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.gruening@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....
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-bounces@lists.galaxyproject.org] on behalf of Christian Brenninkmeijer [christian.brenninkmeijer@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.... 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-bounces@lists.galaxyproject.org] on behalf of Christian Brenninkmeijer [christian.brenninkmeijer@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.gruening@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.gruening@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_27aug2015/77f3...
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@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_... 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@lists.galaxyproject.org] on behalf of Christian Brenninkmeijer [christian.brenninkmeijer@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/b39299b4b6... (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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