bioinformatics - Bowtie package from bioconductor/R - ERROR: compilation failed for package ‘Rbowtie’ -


i'm trying install "rbowtie" package of bioconductor. i'm running r in root mode on ubuntu 12.4 lts latest version of r (3.1.0).

edit : here package container

here did (this works other packages) :

source("http://bioconductor.org/bioclite.r") bioclite("rbowtie")

here complete error message got :

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 `popcnt' ebwt.h:1909: error: invalid instruction suffix `popcnt' ebwt.h:1909: error: invalid instruction suffix `popcnt' ebwt.h:1909: error: invalid instruction suffix `popcnt' make: *** [bowtie-build] erreur 1 error: compilation failed package ‘rbowtie’ * removing ‘/home/retureau/r/i686-pc-linux-gnu-library/3.1/rbowtie’  downloaded source packages 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

thanks.

i adding final message our discussion on bioconductor mailing list solution here, people end on page know it.

i have updated rbowtie include fixed bowtie developers should allow compilation on additional platforms.

an update rbowtie version 1.4.5 (release) or 1.5.5 (development) should solve issue.

best wishes, michael


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