Re: [galaxy-dev] Installing Cairo into Gakaxy

Thank you Björn for the link to the new R package which appears to include cairo. However I am still unable to run an R script which imports cairo the following line in an R Script fails library(Cairo) When I try to do a setup_r_enviromnent I am still getting: ..... install_environment.STDOUT DEBUG 2015-08-28 14:47:00,491 checking cairo.h usability... no install_environment.STDOUT DEBUG 2015-08-28 14:47:00,506 checking for cairo.h... no checking cairo.h usability... no checking cairo.h presence... no checking for cairo.h... no configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly. ERROR: configuration failed for package ‘Cairo’ This time tested on the testtoolshed so directly using the iuc dependencies so using his env vars https://testtoolshed.g2.bx.psu.edu/view/brenninc/test_r_cairo_27aug2015/7... tool_dependency.xml attached. I tried it with a new git clone (Master branch) from this morning Only setting change tool_config_file, tool_dependency_dir, tools_shed_config_file and admin_users Installing all the required packages manually in the order that required packages installed before the using package. Including Cairo before package_3_2_1 On an Ubuntu 14.04.LTS (updated today) Memory 15.6 GiB Processor Intel Xeon(R) CPU E5-1660 v3 @ 3.00Ghz x 16 OS type 64-bit I also tried it on my laptop also with Ubuntu 14.04.LTS Neither machine has R or Cairo installed natively. Any farther help or suggestions greatly appreciated. Christian University of Manchester ________________________________________ From: Björn Grüning [bjoern.gruening(a)gmail.com] Sent: Wednesday, August 26, 2015 7:19 PM To: Christian Brenninkmeijer; galaxy-dev(a)lists.galaxyproject.org Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy Hi Christian, looking at the R package and on the Docker build instructions, R seems to be installed with cairo support: https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_r... https://github.com/natefoo/docker-build/blob/master/R/build.sh Are you using the latest IUC packages? Your script seems to be fine, I can not spot any obvious error. But I don't know how your dependencies are defined and which env vars are exported. Ciao, Bjoern Am 26.08.2015 um 12:18 schrieb Christian Brenninkmeijer: > Still looking for an example tool_dependencies.xml to install R Cairo package > > Farther update. > > package_cairo_1_12_14 needs to be at the same level as package_r_3_1_2 inside of setup_r_environment without the set_environment_for_install > > > I am no longer getting cairo.h No but am still getting > > checking if R was compiled with the RConn patch... no > ... > checking for ATS font support in Cairo... no > .... > checking whether Cairo programs can be compiled... > ERROR: configuration failed for package ‘Cairo’ > > Again updated tool_dependencies.xml attached > > Thanks > > Christian > ________________________________ > From: galaxy-dev [galaxy-dev-bounces(a)lists.galaxyproject.org] on behalf of Christian Brenninkmeijer [christian.brenninkmeijer(a)manchester.ac.uk] > Sent: Wednesday, August 26, 2015 10:18 AM > To: galaxy-dev ‎[galaxy-dev@lists.galaxyproject.org]‎ > Subject: [galaxy-dev] Installing Cairo into Gakaxy > > Hi All, > > Has anyone got a working example tool_dependencies.xml to install the Cairo package into R. > (I actually need a package that depends on R Cairo but the current issue is Cairo) > > I am having the cairo.h not found issue > > I have cloned > https://toolshed.g2.bx.psu.edu/view/devteam/package_cairo_1_12_14/b39299b... > (and its dependencies) > > As well as > https://toolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/9f2fddb9d6e2 > > I am trying to use <action type="setup_r_environment"> > But can not get the package_cairo to be seen by the R > > I have tried <action type="set_environment_for_install"> both inside and outside of the setup_r_environment but it does not appear to be working, > > Full attempted tool_dependencies.xml attached, > > Thanks in advance > > > Christian > University of Manchester > > > > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >