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.gruen...@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-98f3c4d456a8a7bbd94eca94e167c5b8

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.gruen...@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_27aug2015/77f3bd0e4153
>>
>> 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.gruen...@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_2_1/tool_dependencies.xml
>> 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-boun...@lists.galaxyproject.org] on behalf of 
>>> Christian Brenninkmeijer [christian.brenninkmei...@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/b39299b4b6e1
>>> (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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>
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