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 :)).

Martin

On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi <scott.b.szakony...@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
>    - Error downloading from URL
>       ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz:
>       <urlopen error ftp error: [Errno 110] Connection timed out>
>
> Is anyone else having issues with these packages? Any suggestions for
> resolving these problems?
>
> Thanks!
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
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