I opened a new PR here https://github.com/galaxyproject/tools-iuc/pull/459.

This adds the last remaining LD_INCLUDE_PATH's and as a side effect should also help people with cairo problems.

Note that, at the core, Hans' problem stem from an outdated version of fontconfig on the main toolshed, that is not setting FONTCONFIG_LIB_PATH and FONTCONFIG_INCLUDE_PATH,

so updating fontconfig would suffice to get R compiling.

But let's accept the PR and move away from relying on arbitrarily named ENV vars that are subject to change ...

On 3 December 2015 at 09:44, Marius van den Beek <m.vandenbeek@gmail.com> wrote:

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

___________________________________________________________
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/