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INSTALL report for VariantFiltering on tokay2

This page was generated on 2019-10-16 12:29:47 -0400 (Wed, 16 Oct 2019).

Package 1707/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantFiltering 1.20.0
Robert Castelo
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/VariantFiltering
Branch: RELEASE_3_9
Last Commit: cffc85d
Last Changed Date: 2019-05-02 11:53:47 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantFiltering
Version: 1.20.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/VariantFiltering_1.20.0.tar.gz && rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantFiltering.buildbin-libdir VariantFiltering_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL VariantFiltering_1.20.0.zip && rm VariantFiltering_1.20.0.tar.gz VariantFiltering_1.20.0.zip
StartedAt: 2019-10-15 20:58:40 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 21:01:30 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 170.2 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/VariantFiltering_1.20.0.tar.gz && rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantFiltering.buildbin-libdir VariantFiltering_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL VariantFiltering_1.20.0.zip && rm VariantFiltering_1.20.0.tar.gz VariantFiltering_1.20.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 3082k  100 3082k    0     0  34.5M      0 --:--:-- --:--:-- --:--:-- 37.6M

install for i386

* installing *source* package 'VariantFiltering' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/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/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c methods-WeightMatrix.c -o methods-WeightMatrix.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/VariantFiltering.buildbin-libdir/00LOCK-VariantFiltering/00new/VariantFiltering/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'annotateVariants' with signature 'annObj="MafDb"': no definition for class "MafDb"
** help
*** installing help indices
  converting help for package 'VariantFiltering'
    finding HTML links ... done
    GenePhylostrataDb-class                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/GenePhylostrataDb-class.Rd:47: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
    VariantFiltering-defunct                html  
    VariantFiltering-deprecated             html  
    finding level-2 HTML links ... done

    VariantFiltering-package                html  
    VariantFilteringParam-class             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringParam-class.Rd:105: file link 'getGeneticCode' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringParam-class.Rd:123: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
    VariantFilteringResults-class           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:81: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:84: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:101: file link 'isSNV' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:102: file link 'isInsertion' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:103: file link 'isDeletion' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:104: file link 'isSubstitution' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:105: file link 'isDelins' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:120: file link 'predictCoding' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:198: file link 'graphNEL' in package 'graph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:201: file link 'nodeData' in package 'graph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:207: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:211: file link 'VRangesList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:215: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:228: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:235: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:254: file link 'softFilterMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:316: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:317: file link 'predictCoding' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantFilteringResults-class.Rd:332: file link 'AlignmentsTrack' in package 'Gviz' does not exist and so has been treated as a topic
    VariantType-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantType-class.Rd:40: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantType-class.Rd:56: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/VariantType-class.Rd:60: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
    WeightMatrix-class                      html  
    autosomalDominant                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/autosomalDominant.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/autosomalDominant.Rd:29: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/autosomalDominant.Rd:31: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    autosomalRecessiveHeterozygous          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:22: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:26: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:28: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    autosomalRecessiveHomozygous            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/autosomalRecessiveHomozygous.Rd:26: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
    deNovo                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/deNovo.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/deNovo.Rd:29: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/deNovo.Rd:31: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    readAAradicalChangeMatrix               html  
    unrelatedIndividuals                    html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/unrelatedIndividuals.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/unrelatedIndividuals.Rd:27: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/unrelatedIndividuals.Rd:29: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    xLinked                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/xLinked.Rd:24: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/xLinked.Rd:30: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdnP9t/R.INSTALL26f448434daf/VariantFiltering/man/xLinked.Rd:32: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'VariantFiltering' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/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/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c methods-WeightMatrix.c -o methods-WeightMatrix.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/VariantFiltering.buildbin-libdir/VariantFiltering/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantFiltering' as VariantFiltering_1.20.0.zip
* DONE (VariantFiltering)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'VariantFiltering' successfully unpacked and MD5 sums checked