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### Running command:
###
###   rm -rf GenomicRanges.buildbin-libdir && mkdir GenomicRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicRanges.buildbin-libdir GenomicRanges_1.40.0.tar.gz
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install for i386

* installing *source* package 'GenomicRanges' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/GenomicRanges.buildbin-libdir/00LOCK-GenomicRanges/00new/GenomicRanges/libs/i386
** R
** inst
** byte-compile and prepare 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-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GNCList-class.Rd:46: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GNCList-class.Rd:47: file link 'NCLists' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GNCList-class.Rd:48: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GNCList-class.Rd:49: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GNCList-class.Rd:55: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GNCList-class.Rd:79: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GNCList-class.Rd:79: file link 'NCLists' in package 'IRanges' does not exist and so has been treated as a topic
    GPos-class                              html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:78: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:79: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:79: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:82: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:97: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:99: file link 'UnstitchedIPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:100: file link 'StitchedIPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:117: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:137: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:138: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:139: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:141: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:153: file link 'seqlevels' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:155: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:156: file link 'isCircular' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:157: file link 'genome' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:207: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:230: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:259: file link 'snpsBySeqname' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:260: file link 'snpsByOverlaps' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:261: file link 'snpsById' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:262: file link 'SNPlocs' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GPos-class.Rd:265: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    GRanges-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:100: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:102: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:104: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:106: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:124: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:128: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:132: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:183: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:189: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:289: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:313: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:356: file link 'ManyToOneGrouping' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:371: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:408: file link '[' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:436: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:472: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:473: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:476: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:476: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:485: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:493: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:530: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:530: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRanges-class.Rd:531: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
    GRangesFactor-class                     html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesFactor-class.Rd:28: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesFactor-class.Rd:31: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesFactor-class.Rd:32: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesFactor-class.Rd:41: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesFactor-class.Rd:66: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesFactor-class.Rd:69: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesFactor-class.Rd:78: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesFactor-class.Rd:88: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesFactor-class.Rd:93: file link 'unfactor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesFactor-class.Rd:98: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesFactor-class.Rd:127: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
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    GRangesList-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesList-class.Rd:194: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesList-class.Rd:347: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesList-class.Rd:350: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GRangesList-class.Rd:353: file link 'DataFrameList' in package 'IRanges' does not exist and so has been treated as a topic
    GenomicRanges-comparison                html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GenomicRanges-comparison.Rd:115: file link 'reduce' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GenomicRanges-comparison.Rd:115: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
    GenomicRangesList-class                 html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/GenomicRangesList-class.Rd:91: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/strand-utils.Rd:96: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
    tile-methods                            html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/tile-methods.Rd:12: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/tile-methods.Rd:12: file link 'slidingWindows' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/tile-methods.Rd:30: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/tile-methods.Rd:35: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/tile-methods.Rd:65: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
    tileGenome                              html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/tileGenome.Rd:68: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWam4Uw/R.INSTALLc801991079/GenomicRanges/man/tileGenome.Rd:70: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GenomicRanges' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicRanges' as GenomicRanges_1.40.0.zip
* DONE (GenomicRanges)