Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

INSTALL report for VariantAnnotation on tokay1

This page was generated on 2021-05-06 12:34:08 -0400 (Thu, 06 May 2021).

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 1930/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.36.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/VariantAnnotation
Branch: RELEASE_3_12
Last Commit: 9918bd1
Last Changed Date: 2020-10-27 10:42:24 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: VariantAnnotation
Version: 1.36.0
Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/VariantAnnotation_1.36.0.tar.gz && rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL VariantAnnotation_1.36.0.zip && rm VariantAnnotation_1.36.0.tar.gz VariantAnnotation_1.36.0.zip
StartedAt: 2021-05-05 17:59:54 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 18:02:07 -0400 (Wed, 05 May 2021)
EllapsedTime: 132.9 seconds
RetCode: 0
Status:   OK   

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/VariantAnnotation_1.36.0.tar.gz && rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL VariantAnnotation_1.36.0.zip && rm VariantAnnotation_1.36.0.tar.gz VariantAnnotation_1.36.0.zip
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1308k  100 1308k    0     0  21.8M      0 --:--:-- --:--:-- --:--:-- 22.4M

install for i386

* installing *source* package 'VariantAnnotation' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/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-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/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
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dna_hash.c -o dna_hash.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rle.c -o rle.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c strhash.c -o strhash.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utilities.c -o utilities.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcffile.c -o vcffile.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcftype.c -o vcftype.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c writevcf.c -o writevcf.o
C:/rtools40/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/biocbuild/bbs-3.12-bioc/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/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/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/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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/biocbuild/bbs-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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-3.12-bioc/tmpdir/RtmpMZCN5v/R.INSTALLd6850c05216/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
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/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-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/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
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dna_hash.c -o dna_hash.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rle.c -o rle.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c strhash.c -o strhash.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utilities.c -o utilities.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcffile.c -o vcffile.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcftype.c -o vcftype.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c writevcf.c -o writevcf.o
C:/rtools40/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/biocbuild/bbs-3.12-bioc/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/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantAnnotation' as VariantAnnotation_1.36.0.zip
* DONE (VariantAnnotation)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'VariantAnnotation' successfully unpacked and MD5 sums checked