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CHECK report for rtracklayer on tokay2

This page was generated on 2018-10-17 08:33:48 -0400 (Wed, 17 Oct 2018).

Package 1295/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rtracklayer 1.40.6
Michael Lawrence
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/rtracklayer
Branch: RELEASE_3_7
Last Commit: ba9a6e7
Last Changed Date: 2018-08-30 18:09:48 -0400 (Thu, 30 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: rtracklayer
Version: 1.40.6
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rtracklayer.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings rtracklayer_1.40.6.tar.gz
StartedAt: 2018-10-17 04:36:14 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:41:30 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 316.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: rtracklayer.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rtracklayer.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings rtracklayer_1.40.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/rtracklayer.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* this is package 'rtracklayer' version '1.40.6'
* 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:
  ucsc/bPlusTree.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:238:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:319:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/linefile.c:1083:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:668:3: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1112:3: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1136:4: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1361:5: warning: too many arguments for format [-Wformat-extra-args]
  ucsc/udc.c:1497:6: warning: too many arguments for format [-Wformat-extra-args]
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BEDFile-class.Rd:135: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BEDFile-class.Rd:201: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:11: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:12: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:13: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:33: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:46: file link 'filterBam' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:51: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BigWigSelection-class.Rd:15: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BigWigSelection-class.Rd:37: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BigWigSelection-class.Rd:38: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BrowserViewList-class.Rd:13: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/Chain-class.Rd:51: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/FastaFile-class.Rd:50: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/FastaFile-class.Rd:51: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/FastaFile-class.Rd:58: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/FastaFile-class.Rd:59: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/FastaFile-class.Rd:63: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GFFFile-class.Rd:125: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GFFFile-class.Rd:190: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GRangesForUCSCGenome.Rd:31: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GRangesForUCSCGenome.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GRangesForUCSCGenome.Rd:54: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GenomicData.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GenomicSelection.Rd:7: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GenomicSelection.Rd:26: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GenomicSelection.Rd:33: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/IntegerRangesList-methods.Rd:29: missing file link 'names'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/QuickloadGenome-class.Rd:60: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/QuickloadGenome-class.Rd:61: file link 'GenomeDescription' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/TwoBitFile-class.Rd:108: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/UCSCTableQuery-class.Rd:69: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/UCSCTableQuery-class.Rd:70: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/blocks-methods.Rd:9: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:21: file link 'GenomicRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:25: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browserView-methods.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browserView-methods.Rd:16: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/export.Rd:138: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/export.Rd:148: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/liftOver.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:11: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:64: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:68: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:69: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:73: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:75: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/ucscView-class.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/ucscView-class.Rd:43: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  ucsc/udc.c:1111:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'C:/Users/biocbuild/bbs-3.7-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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
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:::open_input_files'
  '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
smoothGaps: no visible binding for global variable 'congruent'
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 congruent end2 start2 strand2
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'IntegerRangesList-methods.Rd':
  '[IRanges]{names}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'readGFFAsGRanges' 'readGFFPragmas' 'sniffGFFVersion'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/rtracklayer/libs/i386/rtracklayer.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
File 'rtracklayer/libs/i386/rtracklayer.dll':
  Found non-API calls to R: 'R_ReadConnection', 'getConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'rtracklayer_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'rtracklayer_unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/rtracklayer.Rcheck/00check.log'
for details.



Installation output

rtracklayer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/rtracklayer_1.40.6.tar.gz && rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rtracklayer.buildbin-libdir rtracklayer_1.40.6.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL rtracklayer_1.40.6.zip && rm rtracklayer_1.40.6.tar.gz rtracklayer_1.40.6.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1053k  100 1053k    0     0  14.3M      0 --:--:-- --:--:-- --:--:-- 15.8M

install for i386

* installing *source* package 'rtracklayer' ...

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


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_rtracklayer.c -o R_init_rtracklayer.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c readGFF.c -o readGFF.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c bigWig.c -o bigWig.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c chain_io.c -o chain_io.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c twoBit.c -o twoBit.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c handlers.c -o handlers.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  itemPos, bpt->itemCount, bpt->fileName);
  ^
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
 bzero(summary, summarySize * sizeof(summary[0]));
 ^
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
  char *blockPt, *blockEnd;
                  ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
 ^
ucsc/cirTree.c:238:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
     ^
ucsc/cirTree.c:319:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
         ^
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u.  childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
 ^
ucsc/cirTree.c:505:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
 ^
ucsc/cirTree.c:585:1: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
     ^
ucsc/common.c:2476:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
  ^
ucsc/common.c:2487:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2489:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("Error reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
  ^
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)result, (long long)size);
      ^
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2660:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ^
ucsc/common.c:2660:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat=]
ucsc/common.c:2660:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
         ^
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
     ^
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
     ^
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
     ^
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
     ^
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/dnautil.c -o ucsc/dnautil.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
 ^
ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
  ^
ucsc/linefile.c:1083:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/linefile.c: At top level:
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
 static char **getDecompressor(char *fileName)
               ^
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
 static char * headerBytes(char *fileName, int numbytes)
               ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
     ^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:52:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)uncompressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:52:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:73:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)compressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:73:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/hmmstats.c -o ucsc/hmmstats.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
     ^
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
     ^
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
     ^
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
     ^
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:574:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
     ^
ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'stringToSlNames':
ucsc/obscure.c:473:8: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if ((s = skipLeadingSpaces(s)) == NULL)
        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/rangeTree.c -o ucsc/rangeTree.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/rbTree.c -o ucsc/rbTree.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  (unsigned long long)size, errno);
  ^
ucsc/memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
          ^
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:326:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:333:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:377:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:385:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:138:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
  ^
ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
     ^
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:234:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:241:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
     ^
ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:290:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
  ^
ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:516:7: warning: unknown conversion type character 'l' in format [-Wformat=]
       fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
       ^
ucsc/udc.c:516:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   file->sparseFileName, version);
   ^
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:668:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:668:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   ((long long)clearBlock * udcBlockSize), (((long long)clearBlock+1) * udcBlockSize));
   ^
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1112:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
    readSize, file->url, startPos, actualSize);
    ^
ucsc/udc.c:1136:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1136:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
ucsc/udc.c:1136:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1361:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
     ^
ucsc/udc.c:1361:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1361:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1361:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      url, (long long)size, (long long)maxSize);
      ^
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1497:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
 static void readAndIgnore(int sd, bits64 size)
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/net.c -o ucsc/net.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/twoBit.c -o ucsc/twoBit.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/internet.c -o ucsc/internet.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bigWig.o chain_io.o twoBit.o handlers.o utils.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/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
Creating a generic function from function 'uri' in package 'rtracklayer'
** help
*** installing help indices
  converting help for package 'rtracklayer'
    finding HTML links ... done
    BEDFile-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BEDFile-class.Rd:135: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BEDFile-class.Rd:201: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
    BamFile-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:11: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:12: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:13: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:33: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:46: file link 'filterBam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BamFile-methods.Rd:51: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
    Bed15TrackLine-class                    html  
    BigWigFile                              html  
    BigWigSelection-class                   html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BigWigSelection-class.Rd:15: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BigWigSelection-class.Rd:37: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BigWigSelection-class.Rd:38: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    BrowserViewList-class                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/BrowserViewList-class.Rd:13: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
    Chain-class                             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/Chain-class.Rd:51: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
    FastaFile-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/FastaFile-class.Rd:50: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/FastaFile-class.Rd:51: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/FastaFile-class.Rd:58: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/FastaFile-class.Rd:59: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/FastaFile-class.Rd:63: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    GFFFile-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GFFFile-class.Rd:125: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GFFFile-class.Rd:190: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
    GRangesForUCSCGenome                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GRangesForUCSCGenome.Rd:31: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GRangesForUCSCGenome.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GRangesForUCSCGenome.Rd:54: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
    GenomicData                             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GenomicData.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    GenomicSelection                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GenomicSelection.Rd:7: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GenomicSelection.Rd:26: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/GenomicSelection.Rd:33: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic
    IntegerRangesList-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/IntegerRangesList-methods.Rd:29: missing file link 'names'
    Quickload-class                         html  
    QuickloadGenome-class                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/QuickloadGenome-class.Rd:60: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/QuickloadGenome-class.Rd:61: file link 'GenomeDescription' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
    RTLFile-class                           html  
    TabixFile-methods                       html  
    TrackDb-class                           html  
    TwoBitFile-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/TwoBitFile-class.Rd:108: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    UCSCData-class                          html  
    UCSCFile-class                          html  
    UCSCSchema-class                        html  
    UCSCTableQuery-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/UCSCTableQuery-class.Rd:69: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/UCSCTableQuery-class.Rd:70: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    WIGFile-class                           html  
    activeView-methods                      html  
    asBED                                   html  
    asGFF                                   html  
    basicTrackLine-class                    html  
    blocks-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/blocks-methods.Rd:9: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    browseGenome                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:21: file link 'GenomicRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browseGenome.Rd:25: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    browserSession-class                    html  
    browserSession-methods                  html  
    browserView-class                       html  
    browserView-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browserView-methods.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/browserView-methods.Rd:16: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    browserViews-methods                    html  
    cpneTrack                               html  
    export                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/export.Rd:138: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/export.Rd:148: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
    genomeBrowsers                          html  
    laySequence-methods                     html  
    layTrack-methods                        html  
    liftOver                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/liftOver.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    readGFF                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:11: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:64: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:68: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:69: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:73: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/readGFF.Rd:75: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
    targets                                 html  
    tracks-methods                          html  
    ucscGenomes                             html  
    ucscSession-class                       html  
    ucscTrackLine-class                     html  
    ucscTrackModes-class                    html  
    ucscTrackModes-methods                  html  
    ucscView-class                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/ucscView-class.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpE3h89l/R.INSTALL51c683b3a57/rtracklayer/man/ucscView-class.Rd:43: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    wigToBigWig                             html  
    wigTrackLine-class                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'rtracklayer' ...

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


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_rtracklayer.c -o R_init_rtracklayer.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c readGFF.c -o readGFF.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bigWig.c -o bigWig.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c chain_io.c -o chain_io.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c twoBit.c -o twoBit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c handlers.c -o handlers.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function 'bptDataOffset':
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  itemPos, bpt->itemCount, bpt->fileName);
  ^
ucsc/bPlusTree.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/bPlusTree.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:635:1: warning: implicit declaration of function 'bzero' [-Wimplicit-function-declaration]
 bzero(summary, summarySize * sizeof(summary[0]));
 ^
ucsc/bbiRead.c:635:1: warning: incompatible implicit declaration of built-in function 'bzero'
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
  char *blockPt, *blockEnd;
                  ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:238:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "Made %d primary index nodes out of %llu items\n", slCount(list), itemCount);
 ^
ucsc/cirTree.c:238:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:319:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     verbose(2, "level %d: size %d, offset %llu\n", i, levelSizes[i], levelOffsets[i]);
     ^
ucsc/cirTree.c:319:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Internal error: offset mismatch (%llu vs %llu) line %d of %s\n", (bits64)ftell(f), levelOffsets[i+1], __LINE__, __FILE__);
         ^
ucsc/cirTree.c:334:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:334:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:505:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u.  childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
 ^
ucsc/cirTree.c:505:1: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:505:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/cirTree.c: In function 'rEnumerateBlocks':
ucsc/cirTree.c:585:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(3, "rEnumerateBlocks %llu childCount %d. isLeaf %d\n", indexFileOffset, (int)childCount, (int)isLeaf);
 ^
ucsc/cirTree.c:585:1: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/cirTree.c:585:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:2476:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Error writing %lld bytes: %s\n", (long long)size, strerror(ferror(file)));
     ^
ucsc/common.c:2476:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2476:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustRead':
ucsc/common.c:2487:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("Error reading %lld bytes: %s", (long long)size, strerror(ferror(file)));
  ^
ucsc/common.c:2487:2: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/common.c:2487:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2489:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2489:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustReadFd':
ucsc/common.c:2630:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("Error reading %lld bytes", (long long)size);
  ^
ucsc/common.c:2630:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errAbort("End of file reading %llu bytes (got %lld)", (unsigned long long)size, (long long)actualSize);
  ^
ucsc/common.c:2632:2: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2632:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustWriteFd':
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)result, (long long)size);
      ^
ucsc/common.c:2648:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2648:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'mustLseek':
ucsc/common.c:2660:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   (whence == SEEK_END) ? "SEEK_END" : "invalid 'whence' value"), whence);
   ^
ucsc/common.c:2660:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'off_t' [-Wformat=]
ucsc/common.c:2660:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'char *' [-Wformat=]
ucsc/common.c:2660:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
         errAbort("Unsorted inList in fileOffsetSizeMerge %llu %llu", oldEl->offset, nextOld->offset);
         ^
ucsc/common.c:2785:9: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:2785:9: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecpy':
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, string size: %lld", (long long)bufSize, (long long)slen);
     ^
ucsc/common.c:3251:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3251:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencpy':
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, substring size: %lld", (long long)bufSize, (long long)n);
     ^
ucsc/common.c:3260:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3260:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safecat':
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+slen));
     ^
ucsc/common.c:3276:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3276:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/common.c: In function 'safencat':
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("buffer overflow, size %lld, new string size: %lld", (long long)bufSize, (long long)(blen+n));
     ^
ucsc/common.c:3285:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/common.c:3285:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/dnaseq.c -o ucsc/dnaseq.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/dnautil.c -o ucsc/dnautil.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:356:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 safef(pidStr, sizeof(pidStr), "%lld",  ptrToLL(pid));
 ^
ucsc/errAbort.c:356:1: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/hash.c -o ucsc/hash.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c: In function 'lineFileCheckAllIntsNoAbort':
ucsc/linefile.c:1083:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  safef(errMsg, errMsgSize, "%s%s overflowed, limit=%s%llu", isSigned ? "signed ":"", typeString, isMinus ? "-" : "", limit);
  ^
ucsc/linefile.c:1083:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/linefile.c: At top level:
ucsc/linefile.c:35:15: warning: 'getDecompressor' defined but not used [-Wunused-function]
 static char **getDecompressor(char *fileName)
               ^
ucsc/linefile.c:112:15: warning: 'headerBytes' defined but not used [-Wunused-function]
 static char * headerBytes(char *fileName, int numbytes)
               ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:38:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("Couldn't allocate %lld bytes", (long long)fullSize);
     ^
ucsc/localmem.c:38:5: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/sqlNum.c -o ucsc/sqlNum.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:52:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)uncompressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:52:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:52:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:73:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      (long long)compressedSize, zlibErrorMessage(err));
      ^
ucsc/zlibFace.c:73:6: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
ucsc/zlibFace.c:73:6: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/dystring.c -o ucsc/dystring.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/hmmstats.c -o ucsc/hmmstats.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
     ^
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:547:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
     ^
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:557:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
     ^
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:565:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld,%03lld", thousands, l);
     ^
ucsc/obscure.c:571:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/obscure.c:571:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c:574:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     sprintf(s, "%lld", l);
     ^
ucsc/obscure.c:574:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/obscure.c: In function 'printVmPeak':
ucsc/obscure.c:789:6: warning: format '%d' expects argument of type 'int', but argument 3 has type 'pid_t' [-Wformat=]
      fprintf(stderr, "# pid=%d: %s\n", pid, line);
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/pipeline.c -o ucsc/pipeline.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/rangeTree.c -o ucsc/rangeTree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/rbTree.c -o ucsc/rbTree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)maxAlloc);
          ^
ucsc/memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  (unsigned long long)size, errno);
  ^
ucsc/memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
          (unsigned long long)size, (unsigned long long)NEEDMEM_LIMIT);
          ^
ucsc/memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              (unsigned long long)size, errno);
              ^
ucsc/memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
ucsc/memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:326:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:326:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:333:14: warning: unknown conversion type character 'l' in format [-Wformat=]
              ptrToLL(vpt));
              ^
ucsc/memalloc.c:333:14: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:377:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:377:18: warning: too many arguments for format [-Wformat-extra-args]
ucsc/memalloc.c:385:18: warning: unknown conversion type character 'l' in format [-Wformat=]
                  ptrToLL(cmb+1));
                  ^
ucsc/memalloc.c:385:18: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/dlist.c -o ucsc/dlist.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'readAndIgnore':
ucsc/udc.c:138:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  errnoAbort("readAndIgnore: error reading socket after %lld bytes", total);
  ^
ucsc/udc.c:138:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("readAndIgnore: got EOF at %lld bytes (wanted %lld)", total, size);
     ^
ucsc/udc.c:143:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:143:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:234:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:234:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:234:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:241:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     warn("udcDataViaLocal failed to fetch %d bytes at %lld", size, offset);
     ^
ucsc/udc.c:241:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:290:1: warning: unknown conversion type character 'l' in format [-Wformat=]
 verbose(2, "slow reading remote data - %d bytes at %lld - on %s\n", size, offset, url);
 ^
ucsc/udc.c:290:1: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:290:1: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c:308:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  warn("udcDataViaSlow failed to fetch %d bytes at %lld", size, offset);
  ^
ucsc/udc.c:308:2: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:516:7: warning: unknown conversion type character 'l' in format [-Wformat=]
       fd, file->bitmapFileName, offset, udcBitmapHeaderSize);
       ^
ucsc/udc.c:516:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long long int' [-Wformat=]
ucsc/udc.c:516:7: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'setInitialCachedDataBounds':
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   file->sparseFileName, version);
   ^
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:668:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:668:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'time_t' [-Wformat=]
ucsc/udc.c:668:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcCheckCacheBits':
ucsc/udc.c:1111:3: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
   (unsigned long)file, clearBlock,
   ^
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   ((long long)clearBlock * udcBlockSize), (((long long)clearBlock+1) * udcBlockSize));
   ^
ucsc/udc.c:1112:3: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1112:3: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
    readSize, file->url, startPos, actualSize);
    ^
ucsc/udc.c:1136:4: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1136:4: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1136:4: warning: format '%d' expects argument of type 'int', but argument 3 has type 'char *' [-Wformat=]
ucsc/udc.c:1136:4: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcMustRead':
ucsc/udc.c:1361:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     errAbort("udc couldn't read %llu bytes from %s, did read %llu", size, file->url, sizeRead);
     ^
ucsc/udc.c:1361:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long unsigned int' [-Wformat=]
ucsc/udc.c:1361:5: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1361:5: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: In function 'udcFileReadAll':
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
      url, (long long)size, (long long)maxSize);
      ^
ucsc/udc.c:1497:6: warning: unknown conversion type character 'l' in format [-Wformat=]
ucsc/udc.c:1497:6: warning: too many arguments for format [-Wformat-extra-args]
ucsc/udc.c: At top level:
ucsc/udc.c:126:13: warning: 'readAndIgnore' defined but not used [-Wunused-function]
 static void readAndIgnore(int sd, bits64 size)
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/net.c -o ucsc/net.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/bits.c -o ucsc/bits.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/twoBit.c -o ucsc/twoBit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/internet.c -o ucsc/internet.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/https.c -o ucsc/https.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/base64.c -o ucsc/base64.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/verbose.c -o ucsc/verbose.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/os.c -o ucsc/os.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/wildcmp.c -o ucsc/wildcmp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ucsc/_portimpl.c -o ucsc/_portimpl.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bigWig.o chain_io.o twoBit.o handlers.o utils.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/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rtracklayer' as rtracklayer_1.40.6.zip
* DONE (rtracklayer)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'rtracklayer' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

rtracklayer.Rcheck/tests_i386/rtracklayer_unit_tests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("rtracklayer") || stop("unable to load rtracklayer package")
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
[1] TRUE
> rtracklayer:::.test()
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Warning in readGFF(filepath, version = version, filter = filter) :
  connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
  connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
  connection is not positioned at the start of the file, rewinding it
For efficiency, consider converting this WIG file to a BigWig file;
see ?wigToBigWig


RUNIT TEST PROTOCOL -- Wed Oct 17 04:40:48 2018 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
rtracklayer RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
There were 14 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
  23.00    2.12   25.54 

rtracklayer.Rcheck/tests_x64/rtracklayer_unit_tests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
[1] TRUE
> rtracklayer:::.test()
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Warning in readGFF(filepath, version = version, filter = filter) :
  connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
  connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
  connection is not positioned at the start of the file, rewinding it
For efficiency, consider converting this WIG file to a BigWig file;
see ?wigToBigWig


RUNIT TEST PROTOCOL -- Wed Oct 17 04:41:15 2018 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
rtracklayer RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
There were 14 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
  25.14    1.14   26.37 

Example timings

rtracklayer.Rcheck/examples_i386/rtracklayer-Ex.timings

nameusersystemelapsed
BEDFile-class2.820.963.79
BamFile-methods0.110.010.13
BigWigFile0.020.000.01
BigWigSelection-class0.030.000.03
GFFFile-class1.730.051.83
GenomicData0.140.030.17
GenomicSelection0.150.000.16
Quickload-class0.250.050.54
QuickloadGenome-class0.250.000.25
TwoBitFile-class0.080.000.08
UCSCSchema-class000
UCSCTableQuery-class000
WIGFile-class0.670.030.70
asBED000
asGFF000
browseGenome000
browserView-methods000
browserViews-methods000
cpneTrack0.470.000.47
export0.050.000.05
layTrack-methods000
liftOver0.020.000.01
readGFF0.360.000.36
targets0.040.020.06
ucscGenomes0.190.000.82
ucscTrackModes-methods0.010.000.02

rtracklayer.Rcheck/examples_x64/rtracklayer-Ex.timings

nameusersystemelapsed
BEDFile-class3.510.644.16
BamFile-methods0.090.020.11
BigWigFile000
BigWigSelection-class0.030.000.03
GFFFile-class1.050.001.05
GenomicData0.190.010.20
GenomicSelection0.150.000.16
Quickload-class0.250.020.47
QuickloadGenome-class0.240.000.23
TwoBitFile-class0.110.000.11
UCSCSchema-class000
UCSCTableQuery-class000
WIGFile-class0.810.000.82
asBED000
asGFF000
browseGenome000
browserView-methods000
browserViews-methods000
cpneTrack0.530.030.56
export0.030.020.04
layTrack-methods000
liftOver000
readGFF0.470.000.47
targets0.040.010.06
ucscGenomes0.190.020.58
ucscTrackModes-methods0.030.000.03