Package: girafe

Version: 1.35.0

Command: rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=girafe.buildbin-libdir girafe_1.35.0.tar.gz

StartedAt: 2019-04-09 08:01:55 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 08:05:11 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 195.9 seconds

RetCode: 0

Status:  OK

PackageFile: girafe_1.35.0.zip

PackageFileSize: 2.11 MiB

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### Running command:
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###   rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=girafe.buildbin-libdir girafe_1.35.0.tar.gz
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install for i386

* installing *source* package 'girafe' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c coverage.cpp -o coverage.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c girafe_init.c -o girafe_init.o
C:/Rtools/mingw_32/bin/g++ -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˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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 request: '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-3.9-bioc/tmpdir/RtmpM5tcyQ/R.INSTALL26704c7a7aa1/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-3.9-bioc/tmpdir/RtmpM5tcyQ/R.INSTALL26704c7a7aa1/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-3.9-bioc/tmpdir/RtmpM5tcyQ/R.INSTALL26704c7a7aa1/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-3.9-bioc/tmpdir/RtmpM5tcyQ/R.INSTALL26704c7a7aa1/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-3.9-bioc/tmpdir/RtmpM5tcyQ/R.INSTALL26704c7a7aa1/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 request: 'sort' when loading 'girafe'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for request: 'sort' when loading 'girafe'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'girafe' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c coverage.cpp -o coverage.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c girafe_init.c -o girafe_init.o
C:/Rtools/mingw_64/bin/g++ -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˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/girafe.buildbin-libdir/girafe/libs/x64
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'sort' when loading 'girafe'
* MD5 sums
packaged installation of 'girafe' as girafe_1.35.0.zip
* DONE (girafe)