Michael Stadler
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Rbowtie |
| Branch: RELEASE_3_10 |
| Last Commit: ce8b181 |
| Last Changed Date: 2019-10-29 13:08:36 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:38:24 -0400 (Wed, 15 Apr 2020).
| Package 1375/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rbowtie 1.26.0 Michael Stadler
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
| Package: Rbowtie |
| Version: 1.26.0 |
| Command: rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbowtie_1.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rbowtie.buildbin-libdir |
| StartedAt: 2020-04-15 08:29:13 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 08:31:23 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 130.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rbowtie_1.26.0.tgz |
| PackageFileSize: 1.232 MiB |
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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_1.26.0.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_1.26.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rbowtie’ ...
** using staged installation
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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rbowtie)