Hello,
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?
Not sure, I will add it if anyone complains :)
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.
Done!
Thanks for testing!
Bjoern
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.vandeweyer@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.vandeweyer@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer