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 | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | [ OK ] | |
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### Running command:
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### rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbowtie_1.10.0.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_1.10.0.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 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 -
clang++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -stdlib=libstdc++ -Wall -mtune=core2 -g -O2 -Wall -mtune=core2 -g -O2 \"" -stdlib=libstdc++ -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 \
-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 \
-lpthread
clang++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -stdlib=libstdc++ -Wall -mtune=core2 -g -O2 -Wall -mtune=core2 -g -O2 \"" -stdlib=libstdc++ -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 \
-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 \
-lpthread
In file included from ebwt_search.cpp:22:
./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: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_;
^
9 warnings 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();
^
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)