Debian Bug report logs - #848326
src:mapdamage: Please add 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: src:mapdamage: Please add autopkgtest

Date: Fri, 16 Dec 2016 11:57:31 +0100

Package: src:mapdamage
Severity: normal
Tags: newcomer

Hi,

I'm filing a set of bugs for packages where an autopkgtest would make
some sense considering its importance due to the number of active users
(based on popcon values).  Since adding tests should be a task for
newcomers the bugs will be tagged that way and I consider these bugs
as reasonable targets for our advent bug squashing party.

So please add an autopkgtest to mapdamage.

Kind regards

      Andreas.


-- System Information:
Debian Release: 8.6
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
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Init: systemd (via /run/systemd/system)

Message #10 received at 848326@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: Debian Med Project List <debian-med@lists.debian.org>, 848326@bugs.debian.org

Subject: Reminding about advent bug squashing party with an easy target (Was: Bug#848326: src:mapdamage: Please add autopkgtest)

Date: Thu, 22 Dec 2016 16:38:24 +0100

Hi,

if you have no idea how to craft the test I just commited some code
piece which runs an internal test of a specific module.  On the home
page you can find detailed instructions for testing:

   https://ginolhac.github.io/mapDamage/#a5

You just need to find a BAM file and a fasta reference as example data
to run these.
 
Kind regards

      Andreas.

-- 
http://fam-tille.de

Message #15 received at 848326@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: debian-med@lists.debian.org, 848326@bugs.debian.org

Subject: Re: Outreachy 2017 (Round 14)

Date: Mon, 27 Mar 2017 08:40:37 +0200

Hi Nadiya,

On Sun, Mar 26, 2017 at 02:31:47PM -0700, Nadiya Sitdykova wrote:
> I generated output files for run-unit-test and run-r-packages-check the
> exact same way you described.

Regarding run-r-package-check.out.  Could you please post the result of

  apt-cache policy r-cran-rcppgsl


> On Sun, Mar 26, 2017 at 1:25 PM, Andreas Tille <andreas@an3as.eu> wrote:
> >
> >  LANG=C . run-unit-test 2>&1 | tee > run-unit-test.out
> >
> > I get the attached build log - but this does not contain the string
> > Rcpp.  This needs to be investigated.

It really seems that your r-cran-rcppgsl installation is broken.  You
might like to try

  apt-get source r-cran-rcppgsl
  LC_ALL=C R --no-save < r-cran-rcppgsl*/tests/doRUnit.R

to make sure this R module works properly.  I admit I have not
experienced severy problems with R modules on clean Debian systems.

Once we get r-cran-rcppgsl working properly you will probably get the
same errors as I observed.

Kind regards

      Andreas.

-- 
http://fam-tille.de

Message #20 received at 848326@bugs.debian.org (full text, mbox, reply):

From: Nadiya Sitdykova <rovenskasa@gmail.com>

To: Andreas Tille <andreas@an3as.eu>

Cc: debian-med@lists.debian.org, 848326@bugs.debian.org

Subject: Re: Outreachy 2017 (Round 14)

Date: Mon, 27 Mar 2017 13:20:30 -0700

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

Here is the output of apt-cache policy r-cran-rcppgsl:

r-cran-rcppgsl:
  Installed: 0.3.2-1
  Candidate: 0.3.2-1
  Version table:
 *** 0.3.2-1 500
        500 http://ftp.us.debian.org/debian sid/main amd64 Packages
        100 /var/lib/dpkg/status

tests for r-cran-rcppgsl crashed because of absence of gsl-config. So I've
done some googling, installed gsl-devel and it helped with
run-r-packages-check but I still didn't get the same error for
run-unit-test as you, I got:

    Compilation ERROR, function(s)/method(s) not created! /usr/bin/ld:
cannot find -llapack
/usr/bin/ld: cannot find -lblas

So I also installed libopenblas-base and libopenblas-dev. NOW I got the
same error as you. I looked into it, and it seems that the problem is that
in the test data nucleotide frequency array looks like 0.5555556 0.2222222
0.2222222 0,
i.e. frequence for T is zero, which is not what expected by mapdamage from
line 4 in
https://github.com/ginolhac/mapDamage/blob/master/mapdamage/Rscripts/stats/function.R#L4
Even though documentation doesn't say that zero frequences are not allowed.

I changed reference file from "CGAGGGCGA" to "TGAAAACGA" (so all frequences
> 0) and now it executes without errors.

Regards, Nadiya

On Sun, Mar 26, 2017 at 11:40 PM, Andreas Tille <andreas@an3as.eu> wrote:

> Hi Nadiya,
>
> On Sun, Mar 26, 2017 at 02:31:47PM -0700, Nadiya Sitdykova wrote:
> > I generated output files for run-unit-test and run-r-packages-check the
> > exact same way you described.
>
> Regarding run-r-package-check.out.  Could you please post the result of
>
>   apt-cache policy r-cran-rcppgsl
>
>
> > On Sun, Mar 26, 2017 at 1:25 PM, Andreas Tille <andreas@an3as.eu> wrote:
> > >
> > >  LANG=C . run-unit-test 2>&1 | tee > run-unit-test.out
> > >
> > > I get the attached build log - but this does not contain the string
> > > Rcpp.  This needs to be investigated.
>
> It really seems that your r-cran-rcppgsl installation is broken.  You
> might like to try
>
>   apt-get source r-cran-rcppgsl
>   LC_ALL=C R --no-save < r-cran-rcppgsl*/tests/doRUnit.R
>
> to make sure this R module works properly.  I admit I have not
> experienced severy problems with R modules on clean Debian systems.
>
> Once we get r-cran-rcppgsl working properly you will probably get the
> same errors as I observed.
>
> Kind regards
>
>       Andreas.
>
> --
> http://fam-tille.de
>
>

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

Message #25 received at 848326@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: debian-med@lists.debian.org, 848326@bugs.debian.org

Subject: Re: Outreachy 2017 (Round 14)

Date: Mon, 27 Mar 2017 23:03:05 +0200

Hi Nadiya,

thanks for your patience.  It seems we have spotted here a really buggy
package with missing dependencies.

On Mon, Mar 27, 2017 at 01:20:30PM -0700, Nadiya Sitdykova wrote:
> Here is the output of apt-cache policy r-cran-rcppgsl:
> 
> r-cran-rcppgsl:
>   Installed: 0.3.2-1
>   Candidate: 0.3.2-1
>   Version table:
>  *** 0.3.2-1 500
>         500 http://ftp.us.debian.org/debian sid/main amd64 Packages
>         100 /var/lib/dpkg/status
> 
> tests for r-cran-rcppgsl crashed because of absence of gsl-config.

Do you want to say that after installing r-cran-rcppgsl on a clean
system is not able to run the test suite of r-cran-rcppgsl itself and
the installation of gsl-config is required to do so?

Or is it rather that gsl-config is required to run the test suite of
mapdamage?

> So I've
> done some googling, installed gsl-devel and it helped with
> run-r-packages-check but I still didn't get the same error for
> run-unit-test as you, I got:
> 
>     Compilation ERROR, function(s)/method(s) not created! /usr/bin/ld:
> cannot find -llapack
> /usr/bin/ld: cannot find -lblas

Hmmm, at what point of the test is the linker ld called?
 
> So I also installed libopenblas-base and libopenblas-dev. NOW I got the
> same error as you.

I wonder in how far the development package is needed in the test suite.
May be it would be enlightening if you always would write down the
command you called and add a larger chunk of the resulting output.

As you describe things it seems this is another missing dependency.

> I looked into it, and it seems that the problem is that
> in the test data nucleotide frequency array looks like 0.5555556 0.2222222
> 0.2222222 0,
> i.e. frequence for T is zero, which is not what expected by mapdamage from
> line 4 in
> https://github.com/ginolhac/mapDamage/blob/master/mapdamage/Rscripts/stats/function.R#L4
> Even though documentation doesn't say that zero frequences are not allowed.
> 
> I changed reference file from "CGAGGGCGA" to "TGAAAACGA" (so all frequences
> > 0) and now it executes without errors.

Would you mind reporting this in the upstream issue tracker?
 
Thanks for your patient work on this

       Andreas.

-- 
http://fam-tille.de

Message #30 received at 848326@bugs.debian.org (full text, mbox, reply):

From: Nadiya Sitdykova <rovenskasa@gmail.com>

To: Andreas Tille <andreas@an3as.eu>

Cc: debian-med@lists.debian.org, 848326@bugs.debian.org

Subject: Re: Outreachy 2017 (Round 14)

Date: Mon, 27 Mar 2017 14:52:25 -0700

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

1) Yes, I mean after I tried

  apt-get source r-cran-rcppgsl
  LC_ALL=C R --no-save < r-cran-rcppgsl*/tests/doRUnit.R

There was an error "gsl-config not found". Unfortunately, I didn't save
that log and can't reproduce it now =(

2) I executed autopkgtest . -- null and run-unit-test failed after linker
call, I saved that log so it's attached

3) Done

On Mon, Mar 27, 2017 at 2:03 PM, Andreas Tille <andreas@an3as.eu> wrote:

> Hi Nadiya,
>
> thanks for your patience.  It seems we have spotted here a really buggy
> package with missing dependencies.
>
> On Mon, Mar 27, 2017 at 01:20:30PM -0700, Nadiya Sitdykova wrote:
> > Here is the output of apt-cache policy r-cran-rcppgsl:
> >
> > r-cran-rcppgsl:
> >   Installed: 0.3.2-1
> >   Candidate: 0.3.2-1
> >   Version table:
> >  *** 0.3.2-1 500
> >         500 http://ftp.us.debian.org/debian sid/main amd64 Packages
> >         100 /var/lib/dpkg/status
> >
> > tests for r-cran-rcppgsl crashed because of absence of gsl-config.
>
> Do you want to say that after installing r-cran-rcppgsl on a clean
> system is not able to run the test suite of r-cran-rcppgsl itself and
> the installation of gsl-config is required to do so?
>
> Or is it rather that gsl-config is required to run the test suite of
> mapdamage?
>
> > So I've
> > done some googling, installed gsl-devel and it helped with
> > run-r-packages-check but I still didn't get the same error for
> > run-unit-test as you, I got:
> >
> >     Compilation ERROR, function(s)/method(s) not created! /usr/bin/ld:
> > cannot find -llapack
> > /usr/bin/ld: cannot find -lblas
>
> Hmmm, at what point of the test is the linker ld called?
>
> > So I also installed libopenblas-base and libopenblas-dev. NOW I got the
> > same error as you.
>
> I wonder in how far the development package is needed in the test suite.
> May be it would be enlightening if you always would write down the
> command you called and add a larger chunk of the resulting output.
>
> As you describe things it seems this is another missing dependency.
>
> > I looked into it, and it seems that the problem is that
> > in the test data nucleotide frequency array looks like 0.5555556
> 0.2222222
> > 0.2222222 0,
> > i.e. frequence for T is zero, which is not what expected by mapdamage
> from
> > line 4 in
> > https://github.com/ginolhac/mapDamage/blob/master/
> mapdamage/Rscripts/stats/function.R#L4
> > Even though documentation doesn't say that zero frequences are not
> allowed.
> >
> > I changed reference file from "CGAGGGCGA" to "TGAAAACGA" (so all
> frequences
> > > 0) and now it executes without errors.
>
> Would you mind reporting this in the upstream issue tracker?
>
> Thanks for your patient work on this
>
>        Andreas.
>
> --
> http://fam-tille.de
>
>

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

[run-unit-test.out (application/octet-stream, attachment)]

Message #35 received at 848326-close@bugs.debian.org (full text, mbox, reply):

From: Nadiya Sitdykova <rovenskasa@gmail.com>

To: 848326-close@bugs.debian.org

Subject: Bug#848326: fixed in mapdamage 2.0.6+dfsg-2

Date: Thu, 30 Mar 2017 11:48:49 +0000

Source: mapdamage
Source-Version: 2.0.6+dfsg-2

We believe that the bug you reported is fixed in the latest version of
mapdamage, 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 848326@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Nadiya Sitdykova <rovenskasa@gmail.com> (supplier of updated mapdamage 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, 23 Mar 2017 21:34:41 -0700
Source: mapdamage
Binary: mapdamage
Architecture: source all
Version: 2.0.6+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nadiya Sitdykova <rovenskasa@gmail.com>
Description:
 mapdamage  - tracking and quantifying damage patterns in ancient DNA sequences
Closes: 848326 859090 859091
Changes:
 mapdamage (2.0.6+dfsg-2) unstable; urgency=medium
 .
   * Team upload
 .
   [ Andreas Tille ]
   * Spelling
 .
   [ Nadiya Sitdykova ]
   * Add simple tests for examples
   * Move pysam dependency from tests/control to control as it's needed
     not only for test, but for package
   * Add test checking stdin redirect
   * Add simple test to demonstrate the problems with installing
     r-cran-rcppgsl package
   * Edit path to seqtk in composition.py
     Closes: #859090
   * Fix typo in tests/control
   * Add patch to fix quantile call to remove NA and NaNs
   * Add dependency providing liblapack.so and libblas.so
     Closes: #859091
   * Add file with reference containing all types of nucleotides
   * Add information how to check R libraries and what to do in case of errors
     to README.test
   * Provide tests for examples from documentation
     Closes: #848326
   * Fixed typo in README.test
Checksums-Sha1:
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 a77076da7aa059f69c41fdb7c898f4c1eedcb239 6928 mapdamage_2.0.6+dfsg-2.debian.tar.xz
 373003c4959296c5c84b60cb09661187b3f54325 38800 mapdamage_2.0.6+dfsg-2_all.deb
 b9633ab8a3dbdd144d71597b02ebff511b71fe66 6027 mapdamage_2.0.6+dfsg-2_amd64.buildinfo
Checksums-Sha256:
 154f033951fd2dd83e89b49cbc4f3aa7852ea4df1ec412c1a1d103039d1cd597 2090 mapdamage_2.0.6+dfsg-2.dsc
 4fe17e581cc172d8feff429be2caed6a29db9ee777f03011dddbc1366c672cb8 6928 mapdamage_2.0.6+dfsg-2.debian.tar.xz
 006f25238ce436c5c0b595bdb03cca26464f6beeb6c4c847ec78a358c5c38e9b 38800 mapdamage_2.0.6+dfsg-2_all.deb
 4a934164110d0ae8f3fa7a43b51ca982bb3da369b3e5c042358c61770c84f458 6027 mapdamage_2.0.6+dfsg-2_amd64.buildinfo
Files:
 62f591c0487e038c18cbb5c35ffe34f5 2090 science optional mapdamage_2.0.6+dfsg-2.dsc
 b7af5a220b8f7549c14e4ff4c21c91bd 6928 science optional mapdamage_2.0.6+dfsg-2.debian.tar.xz
 aff21d92226b52602d776d344588dc7e 38800 science optional mapdamage_2.0.6+dfsg-2_all.deb
 f901d23ec7c23b93aad78d869e0f270d 6027 science optional mapdamage_2.0.6+dfsg-2_amd64.buildinfo

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