Am Mittwoch, den 07.12.2005, 17:06 +0100 schrieb Egon Willighagen: > On Wednesday 07 December 2005 16:49, Daniel Leidert wrote: > > Am Dienstag, den 22.11.2005, 14:41 +0100 schrieb Egon Willighagen:
[..] > > > OK, since Bioclipse almost runs with with free java tools, it can become > > > part of Debian itself (main), > > > > It must completely depend on packages in main to be allowed to go into > > main. > > With 'almost' I meant: Bioclipse itself requires only free java tools. Some > plugins may require non-free stuff (bc_jmol and bc_jcp) and this needs to be > explored. Those would need to go into contrib. > > But to make it clear, bioclipse and bc_cdk: > - can be build with free tools from main (as the build process matches that of > eclipse) > - can run with free tools from main (I have run it with jamvm and classpath) I did not have a look at the source yet. Will do it soon. JFTR: To get a package into main it MUST NOT have any dependencies (build and runtime deps) to packages outside main or precompiled stuff. > > > and making it straightforward for me to add it to > > > the live chemblaics CD I want to release early next year for demoing our > > > favorite software on our friends laptop. > > > > > > Now, Stephan is interested in making debs. Daniel, I was hoping you could > > > help out here too, because the Jmol/JCP plugin debs will depend on debs > > > for Jmol, CDK and JChemPaint... I've done deb packaging in the past too, > > > so can offer testing etc here too... > > > > No problem with that. The whole work is available to the public (ok, > > last solutions are still on my local systems, but if interested I can > > put them online). It would like to see it in Debian. Today I again got > > post asking, why several packages are not part of it :) > > Please do put them online, possibly with a brief explanation on how people > can > build the packages from the deb-src sources. I will try to get it up next weekend. But I stopped work at it some time ago, because of several other projects. It would be quite easier if we could solve several problems in upstream, so it makes the life for the Debian package maintainer easier. > I really interested in getting > things ready for debian, (k)ubuntu and the knoppix-based chemoinformatics > live > CD I want to have ready in May 2006. Of course. > > > Some questions I currently have (Stephan, Daniel, others, please add > > > yours): - how can be build the things from the command line? > > > > Sorry, I don't understand. What do you mean with "build the things from > > the command line"? > > We need a build process for bioclipse framework and the bioclipse plugins. > This will require to build them from the command line, i.e. using the default > Debian build process/daemons. Ant build oder GNU make process? [..] > > > - can we resolve the circular dependencies between the current Jmol/CDK > > > debs? > > > > That's a question for upstream. > > Upstream: that's me right? Yes. Jmol and cdk maintainers/project leaders should make this decision :) I already started a discussion some time ago. > > The current solution is, that there is a > > target in Jmol's build.xml to make a package for the jmolApis.jar and > > jmolIO.jar (IIRC you wrote that). But it still requires heavy patching. > > Can you point out to me what patching you need to do, then I can fix things > upstream. There is a lot of stuff, which needs to be done manually to have a clean source for a debian package. - the source file for jmolApis.jar and jmolIO.jar should not be compild when compiling Jmol (because it depends on jmolApis.jar and jmolIO.jar from the "other" package") Patching stuff: - jar archives provided by Debian should be used instead of the pre-compiled stuff in jars/ or libs/ (same for the docbook stuff). Similar problems inside the cdk source (and because of the circular dependency with JoeLIB some more). I've added some variables to the build.xml file in the Debian package to make the determination for several jars available as command line option. Maybe this is a possible solution for these problems. Maybe(!) it would be better to also(!) have a GNU make framework, where configure can determine the whole locations, paths, .... But this is a lot of work. > > It would be better to find a clear solution, which can be implemented in > > upstream, e.g. moving the cyclic stuff to the cdk sourcs and build > > cdk-jmol.jar. And BTW: There is another cyclic dependency between JoeLIB > > and cdk (cdk-libio.jar). > > OK, lets disregard JOELib for now, as the future of that project is > (unfortunately) uncertain at this moment... There are no dependencies to cdk-libio.jar? Regards, Daniel ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
