Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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 ___ Please keep all replies on the

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

Awesome Marius, thank you very much for looking into this! M. On Fri, Dec 4, 2015 at 12:30 PM Marius van den Beek 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

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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 Note that, at the core, Hans' problem stem from an outdated version of fontconfig on the main toolshed, that

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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 wrote: > Hi, > > I use Mac OS X 10.11.1 (El Capitan) - I append terminal output during

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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 tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2015-12-02 23:04:16,463 Successfully downloaded from url:

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

Hi, I hope I am up-to-date: $ xcode-select —install yields: xcode-select: error: command line tools are already installed, use "Software Update" to install updates and software-update doesn’t show anything Cheers, Hans___ Please keep all

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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-cannot-create-executables It seems to be a fruit problem :) The error message is not so meaningful than I had hoped. Cheers, Bjoern Am

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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 (