Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2022-06-24 12:06:42 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for rtracklayer on palomino3


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.

raw results

Package 1722/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rtracklayer 1.56.1  (landing page)
Michael Lawrence
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/rtracklayer
git_branch: RELEASE_3_15
git_last_commit: 4c6d220
git_last_commit_date: 2022-06-22 15:10:46 -0400 (Wed, 22 Jun 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  YES
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: rtracklayer
Version: 1.56.1
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rtracklayer.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rtracklayer_1.56.1.tar.gz
StartedAt: 2022-06-24 04:30:23 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:34:58 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 275.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rtracklayer.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rtracklayer.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rtracklayer_1.56.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/rtracklayer.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* this is package 'rtracklayer' version '1.56.1'
* 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: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/bigBed.c:314:2: warning: '%s' directive argument is null [-Wformat-overflow=]
  ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/bPlusTree.c:461:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  ucsc/bPlusTree.c:513:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
  ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
  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/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:1088:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  ucsc/udc.c:1446:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  ucsc/udc.c:1445:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1470:11: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1713:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1853:14: warning: too many arguments for format [-Wformat-extra-args]
See 'F:/biocbuild/bbs-3.15-bioc/meat/rtracklayer.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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
* 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 ... OK
* checking Rd cross-references ... OK
* 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 x64 is not available
File 'F:/biocbuild/bbs-3.15-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 'rand', possibly from 'rand' (C)
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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
BEDFile-class 4.47   1.25    5.72
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 3 WARNINGs, 4 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/rtracklayer.Rcheck/00check.log'
for details.



Installation output

rtracklayer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rtracklayer
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'rtracklayer' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c readGFF.c -o readGFF.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bbiHelper.c -o bbiHelper.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bigWig.c -o bigWig.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  148 |   strncpy(keyBuf,item->name, maxBedNameSize);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  338 |   bits64 extraIndexListEndOffset = 0;
      |          ^~~~~~~~~~~~~~~~~~~~~~~
bigBed.c: In function 'BBDFile_query':
bigBed.c:226:22: warning: 'typeId' may be used uninitialized in this function [-Wmaybe-uninitialized]
  226 |         switch(typeId[efIndex]) {
      |                      ^
bigBed.c:236:13: warning: 'lengthIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
  236 |             INTEGER(lengthIndex)[efIndex] = index + 1;
      |             ^~~~~~~~~~~~~~~~~~~~
bigBed.c:218:7: warning: 'blocks' may be used uninitialized in this function [-Wmaybe-uninitialized]
  218 |       SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:209:7: warning: 'itemRgb' may be used uninitialized in this function [-Wmaybe-uninitialized]
  209 |       SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:204:7: warning: 'thickWidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
  204 |       INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1;
      |       ^~~~~~~~~~~~~~~~~~~
bigBed.c:205:7: warning: 'thickStart' may be used uninitialized in this function [-Wmaybe-uninitialized]
  205 |       INTEGER(thickStart)[i] = bed->thickStart;
      |       ^~~~~~~~~~~~~~~~~~~
bigBed.c:198:7: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
  198 |       INTEGER(score)[i] = bed->score;
      |       ^~~~~~~~~~~~~~
bigBed.c:257:5: warning: 'name' may be used uninitialized in this function [-Wmaybe-uninitialized]
  257 |     SET_VECTOR_ELT(ans, index++, name);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c chain_io.c -o chain_io.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c twoBit.c -o twoBit.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c handlers.c -o handlers.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c utils.c -o utils.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/memgfx.c -o ucsc/memgfx.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/aliType.c -o ucsc/aliType.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/binRange.c -o ucsc/binRange.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/htmlColor.c -o ucsc/htmlColor.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
 1041 |     dyStringPrintf(string, "%lld,", array[i]);
      |                               ^
ucsc/sqlList.c:1041:28: warning: too many arguments for format [-Wformat-extra-args]
 1041 |     dyStringPrintf(string, "%lld,", array[i]);
      |                            ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/tokenizer.c -o ucsc/tokenizer.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/asParse.c -o ucsc/asParse.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/basicBed.c -o ucsc/basicBed.o
ucsc/basicBed.c: In function 'loadAndValidateBedExt':
ucsc/basicBed.c:1619:46: warning: unknown conversion type character 'l' in format [-Wformat=]
 1619 |       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=]
 1619 |       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);
      |                                                             ~^                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                              |                                  |
      |                                                              char *                             long long unsigned int
      |                                                             %I64d
ucsc/basicBed.c:1619:25: warning: too many arguments for format [-Wformat-extra-args]
 1619 |       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]
  997 | strncpy(dupe, itemRgb, sizeof(dupe));
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/bigBed.c -o ucsc/bigBed.o
ucsc/bigBed.c: In function 'extractField':
ucsc/bigBed.c:314:2: warning: '%s' directive argument is null [-Wformat-overflow=]
  314 |  warn("Not enough fields in extractField of %s", line);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
  307 |     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=]
  307 |     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=]
  307 |     errAbort("Item index %lld greater than item count %lld in %s",
      |                                                               ~^
      |                                                                |
      |                                                                char *
      |                                                               %I64d
  308 |  itemPos, bpt->itemCount, bpt->fileName);
      |  ~~~~~~~                                                        
      |  |
      |  long long unsigned int
ucsc/bPlusTree.c:307:14: warning: too many arguments for format [-Wformat-extra-args]
  307 |     errAbort("Item index %lld greater than item count %lld in %s",
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'writeIndexLevel',
    inlined from 'bptFileBulkIndexToOpenFile' at ucsc/bPlusTree.c:567:29:
ucsc/bPlusTree.c:461:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  461 | keyBuf[keySize] = 0;
      | ~~~~~~~~~~~~~~~~^~~
ucsc/bPlusTree.c: In function 'bptFileBulkIndexToOpenFile':
ucsc/bPlusTree.c:460:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here
  460 | char keyBuf[keySize+1];
      |      ^~~~~~
In function 'writeLeafLevel',
    inlined from 'bptFileBulkIndexToOpenFile' at ucsc/bPlusTree.c:575:1:
ucsc/bPlusTree.c:513:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  513 | keyBuf[keySize] = 0;
      | ~~~~~~~~~~~~~~~~^~~
ucsc/bPlusTree.c: In function 'bptFileBulkIndexToOpenFile':
ucsc/bPlusTree.c:512:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here
  512 | char keyBuf[keySize+1];
      |      ^~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  635 | bzero(summary, summarySize * sizeof(summary[0]));
      | ^~~~~
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  187 |  char *blockPt, *blockEnd;
      |                  ^~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
  238 | 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]
  238 | 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=]
  319 |     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]
  319 |     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=]
  334 |         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=]
  334 |         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=]
  334 |         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
      |                                                                       ~^           ~~~~~~~~~~~~~~~~
      |                                                                        |           |
      |                                                                        int         long long unsigned int
      |                                                                       %I64d
ucsc/cirTree.c:334:78: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
  334 |         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
      |                                                                             ~^                       ~~~~~~~~~~~~~~~~~
      |                                                                              |                                   |
      |                                                                              char *                              long long unsigned int
      |                                                                             %I64d
ucsc/cirTree.c:334:18: warning: too many arguments for format [-Wformat-extra-args]
  334 |         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=]
  505 | 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=]
  505 | verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u.  childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
      |                                         ~^                                      ~~~~~~~~~~~~~~~
      |                                          |                                      |
      |                                          unsigned int                           long long unsigned int
      |                                         %I64u
ucsc/cirTree.c:505:12: warning: too many arguments for format [-Wformat-extra-args]
  505 | 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=]
  585 | 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=]
  585 | verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
      |                                              ~^                ~~~~~~~~~~~~~~~
      |                                               |                |
      |                                               int              long long unsigned int
      |                                              %I64d
ucsc/cirTree.c:585:12: warning: too many arguments for format [-Wformat-extra-args]
  585 | verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
 2476 |     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=]
 2476 |     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
      |                                         ~^     ~~~~~~~~~~~~~~~
      |                                          |     |
      |                                          |     long long int
      |                                          char *
      |                                         %I64d
ucsc/common.c:2476:14: warning: too many arguments for format [-Wformat-extra-args]
 2476 |     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=]
 2487 |  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=]
 2487 |  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
      |                                      ~^   ~~~~~~~~~~~~~~~
      |                                       |   |
      |                                       |   long long int
      |                                       char *
      |                                      %I64d
ucsc/common.c:2487:11: warning: too many arguments for format [-Wformat-extra-args]
 2487 |  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=]
 2489 |  errAbort("End of file reading %lld bytes", (long long)size);
      |                                  ^
ucsc/common.c:2489:11: warning: too many arguments for format [-Wformat-extra-args]
 2489 |  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=]
 2630 |  errnoAbort("Error reading %lld bytes", (long long)size);
      |                              ^
ucsc/common.c:2630:13: warning: too many arguments for format [-Wformat-extra-args]
 2630 |  errnoAbort("Error reading %lld bytes", (long long)size);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2632:34: warning: unknown conversion type character 'l' in format [-Wformat=]
 2632 |  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=]
 2632 |  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]
 2632 |  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=]
 2647 |         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=]
 2647 |         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]
 2647 |         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=]
 2658 |     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=]
 2658 |     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
      |                                 ~^                    ~~~~~~~~~~~~~~~~~
      |                                  |                    |
      |                                  char *               long long int
      |                                 %I64d
ucsc/common.c:2658:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
 2658 |     errnoAbort("lseek(%d, %lld, %s (%d)) failed", fd, (long long)offset,
      |                                     ~^
      |                                      |
      |                                      int
      |                                     %s
 2659 |         ((whence == SEEK_SET) ? "SEEK_SET" : (whence == SEEK_CUR) ? "SEEK_CUR" :
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            char *
 2660 |   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/common.c:2658:16: warning: too many arguments for format [-Wformat-extra-args]
 2658 |     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=]
 2785 |         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=]
 2785 |         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]
 2785 |         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=]
 3251 |     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=]
 3251 |     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]
 3251 |     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=]
 3260 |     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=]
 3260 |     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]
 3260 |     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=]
 3276 |     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=]
 3276 |     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]
 3276 |     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=]
 3285 |     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=]
 3285 |     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]
 3285 |     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
  356 | safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
      |                                  ^
ucsc/errAbort.c:356:31: warning: too many arguments for format [-Wformat-extra-args]
  356 | safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
      |                               ^~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/hash.c -o ucsc/hash.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
 1083 |  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]
 1083 |  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]
  112 | static char * headerBytes(char *fileName, int numbytes)
      |               ^~~~~~~~~~~
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
   35 | static char **getDecompressor(char *fileName)
      |               ^~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
   38 |     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
      |                                   ^
ucsc/localmem.c:38:14: warning: too many arguments for format [-Wformat-extra-args]
   38 |     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
   51 |     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=]
   51 |     errAbort("Couldn't zCompress %lld bytes: %s",
      |                                              ~^
      |                                               |
      |                                               char *
      |                                              %I64d
   52 |      (long long)uncompressedSize, zlibErrorMessage(err));
      |      ~~~~~~~~~~~~~~~~~~~~~~~~~~~               
      |      |
      |      long long int
ucsc/zlibFace.c:51:14: warning: too many arguments for format [-Wformat-extra-args]
   51 |     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=]
   72 |     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=]
   72 |     errAbort("Couldn't zUncompress %lld bytes: %s",
      |                                                ~^
      |                                                 |
      |                                                 char *
      |                                                %I64d
   73 |      (long long)compressedSize, zlibErrorMessage(err));
      |      ~~~~~~~~~~~~~~~~~~~~~~~~~                   
      |      |
      |      long long int
ucsc/zlibFace.c:72:14: warning: too many arguments for format [-Wformat-extra-args]
   72 |     errAbort("Couldn't zUncompress %lld bytes: %s",
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/dystring.c -o ucsc/dystring.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/obscure.c -o ucsc/obscure.o
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=]
  789 |      fprintf(stderr, "# pid=%d: %s\n", pid, line);
      |                             ~^         ~~~
      |                              |         |
      |                              int       pid_t {aka long long int}
      |                             %lld
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
   90 |     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
      |                                                  ^
ucsc/memalloc.c:90:69: warning: unknown conversion type character 'l' in format [-Wformat=]
   90 |     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
      |                                                                     ^
ucsc/memalloc.c:90:14: warning: too many arguments for format [-Wformat-extra-args]
   90 |     errAbort("needLargeMem: trying to allocate %llu bytes (limit: %llu)",
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:93:60: warning: unknown conversion type character 'l' in format [-Wformat=]
   93 |     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=]
   93 |     errAbort("needLargeMem: Out of memory - request size %llu bytes, errno: %d\n",
      |                                                                             ~^
      |                                                                              |
      |                                                                              int
      |                                                                             %I64d
   94 |              (unsigned long long)size, errno);
      |              ~~~~~~~~~~~~~~~~~~~~~~~~                                         
      |              |
      |              long long unsigned int
ucsc/memalloc.c:93:14: warning: too many arguments for format [-Wformat-extra-args]
   93 |     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=]
  113 |     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
      |                                                        ^
ucsc/memalloc.c:113:75: warning: unknown conversion type character 'l' in format [-Wformat=]
  113 |     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
      |                                                                           ^
ucsc/memalloc.c:113:14: warning: too many arguments for format [-Wformat-extra-args]
  113 |     errAbort("needLargeMemResize: trying to allocate %llu bytes (limit: %llu)",
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:116:66: warning: unknown conversion type character 'l' in format [-Wformat=]
  116 |     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=]
  116 |     errAbort("needLargeMemResize: Out of memory - request size %llu bytes, errno: %d\n",
      |                                                                                   ~^
      |                                                                                    |
      |                                                                                    int
      |                                                                                   %I64d
  117 |              (unsigned long long)size, errno);
      |              ~~~~~~~~~~~~~~~~~~~~~~~~                                               
      |              |
      |              long long unsigned int
ucsc/memalloc.c:116:14: warning: too many arguments for format [-Wformat-extra-args]
  116 |     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=]
  138 |     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=]
  138 |     errAbort("needHugeMem: Out of huge memory - request size %llu bytes, errno: %d\n",
      |                                                                                 ~^
      |                                                                                  |
      |                                                                                  int
      |                                                                                 %I64d
  139 |              (unsigned long long)size, errno);
      |              ~~~~~~~~~~~~~~~~~~~~~~~~                                             
      |              |
      |              long long unsigned int
ucsc/memalloc.c:138:14: warning: too many arguments for format [-Wformat-extra-args]
  138 |     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=]
  160 |     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=]
  160 |     errAbort("needHugeMemResize: Out of memory - request resize %llu bytes, errno: %d\n",
      |                                                                                    ~^
      |                                                                                     |
      |                                                                                     int
      |                                                                                    %I64d
  161 |  (unsigned long long)size, errno);
      |  ~~~~~~~~~~~~~~~~~~~~~~~~                                                            
      |  |
      |  long long unsigned int
ucsc/memalloc.c:160:14: warning: too many arguments for format [-Wformat-extra-args]
  160 |     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=]
  186 |     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
      |                                             ^
ucsc/memalloc.c:186:64: warning: unknown conversion type character 'l' in format [-Wformat=]
  186 |     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
      |                                                                ^
ucsc/memalloc.c:186:14: warning: too many arguments for format [-Wformat-extra-args]
  186 |     errAbort("needMem: trying to allocate %llu bytes (limit: %llu)",
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:189:55: warning: unknown conversion type character 'l' in format [-Wformat=]
  189 |     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=]
  189 |     errAbort("needMem: Out of memory - request size %llu bytes, errno: %d\n",
      |                                                                        ~^
      |                                                                         |
      |                                                                         int
      |                                                                        %I64d
  190 |              (unsigned long long)size, errno);
      |              ~~~~~~~~~~~~~~~~~~~~~~~~                                    
      |              |
      |              long long unsigned int
ucsc/memalloc.c:189:14: warning: too many arguments for format [-Wformat-extra-args]
  189 |     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=]
  325 |     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
      |                                             ^
ucsc/memalloc.c:325:14: warning: too many arguments for format [-Wformat-extra-args]
  325 |     errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/memalloc.c:331:49: warning: unknown conversion type character 'l' in format [-Wformat=]
  331 |     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]
  331 |     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=]
  376 |         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]
  376 |         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=]
  383 |         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]
  383 |         safef(errMsg, sizeof errMsg, "Bad end cookie %x%x%x%x checking %llx\n",
      |                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/dlist.c -o ucsc/dlist.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/hex.c -o ucsc/hex.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/filePath.c -o ucsc/filePath.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/htmlPage.c -o ucsc/htmlPage.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  178 | /* 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=]
  223 |  errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total);
      |                                                             ^
ucsc/udc.c:223:13: warning: too many arguments for format [-Wformat-extra-args]
  223 |  errnoAbort("udcReadAndIgnore: error reading socket after %lld bytes", total);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c:228:46: warning: unknown conversion type character 'l' in format [-Wformat=]
  228 |     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=]
  228 |     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]
  228 |     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=]
  340 | 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=]
  340 | verbose(4, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
      |                                                         ~^           ~~~~~~
      |                                                          |           |
      |                                                          char *      long long unsigned int
      |                                                         %I64d
ucsc/udc.c:340:12: warning: too many arguments for format [-Wformat-extra-args]
  340 | 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=]
  347 |     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]
  347 |     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=]
  396 | 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=]
  396 | verbose(4, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
      |                                                              ~^           ~~~~~~
      |                                                               |           |
      |                                                               char *      long long unsigned int
      |                                                              %I64d
ucsc/udc.c:396:12: warning: too many arguments for format [-Wformat-extra-args]
  396 | 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=]
  414 |  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]
  414 |  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=]
  721 |     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=]
  721 |     errAbort("offset in fd=%d, f=%s is %lld, not expected udcBitmapHeaderSize %d",
      |                                                                               ~^
      |                                                                                |
      |                                                                                int
      |                                                                               %I64d
  722 |       fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
      |                                 ~~~~~~                                          
      |                                 |
      |                                 long long int
ucsc/udc.c:721:14: warning: too many arguments for format [-Wformat-extra-args]
  721 |     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=]
  877 |  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=]
  877 |  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=]
  877 |  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=]
  877 |  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=]
  877 |  verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
      |                                                                      ~^
      |                                                                       |
      |                                                                       char *
      |                                                                      %I64d
  878 |   "new version %d\n",
  879 |   bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
      |   ~~~~~~~~~~~~~~~~~~                                                   
      |       |
      |       long long unsigned int
ucsc/udc.c:877:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
  877 |  verbose(4, "removing stale version (%lld! = %lld or %lld! = %lld or %s doesn't exist or should not be size 0), "
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  878 |   "new version %d\n",
  879 |   bits->remoteUpdate, (long long)file->updateTime, bits->fileSize, file->size,
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       long long int
ucsc/udc.c:878:17: note: format string is defined here
  878 |   "new version %d\n",
      |                ~^
      |                 |
      |                 int
      |                %I64d
ucsc/udc.c:877:13: warning: too many arguments for format [-Wformat-extra-args]
  877 |  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 'djb2_hash':
ucsc/udc.c:1088:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 1088 |     while (c = *str++)
      |            ^
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1446:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 1446 |   (unsigned long)file, clearBlock,
      |   ^
ucsc/udc.c:1445:52: warning: unknown conversion type character 'l' in format [-Wformat=]
 1445 |     warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
      |                                                    ^
ucsc/udc.c:1445:58: warning: unknown conversion type character 'l' in format [-Wformat=]
 1445 |     warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
      |                                                          ^
ucsc/udc.c:1445:10: warning: too many arguments for format [-Wformat-extra-args]
 1445 |     warn("... udcFile 0x%04lx: bit for block %d (%lld..%lld] is not set",
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1470:30: warning: unknown conversion type character 'l' in format [-Wformat=]
 1470 |  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
      |                              ^
ucsc/udc.c:1470:45: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
 1470 |  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
      |                                            ~^
      |                                             |
      |                                             char *
      |                                            %I64d
 1471 |    readSize, file->url, startPos, actualSize);
      |    ~~~~~~~~                                  
      |    |
      |    long long unsigned int
ucsc/udc.c:1470:50: warning: unknown conversion type character 'l' in format [-Wformat=]
 1470 |  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
      |                                                  ^
ucsc/udc.c:1470:59: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
 1470 |  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
      |                                                          ~^
      |                                                           |
      |                                                           int
      |                                                          %s
 1471 |    readSize, file->url, startPos, actualSize);
      |              ~~~~~~~~~                                     
      |                  |
      |                  char *
ucsc/udc.c:1470:11: warning: too many arguments for format [-Wformat-extra-args]
 1470 |  errAbort("unable to fetch %lld bytes from %s @%lld (got %d bytes)",
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1713:35: warning: unknown conversion type character 'l' in format [-Wformat=]
 1713 |     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
      |                                   ^
ucsc/udc.c:1713:50: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
 1713 |     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
      |                                                 ~^                  ~~~~
      |                                                  |                  |
      |                                                  char *             long long unsigned int
      |                                                 %I64d
ucsc/udc.c:1713:64: warning: unknown conversion type character 'l' in format [-Wformat=]
 1713 |     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
      |                                                                ^
ucsc/udc.c:1713:14: warning: too many arguments for format [-Wformat-extra-args]
 1713 |     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:1853:23: warning: unknown conversion type character 'l' in format [-Wformat=]
 1853 |     errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
      |                       ^
ucsc/udc.c:1853:68: warning: unknown conversion type character 'l' in format [-Wformat=]
 1853 |     errAbort("%s is %lld bytes, but maxSize to udcFileReadAll is %lld",
      |                                                                    ^
ucsc/udc.c:1853:14: warning: too many arguments for format [-Wformat-extra-args]
 1853 |     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]
  211 | static void udcReadAndIgnore(struct ioStats *ioStats, int sd, bits64 size)
      |             ^~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/net.c -o ucsc/net.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/bits.c -o ucsc/bits.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
      |  
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/internet.c -o ucsc/internet.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/https.c -o ucsc/https.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/base64.c -o ucsc/base64.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/verbose.c -o ucsc/verbose.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/os.c -o ucsc/os.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/XVector/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
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 -LF:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rtracklayer/00new/rtracklayer/libs/x64
** 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
** 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
* DONE (rtracklayer)

Tests output

rtracklayer.Rcheck/tests/rtracklayer_unit_tests.Rout


R version 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
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 -- Fri Jun 24 04:34:43 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 
  36.90    2.50   50.43 

Example timings

rtracklayer.Rcheck/rtracklayer-Ex.timings

nameusersystemelapsed
BEDFile-class4.471.255.72
BamFile-methods0.140.000.14
BigBedFile000
BigBedSelection0.030.010.05
BigWigFile000
BigWigSelection-class0.030.000.03
GFFFile-class1.240.081.31
GenomicData0.170.030.23
GenomicSelection0.220.030.25
Quickload-class0.200.080.33
QuickloadGenome-class0.170.000.17
TrackHub-class0.060.000.07
TrackHubGenome-class0.020.000.01
TwoBitFile-class0.060.030.10
UCSCSchema-class000
UCSCTableQuery-class000
WIGFile-class0.880.010.89
asBED000
asGFF000
browseGenome000
browserView-methods000
browserViews-methods000
cpneTrack0.650.050.70
layTrack-methods000
liftOver000
readGFF0.320.030.34
targets0.040.000.05
ucscGenomes0.30.00.7
ucscTrackModes-methods0.010.000.02