Re: trinityrnaseq ready for review!!
Hi Michael,
On Fri, Jan 15, 2016 at 11:00:05PM +0000, Michael Crusoe wrote:
> Now that libjung-free-java has been accepted I've updated the trinityrnaseq
> package
:-)
> The tests again pass, this has been tested in a debci virtual machine.
Sounds good.
> All that is left is two spelling corrections
Sometimes I just report this upstream and ignore it for the package ...
> and a mysterious hardening
> warning from Lintian.
I can only see a lintian *info* (not warning) and I admit that I
personally decided to ignore these in several packages where I faced it.
May be it is a false poitive or not - in any case I have done all my
best to propagate the necessary options but the info remained. So this
would not stop me from uploading.
> Given that this package is quite complex I thought I'd ask for a wide
> review before I request an upload.
Patch adjust-trimmomatic-adapters-path looks suspicious. The trimmomatic
package uses /usr/share/trimmomatic (no capital 'T'!). It might be this
could / should be adapted in the trimmomatic package but in the current
situation the patch looks wrong.
The patch jellyfish-path contains a certain jellyfish version (1.1.3).
I just learned that the kraken package does not cope with our current
jellyfish 2.x but needs jellyfish 1.x. I have not yet dealt with this
issue but you might like to re-read the discussion on the mailing list
[1] to verify if this issue possibly affects also trinityrnaseq.
Could you please add a more verbose DEP3 header to noExitTester.
Please git pull for a small typo in a DEP3 header.
Question: I have never seen a debian/autoreconf file. Before I read
the docs could you please explain the sense of this file?
> I will be doing a thorough file-by-file review & copyright audit as well.
Fine.
> Later I will package DESeq2 (I have the packaged locally but need to file
> ITPs & create the repos)
Fine as well.
Thanks for your work on this complex package
Andreas.
[1] https://lists.debian.org/debian-med/2015/11/msg00031.html
--
http://fam-tille.de
Reply to: