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

Wed Jul 2 06:30:09 UTC 2014

Hi Andreas, Yurii,

On 01-07-14 21:33, Andreas Tille wrote:
> Hi Yury,
> 
> On Tue, Jul 01, 2014 at 06:41:19PM +0200, Yury Aulchenko wrote:
>>> 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)
> 
> ??? I admit it sounds pretty strange to me that there should be a policy
> to avoid testing software.  At least in Debian we are doing the contrary
> and try to add tests whereever possible that can run at package build
> time and in periodical tests of the full archive.

Maybe we should try to enable the tests again and see what the CRAN
people say?

> 
>>> 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?

Using a simple SVN checkout is not going to work. Currently we use a
shell script (also in SVN,
pkg/GenABEL-general/distrib_scripts/makedistrib_GenABEL.sh) to prepare
the package before releasing to CRAN. This script copies some stuff
around (e.g. some .cpp/.h files that are shared with DatABEL, but also
files that are in subdirectories in GenABEL/src/ in SVN (e.g. GAlib/,
ITERlib/), but get copied to GenABEL/src/. I guess that a proper
Makevars file would obsolete the need for this file juggling. It's been
on my list for quite some time (also for other packages), but as Yurii
mentioned, we're a bit short on man power.

> 
> I admit that having a canonical way to obtain a tarball from CRAN is
> quite attractive.  Is there any chance to somehow "hide" the tests -
> perhaps by renaming the directory the test files are located in - before
> uploading the tarball to CRAN so the test will not run there but we can
> "uncover" the files again and run the tests.  For me this sounds like a
> good compromise to fullfill all needs without changing the workflow
> drastically.

That should definitely be possible. I'll have a look.

> 
> If you might document this in some README file also other potential
> distributors and users could profit from this. 

Thanks for the suggestion. We should definitely do that.

> 
>> best wishes,
> 
> Same to you and thanks for your quick response
> 
>     Andreas, keeps on shaking head why CRAN refuses testing ...

Thanks for thinking along!

Lennart.

> 
>> Yurii
>>
>>>>> 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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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
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