Debian Bug report logs - #879616
rapmap: 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: rapmap: Please provide autopkgtest

Date: Mon, 23 Oct 2017 15:58:33 +0200

Package: rapmap
Severity: minor

Hi,

please provide an autopkgtest for rapmap.

The commands to run can be obtained from the build time test inside
source code in

    cmake/TestQuasiMap.cmake
    cmake/TestQuasiMapPerfectHash.cmake

Kind regards

        Andreas.


-- 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)

Message #10 received at 879616@bugs.debian.org (full text, mbox, reply):

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

To: 879616@bugs.debian.org

Subject: rapmap: start working on autopkgtest

Date: Sun, 17 Dec 2017 13:42:37 +0200

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

Dear all,

 I will start working on autopkgtest for the rapmap. If anyone has already
started working and/or is
interested in this bug let me know! :)

Kind regards,
Katerina

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

Message #15 received at 879616@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

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

Cc: debian-med@lists.debian.org

Subject: Re: bug_879616 [rapmap_autopkgtest]

Date: Sat, 13 Jan 2018 00:23:51 +0100

Dear Kate,

thanks again for working on the autopkgtest.

On Wed, Jan 10, 2018 at 08:38:32PM +0200, Kalou.Katerina wrote:
> 
> I am currently trying to provide a unit test for rapmap (closing bug n.
> 879616 <879616@bugs.debian.org>). The test until now, is just :
> 
> 'pkg="rapmap"
> ln -s ~/spdlog/include/spdlog/ ~/${pkg}/include

Hmmm, that's wrong as well as the dependencies you added in
debian/tests/control are wrong.  These packages are Build-Depends
to build the package.  However, the test runs on the just built
package to there is no need to compile any more.
 
> cp -a ${pkg}/* $AUTOPKGTEST_TMP

That's also not the best idea.  For the line below you only need
the test data not the whole source tree.

> rapmap quasiindex -t transcripts.fasta -i sample_quasi_index'

To let this work you need the actual data files.  In "usual"
autopkgtests you take these from the source directory.  However, in
Debian Med we established a method where the user can run the test as a
user example as well.  To approach this I added a new package which
included the example data and adds the run-unit-test to this package
(besides a README.test file).

> However, the build fails giving me the error :
> 'In file included from
> /tmp/autopkgtest.LNHf4Z/build.kpG/real-tree/src/RapMapIndexer.cpp:45:0:
> /tmp/autopkgtest.LNHf4Z/build.kpG/real-tree/include/RapMapUtils.hpp:34:29:
> fatal error: spdlog/fmt/ostr.h: No such file or directory
> compilation terminated.
> src/CMakeFiles/rapmap.dir/build.make:89: recipe for target
> 'src/CMakeFiles/rapmap.dir/RapMapIndexer.cpp.o' failed
> make[4]: *** [src/CMakeFiles/rapmap.dir/RapMapIndexer.cpp.o] Error 1'
> 
> When i manually include a symbolic link to the file as
> ln -s ~/spdlog/include/spdlog/ ~/$rapmap/include
> the build succeeds

As I said this is somehow wrong since in autopkgtest no compilation
is needed.  I removed all this.  (Please also make sure you will not
commit swap files ;-) )
 
> However , when i include that line in the autopkgtest it fails. I have read
> that it is not possible to include symbolic links in an autopkgtest? I will
> keep searching for a solution to this, but any helpful hint would be
> appreciated :)

No idea about this and why this is done.
 
I think to finalise the test it would make sense to compare the test
result with the result that was obtained at compile time.  Would you
mind adding this to confirm that you understood the principle and the
changes I did?

Kind regards

        Andreas.

-- 
http://fam-tille.de

Message #20 received at 879616-close@bugs.debian.org (full text, mbox, reply):

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

To: 879616-close@bugs.debian.org

Subject: Bug#879616: fixed in rapmap 0.5.0+dfsg-3

Date: Thu, 18 Jan 2018 13:00:25 +0000

Source: rapmap
Source-Version: 0.5.0+dfsg-3

We believe that the bug you reported is fixed in the latest version of
rapmap, 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 879616@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 rapmap 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: Fri, 12 Jan 2018 18:55:20 +0100
Source: rapmap
Binary: rapmap rapmap-example-data
Architecture: source amd64 all
Version: 0.5.0+dfsg-3
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:
 rapmap     - rapid sensitive and accurate DNA read mapping via quasi-mapping
 rapmap-example-data - example data for rapmap - rapid sensitive and accurate DNA read m
Closes: 879616
Changes:
 rapmap (0.5.0+dfsg-3) unstable; urgency=medium
 .
   * Team upload
 .
   [ Andreas Tille ]
   * Add binary package containing example data
   * debhelper 11
   * Standards-Version: 4.1.3
 .
   [ Katerina Kalou ]
   * Provide autopkgtest
     Closes: #879616
Checksums-Sha1:
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 ead4409c5853a56d5ae49b66e338411f69a157d5 8780 rapmap_0.5.0+dfsg-3.debian.tar.xz
 c8702ef6bdcfe0e64fe11a3e455cd651e109fc66 7226552 rapmap-dbgsym_0.5.0+dfsg-3_amd64.deb
 6d4fa30b1be4cae3adaf82d31c9d76091e095401 411208 rapmap-example-data_0.5.0+dfsg-3_all.deb
 3fab37b84e77d5b8bf4438455a14ec5786a977d0 7533 rapmap_0.5.0+dfsg-3_amd64.buildinfo
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Checksums-Sha256:
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 abfbbcbf76cbb2291c7aece4ab753ba8e518d34e1cc1928e0f2606099917c39b 7533 rapmap_0.5.0+dfsg-3_amd64.buildinfo
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Files:
 3cca0cefb88ebcb2d889251a79ecd8e3 2235 science optional rapmap_0.5.0+dfsg-3.dsc
 a6d81b4ba0ff19f4e971e67f888750d7 8780 science optional rapmap_0.5.0+dfsg-3.debian.tar.xz
 81c540c379e6214875a13332a5f34f03 7226552 debug optional rapmap-dbgsym_0.5.0+dfsg-3_amd64.deb
 6c5ce24f8a8934d22b8ed092d1090cca 411208 science optional rapmap-example-data_0.5.0+dfsg-3_all.deb
 35a1b8d546072f129da46c9b508e2c9c 7533 science optional rapmap_0.5.0+dfsg-3_amd64.buildinfo
 1bf763661de10f45833cefc8f514df46 777208 science optional rapmap_0.5.0+dfsg-3_amd64.deb

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