MF .deps/iit_dump-iit-read.Tpo -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/iit_dump-iit-read.Tpo .deps/iit_dump-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-getopt.o -MD -MP -MF .deps/iit_dump-getopt.Tpo -c -o iit_dump-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/iit_dump-getopt.Tpo .deps/iit_dump-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-getopt1.o -MD -MP -MF .deps/iit_dump-getopt1.Tpo -c -o iit_dump-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/iit_dump-getopt1.Tpo .deps/iit_dump-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DUTILITYP=1 -O3 -MT iit_dump-iit_dump.o -MD -MP -MF .deps/iit_dump-iit_dump.Tpo -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo './'`iit_dump.c
mv -f .deps/iit_dump-iit_dump.Tpo .deps/iit_dump-iit_dump.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -DUTILITYP=1 -O3    -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o  -lm 
libtool: link: gcc -D_THREAD_SAFE -DUTILITYP=1 -O3 -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o  -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-except.o -MD -MP -MF .deps/gsnap-except.Tpo -c -o gsnap-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gsnap-except.Tpo .deps/gsnap-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-assert.o -MD -MP -MF .deps/gsnap-assert.Tpo -c -o gsnap-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gsnap-assert.Tpo .deps/gsnap-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-mem.o -MD -MP -MF .deps/gsnap-mem.Tpo -c -o gsnap-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gsnap-mem.Tpo .deps/gsnap-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-intlist.o -MD -MP -MF .deps/gsnap-intlist.Tpo -c -o gsnap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gsnap-intlist.Tpo .deps/gsnap-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-list.o -MD -MP -MF .deps/gsnap-list.Tpo -c -o gsnap-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gsnap-list.Tpo .deps/gsnap-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-littleendian.o -MD -MP -MF .deps/gsnap-littleendian.Tpo -c -o gsnap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/gsnap-littleendian.Tpo .deps/gsnap-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bigendian.o -MD -MP -MF .deps/gsnap-bigendian.Tpo -c -o gsnap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/gsnap-bigendian.Tpo .deps/gsnap-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-univinterval.o -MD -MP -MF .deps/gsnap-univinterval.Tpo -c -o gsnap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %u
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %u
2 warnings generated.
mv -f .deps/gsnap-univinterval.Tpo .deps/gsnap-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-interval.o -MD -MP -MF .deps/gsnap-interval.Tpo -c -o gsnap-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gsnap-interval.Tpo .deps/gsnap-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-uintlist.o -MD -MP -MF .deps/gsnap-uintlist.Tpo -c -o gsnap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gsnap-uintlist.Tpo .deps/gsnap-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stopwatch.o -MD -MP -MF .deps/gsnap-stopwatch.Tpo -c -o gsnap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gsnap-stopwatch.Tpo .deps/gsnap-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-access.o -MD -MP -MF .deps/gsnap-access.Tpo -c -o gsnap-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/gsnap-access.Tpo .deps/gsnap-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-iit-read-univ.o -MD -MP -MF .deps/gsnap-iit-read-univ.Tpo -c -o gsnap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %u
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %u
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %u
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %u
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %u
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %u
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %u
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %u
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %u
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %u
10 warnings generated.
mv -f .deps/gsnap-iit-read-univ.Tpo .deps/gsnap-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-iit-read.o -MD -MP -MF .deps/gsnap-iit-read.Tpo -c -o gsnap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/gsnap-iit-read.Tpo .deps/gsnap-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-md5.o -MD -MP -MF .deps/gsnap-md5.Tpo -c -o gsnap-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gsnap-md5.Tpo .deps/gsnap-md5.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bzip2.o -MD -MP -MF .deps/gsnap-bzip2.Tpo -c -o gsnap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/gsnap-bzip2.Tpo .deps/gsnap-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-sequence.o -MD -MP -MF .deps/gsnap-sequence.Tpo -c -o gsnap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gsnap-sequence.Tpo .deps/gsnap-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-reader.o -MD -MP -MF .deps/gsnap-reader.Tpo -c -o gsnap-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/gsnap-reader.Tpo .deps/gsnap-reader.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genomicpos.o -MD -MP -MF .deps/gsnap-genomicpos.Tpo -c -o gsnap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gsnap-genomicpos.Tpo .deps/gsnap-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-compress.o -MD -MP -MF .deps/gsnap-compress.Tpo -c -o gsnap-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gsnap-compress.Tpo .deps/gsnap-compress.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome.o -MD -MP -MF .deps/gsnap-genome.Tpo -c -o gsnap-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %u
genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %u
genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %u
genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %u
4 warnings generated.
mv -f .deps/gsnap-genome.Tpo .deps/gsnap-genome.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome_hr.o -MD -MP -MF .deps/gsnap-genome_hr.Tpo -c -o gsnap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gsnap-genome_hr.Tpo .deps/gsnap-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome_sites.o -MD -MP -MF .deps/gsnap-genome_sites.Tpo -c -o gsnap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
mv -f .deps/gsnap-genome_sites.Tpo .deps/gsnap-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bitpack64-read.o -MD -MP -MF .deps/gsnap-bitpack64-read.Tpo -c -o gsnap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/gsnap-bitpack64-read.Tpo .deps/gsnap-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indexdb.o -MD -MP -MF .deps/gsnap-indexdb.Tpo -c -o gsnap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                     ^~~~~~~~
indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
            ^~~
indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
                                    ^~~~~~
indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
7 warnings generated.
mv -f .deps/gsnap-indexdb.Tpo .deps/gsnap-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indexdb_hr.o -MD -MP -MF .deps/gsnap-indexdb_hr.Tpo -c -o gsnap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
mv -f .deps/gsnap-indexdb_hr.Tpo .deps/gsnap-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-oligo.o -MD -MP -MF .deps/gsnap-oligo.Tpo -c -o gsnap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/gsnap-oligo.Tpo .deps/gsnap-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chrom.o -MD -MP -MF .deps/gsnap-chrom.Tpo -c -o gsnap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gsnap-chrom.Tpo .deps/gsnap-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-segmentpos.o -MD -MP -MF .deps/gsnap-segmentpos.Tpo -c -o gsnap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
mv -f .deps/gsnap-segmentpos.Tpo .deps/gsnap-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chrnum.o -MD -MP -MF .deps/gsnap-chrnum.Tpo -c -o gsnap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/gsnap-chrnum.Tpo .deps/gsnap-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-maxent_hr.o -MD -MP -MF .deps/gsnap-maxent_hr.Tpo -c -o gsnap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/gsnap-maxent_hr.Tpo .deps/gsnap-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-samprint.o -MD -MP -MF .deps/gsnap-samprint.Tpo -c -o gsnap-samprint.o `test -f 'samprint.c' || echo './'`samprint.c
mv -f .deps/gsnap-samprint.Tpo .deps/gsnap-samprint.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-mapq.o -MD -MP -MF .deps/gsnap-mapq.Tpo -c -o gsnap-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
mv -f .deps/gsnap-mapq.Tpo .deps/gsnap-mapq.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-shortread.o -MD -MP -MF .deps/gsnap-shortread.Tpo -c -o gsnap-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
mv -f .deps/gsnap-shortread.Tpo .deps/gsnap-shortread.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-substring.o -MD -MP -MF .deps/gsnap-substring.Tpo -c -o gsnap-substring.o `test -f 'substring.c' || echo './'`substring.c
mv -f .deps/gsnap-substring.Tpo .deps/gsnap-substring.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage3hr.o -MD -MP -MF .deps/gsnap-stage3hr.Tpo -c -o gsnap-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
mv -f .deps/gsnap-stage3hr.Tpo .deps/gsnap-stage3hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-goby.o -MD -MP -MF .deps/gsnap-goby.Tpo -c -o gsnap-goby.o `test -f 'goby.c' || echo './'`goby.c
mv -f .deps/gsnap-goby.Tpo .deps/gsnap-goby.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-spanningelt.o -MD -MP -MF .deps/gsnap-spanningelt.Tpo -c -o gsnap-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c
mv -f .deps/gsnap-spanningelt.Tpo .deps/gsnap-spanningelt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-cmet.o -MD -MP -MF .deps/gsnap-cmet.Tpo -c -o gsnap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/gsnap-cmet.Tpo .deps/gsnap-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-atoi.o -MD -MP -MF .deps/gsnap-atoi.Tpo -c -o gsnap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/gsnap-atoi.Tpo .deps/gsnap-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-maxent.o -MD -MP -MF .deps/gsnap-maxent.Tpo -c -o gsnap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/gsnap-maxent.Tpo .deps/gsnap-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pair.o -MD -MP -MF .deps/gsnap-pair.Tpo -c -o gsnap-pair.o `test -f 'pair.c' || echo './'`pair.c
pair.c:2419:24: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^
pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^
pair.c:4651:17: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^
pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^~~
2 warnings generated.
mv -f .deps/gsnap-pair.Tpo .deps/gsnap-pair.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pairpool.o -MD -MP -MF .deps/gsnap-pairpool.Tpo -c -o gsnap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/gsnap-pairpool.Tpo .deps/gsnap-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-diag.o -MD -MP -MF .deps/gsnap-diag.Tpo -c -o gsnap-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/gsnap-diag.Tpo .deps/gsnap-diag.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-diagpool.o -MD -MP -MF .deps/gsnap-diagpool.Tpo -c -o gsnap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/gsnap-diagpool.Tpo .deps/gsnap-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-orderstat.o -MD -MP -MF .deps/gsnap-orderstat.Tpo -c -o gsnap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/gsnap-orderstat.Tpo .deps/gsnap-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-oligoindex_hr.o -MD -MP -MF .deps/gsnap-oligoindex_hr.Tpo -c -o gsnap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/gsnap-oligoindex_hr.Tpo .deps/gsnap-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-cellpool.o -MD -MP -MF .deps/gsnap-cellpool.Tpo -c -o gsnap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/gsnap-cellpool.Tpo .deps/gsnap-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage2.o -MD -MP -MF .deps/gsnap-stage2.Tpo -c -o gsnap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
stage2.c:1329:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
stage2.c:1812:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
2 warnings generated.
mv -f .deps/gsnap-stage2.Tpo .deps/gsnap-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-intron.o -MD -MP -MF .deps/gsnap-intron.Tpo -c -o gsnap-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/gsnap-intron.Tpo .deps/gsnap-intron.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-boyer-moore.o -MD -MP -MF .deps/gsnap-boyer-moore.Tpo -c -o gsnap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/gsnap-boyer-moore.Tpo .deps/gsnap-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-changepoint.o -MD -MP -MF .deps/gsnap-changepoint.Tpo -c -o gsnap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/gsnap-changepoint.Tpo .deps/gsnap-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pbinom.o -MD -MP -MF .deps/gsnap-pbinom.Tpo -c -o gsnap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/gsnap-pbinom.Tpo .deps/gsnap-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-dynprog.o -MD -MP -MF .deps/gsnap-dynprog.Tpo -c -o gsnap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/gsnap-dynprog.Tpo .deps/gsnap-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-gbuffer.o -MD -MP -MF .deps/gsnap-gbuffer.Tpo -c -o gsnap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
mv -f .deps/gsnap-gbuffer.Tpo .deps/gsnap-gbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-translation.o -MD -MP -MF .deps/gsnap-translation.Tpo -c -o gsnap-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/gsnap-translation.Tpo .deps/gsnap-translation.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-doublelist.o -MD -MP -MF .deps/gsnap-doublelist.Tpo -c -o gsnap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/gsnap-doublelist.Tpo .deps/gsnap-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-smooth.o -MD -MP -MF .deps/gsnap-smooth.Tpo -c -o gsnap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/gsnap-smooth.Tpo .deps/gsnap-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chimera.o -MD -MP -MF .deps/gsnap-chimera.Tpo -c -o gsnap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/gsnap-chimera.Tpo .deps/gsnap-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage3.o -MD -MP -MF .deps/gsnap-stage3.Tpo -c -o gsnap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/gsnap-stage3.Tpo .deps/gsnap-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicestringpool.o -MD -MP -MF .deps/gsnap-splicestringpool.Tpo -c -o gsnap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/gsnap-splicestringpool.Tpo .deps/gsnap-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicetrie_build.o -MD -MP -MF .deps/gsnap-splicetrie_build.Tpo -c -o gsnap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
mv -f .deps/gsnap-splicetrie_build.Tpo .deps/gsnap-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicetrie.o -MD -MP -MF .deps/gsnap-splicetrie.Tpo -c -o gsnap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/gsnap-splicetrie.Tpo .deps/gsnap-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splice.o -MD -MP -MF .deps/gsnap-splice.Tpo -c -o gsnap-splice.o `test -f 'splice.c' || echo './'`splice.c
mv -f .deps/gsnap-splice.Tpo .deps/gsnap-splice.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indel.o -MD -MP -MF .deps/gsnap-indel.Tpo -c -o gsnap-indel.o `test -f 'indel.c' || echo './'`indel.c
mv -f .deps/gsnap-indel.Tpo .deps/gsnap-indel.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bitpack64-access.o -MD -MP -MF .deps/gsnap-bitpack64-access.Tpo -c -o gsnap-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
mv -f .deps/gsnap-bitpack64-access.Tpo .deps/gsnap-bitpack64-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-sarray-read.o -MD -MP -MF .deps/gsnap-sarray-read.Tpo -c -o gsnap-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c
sarray-read.c:1399:27: warning: implicit conversion from 'long' to 'int' changes value from 2147483648 to -2147483648 [-Wconstant-conversion]
    base = _mm_set1_epi32(2147483648); /* 2^31 */
           ~~~~~~~~~~~~~~ ^~~~~~~~~~
1 warning generated.
mv -f .deps/gsnap-sarray-read.Tpo .deps/gsnap-sarray-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage1hr.o -MD -MP -MF .deps/gsnap-stage1hr.Tpo -c -o gsnap-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
mv -f .deps/gsnap-stage1hr.Tpo .deps/gsnap-stage1hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-request.o -MD -MP -MF .deps/gsnap-request.Tpo -c -o gsnap-request.o `test -f 'request.c' || echo './'`request.c
mv -f .deps/gsnap-request.Tpo .deps/gsnap-request.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-resulthr.o -MD -MP -MF .deps/gsnap-resulthr.Tpo -c -o gsnap-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
mv -f .deps/gsnap-resulthr.Tpo .deps/gsnap-resulthr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-inbuffer.o -MD -MP -MF .deps/gsnap-inbuffer.Tpo -c -o gsnap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
mv -f .deps/gsnap-inbuffer.Tpo .deps/gsnap-inbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-samheader.o -MD -MP -MF .deps/gsnap-samheader.Tpo -c -o gsnap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
mv -f .deps/gsnap-samheader.Tpo .deps/gsnap-samheader.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-outbuffer.o -MD -MP -MF .deps/gsnap-outbuffer.Tpo -c -o gsnap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
mv -f .deps/gsnap-outbuffer.Tpo .deps/gsnap-outbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-datadir.o -MD -MP -MF .deps/gsnap-datadir.Tpo -c -o gsnap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gsnap-datadir.Tpo .deps/gsnap-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-getopt.o -MD -MP -MF .deps/gsnap-getopt.Tpo -c -o gsnap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gsnap-getopt.Tpo .deps/gsnap-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-getopt1.o -MD -MP -MF .deps/gsnap-getopt1.Tpo -c -o gsnap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gsnap-getopt1.Tpo .deps/gsnap-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-gsnap.o -MD -MP -MF .deps/gsnap-gsnap.Tpo -c -o gsnap-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c
mv -f .deps/gsnap-gsnap.Tpo .deps/gsnap-gsnap.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3     -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o  -lz -lbz2  -lm 
libtool: link: gcc -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o  -lz -lbz2 -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-except.o -MD -MP -MF .deps/gsnapl-except.Tpo -c -o gsnapl-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gsnapl-except.Tpo .deps/gsnapl-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-assert.o -MD -MP -MF .deps/gsnapl-assert.Tpo -c -o gsnapl-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gsnapl-assert.Tpo .deps/gsnapl-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-mem.o -MD -MP -MF .deps/gsnapl-mem.Tpo -c -o gsnapl-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gsnapl-mem.Tpo .deps/gsnapl-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-intlist.o -MD -MP -MF .deps/gsnapl-intlist.Tpo -c -o gsnapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gsnapl-intlist.Tpo .deps/gsnapl-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-list.o -MD -MP -MF .deps/gsnapl-list.Tpo -c -o gsnapl-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gsnapl-list.Tpo .deps/gsnapl-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-littleendian.o -MD -MP -MF .deps/gsnapl-littleendian.Tpo -c -o gsnapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/gsnapl-littleendian.Tpo .deps/gsnapl-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bigendian.o -MD -MP -MF .deps/gsnapl-bigendian.Tpo -c -o gsnapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/gsnapl-bigendian.Tpo .deps/gsnapl-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-univinterval.o -MD -MP -MF .deps/gsnapl-univinterval.Tpo -c -o gsnapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %llu
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %llu
2 warnings generated.
mv -f .deps/gsnapl-univinterval.Tpo .deps/gsnapl-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-interval.o -MD -MP -MF .deps/gsnapl-interval.Tpo -c -o gsnapl-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gsnapl-interval.Tpo .deps/gsnapl-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-uintlist.o -MD -MP -MF .deps/gsnapl-uintlist.Tpo -c -o gsnapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gsnapl-uintlist.Tpo .deps/gsnapl-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-uint8list.o -MD -MP -MF .deps/gsnapl-uint8list.Tpo -c -o gsnapl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
uint8list.c:202:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
      sprintf(Buffer,"%u,",Uint8list_head(p));
                      ~~   ^~~~~~~~~~~~~~~~~
                      %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
uint8list.c:205:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
    sprintf(Buffer,"%u",Uint8list_head(p));
                    ~~  ^~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
uint8list.c:211:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
      sprintf(Buffer,"%u,",Uint8list_head(p));
                      ~~   ^~~~~~~~~~~~~~~~~
                      %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
uint8list.c:214:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
    sprintf(Buffer,"%u",Uint8list_head(p));
                    ~~  ^~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
4 warnings generated.
mv -f .deps/gsnapl-uint8list.Tpo .deps/gsnapl-uint8list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stopwatch.o -MD -MP -MF .deps/gsnapl-stopwatch.Tpo -c -o gsnapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gsnapl-stopwatch.Tpo .deps/gsnapl-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-access.o -MD -MP -MF .deps/gsnapl-access.Tpo -c -o gsnapl-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/gsnapl-access.Tpo .deps/gsnapl-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-iit-read-univ.o -MD -MP -MF .deps/gsnapl-iit-read-univ.Tpo -c -o gsnapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %llu
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %llu
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %llu
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %llu
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %llu
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %llu
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %llu
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %llu
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %llu
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %llu
10 warnings generated.
mv -f .deps/gsnapl-iit-read-univ.Tpo .deps/gsnapl-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-iit-read.o -MD -MP -MF .deps/gsnapl-iit-read.Tpo -c -o gsnapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/gsnapl-iit-read.Tpo .deps/gsnapl-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-md5.o -MD -MP -MF .deps/gsnapl-md5.Tpo -c -o gsnapl-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gsnapl-md5.Tpo .deps/gsnapl-md5.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bzip2.o -MD -MP -MF .deps/gsnapl-bzip2.Tpo -c -o gsnapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/gsnapl-bzip2.Tpo .deps/gsnapl-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-sequence.o -MD -MP -MF .deps/gsnapl-sequence.Tpo -c -o gsnapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gsnapl-sequence.Tpo .deps/gsnapl-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-reader.o -MD -MP -MF .deps/gsnapl-reader.Tpo -c -o gsnapl-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/gsnapl-reader.Tpo .deps/gsnapl-reader.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genomicpos.o -MD -MP -MF .deps/gsnapl-genomicpos.Tpo -c -o gsnapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gsnapl-genomicpos.Tpo .deps/gsnapl-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-compress.o -MD -MP -MF .deps/gsnapl-compress.Tpo -c -o gsnapl-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gsnapl-compress.Tpo .deps/gsnapl-compress.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome.o -MD -MP -MF .deps/gsnapl-genome.Tpo -c -o gsnapl-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
4 warnings generated.
mv -f .deps/gsnapl-genome.Tpo .deps/gsnapl-genome.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome_hr.o -MD -MP -MF .deps/gsnapl-genome_hr.Tpo -c -o gsnapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gsnapl-genome_hr.Tpo .deps/gsnapl-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome_sites.o -MD -MP -MF .deps/gsnapl-genome_sites.Tpo -c -o gsnapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
genome_sites.c:24729:17: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  printf("%u\t",startblock/3*32U);
          ~~    ^~~~~~~~~~~~~~~~
          %llu
genome_sites.c:24744:19: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    printf("%u\t",ptr/3*32U);
            ~~    ^~~~~~~~~
            %llu
genome_sites.c:24751:17: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  printf("%u\t",(endblock+3)/3*32U);
          ~~    ^~~~~~~~~~~~~~~~~~
          %llu
3 warnings generated.
mv -f .deps/gsnapl-genome_sites.Tpo .deps/gsnapl-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bitpack64-read.o -MD -MP -MF .deps/gsnapl-bitpack64-read.Tpo -c -o gsnapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/gsnapl-bitpack64-read.Tpo .deps/gsnapl-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indexdb.o -MD -MP -MF .deps/gsnapl-indexdb.Tpo -c -o gsnapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                     ^~~~~~~~
indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
            ^~~
indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
                                    ^~~~~~
indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
7 warnings generated.
mv -f .deps/gsnapl-indexdb.Tpo .deps/gsnapl-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indexdb_hr.o -MD -MP -MF .deps/gsnapl-indexdb_hr.Tpo -c -o gsnapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c:1008:43: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
      printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm);
                             ~~           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
                             %llu
indexdb_hr.c:1232:45: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("#%d--%d:%u  ",i,batch->nentries,batch->position);
                    ~~                      ^~~~~~~~~~~~~~~
                    %llu
2 warnings generated.
mv -f .deps/gsnapl-indexdb_hr.Tpo .deps/gsnapl-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-oligo.o -MD -MP -MF .deps/gsnapl-oligo.Tpo -c -o gsnapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/gsnapl-oligo.Tpo .deps/gsnapl-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chrom.o -MD -MP -MF .deps/gsnapl-chrom.Tpo -c -o gsnapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gsnapl-chrom.Tpo .deps/gsnapl-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-segmentpos.o -MD -MP -MF .deps/gsnapl-segmentpos.Tpo -c -o gsnapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
segmentpos.c:90:41: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length);
                  ~~                    ^~~~~~~~~~~~~~~~~~~~~~~
                  %llu
1 warning generated.
mv -f .deps/gsnapl-segmentpos.Tpo .deps/gsnapl-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chrnum.o -MD -MP -MF .deps/gsnapl-chrnum.Tpo -c -o gsnapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/gsnapl-chrnum.Tpo .deps/gsnapl-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-maxent_hr.o -MD -MP -MF .deps/gsnapl-maxent_hr.Tpo -c -o gsnapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/gsnapl-maxent_hr.Tpo .deps/gsnapl-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-samprint.o -MD -MP -MF .deps/gsnapl-samprint.Tpo -c -o gsnapl-samprint.o `test -f 'samprint.c' || echo './'`samprint.c
mv -f .deps/gsnapl-samprint.Tpo .deps/gsnapl-samprint.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-mapq.o -MD -MP -MF .deps/gsnapl-mapq.Tpo -c -o gsnapl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
mv -f .deps/gsnapl-mapq.Tpo .deps/gsnapl-mapq.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-shortread.o -MD -MP -MF .deps/gsnapl-shortread.Tpo -c -o gsnapl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
mv -f .deps/gsnapl-shortread.Tpo .deps/gsnapl-shortread.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-substring.o -MD -MP -MF .deps/gsnapl-substring.Tpo -c -o gsnapl-substring.o `test -f 'substring.c' || echo './'`substring.c
substring.c:1005:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend);
                ~~              ^~~~~~~~~~~~~~~~
                %llu
substring.c:1005:50: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend);
                    ~~                           ^~~~~~~~~~~~~~
                    %llu
substring.c:3536:35: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"+%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset + 1U,
                      ~~          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %llu
substring.c:3537:7: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
             substring->alignend_trim - substring->chroffset);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
substring.c:3539:35: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"-%s:%u..%u",chr,substring->alignend_trim - substring->chroffset,
                      ~~          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %llu
substring.c:3540:7: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
             substring->alignstart_trim - substring->chroffset + 1U);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
substring.c:3544:35: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"-%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset,
                      ~~          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %llu
substring.c:3545:7: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
             substring->alignend_trim - substring->chroffset + 1U);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
substring.c:3547:35: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"+%s:%u..%u",chr,substring->alignend_trim - substring->chroffset + 1U,
                      ~~          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %llu
substring.c:3548:7: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
             substring->alignstart_trim - substring->chroffset);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10 warnings generated.
mv -f .deps/gsnapl-substring.Tpo .deps/gsnapl-substring.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage3hr.o -MD -MP -MF .deps/gsnapl-stage3hr.Tpo -c -o gsnapl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
mv -f .deps/gsnapl-stage3hr.Tpo .deps/gsnapl-stage3hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-goby.o -MD -MP -MF .deps/gsnapl-goby.Tpo -c -o gsnapl-goby.o `test -f 'goby.c' || echo './'`goby.c
mv -f .deps/gsnapl-goby.Tpo .deps/gsnapl-goby.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-spanningelt.o -MD -MP -MF .deps/gsnapl-spanningelt.Tpo -c -o gsnapl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c
mv -f .deps/gsnapl-spanningelt.Tpo .deps/gsnapl-spanningelt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-cmet.o -MD -MP -MF .deps/gsnapl-cmet.Tpo -c -o gsnapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/gsnapl-cmet.Tpo .deps/gsnapl-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-atoi.o -MD -MP -MF .deps/gsnapl-atoi.Tpo -c -o gsnapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/gsnapl-atoi.Tpo .deps/gsnapl-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-maxent.o -MD -MP -MF .deps/gsnapl-maxent.Tpo -c -o gsnapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/gsnapl-maxent.Tpo .deps/gsnapl-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pair.o -MD -MP -MF .deps/gsnapl-pair.Tpo -c -o gsnapl-pair.o `test -f 'pair.c' || echo './'`pair.c
pair.c:546:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:573:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:600:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:607:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:1273:3: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                chroffset + this->genomepos + ONEBASEDP,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pair.c:1278:3: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                chroffset + this->genomepos + ONEBASEDP,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pair.c:1790:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                        ~~     ^~~~~~~~~~~~~~~~~~~~~~~~~~
                        %llu
pair.c:1790:52: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                           ~~                             ^~~~~~~~~~~~~~~~~~~~~~~~
                           %llu
pair.c:1799:27: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                         ~~      ^~~~~~~~~~~~~~~~~~~~~~~~~~
                         %llu
pair.c:1799:54: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                            ~~                              ^~~~~~~~~~~~~~~~~~~~~~~~
                            %llu
pair.c:1913:26: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                  ~~     ^~~~~~~~~~~~~~~~~~~~~~~~~~
                  %llu
pair.c:1913:53: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                     ~~                             ^~~~~~~~~~~~~~~~~~~~~~~~
                     %llu
pair.c:1922:28: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                   ~~      ^~~~~~~~~~~~~~~~~~~~~~~~~~
                   %llu
pair.c:1922:55: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                      ~~                              ^~~~~~~~~~~~~~~~~~~~~~~~
                      %llu
pair.c:2419:24: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^
pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^
pair.c:4651:17: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^
pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^~~
pair.c:6986:24: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP);
               ~~      ^~~~~~~~~~~~~~~~~~~~~
               %llu
pair.c:6986:51: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP);
                   ~~                             ^~~~~~~~~~~~~~~~~~~~~
                   %llu
18 warnings generated.
mv -f .deps/gsnapl-pair.Tpo .deps/gsnapl-pair.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pairpool.o -MD -MP -MF .deps/gsnapl-pairpool.Tpo -c -o gsnapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/gsnapl-pairpool.Tpo .deps/gsnapl-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-diag.o -MD -MP -MF .deps/gsnapl-diag.Tpo -c -o gsnapl-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/gsnapl-diag.Tpo .deps/gsnapl-diag.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-diagpool.o -MD -MP -MF .deps/gsnapl-diagpool.Tpo -c -o gsnapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/gsnapl-diagpool.Tpo .deps/gsnapl-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-orderstat.o -MD -MP -MF .deps/gsnapl-orderstat.Tpo -c -o gsnapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/gsnapl-orderstat.Tpo .deps/gsnapl-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-oligoindex_hr.o -MD -MP -MF .deps/gsnapl-oligoindex_hr.Tpo -c -o gsnapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/gsnapl-oligoindex_hr.Tpo .deps/gsnapl-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-cellpool.o -MD -MP -MF .deps/gsnapl-cellpool.Tpo -c -o gsnapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/gsnapl-cellpool.Tpo .deps/gsnapl-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage2.o -MD -MP -MF .deps/gsnapl-stage2.Tpo -c -o gsnapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
stage2.c:1329:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
stage2.c:1812:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
2 warnings generated.
mv -f .deps/gsnapl-stage2.Tpo .deps/gsnapl-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-intron.o -MD -MP -MF .deps/gsnapl-intron.Tpo -c -o gsnapl-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/gsnapl-intron.Tpo .deps/gsnapl-intron.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-boyer-moore.o -MD -MP -MF .deps/gsnapl-boyer-moore.Tpo -c -o gsnapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/gsnapl-boyer-moore.Tpo .deps/gsnapl-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-changepoint.o -MD -MP -MF .deps/gsnapl-changepoint.Tpo -c -o gsnapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/gsnapl-changepoint.Tpo .deps/gsnapl-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pbinom.o -MD -MP -MF .deps/gsnapl-pbinom.Tpo -c -o gsnapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/gsnapl-pbinom.Tpo .deps/gsnapl-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-dynprog.o -MD -MP -MF .deps/gsnapl-dynprog.Tpo -c -o gsnapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/gsnapl-dynprog.Tpo .deps/gsnapl-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-gbuffer.o -MD -MP -MF .deps/gsnapl-gbuffer.Tpo -c -o gsnapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
mv -f .deps/gsnapl-gbuffer.Tpo .deps/gsnapl-gbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-translation.o -MD -MP -MF .deps/gsnapl-translation.Tpo -c -o gsnapl-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/gsnapl-translation.Tpo .deps/gsnapl-translation.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-doublelist.o -MD -MP -MF .deps/gsnapl-doublelist.Tpo -c -o gsnapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/gsnapl-doublelist.Tpo .deps/gsnapl-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-smooth.o -MD -MP -MF .deps/gsnapl-smooth.Tpo -c -o gsnapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/gsnapl-smooth.Tpo .deps/gsnapl-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chimera.o -MD -MP -MF .deps/gsnapl-chimera.Tpo -c -o gsnapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/gsnapl-chimera.Tpo .deps/gsnapl-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage3.o -MD -MP -MF .deps/gsnapl-stage3.Tpo -c -o gsnapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/gsnapl-stage3.Tpo .deps/gsnapl-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicestringpool.o -MD -MP -MF .deps/gsnapl-splicestringpool.Tpo -c -o gsnapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/gsnapl-splicestringpool.Tpo .deps/gsnapl-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicetrie_build.o -MD -MP -MF .deps/gsnapl-splicetrie_build.Tpo -c -o gsnapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
splicetrie_build.c:132:31: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%d %u",(int) leaf,position);
               ~~             ^~~~~~~~
               %llu
splicetrie_build.c:146:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
      printf("%d %u",(int) leaf,position);
                 ~~             ^~~~~~~~
                 %llu
2 warnings generated.
mv -f .deps/gsnapl-splicetrie_build.Tpo .deps/gsnapl-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicetrie.o -MD -MP -MF .deps/gsnapl-splicetrie.Tpo -c -o gsnapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/gsnapl-splicetrie.Tpo .deps/gsnapl-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splice.o -MD -MP -MF .deps/gsnapl-splice.Tpo -c -o gsnapl-splice.o `test -f 'splice.c' || echo './'`splice.c
mv -f .deps/gsnapl-splice.Tpo .deps/gsnapl-splice.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indel.o -MD -MP -MF .deps/gsnapl-indel.Tpo -c -o gsnapl-indel.o `test -f 'indel.c' || echo './'`indel.c
mv -f .deps/gsnapl-indel.Tpo .deps/gsnapl-indel.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bitpack64-access.o -MD -MP -MF .deps/gsnapl-bitpack64-access.Tpo -c -o gsnapl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
mv -f .deps/gsnapl-bitpack64-access.Tpo .deps/gsnapl-bitpack64-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-sarray-read.o -MD -MP -MF .deps/gsnapl-sarray-read.Tpo -c -o gsnapl-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c
sarray-read.c:302:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
        new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T));
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:368:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
        new->lcpcomp = (Univcoord_T *) Access_mmap_and_preload(&new->lcpcomp_fd,&new->lcpcomp_len,&npages,&seconds2,
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:434:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
        new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,filename,sizeof(Univcoord_T),
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:526:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
        new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T));
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:653:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
        new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:1399:27: warning: implicit conversion from 'long' to 'int' changes value from 2147483648 to -2147483648 [-Wconstant-conversion]
    base = _mm_set1_epi32(2147483648); /* 2^31 */
           ~~~~~~~~~~~~~~ ^~~~~~~~~~
sarray-read.c:1667:53: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        printf("%d..%d:%u\t",elt->querystart,elt->queryend,elt->positions[k]);
                       ~~                                  ^~~~~~~~~~~~~~~~~
                       %llu
sarray-read.c:1682:56: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%d..%d:%u\n",elt->querystart,elt->queryend,elt->positions[k]);
                   ~~                                  ^~~~~~~~~~~~~~~~~
                   %llu
sarray-read.c:2170:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types]
    array = Uintlist_to_array(&n,difflist);
          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:2442:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:2442:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:2456:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        /*ambcoords_donor*/NULL,ambcoords,
                                                                                                ^~~~~~~~~
./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                                               ^
sarray-read.c:2499:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:2499:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:2513:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        ambcoords,/*ambcoords_acceptor*/NULL,
                                                                        ^~~~~~~~~
./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                  ^
sarray-read.c:2643:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:2643:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:2656:36: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                                        /*ambcoords_donor*/NULL,ambcoords,
                                                                                                                ^~~~~~~~~
./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                                               ^
sarray-read.c:2699:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:2699:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:2712:12: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                                        ambcoords,/*ambcoords_acceptor*/NULL,
                                                                                        ^~~~~~~~~
./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                  ^
sarray-read.c:2752:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types]
    array = Uintlist_to_array(&n,difflist);
          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:3024:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:3024:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:3038:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        /*ambcoords_donor*/NULL,ambcoords,
                                                                                                ^~~~~~~~~
./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                                               ^
sarray-read.c:3082:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:3082:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:3096:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        ambcoords,/*ambcoords_acceptor*/NULL,
                                                                        ^~~~~~~~~
./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                  ^
sarray-read.c:3217:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:3217:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:3231:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        /*ambcoords_donor*/NULL,ambcoords,
                                                                                                ^~~~~~~~~
./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                                               ^
sarray-read.c:3274:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:3274:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:3288:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        ambcoords,/*ambcoords_acceptor*/NULL,
                                                                        ^~~~~~~~~
./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                  ^
34 warnings generated.
mv -f .deps/gsnapl-sarray-read.Tpo .deps/gsnapl-sarray-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage1hr.o -MD -MP -MF .deps/gsnapl-stage1hr.Tpo -c -o gsnapl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
stage1hr.c:6630:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6630:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6630:76: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6769:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor),
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6769:37: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor),
                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6770:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor),
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6770:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor),
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6771:7: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                    segmenti->diagonal - querylength);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7146:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7146:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7146:76: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7285:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7285:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7285:76: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14 warnings generated.
mv -f .deps/gsnapl-stage1hr.Tpo .deps/gsnapl-stage1hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-request.o -MD -MP -MF .deps/gsnapl-request.Tpo -c -o gsnapl-request.o `test -f 'request.c' || echo './'`request.c
mv -f .deps/gsnapl-request.Tpo .deps/gsnapl-request.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-resulthr.o -MD -MP -MF .deps/gsnapl-resulthr.Tpo -c -o gsnapl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
mv -f .deps/gsnapl-resulthr.Tpo .deps/gsnapl-resulthr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-inbuffer.o -MD -MP -MF .deps/gsnapl-inbuffer.Tpo -c -o gsnapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
mv -f .deps/gsnapl-inbuffer.Tpo .deps/gsnapl-inbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-samheader.o -MD -MP -MF .deps/gsnapl-samheader.Tpo -c -o gsnapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
mv -f .deps/gsnapl-samheader.Tpo .deps/gsnapl-samheader.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-outbuffer.o -MD -MP -MF .deps/gsnapl-outbuffer.Tpo -c -o gsnapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
mv -f .deps/gsnapl-outbuffer.Tpo .deps/gsnapl-outbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-datadir.o -MD -MP -MF .deps/gsnapl-datadir.Tpo -c -o gsnapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gsnapl-datadir.Tpo .deps/gsnapl-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-getopt.o -MD -MP -MF .deps/gsnapl-getopt.Tpo -c -o gsnapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gsnapl-getopt.Tpo .deps/gsnapl-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-getopt1.o -MD -MP -MF .deps/gsnapl-getopt1.Tpo -c -o gsnapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gsnapl-getopt1.Tpo .deps/gsnapl-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-gsnap.o -MD -MP -MF .deps/gsnapl-gsnap.Tpo -c -o gsnapl-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c
mv -f .deps/gsnapl-gsnap.Tpo .deps/gsnapl-gsnap.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3     -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-sarray-read.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o  -lz -lbz2  -lm 
libtool: link: gcc -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-sarray-read.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o  -lz -lbz2 -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-except.o -MD -MP -MF .deps/uniqscan-except.Tpo -c -o uniqscan-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/uniqscan-except.Tpo .deps/uniqscan-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-assert.o -MD -MP -MF .deps/uniqscan-assert.Tpo -c -o uniqscan-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/uniqscan-assert.Tpo .deps/uniqscan-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-mem.o -MD -MP -MF .deps/uniqscan-mem.Tpo -c -o uniqscan-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/uniqscan-mem.Tpo .deps/uniqscan-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-intlist.o -MD -MP -MF .deps/uniqscan-intlist.Tpo -c -o uniqscan-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/uniqscan-intlist.Tpo .deps/uniqscan-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-list.o -MD -MP -MF .deps/uniqscan-list.Tpo -c -o uniqscan-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/uniqscan-list.Tpo .deps/uniqscan-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-littleendian.o -MD -MP -MF .deps/uniqscan-littleendian.Tpo -c -o uniqscan-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/uniqscan-littleendian.Tpo .deps/uniqscan-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bigendian.o -MD -MP -MF .deps/uniqscan-bigendian.Tpo -c -o uniqscan-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/uniqscan-bigendian.Tpo .deps/uniqscan-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-univinterval.o -MD -MP -MF .deps/uniqscan-univinterval.Tpo -c -o uniqscan-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %u
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %u
2 warnings generated.
mv -f .deps/uniqscan-univinterval.Tpo .deps/uniqscan-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-interval.o -MD -MP -MF .deps/uniqscan-interval.Tpo -c -o uniqscan-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/uniqscan-interval.Tpo .deps/uniqscan-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-uintlist.o -MD -MP -MF .deps/uniqscan-uintlist.Tpo -c -o uniqscan-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/uniqscan-uintlist.Tpo .deps/uniqscan-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stopwatch.o -MD -MP -MF .deps/uniqscan-stopwatch.Tpo -c -o uniqscan-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/uniqscan-stopwatch.Tpo .deps/uniqscan-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-access.o -MD -MP -MF .deps/uniqscan-access.Tpo -c -o uniqscan-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/uniqscan-access.Tpo .deps/uniqscan-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-iit-read-univ.o -MD -MP -MF .deps/uniqscan-iit-read-univ.Tpo -c -o uniqscan-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %u
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %u
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %u
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %u
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %u
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %u
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %u
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %u
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %u
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %u
10 warnings generated.
mv -f .deps/uniqscan-iit-read-univ.Tpo .deps/uniqscan-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-iit-read.o -MD -MP -MF .deps/uniqscan-iit-read.Tpo -c -o uniqscan-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/uniqscan-iit-read.Tpo .deps/uniqscan-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-md5.o -MD -MP -MF .deps/uniqscan-md5.Tpo -c -o uniqscan-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/uniqscan-md5.Tpo .deps/uniqscan-md5.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bzip2.o -MD -MP -MF .deps/uniqscan-bzip2.Tpo -c -o uniqscan-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/uniqscan-bzip2.Tpo .deps/uniqscan-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-sequence.o -MD -MP -MF .deps/uniqscan-sequence.Tpo -c -o uniqscan-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/uniqscan-sequence.Tpo .deps/uniqscan-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-reader.o -MD -MP -MF .deps/uniqscan-reader.Tpo -c -o uniqscan-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/uniqscan-reader.Tpo .deps/uniqscan-reader.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genomicpos.o -MD -MP -MF .deps/uniqscan-genomicpos.Tpo -c -o uniqscan-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/uniqscan-genomicpos.Tpo .deps/uniqscan-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-compress.o -MD -MP -MF .deps/uniqscan-compress.Tpo -c -o uniqscan-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/uniqscan-compress.Tpo .deps/uniqscan-compress.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome.o -MD -MP -MF .deps/uniqscan-genome.Tpo -c -o uniqscan-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %u
genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %u
genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %u
genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned int') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %u
4 warnings generated.
mv -f .deps/uniqscan-genome.Tpo .deps/uniqscan-genome.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome_hr.o -MD -MP -MF .deps/uniqscan-genome_hr.Tpo -c -o uniqscan-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/uniqscan-genome_hr.Tpo .deps/uniqscan-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome_sites.o -MD -MP -MF .deps/uniqscan-genome_sites.Tpo -c -o uniqscan-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
mv -f .deps/uniqscan-genome_sites.Tpo .deps/uniqscan-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bitpack64-read.o -MD -MP -MF .deps/uniqscan-bitpack64-read.Tpo -c -o uniqscan-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/uniqscan-bitpack64-read.Tpo .deps/uniqscan-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indexdb.o -MD -MP -MF .deps/uniqscan-indexdb.Tpo -c -o uniqscan-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                     ^~~~~~~~
indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
            ^~~
indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
                                    ^~~~~~
indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
7 warnings generated.
mv -f .deps/uniqscan-indexdb.Tpo .deps/uniqscan-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indexdb_hr.o -MD -MP -MF .deps/uniqscan-indexdb_hr.Tpo -c -o uniqscan-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
mv -f .deps/uniqscan-indexdb_hr.Tpo .deps/uniqscan-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-oligo.o -MD -MP -MF .deps/uniqscan-oligo.Tpo -c -o uniqscan-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/uniqscan-oligo.Tpo .deps/uniqscan-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chrom.o -MD -MP -MF .deps/uniqscan-chrom.Tpo -c -o uniqscan-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/uniqscan-chrom.Tpo .deps/uniqscan-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-segmentpos.o -MD -MP -MF .deps/uniqscan-segmentpos.Tpo -c -o uniqscan-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
mv -f .deps/uniqscan-segmentpos.Tpo .deps/uniqscan-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chrnum.o -MD -MP -MF .deps/uniqscan-chrnum.Tpo -c -o uniqscan-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/uniqscan-chrnum.Tpo .deps/uniqscan-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-maxent_hr.o -MD -MP -MF .deps/uniqscan-maxent_hr.Tpo -c -o uniqscan-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/uniqscan-maxent_hr.Tpo .deps/uniqscan-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-mapq.o -MD -MP -MF .deps/uniqscan-mapq.Tpo -c -o uniqscan-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
mv -f .deps/uniqscan-mapq.Tpo .deps/uniqscan-mapq.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-shortread.o -MD -MP -MF .deps/uniqscan-shortread.Tpo -c -o uniqscan-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
mv -f .deps/uniqscan-shortread.Tpo .deps/uniqscan-shortread.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-substring.o -MD -MP -MF .deps/uniqscan-substring.Tpo -c -o uniqscan-substring.o `test -f 'substring.c' || echo './'`substring.c
mv -f .deps/uniqscan-substring.Tpo .deps/uniqscan-substring.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage3hr.o -MD -MP -MF .deps/uniqscan-stage3hr.Tpo -c -o uniqscan-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
mv -f .deps/uniqscan-stage3hr.Tpo .deps/uniqscan-stage3hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-spanningelt.o -MD -MP -MF .deps/uniqscan-spanningelt.Tpo -c -o uniqscan-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c
mv -f .deps/uniqscan-spanningelt.Tpo .deps/uniqscan-spanningelt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-cmet.o -MD -MP -MF .deps/uniqscan-cmet.Tpo -c -o uniqscan-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/uniqscan-cmet.Tpo .deps/uniqscan-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-atoi.o -MD -MP -MF .deps/uniqscan-atoi.Tpo -c -o uniqscan-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/uniqscan-atoi.Tpo .deps/uniqscan-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-maxent.o -MD -MP -MF .deps/uniqscan-maxent.Tpo -c -o uniqscan-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/uniqscan-maxent.Tpo .deps/uniqscan-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pair.o -MD -MP -MF .deps/uniqscan-pair.Tpo -c -o uniqscan-pair.o `test -f 'pair.c' || echo './'`pair.c
pair.c:2419:24: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^
pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^
pair.c:4651:17: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^
pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^~~
2 warnings generated.
mv -f .deps/uniqscan-pair.Tpo .deps/uniqscan-pair.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pairpool.o -MD -MP -MF .deps/uniqscan-pairpool.Tpo -c -o uniqscan-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/uniqscan-pairpool.Tpo .deps/uniqscan-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-diag.o -MD -MP -MF .deps/uniqscan-diag.Tpo -c -o uniqscan-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/uniqscan-diag.Tpo .deps/uniqscan-diag.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-diagpool.o -MD -MP -MF .deps/uniqscan-diagpool.Tpo -c -o uniqscan-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/uniqscan-diagpool.Tpo .deps/uniqscan-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-orderstat.o -MD -MP -MF .deps/uniqscan-orderstat.Tpo -c -o uniqscan-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/uniqscan-orderstat.Tpo .deps/uniqscan-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-oligoindex_hr.o -MD -MP -MF .deps/uniqscan-oligoindex_hr.Tpo -c -o uniqscan-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/uniqscan-oligoindex_hr.Tpo .deps/uniqscan-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-cellpool.o -MD -MP -MF .deps/uniqscan-cellpool.Tpo -c -o uniqscan-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/uniqscan-cellpool.Tpo .deps/uniqscan-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage2.o -MD -MP -MF .deps/uniqscan-stage2.Tpo -c -o uniqscan-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
stage2.c:1329:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
stage2.c:1812:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
2 warnings generated.
mv -f .deps/uniqscan-stage2.Tpo .deps/uniqscan-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-intron.o -MD -MP -MF .deps/uniqscan-intron.Tpo -c -o uniqscan-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/uniqscan-intron.Tpo .deps/uniqscan-intron.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-boyer-moore.o -MD -MP -MF .deps/uniqscan-boyer-moore.Tpo -c -o uniqscan-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/uniqscan-boyer-moore.Tpo .deps/uniqscan-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-changepoint.o -MD -MP -MF .deps/uniqscan-changepoint.Tpo -c -o uniqscan-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/uniqscan-changepoint.Tpo .deps/uniqscan-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pbinom.o -MD -MP -MF .deps/uniqscan-pbinom.Tpo -c -o uniqscan-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/uniqscan-pbinom.Tpo .deps/uniqscan-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-dynprog.o -MD -MP -MF .deps/uniqscan-dynprog.Tpo -c -o uniqscan-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/uniqscan-dynprog.Tpo .deps/uniqscan-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-translation.o -MD -MP -MF .deps/uniqscan-translation.Tpo -c -o uniqscan-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/uniqscan-translation.Tpo .deps/uniqscan-translation.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-doublelist.o -MD -MP -MF .deps/uniqscan-doublelist.Tpo -c -o uniqscan-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/uniqscan-doublelist.Tpo .deps/uniqscan-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-smooth.o -MD -MP -MF .deps/uniqscan-smooth.Tpo -c -o uniqscan-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/uniqscan-smooth.Tpo .deps/uniqscan-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chimera.o -MD -MP -MF .deps/uniqscan-chimera.Tpo -c -o uniqscan-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/uniqscan-chimera.Tpo .deps/uniqscan-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage3.o -MD -MP -MF .deps/uniqscan-stage3.Tpo -c -o uniqscan-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/uniqscan-stage3.Tpo .deps/uniqscan-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicestringpool.o -MD -MP -MF .deps/uniqscan-splicestringpool.Tpo -c -o uniqscan-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/uniqscan-splicestringpool.Tpo .deps/uniqscan-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicetrie_build.o -MD -MP -MF .deps/uniqscan-splicetrie_build.Tpo -c -o uniqscan-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
mv -f .deps/uniqscan-splicetrie_build.Tpo .deps/uniqscan-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicetrie.o -MD -MP -MF .deps/uniqscan-splicetrie.Tpo -c -o uniqscan-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/uniqscan-splicetrie.Tpo .deps/uniqscan-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splice.o -MD -MP -MF .deps/uniqscan-splice.Tpo -c -o uniqscan-splice.o `test -f 'splice.c' || echo './'`splice.c
mv -f .deps/uniqscan-splice.Tpo .deps/uniqscan-splice.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indel.o -MD -MP -MF .deps/uniqscan-indel.Tpo -c -o uniqscan-indel.o `test -f 'indel.c' || echo './'`indel.c
mv -f .deps/uniqscan-indel.Tpo .deps/uniqscan-indel.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bitpack64-access.o -MD -MP -MF .deps/uniqscan-bitpack64-access.Tpo -c -o uniqscan-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
mv -f .deps/uniqscan-bitpack64-access.Tpo .deps/uniqscan-bitpack64-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-sarray-read.o -MD -MP -MF .deps/uniqscan-sarray-read.Tpo -c -o uniqscan-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c
sarray-read.c:1399:27: warning: implicit conversion from 'long' to 'int' changes value from 2147483648 to -2147483648 [-Wconstant-conversion]
    base = _mm_set1_epi32(2147483648); /* 2^31 */
           ~~~~~~~~~~~~~~ ^~~~~~~~~~
1 warning generated.
mv -f .deps/uniqscan-sarray-read.Tpo .deps/uniqscan-sarray-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage1hr.o -MD -MP -MF .deps/uniqscan-stage1hr.Tpo -c -o uniqscan-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
mv -f .deps/uniqscan-stage1hr.Tpo .deps/uniqscan-stage1hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-resulthr.o -MD -MP -MF .deps/uniqscan-resulthr.Tpo -c -o uniqscan-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
mv -f .deps/uniqscan-resulthr.Tpo .deps/uniqscan-resulthr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-datadir.o -MD -MP -MF .deps/uniqscan-datadir.Tpo -c -o uniqscan-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/uniqscan-datadir.Tpo .deps/uniqscan-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-getopt.o -MD -MP -MF .deps/uniqscan-getopt.Tpo -c -o uniqscan-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/uniqscan-getopt.Tpo .deps/uniqscan-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-getopt1.o -MD -MP -MF .deps/uniqscan-getopt1.Tpo -c -o uniqscan-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/uniqscan-getopt1.Tpo .deps/uniqscan-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-uniqscan.o -MD -MP -MF .deps/uniqscan-uniqscan.Tpo -c -o uniqscan-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c
mv -f .deps/uniqscan-uniqscan.Tpo .deps/uniqscan-uniqscan.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3    -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o  -lz -lbz2 -lm 
libtool: link: gcc -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o  -lz -lbz2 -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-except.o -MD -MP -MF .deps/uniqscanl-except.Tpo -c -o uniqscanl-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/uniqscanl-except.Tpo .deps/uniqscanl-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-assert.o -MD -MP -MF .deps/uniqscanl-assert.Tpo -c -o uniqscanl-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/uniqscanl-assert.Tpo .deps/uniqscanl-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-mem.o -MD -MP -MF .deps/uniqscanl-mem.Tpo -c -o uniqscanl-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/uniqscanl-mem.Tpo .deps/uniqscanl-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-intlist.o -MD -MP -MF .deps/uniqscanl-intlist.Tpo -c -o uniqscanl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/uniqscanl-intlist.Tpo .deps/uniqscanl-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-list.o -MD -MP -MF .deps/uniqscanl-list.Tpo -c -o uniqscanl-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/uniqscanl-list.Tpo .deps/uniqscanl-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-littleendian.o -MD -MP -MF .deps/uniqscanl-littleendian.Tpo -c -o uniqscanl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/uniqscanl-littleendian.Tpo .deps/uniqscanl-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bigendian.o -MD -MP -MF .deps/uniqscanl-bigendian.Tpo -c -o uniqscanl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/uniqscanl-bigendian.Tpo .deps/uniqscanl-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-univinterval.o -MD -MP -MF .deps/uniqscanl-univinterval.Tpo -c -o uniqscanl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %llu
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %llu
2 warnings generated.
mv -f .deps/uniqscanl-univinterval.Tpo .deps/uniqscanl-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-interval.o -MD -MP -MF .deps/uniqscanl-interval.Tpo -c -o uniqscanl-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/uniqscanl-interval.Tpo .deps/uniqscanl-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uintlist.o -MD -MP -MF .deps/uniqscanl-uintlist.Tpo -c -o uniqscanl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/uniqscanl-uintlist.Tpo .deps/uniqscanl-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uint8list.o -MD -MP -MF .deps/uniqscanl-uint8list.Tpo -c -o uniqscanl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
uint8list.c:202:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
      sprintf(Buffer,"%u,",Uint8list_head(p));
                      ~~   ^~~~~~~~~~~~~~~~~
                      %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
uint8list.c:205:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
    sprintf(Buffer,"%u",Uint8list_head(p));
                    ~~  ^~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
uint8list.c:211:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
      sprintf(Buffer,"%u,",Uint8list_head(p));
                      ~~   ^~~~~~~~~~~~~~~~~
                      %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
uint8list.c:214:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
    sprintf(Buffer,"%u",Uint8list_head(p));
                    ~~  ^~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
4 warnings generated.
mv -f .deps/uniqscanl-uint8list.Tpo .deps/uniqscanl-uint8list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stopwatch.o -MD -MP -MF .deps/uniqscanl-stopwatch.Tpo -c -o uniqscanl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/uniqscanl-stopwatch.Tpo .deps/uniqscanl-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-access.o -MD -MP -MF .deps/uniqscanl-access.Tpo -c -o uniqscanl-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/uniqscanl-access.Tpo .deps/uniqscanl-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-iit-read-univ.o -MD -MP -MF .deps/uniqscanl-iit-read-univ.Tpo -c -o uniqscanl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %llu
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %llu
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %llu
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %llu
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %llu
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %llu
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %llu
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %llu
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %llu
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %llu
10 warnings generated.
mv -f .deps/uniqscanl-iit-read-univ.Tpo .deps/uniqscanl-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-iit-read.o -MD -MP -MF .deps/uniqscanl-iit-read.Tpo -c -o uniqscanl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/uniqscanl-iit-read.Tpo .deps/uniqscanl-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-md5.o -MD -MP -MF .deps/uniqscanl-md5.Tpo -c -o uniqscanl-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/uniqscanl-md5.Tpo .deps/uniqscanl-md5.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bzip2.o -MD -MP -MF .deps/uniqscanl-bzip2.Tpo -c -o uniqscanl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/uniqscanl-bzip2.Tpo .deps/uniqscanl-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-sequence.o -MD -MP -MF .deps/uniqscanl-sequence.Tpo -c -o uniqscanl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/uniqscanl-sequence.Tpo .deps/uniqscanl-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-reader.o -MD -MP -MF .deps/uniqscanl-reader.Tpo -c -o uniqscanl-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/uniqscanl-reader.Tpo .deps/uniqscanl-reader.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genomicpos.o -MD -MP -MF .deps/uniqscanl-genomicpos.Tpo -c -o uniqscanl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/uniqscanl-genomicpos.Tpo .deps/uniqscanl-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-compress.o -MD -MP -MF .deps/uniqscanl-compress.Tpo -c -o uniqscanl-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/uniqscanl-compress.Tpo .deps/uniqscanl-compress.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome.o -MD -MP -MF .deps/uniqscanl-genome.Tpo -c -o uniqscanl-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
4 warnings generated.
mv -f .deps/uniqscanl-genome.Tpo .deps/uniqscanl-genome.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome_hr.o -MD -MP -MF .deps/uniqscanl-genome_hr.Tpo -c -o uniqscanl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/uniqscanl-genome_hr.Tpo .deps/uniqscanl-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome_sites.o -MD -MP -MF .deps/uniqscanl-genome_sites.Tpo -c -o uniqscanl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
genome_sites.c:24729:17: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  printf("%u\t",startblock/3*32U);
          ~~    ^~~~~~~~~~~~~~~~
          %llu
genome_sites.c:24744:19: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    printf("%u\t",ptr/3*32U);
            ~~    ^~~~~~~~~
            %llu
genome_sites.c:24751:17: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  printf("%u\t",(endblock+3)/3*32U);
          ~~    ^~~~~~~~~~~~~~~~~~
          %llu
3 warnings generated.
mv -f .deps/uniqscanl-genome_sites.Tpo .deps/uniqscanl-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bitpack64-read.o -MD -MP -MF .deps/uniqscanl-bitpack64-read.Tpo -c -o uniqscanl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/uniqscanl-bitpack64-read.Tpo .deps/uniqscanl-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indexdb.o -MD -MP -MF .deps/uniqscanl-indexdb.Tpo -c -o uniqscanl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                     ^~~~~~~~
indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
            ^~~
indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
                                    ^~~~~~
indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
7 warnings generated.
mv -f .deps/uniqscanl-indexdb.Tpo .deps/uniqscanl-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indexdb_hr.o -MD -MP -MF .deps/uniqscanl-indexdb_hr.Tpo -c -o uniqscanl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c:1008:43: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
      printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm);
                             ~~           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
                             %llu
indexdb_hr.c:1232:45: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("#%d--%d:%u  ",i,batch->nentries,batch->position);
                    ~~                      ^~~~~~~~~~~~~~~
                    %llu
2 warnings generated.
mv -f .deps/uniqscanl-indexdb_hr.Tpo .deps/uniqscanl-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-oligo.o -MD -MP -MF .deps/uniqscanl-oligo.Tpo -c -o uniqscanl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/uniqscanl-oligo.Tpo .deps/uniqscanl-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chrom.o -MD -MP -MF .deps/uniqscanl-chrom.Tpo -c -o uniqscanl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/uniqscanl-chrom.Tpo .deps/uniqscanl-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-segmentpos.o -MD -MP -MF .deps/uniqscanl-segmentpos.Tpo -c -o uniqscanl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
segmentpos.c:90:41: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length);
                  ~~                    ^~~~~~~~~~~~~~~~~~~~~~~
                  %llu
1 warning generated.
mv -f .deps/uniqscanl-segmentpos.Tpo .deps/uniqscanl-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chrnum.o -MD -MP -MF .deps/uniqscanl-chrnum.Tpo -c -o uniqscanl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/uniqscanl-chrnum.Tpo .deps/uniqscanl-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-maxent_hr.o -MD -MP -MF .deps/uniqscanl-maxent_hr.Tpo -c -o uniqscanl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/uniqscanl-maxent_hr.Tpo .deps/uniqscanl-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-mapq.o -MD -MP -MF .deps/uniqscanl-mapq.Tpo -c -o uniqscanl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
mv -f .deps/uniqscanl-mapq.Tpo .deps/uniqscanl-mapq.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-shortread.o -MD -MP -MF .deps/uniqscanl-shortread.Tpo -c -o uniqscanl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
mv -f .deps/uniqscanl-shortread.Tpo .deps/uniqscanl-shortread.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-substring.o -MD -MP -MF .deps/uniqscanl-substring.Tpo -c -o uniqscanl-substring.o `test -f 'substring.c' || echo './'`substring.c
substring.c:1005:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend);
                ~~              ^~~~~~~~~~~~~~~~
                %llu
substring.c:1005:50: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend);
                    ~~                           ^~~~~~~~~~~~~~
                    %llu
substring.c:3536:35: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"+%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset + 1U,
                      ~~          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %llu
substring.c:3537:7: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
             substring->alignend_trim - substring->chroffset);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
substring.c:3539:35: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"-%s:%u..%u",chr,substring->alignend_trim - substring->chroffset,
                      ~~          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %llu
substring.c:3540:7: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
             substring->alignstart_trim - substring->chroffset + 1U);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
substring.c:3544:35: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"-%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset,
                      ~~          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %llu
substring.c:3545:7: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
             substring->alignend_trim - substring->chroffset + 1U);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
substring.c:3547:35: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"+%s:%u..%u",chr,substring->alignend_trim - substring->chroffset + 1U,
                      ~~          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %llu
substring.c:3548:7: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
             substring->alignstart_trim - substring->chroffset);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10 warnings generated.
mv -f .deps/uniqscanl-substring.Tpo .deps/uniqscanl-substring.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage3hr.o -MD -MP -MF .deps/uniqscanl-stage3hr.Tpo -c -o uniqscanl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
mv -f .deps/uniqscanl-stage3hr.Tpo .deps/uniqscanl-stage3hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-spanningelt.o -MD -MP -MF .deps/uniqscanl-spanningelt.Tpo -c -o uniqscanl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c
mv -f .deps/uniqscanl-spanningelt.Tpo .deps/uniqscanl-spanningelt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-cmet.o -MD -MP -MF .deps/uniqscanl-cmet.Tpo -c -o uniqscanl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/uniqscanl-cmet.Tpo .deps/uniqscanl-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-atoi.o -MD -MP -MF .deps/uniqscanl-atoi.Tpo -c -o uniqscanl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/uniqscanl-atoi.Tpo .deps/uniqscanl-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-maxent.o -MD -MP -MF .deps/uniqscanl-maxent.Tpo -c -o uniqscanl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/uniqscanl-maxent.Tpo .deps/uniqscanl-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pair.o -MD -MP -MF .deps/uniqscanl-pair.Tpo -c -o uniqscanl-pair.o `test -f 'pair.c' || echo './'`pair.c
pair.c:546:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:573:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:600:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:607:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
    sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP);
    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                    %llu
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^~~~~~~~~~~
pair.c:1273:3: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                chroffset + this->genomepos + ONEBASEDP,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pair.c:1278:3: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                chroffset + this->genomepos + ONEBASEDP,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pair.c:1790:25: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                        ~~     ^~~~~~~~~~~~~~~~~~~~~~~~~~
                        %llu
pair.c:1790:52: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                           ~~                             ^~~~~~~~~~~~~~~~~~~~~~~~
                           %llu
pair.c:1799:27: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                         ~~      ^~~~~~~~~~~~~~~~~~~~~~~~~~
                         %llu
pair.c:1799:54: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
            fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                            ~~                              ^~~~~~~~~~~~~~~~~~~~~~~~
                            %llu
pair.c:1913:26: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                  ~~     ^~~~~~~~~~~~~~~~~~~~~~~~~~
                  %llu
pair.c:1913:53: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                     ~~                             ^~~~~~~~~~~~~~~~~~~~~~~~
                     %llu
pair.c:1922:28: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                   ~~      ^~~~~~~~~~~~~~~~~~~~~~~~~~
                   %llu
pair.c:1922:55: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                      ~~                              ^~~~~~~~~~~~~~~~~~~~~~~~
                      %llu
pair.c:2419:24: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^
pair.c:2419:24: note: remove the call to 'abs' since unsigned values cannot be negative
          sprintf(token,"N%u",abs(intron_end - intron_start) + 1);
                              ^~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                                                       ^
pair.c:4651:17: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^
pair.c:4651:17: note: remove the call to 'abs' since unsigned values cannot be negative
          genome_gap = abs(intron_end - intron_start) + 1;
                       ^~~
pair.c:6986:24: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP);
               ~~      ^~~~~~~~~~~~~~~~~~~~~
               %llu
pair.c:6986:51: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP);
                   ~~                             ^~~~~~~~~~~~~~~~~~~~~
                   %llu
18 warnings generated.
mv -f .deps/uniqscanl-pair.Tpo .deps/uniqscanl-pair.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pairpool.o -MD -MP -MF .deps/uniqscanl-pairpool.Tpo -c -o uniqscanl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/uniqscanl-pairpool.Tpo .deps/uniqscanl-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-diag.o -MD -MP -MF .deps/uniqscanl-diag.Tpo -c -o uniqscanl-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/uniqscanl-diag.Tpo .deps/uniqscanl-diag.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-diagpool.o -MD -MP -MF .deps/uniqscanl-diagpool.Tpo -c -o uniqscanl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/uniqscanl-diagpool.Tpo .deps/uniqscanl-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-orderstat.o -MD -MP -MF .deps/uniqscanl-orderstat.Tpo -c -o uniqscanl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/uniqscanl-orderstat.Tpo .deps/uniqscanl-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-oligoindex_hr.o -MD -MP -MF .deps/uniqscanl-oligoindex_hr.Tpo -c -o uniqscanl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/uniqscanl-oligoindex_hr.Tpo .deps/uniqscanl-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-cellpool.o -MD -MP -MF .deps/uniqscanl-cellpool.Tpo -c -o uniqscanl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/uniqscanl-cellpool.Tpo .deps/uniqscanl-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage2.o -MD -MP -MF .deps/uniqscanl-stage2.Tpo -c -o uniqscanl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
stage2.c:1329:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1329:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
stage2.c:1812:19: warning: taking the absolute value of unsigned type 'unsigned int' has no effect [-Wabsolute-value]
          diffdistance = abs(gendistance - querydistance);
                         ^
stage2.c:1812:19: note: remove the call to 'abs' since unsigned values cannot be negative
          diffdistance = abs(gendistance - querydistance);
                         ^~~
2 warnings generated.
mv -f .deps/uniqscanl-stage2.Tpo .deps/uniqscanl-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-intron.o -MD -MP -MF .deps/uniqscanl-intron.Tpo -c -o uniqscanl-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/uniqscanl-intron.Tpo .deps/uniqscanl-intron.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-boyer-moore.o -MD -MP -MF .deps/uniqscanl-boyer-moore.Tpo -c -o uniqscanl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/uniqscanl-boyer-moore.Tpo .deps/uniqscanl-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-changepoint.o -MD -MP -MF .deps/uniqscanl-changepoint.Tpo -c -o uniqscanl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/uniqscanl-changepoint.Tpo .deps/uniqscanl-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pbinom.o -MD -MP -MF .deps/uniqscanl-pbinom.Tpo -c -o uniqscanl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/uniqscanl-pbinom.Tpo .deps/uniqscanl-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-dynprog.o -MD -MP -MF .deps/uniqscanl-dynprog.Tpo -c -o uniqscanl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/uniqscanl-dynprog.Tpo .deps/uniqscanl-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-translation.o -MD -MP -MF .deps/uniqscanl-translation.Tpo -c -o uniqscanl-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/uniqscanl-translation.Tpo .deps/uniqscanl-translation.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-doublelist.o -MD -MP -MF .deps/uniqscanl-doublelist.Tpo -c -o uniqscanl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/uniqscanl-doublelist.Tpo .deps/uniqscanl-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-smooth.o -MD -MP -MF .deps/uniqscanl-smooth.Tpo -c -o uniqscanl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/uniqscanl-smooth.Tpo .deps/uniqscanl-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chimera.o -MD -MP -MF .deps/uniqscanl-chimera.Tpo -c -o uniqscanl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/uniqscanl-chimera.Tpo .deps/uniqscanl-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage3.o -MD -MP -MF .deps/uniqscanl-stage3.Tpo -c -o uniqscanl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/uniqscanl-stage3.Tpo .deps/uniqscanl-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicestringpool.o -MD -MP -MF .deps/uniqscanl-splicestringpool.Tpo -c -o uniqscanl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/uniqscanl-splicestringpool.Tpo .deps/uniqscanl-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicetrie_build.o -MD -MP -MF .deps/uniqscanl-splicetrie_build.Tpo -c -o uniqscanl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
splicetrie_build.c:132:31: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%d %u",(int) leaf,position);
               ~~             ^~~~~~~~
               %llu
splicetrie_build.c:146:33: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
      printf("%d %u",(int) leaf,position);
                 ~~             ^~~~~~~~
                 %llu
2 warnings generated.
mv -f .deps/uniqscanl-splicetrie_build.Tpo .deps/uniqscanl-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicetrie.o -MD -MP -MF .deps/uniqscanl-splicetrie.Tpo -c -o uniqscanl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/uniqscanl-splicetrie.Tpo .deps/uniqscanl-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splice.o -MD -MP -MF .deps/uniqscanl-splice.Tpo -c -o uniqscanl-splice.o `test -f 'splice.c' || echo './'`splice.c
mv -f .deps/uniqscanl-splice.Tpo .deps/uniqscanl-splice.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indel.o -MD -MP -MF .deps/uniqscanl-indel.Tpo -c -o uniqscanl-indel.o `test -f 'indel.c' || echo './'`indel.c
mv -f .deps/uniqscanl-indel.Tpo .deps/uniqscanl-indel.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bitpack64-access.o -MD -MP -MF .deps/uniqscanl-bitpack64-access.Tpo -c -o uniqscanl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
mv -f .deps/uniqscanl-bitpack64-access.Tpo .deps/uniqscanl-bitpack64-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-sarray-read.o -MD -MP -MF .deps/uniqscanl-sarray-read.Tpo -c -o uniqscanl-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c
sarray-read.c:302:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
        new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T));
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:368:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
        new->lcpcomp = (Univcoord_T *) Access_mmap_and_preload(&new->lcpcomp_fd,&new->lcpcomp_len,&npages,&seconds2,
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:434:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
        new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,filename,sizeof(Univcoord_T),
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:526:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
        new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T));
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:653:15: warning: incompatible pointer types assigning to 'UINT4 *' (aka 'unsigned int *') from 'Univcoord_T *' (aka 'unsigned long long *') [-Wincompatible-pointer-types]
        new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:1399:27: warning: implicit conversion from 'long' to 'int' changes value from 2147483648 to -2147483648 [-Wconstant-conversion]
    base = _mm_set1_epi32(2147483648); /* 2^31 */
           ~~~~~~~~~~~~~~ ^~~~~~~~~~
sarray-read.c:1667:53: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        printf("%d..%d:%u\t",elt->querystart,elt->queryend,elt->positions[k]);
                       ~~                                  ^~~~~~~~~~~~~~~~~
                       %llu
sarray-read.c:1682:56: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%d..%d:%u\n",elt->querystart,elt->queryend,elt->positions[k]);
                   ~~                                  ^~~~~~~~~~~~~~~~~
                   %llu
sarray-read.c:2170:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types]
    array = Uintlist_to_array(&n,difflist);
          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:2442:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:2442:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:2456:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        /*ambcoords_donor*/NULL,ambcoords,
                                                                                                ^~~~~~~~~
./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                                               ^
sarray-read.c:2499:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:2499:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:2513:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        ambcoords,/*ambcoords_acceptor*/NULL,
                                                                        ^~~~~~~~~
./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                  ^
sarray-read.c:2643:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:2643:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:2656:36: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                                        /*ambcoords_donor*/NULL,ambcoords,
                                                                                                                ^~~~~~~~~
./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                                               ^
sarray-read.c:2699:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:2699:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:2712:12: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                                        ambcoords,/*ambcoords_acceptor*/NULL,
                                                                                        ^~~~~~~~~
./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                  ^
sarray-read.c:2752:11: warning: incompatible pointer types assigning to 'Univcoord_T *' (aka 'unsigned long long *') from 'UINT4 *' (aka 'unsigned int *') [-Wincompatible-pointer-types]
    array = Uintlist_to_array(&n,difflist);
          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:3024:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:3024:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:3038:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        /*ambcoords_donor*/NULL,ambcoords,
                                                                                                ^~~~~~~~~
./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                                               ^
sarray-read.c:3082:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:3082:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:3096:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        ambcoords,/*ambcoords_acceptor*/NULL,
                                                                        ^~~~~~~~~
./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                  ^
sarray-read.c:3217:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:3217:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:3231:34: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        /*ambcoords_donor*/NULL,ambcoords,
                                                                                                ^~~~~~~~~
./stage3hr.h:296:50: note: passing argument to parameter 'ambcoords_acceptor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                                               ^
sarray-read.c:3274:30: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                                           ^~~~~~~~~
./uint8list.h:11:19: note: passing argument to parameter 'list' here
Uint8list_push (T list, UINT8 x);
                  ^
sarray-read.c:3274:13: warning: incompatible pointer types assigning to 'Uintlist_T' (aka 'struct Uintlist_T *') from 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                          ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sarray-read.c:3288:10: warning: incompatible pointer types passing 'Uintlist_T' (aka 'struct Uintlist_T *') to parameter of type 'Uint8list_T' (aka 'struct Uint8list_T *') [-Wincompatible-pointer-types]
                                                                        ambcoords,/*ambcoords_acceptor*/NULL,
                                                                        ^~~~~~~~~
./stage3hr.h:296:21: note: passing argument to parameter 'ambcoords_donor' here
                      Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
                                  ^
34 warnings generated.
mv -f .deps/uniqscanl-sarray-read.Tpo .deps/uniqscanl-sarray-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage1hr.o -MD -MP -MF .deps/uniqscanl-stage1hr.Tpo -c -o uniqscanl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
stage1hr.c:6630:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6630:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6630:76: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6769:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor),
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6769:37: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_genomicstart(donor),Substring_genomicend(donor),Substring_plusp(donor),
                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6770:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor),
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6770:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_genomicstart(acceptor),Substring_genomicend(acceptor),Substring_plusp(acceptor),
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:6771:7: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                    segmenti->diagonal - querylength);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7146:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7146:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7146:76: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7285:7: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7285:40: warning: format specifies type 'unsigned int' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stage1hr.c:7285:76: warning: format specifies type 'unsigned int' but the argument has type 'unsigned long long' [-Wformat]
                    Substring_left_genomicseg(donor),Substring_left_genomicseg(acceptor),segmenti->diagonal - querylength);
                                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14 warnings generated.
mv -f .deps/uniqscanl-stage1hr.Tpo .deps/uniqscanl-stage1hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-resulthr.o -MD -MP -MF .deps/uniqscanl-resulthr.Tpo -c -o uniqscanl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
mv -f .deps/uniqscanl-resulthr.Tpo .deps/uniqscanl-resulthr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-datadir.o -MD -MP -MF .deps/uniqscanl-datadir.Tpo -c -o uniqscanl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/uniqscanl-datadir.Tpo .deps/uniqscanl-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-getopt.o -MD -MP -MF .deps/uniqscanl-getopt.Tpo -c -o uniqscanl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/uniqscanl-getopt.Tpo .deps/uniqscanl-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-getopt1.o -MD -MP -MF .deps/uniqscanl-getopt1.Tpo -c -o uniqscanl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/uniqscanl-getopt1.Tpo .deps/uniqscanl-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uniqscan.o -MD -MP -MF .deps/uniqscanl-uniqscan.Tpo -c -o uniqscanl-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c
mv -f .deps/uniqscanl-uniqscan.Tpo .deps/uniqscanl-uniqscan.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3    -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-sarray-read.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o  -lz -lbz2 -lm 
libtool: link: gcc -D_THREAD_SAFE -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-apple-darwin18.7.0\" -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-sarray-read.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o  -lz -lbz2 -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-except.o -MD -MP -MF .deps/snpindex-except.Tpo -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/snpindex-except.Tpo .deps/snpindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-assert.o -MD -MP -MF .deps/snpindex-assert.Tpo -c -o snpindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/snpindex-assert.Tpo .deps/snpindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-mem.o -MD -MP -MF .deps/snpindex-mem.Tpo -c -o snpindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/snpindex-mem.Tpo .deps/snpindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-intlist.o -MD -MP -MF .deps/snpindex-intlist.Tpo -c -o snpindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/snpindex-intlist.Tpo .deps/snpindex-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-list.o -MD -MP -MF .deps/snpindex-list.Tpo -c -o snpindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/snpindex-list.Tpo .deps/snpindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-littleendian.o -MD -MP -MF .deps/snpindex-littleendian.Tpo -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/snpindex-littleendian.Tpo .deps/snpindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bigendian.o -MD -MP -MF .deps/snpindex-bigendian.Tpo -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/snpindex-bigendian.Tpo .deps/snpindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-univinterval.o -MD -MP -MF .deps/snpindex-univinterval.Tpo -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %llu
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %llu
2 warnings generated.
mv -f .deps/snpindex-univinterval.Tpo .deps/snpindex-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-interval.o -MD -MP -MF .deps/snpindex-interval.Tpo -c -o snpindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/snpindex-interval.Tpo .deps/snpindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-uintlist.o -MD -MP -MF .deps/snpindex-uintlist.Tpo -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/snpindex-uintlist.Tpo .deps/snpindex-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-stopwatch.o -MD -MP -MF .deps/snpindex-stopwatch.Tpo -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/snpindex-stopwatch.Tpo .deps/snpindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-access.o -MD -MP -MF .deps/snpindex-access.Tpo -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/snpindex-access.Tpo .deps/snpindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-iit-read-univ.o -MD -MP -MF .deps/snpindex-iit-read-univ.Tpo -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %llu
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %llu
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %llu
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %llu
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %llu
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %llu
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %llu
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %llu
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %llu
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %llu
10 warnings generated.
mv -f .deps/snpindex-iit-read-univ.Tpo .deps/snpindex-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-iit-read.o -MD -MP -MF .deps/snpindex-iit-read.Tpo -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/snpindex-iit-read.Tpo .deps/snpindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genomicpos.o -MD -MP -MF .deps/snpindex-genomicpos.Tpo -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/snpindex-genomicpos.Tpo .deps/snpindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-compress.o -MD -MP -MF .deps/snpindex-compress.Tpo -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/snpindex-compress.Tpo .deps/snpindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-compress-write.o -MD -MP -MF .deps/snpindex-compress-write.Tpo -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
                                                                     ~~~              ^~~~~~~~~~
                                                                     %llu
compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
3 warnings generated.
mv -f .deps/snpindex-compress-write.Tpo .deps/snpindex-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genome_hr.o -MD -MP -MF .deps/snpindex-genome_hr.Tpo -c -o snpindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/snpindex-genome_hr.Tpo .deps/snpindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bitpack64-read.o -MD -MP -MF .deps/snpindex-bitpack64-read.Tpo -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/snpindex-bitpack64-read.Tpo .deps/snpindex-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bitpack64-write.o -MD -MP -MF .deps/snpindex-bitpack64-write.Tpo -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
mv -f .deps/snpindex-bitpack64-write.Tpo .deps/snpindex-bitpack64-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-indexdb.o -MD -MP -MF .deps/snpindex-indexdb.Tpo -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                     ^~~~~~~~
indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
            ^~~
indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
                                    ^~~~~~
indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
7 warnings generated.
mv -f .deps/snpindex-indexdb.Tpo .deps/snpindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-indexdb-write.o -MD -MP -MF .deps/snpindex-indexdb-write.Tpo -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb-write.c:2495:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                ^~~~~~
indexdb-write.c:2495:10: warning: format specifies type 'int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                       ^
indexdb-write.c:2495:12: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                         ^~~~~~~~
indexdb-write.c:2727:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
              oligok,offsetscomp[gammaptrs[p-1]],cum);
              ^~~~~~
indexdb-write.c:2738:8: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
              oligok-1UL,offsets[oligok-1],cum);
              ^~~~~~~~~~
indexdb-write.c:2761:3: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                oligok-1UL,offsets[oligok-1],cum);
                ^~~~~~~~~~
indexdb-write.c:2788:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
            oligok,offsetscomp[gammaptrs[p-1]],cum);
            ^~~~~~
indexdb-write.c:2799:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
            oligok,offsets[oligok],*ptr);
            ^~~~~~
indexdb-write.c:2888:59: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T));
                             ~~~                          ^~~~~~~~~~~~~~
                             %llu
indexdb-write.c:2895:101: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part);
                                       ~~~                                                          ^~~~~~~~~~~~~~
                                       %llu
indexdb-write.c:2972:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3094:79: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]);
                              ~~~                                             ^~~~~~~~~~~~
                              %llu
indexdb-write.c:3127:101: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                              ~~~                                                                   ^~~~~~~~~~~~~~
                              %llu
indexdb-write.c:3171:102: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                              ~~~                                                                    ^~~~~~~~~~~~~~
                              %llu
indexdb-write.c:3234:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
    fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT4),offset);
                                                           ~~~                      ^~~~~~
                                                           %lld
indexdb-write.c:3246:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
    fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT8),offset);
                                                           ~~~                      ^~~~~~
                                                           %lld
indexdb-write.c:3371:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3601:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3796:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3823:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3838:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                  positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                          ^~~~~~~~
indexdb-write.c:3865:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3892:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3907:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                  positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                          ^~~~~~~~
24 warnings generated.
mv -f .deps/snpindex-indexdb-write.Tpo .deps/snpindex-indexdb-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-chrom.o -MD -MP -MF .deps/snpindex-chrom.Tpo -c -o snpindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/snpindex-chrom.Tpo .deps/snpindex-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-md5.o -MD -MP -MF .deps/snpindex-md5.Tpo -c -o snpindex-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/snpindex-md5.Tpo .deps/snpindex-md5.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bzip2.o -MD -MP -MF .deps/snpindex-bzip2.Tpo -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/snpindex-bzip2.Tpo .deps/snpindex-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-sequence.o -MD -MP -MF .deps/snpindex-sequence.Tpo -c -o snpindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/snpindex-sequence.Tpo .deps/snpindex-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genome.o -MD -MP -MF .deps/snpindex-genome.Tpo -c -o snpindex-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c:10292:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10292:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
genome.c:10392:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                         ~~~                           ^~~~
                         %llu
genome.c:10392:68: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                                                ~~~                ^~~~
                                                %llu
4 warnings generated.
mv -f .deps/snpindex-genome.Tpo .deps/snpindex-genome.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-datadir.o -MD -MP -MF .deps/snpindex-datadir.Tpo -c -o snpindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/snpindex-datadir.Tpo .deps/snpindex-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-getopt.o -MD -MP -MF .deps/snpindex-getopt.Tpo -c -o snpindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/snpindex-getopt.Tpo .deps/snpindex-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-getopt1.o -MD -MP -MF .deps/snpindex-getopt1.Tpo -c -o snpindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/snpindex-getopt1.Tpo .deps/snpindex-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-snpindex.o -MD -MP -MF .deps/snpindex-snpindex.Tpo -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo './'`snpindex.c
snpindex.c:889:75: warning: format specifies type 'unsigned long' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
      fprintf(stderr,"Problem: saw duplicate positions %lu in oligo %s\n",*ptr1,nt);
                                                       ~~~                ^~~~~
                                                       %llu
snpindex.c:1143:71: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  fprintf(stderr,"Allocating %lu*3*%lu bytes for compressed genome\n",nblocks,sizeof(Genomecomp_T));
                             ~~~                                      ^~~~~~~
                             %llu
snpindex.c:1270:66: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(stderr,"Writing %lu offsets with %u total positions\n",oligospace+1,offsets[oligospace]);
                          ~~~                                    ^~~~~~~~~~~~
                          %llu
3 warnings generated.
mv -f .deps/snpindex-snpindex.Tpo .deps/snpindex-snpindex.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3    -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-genome_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o  -lz -lbz2 -lm 
libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-genome_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o  -lz -lbz2 -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-except.o -MD -MP -MF .deps/cmetindex-except.Tpo -c -o cmetindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/cmetindex-except.Tpo .deps/cmetindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-assert.o -MD -MP -MF .deps/cmetindex-assert.Tpo -c -o cmetindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/cmetindex-assert.Tpo .deps/cmetindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-mem.o -MD -MP -MF .deps/cmetindex-mem.Tpo -c -o cmetindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/cmetindex-mem.Tpo .deps/cmetindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-littleendian.o -MD -MP -MF .deps/cmetindex-littleendian.Tpo -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/cmetindex-littleendian.Tpo .deps/cmetindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bigendian.o -MD -MP -MF .deps/cmetindex-bigendian.Tpo -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/cmetindex-bigendian.Tpo .deps/cmetindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-genomicpos.o -MD -MP -MF .deps/cmetindex-genomicpos.Tpo -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/cmetindex-genomicpos.Tpo .deps/cmetindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-stopwatch.o -MD -MP -MF .deps/cmetindex-stopwatch.Tpo -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/cmetindex-stopwatch.Tpo .deps/cmetindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-access.o -MD -MP -MF .deps/cmetindex-access.Tpo -c -o cmetindex-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/cmetindex-access.Tpo .deps/cmetindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-univinterval.o -MD -MP -MF .deps/cmetindex-univinterval.Tpo -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %llu
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %llu
2 warnings generated.
mv -f .deps/cmetindex-univinterval.Tpo .deps/cmetindex-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-interval.o -MD -MP -MF .deps/cmetindex-interval.Tpo -c -o cmetindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/cmetindex-interval.Tpo .deps/cmetindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-iit-read-univ.o -MD -MP -MF .deps/cmetindex-iit-read-univ.Tpo -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %llu
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %llu
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %llu
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %llu
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %llu
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %llu
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %llu
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %llu
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %llu
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %llu
10 warnings generated.
mv -f .deps/cmetindex-iit-read-univ.Tpo .deps/cmetindex-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-iit-read.o -MD -MP -MF .deps/cmetindex-iit-read.Tpo -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/cmetindex-iit-read.Tpo .deps/cmetindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-compress.o -MD -MP -MF .deps/cmetindex-compress.Tpo -c -o cmetindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/cmetindex-compress.Tpo .deps/cmetindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-compress-write.o -MD -MP -MF .deps/cmetindex-compress-write.Tpo -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
                                                                     ~~~              ^~~~~~~~~~
                                                                     %llu
compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
3 warnings generated.
mv -f .deps/cmetindex-compress-write.Tpo .deps/cmetindex-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-genome_hr.o -MD -MP -MF .deps/cmetindex-genome_hr.Tpo -c -o cmetindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/cmetindex-genome_hr.Tpo .deps/cmetindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bitpack64-read.o -MD -MP -MF .deps/cmetindex-bitpack64-read.Tpo -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/cmetindex-bitpack64-read.Tpo .deps/cmetindex-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bitpack64-write.o -MD -MP -MF .deps/cmetindex-bitpack64-write.Tpo -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
mv -f .deps/cmetindex-bitpack64-write.Tpo .deps/cmetindex-bitpack64-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-indexdb.o -MD -MP -MF .deps/cmetindex-indexdb.Tpo -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                     ^~~~~~~~
indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
            ^~~
indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
                                    ^~~~~~
indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
7 warnings generated.
mv -f .deps/cmetindex-indexdb.Tpo .deps/cmetindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-indexdb-write.o -MD -MP -MF .deps/cmetindex-indexdb-write.Tpo -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb-write.c:2495:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                ^~~~~~
indexdb-write.c:2495:10: warning: format specifies type 'int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                       ^
indexdb-write.c:2495:12: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                         ^~~~~~~~
indexdb-write.c:2727:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
              oligok,offsetscomp[gammaptrs[p-1]],cum);
              ^~~~~~
indexdb-write.c:2738:8: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
              oligok-1UL,offsets[oligok-1],cum);
              ^~~~~~~~~~
indexdb-write.c:2761:3: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                oligok-1UL,offsets[oligok-1],cum);
                ^~~~~~~~~~
indexdb-write.c:2788:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
            oligok,offsetscomp[gammaptrs[p-1]],cum);
            ^~~~~~
indexdb-write.c:2799:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
            oligok,offsets[oligok],*ptr);
            ^~~~~~
indexdb-write.c:2888:59: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T));
                             ~~~                          ^~~~~~~~~~~~~~
                             %llu
indexdb-write.c:2895:101: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part);
                                       ~~~                                                          ^~~~~~~~~~~~~~
                                       %llu
indexdb-write.c:2972:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3094:79: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]);
                              ~~~                                             ^~~~~~~~~~~~
                              %llu
indexdb-write.c:3127:101: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                              ~~~                                                                   ^~~~~~~~~~~~~~
                              %llu
indexdb-write.c:3171:102: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                              ~~~                                                                    ^~~~~~~~~~~~~~
                              %llu
indexdb-write.c:3234:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
    fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT4),offset);
                                                           ~~~                      ^~~~~~
                                                           %lld
indexdb-write.c:3246:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
    fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT8),offset);
                                                           ~~~                      ^~~~~~
                                                           %lld
indexdb-write.c:3371:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3601:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3796:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3823:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3838:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                  positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                          ^~~~~~~~
indexdb-write.c:3865:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3892:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3907:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                  positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                          ^~~~~~~~
24 warnings generated.
mv -f .deps/cmetindex-indexdb-write.Tpo .deps/cmetindex-indexdb-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-cmet.o -MD -MP -MF .deps/cmetindex-cmet.Tpo -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/cmetindex-cmet.Tpo .deps/cmetindex-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-list.o -MD -MP -MF .deps/cmetindex-list.Tpo -c -o cmetindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/cmetindex-list.Tpo .deps/cmetindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-datadir.o -MD -MP -MF .deps/cmetindex-datadir.Tpo -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/cmetindex-datadir.Tpo .deps/cmetindex-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-getopt.o -MD -MP -MF .deps/cmetindex-getopt.Tpo -c -o cmetindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/cmetindex-getopt.Tpo .deps/cmetindex-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-getopt1.o -MD -MP -MF .deps/cmetindex-getopt1.Tpo -c -o cmetindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/cmetindex-getopt1.Tpo .deps/cmetindex-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-cmetindex.o -MD -MP -MF .deps/cmetindex-cmetindex.Tpo -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo './'`cmetindex.c
mv -f .deps/cmetindex-cmetindex.Tpo .deps/cmetindex-cmetindex.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3    -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-genome_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o  -lm 
libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-genome_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o  -lm
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-except.o -MD -MP -MF .deps/atoiindex-except.Tpo -c -o atoiindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/atoiindex-except.Tpo .deps/atoiindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-assert.o -MD -MP -MF .deps/atoiindex-assert.Tpo -c -o atoiindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/atoiindex-assert.Tpo .deps/atoiindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-mem.o -MD -MP -MF .deps/atoiindex-mem.Tpo -c -o atoiindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/atoiindex-mem.Tpo .deps/atoiindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-littleendian.o -MD -MP -MF .deps/atoiindex-littleendian.Tpo -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/atoiindex-littleendian.Tpo .deps/atoiindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bigendian.o -MD -MP -MF .deps/atoiindex-bigendian.Tpo -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/atoiindex-bigendian.Tpo .deps/atoiindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-genomicpos.o -MD -MP -MF .deps/atoiindex-genomicpos.Tpo -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/atoiindex-genomicpos.Tpo .deps/atoiindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-stopwatch.o -MD -MP -MF .deps/atoiindex-stopwatch.Tpo -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/atoiindex-stopwatch.Tpo .deps/atoiindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-access.o -MD -MP -MF .deps/atoiindex-access.Tpo -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c
access.c:61:7: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  if (stat64(filename,&sb) == 0) {
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:85:3: warning: 'stat64' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  stat64(filename,&sb);
  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/stat.h:402:9: note: 'stat64' has been explicitly marked deprecated here
int     stat64(const char *, struct stat64 *) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_5, __MAC_10_6, __IPHONE_NA, __IPHONE_NA);
        ^
access.c:358:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
              ^~~~~~
access.c:358:15: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              length,length,errno,strerror(errno));
                     ^~~~~~
access.c:423:11: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                 ^~~~~~
access.c:493:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
access.c:556:8: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              offset,length,errno,strerror(errno));
              ^~~~~~
access.c:641:13: warning: format specifies type 'uintmax_t' (aka 'unsigned long') but the argument has type 'off_t' (aka 'long long') [-Wformat]
              *len,length,errno,strerror(errno));
                   ^~~~~~
8 warnings generated.
mv -f .deps/atoiindex-access.Tpo .deps/atoiindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-univinterval.o -MD -MP -MF .deps/atoiindex-univinterval.Tpo -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c:71:23: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
          ~~~         ^~~~~~~~~
          %llu
univinterval.c:71:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
  printf("%lu %lu %d",this->low,this->high,this->type);
              ~~~               ^~~~~~~~~~
              %llu
2 warnings generated.
mv -f .deps/atoiindex-univinterval.Tpo .deps/atoiindex-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-interval.o -MD -MP -MF .deps/atoiindex-interval.Tpo -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/atoiindex-interval.Tpo .deps/atoiindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-iit-read-univ.o -MD -MP -MF .deps/atoiindex-iit-read-univ.Tpo -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c:507:24: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
             ~~~       ^~~~~~~~
             %llu
iit-read-univ.c:507:33: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf(" %lu..%lu",startpos,endpos);
                  ~~~           ^~~~~~
                  %llu
iit-read-univ.c:544:25: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
            ~~~         ^~~~~~~~
            %llu
iit-read-univ.c:544:34: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
    printf("%lu..%lu\t",startpos,endpos);
                 ~~~             ^~~~~~
                 %llu
iit-read-univ.c:694:27: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ~~~         ^~~~~~~~~~~
              %llu
iit-read-univ.c:694:39: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      printf("%lu..%lu\t",startpos+1U,endpos+1U);
                   ~~~                ^~~~~~~~~
                   %llu
iit-read-univ.c:700:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                ~~~         ^~~~~~~~~
                %llu
iit-read-univ.c:700:32: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",endpos+1U,startpos+1U);
                     ~~~              ^~~~~~~~~~~
                     %llu
iit-read-univ.c:703:22: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                ~~~         ^~~~~~~~~~~
                %llu
iit-read-univ.c:703:34: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("%lu..%lu\t",startpos+1U,endpos+1U);
                     ~~~                ^~~~~~~~~
                     %llu
10 warnings generated.
mv -f .deps/atoiindex-iit-read-univ.Tpo .deps/atoiindex-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-iit-read.o -MD -MP -MF .deps/atoiindex-iit-read.Tpo -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/atoiindex-iit-read.Tpo .deps/atoiindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-compress.o -MD -MP -MF .deps/atoiindex-compress.Tpo -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/atoiindex-compress.Tpo .deps/atoiindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-compress-write.o -MD -MP -MF .deps/atoiindex-compress-write.Tpo -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c:73:80: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
        printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
                                                                     ~~~              ^~~~~~~~~~
                                                                     %llu
compress-write.c:252:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
compress-write.c:300:13: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                Buffer[i],position+i);
                          ^~~~~~~~~~
3 warnings generated.
mv -f .deps/atoiindex-compress-write.Tpo .deps/atoiindex-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-genome_hr.o -MD -MP -MF .deps/atoiindex-genome_hr.Tpo -c -o atoiindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/atoiindex-genome_hr.Tpo .deps/atoiindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bitpack64-read.o -MD -MP -MF .deps/atoiindex-bitpack64-read.Tpo -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/atoiindex-bitpack64-read.Tpo .deps/atoiindex-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bitpack64-write.o -MD -MP -MF .deps/atoiindex-bitpack64-write.Tpo -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
mv -f .deps/atoiindex-bitpack64-write.Tpo .deps/atoiindex-bitpack64-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-indexdb.o -MD -MP -MF .deps/atoiindex-indexdb.Tpo -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c:1363:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1483:58: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                       ^~~~~~~~
indexdb.c:1653:63: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
              filenames->positions_filename,end0*sizeof(Univcoord_T),filesize);
                                                                     ^~~~~~~~
indexdb.c:1792:6: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
            ^~~
indexdb.c:1792:30: warning: format specifies type 'long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
            ptr,sizeof(Univcoord_T),offset);
                                    ^~~~~~
indexdb.c:1934:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
indexdb.c:2026:76: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                                       ~~~                                 ^~~~~~~~~~~~~~
                                       %llu
7 warnings generated.
mv -f .deps/atoiindex-indexdb.Tpo .deps/atoiindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-indexdb-write.o -MD -MP -MF .deps/atoiindex-indexdb-write.Tpo -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb-write.c:2495:3: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                ^~~~~~
indexdb-write.c:2495:10: warning: format specifies type 'int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                       ^
indexdb-write.c:2495:12: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                oligoi,i,oligoi+i,offsets64[i],offsets[oligoi+i]);
                         ^~~~~~~~
indexdb-write.c:2727:8: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
              oligok,offsetscomp[gammaptrs[p-1]],cum);
              ^~~~~~
indexdb-write.c:2738:8: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
              oligok-1UL,offsets[oligok-1],cum);
              ^~~~~~~~~~
indexdb-write.c:2761:3: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
                oligok-1UL,offsets[oligok-1],cum);
                ^~~~~~~~~~
indexdb-write.c:2788:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
            oligok,offsetscomp[gammaptrs[p-1]],cum);
            ^~~~~~
indexdb-write.c:2799:6: warning: format specifies type 'unsigned long' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
            oligok,offsets[oligok],*ptr);
            ^~~~~~
indexdb-write.c:2888:59: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
  fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T));
                             ~~~                          ^~~~~~~~~~~~~~
                             %llu
indexdb-write.c:2895:101: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
    fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part);
                                       ~~~                                                          ^~~~~~~~~~~~~~
                                       %llu
indexdb-write.c:2972:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3094:79: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]);
                              ~~~                                             ^~~~~~~~~~~~
                              %llu
indexdb-write.c:3127:101: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                              ~~~                                                                   ^~~~~~~~~~~~~~
                              %llu
indexdb-write.c:3171:102: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
      fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                              ~~~                                                                    ^~~~~~~~~~~~~~
                              %llu
indexdb-write.c:3234:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
    fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT4),offset);
                                                           ~~~                      ^~~~~~
                                                           %lld
indexdb-write.c:3246:85: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
    fprintf(stderr,"Attempted to do lseek on offset %u*%lu=%lu\n",ptr,sizeof(UINT8),offset);
                                                           ~~~                      ^~~~~~
                                                           %lld
indexdb-write.c:3371:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3601:56: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
        fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                                                     ~~~      ^~~~~~~~
                                                     %llu
indexdb-write.c:3796:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3823:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3838:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                  positionsfile,totalcounts*sizeof(UINT8),filesize);
                                                          ^~~~~~~~
indexdb-write.c:3865:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3892:43: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                        ^~~~~~~~
indexdb-write.c:3907:45: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                  positionsfile,totalcounts*sizeof(UINT4),filesize);
                                                          ^~~~~~~~
24 warnings generated.
mv -f .deps/atoiindex-indexdb-write.Tpo .deps/atoiindex-indexdb-write.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-atoi.o -MD -MP -MF .deps/atoiindex-atoi.Tpo -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/atoiindex-atoi.Tpo .deps/atoiindex-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-list.o -MD -MP -MF .deps/atoiindex-list.Tpo -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/atoiindex-list.Tpo .deps/atoiindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-datadir.o -MD -MP -MF .deps/atoiindex-datadir.Tpo -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/atoiindex-datadir.Tpo .deps/atoiindex-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-getopt.o -MD -MP -MF .deps/atoiindex-getopt.Tpo -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/atoiindex-getopt.Tpo .deps/atoiindex-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-getopt1.o -MD -MP -MF .deps/atoiindex-getopt1.Tpo -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/atoiindex-getopt1.Tpo .deps/atoiindex-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-atoiindex.o -MD -MP -MF .deps/atoiindex-atoiindex.Tpo -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c
mv -f .deps/atoiindex-atoiindex.Tpo .deps/atoiindex-atoiindex.Po
/bin/sh ../libtool  --tag=CC   --mode=link gcc  -D_THREAD_SAFE  -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3    -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-genome_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o  -lm 
libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-genome_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o  -lm
 ../config/install-sh -c -d '/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/install -c gmap gmapl get-genome gmapindex iit_store iit_get iit_dump gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex '/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin'
libtool: install: /usr/bin/install -c gmap /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/gmap
libtool: install: /usr/bin/install -c gmapl /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/gmapl
libtool: install: /usr/bin/install -c get-genome /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/get-genome
libtool: install: /usr/bin/install -c gmapindex /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/gmapindex
libtool: install: /usr/bin/install -c iit_store /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/iit_store
libtool: install: /usr/bin/install -c iit_get /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/iit_get
libtool: install: /usr/bin/install -c iit_dump /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/iit_dump
libtool: install: /usr/bin/install -c gsnap /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/gsnap
libtool: install: /usr/bin/install -c gsnapl /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/gsnapl
libtool: install: /usr/bin/install -c uniqscan /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/uniqscan
libtool: install: /usr/bin/install -c uniqscanl /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/uniqscanl
libtool: install: /usr/bin/install -c snpindex /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/snpindex
libtool: install: /usr/bin/install -c cmetindex /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/cmetindex
libtool: install: /usr/bin/install -c atoiindex /Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin/atoiindex
make[3]: Nothing to be done for `install-data-am'.
Making install in util
cp gmap_compress.pl gmap_compress
chmod +x gmap_compress
cp gmap_uncompress.pl gmap_uncompress
chmod +x gmap_uncompress
cp gmap_process.pl gmap_process
chmod +x gmap_process
cp gmap_setup.pl gmap_setup
chmod +x gmap_setup
cp gmap_build.pl gmap_build
chmod +x gmap_build
cp gmap_reassemble.pl gmap_reassemble
chmod +x gmap_reassemble
cp md_coords.pl md_coords
chmod +x md_coords
cp fa_coords.pl fa_coords
chmod +x fa_coords
cp psl_splicesites.pl psl_splicesites
chmod +x psl_splicesites
cp psl_introns.pl psl_introns
chmod +x psl_introns
cp psl_genes.pl psl_genes
chmod +x psl_genes
cp gtf_splicesites.pl gtf_splicesites
chmod +x gtf_splicesites
cp gtf_introns.pl gtf_introns
chmod +x gtf_introns
cp gtf_genes.pl gtf_genes
chmod +x gtf_genes
cp gff3_splicesites.pl gff3_splicesites
chmod +x gff3_splicesites
cp gff3_introns.pl gff3_introns
chmod +x gff3_introns
cp gff3_genes.pl gff3_genes
chmod +x gff3_genes
cp dbsnp_iit.pl dbsnp_iit
chmod +x dbsnp_iit
cp gvf_iit.pl gvf_iit
chmod +x gvf_iit
cp vcf_iit.pl vcf_iit
chmod +x vcf_iit
 ../config/install-sh -c -d '/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin'
 /usr/bin/install -c gmap_compress gmap_uncompress gmap_process gmap_setup gmap_build gmap_reassemble md_coords fa_coords psl_splicesites psl_introns psl_genes gtf_splicesites gtf_introns gtf_genes gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/Users/biocbuild/bbs-3.15-bioc/meat/gmapR/src/../inst/usr/bin'
make[3]: Nothing to be done for `install-data-am'.
Making install in tests
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-gmapR/00new/gmapR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘directory’ in package ‘gmapR’
Creating a generic function for ‘bamPaths’ from package ‘Rsamtools’ in package ‘gmapR’
Note: ... may be used in an incorrect context 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gmapR)

Tests output

gmapR.Rcheck/tests/gmapR_unit_tests.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> require("gmapR") || stop("unable to load gmapR package")
Loading required package: gmapR
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

[1] TRUE
> gmapR:::.test()
NOTE: genome 'hg19.p53' already exists, not overwriting
Loading required package: BSgenome
Loading required package: rtracklayer
writing chrI sequence to file ... OK
writing chrII sequence to file ... OK
writing chrIII sequence to file ... OK
writing chrIV sequence to file ... OK
writing chrV sequence to file ... OK
writing chrVI sequence to file ... OK
writing chrVII sequence to file ... OK
writing chrVIII sequence to file ... OK
writing chrIX sequence to file ... OK
writing chrX sequence to file ... OK
writing chrXI sequence to file ... OK
writing chrXII sequence to file ... OK
writing chrXIII sequence to file ... OK
writing chrXIV sequence to file ... OK
writing chrXV sequence to file ... OK
writing chrXVI sequence to file ... OK
writing chrM sequence to file ... OK
-k flag specified (not as 15), but not -b, so building with base size == kmer size
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//fa_coords  -c chrM -o ./yeast.coords "/private/tmp/RtmpINmJqX/gmap_build_fasta3fa265280bce"
Opening file /private/tmp/RtmpINmJqX/gmap_build_fasta3fa265280bce
  Processed short contigs (<1000000 nt): ...
  Contig chrIV: concatenated at chromosome end: chrIV:1..1531933 (length = 1531933 nt)
  Processed short contigs (<1000000 nt): ..
  Contig chrVII: concatenated at chromosome end: chrVII:1..1090940 (length = 1090940 nt)
  Processed short contigs (<1000000 nt): ....
  Contig chrXII: concatenated at chromosome end: chrXII:1..1078177 (length = 1078177 nt)
  Processed short contigs (<1000000 nt): ..
  Contig chrXV: concatenated at chromosome end: chrXV:1..1091291 (length = 1091291 nt)
  Processed short contigs (<1000000 nt): ..
============================================================
Contig mapping information has been written to file ./yeast.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
    make gmapdb
============================================================
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmap_process  -c ./yeast.coords "/private/tmp/RtmpINmJqX/gmap_build_fasta3fa265280bce" | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex  -d yeast -D . -A -s none
Reading coordinates from file ./yeast.coords
Logging contig chrI at chrI:1..230218 in genome yeast
Logging contig chrII at chrII:1..813184 in genome yeast
Logging contig chrIII at chrIII:1..316620 in genome yeast
Logging contig chrIV at chrIV:1..1531933 in genome yeast
Logging contig chrV at chrV:1..576874 in genome yeast
Logging contig chrVI at chrVI:1..270161 in genome yeast
Logging contig chrVII at chrVII:1..1090940 in genome yeast
Logging contig chrVIII at chrVIII:1..562643 in genome yeast
Logging contig chrIX at chrIX:1..439888 in genome yeast
Logging contig chrX at chrX:1..745751 in genome yeast
Logging contig chrXI at chrXI:1..666816 in genome yeast
Logging contig chrXII at chrXII:1..1078177 in genome yeast
Logging contig chrXIII at chrXIII:1..924431 in genome yeast
Logging contig chrXIV at chrXIV:1..784333 in genome yeast
Logging contig chrXV at chrXV:1..1091291 in genome yeast
Logging contig chrXVI at chrXVI:1..948066 in genome yeast
Logging contig chrM at chrM:1..85779 in genome yeast
chrM is a circular chromosome
Total genomic length = 12157105 bp
Chromosome chrI has universal coordinates 1..230218
Chromosome chrII has universal coordinates 230219..1043402
Chromosome chrIII has universal coordinates 1043403..1360022
Chromosome chrIV has universal coordinates 1360023..2891955
Chromosome chrV has universal coordinates 2891956..3468829
Chromosome chrVI has universal coordinates 3468830..3738990
Chromosome chrVII has universal coordinates 3738991..4829930
Chromosome chrVIII has universal coordinates 4829931..5392573
Chromosome chrIX has universal coordinates 5392574..5832461
Chromosome chrX has universal coordinates 5832462..6578212
Chromosome chrXI has universal coordinates 6578213..7245028
Chromosome chrXII has universal coordinates 7245029..8323205
Chromosome chrXIII has universal coordinates 8323206..9247636
Chromosome chrXIV has universal coordinates 9247637..10031969
Chromosome chrXV has universal coordinates 10031970..11123260
Chromosome chrXVI has universal coordinates 11123261..12071326
Chromosome chrM has universal coordinates 12071327..12157105
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (17 intervals)
Writing IIT file footer information...done
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (17 intervals)
Writing IIT file footer information...done
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmap_process  -c ./yeast.coords "/private/tmp/RtmpINmJqX/gmap_build_fasta3fa265280bce" | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex  -d yeast -F . -D . -G
Genome length is 12242884 nt
Trying to allocate 1147773*4 bytes of memory...succeeded.  Building genome in memory.
Reading coordinates from file ./yeast.coords
Writing contig chrI to universal coordinates 1..230218 in genome yeast
Writing contig chrII to universal coordinates 230219..1043402 in genome yeast
Writing contig chrIII to universal coordinates 1043403..1360022 in genome yeast
Writing contig chrIV to universal coordinates 1360023..2891955 in genome yeast
Writing contig chrV to universal coordinates 2891956..3468829 in genome yeast
Writing contig chrVI to universal coordinates 3468830..3738990 in genome yeast
Writing contig chrVII to universal coordinates 3738991..4829930 in genome yeast
Writing contig chrVIII to universal coordinates 4829931..5392573 in genome yeast
Writing contig chrIX to universal coordinates 5392574..5832461 in genome yeast
Writing contig chrX to universal coordinates 5832462..6578212 in genome yeast
Writing contig chrXI to universal coordinates 6578213..7245028 in genome yeast
Writing contig chrXII to universal coordinates 7245029..8323205 in genome yeast
Writing contig chrXIII to universal coordinates 8323206..9247636 in genome yeast
Writing contig chrXIV to universal coordinates 9247637..10031969 in genome yeast
Writing contig chrXV to universal coordinates 10031970..11123260 in genome yeast
Writing contig chrXVI to universal coordinates 11123261..12071326 in genome yeast
Writing contig chrM to universal coordinates 12071327..12157105 in genome yeast
Chromosome chrM is circular.  Copying 12071327..12157105 to 12157106..12242884
A total of 0 non-ACGTNX characters were seen in the genome.
Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -d yeast -U > ./yeast.genomebits
Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d yeast -F . -D . -O 
Note: since base size is equal to the k-mer size 12, offsets will not be compressed
Offset compression types:
Allocating 16777217*4 bytes for offsets
Indexing offsets of oligomers in genome yeast (12 bp every 3 bp), position 0
Writing 16777217 offsets to file with total of 4080904 k-mers...done
Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d yeast -F . -D . -P
Looking for index files in directory . (offsets not compressed)
  Offsets file is yeast.ref123offsets
  Positions file is yeast.ref123positions
Trying to allocate 4080904*4 bytes of memory...succeeded.  Building positions in memory.
Indexing positions of oligomers in genome yeast (12 bp every 3 bp), position 0
Writing 4080904 genomic positions to file ./yeast.ref123positions ...
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -d yeast -F . -D . -S
SACA_K called with n = 12242885, K = 5, level 0
SACA_K called with n = 3442582, K = 0, level 1
SACA_K called with n = 1091915, K = 0, level 2
SACA_K called with n = 355699, K = 0, level 3
SACA_K called with n = 115942, K = 0, level 4
SACA_K called with n = 37652, K = 0, level 5
SACA_K called with n = 12156, K = 0, level 6
SACA_K called with n = 4037, K = 0, level 7
SACA_K called with n = 1305, K = 0, level 8
Computing lcp...done
Computing saindex...done
Copying files to directory /private/tmp/RtmpINmJqX/584124234/yeast
-k flag specified (not as 15), but not -b, so building with base size == kmer size
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//fa_coords   -o ./thing.coords "/private/tmp/RtmpINmJqX/file3fa2281f3544"
Opening file /private/tmp/RtmpINmJqX/file3fa2281f3544
  Processed short contigs (<1000000 nt): .
============================================================
Contig mapping information has been written to file ./thing.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
    make gmapdb
============================================================
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmap_process  -c ./thing.coords "/private/tmp/RtmpINmJqX/file3fa2281f3544" | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex  -d thing -D . -A -s none
Reading coordinates from file ./thing.coords
Logging contig sampleDNAStringSet at sampleDNAStringSet:1..2000 in genome thing
Total genomic length = 2000 bp
Chromosome sampleDNAStringSet has universal coordinates 1..2000
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (1 intervals)
Writing IIT file footer information...done
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (1 intervals)
Writing IIT file footer information...done
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmap_process  -c ./thing.coords "/private/tmp/RtmpINmJqX/file3fa2281f3544" | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex  -d thing -F . -D . -G
Genome length is 2000 nt
Trying to allocate 189*4 bytes of memory...succeeded.  Building genome in memory.
Reading coordinates from file ./thing.coords
Writing contig sampleDNAStringSet to universal coordinates 1..2000 in genome thing
A total of 0 non-ACGTNX characters were seen in the genome.
Running cat ./thing.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -d thing -U > ./thing.genomebits
Running cat ./thing.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d thing -F . -D . -O 
Note: since base size is equal to the k-mer size 12, offsets will not be compressed
Offset compression types:
Allocating 16777217*4 bytes for offsets
Indexing offsets of oligomers in genome thing (12 bp every 3 bp), position 0
Writing 16777217 offsets to file with total of 663 k-mers...done
Running cat ./thing.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d thing -F . -D . -P
Looking for index files in directory . (offsets not compressed)
  Offsets file is thing.ref123offsets
  Positions file is thing.ref123positions
Trying to allocate 663*4 bytes of memory...succeeded.  Building positions in memory.
Indexing positions of oligomers in genome thing (12 bp every 3 bp), position 0
Writing 663 genomic positions to file ./thing.ref123positions ...
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -d thing -F . -D . -S
SACA_K called with n = 2001, K = 5, level 0
SACA_K called with n = 575, K = 0, level 1
Computing lcp...done
Computing saindex...done
Copying files to directory /private/tmp/RtmpINmJqX/871805021/thing
-k flag specified (not as 15), but not -b, so building with base size == kmer size
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//fa_coords   -o ./testGenome.coords "/private/tmp/RtmpINmJqX/file3fa223919a53"
Opening file /private/tmp/RtmpINmJqX/file3fa223919a53
  Processed short contigs (<1000000 nt): ..
============================================================
Contig mapping information has been written to file ./testGenome.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
    make gmapdb
============================================================
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmap_process  -c ./testGenome.coords "/private/tmp/RtmpINmJqX/file3fa223919a53" | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex  -d testGenome -D . -A -s none
Reading coordinates from file ./testGenome.coords
Logging contig testA at testA:1..26 in genome testGenome
Logging contig testB at testB:1..13 in genome testGenome
Total genomic length = 39 bp
Chromosome testA has universal coordinates 1..26
Chromosome testB has universal coordinates 27..39
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (2 intervals)
Writing IIT file footer information...done
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (2 intervals)
Writing IIT file footer information...done
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmap_process  -c ./testGenome.coords "/private/tmp/RtmpINmJqX/file3fa223919a53" | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex  -d testGenome -F . -D . -G
Genome length is 39 nt
Trying to allocate 6*4 bytes of memory...succeeded.  Building genome in memory.
Reading coordinates from file ./testGenome.coords
Writing contig testA to universal coordinates 1..26 in genome testGenome
Writing contig testB to universal coordinates 27..39 in genome testGenome
A total of 0 non-ACGTNX characters were seen in the genome.
Running cat ./testGenome.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -d testGenome -U > ./testGenome.genomebits
Running cat ./testGenome.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d testGenome -F . -D . -O 
Note: since base size is equal to the k-mer size 12, offsets will not be compressed
Offset compression types:
Allocating 16777217*4 bytes for offsets
Indexing offsets of oligomers in genome testGenome (12 bp every 3 bp), position 0
Writing 16777217 offsets to file with total of 6 k-mers...done
Running cat ./testGenome.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d testGenome -F . -D . -P
Looking for index files in directory . (offsets not compressed)
  Offsets file is testGenome.ref123offsets
  Positions file is testGenome.ref123positions
Trying to allocate 6*4 bytes of memory...succeeded.  Building positions in memory.
Indexing positions of oligomers in genome testGenome (12 bp every 3 bp), position 0
Writing 6 genomic positions to file ./testGenome.ref123positions ...
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -d testGenome -F . -D . -S
SACA_K called with n = 40, K = 5, level 0
Computing lcp...done
Computing saindex...done
Copying files to directory /private/tmp/RtmpINmJqX/file3fa218e217f0/testGenome
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Finished reading FASTA file -- total entries: 4918
Maximum coordinate: 1968875
Total label length: 29508 + 4918 separators
Total annotation length: 20152 + 4918 separators
Saw 1 distinct divisions/chromosomes
Saw 3 distinct tags/types
Writing IIT file header information...done
Processing null division/chromosome...sorting...writing...done (0 intervals)
Processing division/chromosome chr17...sorting...writing...done (4918 intervals)
Writing IIT file footer information...done
NOTE: genome 'hg19.p53' already exists, not overwriting
Creating directory /tmp/RtmpINmJqX/66073
writing chrI sequence to file ... OK
writing chrII sequence to file ... OK
writing chrIII sequence to file ... OK
writing chrIV sequence to file ... OK
writing chrV sequence to file ... OK
writing chrVI sequence to file ... OK
writing chrVII sequence to file ... OK
writing chrVIII sequence to file ... OK
writing chrIX sequence to file ... OK
writing chrX sequence to file ... OK
writing chrXI sequence to file ... OK
writing chrXII sequence to file ... OK
writing chrXIII sequence to file ... OK
writing chrXIV sequence to file ... OK
writing chrXV sequence to file ... OK
writing chrXVI sequence to file ... OK
writing chrM sequence to file ... OK
-k flag specified (not as 15), but not -b, so building with base size == kmer size
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//fa_coords  -c chrM -o ./yeast.coords "/private/tmp/RtmpINmJqX/gmap_build_fasta3fa228314af3"
Opening file /private/tmp/RtmpINmJqX/gmap_build_fasta3fa228314af3
  Processed short contigs (<1000000 nt): ...
  Contig chrIV: concatenated at chromosome end: chrIV:1..1531933 (length = 1531933 nt)
  Processed short contigs (<1000000 nt): ..
  Contig chrVII: concatenated at chromosome end: chrVII:1..1090940 (length = 1090940 nt)
  Processed short contigs (<1000000 nt): ....
  Contig chrXII: concatenated at chromosome end: chrXII:1..1078177 (length = 1078177 nt)
  Processed short contigs (<1000000 nt): ..
  Contig chrXV: concatenated at chromosome end: chrXV:1..1091291 (length = 1091291 nt)
  Processed short contigs (<1000000 nt): ..
============================================================
Contig mapping information has been written to file ./yeast.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
    make gmapdb
============================================================
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmap_process  -c ./yeast.coords "/private/tmp/RtmpINmJqX/gmap_build_fasta3fa228314af3" | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex  -d yeast -D . -A -s none
Reading coordinates from file ./yeast.coords
Logging contig chrI at chrI:1..230218 in genome yeast
Logging contig chrII at chrII:1..813184 in genome yeast
Logging contig chrIII at chrIII:1..316620 in genome yeast
Logging contig chrIV at chrIV:1..1531933 in genome yeast
Logging contig chrV at chrV:1..576874 in genome yeast
Logging contig chrVI at chrVI:1..270161 in genome yeast
Logging contig chrVII at chrVII:1..1090940 in genome yeast
Logging contig chrVIII at chrVIII:1..562643 in genome yeast
Logging contig chrIX at chrIX:1..439888 in genome yeast
Logging contig chrX at chrX:1..745751 in genome yeast
Logging contig chrXI at chrXI:1..666816 in genome yeast
Logging contig chrXII at chrXII:1..1078177 in genome yeast
Logging contig chrXIII at chrXIII:1..924431 in genome yeast
Logging contig chrXIV at chrXIV:1..784333 in genome yeast
Logging contig chrXV at chrXV:1..1091291 in genome yeast
Logging contig chrXVI at chrXVI:1..948066 in genome yeast
Logging contig chrM at chrM:1..85779 in genome yeast
chrM is a circular chromosome
Total genomic length = 12157105 bp
Chromosome chrI has universal coordinates 1..230218
Chromosome chrII has universal coordinates 230219..1043402
Chromosome chrIII has universal coordinates 1043403..1360022
Chromosome chrIV has universal coordinates 1360023..2891955
Chromosome chrV has universal coordinates 2891956..3468829
Chromosome chrVI has universal coordinates 3468830..3738990
Chromosome chrVII has universal coordinates 3738991..4829930
Chromosome chrVIII has universal coordinates 4829931..5392573
Chromosome chrIX has universal coordinates 5392574..5832461
Chromosome chrX has universal coordinates 5832462..6578212
Chromosome chrXI has universal coordinates 6578213..7245028
Chromosome chrXII has universal coordinates 7245029..8323205
Chromosome chrXIII has universal coordinates 8323206..9247636
Chromosome chrXIV has universal coordinates 9247637..10031969
Chromosome chrXV has universal coordinates 10031970..11123260
Chromosome chrXVI has universal coordinates 11123261..12071326
Chromosome chrM has universal coordinates 12071327..12157105
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (17 intervals)
Writing IIT file footer information...done
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (17 intervals)
Writing IIT file footer information...done
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmap_process  -c ./yeast.coords "/private/tmp/RtmpINmJqX/gmap_build_fasta3fa228314af3" | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex  -d yeast -F . -D . -G
Genome length is 12242884 nt
Trying to allocate 1147773*4 bytes of memory...succeeded.  Building genome in memory.
Reading coordinates from file ./yeast.coords
Writing contig chrI to universal coordinates 1..230218 in genome yeast
Writing contig chrII to universal coordinates 230219..1043402 in genome yeast
Writing contig chrIII to universal coordinates 1043403..1360022 in genome yeast
Writing contig chrIV to universal coordinates 1360023..2891955 in genome yeast
Writing contig chrV to universal coordinates 2891956..3468829 in genome yeast
Writing contig chrVI to universal coordinates 3468830..3738990 in genome yeast
Writing contig chrVII to universal coordinates 3738991..4829930 in genome yeast
Writing contig chrVIII to universal coordinates 4829931..5392573 in genome yeast
Writing contig chrIX to universal coordinates 5392574..5832461 in genome yeast
Writing contig chrX to universal coordinates 5832462..6578212 in genome yeast
Writing contig chrXI to universal coordinates 6578213..7245028 in genome yeast
Writing contig chrXII to universal coordinates 7245029..8323205 in genome yeast
Writing contig chrXIII to universal coordinates 8323206..9247636 in genome yeast
Writing contig chrXIV to universal coordinates 9247637..10031969 in genome yeast
Writing contig chrXV to universal coordinates 10031970..11123260 in genome yeast
Writing contig chrXVI to universal coordinates 11123261..12071326 in genome yeast
Writing contig chrM to universal coordinates 12071327..12157105 in genome yeast
Chromosome chrM is circular.  Copying 12071327..12157105 to 12157106..12242884
A total of 0 non-ACGTNX characters were seen in the genome.
Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -d yeast -U > ./yeast.genomebits
Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d yeast -F . -D . -O 
Note: since base size is equal to the k-mer size 12, offsets will not be compressed
Offset compression types:
Allocating 16777217*4 bytes for offsets
Indexing offsets of oligomers in genome yeast (12 bp every 3 bp), position 0
Writing 16777217 offsets to file with total of 4080904 k-mers...done
Running cat ./yeast.genomecomp | /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d yeast -F . -D . -P
Looking for index files in directory . (offsets not compressed)
  Offsets file is yeast.ref123offsets
  Positions file is yeast.ref123positions
Trying to allocate 4080904*4 bytes of memory...succeeded.  Building positions in memory.
Indexing positions of oligomers in genome yeast (12 bp every 3 bp), position 0
Writing 4080904 genomic positions to file ./yeast.ref123positions ...
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/library/gmapR/usr/bin//gmapindex -d yeast -F . -D . -S
SACA_K called with n = 12242885, K = 5, level 0
SACA_K called with n = 3442582, K = 0, level 1
SACA_K called with n = 1091915, K = 0, level 2
SACA_K called with n = 355699, K = 0, level 3
SACA_K called with n = 115942, K = 0, level 4
SACA_K called with n = 37652, K = 0, level 5
SACA_K called with n = 12156, K = 0, level 6
SACA_K called with n = 4037, K = 0, level 7
SACA_K called with n = 1305, K = 0, level 8
Computing lcp...done
Computing saindex...done
Copying files to directory /private/tmp/RtmpINmJqX/66073/yeast
Creating package in /tmp/RtmpINmJqX/50224/GmapGenome.Scerevisiae.UCSC.sacCer3 


RUNIT TEST PROTOCOL -- Wed Jan 19 01:33:16 2022 
*********************************************** 
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gmapR RUnit Tests - 26 test functions, 0 errors, 0 failures
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
129.890   6.913 203.066 

Example timings

gmapR.Rcheck/gmapR-Ex.timings

nameusersystemelapsed
GmapGenome-class0.0000.0000.001
GmapGenomeDirectory-class0.0020.0010.003
TP53Genome0.0100.0010.013
cmetindex000
gmap_build-methods0.0000.0010.000
makeGmapGenomePackage000