compiler error: Rbowtie
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i'm trying to install the "Rbowtie" package of bioconductor. I'm running R in root mode on ubuntu 12.4 LTS with the latest version of R (3.1.0). I follow the instruction on Rbowtie page : source("http://bioconductor.org/biocLite.R") biocLite("Rbowtie") I got this error message. Can someone help me to identify the problem ? Thanks. -- output of sessionInfo(): BioC_mirror: http://bioconductor.org Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0. Installing package(s) 'Rbowtie' essai de l'URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib /Rbowtie_1.4.4.tar.gz' Content type 'application/x-gzip' length 880659 bytes (860 Kb) URL ouverte ================================================== downloaded 860 Kb * installing *source* package ???Rbowtie??? ... ** libs ** arch - g++ -O3 -m32 -DCOMPILER_OPTIONS=""-O3 -m32 -Wl,--hash-style=both -DPOPCNT_CAPABILITY - g -O2 -fstack-protector --param=ssp- buffer-size=4 -Wformat -Wformat-security -Werror=format- security -D_FORTIFY_SOURCE=2 -g -g -O2 -fstack-protector --param=ssp-buffer- size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g "" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat- security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -fno-strict-aliasing -DBOWTIE_VERSION=""`cat VERSION`"" - DBUILD_HOST=""`hostname`"" -DBUILD_TIME=""`date`"" -DCOMPILER_VERSION=""`g++ -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 -I SeqAn-1.1 -I third_party -o bowtie-build ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp bowtie_build_main.cpp -lpthread ebwt.h: Assembler messages: ebwt.h:1909: Error: invalid instruction suffix for `popcnt' ebwt.h:1909: Error: invalid instruction suffix for `popcnt' ebwt.h:1909: Error: invalid instruction suffix for `popcnt' ebwt.h:1909: Error: invalid instruction suffix for `popcnt' make: *** [bowtie-build] Erreur 1 ERROR: compilation failed for package ???Rbowtie??? * removing ???/home/retureau/R/i686-pc-linux-gnu- library/3.1/Rbowtie??? The downloaded source packages are in ???/tmp/Rtmp1qDuN3/downloaded_packages??? Message d'avis : In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ???Rbowtie??? had non-zero exit status -- Sent via the guest posting facility at bioconductor.org.
Rbowtie Rbowtie • 818 views
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