Add a LD_LIBRARY_PATH does not help.
Changes the error but does not fix the problem.
I now get:
checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
install_environment.STDOUT DEBUG 2015-09-01 12:01:42,121 configure: CAIRO_LIBS=
checking for ATS font support in Cairo... no
checking for library containing deflate... -lz
configure: error: Cannot compile a simple Cairo program. See config.log for details.
A few things I did notice.
1. package_cairo_1_12_14 uses "package_pixman_0_32_4"
while package_r_3_2_1 uses package_pixman_0_32_6
2. R install in dependecy dir for 3.2.1 does not have an include directory
3.1.2 R did have a inlcude directory including the cairo headers.
Attached is the full install log.
Note the CAIRO_CFLAGS line was hard coded into recipe_manager.py for this test.
From: Björn Grüning [bjoern.gruening(a)gmail.com]
Sent: Friday, August 28, 2015 6:05 PM
To: Christian Brenninkmeijer; Bjoern Gruening; galaxy-dev(a)lists.galaxyproject.org; Dave
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
can you put
into your LD_LIBRARY_PATH and test if this helps?
Am 28.08.2015 um 17:12 schrieb Christian Brenninkmeijer:
I did a
find ~ -name cairo.h
and it looks like the header files are being made
So it is more a question of how to get setup_r_enviromnent to find them.
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
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?
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
> 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
> 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
) 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
> 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
> 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.
> 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:
> 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.
> 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
>> 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 [email@example.com]
>> 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
>> I am having the cairo.h not found issue
>> I have cloned
>> (and its dependencies)
>> As well as
>> 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
>> University of Manchester
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