Back to "Blame Jeroen" build/check report for BioC 3.11

INSTALL report for VariantAnnotation on tokay2

This page was generated on 2020-04-15 03:20:11 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
TO THE DEVELOPERS/MAINTAINERS OF THE VariantAnnotation PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 85/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.33.4
Bioconductor Package Maintainer
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/VariantAnnotation
Branch: master
Last Commit: 5f14082
Last Changed Date: 2020-04-08 18:20:28 -0400 (Wed, 08 Apr 2020)
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] ERROR  skipped  skipped 

Summary

Package: VariantAnnotation
Version: 1.33.4
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/VariantAnnotation_1.33.4.tar.gz && rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.33.4.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL VariantAnnotation_1.33.4.zip && rm VariantAnnotation_1.33.4.tar.gz VariantAnnotation_1.33.4.zip
StartedAt: 2020-04-14 18:23:11 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 18:25:09 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 118.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/VariantAnnotation_1.33.4.tar.gz && rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.33.4.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL VariantAnnotation_1.33.4.zip && rm VariantAnnotation_1.33.4.tar.gz VariantAnnotation_1.33.4.zip
###
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100 1308k  100 1308k    0     0  17.1M      0 --:--:-- --:--:-- --:--:-- 18.7M

install for i386

* installing *source* package 'VariantAnnotation' ...
** using staged installation
** libs
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dna_hash.c -o dna_hash.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rle.c -o rle.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c strhash.c -o strhash.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utilities.c -o utilities.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcffile.c -o vcffile.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcftype.c -o vcftype.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c writevcf.c -o writevcf.o
/mingw32/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/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/VariantAnnotation.buildbin-libdir/00LOCK-VariantAnnotation/00new/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/VariantAnnotation/man/VCF-class.Rd:317: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/VariantAnnotation/man/VCF-class.Rd:416: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/VariantAnnotation/man/VCF-class.Rd:417: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/VariantAnnotation/man/VCF-class.Rd:418: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    VCFHeader-class                         html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/VariantAnnotation/man/defunct.Rd:85: 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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmpi8T2Ak/R.INSTALLf345a0324c4/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 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 'VariantAnnotation' ...
** libs
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dna_hash.c -o dna_hash.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rle.c -o rle.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c strhash.c -o strhash.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utilities.c -o utilities.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcffile.c -o vcffile.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcftype.c -o vcftype.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c writevcf.c -o writevcf.o
/mingw64/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/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantAnnotation' as VariantAnnotation_1.33.4.zip
* DONE (VariantAnnotation)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'VariantAnnotation' successfully unpacked and MD5 sums checked