[Debian-med-packaging] Packaging Spades (Was: [spades] branch master created (now a2fa706))

[Andreas Tille]

Hi Afif,

it is **really** welcome that you intend to care for spades.  I will
remove my SVN commits to make sure nobody will be confused.  Please note
that I had trouble with running the test suite and thus failed to do a
final upload.  The problems occured when I tried

    spades -1 ecoli_1K_1.fq.gz -2 ecoli_1K_2.fq.gz -o tmp

I also had *severe* problems to replace some Debian packaged tools (I
guess the deactivated patches might not apply to the latest upstream but
should be easy to adapt).  It turned out that Spades broke in a *very*
strange way and I was not yet able to track this down.

Feel free to discuss any issues here on the list.

I kind regards

       Andreas.


On Mon, Nov 23, 2015 at 11:19:01AM +0000, Afif Elghraoui wrote:
> This is an automated email from the git hooks/post-receive script.
> 
> afif-guest pushed a change to branch master
> in repository spades.
> 
>         at  a2fa706   Set Vcs fields to point to git
> 
> This branch includes the following new commits:
> 
>        new  9728866   Inject initial (not yet working) packaging for spades
>        new  5b01563   Thanks to gregor hermann for the hint to the watch file
>        new  cf53945   Files layout is a bit hackish but works for the first tests
>        new  99af06b   Do not install license copies
>        new  3ad0116   Add help2man based manpages
>        new  67047f2   Do not install code copies of python-yaml and python-joblib and rather use Debian packaged code
>        new  65daf15   Deal with some code copies, document others (more to come)
>        new  5f3cb0f   Add upstream contact
>        new  524a185   Move debian/upstream to debian/upstream/metadata
>        new  531a62a   Some steps forward to adapt to latest version 3.5.  There is a lot work remaining.  For the moment it does not even build in pbuilder since it depends on a cmake control file in a not yet released bamtools package (I'll see whether this can be avoided)
>        new  0a8d3d7   Enable pbuilder builds
>        new  37438f9   Better organising of patches
>        new  c5337b5   Fix spacing in patches
>        new  ac1cfa1   Try to create patches acceptable by upstream
>        new  b3256d5   Get something that somehow builds and passes the test.  Keep on with the replacement of code copies
>        new  c59fd4c   Use debian's own boots library
>        new  519b959   Strange error in test suite is caused by using Debian packaged bamtools - at least when linked this way.
>        new  70ab84e   led to exclude yaml-cpp :-(
>        new  b15cbaf   initial upstream branch
>        new  7dd7202   Merge branch 'upstream'
>        new  14f4c34   Imported Upstream version 3.6.2+dfsg
>        new  a3c9270   Imported Upstream version 3.6.2+dfsg
>        new  9435974   Merge tag 'upstream/3.6.2+dfsg'
>        new  e619f1a   Update changelog for new release
>        new  16ed1d0   Refresh patches
>        new  81d17e9   Join the uploaders list
>        new  a2fa706   Set Vcs fields to point to git
> 
> The 27 revisions listed above as "new" are entirely new to this
> repository and will be described in separate emails.  The revisions
> listed as "adds" were already present in the repository and have only
> been added to this reference.
> 
> 
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