[Debian-med-packaging] Plast packaged for Debian

[Andreas Tille]

Hi,

I'm writing you on behalf of the Debian Med team which is a group inside
Debian with the objective to make Debian the best operating system for
Biology and Medicine by packaging all free software that is relevant for
these fields for official Debian.  You can see the results of our work
for Biology which might be of personal interest for you on our so called
tasks page[1] (may be once you follow the link even with plast included
after the next cron job run).

Last night the package I've greated for plast was accepted in Debian
unstable but our ftpmaster had some remarks to drop the additional
CECILL reference from:
   plast_20160121/scripts/plast.sh
   plast_20160121/scripts/test-plast.sh

Here are some additional remarks from my side which might be interesting
for you for your next release:

1. Please use /bin/bash explicitly in scripts/plast.sh
   In Debian and Ubuntu default /bin/sh is DASH which is loading faster
   than BASH due to a less feature rich interpreter.  Specifically it
   can not deal with the "-e" option of `read` and thus the script turns
   into an endless loop of telling the user not understanding "-e"
   option.  The easy fix is to use

    #!/bin/bash

   in the first line.

Moreover I have created some patches in our packaging git[3] and I will
comment those here that might be relevant for your next release and do
not contain Debian specific things.

2. This patch
    https://anonscm.debian.org/cgit/debian-med/plast.git/tree/debian/patches/fix_format_string.patch
   contains a fix I'd really recommend since when switching on compiler
   hardening options the build will fail otherwise.

3. The Debian quality assurance tool lintian detected some spelling issues
    https://anonscm.debian.org/cgit/debian-med/plast.git/tree/debian/patches/spelling.patch
   In addition it suspected
     ment instead of meant
   and
     algorith instead of algorithm
   but I failed greping for these so this is just a hint.

4. Optionally I would recommend to enable using a system installation
   of libpcre.  I did so in
    https://anonscm.debian.org/cgit/debian-med/plast.git/tree/debian/patches/use_debian_packaged_pcre.patch
   Which you should not simply apply since on the Debian build system
   I can ensure via depencencies that libpcre is really installed.  For
   general use you need to check this via cmake but I'm no cmake expert
   and thus my patch is to weak.  So this is just a hint to keep in mind
   that code duplication would be a thing users might want to avoid.  In
   Debian this will be regarded a potential security issue and thus I
   used the libpcre Debian library.

5. The other patches are more or less Debian specific since I have
   tweaked the path for the test script and droped the -msse3 switch
   which is not recommended since modern compilers do autodetect this.

Two last remarks:  I've fixed the first "bug" against the plast
package[4] since it does only build for intel architectures featuring
SSE by explicitly restrict Debian autobuilders to these architectures.
You must know that Debian runs on more than 10 architectures and
autobuilders try to build for these once a new package might arrive.
I'd consider it a good idea to provide support for those architectures
like arm64 or ppc64 that might play a certain role in some clusters in
the not to far future.  Just a thing you might consider.

Finally I would love to see some expected resultset for the test you are
providing to be able to compare the result.  The script
scripts/test-plast.sh will be run at package build time as well as in
periodic tests of the whole archive (about every second week).  It would
be nice to have a better option to confirm success by just realising
that an output file exists.

Kind regards and thanks for providing plast as free software

    Andreas.

[1] http://blends.debian.org/med/tasks/bio#plast
[2] https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-February/039364.html
[3] https://anonscm.debian.org/cgit/debian-med/plast.git/tree/debian/patches
[4] https://bugs.debian.org/814299

-- 
http://fam-tille.de