Dear Romain,
Thank you for the report. I am also using Ubuntu 12.04 LTS, and cannot
reproduce your issue, however I am using 64-bit R, while you are using
a
32-bit version.
Could you test the following things to narrow down the problem:
1. what is the output of: uname -a
2. can you compile bowtie 1.0.1?
For this, first download bowtie-1.0.1-src.zip from
https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.0.1/ and
then
change on the shell to the directory containing the downloaded file
and
run the following commands:
unzip bowtie-1.0.1-src.zip
cd bowtie-1.0.1/
make
Please send me the console output of the 'make'. In my case, I get
something like:
g++ -O3 -m64 ... -DPOPCNT_CAPABILITY ...
and then I find the bowtie binaries:
./bowtie --version
which produces:
./bowtie version 1.0.1
64-bit
Built on f022c-852634
Don Jun 5 08:47:09 CEST 2014
Compiler: gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
Options: -O3 -m64 -Wl,--hash-style=both -DPOPCNT_CAPABILITY
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8,
8}
3. if the above does not work, try building again using:
cd ..
rm -rf bowtie-1.0.1
unzip bowtie-1.0.1-src.zip
cd bowtie-1.0.1/
POPCNT_CAPABILITY=0 make
and I can test with:
./bowtie version 1.0.1
which gives:
64-bit
Built on f022c-852634
Don Jun 5 08:50:34 CEST 2014
Compiler: gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
Options: -O3 -m64 -Wl,--hash-style=both
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8,
8}
Let me know if this is not clear.
Best,
Michael
On 04.06.2014 09:20, Romain [guest] wrote:
> Hi,
>
> I'm trying to install "Rbowtie" package, following the instructions
here :
http://bioconductor.org/packages/2.12/bioc/html/Rbowtie.html
>
> When I run the command, I got this error message :
>
http://pastebin.com/DkEdCV05
>
> I'm currently running on Ubuntu 12.4 LTS and all others packages
seems to work well. I updated gcc and g++ to the last version aviable.
> May you help me to identify the problem ?
>
> Thanks.
>
> -- output of sessionInfo():
>
> R version 3.1.0 (2014-04-10)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
> [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.14.2
>
> loaded via a namespace (and not attached):
> [1] tools_3.1.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
--
--------------------------------------------
Michael Stadler, PhD
Head of Computational Biology
Friedrich Miescher Institute
Basel (Switzerland)
Phone : +41 61 697 6492
Fax : +41 61 697 3976
Mail : michael.stadler at fmi.ch
