Last data update: 2014.03.03

VariantAnnotation

Package: VariantAnnotation
Type: Package
Title: Annotation of Genetic Variants
Description: Annotate variants, compute amino acid coding changes,
predict coding outcomes.
Version: 1.18.1
Authors@R: c(person("Valerie", "Obenchain", role=c("aut", "cre"),
email="maintainer@bioconductor.org"),
person("Martin", "Morgan", role="aut"),
person("Michael", "Lawrence", role="aut"),
person("Stephanie", "Gogarten", role="ctb"))
License: Artistic-2.0
Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3), GenomeInfoDb
(>= 1.7.1), GenomicRanges (>= 1.19.47), SummarizedExperiment
(>= 0.3.1), Rsamtools (>= 1.23.10)
Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.9.47), IRanges
(>= 2.3.25), XVector (>= 0.5.6), Biostrings (>= 2.33.5),
AnnotationDbi (>= 1.27.9), BSgenome (>= 1.37.6), rtracklayer
(>= 1.25.16), GenomicFeatures (>= 1.19.17)
Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP.20110815,
SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132,
SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats,
ggplot2, BiocStyle
LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rsamtools
LazyLoad: yes
biocViews: DataImport, Sequencing, SNP, Annotation, Genetics,
VariantAnnotation
Video:
https://www.youtube.com/watch?v=Ro0lHQ_J--I&list=UUqaMSQd_h-2EDGsU6WDiX0Q
NeedsCompilation: yes
Packaged: 2016-05-15 03:03:33 UTC; biocbuild
Author: Valerie Obenchain [aut, cre],
Martin Morgan [aut],
Michael Lawrence [aut],
Stephanie Gogarten [ctb]
Maintainer: Valerie Obenchain <maintainer@bioconductor.org>

● BiocViews: Annotation, DataImport, Genetics, SNP, Sequencing, VariantAnnotationVideo: https://www.youtube.com/watch?v=Ro0lHQ_J--I&list=UUqaMSQd_h-2EDGsU6WDiX0Q
● 0 images, 26 functions, 0 datasets
● Reverse Depends: 20

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'VariantAnnotation' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c dna_hash.c -o dna_hash.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c rle.c -o rle.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c strhash.c -o strhash.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c utilities.c -o utilities.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c vcffile.c -o vcffile.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c vcftype.c -o vcftype.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"   -fpic  -g -O2  -c writevcf.c -o writevcf.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o VariantAnnotation.so 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 /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbam.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbcf.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/VariantAnnotation/libs
** R
** inst
** preparing 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: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/VCF-class.Rd:292: missing file link 'BSgenome'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/VCF-class.Rd:389: missing file link 'DataFrame'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/VCF-class.Rd:390: missing file link 'SimpleList'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/VCF-class.Rd:391: missing file link 'RangedSummarizedExperiment'
    VCFHeader-class                         html  
    VRanges-class                           html  
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/VRanges-class.Rd:81: missing file link 'GRanges'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/VRanges-class.Rd:113: missing file link 'FilterMatrix'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/VRanges-class.Rd:171: missing file link 'FilterMatrix'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/VRanges-class.Rd:174: missing file link 'FilterRules'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/VRanges-class.Rd:191: missing file link 'GenomicRanges'
    VRangesList-class                       html  
    VariantType-class                       html  
    VcfFile-class                           html  
    defunct                                 html  
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/defunct.Rd:89: missing file link 'mapToTranscripts'
    filterVcf-methods                       html  
    genotypeToSnpMatrix-methods             html  
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:85: missing file link 'snpStats'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:89: missing file link 'snpStats'
    getTranscriptSeqs-methods               html  
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:14: missing file link 'BSgenome'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:15: missing file link 'FaFile'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:25: missing file link 'GRangesList'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: missing file link 'BSgenome'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: missing file link 'FaFile'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: missing file link 'BSgenome'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: missing file link 'FaFile'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:45: missing file link 'DNAStringSet'
    isSNV-methods                           html  
    locateVariants-methods                  html  
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/locateVariants-methods.Rd:41: missing file link 'Ranges'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/locateVariants-methods.Rd:41: missing file link 'GRanges'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/locateVariants-methods.Rd:48: missing file link 'TxDb'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/locateVariants-methods.Rd:50: missing file link 'TxDb'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/locateVariants-methods.Rd:83: missing file link 'Hits'
    predictCoding-methods                   html  
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/predictCoding-methods.Rd:26: missing file link 'Ranges'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/predictCoding-methods.Rd:41: missing file link 'TxDb'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/predictCoding-methods.Rd:43: missing file link 'TxDb'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/predictCoding-methods.Rd:46: missing file link 'BSgenome'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/predictCoding-methods.Rd:49: missing file link 'DNAStringSet'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/predictCoding-methods.Rd:82: missing file link 'BSgenome'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/predictCoding-methods.Rd:103: missing file link 'GRanges'
    probabilityToSnpMatrix                  html  
    readVcf-methods                         html  
    scanVcf-methods                         html  
    snpSummary                              html  
    summarizeVariants-methods               html  
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/summarizeVariants-methods.Rd:34: missing file link 'TxDb'
Rd warning: /tmp/RtmpTpbOBm/R.INSTALL650b73e2e45e/VariantAnnotation/man/summarizeVariants-methods.Rd:36: missing file link 'TxDb'
    writeVcf-methods                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VariantAnnotation)
Making 'packages.html' ... done

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO