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This page was generated on 2021-10-26 14:08:58 -0400 (Tue, 26 Oct 2021).

BUILD BIN results for Rhisat2 on machv2

To the developers/maintainers of the Rhisat2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhisat2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 1602/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhisat2 1.9.0  (landing page)
Charlotte Soneson
Snapshot Date: 2021-10-25 14:50:11 -0400 (Mon, 25 Oct 2021)
git_url: https://git.bioconductor.org/packages/Rhisat2
git_branch: master
git_last_commit: 411aa77
git_last_commit_date: 2021-05-19 12:40:25 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: Rhisat2
Version: 1.9.0
Command: rm -rf Rhisat2.buildbin-libdir && mkdir Rhisat2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhisat2_1.9.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rhisat2.buildbin-libdir
StartedAt: 2021-10-26 12:47:53 -0400 (Tue, 26 Oct 2021)
EndedAt: 2021-10-26 12:50:40 -0400 (Tue, 26 Oct 2021)
EllapsedTime: 166.8 seconds
RetCode: 0
Status:   OK  
PackageFile: Rhisat2_1.9.0.tgz
PackageFileSize: 1.136 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rhisat2.buildbin-libdir && mkdir Rhisat2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhisat2_1.9.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rhisat2.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rhisat2.buildbin-libdir Rhisat2_1.9.0.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-3.14-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/4.1/Resources/lib/libgcc_s.1.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so"