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(a)gmail.com] Sent: Tuesday, October 06, 2015 2:36 PM
To: Christian Brenninkmeijer; Björn Grüning;
galaxy-dev(a)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-98f3c4d456...
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(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:
>
>
https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456...
>
>
>
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(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)
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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