Hans Rudolph,

thanks to Marius van den Beek this issue should be fixed with this PR: https://github.com/galaxyproject/tools-devteam/pull/299

These changes were already propagated to the Main Tool Shed.

Note for tool developers: for future endeavours please use packages from the IUC repository ( https://github.com/galaxyproject/tools-iuc/tree/master/packages)

Thank you for the report (and for using Galaxy :)).

Martin

On Tue, Dec 1, 2015 at 6:25 AM Hans Rudolph hans.rudolph@sceedo.de wrote:

Hello Galaxy-devs,

I am setting up galaxy on current os x 10.11 and encounter this trouble using galaxy to install pixman-0.32.4: the package gets downloaded successfully from http://cairographics.org/releases/pixman-0.32.4.tar.gz … while following the installation process in terminal I see this output during the process …presumably indicating an gcc problem ... install_environment.STDOUT DEBUG 2015-12-01 10:44:18,096 checking build system type... x86_64-apple-darwin15.0.0 install_environment.STDOUT DEBUG 2015-12-01 10:44:18,099 checking for gcc... gcc checking build system type... x86_64-apple-darwin15.0.0 checking host system type... x86_64-apple-darwin15.0.0 checking for gcc... gcc checking whether the C compiler works... no configure: error: in `/Users/hans/galaxy/database/tmp/tmp-toolshed-mtdKC9F_F/pixman-0.32.4': configure: error: C compiler cannot create executables See `config.log' for more details

Curiously, if I download the pixman package (same URL) outside of galaxy and run ./configure … gcc seems to work : ... checking build system type... x86_64-apple-darwin15.0.0 checking host system type... x86_64-apple-darwin15.0.0 checking for gcc... gcc checking whether the C compiler works… yes ... and ./configure finishes OK.

to actually compile/make pixman properly, I have to use the ./configure —disable-mmx option to avoid another known error (*pixman-mmx.c:100:20: **error: **constraint 'K' expects an integer constant expression* : "y" (__A), "K" (__N))

Perhaps someone is using galaxy on Mac OS X how this difference in gcc handling arises? Thanks very much,

Hans Rudolph ___________________________________________________________ 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/

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Hi,

we just did not updated the packages. Sorry. I have now pushed everything to the TS's.

Hopefully it is working now for you. Cheers, Bjoern

Thanks to Marius and Martin for fixing pixman-0.32.4!

This new pixman-0.32.4 version (owned by devteam) is also used by the new devteam cairo-1-12-14 package … both installed properly into galaxy on OS X.

I am curious/unclear on how to proceed with other packages, e.g. deseq2-1-8-2 (uic), which still seem to use the "old" cairo-1-12-14 (uic) and pixman-0-32-4 (uic) versions … which won’t work on OS X.

What am I missing?

Best regards, Hans

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Hi,

which operating system are you using? We ship precompiled binaries for x64-linux systems. So I wonder why your Galaxy is trying to compile R.

Can you provide us with the INSTALLATION.log from the R package?

Thanks, Bjoern

Am 03.12.2015 um 00:49 schrieb Hans Rudolph:

Hi Björn,

thanks very much for your efforts. Unfortunately, installation of the new deseq2-1-8-2 (uic, 2015-12-02) still fails for me -

apparently due to the included package_r_3_2_1 which fails with "configure: error: C compiler cannot create executables” and the R error status stops deseq2 installation with error "/bin/sh: line 7: Rscript: command not found”.

But all the other dependencies in the deseq2-1-8-2 package:

atlas-3-10 cairo-1-12-14 fontconfig-2-11-1 freetype-2-5-2 libpng-1-6-7 libxml2-2-9-1 ncurses-6-0 pixman-0.32-4 pixman-0-32-6 readline-6-3

show the green label “installed” as installation status.

Best regards, Hans

Hans:

I have had trouble with el capitan and gcc lately, updating the xcode commandlinetools sometimes helps.

$ xcode-select --install

M.

On Wed, Dec 2, 2015 at 7:30 PM Hans Rudolph hans.rudolph@sceedo.de wrote:

Hi,

I use Mac OS X 10.11.1 (El Capitan) - I append terminal output during the r-package installation and R INSTALLATION.LOG Cheers, Hans

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Hi Hans,

as non-Apple user I now a little bit lost here.

Can you please read this one: http://stackoverflow.com/questions/10357804/configure-error-c-compiler-canno...

It seems to be a fruit problem :) The error message is not so meaningful than I had hoped.

Cheers, Bjoern

Am 03.12.2015 um 01:30 schrieb Hans Rudolph:

Hi,

I use Mac OS X 10.11.1 (El Capitan) - I append terminal output during the r-package installation and R INSTALLATION.LOG Cheers, Hans

I could reproduce this, and in fact removing all the export statements would solve the problem. Those shouldn't be necessary in the first place since we consequently modify LD_INCLUDE_PATH and LD_LIBRARY_PATH. I have no proof yet, but I think the underlying problem is that OS Xs GCC compiler doesn't tolerate empty include or library PATHs. Probably one of the variables in the export statement is missing because it was renamed or removed. Yet, it would be much less maintenance work to rely on modified LD_INCLUDE_PATH and LD_LIBRARY_PATH and use the autoconf action. What do you think about this, Bjoern?

Marius

On 3 December 2015 at 09:21, Marius van den Beek m.vandenbeek@gmail.com wrote:

Hi Hans,

I've seen this error (" configure: error: C compiler cannot create executables”) quite a few times on OS X, and contrary to the message, is usually not related to the installed compiler (all your other packages compiled just fine). I'll check this on my macs, to see if we didn't introduce a regression. My feeling is that one of the include PATHS hasn't been set correctly. Could you post the full INSTALLATION.log ?

Marius

On 3 December 2015 at 00:49, Hans Rudolph hans.rudolph@sceedo.de wrote:

...

Hi Björn,

thanks very much for your efforts. Unfortunately, installation of the new deseq2-1-8-2 (uic, 2015-12-02) still fails for me -

apparently due to the included package_r_3_2_1 which fails with " configure: error: C compiler cannot create executables” and the R error status stops deseq2 installation with error " /bin/sh: line 7: Rscript: command not found”.

But all the other dependencies in the deseq2-1-8-2 package:

atlas-3-10 cairo-1-12-14 fontconfig-2-11-1 freetype-2-5-2 libpng-1-6-7 libxml2-2-9-1 ncurses-6-0 pixman-0.32-4 pixman-0-32-6 readline-6-3

show the green label “installed” as installation status.

Best regards, Hans

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Hi,

not sure whether that helps, but I tried to compile r-3-2-1 outside galaxy on the same machine:

1.straight ./configure yields error: "cannot compile a simple Fortran program." To remedie this, I installed gfortran (=gf) 5.2 for OS X (10.11) from https://gcc.gnu.org/wiki/GFortranBinaries https://gcc.gnu.org/wiki/GFortranBinaries

and with gf installed, ./configure now completes, but make fails with "dyld: Symbol not found: _libiconv_open"

2. I then installed libiconv-1.4 as suggested in this tip for R-on-OS X: http://blog.qiubio.com:8080/archives/3897 http://blog.qiubio.com:8080/archives/3897 and put /usr/local/lib into $PATH now make finishes …

I made mistakes running ./configure and make/install first omitting the epxort LD_LIBRARY_PATH= command … and I don’t have proper records ;-)

Not sure how to clean this up - but I wanted to let you know my findings with respect to compiling r-3-2-1

Cheers,

Hans

Hello Hans,

I'm not sure if it would help to use the pre-compiled binaries, as you would still need some of the underlying libraries for building R packages. We're not far from having this fixed ... there is a newer revision of R on the main toolshed, that nevertheless will (probably) fail because of a missing include of what seems to be fontconfig. I had it working yesterday already, I'm trying to see what went wrong in the meantime ...

Marius

On 4 December 2015 at 09:20, Hans Rudolph hans.rudolph@sceedo.de wrote:

Hi,

I now learned that R-3.2.2 binaries for Mac OS X are available ( https://cran.r-project.org/bin/macosx/) - could that be a potential help for R-related problems in galaxy on Mac OS X?

Cheers, Hans

Awesome Marius, thank you very much for looking into this! M.

On Fri, Dec 4, 2015 at 12:30 PM Marius van den Beek m.vandenbeek@gmail.com wrote:

Hello Hans (and other OS X users),

I hope that the last remaining problem should be fixed now. There is a new revision of package_r_3_2_1 and package_cairo_1_12_14 on the toolshed. Make sure you get package_cairo_1_12_14 first when you upgrade. The underlying problem was that cairo was missing the fontconfig dependency, which would still compile correctly, but fail when R is built with `--with-cairo`.

Cheers, Marius

On 4 December 2015 at 09:47, Marius van den Beek m.vandenbeek@gmail.com wrote:

...

Hello Hans,

I'm not sure if it would help to use the pre-compiled binaries, as you would still need some of the underlying libraries for building R packages. We're not far from having this fixed ... there is a newer revision of R on the main toolshed, that nevertheless will (probably) fail because of a missing include of what seems to be fontconfig. I had it working yesterday already, I'm trying to see what went wrong in the meantime ...

Marius

On 4 December 2015 at 09:20, Hans Rudolph hans.rudolph@sceedo.de wrote:

...

Hi,

I now learned that R-3.2.2 binaries for Mac OS X are available ( https://cran.r-project.org/bin/macosx/) - could that be a potential help for R-related problems in galaxy on Mac OS X?

Cheers, Hans

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Hi,

just to mention that deseq2-1-8-2 (requiring r-3-2-1) also installs fine!

Best regards, Hans