Re: Update on Trinityrnaseq packaging

[Andreas Tille <andreas@an3as.eu>]

On Thu, Feb 12, 2015 at 12:16:57AM +0000, Michael Crusoe wrote:
> - [ ] hardening-no-relro usr/lib/trinityrnaseq/Chrysalis/*
> Needs investigation

While fixing this is nice to have I would not insist on it for sponsoring
the package.

> - [ ] jar-not-in-usr-share usr/lib/trinityrnaseq/Butterfly/Butterfly.jar,
> usr/lib/trinityrnaseq/util/support_scripts/ExitTester.jar
> May be fixable with a move + symlink. Need to make sure that they are pure
> Java

I'm not a Java expert but IMHO all JARs are machine independent and thus
should reside in /usr/share.  All Java packages with machine dependant
code I have seen (not too much admittedly) had extra *.so files in
/usr/lib.  If you are unsure asking on debian-java@lists.debian.org is
the best way to clarify.

> - [ ] binary-without-manpage usr/bin/Trinity

Same as above.  It would be nice to have (even nicer than hardening)
there are cases where it is hard to write a sensible manpage.

> - [ ] script-not-executable: several

Usually this is either easy to fix or contains a hidden problem that
should be fixed.

> - [ ] debian/copyright needs audit

 * lacking "Files: debian/*" paragraph
 * `licensecheck -r *` did not uncover anything suspicious to me
 * trinity-plugins/GAL_0.2.1: This third party code should be
   specified separately with the license that can be found in the
   downloadable archive at
    http://www.sequenceontology.org/software/GAL_Code/
   However, I'd prefer packaging GAL separately (in the latest
   version)
 * trinity-plugins/Trimmomatic-0.32: Binary without source!
   Trimmomatic is packaged in this version anyway - so this should
   be simply dropped via Files-Excluded
 * trinity-plugins/collectl: Packaged for Debian.  Once you are
   removing files via Files-Excluded the most easy thing would be
   to delete this as well which saves you the work of mentioning
   it in d/copyright
 * trinity-plugins/fstrozzi-Fastool-7c3e034f05: While mentioned
   properly in d/copyright I'd at least refer to the download
   location
     https://github.com/fstrozzi/Fastool
   in a Comment: field.  I'd regard it as the better solution to
   create a separate package since it might be considered useful
   for people not only using it via trinityrnaseq
 * trinity-plugins/parafly/src/ParaFly.cpp: 
    Authors of this wrapper are MB Couger (mbcouger(AT Symbol)gmail.com, Matt Stowe mstowe(AT Symbol)okstate.edu
   This should at least deserve an extra d/copyright line and you
   should also dig for the original download location.  I can
   not evaluate the sense of a separate package.
 * trinity-plugins/slclust: Same as for Fasttool - I'd really
   love to see a separate package from
     http://sourceforge.net/projects/slclust/
 * trinity-plugins/TransDecoder_r20140704.tar.gz:
   Same as for Fasttool / slclust:
     https://transdecoder.github.io/
 * trinity-plugins/jellyfish-2.1.4.tar.gz: --> Files-Excluded
   since we have a separate package
 * trinity-plugins/rsem-1.2.19.tar.gz: --> Files-Excluded since
   you ITP it as you wrote below

Please feel free to ask for help here if you agree that Fastool, slclust
and transdecoder should be packaged separately.  I could even try to
work in a MoM project with some potential student on these.

> trinityrnaseq has two unfulfilled dependencies: rsem & express
> 
> rsem
> - [ ] lacks manpages
> - [ ] lacks ITP
> 
> express:
> - [ ] lacks ITP

Thanks for sending this kind of status messages.  That's really helpful
and enables team input.

Kind regards

          Andreas.

-- 
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