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BioC 2.14: INSTALL report for Rbowtie on morelia

This page was generated on 2014-10-08 09:06:03 -0700 (Wed, 08 Oct 2014).

Package 635/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie 1.4.5
Michael Stadler
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Rbowtie
Last Changed Rev: 91054 / Revision: 95116
Last Changed Date: 2014-06-06 08:34:15 -0700 (Fri, 06 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64 [ OK ] OK  OK  OK 

Summary

Package: Rbowtie
Version: 1.4.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rbowtie
StartedAt: 2014-10-07 18:05:40 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 18:06:42 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 61.4 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rbowtie
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’
* installing *source* package ‘Rbowtie’ ...
** libs
** arch - 
clang++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -stdlib=libstdc++ -DPOPCNT_CAPABILITY -Wall -mtune=core2 -g -O2   -Wall -mtune=core2 -g -O2  \""  -stdlib=libstdc++ -DPOPCNT_CAPABILITY -Wall -mtune=core2 -g -O2   -Wall -mtune=core2 -g -O2    \
		-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -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 \
		-I SeqAn-1.1 -I third_party/macos \
		-o bowtie-build ebwt_build.cpp \
		ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
		-lpthread 
clang++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -stdlib=libstdc++ -DPOPCNT_CAPABILITY -Wall -mtune=core2 -g -O2   -Wall -mtune=core2 -g -O2  \""  -stdlib=libstdc++ -DPOPCNT_CAPABILITY -Wall -mtune=core2 -g -O2   -Wall -mtune=core2 -g -O2   \
		-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -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 \
		-I SeqAn-1.1 -I third_party/macos \
		-o bowtie 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 \
		-lpthread 
ebwt_search.cpp:992:20: warning: unused function 'finishReadWithHitmask' [-Wunused-function]
static inline void finishReadWithHitmask(PatternSourcePerThread* p,
                   ^
In file included from ebwt_search.cpp:22:
./range_cache.h:340:11: warning: private field 'sanity_' is not used [-Wunused-private-field]
        bool     sanity_;  /// do consistency checks?
                 ^
In file included from ebwt_search.cpp:26:
./aligner_0mm.h:119:22: warning: private field 'ebwtBw_' is not used [-Wunused-private-field]
        Ebwt<String<Dna> >* ebwtBw_;
                            ^
./aligner_0mm.h:136:11: warning: private field 'seed_' is not used [-Wunused-private-field]
        uint32_t seed_;
                 ^
./aligner_0mm.h:351:22: warning: private field 'ebwtBw_' is not used [-Wunused-private-field]
        Ebwt<String<Dna> >* ebwtBw_;
                            ^
./aligner_0mm.h:379:17: warning: private field 'seed_' is not used [-Wunused-private-field]
        const uint32_t seed_;
                       ^
In file included from ebwt_search.cpp:27:
./aligner_1mm.h:173:11: warning: private field 'seed_' is not used [-Wunused-private-field]
        uint32_t seed_;
                 ^
./aligner_1mm.h:491:17: warning: private field 'seed_' is not used [-Wunused-private-field]
        const uint32_t seed_;
                       ^
In file included from ebwt_search.cpp:28:
./aligner_23mm.h:243:11: warning: private field 'seed_' is not used [-Wunused-private-field]
        uint32_t seed_;
                 ^
./aligner_23mm.h:688:17: warning: private field 'seed_' is not used [-Wunused-private-field]
        const uint32_t seed_;
                       ^
10 warnings generated.
mkdir -p ../inst
cp bowtie ../inst/bowtie
cp bowtie-build ../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();
                                     ^
runSpliceMap_QuasR.cpp:191:27: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
            if (head_clip_length < 0) {
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜
2 warnings 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
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rbowtie)