Peter, Björn,

I have restored gfortran to the repository test host. I believe it was inadvertently removed, possibly as a side effect of updating packages or removing packages that were causing conflicts with the Galaxy eggs. Numpy and biopython should now install successfully, as they do in my local environment.

   --Dave B.

On 10/08/2013 05:25 AM, Peter Cock wrote:
On Mon, Oct 7, 2013 at 8:52 PM, Björn Grüning
<bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:

Hi Dave, Bjeorn,

Right now NumPy isn't installing at all on the Test Tool Shed.

Dave - is is possible that the system was updated and the
Fortran compiler removed? e.g.

...

Since this seems to be breaking lapack, perhaps we should
further simplify package_numpy_1_7 not to use lapack or
ATLAS? What do you think Bjoern?

I'm a little bit sceptic to remove features only because the Test
Utility can not handle it.
On the other hand I understand that numpy should just work and that your
test failing since month because of my dependencies. I will get rid of
it tomorrow. As a result we can setup_virtualenv and install numpy from
pip directly I think.

Is that ok for you?
Cheers,
Bjoern

Hi Bjoern,

I think the real problem here is we don't yet have a clear
base installation:
https://trello.com/c/gYlRdqwr/774-toolshed-define-a-base-set-of-utilities-that-can-be-expected-to-be-on-systems-into-which-tool-dependencies-are-being-installed
https://trello.com/c/7VTlX9rD/844-toolshed-tool-dependency-installation-requirements

What is worse is the system used by the ToolShed for
running the nightly tests appears to change without
notice, e.g. here it looks like something with the Fortran
compiler has changed, for the BLAST+ wrappers the
default shell seems to have changed between bash
and sh).

I think the ToolShed system should be a role model of
the agreed standard set of system level dependencies.

Given that, it seems your lapack package has some
dependencies which are not necessarily present, and
this failure is cascading up to break NumPy and then
Biopython, and thus multiple tools on the Tool Shed :(

I do think that in the short term the best option is to
  further simplify package_numpy_1_7 not to use
lapack or ATLAS - although this is not ideal :(

On the positive side, your hard work setting up packages
for NumPy, lapack and Altas is drawing attention to the
need for a clearer set of base packages. :)

Thanks,

Peter

___________________________________________________________
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, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Reply via email to