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

Question

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).

edit : here is the package container

Here what I did (this works for all other packages) :

source("http://bioconductor.org/biocLite.R")
biocLite("Rbowtie")

here is the complete error message i 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 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

Thanks.

Answer 1

I am adding the final message from our discussion on the Bioconductor mailing list with the solution here, so people who end up on this page know about it.

I have updated Rbowtie to include fixed by the bowtie developers that should allow its compilation on additional platforms.

An update to Rbowtie version 1.4.5 (release) or 1.5.5 (development) should solve the issue.

Best wishes, Michael