Re: Packaging Ray for Debian Med
Hi,
On 11/03/2012 01:26 PM, Andreas Tille wrote:
Hi Sébastien,
many thanks for you preparations.
On Fri, Nov 02, 2012 at 05:09:10PM -0400, Sébastien Boisvert wrote:
The Ray Debian package is now at
http://anonscm.debian.org/gitweb/?p=debian-med/ray.git;a=summary
I cloned this and think the packaging is fine so far. However, I do not
see any upstream and pristine-tar branch. Could you please post what a
`git branch` at your site says?
You are right, branches upstream and pristine-tar were missing.
I added them:
$ git branch
* master
pristine-tar
upstream
$ git tag
pristine-tar/2.1.0
upstream/2.1.0
The branch upstream contains commits from git://github.com/sebhtml/ray.git
The tag upstream/2.1.0 is named v2.1.0 on github.
The pristine-tar branch contains the content of Ray-v2.1.0.tar.bz2 (tag pristine-tar/2.1.0)
As I understand, the package will be built using tag pristine-tar/2.1.0 to
generate the orig.tar.gz file and using tag debian/2.1.0-1 to generate the debian.tar.gz
file.
Is that right ?
I fixed everything that lintian reported except these:
W: ray-extra: unusual-interpreter ./usr/share/ray/scripts/plot-color-distributions.R #!/usr/bin/Rscript
W: ray-extra: unusual-interpreter ./usr/share/ray/scripts/plot-coverage-distribution.R #!/usr/bin/Rscript
W: ray-extra: unusual-interpreter ./usr/share/ray/scripts/plot-library-distribution.R #!/usr/bin/Rscript
r-base-core installs /usr/bin/Rscript so it is legit.
Yes. I would consider this a lintian bug.
Maybe /usr/bin/Rscript should be added in
/usr/share/lintian/checks/scripts (package lintian)
Using /usr/bin/env Rscript also throws unusual-interpreter.
I do not see any reason to try tricks to circumvent lintian problems.
If I were you I would use `reportbug lintian` to report this problem.
I reported the bug and provided a patch for lintian:
"lintian says that /usr/bin/Rscript (r-base-core) is unusual"
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=692232
If you are bored by these lintian warnings you could meanwhile add
the lines above in a file
debian/ray.lintian-overrides
and lintian will ignore the warnings.
I added this.
In the Debian Med team we are using the team mailing list as maintainer
so everybody gets informed about uploads, bugs etc. It is easy to add
other uploaders (people feeling responsible and adding code to the
packaging).
Done.
Great.
and install these using a file ray.manpages containing just this string
(see dh_installman). A patch would be fine as well but editing a plain
file is way more comfortable than handling a patch and it is easier to
point upstream to a plain file when asking upstream to include this file.
I added debian/Ray.1 that is simplier than a patch.
Fine.
Keep on your good work and feel free to keep on asking if something else
might remain unclear
My question: what's next ?
I think the package deserves a watch file to enable uscan detecting new
versions. Unfortunately it is not that obvious to me how to download a
versioned source tarball - otherwise I would have just injected such a
watch file.
I added the watch file.
The tarballs are available on
http://sourceforge.net/projects/denovoassembler/files/
I think debian/2.1.0-4 should do it, unless you have other suggestions, in which case
I will gladly implement them.
I just have one remark for the versioning: While it is a good idea to
have differently versioned packages if there are changes it is kind of
usual to uploading a *new* package starting with version 2.1.0-1. The
rationale is that changes done before the first upload to the official
Debian mirror are not really relevant. While this is rather some
"usual" thing to do there is no real need I would like you to consider
this.
I fixed this. Now there is only 2.1.0-1 and I removed the
git tags debian/2.1.0-3 and debian/2.1.0-4.
There are no debian/* tag at the moment.
I guess you (or I) can add the tag debian/2.1.0-1 on the HEAD of branch master
if you feel that everything is fine.
However, if there was some non-Debian upload (I have noticed that
2.1.0-2 was targeting at precise) you should definitely leave the
versioning as it is now.
The precise target was added by Tim Booth. I guess the target for 2.1.0-1
can be edited for Ubuntu releases using the same files. I prefer to start
at 2.1.0-1 in Debian. It makes more sense.
What needs to be done before the upload is to file an so called ITP
(=Intend To Package) bug using
reportbug wnpp
"ITP: ray -- Parallel genome assemblies for parallel DNA sequencing"
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=692238
and following the menu. It makes sense to add a final remark that the
package will be maintained in the Debian Med team and also give the
Vcs-Git location.
Fixed the Vcs-Git in debian/control.
Kind regards and thanks for your work on this
Thank you (and Tim as well) for the mentoring. I really appreciate the time you
have put on this.
Andreas.
Sébastien
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