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 apprec

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

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

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

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: - gf

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 package_cairo_1_12_14 on

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 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 because

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 list

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 i

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 doesn'

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

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

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 0

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

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 the > r-package installa

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: http://cran.rstudio.com/src/ba

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 in

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 cairo-1

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

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

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 (