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This page was generated on 2021-10-15 15:06:49 -0400 (Fri, 15 Oct 2021).

BUILD BIN results for Rbowtie on machv2

To the developers/maintainers of the Rbowtie package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbowtie.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1511/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie 1.32.0  (landing page)
Michael Stadler
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Rbowtie
git_branch: RELEASE_3_13
git_last_commit: 1a56c71
git_last_commit_date: 2021-05-19 11:55:09 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rbowtie
Version: 1.32.0
Command: rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbowtie_1.32.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rbowtie.buildbin-libdir
StartedAt: 2021-10-15 03:39:00 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 03:41:08 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 128.5 seconds
RetCode: 0
Status:   OK  
PackageFile: Rbowtie_1.32.0.tgz
PackageFileSize: 1.244 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_1.32.0.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_1.32.0.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 - 
clang++ -O3 -DCOMPILER_OPTIONS="\"-O3  -stdlib=libc++ -Wall -g -O2   -Wall -g -O2  \""  -stdlib=libc++ -Wall -g -O2   -Wall -g -O2    \
		-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2021-10-15T03:39:02\"" -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 -Wno-unused-parameter -Wno-reorder \
		 -I third_party \
		-o bowtie-build-s ebwt_build.cpp \
		ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp  bowtie_build_main.cpp \
		-L/usr/local/lib  -lz -lpthread 
clang++ -O3 -DCOMPILER_OPTIONS="\"-O3  -stdlib=libc++ -Wall -g -O2   -Wall -g -O2  \""  -stdlib=libc++ -Wall -g -O2   -Wall -g -O2   \
		-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2021-10-15T03:39:16\"" -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 -Wno-unused-parameter -Wno-reorder \
		 -I third_party \
		-o bowtie-align-s ebwt_search.cpp \
		ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \
		-L/usr/local/lib  -lz -lpthread 
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 LDFLAGS` `"/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 LDFLAGS` `"/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 LDFLAGS` `"/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 LDFLAGS` `"/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 LDFLAGS` `"/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 LDFLAGS` `"/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)