[GSoC] Mummer uploaded, next todo list [Was: GDPC Autopkgtes]

[Andreas Tille]

Hi Canberk,

On Wed, Jul 27, 2016 at 01:51:47AM +0300, Canberk Koç wrote:
> I revert your changes due to new Autopkgtest on mummer and look tests but
>  couldn't find what is wrong also there is no bug report on program.

I've uploaded mummer.  Thanks for fixing it.
 
Further todo suggestions:

 fastqc
 kalign
 probcons

Since there were no uploads yesterday and the day before yesterday
would you think you manage two packages per day?

Kind regards

 Andreas.

-- 
http://fam-tille.de

Re: Embassy phylipnew - please use freely licensed source of phylip

[Andreas Tille]

Hi Peter,

On Tue, Jul 26, 2016 at 10:34:21PM +0100, Peter Rice wrote:
> This was a restoration of the 6.6.0 release files which had been lost when
> the FTP server was reset, and a correction of the file names which should
> have been .660 on the original FTP server.

Thanks for the clarification.  However, do you see any chance to fetch
the new phylip sources which are not really different from the old ones
except they now have a free license.  I'd even volunteer to assemble a
new tarball containing the new sources and do the needed patching if
somebody would check this and do an official release.
 
> The same applies to the other EMBASSY packages.

Kind regards

  Andreas.
 
> regards,
> 
> Peter Rice
> EMBOSS Team
> 
> On 25/07/2016 10:55, Andreas Tille wrote:
> >Hi,
> >
> >I realised that at the EMBASSY download ftpserver[1] files with new
> >version numbers appeared.  I was specifically keen to check PHYLIPNEW
> >since I wanted to release a Debian package with the freely licensed
> >phylip.  Unfortunately I realised that PHYLIPNEW-3.69.660.tar.gz is byte
> >identical to PHYLIPNEW-3.69.650.tar.gz - so no change in the source code
> >has happened at all.
> >
> >I wonder whether this is by mistake or what the version rename might
> >mean here.  It would be really great if you could base the code on
> >version 3.696 of phylip since this version has a free license and could
> >be distributed in Debian main.
> >
> >Kind regards
> >
> >   Andreas.
> >
> >
> >[1] ftp://emboss.open-bio.org/pub/EMBOSS/
> >
> 

-- 
http://fam-tille.de

Re: GDPC Autopkgtes [GSOC]

[Canberk Koç]

Hello Andreas,

I revert your changes due to new Autopkgtest on mummer and look tests but
 couldn't find what is wrong also there is no bug report on program.

Best Regards



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


2016-07-25 10:12 GMT+03:00 Canberk Koç :

> Hello Andreas,Sascha,
>
> Thanks for your help first of all. I can't look what you've changed in
> mummer but i'll look it by tommorrow and i will give you more detailed
> report. I am going on list also ;-)
>
> Best Regards
>
>
>
> Canberk Koç
> [image: https://]about.me/canberkkoc
>
> 
>
> 2016-07-25 10:07 GMT+03:00 Andreas Tille :
>
>> Hi Canberk,
>>
>> On Sun, Jul 24, 2016 at 08:13:16AM +0200, Andreas Tille wrote:
>> > > I commit Gdpc to Git here is the problem unit test codes(all of em)
>> from
>> > > Readme file and gives segmentation fault for this issue.
>> >
>> > I think this is a severe bug in the package.  Would you please use
>> >
>> > reportbug
>> >
>> > to report the issue.  Do you feel able to track down the issue?  May be
>> > some debugging of the source code will shade some light.
>>
>> I think this is solved by Sascha's patch and I uploaded the package
>> without an actual autopkgtest but leaving your script for manual testing
>> for the users.
>>
>> > > Second issue Mummer features mummerplot and run-mummer1 has some
>> faults
>> > > mummerplots have a lot of faulty lines i can't manage to solve them
>> > > run-mummer1 also have some problem about tail command neither i can't
>> > > manage to solve it. But i command line these tests and take pass
>> result.
>> >
>> > H, I fixed the line that is uncompressing the data files and now the
>> > test script seems to pass.  What exactly do you think is wrong?
>>
>> Could you please explain what exactly is wrong with the mummer test
>> after I fixed the compression of the test data?  I'd recommend to always
>> use the `find ...` command since it safely unpacks all gzipped files.
>>
>> > gdpc
>>
>> Uploaded.
>>
>> > mummer (I'll convert this to Git as well)
>>
>> Please explain more verbosely what might be wrong.
>>
>> Further todo suggestions:
>>
>> fastqc
>> kalign
>>
>> > I'll convert kalign to Git.
>>
>> Done
>>
>> probcons
>>
>> Kind regards
>>
>>   Andreas.
>>
>>
>> --
>> http://fam-tille.de
>>
>>
>

Re: Embassy phylipnew - please use freely licensed source of phylip

[Peter Rice]

Hi Andreas,

This was a restoration of the 6.6.0 release files which had been lost 
when the FTP server was reset, and a correction of the file names which 
should have been .660 on the original FTP server.


The same applies to the other EMBASSY packages.

regards,

Peter Rice
EMBOSS Team

On 25/07/2016 10:55, Andreas Tille wrote:

Hi,

I realised that at the EMBASSY download ftpserver[1] files with new
version numbers appeared.  I was specifically keen to check PHYLIPNEW
since I wanted to release a Debian package with the freely licensed
phylip.  Unfortunately I realised that PHYLIPNEW-3.69.660.tar.gz is byte
identical to PHYLIPNEW-3.69.650.tar.gz - so no change in the source code
has happened at all.

I wonder whether this is by mistake or what the version rename might
mean here.  It would be really great if you could base the code on
version 3.696 of phylip since this version has a free license and could
be distributed in Debian main.

Kind regards

   Andreas.


[1] ftp://emboss.open-bio.org/pub/EMBOSS/

Re: Sponsoring request: berkeley-express [RC]

[Andreas Tille]

Uploaded, thanks a lot for your gcc-6 effort.  Andreas.

On Tue, Jul 26, 2016 at 09:24:52PM +0200, Gert Wollny wrote:
> Hi all,
> 
> I've prepared a new upload of berkeley-express [1], changelog reads: 
> 
>   * d/p/gcc-6: Fix compilation with gcc-6, Closes: #811859
>   * cme fix dpkg-control: 
> - update standards version to 3.9.8
> - update to secure packaging urls
>   * d/p/correct-debug-flags: don't force debug flags and 
> dynamically link to BOOST, protobuf and tcmalloc_minimal
>   * d/rules: enable hardening 
> 
> Many thanks, 
> Gert 
> 
> [1] git://@git.debian.org/debian-med/express.git
> 
> 
> 

-- 
http://fam-tille.de

Re: Sponsoring request: berkeley-express [RC]

[Andreas Tille]

I'll take it, Andreas.

On Tue, Jul 26, 2016 at 09:24:52PM +0200, Gert Wollny wrote:
> Hi all,
> 
> I've prepared a new upload of berkeley-express [1], changelog reads: 
> 
>   * d/p/gcc-6: Fix compilation with gcc-6, Closes: #811859
>   * cme fix dpkg-control: 
> - update standards version to 3.9.8
> - update to secure packaging urls
>   * d/p/correct-debug-flags: don't force debug flags and 
> dynamically link to BOOST, protobuf and tcmalloc_minimal
>   * d/rules: enable hardening 
> 
> Many thanks, 
> Gert 
> 
> [1] git://@git.debian.org/debian-med/express.git
> 
> 
> 

-- 
http://fam-tille.de

Sponsoring request: berkeley-express [RC]

[Gert Wollny]

Hi all,

I've prepared a new upload of berkeley-express [1], changelog reads: 

  * d/p/gcc-6: Fix compilation with gcc-6, Closes: #811859
  * cme fix dpkg-control: 
- update standards version to 3.9.8
- update to secure packaging urls
  * d/p/correct-debug-flags: don't force debug flags and 
dynamically link to BOOST, protobuf and tcmalloc_minimal
  * d/rules: enable hardening 

Many thanks, 
Gert 

[1] git://@git.debian.org/debian-med/express.git