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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/girafe_1.42.0.tar.gz && rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=girafe.buildbin-libdir girafe_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL girafe_1.42.0.zip && rm girafe_1.42.0.tar.gz girafe_1.42.0.zip
###
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100 1061k  100 1061k    0     0  3862k      0 --:--:-- --:--:-- --:--:-- 3872k

install for i386

* installing *source* package 'girafe' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c coverage.cpp -o coverage.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 girafe_init.c -o girafe_init.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o girafe.dll tmp.def coverage.o girafe_init.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/girafe.buildbin-libdir/00LOCK-girafe/00new/girafe/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for requests: 'score', 'score<-', 'sort' when loading 'girafe'
Creating a generic function for 'sample' from package 'base' in package 'girafe'
** help
*** installing help indices
  converting help for package 'girafe'
    finding HTML links ... done
    AlignedGenomeIntervals-class            html  
    agiFromBam                              html  
    countReadsAnnotated                     html  
    fracOverlap                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/girafe/man/fracOverlap.Rd:38: file link 'interval_overlap' in package 'genomeIntervals' does not exist and so has been treated as a topic
    getFeatureCounts                        html  
    girafe-internal                         html  
    intPhred                                html  
    medianByPosition                        html  
    negbinomsig                             html  
    perWindow                               html  
    plotAligned                             html  
    plotReads                               html  
    plotnegbinomfit                         html  
    reduce-extras                           html  
    trimAdapter                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/girafe/man/trimAdapter.Rd:39: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/girafe/man/trimAdapter.Rd:41: file link 'writeFastq' in package 'ShortRead' does not exist and so has been treated as a topic
    weightedConsensusMatrix                 html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/girafe/man/weightedConsensusMatrix.Rd:23: file link 'consensusMatrix' in package 'Biostrings' does not exist and so has been treated as a topic
    whichNearestMethods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpctpO9i/R.INSTALL1568703d7dfc/girafe/man/whichNearestMethods.Rd:44: file link 'which_nearest' in package 'intervals' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for requests: 'score', 'score<-', 'sort' when loading 'girafe'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for requests: 'score', 'score<-', 'sort' when loading 'girafe'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'girafe' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c coverage.cpp -o coverage.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 girafe_init.c -o girafe_init.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o girafe.dll tmp.def coverage.o girafe_init.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/girafe.buildbin-libdir/girafe/libs/x64
** testing if installed package can be loaded
No methods found in package 'IRanges' for requests: 'score', 'score<-', 'sort' when loading 'girafe'
* MD5 sums
packaged installation of 'girafe' as girafe_1.42.0.zip
* DONE (girafe)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'girafe' successfully unpacked and MD5 sums checked