Re: [galaxy-dev] Installing Cairo into Gakaxy

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?

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(a)gmail.com] Sent: Thursday, September 03, 2015 1:31 PM To: Christian Brenninkmeijer; Björn Grüning; galaxy-dev(a)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_... > > 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(a)lists.galaxyproject.org] on behalf of Christian Brenninkmeijer [christian.brenninkmeijer(a)manchester.ac.uk] > Sent: Wednesday, September 02, 2015 11:40 AM > To: Björn Grüning; galaxy-dev(a)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_... 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(a)lists.galaxyproject.org] on behalf of Christian Brenninkmeijer [christian.brenninkmeijer(a)manchester.ac.uk] > Sent: Tuesday, September 01, 2015 12:17 PM > To: Björn Grüning; galaxy-dev(a)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(a)gmail.com] > Sent: Friday, August 28, 2015 6:05 PM > To: Christian Brenninkmeijer; Bjoern Gruening; galaxy-dev(a)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(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 >> >> 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_27aug2015/7... >>> >>> 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(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: >>> >>> https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_r... >>> 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(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 ‎[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/b39299b... >>>> (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/