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INSTALL report for VariantTools on tokay2

This page was generated on 2019-10-16 12:27:06 -0400 (Wed, 16 Oct 2019).

Package 1708/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantTools 1.26.0
Michael Lawrence
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/VariantTools
Branch: RELEASE_3_9
Last Commit: 780ffb6
Last Changed Date: 2019-05-02 11:53:39 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS 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  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantTools
Version: 1.26.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/VariantTools_1.26.0.tar.gz && rm -rf VariantTools.buildbin-libdir && mkdir VariantTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantTools.buildbin-libdir VariantTools_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL VariantTools_1.26.0.zip && rm VariantTools_1.26.0.tar.gz VariantTools_1.26.0.zip
StartedAt: 2019-10-15 20:32:42 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:34:02 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 79.5 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/VariantTools_1.26.0.tar.gz && rm -rf VariantTools.buildbin-libdir && mkdir VariantTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantTools.buildbin-libdir VariantTools_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL VariantTools_1.26.0.zip && rm VariantTools_1.26.0.tar.gz VariantTools_1.26.0.zip
###
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  % 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 5982k  100 5982k    0     0  27.5M      0 --:--:-- --:--:-- --:--:-- 28.4M

install for i386

* installing *source* package 'VariantTools' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'VariantTools'
    finding HTML links ... done
    FilterConstructors                      html  
    annnotateWithControlDepth               html  
    callGenotypes                           html  
    callSampleSpecificVariants              html  
    callVariants                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwZ4wkD/R.INSTALL21a02c7241e/VariantTools/man/callVariants.Rd:84: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
    callWildtype                            html  
    concordance                             html  
    extractCoverageForPositions             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwZ4wkD/R.INSTALL21a02c7241e/VariantTools/man/extractCoverageForPositions.Rd:16: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
    matchVariants                           html  
    pileupVariants                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwZ4wkD/R.INSTALL21a02c7241e/VariantTools/man/pileupVariants.Rd:21: file link 'PileupFiles' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwZ4wkD/R.INSTALL21a02c7241e/VariantTools/man/pileupVariants.Rd:28: file link 'ApplyPileupsParam' in package 'Rsamtools' does not exist and so has been treated as a topic
    postFilterVariants                      html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwZ4wkD/R.INSTALL21a02c7241e/VariantTools/man/postFilterVariants.Rd:50: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
    qaVariants                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwZ4wkD/R.INSTALL21a02c7241e/VariantTools/man/qaVariants.Rd:51: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
    tallyVariants                           html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwZ4wkD/R.INSTALL21a02c7241e/VariantTools/man/tallyVariants.Rd:60: file link 'stackSamples' in package 'VariantAnnotation' does not exist and so has been treated as a topic
    variantGR2Vcf                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwZ4wkD/R.INSTALL21a02c7241e/VariantTools/man/variantGR2Vcf.Rd:8: file link 'VCF' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwZ4wkD/R.INSTALL21a02c7241e/VariantTools/man/variantGR2Vcf.Rd:10: file link 'writeVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwZ4wkD/R.INSTALL21a02c7241e/VariantTools/man/variantGR2Vcf.Rd:19: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
    vignette                                html  
** building package indices
** installing vignettes
   'VariantTools.Rnw' 
** 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 'VariantTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantTools' as VariantTools_1.26.0.zip
* DONE (VariantTools)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'VariantTools' successfully unpacked and MD5 sums checked