| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:16 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
To the developers/maintainers of the rtracklayer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rtracklayer.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1675/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rtracklayer 1.54.0 (landing page) Michael Lawrence
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: rtracklayer |
| Version: 1.54.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rtracklayer.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings rtracklayer_1.54.0.tar.gz |
| StartedAt: 2022-04-13 02:08:36 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 02:16:25 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 468.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rtracklayer.Rcheck |
| Warnings: 5 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rtracklayer.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings rtracklayer_1.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/rtracklayer.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* this is package 'rtracklayer' version '1.54.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'rtracklayer' can be installed ... WARNING
Found the following significant warnings:
bigBedHelper.c:148:3: warning: 'strncpy' destination unchanged after copying no bytes [-Wstringop-truncation]
ucsc/sqlList.c:1041:28: warning: too many arguments for format [-Wformat-extra-args]
ucsc/basicBed.c:769:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess]
ucsc/basicBed.c:805:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess]
ucsc/basicBed.c:1619:25: warning: too many arguments for format [-Wformat-extra-args]
ucsc/basicBed.c:997:1: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:238:12: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:319:16: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:334:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:505:12: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:585:12: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2476:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2487:11: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2489:11: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2630:13: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2632:11: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2647:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2658:16: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2785:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:3251:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:3260:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:3276:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:3285:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/errAbort.c:356:31: warning: too many arguments for format [-Wformat-extra-args]
ucsc/linefile.c:1083:28: warning: too many arguments for format [-Wformat-extra-args]
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c:51:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c:72:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:90:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:113:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:160:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:186:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:325:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:331:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:376:38: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:383:38: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:223:13: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:228:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:340:12: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:347:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:396:12: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:414:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:721:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:877:13: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:1410:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:1435:11: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:1678:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:1818:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:1411:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/rtracklayer.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
R 1.8Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
Artistic-2.0 + file LICENSE
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
':::' call which should be '::': 'XVector:::open_input_files'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'BiocGenerics:::testPackage' 'GenomicRanges:::INVALID.GR.COLNAMES'
'S4Vectors:::labeledLine'
'S4Vectors:::make_XYZxyz_to_XxYyZz_subscript'
'S4Vectors:::new_SimpleList_from_list' 'XVector:::rewind_filexp'
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
import,BEDPEFile-ANY-ANY: no visible binding for global variable
'chrom2'
import,BEDPEFile-ANY-ANY: no visible binding for global variable
'start2'
import,BEDPEFile-ANY-ANY: no visible binding for global variable 'end2'
import,BEDPEFile-ANY-ANY: no visible binding for global variable
'strand2'
Undefined global functions or variables:
chrom2 end2 start2 strand2
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'uri':
'Quickload-class.Rd' 'TrackHub-class.Rd'
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'IntegerRangesList-methods.Rd':
'[IRanges]{names}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'FileForFormat' 'Genome' 'Track' 'TrackContainer' 'browserSession<-'
'cleanupBigBedCache' 'descriptionUrl' 'descriptionUrl<-' 'email'
'email<-' 'genomeField' 'genomeField<-' 'genomeInfo' 'genomeInfo<-'
'genomesFile' 'genomesFile<-' 'getTracks' 'hub' 'hub<-' 'hubUrl<-'
'longLabel' 'longLabel<-' 'readGFFAsGRanges' 'readGFFPragmas'
'resource' 'shortLabel' 'shortLabel<-' 'sniffGFFVersion' 'trackField'
'trackField<-' 'trackName' 'trackName<-'
Undocumented S4 classes:
'RTLFile' 'Track' 'TrackContainer' 'RTLFileList'
Undocumented S4 methods:
generic 'as.character' and siglist 'RTLFile'
generic 'browserSession' and siglist 'UCSCTableQuery'
generic 'browserSession<-' and siglist 'UCSCTableQuery'
generic 'export' and siglist 'CompressedGRangesList,BEDFile,ANY'
generic 'export' and siglist 'CompressedGRangesList,GFFFile,ANY'
generic 'export' and siglist 'GRangesList,UCSCFile,ANY'
generic 'export' and siglist 'SimpleGRangesList,BEDFile,ANY'
generic 'export' and siglist 'SimpleGRangesList,GFFFile,ANY'
generic 'export' and siglist 'SimpleGRangesList,WIGFile,ANY'
generic 'fileFormat' and siglist 'Bed15TrackLine'
generic 'fileFormat' and siglist 'GraphTrackLine'
generic 'fileFormat' and siglist 'RTLFile'
generic 'fileFormat' and siglist 'TrackLine'
generic 'genomesFile' and siglist 'TrackHub'
generic 'genomesFile<-' and siglist 'TrackHub'
generic 'initialize' and siglist 'RTLFile'
generic 'liftOver' and siglist 'GRangesList,Chain'
generic 'names' and siglist 'GenomeContainer'
generic 'names' and siglist 'Quickload'
generic 'names' and siglist 'TrackContainer'
generic 'names' and siglist 'TrackHub'
generic 'path' and siglist 'RTLFile'
generic 'show' and siglist 'RTLFile'
generic 'show' and siglist 'UCSCSchema'
generic 'track<-' and siglist 'TrackHubGenome,BiocFile'
generic 'track<-' and siglist 'UCSCSession,SimpleGRangesList'
generic 'trackName' and siglist 'UCSCTableQuery'
generic 'trackName<-' and siglist 'UCSCTableQuery'
generic 'trackNames' and siglist 'QuickloadGenome'
generic 'trackNames' and siglist 'TrackHubGenome'
generic 'trackNames' and siglist 'UCSCTableQuery'
generic 'uri' and siglist 'Quickload'
generic 'uri' and siglist 'TrackHub'
generic 'writeTrackHub' and siglist 'TrackHub'
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 ... WARNING
S4 class codoc mismatches from documentation object 'UCSCView-class':
Slots for class 'UCSCView'
Code: form hgsid session
Inherited: session
Docs: hgsid session
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/rtracklayer/libs/i386/rtracklayer.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/rtracklayer/libs/x64/rtracklayer.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
File 'rtracklayer/libs/i386/rtracklayer.dll':
Found non-API calls to R: 'R_ReadConnection', 'getConnection'
File 'rtracklayer/libs/x64/rtracklayer.dll':
Found non-API calls to R: 'R_ReadConnection', 'getConnection'
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.
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BEDFile-class 4.04 1.53 5.56
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BEDFile-class 4.38 0.65 5.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'rtracklayer_unit_tests.R'
OK
** running tests for arch 'x64' ...
Running 'rtracklayer_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, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/rtracklayer.Rcheck/00check.log'
for details.
rtracklayer.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/rtracklayer_1.54.0.tar.gz && rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rtracklayer.buildbin-libdir rtracklayer_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL rtracklayer_1.54.0.zip && rm rtracklayer_1.54.0.tar.gz rtracklayer_1.54.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
21 1126k 21 241k 0 0 522k 0 0:00:02 --:--:-- 0:00:02 522k
100 1126k 100 1126k 0 0 918k 0 0:00:01 0:00:01 --:--:-- 918k
install for i386
* installing *source* package 'rtracklayer' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_rtracklayer.c -o R_init_rtracklayer.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readGFF.c -o readGFF.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bbiHelper.c -o bbiHelper.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigWig.c -o bigWig.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigBedHelper.c -o bigBedHelper.o
bigBedHelper.c: In function 'bbNamedFileChunkKey':
bigBedHelper.c:148:3: warning: 'strncpy' destination unchanged after copying no bytes [-Wstringop-truncation]
strncpy(keyBuf,item->name, maxBedNameSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigBed.c -o bigBed.o
bigBed.c: In function 'BBDFile_write':
bigBed.c:338:10: warning: variable 'extraIndexListEndOffset' set but not used [-Wunused-but-set-variable]
bits64 extraIndexListEndOffset = 0;
^~~~~~~~~~~~~~~~~~~~~~~
bigBed.c: In function 'BBDFile_query':
bigBed.c:226:22: warning: 'typeId' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(typeId[efIndex]) {
^
bigBed.c:236:13: warning: 'lengthIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(lengthIndex)[efIndex] = index + 1;
^~~~~~~~~~~~~~~~~~~~
bigBed.c:270:5: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans, index++, blocks);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:267:5: warning: 'itemRgb' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans, index++, itemRgb);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:263:5: warning: 'thickWidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans, index++, new_IRanges("IRanges", thickStart,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
thickWidth, R_NilValue));
~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:263:5: warning: 'thickStart' may be used uninitialized in this function [-Wmaybe-uninitialized]
bigBed.c:260:5: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans, index++, score);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:257:5: warning: 'name' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans, index++, name);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chain_io.c -o chain_io.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c twoBit.c -o twoBit.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c handlers.c -o handlers.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memgfx.c -o ucsc/memgfx.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/aliType.c -o ucsc/aliType.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/binRange.c -o ucsc/binRange.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/htmlColor.c -o ucsc/htmlColor.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1041:31: warning: unknown conversion type character 'l' in format [-Wformat=]
dyStringPrintf(string, "%lld,", array[i]);
^
ucsc/sqlList.c:1041:28: warning: too many arguments for format [-Wformat-extra-args]
dyStringPrintf(string, "%lld,", array[i]);
^~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/tokenizer.c -o ucsc/tokenizer.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/asParse.c -o ucsc/asParse.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/basicBed.c -o ucsc/basicBed.o
ucsc/basicBed.c: In function 'lmCloneBed':
ucsc/basicBed.c:769:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess]
strncpy(newBed->strand, bed->strand, sizeof(bed->strand));
^
ucsc/basicBed.c: In function 'cloneBed':
ucsc/basicBed.c:805:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess]
strncpy(newBed->strand, bed->strand, sizeof(bed->strand));
^
ucsc/basicBed.c: In function 'loadAndValidateBedExt':
ucsc/basicBed.c:1619:46: warning: unknown conversion type character 'l' in format [-Wformat=]
lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
^
ucsc/basicBed.c:1619:62: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%I64d
ucsc/basicBed.c:1619:25: warning: too many arguments for format [-Wformat-extra-args]
lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/basicBed.c: In function 'bedParseRgb':
ucsc/basicBed.c:997:1: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
strncpy(dupe, itemRgb, sizeof(dupe));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bigBed.c -o ucsc/bigBed.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:307:28: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
^
ucsc/bPlusTree.c:307:57: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
^
ucsc/bPlusTree.c:307:64: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
~^
%I64d
itemPos, bpt->itemCount, bpt->fileName);
~~~~~~~
ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Item index %lld greater than item count %lld in %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
bzero(summary, summarySize * sizeof(summary[0]));
^~~~~
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
char *blockPt, *blockEnd;
^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:50: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^
ucsc/cirTree.c:238:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:45: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^
ucsc/cirTree.c:319:16: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c:334:54: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^
ucsc/cirTree.c:334:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^
ucsc/cirTree.c:334:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:334:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:334:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:38: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
^
ucsc/cirTree.c:505:42: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
~^ ~~~~~~~~~~~~~~~
%I64u
ucsc/cirTree.c:505:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:32: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
^
ucsc/cirTree.c:585:47: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:585:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:31: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2476:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2476:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:28: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2487:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2487:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2489:34: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %lld bytes", (long long)size);
^
ucsc/common.c:2489:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("End of file reading %lld bytes", (long long)size);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:30: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("Error reading %lld bytes", (long long)size);
^
ucsc/common.c:2630:13: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("Error reading %lld bytes", (long long)size);
^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2632:34: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^
ucsc/common.c:2632:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^
ucsc/common.c:2632:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2647:44: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^
ucsc/common.c:2647:52: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^
ucsc/common.c:2647:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2658:29: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
^
ucsc/common.c:2658:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2658:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^
%s
((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2658:16: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:60: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2785:65: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2785:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^
ucsc/common.c:3251:58: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^
ucsc/common.c:3251:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^
ucsc/common.c:3260:61: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^
ucsc/common.c:3260:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^
ucsc/common.c:3276:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^
ucsc/common.c:3276:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^
ucsc/common.c:3285:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^
ucsc/common.c:3285:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnautil.c -o ucsc/dnautil.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:34: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
^
ucsc/errAbort.c:356:31: warning: too many arguments for format [-Wformat-extra-args]
safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
^~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:56: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
^
ucsc/linefile.c:1083:28: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
static char * headerBytes(char *fileName, int numbytes)
^~~~~~~~~~~
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
static char **getDecompressor(char *fileName)
^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:35: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:51:36: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't zCompress %lld bytes: %s",
^
ucsc/zlibFace.c:51:47: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Couldn't zCompress %lld bytes: %s",
~^
%I64d
(long long)uncompressedSize, zlibErrorMessage(err));
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c:51:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't zCompress %lld bytes: %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:72:38: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't zUncompress %lld bytes: %s",
^
ucsc/zlibFace.c:72:49: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Couldn't zUncompress %lld bytes: %s",
~^
%I64d
(long long)compressedSize, zlibErrorMessage(err));
~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c:72:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't zUncompress %lld bytes: %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hmmstats.c -o ucsc/hmmstats.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rangeTree.c -o ucsc/rangeTree.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rbTree.c -o ucsc/rbTree.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:90:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:90:69: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:90:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:60: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:93:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:56: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:113:75: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:113:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:66: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:116:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:138:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:67: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:160:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:160:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:45: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:186:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:186:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:55: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:189:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:325:45: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:325:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:331:49: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
^
ucsc/memalloc.c:331:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:376:70: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:376:38: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:383:74: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
^
ucsc/memalloc.c:383:38: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hex.c -o ucsc/hex.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/filePath.c -o ucsc/filePath.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/htmlPage.c -o ucsc/htmlPage.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/udc.c -o ucsc/udc.o
In file included from ucsc/udc.c:41:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
/* Use byteRange as a work-around alternate method to get file size (content-length).
ucsc/udc.c: In function 'udcReadAndIgnore':
ucsc/udc.c:223:61: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total);
^
ucsc/udc.c:223:13: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:228:46: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^
ucsc/udc.c:228:65: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^
ucsc/udc.c:228:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:340:49: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^
ucsc/udc.c:340:58: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
~^ ~~~~~~
%I64d
ucsc/udc.c:340:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:347:57: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:347:10: warning: too many arguments for format [-Wformat-extra-args]
warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:396:54: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^
ucsc/udc.c:396:63: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
~^ ~~~~~~
%I64d
ucsc/udc.c:396:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:414:53: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:414:7: warning: too many arguments for format [-Wformat-extra-args]
warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:721:42: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
^
ucsc/udc.c:721:80: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
~^
%I64d
fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
~~~~~~
ucsc/udc.c:721:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:877:40: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^
ucsc/udc.c:877:48: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^
ucsc/udc.c:877:56: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^
ucsc/udc.c:877:64: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^
ucsc/udc.c:877:71: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
~^
%I64d
ucsc/udc.c:879:3:
bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
~~~~~~~~~~~~~~~~~~
ucsc/udc.c:877:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:879:23:
bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:878:17: note: format string is defined here
"new version %d\n",
~^
%I64d
ucsc/udc.c:877:13: warning: too many arguments for format [-Wformat-extra-args]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1410:52: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^
ucsc/udc.c:1410:58: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^
ucsc/udc.c:1410:10: warning: too many arguments for format [-Wformat-extra-args]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1435:30: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^
ucsc/udc.c:1435:45: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
~^
%I64d
readSize, file->url, startPos, actualSize);
~~~~~~~~
ucsc/udc.c:1435:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^
ucsc/udc.c:1435:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
~^
%s
readSize, file->url, startPos, actualSize);
~~~~~~~~~
ucsc/udc.c:1435:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1678:35: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^
ucsc/udc.c:1678:50: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
~^ ~~~~
%I64d
ucsc/udc.c:1678:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^
ucsc/udc.c:1678:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1818:23: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^
ucsc/udc.c:1818:68: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^
ucsc/udc.c:1818:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/udc.c:211:13: warning: 'udcReadAndIgnore' defined but not used [-Wunused-function]
static void udcReadAndIgnore(struct ioStats *ioStats, int sd, bits64 size)
^~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/net.c -o ucsc/net.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/twoBit.c -o ucsc/twoBit.o
In file included from ucsc/twoBit.c:15:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
/* Use byteRange as a work-around alternate method to get file size (content-length).
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/internet.c -o ucsc/internet.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/hex.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/rtracklayer.buildbin-libdir/00LOCK-rtracklayer/00new/rtracklayer/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
** help
*** installing help indices
converting help for package 'rtracklayer'
finding HTML links ... done
BEDFile-class html
BamFile-methods html
Bed15TrackLine-class html
BigBedFile html
finding level-2 HTML links ... done
BigBedSelection html
BigWigFile html
BigWigSelection-class html
BrowserViewList-class html
Chain-class html
FastaFile-class html
GFFFile-class html
GRangesForUCSCGenome html
GenomicData html
GenomicSelection html
IntegerRangesList-methods html
Quickload-class html
QuickloadGenome-class html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/rtracklayer.buildbin-libdir/00LOCK-rtracklayer/00new/rtracklayer/help/quickload.html
TabixFile-methods html
TrackDb-class html
TrackHub-class html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/rtracklayer.buildbin-libdir/00LOCK-rtracklayer/00new/rtracklayer/help/uri.html
TrackHubGenome-class html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/rtracklayer.buildbin-libdir/00LOCK-rtracklayer/00new/rtracklayer/help/trackhub.html
TwoBitFile-class html
UCSCData-class html
UCSCFile-class html
UCSCSchema-class html
UCSCTableQuery-class html
WIGFile-class html
activeView-methods html
asBED html
asGFF html
basicTrackLine-class html
blocks-methods html
browseGenome html
browserSession-class html
browserSession-methods html
browserView-class html
browserView-methods html
browserViews-methods html
cpneTrack html
genomeBrowsers html
laySequence-methods html
layTrack-methods html
liftOver html
readGFF html
targets html
tracks-methods html
ucscGenomes html
ucscSession-class html
ucscTrackLine-class html
ucscTrackModes-class html
ucscTrackModes-methods html
ucscView-class html
wigToBigWig html
wigTrackLine-class html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'rtracklayer' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_rtracklayer.c -o R_init_rtracklayer.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readGFF.c -o readGFF.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bbiHelper.c -o bbiHelper.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigWig.c -o bigWig.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigBedHelper.c -o bigBedHelper.o
bigBedHelper.c: In function 'bbNamedFileChunkKey':
bigBedHelper.c:148:3: warning: 'strncpy' destination unchanged after copying no bytes [-Wstringop-truncation]
strncpy(keyBuf,item->name, maxBedNameSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bigBed.c -o bigBed.o
bigBed.c: In function 'BBDFile_write':
bigBed.c:338:10: warning: variable 'extraIndexListEndOffset' set but not used [-Wunused-but-set-variable]
bits64 extraIndexListEndOffset = 0;
^~~~~~~~~~~~~~~~~~~~~~~
bigBed.c: In function 'BBDFile_query':
bigBed.c:226:22: warning: 'typeId' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(typeId[efIndex]) {
^
bigBed.c:236:13: warning: 'lengthIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(lengthIndex)[efIndex] = index + 1;
^~~~~~~~~~~~~~~~~~~~
bigBed.c:270:5: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans, index++, blocks);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:267:5: warning: 'itemRgb' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans, index++, itemRgb);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:263:5: warning: 'thickWidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans, index++, new_IRanges("IRanges", thickStart,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
thickWidth, R_NilValue));
~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:263:5: warning: 'thickStart' may be used uninitialized in this function [-Wmaybe-uninitialized]
bigBed.c:260:5: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans, index++, score);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:257:5: warning: 'name' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans, index++, name);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chain_io.c -o chain_io.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c twoBit.c -o twoBit.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c handlers.c -o handlers.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memgfx.c -o ucsc/memgfx.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/aliType.c -o ucsc/aliType.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/binRange.c -o ucsc/binRange.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/htmlColor.c -o ucsc/htmlColor.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlList.c -o ucsc/sqlList.o
ucsc/sqlList.c: In function 'sqlLongLongArrayToString':
ucsc/sqlList.c:1041:31: warning: unknown conversion type character 'l' in format [-Wformat=]
dyStringPrintf(string, "%lld,", array[i]);
^
ucsc/sqlList.c:1041:28: warning: too many arguments for format [-Wformat-extra-args]
dyStringPrintf(string, "%lld,", array[i]);
^~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/tokenizer.c -o ucsc/tokenizer.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/asParse.c -o ucsc/asParse.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/basicBed.c -o ucsc/basicBed.o
ucsc/basicBed.c: In function 'lmCloneBed':
ucsc/basicBed.c:769:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess]
strncpy(newBed->strand, bed->strand, sizeof(bed->strand));
^
ucsc/basicBed.c: In function 'cloneBed':
ucsc/basicBed.c:805:44: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess]
strncpy(newBed->strand, bed->strand, sizeof(bed->strand));
^
ucsc/basicBed.c: In function 'loadAndValidateBedExt':
ucsc/basicBed.c:1619:46: warning: unknown conversion type character 'l' in format [-Wformat=]
lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
^
ucsc/basicBed.c:1619:62: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%I64d
ucsc/basicBed.c:1619:25: warning: too many arguments for format [-Wformat-extra-args]
lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/basicBed.c: In function 'bedParseRgb':
ucsc/basicBed.c:997:1: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
strncpy(dupe, itemRgb, sizeof(dupe));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bigBed.c -o ucsc/bigBed.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:307:28: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
^
ucsc/bPlusTree.c:307:57: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
^
ucsc/bPlusTree.c:307:64: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("Item index %lld greater than item count %lld in %s",
~^
%I64d
itemPos, bpt->itemCount, bpt->fileName);
~~~~~~~
ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Item index %lld greater than item count %lld in %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
bzero(summary, summarySize * sizeof(summary[0]));
^~~~~
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
char *blockPt, *blockEnd;
^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:50: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^
ucsc/cirTree.c:238:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:45: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^
ucsc/cirTree.c:319:16: warning: too many arguments for format [-Wformat-extra-args]
verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c:334:54: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^
ucsc/cirTree.c:334:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^
ucsc/cirTree.c:334:72: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:334:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:334:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:38: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
^
ucsc/cirTree.c:505:42: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
~^ ~~~~~~~~~~~~~~~
%I64u
ucsc/cirTree.c:505:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:32: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
^
ucsc/cirTree.c:585:47: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/cirTree.c:585:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:31: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2476:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2476:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:28: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^
ucsc/common.c:2487:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
~^ ~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2487:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2489:34: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %lld bytes", (long long)size);
^
ucsc/common.c:2489:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("End of file reading %lld bytes", (long long)size);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:30: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("Error reading %lld bytes", (long long)size);
^
ucsc/common.c:2630:13: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("Error reading %lld bytes", (long long)size);
^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2632:34: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^
ucsc/common.c:2632:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^
ucsc/common.c:2632:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2647:44: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^
ucsc/common.c:2647:52: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^
ucsc/common.c:2647:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("mustWriteFd only wrote %lld of %lld bytes. Likely the disk is full.",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2658:29: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
^
ucsc/common.c:2658:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^ ~~~~~~~~~~~~~~~~~
%I64d
ucsc/common.c:2658:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
~^
%s
((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2658:16: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:60: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2785:65: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^
ucsc/common.c:2785:18: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^
ucsc/common.c:3251:58: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^
ucsc/common.c:3251:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^
ucsc/common.c:3260:61: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^
ucsc/common.c:3260:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^
ucsc/common.c:3276:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^
ucsc/common.c:3276:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:39: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^
ucsc/common.c:3285:62: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^
ucsc/common.c:3285:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnaseq.c -o ucsc/dnaseq.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dnautil.c -o ucsc/dnautil.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:34: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
^
ucsc/errAbort.c:356:31: warning: too many arguments for format [-Wformat-extra-args]
safef(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
^~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hash.c -o ucsc/hash.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:56: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
^
ucsc/linefile.c:1083:28: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
static char * headerBytes(char *fileName, int numbytes)
^~~~~~~~~~~
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
static char **getDecompressor(char *fileName)
^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:35: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/sqlNum.c -o ucsc/sqlNum.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:51:36: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't zCompress %lld bytes: %s",
^
ucsc/zlibFace.c:51:47: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Couldn't zCompress %lld bytes: %s",
~^
%I64d
(long long)uncompressedSize, zlibErrorMessage(err));
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c:51:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't zCompress %lld bytes: %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:72:38: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Couldn't zUncompress %lld bytes: %s",
^
ucsc/zlibFace.c:72:49: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
errAbort("Couldn't zUncompress %lld bytes: %s",
~^
%I64d
(long long)compressedSize, zlibErrorMessage(err));
~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/zlibFace.c:72:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Couldn't zUncompress %lld bytes: %s",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dystring.c -o ucsc/dystring.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hmmstats.c -o ucsc/hmmstats.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:547:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:47: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^
ucsc/obscure.c:547:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:557:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:40: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^
ucsc/obscure.c:557:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:565:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:33: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^
ucsc/obscure.c:565:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
^~~~~~~~~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:571:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:26: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld,%03lld", thousands, l);
^
ucsc/obscure.c:571:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld,%03lld", thousands, l);
^~~~~~~~~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
ucsc/obscure.c:574:19: warning: unknown conversion type character 'l' in format [-Wformat=]
sprintf(s, "%lld", l);
^
ucsc/obscure.c:574:16: warning: too many arguments for format [-Wformat-extra-args]
sprintf(s, "%lld", l);
^~~~~~
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:789:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' {aka 'long long int'} [-Wformat=]
fprintf(stderr, "# pid=%d: %s\n", pid, line);
~^ ~~~
%I64d
ucsc/obscure.c:789:30: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' {aka 'long long int'} [-Wformat=]
fprintf(stderr, "# pid=%d: %s\n", pid, line);
~^ ~~~
%I64d
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/pipeline.c -o ucsc/pipeline.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rangeTree.c -o ucsc/rangeTree.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/rbTree.c -o ucsc/rbTree.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:90:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:90:69: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:90:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:60: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:93:78: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:113:56: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:113:75: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:113:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:66: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:116:84: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:138:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:138:82: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:160:67: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:160:85: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:160:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:186:45: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:186:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^
ucsc/memalloc.c:186:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:55: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
^
ucsc/memalloc.c:189:73: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
~^
%I64d
(unsigned long long)size, errno);
~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:325:45: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:325:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:331:49: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
^
ucsc/memalloc.c:331:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:376:70: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
^
ucsc/memalloc.c:376:38: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, sizeof errMsg, "Bad start cookie %x checking %llx\n", cmb->startCookie,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:383:74: warning: unknown conversion type character 'l' in format [-Wformat=]
safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
^
ucsc/memalloc.c:383:38: warning: too many arguments for format [-Wformat-extra-args]
safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/dlist.c -o ucsc/dlist.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/hex.c -o ucsc/hex.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/filePath.c -o ucsc/filePath.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/htmlPage.c -o ucsc/htmlPage.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/udc.c -o ucsc/udc.o
In file included from ucsc/udc.c:41:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
/* Use byteRange as a work-around alternate method to get file size (content-length).
ucsc/udc.c: In function 'udcReadAndIgnore':
ucsc/udc.c:223:61: warning: unknown conversion type character 'l' in format [-Wformat=]
errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total);
^
ucsc/udc.c:223:13: warning: too many arguments for format [-Wformat-extra-args]
errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:228:46: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^
ucsc/udc.c:228:65: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^
ucsc/udc.c:228:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("udcReadAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:340:49: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^
ucsc/udc.c:340:58: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
~^ ~~~~~~
%I64d
ucsc/udc.c:340:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:347:57: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:347:10: warning: too many arguments for format [-Wformat-extra-args]
warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:396:54: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^
ucsc/udc.c:396:63: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
~^ ~~~~~~
%I64d
ucsc/udc.c:396:12: warning: too many arguments for format [-Wformat-extra-args]
verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:414:53: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
^
ucsc/udc.c:414:7: warning: too many arguments for format [-Wformat-extra-args]
warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:721:42: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
^
ucsc/udc.c:721:80: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
~^
%I64d
fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
~~~~~~
ucsc/udc.c:721:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:877:40: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^
ucsc/udc.c:877:48: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^
ucsc/udc.c:877:56: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^
ucsc/udc.c:877:64: warning: unknown conversion type character 'l' in format [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^
ucsc/udc.c:877:71: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
~^
%I64d
ucsc/udc.c:879:3:
bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
~~~~~~~~~~~~~~~~~~
ucsc/udc.c:877:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:879:23:
bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:878:17: note: format string is defined here
"new version %d\n",
~^
%I64d
ucsc/udc.c:877:13: warning: too many arguments for format [-Wformat-extra-args]
verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1411:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
(unsigned long)file, clearBlock,
^
ucsc/udc.c:1410:52: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^
ucsc/udc.c:1410:58: warning: unknown conversion type character 'l' in format [-Wformat=]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^
ucsc/udc.c:1410:10: warning: too many arguments for format [-Wformat-extra-args]
warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1435:30: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^
ucsc/udc.c:1435:45: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
~^
%I64d
readSize, file->url, startPos, actualSize);
~~~~~~~~
ucsc/udc.c:1435:50: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^
ucsc/udc.c:1435:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
~^
%s
readSize, file->url, startPos, actualSize);
~~~~~~~~~
ucsc/udc.c:1435:11: warning: too many arguments for format [-Wformat-extra-args]
errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1678:35: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^
ucsc/udc.c:1678:50: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
~^ ~~~~
%I64d
ucsc/udc.c:1678:64: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^
ucsc/udc.c:1678:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1818:23: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^
ucsc/udc.c:1818:68: warning: unknown conversion type character 'l' in format [-Wformat=]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^
ucsc/udc.c:1818:14: warning: too many arguments for format [-Wformat-extra-args]
errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
At top level:
ucsc/udc.c:211:13: warning: 'udcReadAndIgnore' defined but not used [-Wunused-function]
static void udcReadAndIgnore(struct ioStats *ioStats, int sd, bits64 size)
^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/net.c -o ucsc/net.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/bits.c -o ucsc/bits.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/twoBit.c -o ucsc/twoBit.o
In file included from ucsc/twoBit.c:15:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
/* Use byteRange as a work-around alternate method to get file size (content-length).
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/internet.c -o ucsc/internet.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/https.c -o ucsc/https.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/base64.c -o ucsc/base64.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/verbose.c -o ucsc/verbose.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/os.c -o ucsc/os.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/wildcmp.c -o ucsc/wildcmp.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/hex.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rtracklayer' as rtracklayer_1.54.0.zip
* DONE (rtracklayer)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'rtracklayer' successfully unpacked and MD5 sums checked
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rtracklayer.Rcheck/tests_i386/rtracklayer_unit_tests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("rtracklayer") || stop("unable to load rtracklayer package")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
[1] TRUE
> rtracklayer:::.test()
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
For efficiency, consider converting this WIG file to a BigWig file;
see ?wigToBigWig
RUNIT TEST PROTOCOL -- Wed Apr 13 02:15:21 2022
***********************************************
Number of test functions: 11
Number of errors: 0
Number of failures: 0
1 Test Suite :
rtracklayer RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11
Number of errors: 0
Number of failures: 0
There were 16 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
38.34 2.93 56.01
|
rtracklayer.Rcheck/tests_x64/rtracklayer_unit_tests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("rtracklayer") || stop("unable to load rtracklayer package")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
[1] TRUE
> rtracklayer:::.test()
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
For efficiency, consider converting this WIG file to a BigWig file;
see ?wigToBigWig
RUNIT TEST PROTOCOL -- Wed Apr 13 02:16:14 2022
***********************************************
Number of test functions: 11
Number of errors: 0
Number of failures: 0
1 Test Suite :
rtracklayer RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11
Number of errors: 0
Number of failures: 0
There were 16 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
38.37 1.64 52.62
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rtracklayer.Rcheck/examples_i386/rtracklayer-Ex.timings
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rtracklayer.Rcheck/examples_x64/rtracklayer-Ex.timings
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