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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Sounds great Hans,

gfortran is only needed on OS-X for Linux we can ship precompiled binaries. Moreover if you setup your production instance keep this list in mind.

https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList

Cheers, Bjoern

Hi Marius,

I bow to your efforts in appreciation - it seems to install without flaws!!

I tried the new cairo-1-12-14 and then r-3-2-1 in a frest postgresqldb/galaxy instance … everything got installed and shows the green label ;-)

requirements on top of Mac OS Xcode/command line tools are: - gfortran (I used the OS X 10.11 gfortran 5.2 installer from here https://gcc.gnu.org/wiki/GFortranBinaries https://gcc.gnu.org/wiki/GFortranBinaries) - libiconv-1.14 (from http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.14.tar.gz http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.14.tar.gz) - (which I put into /usr/local where it seems to be found without editing my $PATH)

This is great! Many thanks again! Hans

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