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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/crlmm_1.46.0.tar.gz && rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crlmm.buildbin-libdir crlmm_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL crlmm_1.46.0.zip && rm crlmm_1.46.0.tar.gz crlmm_1.46.0.zip
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100 3494k  100 3494k    0     0  29.0M      0 --:--:-- --:--:-- --:--:-- 31.0M

install for i386

* installing *source* package 'crlmm' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gtypeCaller.c -o gtypeCaller.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trimmed.c -o trimmed.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
C:/rtools40/mingw32/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/crlmm.buildbin-libdir/00LOCK-crlmm/00new/crlmm/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
** help
*** installing help indices
  converting help for package 'crlmm'
    finding HTML links ... done
    ABpanel                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpBIcE/R.INSTALL1640331442ec/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-3.11-bioc/tmpdir/RtmpIpBIcE/R.INSTALL1640331442ec/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-3.11-bioc/tmpdir/RtmpIpBIcE/R.INSTALL1640331442ec/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 from temporary location
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
** testing if installed package can be loaded from final location
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'crlmm' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gtypeCaller.c -o gtypeCaller.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trimmed.c -o trimmed.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
C:/rtools40/mingw64/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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/crlmm.buildbin-libdir/crlmm/libs/x64
** testing if installed package can be loaded
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
* MD5 sums
packaged installation of 'crlmm' as crlmm_1.46.0.zip
* DONE (crlmm)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'crlmm' successfully unpacked and MD5 sums checked