Re: [Outreachy] predictprotein and other RostLab packages
Hi Tanya,
On Fri, Jul 08, 2016 at 07:28:09PM +0300, merlettaia wrote:
> Your solution for reprof works, I've added README.test and for now it's
> ready (current testsuite checks only perl portion of code, I'll probably
> later add other test).
Having any test for the moment is helpful. Its uploaded now.
> I've made tests for profphd-utils, it's ready for upload. For now I took 2
> example files from profphd package - to test profphd-utils independently
> from profphd. If you think it's better to take them directly from profphd
> package installation (and mention profphd in 'Depends:' section in
> debian/tests/control), I can fix this.
I uploaded as is. While your idea has some charm I think its OK as is
as well.
> I also tried to make tests for profnet. This package generates 8 packages
> (and profphd-net), with commands which can be run in similar manner. But
> there are no enough example files. I found correct example file for these
> tests in profphd source package, but it works for 5 of 8 packages. Other 3
> packages (profnet-bval, profnet-md, profnet-norsnet) with the same input
> files raise Segmentation fault.
Hmmm, segmentation fault is not good. I wonder, whether we should
upload with the 5 working tests and report upstream the failures. The
program should not segfault in any case.
> The main difference between sources of these executables can be found in
> upstream's patch files mainly in space character (like in these two lines
> from upstream's bval.patch file):
> - CALL RDPAR_ERR('NUMIN ',VARIN)
> + CALL RDPAR_ERR('NUMIN',VARIN)
>
> For now I couldn't find correct set of example files which works with
> profnet-bval, profnet-md or profnet-norsnet.
Could you provide example command lines and send these upstream to at
least fix the segfault and interrupt at least with a proper error
message?
> For other 5 packages (profnet-chop, profnet-con, profnet-isis,
> profnet-prof, profnet-snapfun) I wrote testsuite which passes.
That's a nice improvement.
> The main problem is profnet is utility package and packages it generates
> are not made to be used by itself, without packages they are supposed to be
> used with.
I can't parse this sentence, sorry.
> I think it's better to return later to this package and search example
> files which works correctly in related packages (for now I couldn't find
> any which doesn't produce segfault). How do you think?
I think having found examples that crash is some valuable information.
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: