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INSTALL report for Biobase on tokay1

This page was generated on 2020-08-07 11:55:54 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Biobase PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 144/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.49.0
Bioconductor Package Maintainer
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/Biobase
Branch: master
Last Commit: 90d7ace
Last Changed Date: 2020-04-27 14:07:40 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Biobase
Version: 2.49.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/Biobase_2.49.0.tar.gz && rm -rf Biobase.buildbin-libdir && mkdir Biobase.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Biobase.buildbin-libdir Biobase_2.49.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Biobase_2.49.0.zip && rm Biobase_2.49.0.tar.gz Biobase_2.49.0.zip
StartedAt: 2020-08-06 16:38:15 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 16:39:35 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 79.8 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/Biobase_2.49.0.tar.gz && rm -rf Biobase.buildbin-libdir && mkdir Biobase.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Biobase.buildbin-libdir Biobase_2.49.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Biobase_2.49.0.zip && rm Biobase_2.49.0.tar.gz Biobase_2.49.0.zip
###
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1156k  100 1156k    0     0  23.4M      0 --:--:-- --:--:-- --:--:-- 25.0M

install for i386

* installing *source* package 'Biobase' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c anyMissing.c -o anyMissing.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c envir.c -o envir.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matchpt.c -o matchpt.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rowMedians.c -o rowMedians.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublist_extract.c -o sublist_extract.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o Biobase.dll tmp.def Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/Biobase.buildbin-libdir/00LOCK-Biobase/00new/Biobase/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Biobase'
    finding HTML links ... done
    Aggregate                               html  
    Biobase-package                         html  
    ScalarObject-class                      html  
    abstract                                html  
    addVig2Menu                             html  
    annotatedDataFrameFrom-methods          html  
    anyMissing                              html  
    assayData                               html  
    cache                                   html  
    channel                                 html  
    channelNames                            html  
    class.AnnotatedDataFrame                html  
    finding level-2 HTML links ... done

    class.AssayData                         html  
    class.ExpressionSet                     html  
    class.MIAME                             html  
    class.MIAxE                             html  
    class.MultiSet                          html  
    class.NChannelSet                       html  
    class.SnpSet                            html  
    class.Versioned                         html  
    class.VersionedBiobase                  html  
    class.Versions                          html  
    class.VersionsNull                      html  
    class.aggregator                        html  
    class.characterORmiame                  html  
    class.container                         html  
    class.eSet                              html  
    classVersion                            html  
    contents                                html  
    copyEnv                                 html  
    copySubstitute                          html  
    createPackage                           html  
    data.aaMap                              html  
    data.geneData                           html  
    data.reporter                           html  
    data.sample.ExpressionSet               html  
    data.sample.MultiSet                    html  
    defunct                                 html  
    description                             html  
    dumpPackTxt                             html  
    esApply                                 html  
    exprs                                   html  
    featureData                             html  
    featureNames                            html  
    getPkgVigs                              html  
    internals                               html  
    isCurrent                               html  
    isUnique                                html  
    isVersioned                             html  
    lcSuffix                                html  
    listLen                                 html  
    makeDataPackage                         html  
    matchpt                                 html  
    multiassign                             html  
    note                                    html  
    notes                                   html  
    openPDF                                 html  
    openVignette                            html  
    package.version                         html  
    phenoData                               html  
    protocolData                            html  
    read.AnnotatedDataFrame                 html  
    read.MIAME                              html  
    readExpressionSet                       html  
    reverseSplit                            html  
    rowMedians                              html  
    rowQ                                    html  
    selectChannels                          html  
    selectSome                              html  
    snpCall                                 html  
    storageMode                             html  
    strbreak                                html  
    subListExtract                          html  
    testBioCConnection                      html  
    updateObjectTo                          html  
    updateOldESet                           html  
    userQuery                               html  
    validMsg                                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 'Biobase' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c anyMissing.c -o anyMissing.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c envir.c -o envir.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matchpt.c -o matchpt.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rowMedians.c -o rowMedians.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublist_extract.c -o sublist_extract.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o Biobase.dll tmp.def Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/Biobase.buildbin-libdir/Biobase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Biobase' as Biobase_2.49.0.zip
* DONE (Biobase)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'Biobase' successfully unpacked and MD5 sums checked