Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-09-21

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All times shown according to UTC.

Time Nick Message
01:26 samuell left #bioclipse
04:55 egonw joined #bioclipse
06:29 * sneumann just had a failure upgrading bc qsar to 2.4.X
06:30 egonw any details available? like stacktrace or so?
06:30 sneumann no, just a popup. is there a logfile ?
06:30 egonw yeah, should be in your home folder
06:30 sneumann found
06:35 egonw we have had a lot of problems with upgrading in the 2.4 series...
06:35 egonw please talk to jonalv
06:35 egonw @tell jonalv sneumann has more upgrade problems...
06:35 zarah Consider it noted.
06:35 egonw @tell olas the sooner we get p2, the better... sneumann had upgrade problems with 2.4 too
06:35 zarah Consider it noted.
06:36 sneumann Ah, I thought p2 was already released and it'd be a good moment to upgrade
06:37 egonw yeah, there is work to be done to integrate it into your own rcp apps
06:37 egonw it's now scheduled for 2.6
06:38 sneumann Is there a way to use BC to make a clustering of molecules in an SDF based on tanimoto distances and afterwards do an MCS on the clusters ?
06:38 sneumann Usually we'd do that with pure CDK
06:40 Gpox joined #bioclipse
06:42 egonw ping olas when he gets online
06:42 egonw he had a student working on making dendrograms
06:42 egonw not sure about the state of that
06:42 egonw or where that code hangs out...
06:42 egonw the cdk manager should have stuff to calculate the MCS for each cluster, I think
06:49 sneumann QSAR feature has a digital signature signed by the Eclipse foundation ?! How that ?
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06:55 sneumann Things worked out after updating QSAR alone, and then update all offered features. Looks like a dependency problem
06:55 sneumann similar with decision support
07:02 sneumann Then I tried to download stuff from PubChem following
07:02 sneumann the cheat sheet
07:03 sneumann So I searched for C15H12O5 and got three (!) hits
07:03 sneumann where MetFrag found ~468 hits.
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07:09 sneumann Has the user database of http://pele.farmbio.uu.se/cgi-bin/bugzilla changed =
07:09 sneumann Has the user database of http://pele.farmbio.uu.se/cgi-bin/bugzilla changed ?
07:10 sneumann Password is incorrect, and it forgot my user name to reset the password ?
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08:20 samuell joined #bioclipse
08:55 samuell Gpox: Are you using ant at all in Bioclipse?
08:55 samuell And in particular, for the documentation generation?
08:57 samuell ... found mostly shell scripts in net.bioclipse.doc ... but I'm quite new to ant, so I might miss some place where things might be defined
08:58 Gpox Eclipse uses ant to build stuff, bioclipse I thing have a perl script that dose some thing
08:58 samuell Ok ...
08:58 samuell ... I'm wondering, since ant seems to have the functionality needed for generation from (MediaWiki) WikiText to HTML
08:59 samuell So, I hope there won't be a problem to use ant, at least ...
09:00 samuell But I guess the perl script would have to execute the ant I create, if so ... hope that's not too hard to fix.
09:00 Gpox buckminster can be used to invoke ant scripts, so it should not be a problem to do it when building a release
09:00 samuell Gpox: Ok, good!
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10:06 egonw sneumann: did someone reply to you about pelezilla?
10:06 egonw sneumann: bugzilla db was lost in the upgrade...
10:06 egonw that is, we still have the backup
10:06 egonw but the backup does not import into the current bugzilla :(
10:06 egonw will decide today with ola about next steps
10:11 sneumann Ack.
10:12 sneumann My bugreport would've been on the pubchem stuff,
10:12 egonw ack, yeah, important
10:12 egonw I'm waiting for Ola to come online
10:12 sneumann But the URL used is kinda correct
10:12 sneumann http://www.ncbi.nlm.nih.gov/entrez/eutils/esear​ch.fcgi?db=pccompound&retmax=50&usehist​ory=n&tool=bioclipse.net&term=C15H12O5
10:12 zarah sneumann's link is also http://tinyurl.com/27dmgzg
10:12 sneumann and really returns only 3 compounds
10:12 sneumann which is a bug in the URL :-)
10:12 sneumann Or my search terms :-(
10:13 sneumann which is a bug in PubChem. Sorry
10:13 egonw dunno
10:13 egonw I am not user term= is the proper field to use for MFs
10:19 sneumann Is that dump a database dump or a bugzilla dump or is that the same ?
10:19 sneumann Is it mysql ?
10:44 egonw yes
10:44 egonw mysql dump
10:44 egonw but the tables seem to have changed
10:45 egonw it was both 3.2.x :(
11:25 egonw samuell:
11:25 egonw http://packages.ubuntu.com/jaunty/bugzilla3
11:29 samuell https://launchpad.net/ubuntu/intrep​id/+source/bugzilla/3.0.4-0ubuntu1
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12:38 sneumann egonw: just tried to run http://www.myexperiment.org/workflows/934.html
12:38 sneumann in my (now updated) BC 2.4.1
12:38 sneumann It bails out with
12:38 sneumann ui.open(mcss)
12:38 sneumann The object could not be opened. No suitable editor could be found for object:
12:38 sneumann CDKMolecule:C2H5NO
12:39 egonw sneumann: we're hard working on getting the bugzilla back online...
12:39 egonw sneumann: bad regression
12:39 egonw bugger...
12:39 sneumann I'll queue my reports here :-)
12:40 egonw thanx...
12:41 sneumann and I'll ask olass later about
12:41 sneumann [08:42] <egonw> he had a student working on making dendrograms
12:41 egonw yes, please do
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13:38 samuell Någon, vet ni om det var bugzilla 2 eller 3 tidigare?
13:38 samuell Eller om pele körde Ubuntu 8.04 eller 8.10?
13:39 samuell Sorry, forgot to speak englith
13:39 samuell ping olass, masak
13:39 masak pong
13:39 zarah masak: You have new messages. Write '/msg zarah @messages' to read them.
13:40 samuell Anybody knows if bugzilla was version 2 or 3 before?
13:40 samuell Or if pele was running Ubuntu 8.04 or 8.10 (or other)?
13:40 * masak doesn't know about the prior bugzilla version
13:41 masak I checked the Ubuntu version before the reinstall. but I already forgot what it was.
13:55 * sneumann mubles "tar up at least  /etc before an upgrade ..."
13:55 * sneumann mumbles "tar up at least  /etc before an upgrade ..."
13:55 egonw sneumann: done that
13:56 egonw important indeed
13:56 egonw the system originally had hardy, with BZ 2.22
13:57 egonw then was upgraded to intrepid for Mylyn 1-1.5 years ago
13:57 egonw with BZ 3.2
13:57 egonw last week it was upgraded to jaunty, also with 3.2
13:57 egonw later minor release
13:58 egonw then the upgrade the karmic failed
13:58 egonw which is when I had to reinstall, and installed lucid LTS
13:58 sneumann "So Canonical recently spent tens of thousands of USD to upgrade the GNOME Bugzilla instance from 2.20 to 3.4"
13:58 egonw also with BZ 3.2
13:58 sneumann http://www.google.com/url?sa=t&amp;source=web&a​mp;cd=3&amp;sqi=2&amp;ved=0CCIQFjAC&amp;url=htt​p%3A%2F%2Fgnomejournal.org%2Farticle%2F96%2Fcan​onical-upgrading-gnome-bugzilla-and-commercial-​sponsorship&amp;rct=j&amp;q=gnome%20update%20bu​gzilla&amp;ei=2LmYTM6HDovLswbamcS1DA&amp;usg=AF​QjCNE85a1lTUjwb8DPeXyepWJ9qtWyVA&amp;cad=rja
13:58 zarah sneumann's link is also http://tinyurl.com/32vogms
14:01 sneumann So you are looking for bugzilla packages with karmic's BZ3.2  or a way to import that dump into current BZ 3.2.5.1-2 ?
14:06 egonw samuell is looking at it...
14:06 egonw comparing schema...
14:06 egonw the schema does not really match...
14:06 egonw which may be caused by the 2.22->3.2 upgrade...
14:22 sneumann http://www.ravenbrook.com/project/p4dti/tool/​cgi/bugzilla-schema/index.cgi?action=range&am​p;from=2.22&amp;to=3.2&amp;view=View+schema
14:22 zarah sneumann's link is also http://tinyurl.com/3932kur
14:23 sneumann Bugzilla Schema for Versions 2.22 to 3.2
14:24 egonw indeed...
14:25 egonw and it is completely off with our backup
14:25 egonw there is no logic
14:25 egonw but there seems to be a possible mapping, though
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16:51 egonw hi samuell
16:51 samuell hi egonw
16:51 egonw samuell: thanx, got your mails about the mysql BU
16:51 samuell Yeah ... think this might work out pretty well
16:52 samuell It's some work, but not as much as I thought at least
16:53 masak left #bioclipse
16:56 egonw OK, please keep emailing...
16:56 egonw I won't have time for anything until Fri
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