Hi,

Compilation/installing works now. Using this R from the commandline no longer complains about missing X. With regards to cairo, I don't think I explicitly need it, but as I understood it, it was used in case there was no X11 server on the system?


would you add it to the main toolshed? Then I can put is as a dependency on my tools that create plots from R (coverage_report), which has now the system version hardcoded.

Best,

Geert

On 02/20/2014 01:45 AM, Björn Grüning wrote:

Hi Geert,

can you retest please, I had a typo. Unfortunately, I can't test it by myself since my internet connection is to bad here in Slovenia to download that R-tarball.

Sorry,
Bjoern

hi,

The dependencies installed fine, but R itself gave this error:

configure: error: unrecognized option: `-I/galaxy/galaxy_tool_binaries/libpng/1.6.7/devteam/package_libpng_1_6_7/a0b0e0281cc4/include' Try `./configure --help' for more information


Any idea what might be wrong?

Best,

Geert


On 02/19/2014 12:55 PM, Björn Grüning wrote:
Hi Geert,

I tried to update the R package to include the libpng dependency, if you like to test it ...

http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_2

Do you know if cairo is really needed? If I can I would omit to have a dependency on cairo :)

Cheers,
Bjoern

Hi all,

I installed to package_r_2.11 and r_3x from the devteam to use as tool dependency. All installation goes fine, but when I run my tool I get the following error:

Error in png(file = "../Plots/outname.png", bg = "white", width = 480, :
  X11 is not available

The tool uses the installed R : /galaxy/galaxy_tool_binaries/R/2.11.0/devteam/package_r_2_11_0/8d0a55bf7aaf/lib/R/bin/R

If I force the tool to use the system installed version of R, it works fine. Are there packages available in the toolsheds that allow the 'png' function to work? I already tried the R-packages from boris, but they gave compilation errors... I also tried to install the R-png package from cran as a galaxy dependency, but that didn't help either.


Thanks for the help,

Geert




--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail:geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer



--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer

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