Re: Macsyfinder Test Issues

[Canberk Koç]

Hello Andreas,

I commit autopkgtest can you check .

Best Regards



Canberk Koç
[image: https://]about.me/canberkkoc


2016-12-12 18:42 GMT+03:00 Canberk Koç :

> Indeed mentor indeed :)
>
>
>
> Canberk Koç
> [image: https://]about.me/canberkkoc
>
> 
>
> 2016-12-12 14:23 GMT+03:00 Andreas Tille :
>
>> On Mon, Dec 12, 2016 at 01:55:06PM +0300, Canberk Koç wrote:
>> > My hdd also my test is gone i'll write it again today.
>>
>> Lesson learned why I suggest early commits? :-P
>>
>>
>>
>> --
>> http://fam-tille.de
>>
>>
>

Re: Macsyfinder Test Issues

[Canberk Koç]

Indeed mentor indeed :)



Canberk Koç
[image: https://]about.me/canberkkoc


2016-12-12 14:23 GMT+03:00 Andreas Tille :

> On Mon, Dec 12, 2016 at 01:55:06PM +0300, Canberk Koç wrote:
> > My hdd also my test is gone i'll write it again today.
>
> Lesson learned why I suggest early commits? :-P
>
>
>
> --
> http://fam-tille.de
>
>

Re: Macsyfinder Test Issues

[Andreas Tille]

On Mon, Dec 12, 2016 at 01:55:06PM +0300, Canberk Koç wrote:
> My hdd also my test is gone i'll write it again today.

Lesson learned why I suggest early commits? :-P



-- 
http://fam-tille.de

Re: Macsyfinder Test Issues

[Canberk Koç]

Hello Andreas,

My hdd also my test is gone i'll write it again today.

Best regards

12 Ara 2016 10:38 tarihinde "Andreas Tille"  yazdı:

> Hi again,
>
> is there any chance to at least commit your test suite to enable me
> reproducing the problem you faced?  As you know I respect your exams but
> you said you had written a test suite which uncovered a problem.  I
> think I solved the problem but I would like to verify this.  Committing
> what you just have should not be that time consuming, thought.
>
> Thanks a lot
>
>   Andreas.
>
> On Thu, Dec 01, 2016 at 08:46:15PM +0300, Canberk Koç wrote:
> > Hello Andreas,
> >
> > Due to my exams i can not find any time to look this issue i will take
> care
> > of it and return to you.
> >
> > Best Regards
> >
> >
> >
> > Canberk Koç
> > [image: https://]about.me/canberkkoc
> >  email_sig_medium=email_sig_campaign=external_links>
> >
> > 2016-12-01 16:05 GMT+03:00 Andreas Tille :
> >
> > > Hi Canberk,
> > >
> > > any news?  Its *really* high time to get this issue settled.  It would
> > > be extremely helpful if you could at least submit your test suite to
> Git
> > > to let me reproduce the test results if you do not manage to check the
> > > issue yourself.
> > >
> > > BTW, adding tests to packages could als made part of our bug squashing
> > > party by filing bugs "Please add autopkgtest to package xy" and than
> > > you close the bug with a test ...
> > >
> > > Kind regards
> > >
> > >   Andreas.
> > >
> > > On Thu, Nov 03, 2016 at 05:27:09PM +0100, Andreas Tille wrote:
> > > > Hi Canberk,
> > > >
> > > > On Thu, Nov 03, 2016 at 08:19:19AM +0300, Canberk Koç wrote:
> > > > > Hello Andreas,
> > > > >
> > > > > I made a bug report and will make a test soon. System said there
> will
> > > be a
> > > > > mail to come but if it won't come what should i do for take this
> mail.
> > > >
> > > > I think the answer to your question was given here:
> > > >
> > > >https://lists.debian.org/debian-med/2016/11/msg3.html
> > > >
> > > > Are you able to run your test with the fixed version I mentioned:
> > > >
> > > > > > That's done now.  The fix (=hack) is in
> > > > > >
> > > > > > https://anonscm.debian.org/git/debian-med/macsyfinder.git
> > > >
> > > > If yes, we can even close your proposed bug report with the next
> > > > upload ...
> > > >
> > > > Kind regards
> > > >
> > > >   Andreas.
> > > >
> > > >
> > > > --
> > > > http://fam-tille.de
> > > >
> > > >
> > >
> > > --
> > > http://fam-tille.de
> > >
>
> --
> http://fam-tille.de
>

Re: Macsyfinder Test Issues

[Andreas Tille]

Hi again,

is there any chance to at least commit your test suite to enable me
reproducing the problem you faced?  As you know I respect your exams but
you said you had written a test suite which uncovered a problem.  I
think I solved the problem but I would like to verify this.  Committing
what you just have should not be that time consuming, thought.

Thanks a lot

  Andreas.

On Thu, Dec 01, 2016 at 08:46:15PM +0300, Canberk Koç wrote:
> Hello Andreas,
> 
> Due to my exams i can not find any time to look this issue i will take care
> of it and return to you.
> 
> Best Regards
> 
> 
> 
> Canberk Koç
> [image: https://]about.me/canberkkoc
> 
> 
> 2016-12-01 16:05 GMT+03:00 Andreas Tille :
> 
> > Hi Canberk,
> >
> > any news?  Its *really* high time to get this issue settled.  It would
> > be extremely helpful if you could at least submit your test suite to Git
> > to let me reproduce the test results if you do not manage to check the
> > issue yourself.
> >
> > BTW, adding tests to packages could als made part of our bug squashing
> > party by filing bugs "Please add autopkgtest to package xy" and than
> > you close the bug with a test ...
> >
> > Kind regards
> >
> >   Andreas.
> >
> > On Thu, Nov 03, 2016 at 05:27:09PM +0100, Andreas Tille wrote:
> > > Hi Canberk,
> > >
> > > On Thu, Nov 03, 2016 at 08:19:19AM +0300, Canberk Koç wrote:
> > > > Hello Andreas,
> > > >
> > > > I made a bug report and will make a test soon. System said there will
> > be a
> > > > mail to come but if it won't come what should i do for take this mail.
> > >
> > > I think the answer to your question was given here:
> > >
> > >https://lists.debian.org/debian-med/2016/11/msg3.html
> > >
> > > Are you able to run your test with the fixed version I mentioned:
> > >
> > > > > That's done now.  The fix (=hack) is in
> > > > >
> > > > > https://anonscm.debian.org/git/debian-med/macsyfinder.git
> > >
> > > If yes, we can even close your proposed bug report with the next
> > > upload ...
> > >
> > > Kind regards
> > >
> > >   Andreas.
> > >
> > >
> > > --
> > > http://fam-tille.de
> > >
> > >
> >
> > --
> > http://fam-tille.de
> >

-- 
http://fam-tille.de

Re: Macsyfinder Test Issues

[Canberk Koç]

Hello Andreas,

Due to my exams i can not find any time to look this issue i will take care
of it and return to you.

Best Regards



Canberk Koç
[image: https://]about.me/canberkkoc


2016-12-01 16:05 GMT+03:00 Andreas Tille :

> Hi Canberk,
>
> any news?  Its *really* high time to get this issue settled.  It would
> be extremely helpful if you could at least submit your test suite to Git
> to let me reproduce the test results if you do not manage to check the
> issue yourself.
>
> BTW, adding tests to packages could als made part of our bug squashing
> party by filing bugs "Please add autopkgtest to package xy" and than
> you close the bug with a test ...
>
> Kind regards
>
>   Andreas.
>
> On Thu, Nov 03, 2016 at 05:27:09PM +0100, Andreas Tille wrote:
> > Hi Canberk,
> >
> > On Thu, Nov 03, 2016 at 08:19:19AM +0300, Canberk Koç wrote:
> > > Hello Andreas,
> > >
> > > I made a bug report and will make a test soon. System said there will
> be a
> > > mail to come but if it won't come what should i do for take this mail.
> >
> > I think the answer to your question was given here:
> >
> >https://lists.debian.org/debian-med/2016/11/msg3.html
> >
> > Are you able to run your test with the fixed version I mentioned:
> >
> > > > That's done now.  The fix (=hack) is in
> > > >
> > > > https://anonscm.debian.org/git/debian-med/macsyfinder.git
> >
> > If yes, we can even close your proposed bug report with the next
> > upload ...
> >
> > Kind regards
> >
> >   Andreas.
> >
> >
> > --
> > http://fam-tille.de
> >
> >
>
> --
> http://fam-tille.de
>

Re: Macsyfinder Test Issues

[Andreas Tille]

Hi Canberk,

any news?  Its *really* high time to get this issue settled.  It would
be extremely helpful if you could at least submit your test suite to Git
to let me reproduce the test results if you do not manage to check the
issue yourself.

BTW, adding tests to packages could als made part of our bug squashing
party by filing bugs "Please add autopkgtest to package xy" and than
you close the bug with a test ...

Kind regards

  Andreas.

On Thu, Nov 03, 2016 at 05:27:09PM +0100, Andreas Tille wrote:
> Hi Canberk,
> 
> On Thu, Nov 03, 2016 at 08:19:19AM +0300, Canberk Koç wrote:
> > Hello Andreas,
> > 
> > I made a bug report and will make a test soon. System said there will be a
> > mail to come but if it won't come what should i do for take this mail.
> 
> I think the answer to your question was given here:
> 
>https://lists.debian.org/debian-med/2016/11/msg3.html
> 
> Are you able to run your test with the fixed version I mentioned:
>  
> > > That's done now.  The fix (=hack) is in
> > >
> > > https://anonscm.debian.org/git/debian-med/macsyfinder.git
> 
> If yes, we can even close your proposed bug report with the next
> upload ...
> 
> Kind regards
> 
>   Andreas.
> 
> 
> -- 
> http://fam-tille.de
> 
> 

-- 
http://fam-tille.de

Re: Macsyfinder Test Issues

[Andreas Tille]

Hi again,

On Thu, Oct 27, 2016 at 09:16:06AM +0200, Andreas Tille wrote:
> On Thu, Oct 27, 2016 at 03:53:59AM +0300, Canberk Koç wrote:
> > I try to make a test for macsyfinder but when i try quick start guide like:
> > 
> > macsyfinder --db-type unordered --sequence-db metagenome.fasta all
> > 
> > it gives an error message like:
> > 
> > ValueError: debian/macsyfinder/usr/share/macsyfinder/DEF: No such
> > definition directory
> > 
> > I control theres is a DEF directory in /usr/share i think developer gave
> > path wrong.
> > Is anybody came across something like that or this program have a bug ?
> 
> I admit that I wonder how these currently 25 regular users (according to
> popcon) did not stumbled upon this.  You definitely hit a bug in the
> packaging.  You should report this via
> 
>  reportbug macsyfinder
>  
> The cause is that in
> 
>/usr/lib/python2.7/dist-packages/macsypy/config.py
> 
> the temporary location that is used for packaging ended up hardcoded as
> 
>debian/macsyfinder/usr/
> 
> I'll check how to fix this but a bug report seems apropriate here.

I found a *hack* to solve the issue.  It would be better to fix setup.py
to provide a root dir there.  You might like to ask on
debian-pyt...@lists.debian.org list if you want to solve the issue
properly but have no idea how to do this.
 
> BTW, I'll also convert the packaging from SVN to Git as you prefer.

That's done now.  The fix (=hack) is in

https://anonscm.debian.org/git/debian-med/macsyfinder.git

Kind regards

 Andreas.

-- 
http://fam-tille.de

Re: Macsyfinder Test Issues

[Andreas Tille]

Hi Canberk,

On Thu, Oct 27, 2016 at 03:53:59AM +0300, Canberk Koç wrote:
> Hello All,
> 
> I try to make a test for macsyfinder but when i try quick start guide like:
> 
> macsyfinder --db-type unordered --sequence-db metagenome.fasta all
> 
> it gives an error message like:
> 
> ValueError: debian/macsyfinder/usr/share/macsyfinder/DEF: No such
> definition directory
> 
> I control theres is a DEF directory in /usr/share i think developer gave
> path wrong.
> Is anybody came across something like that or this program have a bug ?

I admit that I wonder how these currently 25 regular users (according to
popcon) did not stumbled upon this.  You definitely hit a bug in the
packaging.  You should report this via

 reportbug macsyfinder
 
The cause is that in

   /usr/lib/python2.7/dist-packages/macsypy/config.py

the temporary location that is used for packaging ended up hardcoded as

   debian/macsyfinder/usr/

I'll check how to fix this but a bug report seems apropriate here.

BTW, I'll also convert the packaging from SVN to Git as you prefer.

Bertrand, assuming that the source code is on Github I assume you are
fine with maintaining the package in Git (git.debian.org) as well,
right?

Canberk, I updated the list of packages that might deserve an
autopkttest.  Please note that njplot is specifically interesting
since I would like to publish the new packaging location in an
uploaded package and its popcon is also quite high.  Please let
me know if there might be problems with njplot.


 njplot (https://anonscm.debian.org/git/debian-med/njplot.git)
 macsyfinder
 dialign-t
 poa
 proda
 picard-tools
 filo


Kind regards

   Andreas.


-- 
http://fam-tille.de