Re: trinityrnaseq ready for review!!
Uploaded (my upload cable is glowing ;-)). Thanks for your work on this. Andreas.
On Fri, Jan 29, 2016 at 03:26:58PM +0000, Michael Crusoe wrote:
> On Sat, Jan 16, 2016 at 2:36 PM Andreas Tille <andreas@an3as.eu> wrote:
>
> > Hi Michael,
> >
> > On Fri, Jan 15, 2016 at 11:00:05PM +0000, Michael Crusoe wrote:
> >
> > All that is left is two spelling corrections
> >
> > Sometimes I just report this upstream and ignore it for the package ...
> >
>
> Done
>
>
> > > 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.
> >
>
> okay.
>
> >
> > > 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.
> >
>
> Fixed
>
>
> > 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.
> >
>
> Trinity passes all its tests despite the newer version of Jellyfish
>
>
> > Could you please add a more verbose DEP3 header to noExitTester.
> >
> Done
>
> > Please git pull for a small typo in a DEP3 header.
> >
> Done
>
> >
> >
> > Question: I have never seen a debian/autoreconf file. Before I read
> > the docs could you please explain the sense of this file?
> >
>
> It tells dh_autoreconf in which directories it should run
>
> >
> > Thanks for your work on this complex package
> >
>
> My pleasure
> --
> Michael R. Crusoe CWL Community Engineer crusoe@ucdavis.edu
> <mcrusoe@msu.edu>
> Common Workflow Language project University of California, Davis
> https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe
--
http://fam-tille.de
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