Hello Scott,

thanks to Marius van den Beek the first two issues 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)

As of the timeout for the readline package it seems the problem was on the ftp.gnu side and it is now resolved.
In the future Galaxy plans to use a smart caching proxy to handle&mirror all source codes required by the Tool Shed installations. This effort is lead by Eric Rasche and you can see it here https://github.com/galaxyproject/cargo-port

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


On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu> wrote:
Hi all,

I'm installing the latest revision of Picard tools (efc56ee1ade4). Picard installs successfully, and the tools are appearing in the appropriate menu, but several packages that install with Picard are reporting dependency issues, and I'm concerned that not all the tools will work appropriately. The tools reporting issues are:
  • package_cairo_1_12_14 (last lines of long warning/error sequence)
    • /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: file not recognized: Is a directory
      collect2: ld returned 1 exit status
      make[3]: *** [libcairo.la] Error 1
      make[2]: *** [all] Error 2
      make[1]: *** [all-recursive] Error 1
      make: *** [all] Error 2
  • package_pixman_0_32_4
    • /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start':
      (.text+0x20): undefined reference to `main'
      collect2: ld returned 1 exit status
      make[2]: *** [clip-test] Error 1
      make[1]: *** [all-recursive] Error 1
      make: *** [all] Error 2
  • package_readline_6_2
Is anyone else having issues with these packages? Any suggestions for resolving these problems?


Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556


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