Re: [galaxy-dev] Installing Cairo into Gakaxy

i finally got Cairo installed into R inside galaxy. As well as cairo needing fontconfig to add cairo into R also requires libmxl2 I also changed the R install. 1. Never use the zip as it has hard coded environment variables in it 2. The set_environment variable in the R install to "prepend_to" PKG_CONFIG_DIR and PKG_CONFIG_PATH I have some examples in the test tool shed test section but I would like to clean these up first. Once done I will post a link in this thread. Christian University of Manchester ________________________________________ From: Björn Grüning [bjoern.gruening(a)gmail.com] Sent: Sunday, September 27, 2015 10:40 PM To: Christian Brenninkmeijer; Bjoern Gruening; galaxy-dev(a)lists.galaxyproject.org; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy Hi Christian, I think I found the problem and fixed it in the Test Tool Shed. The root problem was that cairo was not compiled with fontconfig and therefore the freetype-cairo module was not working properly, which causes R-Cairo do give us such an unusable error message. I tested it with our new DEXSeq wrapper, which also needs Cairo if you want to create SVGs. Have a look how to define dependencies here: https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456... This PR will also help you to get all needed R packages in the correct order: https://github.com/bioarchive/aRchive_source_code/pull/20 Keep in mind to mirror your tarballs somewhere. BioC tends to remove older tarballs. Let me know how it goes and I will move everything over into the Main Tool Shed Hope this fixes your issues, Bjoern > Thanks Guys, > Help greatly appreciated. > > I need this as my team are thinking of using > SCDE see http://pklab.med.harvard.edu/scde/index.html > which uses cairo. > > Monday in a bank holiday here so even if you guys are super fast I will not be able to test until Tuesday. > > Christian > University of Manchester > ________________________________________ > From: Bjoern Gruening [bjoern.gruening(a)gmail.com] > Sent: Friday, August 28, 2015 3:19 PM > To: Christian Brenninkmeijer; galaxy-dev(a)lists.galaxyproject.org; Dave Bouvier > Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy > > Hi, > > I have CCed Dave here. He took over the maintenance of R many moons ago. > Dave can it be that we need to include some cairo headers, shared > objects into the tarball from docker-build? > > Thanks, > Bjoern > > On 28.08.2015 16:16, Christian Brenninkmeijer wrote: >> 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. 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