Hi Bjoern & devteam members,
I tried to install R_3_0_2 iuc version from the main toolshed, but got an error from the package_libpng from the devteam. I checked between the working tool_dependency from the testtoolshed and the failing one from the main.
working: <action type="download_by_url">http://downloads.sourceforge.net/project/libpng/libpng16/older-releases/1.6....</action>
failing : <action type="download_by_url">http://downloads.sourceforge.net/project/libpng/libpng16/1.6.7/libpng-1.6.7....</action>
The package_libpng from the devteam is downloading a different version on test and main.
Best,
Geert
On 02/20/2014 12:56 PM, Björn Grüning wrote:
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