Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-03-14

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All times shown according to UTC.

Time Nick Message
04:17 egonw joined #bioclipse
04:45 CIA-137 chembl.rdf: Egon Willighagen master * r370254e / targets.php : Another assignment/equivalence test fix (it's those mysql_fetch_assoc if clauses...) - http://git.io/UzOHzQ
06:22 sneumann joined #bioclipse
07:08 zaetnick joined #bioclipse
07:12 egonw joined #bioclipse
07:15 egonw joined #bioclipse
07:29 konditorn joined #bioclipse
07:30 CIA-137 chembl.rdf: Egon Willighagen master * r9f727a4 / properties.php : Draft for adding the physchem props - http://git.io/4DmEdQ
07:30 CIA-137 chembl.rdf: Egon Willighagen master * reaeff6c / properties.php : Added all mapping but the ACID/BASE (role or descriptor?), and mw_freebase (no CHEMINF id yet) - http://git.io/gFLwWA
07:55 jonalv joined #bioclipse
08:01 Gpox joined #bioclipse
08:04 CIA-137 bioclipse.vscreen: Klas Jönsson 2.4.x * r8c8bbe4 / net.bioclipse.vscreen.ui/ch​eatsheets/vscreen-intro.xml : Changed the title. - http://git.io/P2SpzQ
08:04 CIA-137 bioclipse.vscreen: Klas Jönsson 2.4.x * rd181090 / net.bioclipse.vscreen.ui/ch​eatsheets/vscreen-intro.xml :
08:04 CIA-137 bioclipse.vscreen: Changed from "<b>Vscreen Perspective</b>" to "<b>VScreen
08:04 CIA-137 bioclipse.vscreen: Perspective</b>" in step 1. - http://git.io/VKNKpA
08:04 CIA-137 bioclipse.vscreen: Klas Jönsson 2.4.x * r363b280 / net.bioclipse.vscreen.ui/ch​eatsheets/vscreen-intro.xml : Updated the path to "Screening file" in the File > New.. wizard - http://git.io/jaYFgw
08:04 CIA-137 bioclipse.vscreen: Jonathan Alvarsson 2.4.x * r6308241 / net.bioclipse.vscreen.ui/ch​eatsheets/vscreen-intro.xml :
08:04 CIA-137 bioclipse.vscreen: Merge pull request #1 from KlasJoenssson/UpdateCheatSheet
08:04 CIA-137 bioclipse.vscreen: Update cheat sheet - http://git.io/YLyBCA
08:08 jonalv Gpox, konditorn: Are we waiting woth this pull request: https://github.com/bioclipse/bioclipse.ons/pull/2 because of some reason?
08:11 konditorn jonalv: egonw wanted to wait with it "until the google manager uses the account info too".
08:11 jonalv okey
09:09 amarillion joined #bioclipse
10:09 egonw hi jonalv, konditorn
10:09 konditorn hi egonw
10:13 egonw konditorn: we have a call for this afternoon
10:13 stain_ hi
10:13 zarah privet stain_
10:13 stain_ ?
10:14 stain_ privet
10:14 egonw hi stain
10:14 egonw zarah is our irc bot
10:14 egonw privet == hello
10:14 egonw dunno what language...
10:14 egonw how's the taverna rdf coming along?
10:14 egonw I saw a post on an upcoming release?
10:16 stain_ ah :)
10:16 stain_ egonw: the taverna rdf.. well, scufl2 was released a mnth ago or so?
10:16 stain_ there's Taverna 2.4 coming out next week I think
10:16 stain_ we'll see if Alan will do the build without me there ;)
10:16 egonw based on that new scufl2 format?
10:16 stain_ no
10:16 stain_ that's for Tavern 3
10:16 stain_ Taverna 3
10:16 zaetnick privet is russian, for the record
10:17 stain_ although I'll make a plugin for 2.4 as well
10:17 egonw zaetnick++
10:17 stain_ we won't change the whole internal model for 2.x
10:17 egonw make sense
10:18 konditorn egonw: I thought it was next Wednesday… But today works as well for me.=)
10:18 stain_ egonw: are you involved with the nanopublication thingie in OpenPhacts?
10:18 konditorn it was at 14, wasn't it?
10:18 egonw konditorn: sorry, you're right
10:18 egonw yeah, I have lectures today...
10:18 egonw gave 2.5 hours of Perl education this morning
10:19 egonw mind if not working
10:19 konditorn then i guess we take it next week. =)
10:19 egonw hence I did not schedule for today :)
10:19 egonw yeah, that's after me giving Protein Structure education :)
10:19 egonw stain_: not formally
10:20 jonalv egonw++ // For directing me to prince. http://www.princexml.com/
10:21 egonw stain_: that doc was started before I joine Open PHACTS
10:21 stain_ ok
10:21 egonw stain_: but I did see your comments :)
10:21 stain_ ;)
10:21 egonw dc terms / elements is a recurrent thing...
10:21 egonw I think I take the wrong one now and then too
10:22 egonw good you corrected that
10:22 egonw jonalv: I should perhaps make that part of the PharmBio book chapter too...
10:25 stain_ yes.. and dcterms is not perfect either as almost everything appears as annotation properties in OWL..
10:25 stain_ but at least it's clear if something is a string or resource ;)
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12:30 egonw can someone test the downloading of PDB files, with the download wizard?
12:30 egonw doesn't work for me
12:31 egonw 13:31:24.274 ERROR [n.b.w.w.newwizards.DownloadPDBWizard] Error downloading PDBs: null
12:38 olass file a bug plz
12:47 egonw ack
12:48 Gpox @pz 3084
12:48 zarah http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3084
12:49 egonw oh, ok
12:52 jonalv zaetnick: regarding bug 3147
12:52 zarah bug #3147 | http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3147
12:52 jonalv zaetnick: Can we inform our users about this somehow. I am not espacially happy about having the entire Bioclipse platform crashing because R is missing a dependency...
13:04 zaetnick jonalv: indeed, we have to come up with something
13:04 jonalv zaetnick: okey, see the bug ticket...
13:05 zaetnick jonalv: it's not a R thing, I think
13:06 jonalv zaetnick: okey, what is it then?
13:07 zaetnick not sure, but I understand it as a library
13:08 jonalv sounds like an R thing to me. Defnitely gonna sound like an R thing to our users
13:08 zaetnick jonalv: http://cran.r-project.org/bin/macosx/tools/
13:08 jonalv but are you saying it's a missing dependency?
13:08 zaetnick jonalv: " This library is necessary in order to use the tcltk R package"
13:09 jonalv "tools and libraries that are part of the base distribution of R for Mac OS X."
13:10 jonalv how come it isnt installed then I wonder...
13:10 jonalv zaetnick: But do you know if we can check for these things?
13:11 zaetnick jonalv: they provide it as a .dmg installable package
13:12 jonalv I am still confused. It works fine ton install packages from the terminal but not from inside Bioclipse. What exactly does this tcl thing do? Do you know that?
13:12 zaetnick jonalv: do you know if we can and how we can install such thing
13:12 jonalv zaetnick: no :( Probaly we can't autoinstall it. If can detect it we can at least warn if it isn't there...
13:13 zaetnick jonalv: without it the mirror selection dialog opens directly in the console where you're running R (this is outside BC)
13:13 zaetnick jonalv: with it the selection dialog opens in a separate window
13:14 jonalv okey
13:14 zaetnick jonalv: and the BC crash comes when R tries to open the dialog without the possibility for that separate window
13:16 zaetnick jonalv: yes, we should be able to check if it's installed or not, and warn the user
13:16 jonalv very good
13:16 jonalv that would be enough I think
13:17 zaetnick jonalv: another thing is that there is more than one workarounds and we need to figure out good interface for warning
13:18 jonalv prining the warning in the R console is not good enough?
13:18 zaetnick konditorn: you're looking at the cheat sheets, don't you
13:18 konditorn yes...
13:21 zaetnick jonalv: isn't it good idea to inform the user how to handle it - i) to install the library; ii) to install the R packages that require mirror selection outside of BC; iii) to set a default mirror via Rprofile file in the wd
13:22 jonalv zaetnick: yea I suppose. I was hoping we could just link to some install instructions page...
13:22 zaetnick konditorn: have you gone through the DS cheat sheet, I'm getting an error on step 3
13:23 zaetnick konditorn: the tests running, did you have problems with that
13:24 konditorn I have no notes of any problems in step 3...
13:27 zaetnick konditorn: actually this a problem with DS, not with the cheat sheet
13:27 konditorn … but when I look att the cheat sheet I do remember some thing like that.
13:28 konditorn yes, I'm looking to se if I filed a bug about it...
13:32 zaetnick konditorn: does it run for you now
13:32 konditorn I can't find any bug.
13:36 zaetnick konditorn: can you try to run DS tests if you have BC with DS installed on hand
13:36 konditorn I'm trying...=)
13:37 konditorn …But I can't find any tests to run….
13:39 konditorn zaetnick: I got this error:
13:39 konditorn An internal error occurred during: "Initializing decision support tests".
13:39 konditorn Failed to run method (Message was: null)
13:42 zaetnick konditorn: for which molecule you tried to run
13:43 zaetnick konditorn: actually in my case it fails for any molecule I try
13:47 konditorn That is what I remember as well, but right now I can't run any tests 'cos I don't have any tests to run...
13:48 zaetnick konditorn: you have BC with DS installed, don't you
13:49 konditorn yes...
13:49 zaetnick konditorn: and you have the Decision Support view in your perspective
13:50 konditorn yes...
13:50 konditorn I run the cheat sheet and it worked until step 3...
13:50 zaetnick konditorn: …with two tests in it - Cancer growth inhibition and one more
13:52 konditorn mm, the error I wrote earlier came up when I changed to the DS-view, i.e. when it initializating
13:53 zaetnick konditorn: already! I see
13:56 zaetnick it initializes here, but then when I open a molecule and hit Run Tests I get an "Unexpected error"
13:56 zaetnick :)
13:58 zaetnick it's an issue with the Mutagenicity test only
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20:04 zaetnick olass: ping
20:05 zaetnick olass: in which Component should bugs in the BC help system be reported
20:07 zaetnick olass: BC core system, I guess
20:12 olass zaetnick: yes, seems logical
20:12 olass if nothing else fits then it's a good place for everything
20:17 zaetnick olass: indeed, but should I leave Arvid as an assignee for small errors/typos in the DS help pages, for example
20:18 zaetnick …or put you as an assignee
20:18 olass put me if you like
20:19 zaetnick ok :)
20:27 olass as long as the bug is there so we follow it up
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