Bug#731190: qiime REMOVED from testing
Hi Steven, On Wed, Jan 22, 2014 at 11:45:50AM +, Steven Chamberlain wrote: On 22/01/14 10:49, Andreas Tille wrote: Well, for king we have another problem that it depends from the deprecated libjogl-java and should be replaced by libjogl2-java. I tried removing libjogl-java, and KiNG still seems to work? I admit that I was quite astonished that the package builds despite the errors. I don't know if the graphics are being 'accelerated' or not, but: http://kinemage.biochem.duke.edu/kinemage/king-manual.html#tth_sEc3.3.2 This feature has been tested with various combinations of Java 1.4.2 through Java 1.6.0 and JOGL 1.1 through JOGL 1.1.1. JOGL is still under development, as is this feature, and interacting so directly with the hardware is always risky, so it's possible that OpenGL rendering may hang KiNG on your computer. You've been warned. Hopefully, a future version of Java (possibly the 1.6.x series) will use OpenGL behind the scenes for all graphics operations, making KiNG much faster and making this feature obsolete. Until then, this is a work-around for large kinemages where performance is an issue. So it may be that graphics rendering is fast enough in openjdk-6 and -7 that KiNG's use of JOGL is obsolete anyway? This would be cool and I'd be very happy if somebody of the Java team would comment on this. If the libjogl-java dependency is dropped, king should be installable on kfreebsd and then so would qiime. And libjogl2-java transition can go ahead. Most probably this would be the most simple solution. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#731190: qiime REMOVED from testing
Hi, thanks to the hint od Steven below I wonder if I could get more help to solve #731190 which boils down to the question why libjogl-java is not available on kfreebsd. I addressed this to the maintainer (debian-java) but his new upload did not fixed the issue obviously. It even seemed to make things worse, since the package now fails to build on even more architectures as http://buildd.debian-ports.org/status/package.php?p=libjogl-java shows and kfreebsd is not even on the list of architectures any more. Hope anybody will have a clue - otherwise I will restrict the qiime to the architectures that do not have trouble with libjogl-java. Kind regards Andreas. On Tue, Jan 21, 2014 at 08:21:15PM +, Steven Chamberlain wrote: On 21/01/14 20:10, Niels Thykier wrote: On 2014-01-21 19:45, Andreas Tille wrote: I know that qiime has a serious bug (#731190) where I was seeking for help six weeks ago with no real result. So I would have expected to become kicked from testing because of this bug which would be fine. Please, please Cc: debian-...@lists.debian.org for help with something like this. I only noticed that bug today because I happen to read -release@ ... -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#731190: qiime REMOVED from testing
On 21/01/14 20:32, Andreas Tille wrote: [...] #731190 which boils down to the question why libjogl-java is not available on kfreebsd. AFAICT that package has never been available on kfreebsd: https://buildd.debian.org/status/logs.php?pkg=libjogl-javaarch=kfreebsd-amd64 I'm currently not sure of the best action to take: If that package is only needed for qiime to work on Linux, the dependency could be limited to [linux-any]. Or if that package crucial for qiime to work at all, you can only request its removal from kfreebsd. (From unstable - by filing a bug with ftpmaster). Or with luck, someone might be able to get libjogl-java built on kfreebsd. (I think changes to gluegen2 are needed). There's a more immediate problem that qiime now FTBFS on kfreebsd-*: http://buildd.debian-ports.org/status/package.php?p=libjogl-java shows and kfreebsd is not even on the list of architectures any more. That's the wrong page - that's the debian-ports.org infrastructure. Architectures for Debian sid are here: https://buildd.debian.org/status/package.php?p=libjogl-java I'm curious why it talks about 'downloading', it's not really downloading source code during the build, I hope? FastTree.c downloaded successfully. FastTree built. Traceback (most recent call last): File setup.py, line 183, in module if download_UCLUST(): File setup.py, line 140, in download_UCLUST raise SystemError, (Platform not supported by UCLUST) SystemError: Platform not supported by UCLUST Seems like some porting is needed, maybe not much. I'm looking into it right now... Thanks! Regards, -- Steven Chamberlain ste...@pyro.eu.org -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#731190: qiime REMOVED from testing
Hi Steven, thanks for your quick response. On Tue, Jan 21, 2014 at 08:44:27PM +, Steven Chamberlain wrote: On 21/01/14 20:32, Andreas Tille wrote: [...] #731190 which boils down to the question why libjogl-java is not available on kfreebsd. AFAICT that package has never been available on kfreebsd: https://buildd.debian.org/status/logs.php?pkg=libjogl-javaarch=kfreebsd-amd64 I'm currently not sure of the best action to take: If that package is only needed for qiime to work on Linux, the dependency could be limited to [linux-any]. I admit I have no idea about the usage of libjogl-java in qiime, but since it is no direct dependency but it is introduced by a dependency of king and libjogl-java is deprecated (see #706922) we most probably will not be very lucky. Or if that package crucial for qiime to work at all, you can only request its removal from kfreebsd. (From unstable - by filing a bug with ftpmaster). Or with luck, someone might be able to get libjogl-java built on kfreebsd. (I think changes to gluegen2 are needed). I have no idea what gluegen2 might be. There's a more immediate problem that qiime now FTBFS on kfreebsd-*: http://buildd.debian-ports.org/status/package.php?p=libjogl-java shows and kfreebsd is not even on the list of architectures any more. That's the wrong page - that's the debian-ports.org infrastructure. Architectures for Debian sid are here: https://buildd.debian.org/status/package.php?p=libjogl-java I'm curious why it talks about 'downloading', it's not really downloading source code during the build, I hope? No, it is not. At least under amd64 is builds fine in pbuilder. FastTree.c downloaded successfully. FastTree built. Traceback (most recent call last): File setup.py, line 183, in module if download_UCLUST(): File setup.py, line 140, in download_UCLUST raise SystemError, (Platform not supported by UCLUST) SystemError: Platform not supported by UCLUST Seems like some porting is needed, maybe not much. I'm looking into it right now... From where did you got this line. I'm aware of it from the test suite which is known to fail for this reason. UCLUST is non-free and was removed from the soures - so this must fail obviously (patching the test suite is work in progress). Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#731190: qiime REMOVED from testing
On 21/01/14 21:05, Andreas Tille wrote: https://buildd.debian.org/status/package.php?p=libjogl-java FastTree.c downloaded successfully. FastTree built. Traceback (most recent call last): File setup.py, line 183, in module if download_UCLUST(): File setup.py, line 140, in download_UCLUST raise SystemError, (Platform not supported by UCLUST) SystemError: Platform not supported by UCLUST From where did you got this line. I'm aware of it from the test suite which is known to fail for this reason. UCLUST is non-free and was removed from the soures - so this must fail obviously (patching the test suite is work in progress). It's quoted from the link above, Tail of log for qiime on kfreebsd-amd64. It's an excerpt from near the end of the build log on kfreebsd: https://buildd.debian.org/status/fetch.php?pkg=qiimearch=kfreebsd-amd64ver=1.8.0%2Bdfsg-2stamp=1388360126 UCLUST is non-free and was removed from the soures setup.py is trying to 'download' it, at least. Whatever that means. On i386 that step is successful. I hope to get a closer look at this soon (waiting for qiime source to unpack on a verrry overloaded machine). Regards, -- Steven Chamberlain ste...@pyro.eu.org -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#731190: qiime REMOVED from testing
https://buildd.debian.org/status/package.php?p=libjogl-java FastTree.c downloaded successfully. FastTree built. Traceback (most recent call last): File setup.py, line 183, in module if download_UCLUST(): File setup.py, line 140, in download_UCLUST raise SystemError, (Platform not supported by UCLUST) SystemError: Platform not supported by UCLUST Oddly, I didn't get that error building qiime 1.7.0+dfsg-1 just now, it built successfully. But the resulting package is going to be uninstallable on kfreebsd unless we manage to port packages (gluegen2 first I think, and then) libjogl-jni, libjogl-java, king. If king is absolutely needed for qiime to be useful, I think the only available option currently is to make it Architecture: linux-any and request that ftpmaster remove the old packages built for kfreebsd-* from sid. Regards, -- Steven Chamberlain ste...@pyro.eu.org -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
