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BUILD BIN report for Rbowtie on merida2

This page was generated on 2019-04-09 13:27:50 -0400 (Tue, 09 Apr 2019).

Package 1293/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie 1.23.3
Michael Stadler
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Rbowtie
Branch: master
Last Commit: 35e186a
Last Changed Date: 2019-03-15 04:50:39 -0400 (Fri, 15 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]

Summary

Package: Rbowtie
Version: 1.23.3
Command: rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbowtie_1.23.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rbowtie.buildbin-libdir
StartedAt: 2019-04-09 06:15:59 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:18:21 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 141.8 seconds
RetCode: 0
Status:  OK 
PackageFile: Rbowtie_1.23.3.tgz
PackageFileSize: 1.237 MiB

Command output

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###
### Running command:
###
###   rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbowtie_1.23.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rbowtie.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rbowtie.buildbin-libdir Rbowtie_1.23.3.tar.gz'
>>>>>>> 

* installing *source* package ‘Rbowtie’ ...
rm -f bowtie-build-s bowtie-align-s  \
	bowtie_prof \
	bowtie-build-s.exe bowtie-align-s.exe bowtie_prof.exe \
	bowtie-src.zip bowtie-bin.zip
rm -f core.*
rm -f bowtie-align-s-master* bowtie-align-s-no-io* 
rm -rf .lib .include
rm -f SpliceMap/*.o SpliceMap/SpliceMap SpliceMap/amalgamateSAM SpliceMap/getSpliceMapUnmapped SpliceMap/fuseReorder SpliceMap/runSpliceMap_QuasR SpliceMap/sortsam
rm -f ../inst/bowtie ../inst/bowtie-build ../inst/SpliceMap ../inst/amalgamateSAM ../inst/getSpliceMapUnmapped ../inst/fuseReorder ../inst/runSpliceMap_QuasR ../inst/sortsam
** libs
** arch - 
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wall -g -O2   -Wall -g -O2  \""  -Wall -g -O2   -Wall -g -O2    \
		-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \
		 -isystem ./SeqAn-1.1 -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 \
		-L/usr/local/lib  -lz -lpthread 
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wall -g -O2   -Wall -g -O2  \""  -Wall -g -O2   -Wall -g -O2   \
		-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \
		 -isystem ./SeqAn-1.1 -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 sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
		-L/usr/local/lib  -lz -lpthread 
In file included from ebwt_search.cpp:29:
./range_cache.h:338:11: warning: private field 'sanity_' is not used [-Wunused-private-field]
        bool     sanity_;  /// do consistency checks?
                 ^
In file included from ebwt_search.cpp:31:
./aligner_0mm.h:118:22: warning: private field 'ebwtBw_' is not used [-Wunused-private-field]
        Ebwt<String<Dna> >* ebwtBw_;
                            ^
./aligner_0mm.h:348:22: warning: private field 'ebwtBw_' is not used [-Wunused-private-field]
        Ebwt<String<Dna> >* ebwtBw_;
                            ^
3 warnings generated.
In file included from pat.cpp:9:
./pat.h:743:7: warning: private field 'solexa64_' is not used [-Wunused-private-field]
        bool solexa64_;
             ^
./pat.h:744:7: warning: private field 'phred64_' is not used [-Wunused-private-field]
        bool phred64_;
             ^
./pat.h:745:7: warning: private field 'intQuals_' is not used [-Wunused-private-field]
        bool intQuals_;
             ^
3 warnings generated.
In file included from sam.cpp:13:
./sam.h:119:7: warning: private field 'offBase_' is not used [-Wunused-private-field]
        int  offBase_;        /// Add this to reference offsets before outputting.
             ^
1 warning generated.
mkdir -p ../inst
cp bowtie-align-s ../inst/bowtie
cp bowtie-build-s ../inst/bowtie-build
cd SpliceMap; \
	make -f Makefile; \
	echo "MAKE of SpliceMap DONE"	
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
runSpliceMap_QuasR.cpp:108:31: warning: unused variable 'chr_file_list_it' [-Wunused-variable]
            vector<string>::iterator chr_file_list_it = chr_file_list.begin();
                                     ^
1 warning generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
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
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rbowtie)