Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-08-07

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All times shown according to UTC.

Time Nick Message
01:11 miguelrojasch joined #bioclipse
06:35 egonw joined #bioclipse
06:57 olass joined #bioclipse
06:57 olass moin
06:57 zarah hi olass
07:08 Gpox joined #bioclipse
07:10 olass egonw: ping
07:10 olass what is wrong with:
07:10 olass git remote add upstream git://github.com/jonalv/bioclipse.structuredb.git
07:10 olass after I clone my fork?
07:10 olass Gpox: do you know?
07:11 Gpox git remote add upstream <name> ...
07:12 olass so is upstream not the name?
07:13 egonw i think it's a keyword
07:13 egonw indicating that you define an 'upstream' repository
07:13 egonw which is prob a remote repository...
07:13 egonw but to which you like to synch frequently...
07:13 egonw and compare too...
07:13 egonw such as 'git status' does
07:13 olass fatal: Not a git repository (or any of the parent directories): .git
07:14 egonw "your branch is 5227 commits behind"
07:14 egonw olass: unintended extra space?
07:15 * egonw is leaving for lunch
07:15 egonw bbl
07:20 egonw back
07:20 egonw BTW, it occured to me that we will be able to run BSL scripts from the command line
07:20 egonw without having to boot Bioclipse at all
07:21 olass sure
07:21 olass we just need a daemon
07:24 olass egonw: and we could produce a worker/node for BSL snippets (gists) for Taverna or Knime
07:25 egonw right :)
07:27 olass that would make a nice app note
07:32 egonw OK, back to 2.1
07:32 CIA-63 bioclipse.balloon: Ola Spjuth master * r3da3373 / (6 files in 6 dirs): Set version to 2.1.0 - http://bit.ly/2Aafc5
07:34 CIA-63 bioclipse.core: Ola Spjuth master * r7ad7fa3 / (4 files in 3 dirs): Set version for 2.1.0. - http://bit.ly/KKUR3
07:41 jonalv joined #bioclipse
07:41 jonalv o/
07:42 egonw hi jonalv
07:42 egonw jonalv:
07:42 egonw [08/07/09 09:20] <egonw> BTW, it occured to me that we will be able to run BSL scripts from the command line
07:42 jonalv egonw: well that has occured to me as well but then I realized that: Oh hang on. How would we go about doing that?
07:43 egonw ha, a puzzle!
07:43 olass a riddle
07:43 egonw well, Spring works from the command line too...
07:43 olass a quest!
07:43 jonalv egonw: no really what was your thought?
07:43 egonw so, we need only worry about the eclipse stuff inherited?
07:44 egonw there is the issue of lack of a 'workspace'...
07:44 egonw we would have to dynamically boot one based on the current folder
07:45 olass egonw: we need an app like the infosys
07:45 olass like how we run the help system
07:45 olass then we can have Bioclispe-REST!
07:45 egonw it seems to me that the CmlFileDescriber is processing the complete XML document!
07:46 olass did you not see me filing you a bug about that?
07:47 olass it is very annoying
07:47 egonw yes, that's the bug I am looking at
07:47 olass ah, good
07:47 olass yes, I got that feeling too
07:48 egonw damn
07:48 egonw no unit tests...
07:50 jonalv egonw: it seems that you instructions for making git repos from SVN has not quite worked. The .get folder in bioclipse.structredb is appharently 75MB. Do you think you could help me with that some time?
07:51 egonw jonalv: how do you envision me to help?
07:51 olass fix it?
07:51 jonalv egonw: well yea...
07:51 jonalv egonw: you seem to know how that works...
07:51 olass fix git?
07:52 olass 'git fix structuredb'
07:52 olass it's like 'git make coffee'
07:52 olass you expect it to work..
07:52 olass but it doesn't
07:53 egonw jonalv: how what works?
07:53 jonalv egonw: the history rewriting
07:53 egonw with what purpose?
07:53 olass egonw: is speclipse developed against 2.0.x or master?
07:53 jonalv egonw: I don't really care if the Structuredb repo is 80MB but is seems olass do..
07:53 egonw olass: is it not large enough?!?!
07:53 olass it is much larger than core and cheminfo
07:54 egonw olass: 80MB is not the limit of what you can put in it?
07:54 olass github has limited space
07:54 egonw jonalv: what path did you use?
07:54 olass egonw: stop being a smartass
07:54 egonw jonalv: removing stuff or adding stuff?
07:54 jonalv olass: stop being me? How do one do that? ;)
07:55 olass take a knife...
07:55 olass imagine the rest
07:55 olass (poison just as good)
07:55 jonalv olass: oh you can cut out the "me" part being the smartass? ;)
07:55 olass jonalv: please try, it is in the chest
07:55 olass egonw: is speclipse developed against 2.0.x or master?
07:56 olass or both?
07:56 egonw olass: why do you think I have any clue?
07:56 olass you commit there
07:56 egonw I'm a smartass, not omniscient
07:56 olass I'd ask shk3, but he's not around
07:56 olass ok, then I will remove speclipse update site from 2.1.0
07:56 jonalv egonw: but if we could have a look at it sometime that would be really nice...
07:56 egonw olass: I guess he will be around shortly
07:57 egonw it's almost 9am in the UK now
07:57 egonw [08/07/09 09:54] <egonw> jonalv: removing stuff or adding stuff?
07:57 * jonalv semi-afk reading the Bioclipse 2 application note
07:57 egonw jonalv: I suggest you try the second alternative mentioned in the wiki
07:57 egonw adding folders...
07:57 jonalv egonw: well we don't need to add stuff it's already too much in there...
07:57 egonw jonalv: start with a new empty git
07:57 egonw and copy in plugin folder one by one
07:58 egonw jonalv: please read the wiki
07:58 egonw or, in more common language: RTFM
07:58 jonalv egonw: I thought I did that the first time...
07:58 egonw yes, guess so
07:59 egonw but you picked the wrong alternative
07:59 olass well it's not urgent
07:59 egonw I hope
07:59 olass but at some time it would be nice
07:59 egonw otherwise the repos size will not shrink anyway
07:59 olass indeed
07:59 egonw olass: yeah, it would be good if you did that too
07:59 olass did what?
07:59 egonw bioclipse.core is also larger than it needs to be
08:00 olass you set it up!
08:00 jonalv okey...
08:00 egonw olass: yes, and I chose the wrong alternative :)
08:00 egonw which is the whole reason why there now is an alternative
08:00 olass I will do that "some day(tm)"
08:00 egonw yes
08:01 egonw because everyone will have to remove all current checks outs, forks, etc
08:01 egonw and start from scratch from the new copy
08:01 olass let's do that the last day before a release
08:01 jonalv awesome, let's do all repos at the same time then shall we... :)
08:01 egonw or maybe we should just not care about 80MB?
08:02 olass jonalv: yes, I have time 2014 in the fall...
08:02 jonalv olass: yea I think I can book a week there...
08:02 olass let's care when we reach github limit
08:02 egonw 2014... as an Nov 2009 19 ?
08:02 egonw 2014... as an Nov 2009 14 ?
08:02 olass jonalv: oh, I only have 5 mins
08:02 olass you want a week?
08:02 jonalv olass: oh so one minute a day during that week? :)
08:02 olass that's not until year 2177
08:03 olass sry
08:03 olass quite fully booked
08:03 jonalv so let's igore it all for now then?
08:05 CIA-63 bioclipse.core: Ola Spjuth master * r5037728 / (3 files in 3 dirs): Set update site for 2.1.0 devel release: http://bioclipse-devel.bioclipse.net - http://bit.ly/j6Vj5
08:05 zarah CIA-63's link is also http://tinyurl.com/ms8xul
08:12 CIA-63 bioclipse.qsar: Ola Spjuth master * rce0e8d3 / (11 files in 11 dirs): Set versions for 2.1.0 release. - http://bit.ly/HsN0y
08:13 olass egonw: does the rdf feature work with master or 2.0.x?
08:13 olass is there a branch?
08:15 egonw I tested it more recent with 2.1
08:15 egonw and not tested lately with 2.0
08:15 egonw but it should work
08:18 olass egonw: have you set version for 2.1.0?
08:18 olass jonalv: should structuredb go in 2.1.0 devel update site?
08:18 egonw yes, see bug report
08:18 jonalv olass: will that be built today?
08:18 olass jonalv: if so, please set version to 2.1.0.v20090807
08:18 olass yes
08:19 olass but we can easily add sdb later if you so wish
08:19 jonalv olass: honestly I don't know. :) What do you think?
08:19 olass note it is DEVEL version
08:19 olass if you can try ANYTHING, we should add it
08:19 egonw jonalv: release soon, release often
08:19 egonw if you do not release, you won't get feedback
08:19 jonalv there are lot's of things you can try in it
08:19 olass then please set version correctly
08:19 jonalv there are alos quite some things that you can't do...
08:19 olass egonw: please bug number?
08:20 jonalv olass: oki will do
08:20 egonw and certainly not interested developers
08:20 olass egonw: have you set version for rdf feature?
08:20 egonw olass: no, will do so now
08:23 olass egonw: structruredb.rdf does not compile
08:23 egonw btw, me can recommend the util 'tig'
08:23 olass jonalv: structuredb does not compile, missing import: net.bioclipse.chemoinformatics.PickMoleculeDialog
08:24 egonw olass: very likely
08:24 jonalv olass: update chemoinformatics
08:24 egonw olass: structuredb.rdf is not updated for jonalv's recent work
08:24 olass hmm, thought I did that..
08:24 egonw jonalv: no, have not applied your patch yet
08:24 jonalv I think egonw  applied my commit.
08:24 jonalv I am pretty sure I saw it listed here
08:24 jonalv oh
08:24 jonalv okey then I was dreaming :)
08:25 CIA-63 bioclipse.rdf: Egon Willighagen master * r14a34f1 / plugins/net.bioclipse.structuredb.r​df/src/net/bioclipse/structuredb/rd​f/business/StructureRDFManager.java : Updated for recent structuredb API changes - http://bit.ly/WfEFF
08:25 CIA-63 bioclipse.rdf: Egon Willighagen master * re25de02 / (9 files in 9 dirs): Updated versions to 2.1.0.v20090807 for the update site - http://bit.ly/19P56o
08:26 CIA-63 bioclipse.cheminformatics: jonalv master * r9d125d7 / plugins/net.bioclipse.chemoinformatics/src/net/bi​oclipse/chemoinformatics/PickMoleculeDialog.java :
08:26 CIA-63 bioclipse.cheminformatics: A first candidate for a dialog for picking a molecule from the worskpace.
08:26 CIA-63 bioclipse.cheminformatics: It looks terrible and in the best of worlds it would be possible to resize it
08:26 CIA-63 bioclipse.cheminformatics: but we are not there yet. However it seems impossible to that with a
08:26 CIA-63 bioclipse.cheminformatics: TitleAreaDialog so it probably have to be rewritten from scratch based on some
08:26 CIA-63 bioclipse.cheminformatics: other class.
08:26 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/Vnak9
08:27 olass jonalv: version in structuredb, is that on its way or will it take time?
08:27 olass you can still work for this entire day
08:27 jonalv olass: oh I didn't realise I needed to stop everything I was doing and fix it. I will do so now though.
08:27 olass possibly tomorrow as well
08:27 olass thx
08:27 * olass is building and wants to test
08:27 olass if things fail, it takes time to fix
08:28 * olass is not optimistic anymore
08:28 olass core export seem to work at least
08:28 jonalv olass: velcome to my world :)
08:28 olass jonalv==ior
08:28 olass :)
08:28 jonalv ior == my greatest hero
08:28 jonalv :)
08:35 olass jonalv: ping me when done
08:35 CIA-63 bioclipse.core: jonalv master * rd6c0c0f / plugins/net.bioclipse.data​bases/META-INF/MANIFEST.MF : set version to 2.1.0.v20090807 - http://bit.ly/HmI8x
08:35 CIA-63 bioclipse.structuredb: jonalv master * rbf67361 / (2 files in 2 dirs): Set version to 2.1.0.v20090807 - http://bit.ly/TcOlD
08:35 olass egonw: ping
08:36 jonalv olass: ping
08:36 olass cheminfo feature must depend on core feature version 2.0.0.v20090807 could you commit this?
08:36 egonw pong
08:36 olass jonalv: pon
08:36 olass g
08:36 egonw olass: 2.0.1.foo you mean?
08:36 jonalv olass: I think I am done
08:36 olass egonw: 2.1.0
08:36 olass this is devel release
08:36 olass towards 2.2.0
08:37 olass we are in master
08:37 olass egonw: capice?
08:37 olass (btw, this was your suggestion)
08:37 CIA-63 bioclipse.rdf: Egon Willighagen master * r72787f7 / (2 files in 2 dirs): Versioned the feature dependencies to 2.1.0.v20090807 too - http://bit.ly/3QPS7Z
08:37 olass thx
08:38 egonw olass: then why did you say 2.0.0 in the first place?!?!?!
08:38 egonw olass--
08:38 olass just kidding :)
08:38 olass egonw-- //for forgetting it in the first place
08:38 jonalv olass: is the funny one
08:40 olass egonw: and cheminfo_feature?
08:40 olass on the way?
08:40 egonw yes, on its way
08:41 olass jonalv: this goes for sdb too
08:41 jonalv olass: sry what do you want me to do?
08:42 olass add dep from sdb_feature to core_feature version 2.1.0.v20090807
08:42 olass maybe not overly important
08:42 jonalv olass: change sdbfeature dep?
08:42 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r0380c04 / plugins/net.bioclipse.cml/src/net/bioclip​se/cml/contenttypes/CmlFileDescriber.java : Limit the amount of XML to be processed, before giving up any further analyses, to not make it crash on multi MB files (fixes #1446) - http://bit.ly/wOJSJ
08:42 zarah bug #1446 | http://tinyurl.com/nn32py
08:42 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * rcc7bcf2 / (2 files in 2 dirs): Versioned the feature dependencies to 2.1.0.v20090807 too - http://bit.ly/wAPsW
08:42 olass jonalv: yes, now it is incorrect
08:42 olass it depends on old versions
08:43 olass please fix
08:43 * olass wishes he could just fix these things
08:43 egonw olass: you can
08:43 olass this procedure is really slowed down now
08:43 * olass does not have commit rights to sdb
08:43 egonw so what?
08:44 olass jonalv: let me know
08:44 jonalv olass: okey you can do this locally on your own machine, push it to your fork and ask me to pull you know...
08:45 CIA-63 bioclipse.structuredb: jonalv master * radb335b / features/net.bioclipse.stru​cturedb_feature/feature.xml : Updated version deps for structuredb feature - http://bit.ly/16UmMu
08:45 jonalv olass: done
08:46 egonw 'Preemptive Guilt': http://feedproxy.google.com/~r/D​ilbertDailyStrip/~3/sGve_2rXifM/
08:47 zarah egonw's link is also http://tinyurl.com/mnp8fg
08:52 CIA-63 bioclipse: ospjuth * r11724 /bioclipse2/trunk/features/net.bi​oclipse.sdk_feature/feature.xml: Removed redundant dep for sdk feature.
08:53 * olass is now happy to start building update site
08:53 olass there might be mor eissues, but none that I can spot out of the box
08:53 jonalv \o/
08:54 olass ARGH
08:54 jonalv olass?
08:55 olass sdb has classpath cycle
08:55 jonalv olass: huh?
08:55 * jonalv mumbles some evil words about Eclipse
08:56 olass "a cycle was detected when generating the classpath net.bioclipse.structuredb_2.1.0.v20090807, net.bioclipse.bundle.spring.orm_2.5.1, net.bioclipse.structuredb_2.1.0.v20090807
08:56 olass jonalv: please see if you can fix this
08:56 olass I have no clue
08:57 jonalv olass: I am on it
08:57 jonalv *not that I ahve a clue either though...)
08:59 jonalv olass: seems like I have to move iBatis outside the StrucutreDB plugin...
08:59 olass one more plugin?
08:59 olass ok
08:59 jonalv olass: yup
08:59 olass do that
09:00 * olass is testing the rest in the meantime
09:07 * egonw notes he has 138 open bugs
09:10 * jonalv is stuck in the deps jungle again
09:10 jonalv why oh why doesn't it just work?
09:10 * olass is happy to see that egonw's gist works up to the point where balloon is used
09:11 egonw hahaha
09:11 olass you did not test it, right?
09:11 egonw no, not the balloon
09:11 olass why not?
09:11 egonw because I had no time up update that yet
09:11 olass ok
09:11 egonw and needed some sleep
09:11 olass what is a reasonable timeout for balloon?
09:12 olass clearly generating conformers is a tedious task
09:12 olass 2 mins is NOT enough
09:12 * olass hopes it is not another problem
09:13 egonw wow: http://9elements.com/io/projects/html5/canvas/
09:13 zarah egonw's link is also http://tinyurl.com/nsfqd4
09:13 * olass is testing 10 minuts now and only generating 2 conformers each
09:16 olass egonw: did you look at the downloaded molecules?
09:16 egonw yes
09:16 olass some are huge, and seems to take forever with balloon
09:16 egonw yes
09:16 egonw HIV
09:16 egonw remember
09:16 olass yes
09:16 olass hmm
09:16 olass not good
09:16 egonw many small protein sequences
09:17 egonw which is why I picked C1CNCC1 as SMILES
09:17 egonw == proline
09:17 jonalv maybe you can run them one at a time so you only time out on the big ones and still get the small ones?
09:17 egonw but also found in a old fashion drug in the search results
09:17 jonalv GAH
09:17 * jonalv restarts Eclipse something is seriously wrong here
09:19 jonalv But the class file is in the jar file why can't the freaking plugin find it?
09:21 olass egonw: can you update the gist and change last line to: balloon.generateMultiple3Dconformations(..)
09:21 olass then it works
09:21 olass however
09:22 olass is times out
09:22 olass any idea how to change it?
09:22 olass hmm
09:22 egonw no
09:22 olass then please wait
09:22 egonw just run it on one structure?
09:22 olass yes
09:22 olass sounds good
09:23 jonalv guys I think I need help
09:24 olass egonw: change the line to: balloon.generate3Dconformations(matches.get(0), 5);
09:24 olass 51 chars
09:24 olass should be fine
09:24 olass egonw: ok?
09:24 olass jonalv: what can I do?
09:24 jonalv fuck
09:24 jonalv I did this all wrong
09:24 * jonalv redoes it and hopes it will work better this time
09:26 egonw olass: like this: http://gist.github.com/163575 ?
09:26 olass yes
09:26 * olass is confirming
09:30 olass it works, but look crappy
09:30 olass will add some visu
09:30 olass that can go in the gist, but not in the paper
09:32 olass egonw: maybe we should save to SDF after all..
09:32 * olass is doing so
09:35 egonw I think this is a good thing
09:35 egonw people like looking at 2D diagrams
09:35 olass it is in 3d, but anyway
09:36 olass you can look at it in 2d
09:37 * egonw moved to reviewing paper drafts
09:41 olass egonw: please change last two lines in gist to:
09:41 olass conf=balloon.generate3Dcon​formations(matches.get(0), 5);
09:41 olass cdk.saveSDFile("Virtual/conf.sdf", conf);
09:41 olass that should do it
09:42 egonw no ui.open("Virtual/conf.sdf") ?
09:46 olass no
09:46 olass that does not work
09:46 olass and besides, not important
09:46 olass users can do that themselves
09:46 olass ok, that is pretty much it
09:46 olass export seems to work
09:46 olass update site seems to work
09:47 olass the 2 gists seems to work
09:47 * olass will put all together after lunch
09:47 olass egonw: does the ui.open(..) work for you?
09:48 olass not here
09:48 egonw oh, OK
09:50 olass egonw: Pubchem is queried for compounds matching the name "HIV" using a Web service
09:50 olass is that really true?
09:50 olass don't you just put together a URL?
09:50 egonw it's not using SOAP
09:50 egonw if that is what you mean
09:50 olass REST?
09:50 egonw REST is just using a URL
09:50 egonw but it is not REST
09:50 olass ok
09:50 egonw it's the PubChem eUtilz
09:51 olass ok
09:53 olass egonw: can I expect any more bugfixes to cheminfo very soon?
09:53 egonw no
09:53 olass ok, then I will build 2.1.0
09:53 egonw the rest all takes much more time
09:54 olass ack
09:54 CIA-63 bioclipse.structuredb: jonalv master * r9ed78a2 / (11 files in 8 dirs): moved iBatis out of net.bioclipse.structuredb into net.bioclipse.databases.iBatis - http://bit.ly/ji9tk
09:56 jonalv olass: now I manage to build but for some reason the databaess view does not make it into the build
10:05 jonalv olass: ping
10:05 olass jonalv: pong
10:05 * olass is in the middle of lunch
10:05 jonalv olass: have yout ried to build StructureDB after my changes?
10:06 jonalv aha
10:06 olass nope
10:06 olass give me 10 mins
10:06 olass and I will try
10:06 jonalv maybe I should go for lunch as well
10:06 olass jonalv: is teh DB plugin in structuredb feature now?
10:06 jonalv olass: yes
10:06 olass ok
10:17 jonalv now, where to eat? :)
10:24 * olass recommends the mouth
10:31 olass jonalv: ping
10:42 olass egonw: ping
10:42 olass please do not use ArrayList as impl in managers, use RecordableList. Else it is not possible to use ui.open() on the results
10:46 olass I fixed this
11:04 jonalv olass: pong
11:04 olass jonalv: sdb builds now
11:04 olass I fixed the build.props in databases
11:04 jonalv good, and cam you run it?
11:05 olass so view appears
11:05 jonalv good
11:05 olass have not tried yet
11:05 jonalv what was wronmg?
11:05 olass I fixed the build.props in databases
11:05 * jonalv has no idea what that means :)
11:05 olass build.properties specifies what goes in the binary build
11:05 olass plugin.xml was not checked
11:05 jonalv olass: ah
11:06 jonalv olass: that explains that. good. olass++
11:06 olass please verify this for all structuredb plugins
11:06 olass I have not done that
11:06 * olass is exportin g2.1.0 for the moment
11:06 jonalv olass: so I ahve a pull request waiting for me now? :)
11:07 olass no
11:07 olass it was in core
11:07 olass I committed it
11:07 olass net.bc.databases is in core
11:07 jonalv olass: ah right
11:07 jonalv true that
11:07 olass not sure if that is good, but that is how we have it
11:08 jonalv yea
11:08 jonalv I don't know eiehter
11:09 * jonalv goes and fetches some water. it's hot. is it summer perchance? :)
11:23 CIA-63 bioclipse.cheminformatics: Ola Spjuth master * r025a457 / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/CDKManager.java :
11:23 CIA-63 bioclipse.cheminformatics: Use RecordableList instead of ArrayList to make it possible to use ui.open(list).
11:23 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/18YmFD
11:28 jonalv olass: ping
11:28 olass pong
11:28 jonalv olass: have you exported SDB now so any thing new that I does won't go in?
11:28 olass no
11:28 jonalv oh
11:28 olass sdb is on update site
11:28 jonalv hm..
11:28 olass that is just to upload
11:29 olass exporting is core, ballon and cheminf
11:29 jonalv oh I mean have you built it?
11:29 olass feel free to continue working
11:29 olass define built
11:29 olass compiled? yes
11:29 jonalv uploaded
11:29 olass no
11:30 jonalv I need to make changes in multiple places and I don't want version trouble after the export just because some patches aren't along...
11:30 olass jonalv: sdb seems to work fine
11:30 olass jonalv: no worries
11:30 jonalv olass: sounds good
11:30 olass as long as you don't update cheminf
11:30 olass cheminf will be as it is now
11:30 egonw olass: hang on
11:30 egonw I think I got one fix
11:30 jonalv olass: ah that is what I am doing..
11:30 olass egonw: can you tag 2.1.0 ?
11:30 olass oh
11:30 olass :(
11:30 egonw minor one
11:30 egonw never mind
11:31 olass me has already exported
11:31 egonw no worries
11:31 olass please tag and go ahead
11:31 olass 2.1.0
11:31 * egonw will tag 2.1.0 for bioclipse.cheminformatics and bioclipse.rdf
11:31 * olass will tag core now
11:31 olass and balloon
11:31 olass etc
11:31 jonalv olass: so please don't update Structuredb before you upload StructureDB to the update site then...
11:31 jonalv olass: will that work?
11:31 olass jonalv: please tag
11:31 olass jonalv: sorry?
11:31 jonalv olass: sry tag what?
11:31 olass upload but don't update?
11:32 olass 2.1.0
11:32 jonalv olass: upload but don't pull
11:32 olass ok
11:32 olass but please tag anyway
11:32 egonw .cheminformatics and .rdf tagged
11:32 jonalv (jonalv still talks SVN wording...)
11:32 olass super
11:32 jonalv olass: we should have a git repo containing links to all other git repos with a certain version
11:33 jonalv olass: so if someone want's to check out the code for 2.1 he she just checks out  a tah in that repo and get everything
11:33 olass set it up if you like
11:33 olass hmm
11:33 * jonalv might do that some day... :)
11:33 olass is that the bioclipse repo?
11:34 olass jonalv: you forgit the (tm)
11:34 olass I have trademarked that
11:34 olass else I will sue you
11:34 jonalv olass: sry what?
11:34 olass some day(tm)
11:35 olass and, btw, never use "some day" with an alligator; I have TMed that too
11:36 jonalv oh okey I might do it some-day™
11:36 egonw any reason why a List<Integer> should not be recordable?
11:37 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r34476e0 / plugins/net.bioclipse.pubchem/src/net/bioc​lipse/pubchem/business/PubChemManager.java : Use RecordableList instead of List for all Bioclipse resources - http://bit.ly/yyzuT
11:37 jonalv egonw: I am not sure. It's complicated...
11:47 jonalv github is cool: <http://github.com/egonw/biocl​ipse.cheminformatics/network>
11:48 zarah jonalv's link is also http://tinyurl.com/nz6cg2
11:48 egonw :)
11:48 egonw you'd no seen that before?
11:48 jonalv egonw: not with 4 diffferent repos at the same time
11:48 egonw heheheh
11:49 jonalv egonw: I huess that repo keeps you busy? :)
11:49 egonw yes
11:49 egonw but at least I can control now what goes in
11:50 jonalv yea
11:50 jonalv that is very nice
11:50 egonw but I will start bugging people to not ask me to pull upon every single bit changed...
11:50 egonw but actually work with somewhat larger patch sets
11:50 egonw :)
11:50 jonalv hehe
11:51 egonw I can also suggest people to use rebase for their private copies a bit more
11:51 jonalv egonw: yea I always forget that and realises after I ahve already pushed that "ooops I should ahve rebased...."
11:52 egonw did you commit SingleMoleculeContentTypeViewerFilter too?
11:52 egonw I don't seem to have that in my copy
11:52 egonw find . -name SingleMoleculeContentTypeViewerFilter.java
11:52 jonalv egonw: yes
11:53 egonw ha, indeed
11:53 egonw I see it now
11:53 jonalv egonw: commit: 21e663627f03622ec085dd9525f9c0d6c18a9f52
11:53 egonw apparently GitHub does not show the source for new files...
11:53 egonw I see it now
11:53 jonalv okey
11:53 jonalv neither does gitx actually
11:53 jonalv it sort of sucks...
11:54 CIA-63 bioclipse.cheminformatics: jonalv master * r0de28d5 / plugins/net.bioclipse.chemoinformatics/​src/net/bioclipse/chemoinformatics/util​/MoleculeContentTypeViewerFilter.java :
11:54 CIA-63 bioclipse.cheminformatics: layout (80 cols)
11:54 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/NyFsJ
11:54 CIA-63 bioclipse.cheminformatics: jonalv master * r173941c / (2 files in 2 dirs):
11:54 CIA-63 bioclipse.cheminformatics: Wrote a SingleMoleculeContentTypeViewerFilter and switched to using that instead in the PickMoleculeDialog.
11:54 CIA-63 bioclipse.cheminformatics: The PickMoleculeDialog should only pick one molecule.
11:54 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/BV5K
11:54 CIA-63 bioclipse.cheminformatics: jonalv master * rc6ac21f / plugins/net.bioclipse.chemoinformatics/src/net/bi​oclipse/chemoinformatics/PickMoleculeDialog.java :
11:54 CIA-63 bioclipse.cheminformatics: Changed the treeviewer in PickMoleculeDialog to only allow selection of one resource.
11:54 CIA-63 bioclipse.cheminformatics: The PickMoleculeDialog should be used for picking one molecule.
11:54 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/BsF8c
12:00 olass egonw: http://pele.farmbio.uu.se/b​ioclipse/help/2.0/index.jsp
12:00 zarah olass's link is also http://tinyurl.com/kw5yxj
12:01 egonw wow
12:01 egonw olass: did you try rebooting the help server?
12:01 olass tomcat?
12:01 olass or the infosys?
12:01 olass no
12:01 egonw the eclipse help system
12:01 olass that is the infosys
12:02 olass nope
12:02 olass I can try
12:03 olass ola@pele:/var/www$ java.io.FileNotFoundException: /var/www/workspace/.metadata/.helplock (No such file or directory)
12:03 olass hmm
12:03 olass ah
12:03 olass sry
12:04 olass ok, fixed it
12:06 olass egonw/jonalv: comments on http://pele.farmbio.uu.se/bioclipse-devel/ ?
12:06 zarah olass's link is also http://tinyurl.com/l7lteh
12:06 olass I am still uploading the files
12:07 olass but do you have comments on text?
12:07 olass add something?
12:08 egonw I suggest adding links to the source?
12:08 olass the git repos?
12:08 egonw yeah, all three: .core, .balloon and .cheminformatics
12:08 olass I can link to the wiki page listing the repos
12:08 egonw yeah, that should be fine too
12:08 jonalv olass: I like
12:09 jonalv but yes links to source wouldnät hurt
12:09 egonw oh, and link to Planet Bioclipse instead of the Bioclipse Blog?
12:09 jonalv what egonw said
12:11 olass yes
12:11 olass thx
12:15 jonalv olass: our rcpdeveloper key has already expired... :( Did we pay for that or was that some sort of free for academics?
12:15 olass we got it for free
12:15 olass feel free to ask them again
12:15 olass I am getting tired of this
12:15 jonalv olass: do you remember how you did that?
12:15 olass email
12:15 egonw "our rcpdeveloper key" ?
12:16 jonalv olass: I will try the free version and see if I can live wioth that...
12:16 olass ok
12:16 jonalv that is much easier...
12:17 olass egonw/jonalv: is http://pele.farmbio.uu.se/bioclipse-devel/ better now?
12:17 zarah olass's link is also http://tinyurl.com/l7lteh
12:17 egonw The source code for Bioclispe is available
12:17 egonw typo
12:18 egonw link to bugzilla missing
12:18 egonw maybe also mention IRC
12:20 olass hmm
12:20 olass there is a link to the wiki
12:20 olass I do not intend to duplicate everything there
12:20 egonw :)
12:20 egonw but bugzilla is a must
12:20 olass ok
12:21 egonw in the section
12:21 egonw support for development versions
12:43 olass egonw, jonalv: could you please test downloading a version at http://pele.farmbio.uu.se/bioclipse-devel/ and try the update site, and verify that the two gists 163575 and 163440 work?
12:43 zarah olass's link is also http://tinyurl.com/l7lteh
12:43 olass jonalv: windows please :L
12:44 * olass ducks and covers
12:44 jonalv olass: when do you need that?
12:44 jonalv olass: is it okey if I do it at home druing the weekend?
12:44 olass now?
12:44 olass want to submit the paper
12:44 olass hmm
12:44 jonalv olass: running Windows on this machine sucks but running it for real at home is slighlty better
12:45 olass ok, I can boot my windows machine I guess
12:45 olass ok, I'll do it *sigh*
12:45 olass jonalv: please test mac then
12:45 jonalv olass: oki
12:46 olass http://bioclipse.blogspot.com/2009/08/​bioclipse-210-development-release.html
12:46 zarah olass's link is also http://tinyurl.com/mdwwax
12:46 * olass hopws it owrks ;)
12:47 * olass hopes it works ;)
12:48 jonalv olass: what's the point in generating 3d coords when the sdf editor only shows 2d?
12:48 olass jonalv: it's a demo
12:49 olass it's not solving real world problems
12:49 olass it shows what you CAN do
12:49 jonalv olass: okey but How can I see that it worked?
12:49 olass DC the file if you like
12:49 jonalv olass: DC?
12:49 olass hmm, right-click and open in jmol
12:49 olass doubleclick?
12:50 jonalv olass: could I suggest that the script opens the generated file as well?
12:51 olass not possible
12:51 jonalv oh why not?
12:51 olass jmol does not support this
12:51 jonalv oh yea it just sort of support it...
12:52 jonalv this really sucks... :(
12:52 jonalv the Outline in jMol needs more love but I know what a messy problem that is... :(
12:54 jonalv olass: the second script give: org.mozilla.javascript.EcmaError: ReferenceError: "biows" is not defined. (line: #2)
12:55 jonalv olass: O hang on. bioinformatics feature is on the update site but vheminformatics feature is in build? That's unintuitive...
12:56 jonalv olass: maybe this update site should have another name than "Bioclipse Update Site" something like experimental och devlopment or something?
12:59 jonalv olass: they seem to be working
13:02 olass jonalv: it is clearly stated on page http://pele.farmbio.uu.se/bioclipse-devel/ that you need to use the update site
13:02 zarah olass's link is also http://tinyurl.com/l7lteh
13:02 olass you probably missed that, right?
13:03 olass but there are bugs for assertFeatureInstalled(...)
13:03 olass jonalv: about the update site name: I agree
13:03 olass will change that
13:03 olass for the next update :)
13:04 olass hmm, no, for the next release
13:04 jonalv olass: yes I missed that. Maybe us bioinformaticians feel misstreated when the cheminformatics feature is bundled with Bioclipse but bioinformatics feature is not?
13:04 olass would need to re-export all
13:04 jonalv :)
13:04 olass jonalv: RTFM
13:04 jonalv olass: what has that got to do with anything?
13:04 olass it explains it
13:04 jonalv olass: I am not saying that it is not documented
13:04 olass good
13:04 olass then why the complaints?
13:05 olass you want a reason why?
13:05 jonalv olass: "Jag kaenner mig kraenkt" ;)
13:05 jonalv olass: do you ahve one?
13:05 olass kraenka mig hit och dit
13:05 jonalv haha
13:05 olass :)
13:05 olass nja, bioinfo känns väldigt mycket mer beta än chemifno
13:06 jonalv olass: tja det aer ju sant men hela releasen aer ju beta...
13:06 olass hmm swe?
13:06 jonalv olass: oops
13:06 olass egonw: did it work on linux?
13:06 jonalv let's use english in here shall we :)
13:06 egonw still downloading
13:09 jonalv egonw: aren't you the slow one :)
13:17 olass damn
13:17 olass jmol does not open on windows
13:17 olass classformatexception
13:17 olass what does that mean?
13:18 egonw 49.0 ?
13:18 olass egonw: have you ever tried latest Jmol on windows?
13:18 egonw sure
13:18 olass 49.0?
13:18 egonw oh, on windows
13:18 olass what is that?
13:18 egonw no
13:19 egonw you did not see that?
13:19 olass egonw: can you confirm the gists work on linux?
13:19 olass and that jmol can be used?
13:19 olass works on mac
13:19 egonw olass: slow down...
13:19 egonw still downloading
13:19 olass no, you speed up!
13:19 olass :)
13:20 olass Illegal exception table range in class file org/jmol/viewer/ScriptEvaluator
13:21 olass egonw: any idea?
13:21 egonw update 38%
13:21 olass jonalv: any idea?
13:21 egonw @gg "Illegal exception table range"
13:21 zarah egonw: http://lists.jboss.org/pipermail/jbos​s-dev-forums/2006-August/000781.html
13:23 olass egonw: why would that help me?
13:23 egonw google is always helpful
13:23 zarah egonw: http://www.judithshoemaker.com/
13:24 egonw hahahaha
13:24 olass egonw: why would that help me?
13:24 olass :)
13:24 egonw zarah: funny you!
13:24 zarah egonw: excuse me?
13:24 egonw you always need good shoes
13:24 olass egonw: seriously, do you have any idea?
13:24 egonw without good shoes, no bioclipse
13:24 egonw no clue
13:24 egonw but I think your windows has a crappy old JVM
13:24 egonw pre 1.5
13:24 egonw or so
13:24 egonw dunno
13:25 olass hmm
13:25 olass no
13:25 olass but I have an idea...
13:27 olass no
13:27 olass that did not work
13:27 olass I'm out pf ideas
13:27 egonw update manager 33%
13:27 olass ok, should we ignore this for now?
13:27 egonw that 5% point less then earlier ?!?!?
13:28 * olass will ignore that jmol does not work on windows if he doesn't get any help from jonalv and egonw
13:28 * jonalv is back
13:28 * egonw cannot help without a good bug report
13:29 olass well you know what I know
13:29 jonalv olass: sry I don't really know what's going on. Didn't Jmol use to work?
13:29 egonw then I cannot help
13:29 jonalv what has changed?
13:29 olass yes
13:29 olass I can confirm in 2.0
13:29 egonw but likely any reviewer will run windows
13:29 olass that it works
13:30 olass egonw: please downgrade jmol to latest version that worked
13:30 egonw I have no means of testing that right now
13:30 jonalv are we running a later Jmol version than we used to?
13:30 egonw and moreover still testing the Linux version
13:30 olass I am not talking testing, I am talking downgrading
13:30 olass I'll test
13:30 egonw no, read what you wrote
13:30 egonw "latest version that worked"
13:31 egonw I'm not on windows
13:31 olass 2.0.x version works
13:31 egonw I do not know what that is
13:31 jonalv olass: jsut revert the commit that upgraded jmol and test again
13:31 egonw .x ?
13:31 egonw or .0?
13:31 egonw olass: which commit?
13:31 olass you find out
13:31 olass you upgraded it
13:31 egonw olass: tell me which commit worked, and I'll downgrade
13:31 olass and broke it
13:31 olass no, this is your bug
13:31 egonw yeah, which commit broke it?
13:31 egonw I cannot help that windows is broken
13:31 olass you tell me
13:31 olass what?
13:32 olass you install a new Jmol that is not operational, and you say it is not your fault?
13:32 olass come on
13:32 egonw no, the new Jmol works fine
13:32 olass be reasonable
13:32 olass on windows?
13:32 egonw no clue
13:32 olass you see?
13:32 olass please downgrade
13:32 egonw but I already said that I need to know what version did work on windows
13:32 * jonalv feels that he just loves fridays afternnons the time of the week that just can't spell to pordcutivity
13:32 olass 2.0.0
13:33 olass tag 2.0.0 works on windows
13:33 olass I just confirmd it
13:33 egonw I'll downgrade by you'll have to test
13:33 olass *sigh* yes
13:33 egonw I'll downgrade but you'll have to test
13:33 olass can I downgrade myself?
13:34 egonw yes, sure
13:34 olass how?
13:34 egonw that's what I suggested
13:34 olass in my local branch?
13:34 olass please tell me how
13:34 egonw then you can let me know what version of Jmol does work in 2.1
13:34 egonw *sigh*
13:34 steinbeck joined #bioclipse
13:35 jonalv hi steinbeck
13:35 olass egonw: so, how do I do it?
13:35 egonw git revert
13:36 olass only that?
13:36 * olass is testing
13:36 olass nope
13:36 olass should I not say what to revert?
13:37 egonw sure you do
13:37 olass how?
13:37 egonw @gg git revert
13:37 zarah egonw: http://www.kernel.org/pub/softwa​re/scm/git/docs/git-revert.html
13:37 jonalv zarah++
13:37 egonw olass: did Apple remove google support?
13:37 olass egonw: could you please tell me what commit I should revert?
13:37 egonw git log ?
13:37 egonw no, I cannot
13:37 olass and then by hand look?
13:38 egonw I said all the time, I do not know what commit broke things
13:38 egonw git log <FILE>?
13:38 jonalv google git intersect
13:38 zarah jonalv: http://github.com/intersect/qadmin/tree/master
13:38 olass are you saying that someone else than you uploded the latest jmol.jar?
13:38 jonalv hm no it's soemthing else...
13:38 egonw olass: what about this:
13:38 egonw java -jar bioclipse.cheminformatics/plugins​/net.bioclipse.jmol/jar/Jmol.jar
13:39 egonw olass: please try that first
13:39 olass ok
13:39 egonw and make sure it really is a Jmol problem
13:40 olass hmm, in a release, cheminfo is a jar
13:40 olass not a folder
13:41 olass ok, managed to unpack it
13:41 * olass hates windows
13:41 olass no, Jmol does not seem to open
13:41 olass it is suck in splash "Initializing 3D display"
13:43 egonw ok, good
13:43 egonw so, it sort of boots
13:43 egonw what's the output of: java -version ?
13:44 olass 1.5.0_06
13:44 olass hmm
13:45 olass I get this error when starting jmol from cmd in window:
13:45 olass SHA1 digest error
13:45 olass for org/jmol/viewer/ScriptEvaluator.class
13:45 olass I womder how it can work on mac/linux...
13:46 olass can I download the Jar directly from jmol.org?
13:46 egonw yes
13:48 olass what version do we have?
13:48 olass 11.6?
13:48 * olass assumes so
13:48 olass it is the latest stable
13:49 egonw no, please try 11.8
13:49 olass oh?
13:49 egonw wihch is the stable version next week
13:49 olass ok
13:50 egonw Bob is way down the RC releases
13:50 olass testin 11.8RC4 binary then
13:50 egonw ack
13:50 egonw the zip files comes with several jars
13:51 egonw in principle the Jmol.jar should work
13:51 jonalv this is probably a stupid question but how do I push a tag?
13:51 egonw git push --tags
13:52 egonw @gg git push
13:52 zarah egonw: http://www.kernel.org/pub/softw​are/scm/git/docs/git-push.html
13:53 egonw /usr/lib/jvm/java-1.5.0-sun/bin/java -jar Jmol.jar
13:53 egonw works fine here...
13:54 egonw olass: please also ensure you have the latest Sun 1.5.0 Java release on that windows machine
14:04 olass egonw: did all gists work on linux?
14:04 egonw no idea
14:04 egonw have not tested yet
14:04 egonw you intervened with the Jmol trouble
14:04 olass Jmol.jar works in RC4 11.8
14:04 olass on win
14:05 egonw fucking weird
14:05 egonw because that's the jar I uploaded...
14:05 olass hmm
14:05 egonw sorry for the language
14:05 olass I will copy the jar on USB stock to win and try again
14:07 olass seems the jar works
14:07 olass could the zipping/upload break it?
14:07 * olass will test again
14:07 egonw yeah, guess so
14:07 olass damn annoying
14:08 egonw can you verify this:
14:08 egonw copy the Jmol.jar from your mac git checkout
14:08 egonw to the windows machine
14:08 egonw and run that with java -jar
14:09 olass that's what I did
14:09 olass and it worked
14:10 egonw ah, ok
14:10 egonw then the commit and Jmol in git is fine
14:10 egonw and it must be Eclipse fucking up the export in some way
14:11 egonw hej steinbeck!
14:11 egonw olass: btw, I'm proof reading the full app note text now
14:11 olass oh
14:11 olass that is sort of finalized
14:12 olass but thx
14:12 * olass hopes no more errors
14:12 egonw really... just minor things
14:12 olass :)
14:15 * jonalv is doing his first real ui programming using multiple managers
14:15 jonalv basically I am eating my own food
14:15 jonalv it sort of tastes fine for the moment... :)
14:16 olass ok, copied a new version of 2.1 win and jmol works
14:17 jonalv olass++ ?
14:17 olass must have been zip/upload error
14:17 olass wil reupload win version
14:17 olass damn this took me 2 hours
14:17 olass :(
14:17 jonalv olass: you fixed it today though
14:17 jonalv olass: that's good
14:17 olass *grmf*
14:19 jonalv uhm guys doesn't ui.open open a list of molecules in the molecuels editor?
14:23 olass yes
14:25 jonalv olass: w00t
14:26 * jonalv has a somewhat working substructuresearch from ui for Structuredb now
14:26 jonalv the entire result is saved in memory though which might be problematic...
14:27 jonalv +there seems to be some problems with running as jobs... *suprise* :/
14:31 egonw olass: all two scripts work fine here
14:32 olass excellent
14:32 olass if I can just boot it on windows too...
14:32 egonw yes
14:33 egonw oh, one more typo
14:33 egonw section 3
14:33 egonw (offline-) -> (offline)
14:35 CIA-63 bioclipse.structuredb: jonalv master * r81d4ae8 / (3 files in 3 dirs):
14:35 CIA-63 bioclipse.structuredb: A basic ui for doing substructure searches.
14:35 CIA-63 bioclipse.structuredb: It performs the searcg in ui thread for the moment (d'oh) and it saves all the results in a list in memory. Two problems that need solutions if we are going to be able to scale up... - http://bit.ly/4sVsVK
14:41 olass jonalv++ //Progress on StructureDB!
14:45 shk3 joined #bioclipse
14:56 olass egonw: did you test the 64 or 32 bit version of BC 2.1 ?
14:56 egonw 64 bit
14:57 olass ok
15:03 olass jonalv: I'm gonna have to ask to to try windows :(
15:03 olass my machine/network clearly is not working
15:03 olass could you please do it?
15:03 egonw try windows?
15:04 olass bc 2.1 on win
15:04 egonw on that old bmc laptop?
15:04 * jonalv starts Windows if he disappears it's becasue the crap crashed the entire system...
15:04 egonw does it even haz Java?
15:04 egonw oh, jonalv
15:04 egonw phew
15:05 * olass suspects his wireless drivers produce corrupt downloads
15:05 * olass will shut down his windows machine now and not boot it until next spring
15:07 jonalv /me's Windows refuses to start :(
15:08 egonw oh no
15:08 egonw a PDF of 23MB !
15:08 egonw that better be many fancy graphics
15:08 egonw and not plain text to review!
15:09 jonalv egonw: do you ahve any idea how much 23MB text is? :)
15:09 * jonalv finally got his Windows up an running
15:10 egonw jonalv: a book
15:10 jonalv bah how do I find Bioclipse experimental builds now?
15:10 jonalv 2.1
15:11 egonw pele/bioclipse-devel/ ?
15:11 jonalv there is no link on the Bioclipse web page for example is there?
15:12 jonalv there was a webpage...
15:12 jonalv olass: how do I find that page?
15:13 olass http://pele.farmbio.uu.se/bioclipse-devel/
15:13 zarah olass's link is also http://tinyurl.com/l7lteh
15:13 jonalv ah
15:13 jonalv thanx
15:13 jonalv we need to make links for that one
15:13 olass devel.biocloipse.net?
15:13 jonalv perhaps on the Bioclispe site?
15:13 olass its on the wiki
15:13 olass I put it there
15:13 olass should be enough
15:13 jonalv that wiki is a mess...
15:13 olass so is my hair
15:14 jonalv yea welcome to the club :)
15:14 * olass just shoved a big steak in the oven
15:14 olass BBQ-flavored
15:14 olass mmm
15:14 jonalv nice
15:14 olass friday evening roast
15:15 jonalv olass++ makes good steaks
15:15 olass :D
15:15 olass jonalv: let me know if it works on windows
15:16 olass then I'll open a beer
15:16 * egonw is exhausted and going offline for some air and dinner
15:17 olass nice combo
15:17 olass air and dinner
15:19 egonw and I'll add that beer
15:19 egonw bbl
15:22 jonalv olass: did you have those gist ids again?
15:23 olass mom
15:23 olass : a) 163575 and b) 163440.}
15:25 * jonalv wonders if not pubchem supports giving number of hits in the search so that the progressmonitor can be for the complete download...
15:25 jonalv egonw: actually it seems to me like that there is something wrong the way that progressmonitor jumps around
15:26 jonalv anyway, first seems to work
15:27 jonalv and the other one seems to work
15:27 jonalv olass: I think you can take that beer
15:27 olass aaah :)
15:28 olass jonalv++ thx for testing in such an unfriendly environment
15:28 * jonalv closes down Windwos now (brrrr)
15:28 olass jonalv: have you tested StructureDB performance now?
15:29 jonalv olass: uhm no? yes?
15:29 jonalv some
15:29 jonalv olass: it's worrying...
15:50 egonw jonalv: Jmol works for you?
15:51 jonalv egonw: no idea
15:51 egonw jonalv: yes, the pubchem progress monitor is not working properly...
15:51 jonalv egonw: jmol on mac?
15:51 egonw jmol in win
15:51 jonalv egonw: I did not try
15:51 egonw I though you were gonna test that too
15:51 egonw ack
15:52 egonw gone again
15:58 olass jonalv: testing jmol was the big thing
15:58 olass did you not test that on windows?
15:59 olass that was what was failing here..
15:59 jonalv olass: you told me to test thsoe two gist scripts
15:59 olass have you not read anything here in the afternoon?
15:59 olass I spent 3 hours testing jmol on windows and failed!
15:59 jonalv clearly we need to start using well written bug reports and not irc for this sort of things
16:00 * olass thought that it was impossible to miss this
16:00 olass I see
16:00 olass I guess I was not clear enough
16:06 * jonalv is unpacking that Bioclispe zip file again...
16:07 * jonalv will ahve to leave in about half an hour 45 min but if Windows does not crash I might be able to test Jmol in that time at least :)
16:09 olass win--
16:09 * jonalv is spinning a molecule in jmol on windows now
16:10 olass jonalv++
16:10 jonalv olass: do you feel okey now?
16:10 olass yees
16:10 * olass has another sip from the beer that he paused
16:10 jonalv olass: good, I am looking forward to reading that qsar article some-day-now™
16:10 olass maybe :)
16:10 jonalv mm beer
16:10 jonalv :)
16:11 olass mmmm
16:11 * olass has some hot chorizo as snack waiting for the roast to cook
16:13 * jonalv shuts down Windows now if that is okey?
16:14 olass sure
16:14 olass the sooner the better
16:23 steinbeck joined #bioclipse
16:54 * egonw is happy to hear that the win/jmol problem is machine specific
16:54 egonw bbl
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