On Thu Feb 12 2015 at 9:53:12 AM Andreas Tille <[email protected]> wrote:
> 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. > Good to know! > > > - [ ] 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 [email protected] is the best way to clarify. > Upon review they are pure Java > > > - [ ] 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. > I've produced one with help2man. > > - [ ] script-not-executable: several > > Usually this is either easy to fix or contains a hidden problem that > should be fixed. > Fixed > > > - [ ] debian/copyright needs audit > > * lacking "Files: debian/*" paragraph > Fixed. > * `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) > Sure, for another day :-) > * trinity-plugins/Trimmomatic-0.32: Binary without source! > Trimmomatic is packaged in this version anyway - so this should > be simply dropped via Files-Excluded > Done > * 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 > Only used via a hidden option. Excluded and added as a 'suggests' > * 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 > I've added the comment. As for packaging it separately I'll leave this to some other motivated individual to do so. There are a lot of bioinformatics libraries that are functionally single use. > * 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. > Nothing coming up. Probably Broad Foundation employees / interns. I think they are covered by the existing entry. > * trinity-plugins/slclust: Same as for Fasttool - I'd really > love to see a separate package from > http://sourceforge.net/projects/slclust/ See above :-) > > * trinity-plugins/TransDecoder_r20140704.tar.gz: > Same as for Fasttool / slclust: > https://transdecoder.github.io/ Gah, this contains two programs already packaged (cd-hit & ffindex (two versions!)) and another copy of Parafly. Looks like this will require a separate package just to keep the source clean. Trinity can use the Parafly from this (yet to be created) package. > * 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 > Done. > 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. > Go team!
