Hi, Am 06.10.2015 um 15:48 schrieb Christian Brenninkmeijer:
HI Bjorn,
I now see you are bringing in libmxl2 in dexseq. As this is needed by various R packages and already installed by fontconfig would it be worth making it a first class dependency of package_r_3_2_1
We could think about this, yes. Although it is not a strict dependency of R.
I also see that in dexseg you specifically say "libxml2 needs to be sourced after R"
Is this not because if you source it before R the current <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
Yes, I have fixed this here: https://github.com/galaxyproject/tools-iuc/pull/298 Thanks, Bjoern
Christian
________________________________________ From: Björn Grüning [bjoern.gruening@gmail.com] Sent: Tuesday, October 06, 2015 2:36 PM To: Christian Brenninkmeijer; Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
Hi Christian,
what is needed from the TS site? Do you have any changes that are needed in the cairo package or R package?
For me everything is now working and the only thing you need to do is to specify the Rcairo tarball in your tool_dependendy file. Like here:
https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a...
Cheers, Bjoern
Am 06.10.2015 um 15:21 schrieb Christian Brenninkmeijer:
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@gmail.com] Sent: Sunday, September 27, 2015 10:40 PM To: Christian Brenninkmeijer; Bjoern Gruening; galaxy-dev@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-98f3c4d456a8a...
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@gmail.com] Sent: Friday, August 28, 2015 3:19 PM To: Christian Brenninkmeijer; galaxy-dev@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_27aug2015/77f3...
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@gmail.com] Sent: Wednesday, August 26, 2015 7:19 PM To: Christian Brenninkmeijer; galaxy-dev@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_3_...
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@lists.galaxyproject.org] on behalf of Christian Brenninkmeijer [christian.brenninkmeijer@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/b39299b4b6...
(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
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