[Debian-med-packaging] r5655 - trunk/packages/biomaj/trunk/debian
Andreas Tille
andreas at an3as.eu
Tue Jan 11 16:27:06 UTC 2011
Hi Oliver,
it seems you are proceeding with the packaging which is great.
I have some additional remarks regarding to your commit:
On Tue, Jan 11, 2011 at 03:51:26PM +0000, olivier sallou wrote:
>
> Added: trunk/packages/biomaj/trunk/debian/biomaj-watcher.README.source
> ===================================================================
> --- trunk/packages/biomaj/trunk/debian/biomaj-watcher.README.source (rev 0)
> +++ trunk/packages/biomaj/trunk/debian/biomaj-watcher.README.source 2011-01-11 15:51:24 UTC (rev 5655)
> @@ -0,0 +1,3 @@
> +The BmajWatcher war application is made with GWT toolkit. Once compiled and war directory is produced, war file must be uploaded on a repository. The generation must be done before package creation, GWT is not executed at package build time nor installation.
> +
> +To recreate the debian package structure, a script biomajwatcher_deb.sh is available in packaging directory in svn structure. It copies necessary files from svn to a debian structure. For BmajWatcher, the war file must have been uploaded to a repository. The scripts define 2 versions for each element (biomaj/bmajwatcher) at the beginning of the file. It must be updated to the required version prior to execution.
Hmmm, this does sound a bit suspicious to me. Usually a text which is
intended to give advise how to build a Debian package contains something
like:
Call dpkg-buildpackage / debuild / pdebuild / ... as you prefer.
I have not checked biomajwatcher_deb.sh to find out what it really does.
What I'm actually missing is some code to fetch the upstream code. This
can either be done using a debian/watch file as input for uscan or you
might provide a get-orig-source target in debian/rules which fetches the
upstream source tarball. This would be needed before one of us can check
the packaging.
> Property changes on: trunk/packages/biomaj/trunk/debian/biomaj-watcher.config
> ___________________________________________________________________
> Added: svn:executable
> + *
As Charles previosely pointed out: The executable flag is only
necessary for debian/rules. All other files in debian/ directory
do not need (read: for esthetical reasons should not even if there
is no real harm done) to be executable. I'm not sure whether there
is a more easy way in svn to reset the executable flag rather than
removing and adding the file again.
> Added: trunk/packages/biomaj/trunk/debian/biomaj-watcher.templates
> ===================================================================
> --- trunk/packages/biomaj/trunk/debian/biomaj-watcher.templates (rev 0)
> +++ trunk/packages/biomaj/trunk/debian/biomaj-watcher.templates 2011-01-11 15:51:24 UTC (rev 5655)
For consistency reasons I would rename debian/templates to
biomaj.templates to make sure debhelper has good chances to put the
template into the right package.
> Modified: trunk/packages/biomaj/trunk/debian/control
> ===================================================================
> --- trunk/packages/biomaj/trunk/debian/control 2011-01-11 13:38:28 UTC (rev 5654)
> +++ trunk/packages/biomaj/trunk/debian/control 2011-01-11 15:51:24 UTC (rev 5655)
> @@ -21,9 +21,10 @@
> bioinformaticians. For example, it can transform original fasta files to blast
> indexes. It is very flexible and post-processes can be extended very easily.
>
> -### PLEASE FIXME HERE
> Package: biomaj-watcher
> Architecture: all
> -Depends: biomaj
> -Description: <INSERT DESCRIPTION HERE>
> - <INSERT LONG DESCRIPTION HERE>
> +Depends: openjdk-6-jdk, tomcat6, zip, biomaj (>= 1.1), debconf, ${misc:Depends}
> +Description: BioMAJ web interface
> + BioMAJ watcher provide a management interface for the BiomAJ tool.
> + It runs in a web container (tomcat) and is accessible at address:
> + http://myhost:myport/BmajWatcher
That's not a good long description: It basically consists of advises
how to use the package and not what it really does. The advises could
be rather putted into debian/biomaj-watcher.README.Debian or raised
in a debconf notice if necessary.
A further advise: I think myport should be defined by the Debian default
tomcat port. If I'm not totally wrong this was discussed in the OpenMRS
packaging - perhaps you might like to have a look into SVN for this
package.
> Modified: trunk/packages/biomaj/trunk/debian/rules
> ===================================================================
> --- trunk/packages/biomaj/trunk/debian/rules 2011-01-11 13:38:28 UTC (rev 5654)
> +++ trunk/packages/biomaj/trunk/debian/rules 2011-01-11 15:51:24 UTC (rev 5655)
> @@ -1,85 +1,99 @@
> #!/usr/bin/make -f
> -# Partie de debian/rules utilisant debhelper.
> -# GNU copyright 1997-1999 par Joey Hess.
> +# -*- makefile -*-
> +# Sample debian/rules that uses debhelper.
> ...
Thanks for the English translations. :-)
> -binary-indep: build install
> - # ant -f usr/local/biomaj/build.xml
> - # Il n'y a rien à faire par défaut
> - #dh_installdirs /etc/biomaj
> - #dh_installdirs /var/log/biomaj
> - #dh_installdirs /usr/local
> - # DESTDIR Doit Etre Exctement /usr/src/packages/BUILD/debian/<nomDuPaquet>
> - #dh_install general.conf.deb /etc/biomaj/general.conf
> - #dh_install conf/* /etc/biomaj/
> - #dh_install * /usr/local/biomaj/
> - #dh_link /etc/biomaj/general.conf /usr/local/biomaj/general.conf
> - dh_installdirs
> - dh_install
> - dh_install usr
> - dh_install var
> - dh_install etc
> +# Compile here architecture independant files
> +binary-indep: build install biomaj biomaj-watcher
> dh_testdir
> dh_testroot
> - dh_installdebconf
> - dh_installdocs
> - dh_installexamples
> - dh_installmenu
> -# dh_installlogrotate
> -# dh_installemacsen
> -# dh_installpam
> -# dh_installmime
> -# dh_installinit
> - dh_installcron
> - dh_installman
> - dh_installinfo
> -# dh_undocumented
> - dh_installchangelogs
> - dh_link
> - dh_strip
> - dh_compress
> - dh_fixperms
> -# dh_makeshlibs
> - dh_installdeb
> -# dh_perl
> - dh_shlibdeps
> - dh_gencontrol
> - dh_md5sums
> - dh_builddeb
>
> +biomaj:
Uhm, that's not good. Why did you replaced
binary-indep: build install
??? There should be no need at all to do this. You are trying to
circumvent debhelper logic which makes the packaging really hard to
maintain.
> + dh_installdirs -p$@
> + dh_install -p$@
> + dh_install -p$@ usr/share/biomaj
> + dh_install -p$@ usr/share/doc
> + dh_install -p$@ usr/bin/biomaj
> + dh_install -p$@ var/lib/biomaj
> + dh_install -p$@ var/log/biomaj
> + dh_install -p$@ etc/biomaj
I guess you was trying to force -p<packagename> when changing the
target.
I think you missinterpreted the usage of dh_install. Please have a look
into other packages in our SVN which are providing install files. Debhelper
is *very* clever and is doing a lot automatically. There is never any
need to do such stuff as you are trying here.
I'd recommend you try to provide a means to enable others to download
your upstream source tarball (either via watch file or a get-orig-source
target) to make sure we are working on the same base. Then I will try
to work on the debian/rules file to avoid those hacks.
Kind regards and thanks for your patience
Andreas.
--
http://fam-tille.de
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