Re: bioformats (re-resume work)
On 13/09/2012 09:59, Mathieu Malaterre wrote:
On Thu, Aug 2, 2012 at 5:44 PM, Roger Leigh <r.leigh@dundee.ac.uk> wrote:
[...]
With this and my patch for the missing build-deps, it sort-of works.
With this patch applied, bioformats will now build. However, there are
two problems which will still need attention:
1) The following jars are still required:
jar/ome-java-deprecated.jar
jar/ome-java.jar
jar/omero_client.jar
None of these are non-free; they are part of the OMERO build
AFAICT. However, they do represent a nasty circular dependency
between bioformats and omero. That's something that I think we'll
need to address if building without embedded jars is going to be
possible, which I think is quite an important thing to achieve.
Note that these are only used for building other jars which are not
needed, so can be deleted as well (you just need to build specific
targets rather than use the generic "jars" target). It would be nice to
add a generic target for this.
I'm getting build errors for unrelated reasons; it probably just needs
the classpath tweaking--some parts of the build depend upon jars built
earlier, and it looks like it's not finding jars when building other parts.
2) Even with the above jars, the build fails due to perf4j being
missing. It looks like this is missing from Debian at present,
unless I'm just not finding it.
So hopefully this represents some sort of forward progress, since
non-free jars are now eliminated completely, despite this exposing some
additional complications with the circular dependencies which need
addressing. The missing perf4j, if not in Debian, just needs packaging
and adding to the build-deps.
Thanks a bunch ! The patch looks a bit scary to me (*). I do not feel
very confortable with such a big patch to maintain in the long term.
Since upstream seems to be interested in having bio-formats in debian,
wouldn't it be better is this patch was somehow applied upstream ?
Sorry if I was unclear in my previous mail. This patch is already
merged upstream for over a month--it went in once we had tested it; I
just attached the patch for reference and in case you wanted to test
with it before it made it into a stable release.
With current upstream, all you need to do is "rm jars/*" and then build
the various jars as you do now.
As for perf4j, it looks like no-one work on it:
http://lists.debian.org/debian-java/2011/09/msg00056.html
If this package is important, I can start working on this while the
large patch issue can be discussed. Thanks again for your help !
AFAICT, this is only needed for running the testsuite, so it can
probably be skipped for package building for the time being.
Regards,
Roger
--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK Tel: (01382) 386364
The University of Dundee is a registered Scottish Charity, No: SC015096
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