Debian Bug report logs - #890783
prodigal: Please provide autopkgtest

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: prodigal: Please provide autopkgtest

Date: Sun, 18 Feb 2018 22:07:32 +0100

Package: prodigal
Severity: minor

Please provide autopkgtest.

-- System Information:
Debian Release: 9.0
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.9.0-5-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages prodigal depends on:
ii  libc6  2.24-11+deb9u1

prodigal recommends no packages.

prodigal suggests no packages.

Message #10 received at 890783@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: debian-med@lists.debian.org

Subject: Re: Autopkgtest for prodigal (#890783)

Date: Fri, 16 Mar 2018 17:48:35 +0100

Dear Liubov,

On Fri, Mar 16, 2018 at 01:26:18PM +0000, Liubov Chuprikova wrote:
> I have finished and pushed an *autopkgtest *for *prodigal

:-)

> *and also updated
> to the resent standards (by analogy with those changes you've made for
> *coils*).

Very good.  You seem to gain for extra scoring points. ;-)
BTW, when adapting debhelper you need to change two things:

   d/compat (I did so)
   d/control (which you did)

>  Please, have a look at this commit
> <https://salsa.debian.org/med-team/prodigal/commit/10458cc5b6f9e9f9116206f50e291971e2132744>
> .

I'll check soon.
 
> I included a genome sequence from NCBI as test data. Should I indicate the
> source of this data somewhere in the package (e.g., in Readme.tests)?

I think the best place would be debian/copyright since a data file
should come with a license.  I would say something like


Files: debian/tests/test-data
Copyright: yyyy-yyyy Copyright-Owner
License:
Comment:
  This file was obtained by
    wget URL


would be the most precise form we could use.

> Could you please help me with *lintian* messages 1
> <https://lintian.debian.org/tags/hardening-no-fortify-functions.html> and 2

I consider this a false positive - feel free to ignore (but extra
points that you care for the lintian info!)

> <https://lintian.debian.org/tags/hardening-no-bindnow.html>?

Pushed a fix for the hardening options.

> I try not to
> be neglectful about *E *and *W* flags, but there are always some
> information messages. Should I be worried about them?

I usually try to get rid of these to some extend.  Sometimes I'm fixing
even spellings in quilt patches.  I'm doing so if I consider "my time
well spent".  The latter is not always the case.  Two reasons would be:

   1. Upstream is dead any nobody will care (so my patches will not
      become invalid by frequent upstream updates)

   2. Upstream is very active and I have good reasons to assume that
      they will care and take over the patch (in this case I decide
      between quilt patches and using the issue tracker of upstream.

The short answer about lintian issues is: It depends.
 
> With regards,

I'm very happy about your work and your extra care that reaches
beyond the actual task to write tests.

Kind regards

       Andreas.

-- 
http://fam-tille.de

Message #15 received at 890783@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: debian-med@lists.debian.org

Cc: 890783@bugs.debian.org

Subject: Re: Bug#890783: Autopkgtest for prodigal (#890783)

Date: Fri, 16 Mar 2018 18:45:36 +0100

On Fri, Mar 16, 2018 at 05:48:35PM +0100, Andreas Tille wrote:
> 
> >  Please, have a look at this commit
> > <https://salsa.debian.org/med-team/prodigal/commit/10458cc5b6f9e9f9116206f50e291971e2132744>
> > .
> 
> I'll check soon.

The test itself seems technically OK.  Once we have the proper copyright
for it I'd upload.
  
> > I included a genome sequence from NCBI as test data. Should I indicate the
> > source of this data somewhere in the package (e.g., in Readme.tests)?
> 
> I think the best place would be debian/copyright since a data file
> should come with a license.  I would say something like
> 
> 
> Files: debian/tests/test-data
> Copyright: yyyy-yyyy Copyright-Owner
> License:
> Comment:
>   This file was obtained by
>     wget URL

Please let us know here on the list if you spot any problem to fill
in the details.
 
Kind regards

       Andreas. 

-- 
http://fam-tille.de

Message #20 received at 890783@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: Andreas Tille <andreas@an3as.eu>

Cc: debian-med@lists.debian.org, 890783@bugs.debian.org

Subject: Re: Bug#890783: Autopkgtest for prodigal (#890783)

Date: Mon, 19 Mar 2018 12:47:38 +0000

[Message part 1 (text/plain, inline)]

Hi Andreas,


> On Fri, Mar 16, 2018 at 05:48:35PM +0100, Andreas Tille wrote:
>
> > > I included a genome sequence from NCBI as test data. Should I indicate
> the
> > > source of this data somewhere in the package (e.g., in Readme.tests)?
> >
> > I think the best place would be debian/copyright since a data file
> > should come with a license.  I would say something like
> >
> >
> > Files: debian/tests/test-data
> > Copyright: yyyy-yyyy Copyright-Owner
> > License:
> > Comment:
> >   This file was obtained by
> >     wget URL
>
> Please let us know here on the list if you spot any problem to fill
> in the details.


I have tried to find the information that should be placed in d/copyright,
but unfortunately, I don't have any experience with this kind of stuff. So
this is what I have found so far:

   - I downloaded the test sequence from the Ensemble Bacteria, which is an
   online database of EMBL-EBI. At the bottom of the sequence page
   <http://bacteria.ensembl.org/Candidatus_carsonella_ruddii_dc/Info/Index>,
   it is indicated "Ensembl Bacteria release 38 - January 2018 © EMBL-EBI". I
   couldn't find any license they may have for the data, except that Terms
   of Use <https://www.ebi.ac.uk/about/terms-of-use> states: "EMBL-EBI
   itself places no additional restrictions on the use or redistribution of
   the data available via its online services other than those provided by the
   original data owners."
   - At first, the sequence was deposited in the GenBank database (as said
   in this paper
   <http://www.cell.com/current-biology/fulltext/S0960-9822(13)00752-5>). I
   didn't find if the GenBank has copyright, but they say here
   <https://www.ncbi.nlm.nih.gov/genbank/>: "NCBI places no restrictions on
   the use or distribution of the GenBank data. However, some submitters
   may claim patent, copyright, or other intellectual property rights in all
   or a portion of the data they have submitted."
   - Finally, I have found that the sequence itself has no patent (this had
   to be indicated in the field LOCUS of the GenBank file
   <https://www.ncbi.nlm.nih.gov/nuccore/CP003467?report=genbank> as PAT).
   I suspect the sequence has no copyright as well, although I can't find a
   confirmation.

Could you, please, point me in the right direction. I feel like I'm getting
stuck.

Thank you,
Liubov

[Message part 2 (text/html, inline)]

Message #25 received at 890783@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: Debian Med Project List <debian-med@lists.debian.org>

Cc: 890783@bugs.debian.org

Subject: Re: Bug#890783: Autopkgtest for prodigal (#890783)

Date: Mon, 19 Mar 2018 14:14:33 +0100

Dear Liubov,

On Mon, Mar 19, 2018 at 12:47:38PM +0000, Liubov Chuprikova wrote:
> > Please let us know here on the list if you spot any problem to fill
> > in the details.
> 
> 
> I have tried to find the information that should be placed in d/copyright,
> but unfortunately, I don't have any experience with this kind of stuff. So
> this is what I have found so far:
> 
>    - I downloaded the test sequence from the Ensemble Bacteria, which is an
>    online database of EMBL-EBI. At the bottom of the sequence page
>    <http://bacteria.ensembl.org/Candidatus_carsonella_ruddii_dc/Info/Index>,
>    it is indicated "Ensembl Bacteria release 38 - January 2018 © EMBL-EBI". I
>    couldn't find any license they may have for the data, except that Terms
>    of Use <https://www.ebi.ac.uk/about/terms-of-use> states: "EMBL-EBI
>    itself places no additional restrictions on the use or redistribution of
>    the data available via its online services other than those provided by the
>    original data owners."
>    - At first, the sequence was deposited in the GenBank database (as said
>    in this paper
>    <http://www.cell.com/current-biology/fulltext/S0960-9822(13)00752-5>). I
>    didn't find if the GenBank has copyright, but they say here
>    <https://www.ncbi.nlm.nih.gov/genbank/>: "NCBI places no restrictions on
>    the use or distribution of the GenBank data. However, some submitters
>    may claim patent, copyright, or other intellectual property rights in all
>    or a portion of the data they have submitted."
>    - Finally, I have found that the sequence itself has no patent (this had
>    to be indicated in the field LOCUS of the GenBank file
>    <https://www.ncbi.nlm.nih.gov/nuccore/CP003467?report=genbank> as PAT).
>    I suspect the sequence has no copyright as well, although I can't find a
>    confirmation.
> 
> Could you, please, point me in the right direction. I feel like I'm getting
> stuck.

Thanks for this elaborate information.  I tried my best to condensate it
into d/copyright.  The rule should be that we provide information to the
best of our knowledge (but not more ;-) ).  Please review and add at
least a line

   wget ...

(see FIXME) and may be other information you (as a scientist) might
consider helpful which I might have missed.

Hope this helps

       Andreas.

-- 
http://fam-tille.de

Message #30 received at 890783@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: Andreas Tille <andreas@an3as.eu>

Cc: Debian Med Project List <debian-med@lists.debian.org>, 890783@bugs.debian.org

Subject: Re: Bug#890783: Autopkgtest for prodigal (#890783)

Date: Mon, 19 Mar 2018 15:45:38 +0000

[Message part 1 (text/plain, inline)]

Dear Andreas,

пн, 19 мар. 2018 г. в 14:14, Andreas Tille <andreas@an3as.eu>:

> Dear Liubov,
>
> On Mon, Mar 19, 2018 at 12:47:38PM +0000, Liubov Chuprikova wrote:
>
> > I have tried to find the information that should be placed in
> d/copyright,
> > but unfortunately, I don't have any experience with this kind of stuff.
> So
> > this is what I have found so far:
> >
> >    - I downloaded the test sequence from the Ensemble Bacteria, which is
> an
> >    online database of EMBL-EBI. At the bottom of the sequence page
> >    <
> http://bacteria.ensembl.org/Candidatus_carsonella_ruddii_dc/Info/Index>,
> >    it is indicated "Ensembl Bacteria release 38 - January 2018 ©
> EMBL-EBI". I
> >    couldn't find any license they may have for the data, except that
> Terms
> >    of Use <https://www.ebi.ac.uk/about/terms-of-use> states: "EMBL-EBI
> >    itself places no additional restrictions on the use or redistribution
> of
> >    the data available via its online services other than those provided
> by the
> >    original data owners."
> >    - At first, the sequence was deposited in the GenBank database (as
> said
> >    in this paper
> >    <http://www.cell.com/current-biology/fulltext/S0960-9822(13)00752-5>).
> I
> >    didn't find if the GenBank has copyright, but they say here
> >    <https://www.ncbi.nlm.nih.gov/genbank/>: "NCBI places no
> restrictions on
> >    the use or distribution of the GenBank data. However, some submitters
> >    may claim patent, copyright, or other intellectual property rights in
> all
> >    or a portion of the data they have submitted."
> >    - Finally, I have found that the sequence itself has no patent (this
> had
> >    to be indicated in the field LOCUS of the GenBank file
> >    <https://www.ncbi.nlm.nih.gov/nuccore/CP003467?report=genbank> as
> PAT).
> >    I suspect the sequence has no copyright as well, although I can't
> find a
> >    confirmation.
> >
> > Could you, please, point me in the right direction. I feel like I'm
> getting
> > stuck.
>
> Thanks for this elaborate information.  I tried my best to condensate it
> into d/copyright.  The rule should be that we provide information to the
> best of our knowledge (but not more ;-) ).  Please review and add at
> least a line
>
>    wget ...


>
(see FIXME) and may be other information you (as a scientist) might
> consider helpful which I might have missed.
>
>
Thank you for help! I have added wget link, but it is quite long. Is it ok
or it would be better to split it into several lines? Plus, I have replaced
the link to the journal article by the one containing DOI (which is more
stable).

If there is nothing additional to change, could you please check and upload
the package?

Regards,
Liubov

[Message part 2 (text/html, inline)]

Message #35 received at 890783-close@bugs.debian.org (full text, mbox, reply):

From: Liubov Chuprikova <chuprikovalv@gmail.com>

To: 890783-close@bugs.debian.org

Subject: Bug#890783: fixed in prodigal 1:2.6.3-2

Date: Mon, 19 Mar 2018 18:40:03 +0000

Source: prodigal
Source-Version: 1:2.6.3-2

We believe that the bug you reported is fixed in the latest version of
prodigal, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 890783@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Liubov Chuprikova <chuprikovalv@gmail.com> (supplier of updated prodigal package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Thu, 15 Mar 2018 23:36:47 +0000
Source: prodigal
Binary: prodigal
Architecture: source
Version: 1:2.6.3-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Liubov Chuprikova <chuprikovalv@gmail.com>
Description:
 prodigal   - Microbial (bacterial and archaeal) gene finding program
Closes: 890783
Changes:
 prodigal (1:2.6.3-2) unstable; urgency=medium
 .
   [ Liubov Chuprikova ]
   * Team upload.
   * Fix "Please provide autopkgtest" Autopkgtest added
     (Closes: #890783)
   * Standards-Version: 4.1.3
   * debhelper 11
 .
   [ Andreas Tille ]
   * Fix hardening options
Checksums-Sha1:
 128711bc62f526b11dd54a620e3dd4a5da49cf50 2004 prodigal_2.6.3-2.dsc
 102e7d500570f1c4702e806173aa19807f1550e1 48596 prodigal_2.6.3-2.debian.tar.xz
 ce946ac52a0e762bf487c0b6d93bb95a22d069b5 13268 prodigal_2.6.3-2_source.buildinfo
Checksums-Sha256:
 ed51ae4d970f8ddc5df7781ec7aec7daacb0e379a61e539f293c81bb4ebc60d7 2004 prodigal_2.6.3-2.dsc
 59390650a1a833ef2e76f4bbb50259b9a878e106f0097eb4c2de1c493b47a5dd 48596 prodigal_2.6.3-2.debian.tar.xz
 4dbbc6a0a576b227c2d26d04ecde632331250f89d9ff54d41b1749ac243e7aba 13268 prodigal_2.6.3-2_source.buildinfo
Files:
 0c848b9e0a61fb1b7088bf8c7eee556b 2004 science optional prodigal_2.6.3-2.dsc
 0128cc6accbe81e130948738d5fdcd53 48596 science optional prodigal_2.6.3-2.debian.tar.xz
 93b4de1f727fab215f848ede8b142759 13268 science optional prodigal_2.6.3-2_source.buildinfo

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