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BUILD BIN report for VariantTools on tokay2

This page was generated on 2020-10-16 11:59:08 -0400 (Fri, 16 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE VariantTools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1867/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantTools 1.30.0
Michael Lawrence
Snapshot Date: 2020-10-15 14:40:03 -0400 (Thu, 15 Oct 2020)
URL: https://git.bioconductor.org/packages/VariantTools
Branch: RELEASE_3_11
Last Commit: 845c555
Last Changed Date: 2020-04-27 14:31:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantTools
Version: 1.30.0
Command: rm -rf VariantTools.buildbin-libdir && mkdir VariantTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantTools.buildbin-libdir VariantTools_1.30.0.tar.gz
StartedAt: 2020-10-16 11:33:20 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 11:34:48 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 87.8 seconds
RetCode: 0
Status:  OK  
PackageFile: VariantTools_1.30.0.zip
PackageFileSize: 6.392 MiB

Command output

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### Running command:
###
###   rm -rf VariantTools.buildbin-libdir && mkdir VariantTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantTools.buildbin-libdir VariantTools_1.30.0.tar.gz
###
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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-3.11-bioc/tmpdir/RtmpSib9Kh/R.INSTALL1698c0b4a64/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-3.11-bioc/tmpdir/RtmpSib9Kh/R.INSTALL1698c0b4a64/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-3.11-bioc/tmpdir/RtmpSib9Kh/R.INSTALL1698c0b4a64/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-3.11-bioc/tmpdir/RtmpSib9Kh/R.INSTALL1698c0b4a64/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-3.11-bioc/tmpdir/RtmpSib9Kh/R.INSTALL1698c0b4a64/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-3.11-bioc/tmpdir/RtmpSib9Kh/R.INSTALL1698c0b4a64/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-3.11-bioc/tmpdir/RtmpSib9Kh/R.INSTALL1698c0b4a64/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-3.11-bioc/tmpdir/RtmpSib9Kh/R.INSTALL1698c0b4a64/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-3.11-bioc/tmpdir/RtmpSib9Kh/R.INSTALL1698c0b4a64/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-3.11-bioc/tmpdir/RtmpSib9Kh/R.INSTALL1698c0b4a64/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
** 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_1.30.0.zip
* DONE (VariantTools)