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BUILD BIN report for VariantAnnotation on tokay1

This page was generated on 2019-04-13 11:21:45 -0400 (Sat, 13 Apr 2019).

Package 1617/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.28.13
Valerie Obenchain
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/VariantAnnotation
Branch: RELEASE_3_8
Last Commit: 0393347
Last Changed Date: 2019-03-19 13:28:03 -0400 (Tue, 19 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantAnnotation
Version: 1.28.13
Command: rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.28.13.tar.gz
StartedAt: 2019-04-13 08:03:26 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 08:06:17 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 170.5 seconds
RetCode: 0
Status:  OK  
PackageFile: VariantAnnotation_1.28.13.zip
PackageFileSize: 3.516 MiB

Command output

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###
### Running command:
###
###   rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.28.13.tar.gz
###
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install for i386

* installing *source* package 'VariantAnnotation' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c dna_hash.c -o dna_hash.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c rle.c -o rle.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c strhash.c -o strhash.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c vcffile.c -o vcffile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c vcftype.c -o vcftype.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c writevcf.c -o writevcf.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o VariantAnnotation.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'tabulate' in package 'VariantAnnotation'
** help
*** installing help indices
  converting help for package 'VariantAnnotation'
    finding HTML links ... done
    GLtoGP                                  html  
    PROVEANDb-class                         html  
    PolyPhenDb-class                        html  
    PolyPhenDbColumns                       html  
    SIFTDb-class                            html  
    SIFTDbColumns                           html  
    ScanVcfParam-class                      html  
    finding level-2 HTML links ... done

    VCF-class                               html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VCF-class.Rd:241: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VCF-class.Rd:316: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VCF-class.Rd:415: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VCF-class.Rd:416: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VCF-class.Rd:417: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    VCFHeader-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VCFHeader-class.Rd:114: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
    VRanges-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VRanges-class.Rd:81: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VRanges-class.Rd:113: file link 'FilterMatrix' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VRanges-class.Rd:171: file link 'FilterMatrix' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VRanges-class.Rd:174: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VRanges-class.Rd:191: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    VRangesList-class                       html  
    VariantType-class                       html  
    VcfFile-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/VcfFile-class.Rd:138: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
    defunct                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/defunct.Rd:89: file link 'mapToTranscripts' in package 'GenomicFeatures' does not exist and so has been treated as a topic
    filterVcf-methods                       html  
    genotypeToSnpMatrix-methods             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:85: file link 'snpStats' in package 'snpStats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:89: file link 'snpStats' in package 'snpStats' does not exist and so has been treated as a topic
    getTranscriptSeqs-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:14: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:15: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:25: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:45: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    indexVcf-method                         html  
    isSNV-methods                           html  
    locateVariants-methods                  html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/locateVariants-methods.Rd:41: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/locateVariants-methods.Rd:41: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/locateVariants-methods.Rd:48: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/locateVariants-methods.Rd:50: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/locateVariants-methods.Rd:83: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
    predictCoding-methods                   html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/predictCoding-methods.Rd:26: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/predictCoding-methods.Rd:41: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/predictCoding-methods.Rd:43: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/predictCoding-methods.Rd:46: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/predictCoding-methods.Rd:49: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/predictCoding-methods.Rd:82: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/predictCoding-methods.Rd:103: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    probabilityToSnpMatrix                  html  
    readVcf-methods                         html  
    scanVcf-methods                         html  
    seqinfo-method                          html  
    snpSummary                              html  
    summarizeVariants-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/summarizeVariants-methods.Rd:34: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUzY2jL/R.INSTALL3f44650b4e95/VariantAnnotation/man/summarizeVariants-methods.Rd:36: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
    writeVcf-methods                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'VariantAnnotation' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/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-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dna_hash.c -o dna_hash.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rle.c -o rle.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c strhash.c -o strhash.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c vcffile.c -o vcffile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c vcftype.c -o vcftype.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c writevcf.c -o writevcf.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o VariantAnnotation.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantAnnotation' as VariantAnnotation_1.28.13.zip
* DONE (VariantAnnotation)
In R CMD INSTALL
In R CMD INSTALL