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:
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
I have some examples in the test tool shed test section but I would like to clean these
Once done I will post a link in this thread.
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
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
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:
This PR will also help you to get all needed R packages in the correct
Keep in mind to mirror your tarballs somewhere. BioC tends to remove
Let me know how it goes and I will move everything over into the Main
Hope this fixes your issues,
> 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.
> 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
> 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?
> On 28.08.2015 16:16, Christian Brenninkmeijer wrote:
>> Thank you Björn for the link to the new R package which appears to include
>> However I am still unable to run an R script which imports cairo
>> the following line in an R Script fails
>> 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
>> install_environment.STDOUT DEBUG 2015-08-28 14:47:00,506 checking for cairo.h...
>> checking cairo.h usability... no
>> checking cairo.h presence... no
>> checking for cairo.h... no
>> configure: error: Cannot find cairo.h! Please install cairo
) 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
>> 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
>> 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.
>> 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:
>> 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.
>> Am 26.08.2015 um 12:18 schrieb Christian Brenninkmeijer:
>>> Still looking for an example tool_dependencies.xml to install R Cairo
>>> 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
>>> 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 [firstname.lastname@example.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
>>> I am having the cairo.h not found issue
>>> I have cloned
>>> (and its dependencies)
>>> As well as
>>> 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
>>> 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:
>>> To search Galaxy mailing lists use the unified search at: