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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