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

___________________________________________________________ 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/

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

___________________________________________________________ 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/

Hi Christian, I think I found the problem and fixed it in the Test Tool Shed. The root problem was that cairo was not compiled with fontconfig and therefore the freetype-cairo module was not working properly, which causes R-Cairo do give us such an unusable error message. I tested it with our new DEXSeq wrapper, which also needs Cairo if you want to create SVGs. Have a look how to define dependencies here: https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a... This PR will also help you to get all needed R packages in the correct order: https://github.com/bioarchive/aRchive_source_code/pull/20 Keep in mind to mirror your tarballs somewhere. BioC tends to remove older tarballs. Let me know how it goes and I will move everything over into the Main Tool Shed Hope this fixes your issues, Bjoern

Thanks Guys, Help greatly appreciated.

I need this as my team are thinking of using SCDE see http://pklab.med.harvard.edu/scde/index.html which uses cairo.

Monday in a bank holiday here so even if you guys are super fast I will not be able to test until Tuesday.

Christian University of Manchester ________________________________________ 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

___________________________________________________________ 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/

Hi Christian, what is needed from the TS site? Do you have any changes that are needed in the cairo package or R package? For me everything is now working and the only thing you need to do is to specify the Rcairo tarball in your tool_dependendy file. Like here: https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a... Cheers, Bjoern Am 06.10.2015 um 15:21 schrieb Christian Brenninkmeijer:

i finally got Cairo installed into R inside galaxy.

As well as cairo needing fontconfig to add cairo into R also requires libmxl2

I also changed the R install. 1. Never use the zip as it has hard coded environment variables in it 2. The set_environment variable in the R install to "prepend_to" PKG_CONFIG_DIR and PKG_CONFIG_PATH

I have some examples in the test tool shed test section but I would like to clean these up first.

Once done I will post a link in this thread.

Christian University of Manchester ________________________________________ From: Björn Grüning [bjoern.gruening@gmail.com] Sent: Sunday, September 27, 2015 10:40 PM To: Christian Brenninkmeijer; Bjoern Gruening; galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

I think I found the problem and fixed it in the Test Tool Shed. The root problem was that cairo was not compiled with fontconfig and therefore the freetype-cairo module was not working properly, which causes R-Cairo do give us such an unusable error message.

I tested it with our new DEXSeq wrapper, which also needs Cairo if you want to create SVGs. Have a look how to define dependencies here:

https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a...

This PR will also help you to get all needed R packages in the correct order:

https://github.com/bioarchive/aRchive_source_code/pull/20

Keep in mind to mirror your tarballs somewhere. BioC tends to remove older tarballs.

Let me know how it goes and I will move everything over into the Main Tool Shed

Hope this fixes your issues, Bjoern

...

Thanks Guys, Help greatly appreciated.

I need this as my team are thinking of using SCDE see http://pklab.med.harvard.edu/scde/index.html which uses cairo.

Monday in a bank holiday here so even if you guys are super fast I will not be able to test until Tuesday.

Christian University of Manchester ________________________________________ 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

___________________________________________________________ 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/

Hi, Am 06.10.2015 um 15:48 schrieb Christian Brenninkmeijer:

HI Bjorn,

I now see you are bringing in libmxl2 in dexseq. As this is needed by various R packages and already installed by fontconfig would it be worth making it a first class dependency of package_r_3_2_1

We could think about this, yes. Although it is not a strict dependency of R.

I also see that in dexseg you specifically say "libxml2 needs to be sourced after R"

Is this not because if you source it before R the current <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>

Yes, I have fixed this here: https://github.com/galaxyproject/tools-iuc/pull/298 Thanks, Bjoern

Christian

________________________________________ From: Björn Grüning [bjoern.gruening@gmail.com] Sent: Tuesday, October 06, 2015 2:36 PM To: Christian Brenninkmeijer; Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

what is needed from the TS site? Do you have any changes that are needed in the cairo package or R package?

For me everything is now working and the only thing you need to do is to specify the Rcairo tarball in your tool_dependendy file. Like here:

https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a...

Cheers, Bjoern

Am 06.10.2015 um 15:21 schrieb Christian Brenninkmeijer:

...

i finally got Cairo installed into R inside galaxy.

As well as cairo needing fontconfig to add cairo into R also requires libmxl2

I also changed the R install. 1. Never use the zip as it has hard coded environment variables in it 2. The set_environment variable in the R install to "prepend_to" PKG_CONFIG_DIR and PKG_CONFIG_PATH

I have some examples in the test tool shed test section but I would like to clean these up first.

Once done I will post a link in this thread.

Christian University of Manchester ________________________________________ From: Björn Grüning [bjoern.gruening@gmail.com] Sent: Sunday, September 27, 2015 10:40 PM To: Christian Brenninkmeijer; Bjoern Gruening; galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

I think I found the problem and fixed it in the Test Tool Shed. The root problem was that cairo was not compiled with fontconfig and therefore the freetype-cairo module was not working properly, which causes R-Cairo do give us such an unusable error message.

I tested it with our new DEXSeq wrapper, which also needs Cairo if you want to create SVGs. Have a look how to define dependencies here:

https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a...

This PR will also help you to get all needed R packages in the correct

...

order:

https://github.com/bioarchive/aRchive_source_code/pull/20

Keep in mind to mirror your tarballs somewhere. BioC tends to remove older tarballs.

Let me know how it goes and I will move everything over into the Main Tool Shed

Hope this fixes your issues, Bjoern

...

Thanks Guys, Help greatly appreciated.

I need this as my team are thinking of using SCDE see http://pklab.med.harvard.edu/scde/index.html which uses cairo.

Monday in a bank holiday here so even if you guys are super fast I will not be able to test until Tuesday.

Christian University of Manchester ________________________________________ 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

___________________________________________________________ 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/

Hello Christian, this is known and fixed (https://github.com/galaxyproject/tools-iuc/pull/310 ), but the toolshed needs to be updated. I am thinking that this is not the only problem we currently have with cairo. I am working on the cairo issues right now and I'll give an update once the things work out, plus a brand new package_r_3_2_2_cairo, that will hopefully fix your issues. Best, Marius On 9 October 2015 at 14:15, Christian Brenninkmeijer < christian.brenninkmeijer@manchester.ac.uk> wrote:

The cairo package in the testtool shed appears to have become corrupted.

If you try to download

https://testtoolshed.g2.bx.psu.edu/view/iuc/package_cairo_1_14_2/9fe5875b0ed... or any tool that depends on that. The first page looks fine. The second pages as an extra dependency iuc/1.6.7

This because the encoded version return to create that second page includes this for some reason. Reported to bugs as well.

Christian ________________________________________ From: Björn Grüning [bjoern.gruening@gmail.com] Sent: Tuesday, October 06, 2015 3:28 PM To: Christian Brenninkmeijer; Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi,

Am 06.10.2015 um 15:48 schrieb Christian Brenninkmeijer:

...

HI Bjorn,

I now see you are bringing in libmxl2 in dexseq. As this is needed by various R packages and already installed by fontconfig would it be worth making it a first class dependency of package_r_3_2_1

We could think about this, yes. Although it is not a strict dependency of R.

...

I also see that in dexseg you specifically say "libxml2 needs to be sourced after R"

Is this not because if you source it before R the current <environment_variable action="set_to"

name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>

...

Yes, I have fixed this here: https://github.com/galaxyproject/tools-iuc/pull/298

Thanks, Bjoern

...

Christian

________________________________________ From: Björn Grüning [bjoern.gruening@gmail.com] Sent: Tuesday, October 06, 2015 2:36 PM To: Christian Brenninkmeijer; Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

what is needed from the TS site? Do you have any changes that are needed in the cairo package or R package?

For me everything is now working and the only thing you need to do is to specify the Rcairo tarball in your tool_dependendy file. Like here:

https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a...

...

Cheers, Bjoern

Am 06.10.2015 um 15:21 schrieb Christian Brenninkmeijer:

...

i finally got Cairo installed into R inside galaxy.

As well as cairo needing fontconfig to add cairo into R also requires libmxl2

I also changed the R install. 1. Never use the zip as it has hard coded environment variables in it 2. The set_environment variable in the R install to "prepend_to" PKG_CONFIG_DIR and PKG_CONFIG_PATH

I have some examples in the test tool shed test section but I would like to clean these up first.

Once done I will post a link in this thread.

Christian University of Manchester ________________________________________ From: Björn Grüning [bjoern.gruening@gmail.com] Sent: Sunday, September 27, 2015 10:40 PM To: Christian Brenninkmeijer; Bjoern Gruening; galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

I think I found the problem and fixed it in the Test Tool Shed. The root problem was that cairo was not compiled with fontconfig and therefore the freetype-cairo module was not working properly, which causes R-Cairo do give us such an unusable error message.

I tested it with our new DEXSeq wrapper, which also needs Cairo if you want to create SVGs. Have a look how to define dependencies here:

https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a...

...

...

This PR will also help you to get all needed R packages in the correct

...

order:

https://github.com/bioarchive/aRchive_source_code/pull/20

Keep in mind to mirror your tarballs somewhere. BioC tends to remove older tarballs.

Let me know how it goes and I will move everything over into the Main Tool Shed

Hope this fixes your issues, Bjoern

...

Thanks Guys, Help greatly appreciated.

I need this as my team are thinking of using SCDE see http://pklab.med.harvard.edu/scde/index.html which uses cairo.

Monday in a bank holiday here so even if you guys are super fast I will not be able to test until Tuesday.

Christian University of Manchester ________________________________________ 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

___________________________________________________________ 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/

Thanks all for the help, Using Marius's Cairo https://testtoolshed.g2.bx.psu.edu/view/mvdbeek/package_cairo_1_14_2/83f00b6... And a slightly changed R https://testtoolshed.g2.bx.psu.edu/view/brenninc/brenninc_r_sept32105/83005a... This is based on: https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/e36e1db5e729 Except. I removed the option to use the zip <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tar.gz</action> As it has hard coded environment paths in env.sh I used Marius's Cairo, freetype and fontconfig regards Christian ________________________________ From: Marius van den Beek [m.vandenbeek@gmail.com] Sent: Friday, October 09, 2015 1:50 PM To: Christian Brenninkmeijer Cc: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy Hello Christian, this is known and fixed (https://github.com/galaxyproject/tools-iuc/pull/310), but the toolshed needs to be updated. I am thinking that this is not the only problem we currently have with cairo. I am working on the cairo issues right now and I'll give an update once the things work out, plus a brand new package_r_3_2_2_cairo, that will hopefully fix your issues. Best, Marius On 9 October 2015 at 14:15, Christian Brenninkmeijer <christian.brenninkmeijer@manchester.ac.uk<mailto:christian.brenninkmeijer@manchester.ac.uk>> wrote: The cairo package in the testtool shed appears to have become corrupted. If you try to download https://testtoolshed.g2.bx.psu.edu/view/iuc/package_cairo_1_14_2/9fe5875b0ed... or any tool that depends on that. The first page looks fine. The second pages as an extra dependency iuc/1.6.7 This because the encoded version return to create that second page includes this for some reason. Reported to bugs as well. Christian ________________________________________ From: Björn Grüning [bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>] Sent: Tuesday, October 06, 2015 3:28 PM To: Christian Brenninkmeijer; Björn Grüning; galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy Hi, Am 06.10.2015 um 15:48 schrieb Christian Brenninkmeijer:

HI Bjorn,

I now see you are bringing in libmxl2 in dexseq. As this is needed by various R packages and already installed by fontconfig would it be worth making it a first class dependency of package_r_3_2_1

We could think about this, yes. Although it is not a strict dependency of R.

I also see that in dexseg you specifically say "libxml2 needs to be sourced after R"

Is this not because if you source it before R the current <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>

Yes, I have fixed this here: https://github.com/galaxyproject/tools-iuc/pull/298 Thanks, Bjoern

Christian

________________________________________ From: Björn Grüning [bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>] Sent: Tuesday, October 06, 2015 2:36 PM To: Christian Brenninkmeijer; Björn Grüning; galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

what is needed from the TS site? Do you have any changes that are needed in the cairo package or R package?

For me everything is now working and the only thing you need to do is to specify the Rcairo tarball in your tool_dependendy file. Like here:

https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a...

Cheers, Bjoern

Am 06.10.2015 um 15:21 schrieb Christian Brenninkmeijer:

...

i finally got Cairo installed into R inside galaxy.

As well as cairo needing fontconfig to add cairo into R also requires libmxl2

I also changed the R install. 1. Never use the zip as it has hard coded environment variables in it 2. The set_environment variable in the R install to "prepend_to" PKG_CONFIG_DIR and PKG_CONFIG_PATH

I have some examples in the test tool shed test section but I would like to clean these up first.

Once done I will post a link in this thread.

Christian University of Manchester ________________________________________ From: Björn Grüning [bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>] Sent: Sunday, September 27, 2015 10:40 PM To: Christian Brenninkmeijer; Bjoern Gruening; galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

I think I found the problem and fixed it in the Test Tool Shed. The root problem was that cairo was not compiled with fontconfig and therefore the freetype-cairo module was not working properly, which causes R-Cairo do give us such an unusable error message.

I tested it with our new DEXSeq wrapper, which also needs Cairo if you want to create SVGs. Have a look how to define dependencies here:

https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a...

This PR will also help you to get all needed R packages in the correct

...

order:

https://github.com/bioarchive/aRchive_source_code/pull/20

Keep in mind to mirror your tarballs somewhere. BioC tends to remove older tarballs.

Let me know how it goes and I will move everything over into the Main Tool Shed

Hope this fixes your issues, Bjoern

...

Thanks Guys, Help greatly appreciated.

I need this as my team are thinking of using SCDE see http://pklab.med.harvard.edu/scde/index.html which uses cairo.

Monday in a bank holiday here so even if you guys are super fast I will not be able to test until Tuesday.

Christian University of Manchester ________________________________________ From: Bjoern Gruening [bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>] Sent: Friday, August 28, 2015 3:19 PM To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org<mailto: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<mailto:bjoern.gruening@gmail.com>] Sent: Wednesday, August 26, 2015 7:19 PM To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org<mailto: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<mailto:galaxy-dev-bounces@lists.galaxyproject.org>] on behalf of Christian Brenninkmeijer [christian.brenninkmeijer@manchester.ac.uk<mailto:christian.brenninkmeijer@manchester.ac.uk>] Sent: Wednesday, August 26, 2015 10:18 AM To: galaxy-dev ‎[galaxy-dev@lists.galaxyproject.org<mailto: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

___________________________________________________________ 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/

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

___________________________________________________________ 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/

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

___________________________________________________________ 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/

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

___________________________________________________________ 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/

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

___________________________________________________________ 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/

Doing farther testing to installing Cairo into R I get to the point where the follow test done by the config file fails. gcc -std=gnu99 -o conftest.output -g -O2 -I/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/include/cairo -I/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/include/freetype2 -I/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/include/libpng16 -I/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/include/pixman-1 -I/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/include/freetype2 conftest.c -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 -L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib -lfreetype Error is: conftest.c: In function ‘main’: conftest.c:28:4: warning: implicit declaration of function ‘cairo_ft_font_face_create_for_pattern’ [-Wimplicit-function-declaration] cairo_ft_font_face_create_for_pattern(0); ^ /tmp/ccbxU9HY.o: In function `main': /home/christian/Dropbox/Manchester/galaxy_shed_tools/test/conftest.c:28: undefined reference to `cairo_ft_font_face_create_for_pattern' collect2: error: ld returned 1 exit status So it looks like cairo is not installed properly. Christian PS. conftest.c is: ==== /* confdefs.h */ #define PACKAGE_NAME "Cairo" #define PACKAGE_TARNAME "cairo" #define PACKAGE_VERSION "1.3" #define PACKAGE_STRING "Cairo 1.3" #define PACKAGE_BUGREPORT "Simon.Urbanek@r-project.org" #define PACKAGE_URL "" #define STDC_HEADERS 1 #define HAVE_SYS_WAIT_H 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_SYS_STAT_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_MEMORY_H 1 #define HAVE_STRINGS_H 1 #define HAVE_INTTYPES_H 1 #define HAVE_STDINT_H 1 #define HAVE_UNISTD_H 1 #define HAVE_STRING_H 1 #define HAVE_SYS_TIME_H 1 #define HAVE_UNISTD_H 1 #define HAVE_DECL_CAIRO_IMAGE_SURFACE_GET_FORMAT 0 /* end confdefs.h. */ #include <cairo.h> #include <cairo-ft.h> int main(void) { cairo_ft_font_face_create_for_pattern(0); return 0; } ________________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of Christian Brenninkmeijer [christian.brenninkmeijer@manchester.ac.uk] Sent: Thursday, September 03, 2015 2:34 PM To: Bjoern Gruening; galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy Thanks Bjoern, At this point I am looking to run a tiny R script which just loads Cairo and reports the session Info. Full Rscript which would be run via r_wrapper.sh === library(Cairo) args<-commandArgs(TRUE) writeLines(capture.output(sessionInfo()), args[1]) sessionInfo() ==== Even that fails so at the moment saying Cairo library can not be found. This is because SCDE we want to use depends on Cairo Christian ________________________________________ From: Bjoern Gruening [bjoern.gruening@gmail.com] Sent: Thursday, September 03, 2015 2:20 PM To: Christian Brenninkmeijer; Bjoern Gruening; galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy 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

___________________________________________________________ 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/

___________________________________________________________ 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/