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INSTALL report for gQTLstats on tokay2

This page was generated on 2019-10-16 12:32:06 -0400 (Wed, 16 Oct 2019).

Package 710/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gQTLstats 1.16.0
VJ Carey
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/gQTLstats
Branch: RELEASE_3_9
Last Commit: c68a9cf
Last Changed Date: 2019-05-02 11:53:51 -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: gQTLstats
Version: 1.16.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/gQTLstats_1.16.0.tar.gz && rm -rf gQTLstats.buildbin-libdir && mkdir gQTLstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gQTLstats.buildbin-libdir gQTLstats_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL gQTLstats_1.16.0.zip && rm gQTLstats_1.16.0.tar.gz gQTLstats_1.16.0.zip
StartedAt: 2019-10-15 20:54:37 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:57:49 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 192.2 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/gQTLstats_1.16.0.tar.gz && rm -rf gQTLstats.buildbin-libdir && mkdir gQTLstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gQTLstats.buildbin-libdir gQTLstats_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL gQTLstats_1.16.0.zip && rm gQTLstats_1.16.0.tar.gz gQTLstats_1.16.0.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
  1 62.6M    1 1040k    0     0  1416k      0  0:00:45 --:--:--  0:00:45 1428k
100 62.6M  100 62.6M    0     0  39.7M      0  0:00:01  0:00:01 --:--:-- 39.9M

install for i386

* installing *source* package 'gQTLstats' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gQTLstats'
    finding HTML links ... done
    FDRsupp-class                           html  
    TransStore-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/TransStore-class.Rd:19: file link 'Registry' in package 'BatchJobs' does not exist and so has been treated as a topic
    TransStore                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/TransStore.Rd:18: file link 'Registry' in package 'BatchJobs' does not exist and so has been treated as a topic
    cisAssoc                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/cisAssoc.Rd:37: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/cisAssoc.Rd:40: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/cisAssoc.Rd:63: file link 'col.summary' in package 'snpStats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/cisAssoc.Rd:75: file link 'isSNV' in package 'VariantAnnotation' does not exist and so has been treated as a topic
    clipPCs                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/clipPCs.Rd:24: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/clipPCs.Rd:50: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    directPlot                              html  
    enumerateByFDR                          html  
    finding level-2 HTML links ... done

    eqBox2                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/eqBox2.Rd:27: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    filtFDR                                 html  
    gQTLs                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/gQTLs.Rd:29: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
    gQTLstats-package                       html  
    hmm878                                  html  
    manhWngr                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/manhWngr.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    mixedVCFtoSnpMatrix                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:18: file link 'CollapsedVCF-class' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:24: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:32: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:50: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
    pifdr                                   html  
    qqStore                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/qqStore.Rd:28: file link 'storeToQuantiles' in package 'gQTLstats' does not exist and so has been treated as a topic
    queryVCF                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/queryVCF.Rd:29: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
    senstab                                 html  
    setFDRfunc                              html  
    storeToStats                            html  
    tqbrowser                               html  
    transAssoc                              html  
    transBrowse                             html  
    tsByRank                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp426Uxf/R.INSTALL24943922e62/gQTLstats/man/tsByRank.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    txsPlot                                 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 'gQTLstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gQTLstats' as gQTLstats_1.16.0.zip
* DONE (gQTLstats)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'gQTLstats' successfully unpacked and MD5 sums checked