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INSTALL report for affy on riesling1

This page was generated on 2020-10-21 12:13:38 -0400 (Wed, 21 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE affy PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 23/1939HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.67.1
Rafael A. Irizarry
Snapshot Date: 2020-10-20 14:40:34 -0400 (Tue, 20 Oct 2020)
URL: https://git.bioconductor.org/packages/affy
Branch: master
Last Commit: 3cb910e
Last Changed Date: 2020-09-20 15:28:21 -0400 (Sun, 20 Sep 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64 [ OK ] OK  WARNINGS  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: affy
Version: 1.67.1
Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/affy_1.67.1.tar.gz && rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affy.buildbin-libdir affy_1.67.1.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL affy_1.67.1.zip && rm affy_1.67.1.tar.gz affy_1.67.1.zip
StartedAt: 2020-10-20 16:42:02 -0400 (Tue, 20 Oct 2020)
EndedAt: 2020-10-20 16:43:24 -0400 (Tue, 20 Oct 2020)
EllapsedTime: 82.3 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/affy_1.67.1.tar.gz && rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affy.buildbin-libdir affy_1.67.1.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL affy_1.67.1.zip && rm affy_1.67.1.tar.gz affy_1.67.1.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  283k  100  283k    0     0  17.3M      0 --:--:-- --:--:-- --:--:-- 17.3M

install for i386

* installing *source* package 'affy' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chipbackground.c -o chipbackground.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getall_locations.c -o getall_locations.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mas5calls.c -o mas5calls.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma2.c -o rma2.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -LD:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.12-bioc/meat/affy.buildbin-libdir/00LOCK-affy/00new/affy/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'affy'
    finding HTML links ... done
    AffyBatch-class                         html  
    finding level-2 HTML links ... done

    AffyRNAdeg                              html  
    MAplot                                  html  
    ProbeSet-class                          html  
    ProgressBarText-class                   html  
    SpikeIn                                 html  
    affy-deprecated                         html  
    affy-options                            html  
    affy.scalevalue.exprSet                 html  
    barplot.ProbeSet                        html  
    bg.adjust                               html  
    bgc                                     html  
    cdfFromBioC                             html  
    cdfenv.example                          html  
    cleancdfname                            html  
    debug.affy123                           html  
    expresso                                html  
    expressoWidget                          html  
    fit.li.wong                             html  
    generateExprSet-methods                 html  
    generateExprVal-methods                 html  
    generateExprVal.method.avgdiff          html  
    generateExprVal.method.playerout        html  
    hlog                                    html  
    justrma                                 html  
    list.celfiles                           html  
    maffy.subset                            html  
    mas5                                    html  
    mas5calls                               html  
    merge.AffyBatch                         html  
    mva.pairs                               html  
    normalize-methods                       html  
    normalize.constant                      html  
    normalize.contrast                      html  
    normalize.invariantset                  html  
    normalize.loess                         html  
    normalize.qspline                       html  
    normalize.quantiles                     html  
    normalize.quantiles.robust              html  
    pairs.AffyBatch                         html  
    plot.ProbeSet                           html  
    plot.density                            html  
    plotLocation                            html  
    pmcorrect                               html  
    ppsetApply                              html  
    probeMatch-methods                      html  
    probeNames-methods                      html  
    read.affybatch                          html  
    read.probematrix                        html  
    rma                                     html  
    setAffyOptions                          html  
    summary                                 html  
    tukey.biweight                          html  
    whatcdf                                 html  
    xy2indices                              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 'affy' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chipbackground.c -o chipbackground.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getall_locations.c -o getall_locations.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mas5calls.c -o mas5calls.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma2.c -o rma2.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -LD:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.12-bioc/meat/affy.buildbin-libdir/affy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affy' as affy_1.67.1.zip
* DONE (affy)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'affy' successfully unpacked and MD5 sums checked