Josh, On Wed, Apr 11, 2012 at 10:53 AM, Josh Moore <[email protected]> wrote: > On Apr 10, 2012, at 12:13 PM, Mathieu Malaterre wrote: >> On Mon, Jan 16, 2012 at 6:37 PM, Mark Longair >> <[email protected]> wrote: >>> Hi Mathieu, >>> >>> Mathieu Malaterre <[email protected]> wrote: >>>> >>>> Hi Mark ! >>>> >>>> On Sat, Jan 7, 2012 at 1:35 PM, Mark Longair >>>> <[email protected]> wrote: >>> [..] >>>>> NetCDF Java itself also bundles a huge number of jar files in >>>>> the source distribution, but to build the core of NetCDF you >>>>> actually need relatively few dependencies. I made a package >>>>> that builds just the core of NetCDF (i.e. the makeCore ant >>>>> target) and only relies on Debian-packaged dependencies. (The >>>>> NetCDF core is all that bio-formats requires, I believe.) That >>>>> repository is here: >>>>> >>>>> https://github.com/mhl/libnetcdf-java >>>> >>>> Cool. I'll import that into the debian-med svn if this is ok with you: >>>> svn.debian.org/svn/debian-med/trunk/packages/netcdf-java >>> [..] >>>>> The repository with my Debian packaging of bio-formats is here: >>>>> >>>>> https://github.com/mhl/libbio-formats-java >>>> >>>> cool. If this is ok with you I'll import this into debian-med svn at: >>>> svn.debian.org/svn/debian-med/trunk/packages/bio-formats >>> [..] >>> >>> That's great in both cases - thanks for doing that. >> >> ref: >> http://ftp-master.debian.org/new/netcdf-java_4.3.8-BETA-1.html >> >> Assuming everyting goes smoothly, I can now move on to bio-formats itself. > > Hi Mathieu, > > Looking at Mark's repo (mhl/libbio-formats-java) and the patches under > http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bio-formats/trunk/debian/patches/, > much of what was necessary was to remove the jars and configure the build > for using /usr/share, a source drop, etc. Would it help if we modified the > build so there's a global switch (e.g. ant -Ddebian=true) to allow these > commits to live in the mainline? (Would the jars be allowed to remain unused, > or must they be deleted to adhere to the Debian guidelines?)
I am not too keen on the whole "-Ddebian=true". Even if I only use debian distribution, there are other distros out there. Also this puts the burden of maintaining debian related material outside of debian organisation. I do not believe this will be beneficial for both communities. Instead what I have been trying to do is simply use the documented 'build.sysclasspath' [1], ant option. Mark's solution was more invasive even if he used json scripts to automagically fix ant build files. So really as long as netcdf/bioformats allow use of build.sysclasspath=first then all is fine with me. There are still a couple of tiny patches but that was mostly me banging my head trying to get things moving. I believe in the end the number of patches should be much smaller. The only patch, I really dislike so far is the following: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bio-formats/trunk/debian/patches/ij.patch?view=markup I guess I need to check if using newer imagej release this patch goes away. > Where possible we'd certainly like to make Debian packaging simpler. A new > stable release of Bio-Formats (4.4) is planned for the summer which it would > be ideal to target, giving us a chance to merge in patches and the bulk of > Mark's work (especially having seen some of how he suffered!) Again the number of patch should really be minimalistic in the end. > I've CC'd Melissa Linkert, the Bio-Formats lead. Roger Leigh, a (previously > non-Java) Debian maintainer who's recently joined the Bio-Formats project, is > already subscribed to the list. The biggest issue is that I do not believe I will be ready for the debian freeze (should happen before summer if I recall correctly). The whole bio-formats packaging seems very difficult to me, this is why I can only build a minimal number of targets right now: "jar-autogen jar-common jar-formats jar-jai jar-loci-plugins jar-lwf-stubs jar-mdbtools jar-metakit jar-ome-xml jar-poi-loci" Thanks for your interest and CCing people to help out ! And thanks for bio-formats ! -M [1] http://ant.apache.org/manual/sysclasspath.html -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/ca+7wuswb6jxcvz64jrmt44tfkmbcgy6-bncld10kyr18ncp...@mail.gmail.com
