Debian Bug report logs - #879622
macs: 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: macs: Please provide autopkgtest

Date: Mon, 23 Oct 2017 16:28:53 +0200

Package: macs
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 4.9.0-3-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 macs depends on:
pn  cython        <none>
ii  libc6         2.24-11+deb9u1
ii  python        2.7.13-2
pn  python-numpy  <none>

macs recommends no packages.

macs suggests no packages.

Message #10 received at 879622@bugs.debian.org (full text, mbox, reply):

From: "Kalou.Katerina" <aik.kalou@gmail.com>

To: 879622@bugs.debian.org

Subject: start working on an autopkgtest

Date: Thu, 18 Jan 2018 14:24:27 +0200

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

Dear all,

 I am starting to work on an autopkgtest for this package. If anyone has
already started working and/or is  interested in this bug , please let me
know :)

Kind regards,

Kate

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

Message #15 received at 879622@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: debian-med@lists.debian.org, 879622@bugs.debian.org

Subject: Re: [autopkgtest 879622]

Date: Sun, 18 Feb 2018 22:24:04 +0100

Dear Katerina,

On Sun, Feb 18, 2018 at 08:32:05PM +0200, Kalou.Katerina wrote:
> I am sorry for the long absence / my PhD thesis is almost finished but it
> took almost all my time the last month! ;)
> 
> I have pushed an new test suite for autopkgtest for the macs package.

Are you sure you pushed the changes.  Please note that all Debian Med
packages were moved to salsa.  Thus you need to set origin to

   git@salsa.debian.org:med-team/macs.git


> Any
> comments and corrections will be much welcome!! In my linux machine the
> 'autopkgtest -- null' command reports a pass.
> 
> In the example folder i have put two sample data that i managed to found at
> 'https://github.com/arq5x/bedtools2'. These two files are '.BED' file
> extensions. The example at the macs package install instructions is using
> the 'BAM' extension , if anyone has any recommendation on where to find
> these, it will be much appreciated!! :)

In any case make sure you document the origin of the example filese in
debian/README.source (may be you add your question also in this file). 

> Finally , i included the files 'README.test',  'macs-example-data.install'
> and 'macs.install', taking inspiration from the previous packages like
> rapmap i worked on. The purpose was to send the examples folder to the
> 'usr/share/doc' directory during installation , i do not know if i did it
> right!

Sounds sensible - I'll check.
 
> Thank you for all the help!!

Thanks to you for working on the test

       Andreas.

-- 
http://fam-tille.de

Message #20 received at 879622@bugs.debian.org (full text, mbox, reply):

From: "Kalou.Katerina" <aik.kalou@gmail.com>

To: Andreas Tille <andreas@an3as.eu>

Cc: debian-med@lists.debian.org, 879622@bugs.debian.org

Subject: Re: [autopkgtest 879622]

Date: Mon, 19 Feb 2018 00:21:35 +0200

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

Dear Andreas,

Thank you for your comments!! I tried to push the files again , i think
that now it worked :)

Kind regards,
Kate

On Sun, Feb 18, 2018 at 11:24 PM, Andreas Tille <andreas@an3as.eu> wrote:

> Dear Katerina,
>
> On Sun, Feb 18, 2018 at 08:32:05PM +0200, Kalou.Katerina wrote:
> > I am sorry for the long absence / my PhD thesis is almost finished but it
> > took almost all my time the last month! ;)
> >
> > I have pushed an new test suite for autopkgtest for the macs package.
>
> Are you sure you pushed the changes.  Please note that all Debian Med
> packages were moved to salsa.  Thus you need to set origin to
>
>    git@salsa.debian.org:med-team/macs.git
>
>
> > Any
> > comments and corrections will be much welcome!! In my linux machine the
> > 'autopkgtest -- null' command reports a pass.
> >
> > In the example folder i have put two sample data that i managed to found
> at
> > 'https://github.com/arq5x/bedtools2'. These two files are '.BED' file
> > extensions. The example at the macs package install instructions is using
> > the 'BAM' extension , if anyone has any recommendation on where to find
> > these, it will be much appreciated!! :)
>
> In any case make sure you document the origin of the example filese in
> debian/README.source (may be you add your question also in this file).
>
> > Finally , i included the files 'README.test',
> 'macs-example-data.install'
> > and 'macs.install', taking inspiration from the previous packages like
> > rapmap i worked on. The purpose was to send the examples folder to the
> > 'usr/share/doc' directory during installation , i do not know if i did it
> > right!
>
> Sounds sensible - I'll check.
>
> > Thank you for all the help!!
>
> Thanks to you for working on the test
>
>        Andreas.
>
> --
> http://fam-tille.de
>
>

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

Message #25 received at 879622@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

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

Cc: 879622@bugs.debian.org

Subject: Re: [autopkgtest 879622]

Date: Mon, 19 Feb 2018 10:01:55 +0100

Dear Kate,

On Mon, Feb 19, 2018 at 12:21:35AM +0200, Kalou.Katerina wrote:
> Thank you for your comments!! I tried to push the files again , i think
> that now it worked :)

I confirm the push worked now.  I've pushed some more commits - partly
related to your work.  Please keep on reading my comments below.
 
> > > Any
> > > comments and corrections will be much welcome!! In my linux machine the
> > > 'autopkgtest -- null' command reports a pass.
> > >
> > > In the example folder i have put two sample data that i managed to found
> > at
> > > 'https://github.com/arq5x/bedtools2'. These two files are '.BED' file
> > > extensions. The example at the macs package install instructions is using
> > > the 'BAM' extension , if anyone has any recommendation on where to find
> > > these, it will be much appreciated!! :)
> >
> > In any case make sure you document the origin of the example filese in
> > debian/README.source (may be you add your question also in this file).

I've seen you have give some (rather vague) pointer in README.test
(which is fine - no need to create an extra README.source.  Besides the
fact that all Debian related stuff needs to be in debian/ dir (I just
moved the file) I wished you would add some more specific pointer.  The
best thing would be something like

    wget URL_to_example_file1
    wget URL_to_example_file2

So everybody can immediately reproduce what you did to get the files.
To express what I mean I did so in the latest commit.  I also left the
files compressed as downloaded which requires an extra file

    debian/source/include-binaries

(dpkg-buildpackage will tell you about this so this is no knowledge you
need to keep by heart. ;-) )

Regarding how to get BAM files instead of BED files I'm hoping for
comments here on the list but for the moment macs2 seems to do something
sensible which should qualify for a first test.

> > > Finally , i included the files 'README.test',
> > 'macs-example-data.install'

The file macs-example-data.install is wrong.  In the other package you
worked on we have created an extra data package.  I do not think that
the amount of extra data in the macs example rectifies an additional
package and thus we have no such package macs-example-data defined in
debian/control.  Thus this file is simply ignored.  You rather need to
put files in debian/macs.examples (and make sure those files are really
existing - since I bumped debian/compat in some unrelated change
mentioning non-existing files has lead to build problems).

> > > and 'macs.install', taking inspiration from the previous packages like
> > > rapmap i worked on. The purpose was to send the examples folder to the
> > > 'usr/share/doc' directory during installation , i do not know if i did it
> > > right!

I've now fixed it - please check all my according commits.

Finally please always add a changelog entry to the package documenting
your changes.  I'd recommen to use the dch tool for this.  For instance
you can do

    dch --team "Add autopkgtest (Closes: #879622)"

specifically the "Closes:" is important to automatically close the bug.
(You can also use `dch --team` and add the string manually with the
editor.)

I would like you to take over the changelog entry (that's why the --team
option - see `man dch`) since I want to give credit to the person who
has written the test and has fixed the bug.

I think the package is ready once you have done the changelog entry and
I'll upload once I have seen your commit.  Yesterday I added a set of
new bugs for packages in need of an autopkgtest.  So there is a plenty
to pick from and as I wrote here before I issued an according GSoC
project proposal (which can be also picked for outreachy as far as I
know).

Kind regards

       Andreas.

-- 
http://fam-tille.de

Message #30 received at 879622@bugs.debian.org (full text, mbox, reply):

From: "Kalou.Katerina" <aik.kalou@gmail.com>

To: Andreas Tille <andreas@an3as.eu>

Cc: Debian Med Project List <debian-med@lists.debian.org>, 879622@bugs.debian.org

Subject: Re: [autopkgtest 879622]

Date: Mon, 19 Feb 2018 20:03:50 +0200

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

Dear Andreas,

Thank you so much for all your comments! I confirm i pushed the changelog
entry , i hope i did it right ;)

I would love to go on with adding an autopkgtest to another package, i was
thinking to continue with rsem (n.890792
<https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=890782> ), if that is ok
for everyone!

I would also kindly like to express my interest to apply to either
outreachy or GSoC. I had a look to the Outreachy announcement for this
round of applications and as i did not see any proposed project by the
debian med team (especially the one about adding autopkgtest suites),  i
was thinking about the GSoC as an alternative. As my PhD thesis will be
ready in the end of March but i will still be a student until the beginning
of June, i was thinking if it would be possible for me to apply.

Anyway, apart of the internships, i would like to continue contributing to
the debian med project , it is a truly unique experience!

Thank you so much again for all the help and comments!

Kind regards,
Kate

On Mon, Feb 19, 2018 at 11:01 AM, Andreas Tille <andreas@an3as.eu> wrote:

> Dear Kate,
>
> On Mon, Feb 19, 2018 at 12:21:35AM +0200, Kalou.Katerina wrote:
> > Thank you for your comments!! I tried to push the files again , i think
> > that now it worked :)
>
> I confirm the push worked now.  I've pushed some more commits - partly
> related to your work.  Please keep on reading my comments below.
>
> > > > Any
> > > > comments and corrections will be much welcome!! In my linux machine
> the
> > > > 'autopkgtest -- null' command reports a pass.
> > > >
> > > > In the example folder i have put two sample data that i managed to
> found
> > > at
> > > > 'https://github.com/arq5x/bedtools2'. These two files are '.BED'
> file
> > > > extensions. The example at the macs package install instructions is
> using
> > > > the 'BAM' extension , if anyone has any recommendation on where to
> find
> > > > these, it will be much appreciated!! :)
> > >
> > > In any case make sure you document the origin of the example filese in
> > > debian/README.source (may be you add your question also in this file).
>
> I've seen you have give some (rather vague) pointer in README.test
> (which is fine - no need to create an extra README.source.  Besides the
> fact that all Debian related stuff needs to be in debian/ dir (I just
> moved the file) I wished you would add some more specific pointer.  The
> best thing would be something like
>
>     wget URL_to_example_file1
>     wget URL_to_example_file2
>
> So everybody can immediately reproduce what you did to get the files.
> To express what I mean I did so in the latest commit.  I also left the
> files compressed as downloaded which requires an extra file
>
>     debian/source/include-binaries
>
> (dpkg-buildpackage will tell you about this so this is no knowledge you
> need to keep by heart. ;-) )
>
> Regarding how to get BAM files instead of BED files I'm hoping for
> comments here on the list but for the moment macs2 seems to do something
> sensible which should qualify for a first test.
>
> > > > Finally , i included the files 'README.test',
> > > 'macs-example-data.install'
>
> The file macs-example-data.install is wrong.  In the other package you
> worked on we have created an extra data package.  I do not think that
> the amount of extra data in the macs example rectifies an additional
> package and thus we have no such package macs-example-data defined in
> debian/control.  Thus this file is simply ignored.  You rather need to
> put files in debian/macs.examples (and make sure those files are really
> existing - since I bumped debian/compat in some unrelated change
> mentioning non-existing files has lead to build problems).
>
> > > > and 'macs.install', taking inspiration from the previous packages
> like
> > > > rapmap i worked on. The purpose was to send the examples folder to
> the
> > > > 'usr/share/doc' directory during installation , i do not know if i
> did it
> > > > right!
>
> I've now fixed it - please check all my according commits.
>
> Finally please always add a changelog entry to the package documenting
> your changes.  I'd recommen to use the dch tool for this.  For instance
> you can do
>
>     dch --team "Add autopkgtest (Closes: #879622)"
>
> specifically the "Closes:" is important to automatically close the bug.
> (You can also use `dch --team` and add the string manually with the
> editor.)
>
> I would like you to take over the changelog entry (that's why the --team
> option - see `man dch`) since I want to give credit to the person who
> has written the test and has fixed the bug.
>
> I think the package is ready once you have done the changelog entry and
> I'll upload once I have seen your commit.  Yesterday I added a set of
> new bugs for packages in need of an autopkgtest.  So there is a plenty
> to pick from and as I wrote here before I issued an according GSoC
> project proposal (which can be also picked for outreachy as far as I
> know).
>
> Kind regards
>
>        Andreas.
>
> --
> http://fam-tille.de
>
>

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

Message #35 received at 879622@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: Debian Med Project List <debian-med@lists.debian.org>, 890792@bugs.debian.org

Cc: 879622@bugs.debian.org

Subject: Re: [autopkgtest 879622]

Date: Mon, 19 Feb 2018 19:53:55 +0100

Dear Katerina,

On Mon, Feb 19, 2018 at 08:03:50PM +0200, Kalou.Katerina wrote:
> Dear Andreas,
> 
> Thank you so much for all your comments! I confirm i pushed the changelog
> entry , i hope i did it right ;)

There is some room for enhancement. ;-)

I'd suggest to use

export DEBEMAIL=aik.kalou@gmail.com
export DEBFULLNAME='Katerina Kalou'

in your environment - than dch knows for sure what user ID to choose.

There is also some care needed to make sure that there is no changelog
entry left for UNRELEASED.  I merged those two entries.  I've pushed and
uploaded now.

> I would love to go on with adding an autopkgtest to another package, i was
> thinking to continue with rsem (n.890792
> <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=890782> ), if that is ok
> for everyone!

I've put the rsem bug in CC.
 
> I would also kindly like to express my interest to apply to either
> outreachy or GSoC. I had a look to the Outreachy announcement for this
> round of applications and as i did not see any proposed project by the
> debian med team (especially the one about adding autopkgtest suites),  i
> was thinking about the GSoC as an alternative. As my PhD thesis will be
> ready in the end of March but i will still be a student until the beginning
> of June, i was thinking if it would be possible for me to apply.

Please note:  I'm *always* confused about all the bureaucracy around.  I
remember that in the past GSoC *and* Outreachy picked from the project
list that has the GSoC headline.  I as a mentor do not mind at all to
what project you subscribe.  I do not even have a clear advise whom to
ask for clarification - sorry. :-(
 
> Anyway, apart of the internships, i would like to continue contributing to
> the debian med project , it is a truly unique experience!

That's really appreciated.  Thank you for this.

> Thank you so much again for all the help and comments!

You are welcome as any contributor

        Andreas.

-- 
http://fam-tille.de

Message #40 received at 879622-close@bugs.debian.org (full text, mbox, reply):

From: Katerina Kalou <aik.kalou@gmail.com>

To: 879622-close@bugs.debian.org

Subject: Bug#879622: fixed in macs 2.1.1.20160309-2

Date: Mon, 19 Feb 2018 19:06:42 +0000

Source: macs
Source-Version: 2.1.1.20160309-2

We believe that the bug you reported is fixed in the latest version of
macs, 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 879622@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Katerina Kalou <aik.kalou@gmail.com> (supplier of updated macs 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: SHA512

Format: 1.8
Date: Mon, 19 Feb 2018 20:00:45 +0200
Source: macs
Binary: macs
Architecture: source
Version: 2.1.1.20160309-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Katerina Kalou <aik.kalou@gmail.com>
Description:
 macs       - Model-based Analysis of ChIP-Seq on short reads sequencers
Closes: 879622
Changes:
 macs (2.1.1.20160309-2) unstable; urgency=medium
 .
   * Team upload.
 .
   [ Andreas Tille ]
   * debian/upstream/metadata:
      - UTF-8 notation of names rather than TeX syntax
      - added eprint
   * d/rules: Do not parse d/changelog
   * Remove Tim Booth and H. Soon Gweon from Uploaders
   * Standards-Version: 4.1.3
   * hardening=+all
   * debhelper 11
 .
   [ Katerina Kalou ]
   * Add autopkgtest (Closes: #879622)
Checksums-Sha1:
 33a4987bffcfbffc0fbfc37abc93f1c21248e8a1 2122 macs_2.1.1.20160309-2.dsc
 ca12f93b4f26a04cf822aaf649af145ee8624e2b 1268092 macs_2.1.1.20160309-2.debian.tar.xz
 35c61957024ad203c14f993b9314f9fe37a924a1 6845 macs_2.1.1.20160309-2_amd64.buildinfo
Checksums-Sha256:
 d9c82f25e5b36088e03f46ae4fa5e695d009920a7846cbab859f39938027b551 2122 macs_2.1.1.20160309-2.dsc
 26a040c1d933c527e50ff4f978620f5ab31f82b87016a04d1d57f291ff545570 1268092 macs_2.1.1.20160309-2.debian.tar.xz
 6c63425f72159e7b69bd54585d0e72e2136e747cdec60af25285321920e351c1 6845 macs_2.1.1.20160309-2_amd64.buildinfo
Files:
 34d7bf624a4a4a20ada556abd6d7719c 2122 science optional macs_2.1.1.20160309-2.dsc
 7e985c10fecbb4df91a6406b71a11dea 1268092 science optional macs_2.1.1.20160309-2.debian.tar.xz
 0020e12825a0fd3a64d654ec728655cb 6845 science optional macs_2.1.1.20160309-2_amd64.buildinfo

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