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INSTALL report for GenomicRanges on tokay1

This page was generated on 2018-04-12 13:20:05 -0400 (Thu, 12 Apr 2018).

Package 567/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicRanges 1.30.3
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GenomicRanges
Branch: RELEASE_3_6
Last Commit: e999790
Last Changed Date: 2018-02-21 12:07:02 -0400 (Wed, 21 Feb 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicRanges
Version: 1.30.3
Command: rm -rf GenomicRanges.buildbin-libdir && mkdir GenomicRanges.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/GenomicRanges_1.30.3.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicRanges.buildbin-libdir --merge-multiarch GenomicRanges_1.30.3.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL GenomicRanges_1.30.3.zip && rm GenomicRanges_1.30.3.tar.gz GenomicRanges_1.30.3.zip
StartedAt: 2018-04-11 18:36:35 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 18:38:02 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 87.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf GenomicRanges.buildbin-libdir && mkdir GenomicRanges.buildbin-libdir  && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/GenomicRanges_1.30.3.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicRanges.buildbin-libdir --merge-multiarch GenomicRanges_1.30.3.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL GenomicRanges_1.30.3.zip  && rm GenomicRanges_1.30.3.tar.gz GenomicRanges_1.30.3.zip
###
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install for i386

* installing *source* package 'GenomicRanges' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:24: note: 'end' was declared here
  int nexons, j, start, end, width;
                        ^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:17: note: 'start' was declared here
  int nexons, j, start, end, width;
                 ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicRanges'
    finding HTML links ... done
    DelegatingGenomicRanges-class           html  
    GNCList-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GNCList-class.Rd:46: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GNCList-class.Rd:47: missing file link 'NCLists'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GNCList-class.Rd:48: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GNCList-class.Rd:49: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GNCList-class.Rd:55: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCLists'
    GPos-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:63: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:64: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:65: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:67: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:82: missing file link 'seqlevels'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:84: missing file link 'seqlengths'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:85: missing file link 'isCircular'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:86: missing file link 'genome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:134: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:152: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:171: missing file link 'snpsBySeqname'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:172: missing file link 'snpsByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:173: missing file link 'snpsById'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:174: missing file link 'SNPlocs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GPos-class.Rd:177: missing file link 'SummarizedExperiment'
    GRanges-class                           html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:96: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:98: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:100: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:102: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:120: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:124: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:128: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:173: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:345: missing file link 'ManyToOneGrouping'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:523: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:524: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:527: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:527: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:537: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:575: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:577: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:577: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRanges-class.Rd:578: missing file link 'DataFrame'
    GRangesList-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRangesList-class.Rd:208: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GRangesList-class.Rd:368: missing file link 'RleList-class'
    GenomicRanges-comparison                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GenomicRanges-comparison.Rd:113: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GenomicRanges-comparison.Rd:113: missing file link 'disjoin'
    GenomicRangesList-class                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/GenomicRangesList-class.Rd:16: missing file link 'List'
    absoluteRanges                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/absoluteRanges.Rd:39: missing file link 'seqlengths'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/absoluteRanges.Rd:41: missing file link 'seqlengths'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/absoluteRanges.Rd:50: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/absoluteRanges.Rd:65: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/absoluteRanges.Rd:86: missing file link 'IRanges'
    constraint                              html  
    coverage-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:12: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:15: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:16: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:16: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:18: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:19: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:45: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:54: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:67: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:71: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:82: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:90: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/coverage-methods.Rd:95: missing file link 'RleList'
    findOverlaps-methods                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/findOverlaps-methods.Rd:26: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/findOverlaps-methods.Rd:27: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/findOverlaps-methods.Rd:27: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/findOverlaps-methods.Rd:29: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/findOverlaps-methods.Rd:30: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/findOverlaps-methods.Rd:31: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/findOverlaps-methods.Rd:59: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/findOverlaps-methods.Rd:99: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/findOverlaps-methods.Rd:113: missing file link 'findOverlaps'
    genomic-range-squeezers                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:16: missing file link 'ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:17: missing file link 'rglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:19: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:19: missing file link 'ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:21: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:21: missing file link 'rglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:32: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:33: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:34: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:35: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:36: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:37: missing file link 'Pairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:40: missing file link 'ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:46: missing file link 'ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:49: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:50: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:63: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:79: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:82: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:83: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomic-range-squeezers.Rd:84: missing file link 'GAlignmentsList'
    genomicvars                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomicvars.Rd:20: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomicvars.Rd:49: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomicvars.Rd:60: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomicvars.Rd:80: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomicvars.Rd:91: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/genomicvars.Rd:105: missing file link 'RleList'
    inter-range-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/inter-range-methods.Rd:104: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/inter-range-methods.Rd:112: missing file link 'gaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/inter-range-methods.Rd:121: missing file link 'disjoin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/inter-range-methods.Rd:145: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/inter-range-methods.Rd:153: missing file link 'endoapply'
    intra-range-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/intra-range-methods.Rd:53: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/intra-range-methods.Rd:54: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/intra-range-methods.Rd:118: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/intra-range-methods.Rd:122: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/intra-range-methods.Rd:126: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/intra-range-methods.Rd:194: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/intra-range-methods.Rd:196: missing file link 'endoapply'
    makeGRangesFromDataFrame                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:16: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:37: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:120: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:142: missing file link 'getTable'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:146: missing file link 'DataFrame'
    makeGRangesListFromDataFrame            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/makeGRangesListFromDataFrame.Rd:15: missing file link 'split'
    nearest-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/nearest-methods.Rd:69: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/nearest-methods.Rd:141: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/nearest-methods.Rd:144: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/nearest-methods.Rd:157: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/nearest-methods.Rd:158: missing file link 'Hits'
    phicoef                                 html  
    setops-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/setops-methods.Rd:45: missing file link 'punion'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/setops-methods.Rd:45: missing file link 'pintersect'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/setops-methods.Rd:46: missing file link 'psetdiff'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/setops-methods.Rd:46: missing file link 'pgap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/setops-methods.Rd:47: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/setops-methods.Rd:155: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/setops-methods.Rd:155: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/setops-methods.Rd:167: missing file link 'mendoapply'
    strand-utils                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/strand-utils.Rd:52: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/strand-utils.Rd:64: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/strand-utils.Rd:65: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/strand-utils.Rd:73: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/strand-utils.Rd:96: missing file link 'Rle'
    tile-methods                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/tile-methods.Rd:12: missing file link 'tile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/tile-methods.Rd:12: missing file link 'slidingWindows'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/tile-methods.Rd:30: missing file link 'tile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/tile-methods.Rd:35: missing file link 'tile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/tile-methods.Rd:65: missing file link 'tile'
    tileGenome                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/tileGenome.Rd:68: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiYdw8z/R.INSTALL16604670267b/GenomicRanges/man/tileGenome.Rd:70: missing file link 'Views'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GenomicRanges' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:24: note: 'end' was declared here
  int nexons, j, start, end, width;
                        ^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:17: note: 'start' was declared here
  int nexons, j, start, end, width;
                 ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicRanges' as GenomicRanges_1.30.3.zip
* DONE (GenomicRanges)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'GenomicRanges' successfully unpacked and MD5 sums checked
In R CMD INSTALL