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Yikun / BBS

The Bioconductor Build System
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Rhisat2.install #21

Open Yikun opened 1 year ago

Yikun commented 1 year ago 
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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rhisat2
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Rhisat2’ ...
** using staged installation
** libs
/usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"2.2.1\"" -DBUILD_HOST="\"kunpeng1\"" -DBUILD_TIME="\"Mon  6 Feb 02:48:28 UTC 2023\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DUSESIMDE -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \
-I. -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 
g++: error: unrecognized command-line option ‘-m64’
g++: error: unrecognized command-line option ‘-msse2’
make: *** [Makefile:363: hisat2-build-s] Error 1
ERROR: compilation failed for package ‘Rhisat2’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/Rhisat2’
martin-g commented 1 year ago

Related to https://github.com/DaehwanKimLab/hisat2/pull/251

martin-g commented 1 year ago

Once the issue in hisat2 is resolved we will have to ping https://github.com/fmicompbio/Rhisat2 to get the updates.

martin-g commented 1 year ago

Bioc package CircSeqAlignTk depends on this