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:
This PR will also help you to get all needed R packages in the correct
order:
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
>>
>>
>>
>>
>>
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