Hi Christian,
On 03.09.2015 15:14, Christian Brenninkmeijer wrote:
Hi,
Have you ever actually been able to run an rscript which uses the library cairo
using this build outside of docker?
Especially on a machine that does not have a /galaxy folder?
Not sure about this, I simply don't know how R plots ... but we are able
to produce a lot of different plots in a lot of different formats.
If so did you have to install cairo into R?
Using Rscript -e "install.packages(c('Cairo_1.5-8.tar.gz')
Either directly or indirect vai a tool dependency with <action
type="setup_r_environment">
If you did install cairo into R where did you get the cairo R package from?
Christian
________________________________________
From: Bjoern Gruening [bjoern.gruen...@gmail.com]
Sent: Thursday, September 03, 2015 1:31 PM
To: Christian Brenninkmeijer; Björn Grüning;
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
Hi Christian,
thanks for debugging. For your information we use this Docker container
to pre-build the binaries.
https://github.com/galaxyproject/docker-build/tree/master/R
So this is the place we need to fix the binaries.
Hope this helps, if I find time I will also have a look,
Bjoern
On 03.09.2015 12:10, Christian Brenninkmeijer wrote:
In the continued effort to track down the issue of installing cairo into R
I found a bug in
https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/41f43a2064ba
which installs
https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.2-Linux-x84_64.tgz
This has hard code paths in it.
For example lib//pkgconfig/cairo.pc
prefix=/galaxy/builds/Linux-x86_64/install_dir
This is then picked up by cairo's configure script resulting in cairo not being
found as it s clearly not where galaxy said it is!
Debugging continue!
Christian
University of Manchester
________________________________________
From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Wednesday, September 02, 2015 11:40 AM
To: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
I am still having issues installing Cairo into R
I have tracked part of the problem down to:
https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tgz
does have any include files so no headers.
https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/3d28600fc82c has:
<environment_variable action="set_to"
name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
<environment_variable action="set_to"
name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
The set_to overwrites any environment_variable PKG_CONFIG values set by other
packages
I changed the PKG_CONFIG setting to prepend to previous values and got:
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 2015-09-02 11:27:12,315 configure:
CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
-L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
-lfreetype -lpng16 -lz -lcairo
checking for ATS font support in Cairo... no
configure:
CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
-L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
-lfreetype -lpng16 -lz -lcairo
checking for library containing deflate... none required
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,426 checking whether Cairo
programs can be compiled... yes
checking whether Cairo programs can be compiled... yes
checking whether cairo_image_surface_get_format is declared... no
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,499 checking for FreeType
support in cairo... yes
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,576 checking whether
pkg-config knows about fontconfig or freetype2... yes
checking for FreeType support in cairo... yes
checking whether FreeType needs additional flags... yes
checking whether pkg-config knows about fontconfig or freetype2... yes
checking whether additional flags work... no
configure: error: Cannot use cairo-ft backend, although cairo claims it is
working. Please check your caito installation and/or update cairo if necessary
or set CAIRO_CFLAGS/CAIRO_LIBS accordingly.
ERROR: configuration failed for package ‘Cairo’
====
For the record the full cmd to setup R is:
PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/bin:$PATH;
export PATH
PIXMAN_LIB_PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/lib;
export PIXMAN_LIB_PATH
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/lib/pkgconfig:$PKG_CONFIG_PATH;
export PKG_CONFIG_PATH
PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/bin:$PATH;
export PATH
LIBPNG_ROOT=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6;
export LIBPNG_ROOT
LIBPNG_LIB_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib;
export LIBPNG_LIB_PATH
LIBPNG_INCLUDE_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/include;
export LIBPNG_INCLUDE_PATH
LD_LIBRARY_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib:$LD_LIBRARY_PATH;
export LD_LIBRARY_PATH
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib/pkgconfig:$PKG_CONFIG_PATH;
export PKG_CONFIG_PATH
FREETYPE_LIB_PATH=/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib;
export FREETYPE_LIB_PATH
PATH=/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/bin:$PATH;
export PATH
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib/pkgconfig:$PKG_CONFIG_PATH;
export PKG_CONFIG_PATH
FONTCONFIG_ROOT_PATH=/home/christian/galaxy/dependency_dir/fontconfig/2.11.1/iuc/package_fontconfig_2_11_1/1db671dd3e91/lib;
export FONTCONFIG_ROOT_PATH
PATH=/home/christian/galaxy/dependency_dir/fontconfig/2.11.1/iuc/package_fontconfig_2_11_1/1db671dd3e91/bin:$PATH;
export PATH
FONTCONFIG_FILE=/home/christian/galaxy/dependency_dir/fontconfig/2.11.1/iuc/package_fontconfig_2_11_1/1db671dd3e91/etc/fonts/fonts.conf;
export FONTCONFIG_FILE
PATH=/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/bin:$PATH;
export PATH
CAIRO_LIB_PATH=/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib:$CAIRO_LIB_PATH;
export CAIRO_LIB_PATH
CAIRO_INCLUDE_PATH=/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/include:$CAIRO_INCLUDE_PATH;
export CAIRO_INCLUDE_PATH
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib/pkgconfig:$PKG_CONFIG_PATH;
export PKG_CONFIG_PATH
TCL_LIBRARY=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/libtcl8.4.so;
export TCL_LIBRARY
TK_LIBRARY=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/libtk8.4.so;
export TK_LIBRARY
R_DOC_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R/doc;
export R_DOC_DIR
R_HOME_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R;
export R_HOME_DIR
R_INCLUDE_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R/include;
export R_INCLUDE_DIR
R_SHARE_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R/share;
export R_SHARE_DIR
R_ROOT_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c;
export R_ROOT_DIR
R_HOME=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R;
export R_HOME
RHOME=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R;
export RHOME
R_LIBS=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R/library;
export R_LIBS
PKG_CONFIG_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/pkgconfig:/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/share/pkgconfig:$PKG_CONFIG_DIR;
export PKG_CONFIG_DIR
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/pkgconfig:/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/share/pkgconfig:$PKG_CONFIG_PATH;
export PKG_CONFIG_PATH
PATH=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/bin:$PATH;
export PATH
PATH=$PATH:$R_HOME/bin; export PATH;
R_LIBS=/home/christian/galaxy/dependency_dir/R_cairo/0.0.2/brenninc/test_r_cairo_27aug2015/25473b0ac364;
export R_LIBS;
Rscript -e
"install.packages(c('Cairo_1.5-8.tar.gz'),lib='/home/christian/galaxy/dependency_dir/R_cairo/0.0.2/brenninc/test_r_cairo_27aug2015/25473b0ac364',
repos=NULL, dependencies=FALSE)"
________________________________________
From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Tuesday, September 01, 2015 12:17 PM
To: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
Thanks Björn,
Add a LD_LIBRARY_PATH does not help.
Adding
CAIRO_CFLAGS=-I/home/christian/galaxy_test/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/include/cairo;
export CAIRO_CFLAGS
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
configure: CAIRO_LIBS=
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
example:
/galaxy_test/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c
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.
Thanks
Christian
________________________________________
From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Friday, August 28, 2015 6:05 PM
To: Christian Brenninkmeijer; Bjoern Gruening;
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
Hi,
can you put
/home/christian/galaxy/dependency_dir/R/3.1.2/brenninc/package_r_3_1_2/655087f549e9/include/
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
/home/christian/galaxy_test/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/include/cairo/cairo.h
and
/home/christian/galaxy/dependency_dir/R/3.1.2/brenninc/package_r_3_1_2/655087f549e9/include/cairo/cairo.h
So it is more a question of how to get setup_r_enviromnent to find them.
Christian
________________________________________
From: Bjoern Gruening [bjoern.gruen...@gmail.com]
Sent: Friday, August 28, 2015 3:19 PM
To: Christian Brenninkmeijer; galaxy-dev@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_27aug2015/77f3bd0e4153
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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___________________________________________________________
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and other Galaxy lists, please use the interface at:
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