Re: [galaxy-dev] Installing Cairo into Gakaxy

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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