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

1
votes

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.

1
rbioinformaticsbioconductor
It's better not to install packages as root, but rather as individual user, or as user with privileges to install packages in a (world) readable location. It's also better to address or include the package maintainer (from the package landing page) in the conversation, and to ask questions about Bioconductor packages on the Bioconductor mailing list (no subscription required). Sorry not to be directly helpful. – Martin Morgan
I asked them with the mailing list. No answer. I finally download the source files and "install" with "make". It works but without R and I have no idea how to do to get hime inside R (except making a script myself :/). If I make a script, have I to make a package for R or can I just drop those file in a "lib" directory ? I tried to make a package once, it's just horrible >.< – user3703297
Your email should have included the package maintainer (I have forwarded the email to him). The package builds successfully on the ubuntu 12.04 Bioconductor build machine, so there is something particular about your set-up, e.g., g++ --version. I am confident the package author will reply, but of course he has to know that there is an issue first! – Martin Morgan
Ok, thank you very much. I never used this kind of "mailing" list before ^^ that's why i'm kind of lost, but I think I get it. Actually I upgrade my g++ to the latest version, but it didn't work. So, I downloaded the package, and install bowtie directly on Ubuntu (I can launch it with the Terminal). Then I found an older version of Rbowtie here : bioconductor.org/packages/2.12/bioc/html/Rbowtie.html This one works (I installed it with "install.packages" after donwloading the pkg) but always ask me to update (which does the same error). – user3703297

1 Answers

1
votes

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