Hi Christoph, On Thu, Oct 20, 2011 at 09:15:38PM +0200, Dr. med. Christoph Gille wrote: > Thanks Olivier and Andreas, both, ssh and svn co > svn+ssh://svn.debian.org/svn/debian-med/trunk work very well now. I > can even commit changes.
:-) I have noticed that you created trunk/packages/neobio/trunk/debian. Looking foreward to see some content in this dir. Just do not be afraid about making mistakes - we will help correcting them. > When I had a look at the other projects, I noticed, that I > probably did everything wrong. )-: Well, everything is a bit hard: At least you were looking at the other projects - this is perfectly right. :-) > For the Fortran program tm-align I followed > http://wiki.debian.org/IntroDebianPackaging. I created a source > package using debuild -us -uc. The directory structure looked like the > ones in the svn directory, but finally I realized that tm-align > already existed. Someone is already working on it. )-: Nevertheless, > it was a good training. Before I start working on (any, not necessarily Debian Med related) package I do an "apt-cache search <pkg>" which in this case shows: $ apt-cache search tm-align tm-align - structual alignment of proteins I also can not recommend frequently enough to closely watch our tasks page http://debian-med.alioth.debian.org/tasks/bio which shows a (hopefully) complete overview about the packages we just included and those we are working on. Please, before anybody starts working on a package, just look at this (or the other categories) pages. > For the other programs I followed > http://tldp.org/HOWTO/html_single/Debian-Binary-Package-Building-HOWTO/ > since being Java-programs they are architecture independent and > do not need compilation. Here I created the dot deb files with > fakeroot dpkg-deb -b. Was it a mistake not creating a source > package? Yes. Well, OK, at least now I understand from where so many people get a wrong understanding of building Debian packages. I was always wondering where people get this information and now I know ... As a rule of thumb: Never (I really mean NEVER) start with an upper case DEBIAN directory. We are not shouting - we are building Debian packages, right? The only way to the official Debian mirror leads via creating source packages and it is described in the "Debian New Maintainers' Guide"[1]. (I personally wished that those other docs would vanish from the web - ar at least would be ranked at rank >= 100.) > My directories look different to those on the svn server because > it is not a source package. For example I wrote DEBIAN/control > files but no debian/rules files. General rule: These two features (DEBIAN/* and no debian/rules) are a clear sign that you did packaging wrong (not everything - you just asked here and this is right :-)). > THE QUESTION: > > Do I need to change all java based packages and > create source packagess Yes. > in the same style as > /srv/home/groups/pkg-escience/htdocs/debian/? I see no reason to follow specifically pkg-escience rather than any other repository, but in principle yes. I usually copy-n-paste from other projects inside the Debian Med repository. So if I would start packaging a Java package at first I would checkout the complete Debian Med SVN and then I would grep for similar packages like this: $ grep -l "Depends:.*java" trunk/packages/*/trunk/debian/control Currently you get 26 examples which are listing java in the Dependency list (note: there are probably more because my quick shot does not regard potential line breaks before the first java dependency). Just look at these and find something which looks similar to your program in question. > SECOND QUESTION: > > On alioth in /srv/home/groups/pkg-escience/htdocs/debian I find dot > deb files for example for biojava. How did these files get there? In general: pkg-escience was as far as I can tell a small experiment for only a view packages. Do not use it as your reference example. You might become missleaded. (The existance of this project has leaded to some confusion in the past, sorry for you beeing trapped as well.) There are several ways to find out the location of the repository of some package in question. For the BioJava example you could do the following: 1. BioJava is for *developing* biological applications. Thus it can be found in the according task bio-dev of the Debian Med project and is listed on the tasks page: http://debian-med.alioth.debian.org/tasks/bio-dev You can seek there for the string biojava or you learned via $ apt-cache search biojava that the name of the package is actually libbiojava-java and go staight to http://debian-med.alioth.debian.org/tasks/bio-dev#libbiojava-java In the right column of the metainformation you will find the Link to the repositiory (SVN). 2. A more generic way (which works for all packages not only Debian Med stuff is debcheckout libbiojava-java 3. Also very generic: http://packages.debian.org/biojava (even if you did not found out the name via apt-cache before) Following one link to a certain release will bring you to a page which has in the right column links to *.dsc. This file contains information about the repository in the Vcs-fields. 4. Because I suggested to download the full Debian Med repository you can also do find trunk -name "*biojava*" However, this only works for packages in our SVN (some are maintained in Git). These are just four examples how to find out a repository where a package is maintained - there are definitely several more. > find /srv/home/groups/pkg-escience/htdocs | fgrep biojava Easy: Because it is NOT there. Where did you git the impression from that pkg-escience is connected with biojava? We should fix this source of information. > Where do I find the dot deb file for tm-align? Well, I do not know what you mean by "dot deb" file, but if you are seeking the repository where tm-align is maintained I'll leave this for you as exercise now (while I'm going on updating tm-align to latest version ...) > The packages I am working on are stored in > http://www.bioinformatics.org/strap/debian/ They are already > working and above URL can be added to /etc/apt/sources.list for testing While this is definitely interesting you must know that everybody of us has some certain job to do. Chances that somebody is waiting for anybody to recommend some repository to browse are quite low. It works much better if you say: My next target is program X and I have the following question. I'm pretty sure that you will get a helpful answer in the next 24 hours (at least). Kind regards and I really hope that I did not pushed to many information in one rush onto you Andreas. [1] http://www.debian.org/doc/manuals/maint-guide/ -- http://fam-tille.de -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
