On Fri Feb 13 2015 at 12:55:49 AM Andreas Tille <andr...@an3as.eu> wrote:
> [Reply to list only] > We are oppositely calibrated :-D I prefer to be CC'd even when I am a subscriber and you don't. > On Thu, Feb 12, 2015 at 09:42:45PM +0000, Michael Crusoe wrote: > > > > - [ ] 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. > > That's usually the cheapest way and fine for the most cases. > Unfortunately it did not worked in this case - I commited a manually > edited manpage based on yours. The result at least fits nroff syntax. > :-) Thanks! > > > * 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 > > OK - but the dir remains in the Git repository. You should import > a cleaned up archive. You can get this by > > debian/rules get-orig-source > > ... or if you want to save your bandwidth via > > mk-origtargz --repack --compress xz <path_to_original_download_source> > Yeah, I had tried that; I get this head-scratching response: mcrusoe@athyra:~/debian/trinityrnaseq$ mk-origtargz --repack --compress xz ../v2.0.3.tar.gz tar: trinityrnaseq-2.0.3/Butterfly/src/lib/jung-graph-impl-2.0.1.jar: Not found in archive tar: trinityrnaseq-2.0.3/Butterfly/src/lib/jung-api-2.0.1.jar: Not found in archive tar: trinityrnaseq-2.0.3/Butterfly/src/lib/jung-algorithms-2.0.1.jar: Not found in archive tar: trinityrnaseq-2.0.3/Butterfly/src/lib/java-getopt-1.0.13.jar: Not found in archive tar: trinityrnaseq-2.0.3/Butterfly/src/lib/collections-generic-4.01.jar: Not found in archive tar: trinityrnaseq-2.0.3/Butterfly/src/lib/Jaligner.jar: Not found in archive tar: trinityrnaseq-2.0.3/Butterfly/prev_vers/Butterfly_r2013_08_14.jar: Not found in archive tar: Exiting with failure status due to previous errors (I checked and they do exist) > > > * 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. > > May be I'll care for this in some MoM project. Usually these small > tools are easy targets and than it should be done also for the sake of > separate testing. > Have fun! > > > > * 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. > > Finally it does not matter what you think but what you can convince > ftpmaster to accept. ;-) > Indeed, but it'll get properly packaged with transdecoder. Lacking an upstream distribution site makes a pretty clear case for not having its own package.
