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BioC 3.2: BUILD BIN report for Rbowtie on moscato1

This page was generated on 2016-04-23 10:19:01 -0700 (Sat, 23 Apr 2016).

Package 846/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie 1.10.0
Michael Stadler
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Rbowtie
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rbowtie
Version: 1.10.0
Command: rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe --arch x64 CMD INSTALL --build --no-multiarch --library=Rbowtie.buildbin-libdir Rbowtie_1.10.0.tar.gz
StartedAt: 2016-04-23 09:46:57 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 09:48:47 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 109.9 seconds
RetCode: 0
Status:  OK  
PackageFile: Rbowtie_1.10.0.zip
PackageFileSize: 4.095 MiB

Command output

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###
### Running command:
###
###   rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe --arch x64 CMD INSTALL --build --no-multiarch --library=Rbowtie.buildbin-libdir Rbowtie_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'Rbowtie' ...
** libs
  running 'src/Makefile.win' ...
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY  \""  -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY    \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2   -DNDEBUG -Wall \
	-I SeqAn-1.1 -I third_party -I third_party \
	-o bowtie-build-s ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
	 
In file included from ebwt.h:40:0,
                 from ebwt_build.cpp:11:
reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY  \""  -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2   -DNDEBUG -Wall \
	-I SeqAn-1.1 -I third_party -I third_party \
	-o bowtie-align-s ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
	 
In file included from ebwt.h:40:0,
                 from ebwt_search.cpp:14:
reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
mkdir -p ../inst
cp bowtie-align-s ../inst/bowtie
cp bowtie-build-s ../inst/bowtie-build
cd SpliceMap; \
make -f Makefile.win; \
echo "MAKE of SpliceMap DONE"	
`"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXX` `"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp  -static-libgcc
`"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXX` `"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp -static-libgcc
`"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXX` `"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp -static-libgcc
`"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXX` `"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o -static-libgcc
runSpliceMap_QuasR.cpp: In function 'int main(int, char* const*)':
runSpliceMap_QuasR.cpp:108:31: warning: variable 'chr_file_list_it' set but not used [-Wunused-but-set-variable]
runSpliceMap_QuasR.cpp: In function 'void processbowtie(std::string&, std::string&)':
runSpliceMap_QuasR.cpp:1327:9: warning: variable 'min_mismatch' set but not used [-Wunused-but-set-variable]
`"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXX` `"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc
`"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXX` `"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc
amalgamateSAM.cpp: In function 'int extractId(const string&)':
amalgamateSAM.cpp:19:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
amalgamateSAM.cpp:19:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
amalgamateSAM.cpp: In function 'void update_jun_coverage(std::map<std::basic_string<char>, std::map<int, std::map<int, jun_store_ij> > >&, std::string, bool)':
amalgamateSAM.cpp:695:17: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable]
`"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXX` `"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp -static-libgcc
getSpliceMapUnmapped.cpp: In function 'int extractNextId(const string&)':
getSpliceMapUnmapped.cpp:88:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
getSpliceMapUnmapped.cpp:88:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
`"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXX` `"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp -static-libgcc
`"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXX` `"D:/biocbld/bbs-3.2-bioc/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o -static-libgcc
MAKE of SpliceMap DONE
mkdir -p ../inst
cp SpliceMap/SpliceMap ../inst/SpliceMap
cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM
cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped
cp SpliceMap/fuseReorder ../inst/fuseReorder
cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR
cp SpliceMap/sortsam ../inst/sortsam
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rbowtie' as Rbowtie_1.10.0.zip
* DONE (Rbowtie)