[BioC] Rbowtie - compilation error

[Michael Stadler]

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