[Debian-med-packaging] Missing file for unit test in GenABEL

[Yury Aulchenko]

Dear Andreas,

On Jun 27, 2014, at 14:34, Andreas Tille <andreas at an3as.eu> wrote:

> Hi Yurii,
> 
> On Fri, Jun 27, 2014 at 02:29:11PM +0200, Yurii Aulchenko wrote:
>> Dear Andreas,
>> 
>> Sorry it delay with answer.
> 
> No problem. :-)
> 
>> We specifically remove unit tests before submitting to cran. Our dev
>> repo does contain a version with unit tests, also tags for the
>> versions.
> 
> Do you have any reasons to remove the tests from the tarball?  I could
> imagine that larger chunks of data might be used but I assumed that for
> this very purpose GenABEL.data exists ... and so I did package it for
> Debian as well.

This was requested by CRAN maintenance team some time (a year?) ago. My understanding this first takes long time to run these tests and secondly RUnit tests are somehow not very stable. Apparently this is not only for GenABEL, but is a general policy (not 100% sure though)


> 
>> So one option would be to use our code repo instead of what is on
>> cran. What do you think?
> 
> While this would possible in prinziple I personally really prefer a
> downloadable source tarball including testing features if any possible.
> However, if you might have strong reasons I would find ways to drain
> the stuff needed from the repository.

Not sure what is the best option, but we have a few

1. use CRAN release, no unit tests

2. use SVN tag for latest release - easiest for us (but I understand you'd prefer tarball)

3. we provide the tarball for latest release, including RUnit part on the code on our web-site http://www.genabel.org/

what do you think? I am somewhat afraid that it may be difficult to implement/keep coherent option 3. - to be fair, with me being overstretched, we struggle a bit with keeping sustainable maintenance of the GenABEL-package. 

Any other options, anyone?

best wishes,
Yurii

> 
> Kind regards
> 
>      Andreas.
> 
>> ----------------------
>> Yurii Aulchenko
>> (sent from mobile device)
>> 
>>> On Jun 26, 2014, at 15:47, Andreas Tille <andreas at an3as.eu> wrote:
>>> 
>>> Hi Yurii,
>>> 
>>>> On Fri, Jun 20, 2014 at 10:44:43AM +0200, Andreas Tille wrote:
>>>> Hi Yurii,
>>>> 
>>>> I'm trying to update the Debian package of GenABEL.  Since some time
>>>> there is an effort to automatically run unit tests of software if
>>>> available.  Since I noticed that GenABEL comes with unit tests I
>>>> tried
>>>> 
>>>> $ make test
>>>> export RCMDCHECK=FALSE;\
>>>>       cd ../../tests;\
>>>>       R --vanilla --slave < doRUnit.R
>>>> /bin/sh: 2: cd: can't cd to ../../tests
>>>> /bin/sh: 3: cannot open doRUnit.R: No such file
>>>> make: *** [test] Error 2
>>>> 
>>>> 
>>>> As you can see the file doRUnit.R is missing.  It would be great if you
>>>> could include this file into the source diustribution to make sure we
>>>> can reproduce your exact test procedure in the Debian package.
>>> 
>>> I cloned https://github.com/cran/GenABEL.git and had a look into the
>>> code.  I realised that the last tag containing the file doRUnit.R was
>>> 1.6-7.  I wonder how you are doing unit testing in the current version.
>>> 
>>> Thanks for any enlightenment
>>> 
>>>     Andreas.
>>> 
>>> --
>>> http://fam-tille.de
>> 
> 
> -- 
> http://fam-tille.de

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