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INSTALL report for crlmm on tokay2

This page was generated on 2018-10-17 08:34:13 -0400 (Wed, 17 Oct 2018).

Package 324/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crlmm 1.38.0
Benilton S Carvalho
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/crlmm
Branch: RELEASE_3_7
Last Commit: cc1a98e
Last Changed Date: 2018-04-30 10:35:10 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: crlmm
Version: 1.38.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/crlmm_1.38.0.tar.gz && rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crlmm.buildbin-libdir crlmm_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL crlmm_1.38.0.zip && rm crlmm_1.38.0.tar.gz crlmm_1.38.0.zip
StartedAt: 2018-10-16 19:45:18 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:47:15 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 117.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/crlmm_1.38.0.tar.gz && rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crlmm.buildbin-libdir crlmm_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL crlmm_1.38.0.zip && rm crlmm_1.38.0.tar.gz crlmm_1.38.0.zip
###
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100 3494k  100 3494k    0     0  36.1M      0 --:--:-- --:--:-- --:--:-- 38.7M

install for i386

* installing *source* package 'crlmm' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c gtypeCaller.c -o gtypeCaller.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c trimmed.c -o trimmed.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/crlmm.buildbin-libdir/crlmm/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'crlmm'
    finding HTML links ... done
    ABpanel                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpS6EBVZ/R.INSTALL1ca8656bd0e/crlmm/man/ABpanel.Rd:57: file link 'lpolygon' in package 'lattice' does not exist and so has been treated as a topic
    AssayData-methods                       html  
    finding level-2 HTML links ... done

    CNSet-methods                           html  
    ListClassConstructors                   html  
    PredictionRegion-class                  html  
    batchStatisticAccessors                 html  
    calculateRBaf                           html  
    celfile-utils                           html  
    cnSetExample                            html  
    cnrmaAffy                               html  
    constructAffyCNSet                      html  
    constructInf                            html  
    copynumberAccessors                     html  
    crlmm-package                           html  
    crlmm                                   html  
    crlmmCopynumber                         html  
    genotype.Illumina                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpS6EBVZ/R.INSTALL1ca8656bd0e/crlmm/man/genotype.Illumina.Rd:148: file link 'ocSamples' in package 'oligoClasses' does not exist and so has been treated as a topic
    genotype                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpS6EBVZ/R.INSTALL1ca8656bd0e/crlmm/man/genotype.Rd:88: file link 'ocSamples' in package 'oligoClasses' does not exist and so has been treated as a topic
    genotypeAffy                            html  
    genotypeInf                             html  
    genotypes                               html  
    plotSNPs                                html  
    posteriorProbability                    html  
    predictionRegion                        html  
    preprocessInf                           html  
    readGenCallOutput                       html  
    readIdatFiles                           html  
    snprma                                  html  
    snprmaAffy                              html  
    validCdfNames                           html  
    xyplot                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'crlmm' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gtypeCaller.c -o gtypeCaller.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c trimmed.c -o trimmed.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/crlmm.buildbin-libdir/crlmm/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'crlmm' as crlmm_1.38.0.zip
* DONE (crlmm)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'crlmm' successfully unpacked and MD5 sums checked
In R CMD INSTALL