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INSTALL report for HTSanalyzeR on tokay1

This page was generated on 2020-04-15 12:19:22 -0400 (Wed, 15 Apr 2020).

Package 802/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSanalyzeR 2.38.0
Xin Wang
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/HTSanalyzeR
Branch: RELEASE_3_10
Last Commit: eec27b7
Last Changed Date: 2019-10-29 13:08:17 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: HTSanalyzeR
Version: 2.38.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/HTSanalyzeR_2.38.0.tar.gz && rm -rf HTSanalyzeR.buildbin-libdir && mkdir HTSanalyzeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HTSanalyzeR.buildbin-libdir HTSanalyzeR_2.38.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL HTSanalyzeR_2.38.0.zip && rm HTSanalyzeR_2.38.0.tar.gz HTSanalyzeR_2.38.0.zip
StartedAt: 2020-04-14 20:39:01 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 20:39:51 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 49.4 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/HTSanalyzeR_2.38.0.tar.gz && rm -rf HTSanalyzeR.buildbin-libdir && mkdir HTSanalyzeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HTSanalyzeR.buildbin-libdir HTSanalyzeR_2.38.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL HTSanalyzeR_2.38.0.zip && rm HTSanalyzeR_2.38.0.tar.gz HTSanalyzeR_2.38.0.zip
###
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install for i386

* installing *source* package 'HTSanalyzeR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
** help
*** installing help indices
  converting help for package 'HTSanalyzeR'
    finding HTML links ... done
    FDRcollectionGsea                       html  
    GOGeneSets                              html  
    GSCA-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/GSCA-class.Rd:112: file link 'writeHits' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    GenHTSAHtmlRowUnit                      html  
    HTSanalyzeR                             html  
    HTSanalyzeR4cellHTS2                    html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:8: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:9: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:207: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:218: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:218: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    KeggGeneSets                            html  
    NWA-class                               html  
    aggregatePvals                          html  
    analyze                                 html  
    analyzeGeneSetCollections               html  
    annotationConvertor                     html  
    appendGSTerms                           html  
    biogridDataDownload                     html  
    celAnnotationConvertor                  html  
    cellHTS2OutputStatTests                 html  
    changes                                 html  
    collectionGsea                          html  
    data-KcViab                             html  
    drosoAnnotationConvertor                html  
    duplicateRemover                        html  
    getTopGeneSets                          html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/getTopGeneSets.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/getTopGeneSets.Rd:18: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/getTopGeneSets.Rd:27: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/getTopGeneSets.Rd:28: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/getTopGeneSets.Rd:32: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    gseaPlots                               html  
    gseaScores                              html  
    htmlAttrVectorPaste                     html  
    hyperGeoTest                            html  
    interactome                             html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/interactome.Rd:10: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/interactome.Rd:13: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/interactome.Rd:23: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/interactome.Rd:28: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/interactome.Rd:69: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/interactome.Rd:81: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    makeGSEAplots                           html  
    makeOverlapTable                        html  
    mammalAnnotationConvertor               html  
    multiHyperGeoTest                       html  
    networkAnalysis                         html  
    networkPlot                             html  
    pairwiseGsea                            html  
    pairwiseGseaPlot                        html  
    pairwisePhenoMannWhit                   html  
    paraCheck                               html  
    permutationPvalueCollectionGsea         html  
    plotEnrichMap                           html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotEnrichMap.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotEnrichMap.Rd:13: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotEnrichMap.Rd:25: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotEnrichMap.Rd:26: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotEnrichMap.Rd:30: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    plotGSEA                                html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotGSEA.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotGSEA.Rd:14: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotGSEA.Rd:24: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotGSEA.Rd:25: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotGSEA.Rd:29: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    plotSubNet                              html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotSubNet.Rd:10: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotSubNet.Rd:23: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotSubNet.Rd:24: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/plotSubNet.Rd:28: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    preprocess                              html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/preprocess.Rd:11: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/preprocess.Rd:11: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/preprocess.Rd:15: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/preprocess.Rd:20: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/preprocess.Rd:30: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/preprocess.Rd:31: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/preprocess.Rd:35: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/preprocess.Rd:35: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/preprocess.Rd:112: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/preprocess.Rd:113: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    report                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:11: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:11: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:15: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:15: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:25: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:25: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:26: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:26: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:30: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:30: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:69: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/report.Rd:70: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    reportAll                               html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/reportAll.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
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    summarize                               html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/summarize.Rd:14: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/summarize.Rd:28: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/summarize.Rd:28: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/summarize.Rd:33: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpei9JmD/R.INSTALL27f05b70ae/HTSanalyzeR/man/summarize.Rd:33: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
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    viewEnrichMap                           html  
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    viewGSEA                                html  
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    writeHTSAHtmlHead                       html  
    writeHTSAHtmlSummary                    html  
    writeHTSAHtmlTab                        html  
    writeHTSAHtmlTable                      html  
    writeHTSAHtmlTail                       html  
    writeReportHTSA                         html  
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** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
Warning: Package 'HTSanalyzeR' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package can be loaded from final location
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
Warning: Package 'HTSanalyzeR' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'HTSanalyzeR' ...
** testing if installed package can be loaded
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
Warning: Package 'HTSanalyzeR' is deprecated and will be removed from
  Bioconductor version 3.11
* MD5 sums
packaged installation of 'HTSanalyzeR' as HTSanalyzeR_2.38.0.zip
* DONE (HTSanalyzeR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'HTSanalyzeR' successfully unpacked and MD5 sums checked