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BUILD BIN report for Rhisat2 on celaya2

This page was generated on 2020-01-16 13:53:11 -0500 (Thu, 16 Jan 2020).

Package 1428/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhisat2 1.3.0
Charlotte Soneson
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/Rhisat2
Branch: master
Last Commit: c9f1c50
Last Changed Date: 2019-10-29 13:43:26 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: Rhisat2
Version: 1.3.0
Command: rm -rf Rhisat2.buildbin-libdir && mkdir Rhisat2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhisat2_1.3.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhisat2.buildbin-libdir
StartedAt: 2020-01-16 11:39:26 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 11:42:14 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 167.8 seconds
RetCode: 0
Status:  OK 
PackageFile: Rhisat2_1.3.0.tgz
PackageFileSize: 1.155 MiB

Command output

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###
### Running command:
###
###   rm -rf Rhisat2.buildbin-libdir && mkdir Rhisat2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhisat2_1.3.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhisat2.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rhisat2.buildbin-libdir Rhisat2_1.3.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Rhisat2’ ...
** using staged installation
rm -f hisat2-build-s hisat2-align-s  \
	hisat2-build-s.exe hisat2-align-s.exe \
	hisat2-src.zip hisat2-bin.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
rm -f *.so
rm -f ../inst/hisat2 ../inst/hisat2-build
** libs
** arch - 
/usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
	-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \
	 -I third_party \
	-o hisat2-build-s hisat2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
	-lpthread 
/usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
	-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM   -DBOWTIE2 -DNDEBUG -Wall \
	 -I third_party  \
	-o hisat2-align-s hisat2.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp  hisat2_main.cpp \
	-lpthread  
mkdir -p ../inst
cp hisat2-align-s ../inst/hisat2
cp hisat2-build-s ../inst/hisat2-build
/usr/bin/g++ -shared -fPIC -o Rhisat2.so get_info.cpp
installing to /Users/biocbuild/bbs-3.11-bioc/meat/Rhisat2.buildbin-libdir/00LOCK-Rhisat2/00new/Rhisat2/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rhisat2)


>>>>>>> 
>>>>>>> FIXING LINKS FOR Rhisat2.buildbin-libdir/Rhisat2/libs//Rhisat2.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs//Rhisat2.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs//Rhisat2.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs//Rhisat2.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs//Rhisat2.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs//Rhisat2.so"