Hi,

here is the output of uname -a :

*"Linux retureau-MacBookPro 3.2.0-63-generic-pae #95-Ubuntu SMP Thu May 15
23:26:11 UTC 2014 i686 i686 i386 GNU/Linux**"*

I didn't specify it, but i'm running ubuntu in dual bot on a mac book pro.

Here is the output of "make" inside the right folder :
http://pastebin.com/NZGX9YH0  (it's huge, that's why i'm using pastebin).

I tried "./bowtie version 1.0.1" but it doesn't work :
*"Could not locate a Bowtie index corresponding to basename "version"*
*Command: ./bowtie version 1.0.1 "*

So I tried with this : "./bowtie --version" and get that :

*"./bowtie version 1.0.1*
*32-bit*
*Built on retureau-MacBookPro*
*jeudi 5 juin 2014, 10:57:41 (UTC+0200)*
*Compiler: gcc version 4.8.1 (Ubuntu 4.8.1-2ubuntu1~12.04) *
*Options: -O3 -m32  -Wl,--hash-style=both  *
*Sizeof {int, long, long long, void*, size_t, off_t}: {4, 4, 8, 4, 4, 8}"*



Actually, I installed an older version of "Rbowtie" with install.package
(here is the link :
http://bioconductor.org/packages/2.12/bioc/html/Rbowtie.html)
This one seems to works.

Thanks for your help !

Romain.



2014-06-05 8:52 GMT+02:00 Michael Stadler <michael.stadler@fmi.ch>:

> 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@fmi.ch
> --------------------------------------------
>
>

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