Re: trinityrnaseq ready for review!!

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