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 [[email protected]]
Sent: Wednesday, August 26, 2015 7:19 PM
To: Christian Brenninkmeijer; [email protected]
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 [[email protected]] on behalf of
Christian Brenninkmeijer [[email protected]]
Sent: Wednesday, August 26, 2015 10:18 AM
To: galaxy-dev [[email protected]]
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
___________________________________________________________
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
