[Debian-med-packaging] Please check whether I fixed syntax error in proteinortho properly

[Marcus Lechner]

Hi Andreas,

sorry for not responding earlier - there is a lot going on right know.

I followed your suggestions regarding the Makefile (also added 
proteinortho5_tree for install, thanks) in the new update (5.13 -> 
http://www.bioinf.uni-leipzig.de/Software/proteinortho/).
As there was a quite bad bug in 5.12, I kindly ask whether you could 
pack the new version?

Regarding the stripping of all binaries: From my experience, many users 
that download the tar-ball are actually not familiar with compiling and 
can get started with the binaries. That's why they are inside. Would it 
be a useful option to provide two tar-balls, one with and one without 
binaries for either purpose?

Thanks a lot and best regards,
Marcus

Dr. Marcus Lechner
Bioinformatics Junior Group
Department of Pharmaceutical Chemistry
Philipps-University Marburg
Marbacher Weg 6, 35037 Marburg, Germany
Phone:  +49 (0)6421 2825925
Mobile: +49 (0)176 38733610
Web: http://bioinf.pharmazie.uni-marburg.de

On 03/17/2016 09:02 PM, Andreas Tille wrote:
> Hi Marcus,
>
> thanks for the effort you did to enable us to build the Debian package
> properly.  I have some additional remarks:
>
>    1. I'd recommend to strip all binaries from the source tarball.
>       These should be the result of the build process.  For Debian
>       we need to strip the binaries and thus the Debian source tarball
>       is different from the download from your homepage which is not
>       unusual but also not the prefered situation.
>
>    2. It would be nice if you could change your Makefile in a way that
>       external set CPPFLAGS and LDFLAGS are respected to propagate the
>       hardening options which are usually set in Debian.  Here
>        https://anonscm.debian.org/git/debian-med/proteinortho.git/tree/debian/patches/hardening.patch
>       you can see, how to do this.
>
>    3. If looking at your install target one of your build targets
>       proteinortho5_tree is not mentioned in the install command.
>       I suspect this is a remaining bug, right?
>
> I have just uploaded the current state of 5.12 since it passes the
> shipped test suite.  In case you might confirm and further issues I will
> fix these as soon as possible.
>      
> Thanks a lot for your cooperation
>
>        Andreas.
>
> On Thu, Mar 17, 2016 at 12:59:43PM +0100, Marcus Lechner wrote:
>> Hi Andreas,
>>
>> thanks a lot for your feedback again. Obviously, the makefile was not
>> adapted to the most recent changes in the tool. E.g. po_tree.pl needs to be
>> become po2tree.pl. I have done this now and attached the full tarball with
>> fixed makefile and po_tree.c. Should be fine now.
>>
>> Best regards,
>> Marcus
>>
>> Dr. Marcus Lechner
>> Bioinformatics Junior Group
>> Department of Pharmaceutical Chemistry
>> Philipps-University Marburg
>> Marbacher Weg 6, 35037 Marburg, Germany
>> Phone:  +49 (0)6421 2825925
>> Mobile: +49 (0)176 38733610
>> Web: http://bioinf.pharmazie.uni-marburg.de
>>
>> On 03/16/2016 06:02 PM, Andreas Tille wrote:
>>> Hi Marcus,
>>>
>>> thanks for confirming.  Unfortunately there is another build issue:
>>>
>>> ...
>>> po_tree.c:378:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
>>>      fscanf (datei, "%c ",&(matrix[i][*ccs]));
>>>      ^
>>> po_tree.c:381:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
>>>     fscanf (datei, "%c \n",&(matrix[(*viecher)-1][*ccs]));
>>>     ^
>>> make[2]: *** No rule to make target 'po_tree.pl', needed by 'install'.  Stop.
>>> make[2]: Leaving directory '/build/proteinortho-5.12+dfsg'
>>>
>>>
>>> Any idea from where I can get po_tree.pl?  Are you possibly some
>>> repository like Github where somebody could sneak into the full source
>>> that might contain pieces missing inside the tarball?
>>>
>>> Kind regards
>>>
>>>        Andreas.
>>>
>>> On Wed, Mar 16, 2016 at 03:18:37PM +0100, Marcus Lechner wrote:
>>>> Hi Andreas,
>>>>
>>>> thanks a lot for your work and feedback. You've fixed the error correctly (/
>>>> need be be removed). I'll merge this in the next version of Proteinortho.
>>>>
>>>> Best regards,
>>>> Marcus
>>>>
>>>> Dr. Marcus Lechner
>>>> Bioinformatics Junior Group
>>>> Department of Pharmaceutical Chemistry
>>>> Philipps-University Marburg
>>>> Marbacher Weg 6, 35037 Marburg, Germany
>>>> Phone:  +49 (0)6421 2825925
>>>> Mobile: +49 (0)176 38733610
>>>> Web: http://bioinf.pharmazie.uni-marburg.de
>>>>
>>>> On 03/16/2016 02:09 PM, Andreas Tille wrote:
>>>>> Hi Marcus,
>>>>>
>>>>> I'm not sure whether it becomes clear that the last release of
>>>>> proteinortho (5.12) has a serious syntax error which makes the build
>>>>> fail.  The patch below fixes the syntax issue but I'm not 100% sure
>>>>> whether it is correct in terms of content.
>>>>>
>>>>> Please check your code accordingly.
>>>>>
>>>>> Kind regards
>>>>>
>>>>>       Andreas
>>>>>
>>>>> On Thu, Mar 10, 2016 at 08:57:55PM +0100, Andreas Tille wrote:
>>>>>> Hi Marcus,
>>>>>>
>>>>>> when trying to upgrade proteinortho Debian package to version 5.12 I
>>>>>> faced a syntax error which is most probably a typo.  Please verify
>>>>>> that the intention was to *remove* the comment sign as I did in this
>>>>>> patch:
>>>>>>
>>>>>>      https://anonscm.debian.org/cgit/debian-med/proteinortho.git/tree/debian/patches/fix_syntax.patch
>>>>>>
>>>>>> Kind regards
>>>>>>
>>>>>>        Andreas.
>>>>>>
>>>>>> -- 
>>>>>> http://fam-tille.de
>
>