Re: [galaxy-dev] package_r_xx problem: X11 is not available
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] package_r_xx problem: X11 is not available
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.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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] package_r_xx problem: X11 is not available
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] package_r_xx problem: X11 is not available
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] package_r_xx problem: X11 is not available
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] package_r_xx problem: X11 is not available
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
