Charlotte Soneson
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Rhisat2 |
| Branch: RELEASE_3_10 |
| Last Commit: 458e19e |
| Last Changed Date: 2019-10-29 13:11:28 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:48:37 -0400 (Wed, 15 Apr 2020).
| Package 1431/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rhisat2 1.2.0 Charlotte Soneson
| 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: Rhisat2 |
| Version: 1.2.0 |
| Command: rm -rf Rhisat2.buildbin-libdir && mkdir Rhisat2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhisat2_1.2.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhisat2.buildbin-libdir |
| StartedAt: 2020-04-15 08:33:42 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 08:35:56 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 134.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rhisat2_1.2.0.tgz |
| PackageFileSize: 1.155 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Rhisat2.buildbin-libdir && mkdir Rhisat2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhisat2_1.2.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhisat2.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rhisat2.buildbin-libdir Rhisat2_1.2.0.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-3.10-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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/Resources/lib/libquadmath.0.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs//Rhisat2.so"