Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-19

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All times shown according to UTC.

Time Nick Message
05:59 Gpox joined #bioclipse
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07:08 ilbot2 joined #bioclipse
07:08 Topic for #bioclipseis now An open source workbench for chemo- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 alpha released! See http://bioclipse.blogspot.com/ || Your mail to 'Bioclipse-commit'  Is being held. The reason .. Message body is too big: 263689 bytes with a limit of 100 KB: OK
07:26 masak joined #bioclipse
07:31 Gpox joined #bioclipse
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08:04 maclean joined #bioclipse
08:05 jonalv joined #bioclipse
08:06 jonalv moin
08:06 zarah hi jonalv
08:07 egonw hi jonalv
08:09 masak hi jonalv
08:15 olas joined #bioclipse
08:15 olas hi
08:15 zarah hi olas
08:15 zarah olas: You have new messages. Write '@messages' to read them.
08:15 olas @msg
08:15 zarah olas: masak said http://en.wikipedia.org/wiki/​The_Village_of_Stepanchikovo http://en.wikipedia.org/wiki/The_Gambler_(novel) http://en.wikipedia.org/wi​ki/Notes_from_Underground
08:16 olas aah
08:16 olas @thank masak
08:16 zarah masak: olas says thank you
08:16 masak takes ages to type out Russian letters :)
08:16 olas :-)
08:16 masak olas: Yukikos today?
08:16 olas *mums*
08:17 masak that a yes?
08:17 olas indeed
08:17 masak \i/
08:17 masak s/i/o/ :)
08:17 olas hahaha
08:17 olas A very small head on a very thin person
08:17 olas \i/
08:18 masak yes... :)
08:18 masak a very nimble person, with the legs in the air
08:18 masak maybe a skier
08:19 olas oh yes
08:24 egonw google insight on searches for 'eclipse rcp'
08:24 zarah egonw: I can't do that; complain with masak and jonalv
08:24 egonw http://google.com/insights/search/#cat&q=ecl​ipse+rcp&cmpt=q&date&clp&geo=SE
08:24 zarah egonw's link is also http://tinyurl.com/5zotpl
08:24 egonw I think that's Ola :)
08:25 masak hehe :)
08:28 masak http://google.com/insights/search/#cat=&q=b​ioclipse&geo=&date=&clp=&cmpt=q
08:28 zarah masak's link is also http://tinyurl.com/5zotpl
09:08 edrin joined #bioclipse
09:24 EskilA joined #bioclipse
09:50 edrin hi
09:50 zarah hi edrin
09:50 edrin is there a wiki howto for creating bio clipse 2 modules
10:31 egonw joined #bioclipse
11:03 jonalv joined #bioclipse
11:03 jonalv ping
11:03 jonalv ehlo
11:03 zarah hi jonalv
11:04 olas edrin: hi
11:04 olas I suspect you are talking about managers
11:04 olas jonalv: is there?
11:05 jonalv sry I jsut arrived. What was the question?
11:05 olas edrin (11:54:26 AM): is there a wiki howto for creating bio clipse 2 modules
11:05 jonalv left #bioclipse
11:05 jonalv joined #bioclipse
11:05 olas otherwise there are some development tutorials on: http://wiki.bioclipse.net/index.php?t​itle=Bioclipse2#Development_tutorials
11:05 zarah olas's link is also http://tinyurl.com/6h4zlk
11:05 jonalv hm back again
11:05 jonalv :)
11:07 jonalv http://www.comics.com//comics/getfu​zzy/archive/getfuzzy-20080817.html
11:07 zarah jonalv's link is also http://tinyurl.com/6ybx5v
11:11 jonalv okey I have problems in structuredb but I get the same exception when running cdk.business.tests
11:12 jonalv Is there no cdk hacker in Bioclispe that can have a look at this?
11:16 jonalv https://sourceforge.net/tracker/ind​ex.php?func=detail&aid=2027771&​amp;group_id=150681&atid=778609
11:16 jonalv https://sourceforge.net/tracker/ind​ex.php?func=detail&aid=2027767&​amp;group_id=150681&atid=778609
11:17 jonalv https://sourceforge.net/tracker/ind​ex.php?func=detail&aid=2027764&​amp;group_id=150681&atid=778609
11:17 jonalv these are SHOWSTOPPERS!
11:17 jonalv My show is stopped. I'll be working on Brunn now.
11:21 olas jonalv: why the anger?
11:22 olas I'll look at it soon
11:22 olas just need to fix some things first
12:20 zarah joined #bioclipse
12:22 egonw zarah: do you have an email address?
12:22 zarah egonw: please rephrase or stop trying to be witty :)
12:22 masak egonw: type /whois zarah
12:22 egonw so that I may send you new bug reports, which you could summarize here?
12:23 masak egonw: just @tell me and jonalv, that worksforus
12:25 egonw :)
12:26 jonalv best is to @tell masak
12:27 masak I guess
12:27 masak between me and jonalv, I get 90% of the parenting of zarah :)
12:28 edrin yesterday i played around with the bc2 alpha release, looks great, much more professional than the bc1 versions...
12:29 edrin especially from the debugging/stability point of view
12:29 masak edrin: glad to hear it
12:38 jonalv egonw: around?
12:38 egonw jonalv: yes
12:38 jonalv we have problems with cml initializing
12:39 jonalv it complains about not finding typs.xsd
12:39 jonalv types.xsd
12:39 egonw no clue
12:39 egonw that's CML internals...
12:39 jonalv this has happened after new jumbo
12:39 jonalv but cml tests passes in cdk!
12:39 egonw right
12:39 jonalv this is olas
12:39 egonw what is?
12:39 jonalv me
12:40 egonw ah
12:40 * jonalv is olas
12:40 jonalv now
12:40 jonalv :-)
12:40 egonw /nick olas2
12:40 egonw ?
12:40 egonw det var inte
12:40 zarah2 det var inte... ja vad då?
12:40 egonw oh boy, you're going to have so much fun with me misusing swedish phrases :)
12:41 olas2 I know!
12:41 olas2 MOHAHAHAHA
12:41 olas2 anyway, the cml problem
12:41 egonw seriously, no clue
12:41 olas2 me neither :-(
12:41 egonw email Dan and sorts
12:41 olas2 ok, will try some more and then sue you
12:41 olas2 ok?
12:41 egonw in reply to that other email on 1.5/1.6 earlier
12:42 egonw no, sue camb
12:42 olas2 comb?
12:42 olas2 who is he?
12:42 egonw seriously, best to actually email cml-discuss
12:42 olas2 I'll just sue ellen
12:42 egonw camb -> cambridge
12:42 maclean if it helps, there's a file "types.xsd" in src/main/java/org/xmlcml/base
12:42 olas2 did see that
12:42 olas2 that's what ir complains about not finding
12:43 egonw maclean: it's in the jar in CDK too?
12:43 olas2 hmm
12:43 * egonw checks
12:43 egonw but assume so
12:43 olas2 it's in the jumbo jar
12:43 egonw otherwise the CDK tests would fail too...
12:43 egonw so, the question is...
12:43 olas2 is this file duplicated?
12:43 egonw why does loading of that file from that jar fail in bioclipse
12:43 maclean some things seem to have moved around in jumbo54.
12:43 olas2 but some cml serialization do work!
12:43 olas2 just not all
12:44 egonw olas2: you did check that no cdk10 classpath sneaked in, correct?
12:44 olas2 right
12:44 egonw I mean, your 200% sure about that, right?
12:44 olas2 286%
12:44 olas2 (I think)
12:44 egonw that should do
12:44 egonw give and take
12:45 egonw ok, please paste me the URL to webview of SVN on SF...
12:45 egonw of the manager tests...
12:45 egonw maybe I see what makes those tests different
12:45 egonw point me to a working and a failing one
12:59 olas hmm
12:59 olas one test works in my office
12:59 olas the same fails in jonalvs office
12:59 olas we are investigating
13:00 egonw ok
13:00 egonw olas: is the @sourcepath important?
13:00 egonw I noted it was missing, but can't imagine how that could cause the problem
13:06 olas2 hi
13:06 zarah hi olas2
13:07 olas2 egonw: we resolved the problem (we think)
13:07 egonw how?
13:07 egonw what was the problem?
13:07 olas2 it goes away if we run with java 1.6
13:07 olas2 so either the jumbo in cdk svn is not updated properly
13:07 olas2 or jonalvs jumbo is not
13:07 olas2 we will look at this now
13:07 egonw ack
13:12 olas same vers from svn
13:12 olas REALLY strange
13:12 olas I don't even have java 1.6 installed
13:13 olas and it works here
13:20 olas /nick jonalv
13:20 olas damn
13:20 olas jonalv: mail sent
13:22 olas zarah: clone olas
13:22 zarah olas: olas: careful. remember when I called YOU stupid? :)
13:22 olas olas: olas: ?
13:24 masak olas: you got cloned, just like you asked :)
13:25 masak @update
13:26 zarah joined #bioclipse
13:35 jonalv zarah: clone zarah
13:35 zarah jonalv: you've just exceeded my capabilities :/
13:41 masak zarah: you're the uncloneable one. :)
13:41 zarah masak: no, YOU'RE the uncloneable one! :)
13:41 masak zarah: no, YOU'RE the uncloneable one! :)
13:41 zarah masak: oh, shut up :)
13:41 masak :)
14:09 olas 156564
14:09 olas just testing :-)
14:10 olas zarah: clone olas
14:10 zarah olas: excuse me?
14:10 olas *puh*
14:12 masak :)
14:29 jonalv http://xkcd.com/463/
14:58 egonw disturbinh
15:13 jonalv egonw: how do I build cdk in Windows?
15:13 egonw ant?
15:13 jonalv it can't run program bash... :)
15:13 egonw ant clean dist-large
15:13 egonw from cmd.exe
15:13 egonw should work
15:14 jonalv I am just trying to follow your instructions for building cdk as descibed on the bioclipse wiki...
15:14 masak Windows doesn't run bash? I'm SHOCKED!
15:15 jonalv C:\Documents and Settings\Administrator\Desktop\Bioclipse2\e​xternals\org.openscience.cdk\build.xml:45: Execute failed: java.io.IOException: Cannot run program "bash": CreateProcess error=2, The system cannot find the file specified
15:15 jonalv
15:15 egonw mmm...
15:16 masak jonalv: the slashes are the wrong way :)
15:16 egonw never knew the build.xml uses bash...
15:16 jonalv masak: they look windowsy enough...
15:16 egonw I don't think it does...
15:17 egonw jonalv: you're sure it's not a problem with your ant install?
15:17 egonw do other build.xml's work?
15:17 jonalv egonw: I am not sure of anything
15:17 egonw ha, the open world philosophie
15:17 jonalv I have only ever used Ant to build cdk in exactly this way...
15:18 jonalv I am not very familiar with ant at all....
15:19 egonw jonalv: what is the output of 'ant info'
15:19 egonw that's most certainly not using bash
15:19 egonw if anything at all
15:19 jonalv how do I run that?
15:19 egonw just like you run 'ant' from the command line
15:20 jonalv I didn't
15:20 jonalv from Eclipse...
15:20 egonw masak: install cygwin
15:20 egonw then it runs bash
15:21 egonw jonalv: how did you run the ant in eclipse then?
15:21 masak egonw: oh great.
15:21 masak egonw: I have an easier solution: don't use Windows.
15:21 egonw :)
15:21 egonw same here
15:21 egonw I was so relieved to get rid of windows...
15:21 masak it's worked very well for me for seven years
15:21 egonw I worked so much more efficient
15:22 masak indeed
15:22 egonw windows was really holding m eback
15:22 masak windows is positively crippling!
15:22 jonalv egonw: just right klick the build.xml or followed your instructions
15:22 egonw if not for the obligatory reinstalls every 3 months
15:22 masak egonw: that wasn't necessary for the versions I used (3.11 and 95)
15:22 masak those were the days...
15:22 egonw ah, I enjoyed 98
15:23 jonalv 95 needed reinstalls all the time
15:23 jonalv 98 too
15:23 masak I only saw 95 at a distance
15:23 masak s/95/98/
15:23 masak I used 95 a lot, never reinstalled it
15:23 masak it crashed all the time, tho'
15:23 masak :(
15:23 jonalv but that's beside the point, I want to test Bioclipse on windows. After all, 99% of oour users run windows...
15:23 masak poor 99%
15:24 masak think of all the HATE they must be accumulating
15:24 jonalv masak: Think of all the hate I am accumulating...
15:24 masak jonalv: noted.
15:24 egonw do you now understand why 99% of the  chemists think computers suck :)
15:24 masak yes.
15:24 jonalv yea
15:24 jonalv :)
15:25 jonalv for them they do...
15:25 masak it's not just windows, by the way.
15:25 masak software in general sucks
15:26 egonw ok, time to go home
16:47 olas edrin: around?
16:47 olas left #bioclipse
16:47 olas joined #bioclipse
16:48 olas edrin: masak is a damn good perl coder
16:49 olas would it not be good to have a perl module for XWS? xwsperl?
16:49 olas he doesn't have much time though
16:49 olas but could be an option for the future :-)
16:49 olas anyway, gotta go now
16:49 * olas is off to the gym
16:50 olas be back in 1 hour
16:50 olas tops
16:52 CIA-50 joined #bioclipse
17:14 edrin olas: now i am
17:15 edrin left #bioclipse
17:45 olas left #bioclipse
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18:58 CIA-50 bioclipse: shk3 * r6651 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: the tests for save were not finished
19:13 CIA-50 bioclipse: shk3 * r6652 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (11 files in 3 dirs): Added help

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