Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-01-27

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All times shown according to UTC.

Time Nick Message
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07:52 egonw moin
07:52 zarah oh hai egonw
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08:28 * egonw is updating the Bioclipse tutorial for the PharmBio course
08:35 olass joined #bioclipse
08:37 olass moin
08:37 zarah hello olass, you fantastic person you
08:37 egonw hi olass
08:37 olass zarah: you are not so bad either
08:37 zarah olass: I'm just a bot, you expect me to understand that?
08:37 olass egonw: hi
08:37 olass zarah: *sigh*
08:37 zarah olass: please rephrase or stop trying to be witty :)
08:38 * olass stops being witty
08:38 egonw [01/27/10 09:28] * egonw is updating the Bioclipse tutorial for the PharmBio course
08:38 olass egonw++
08:38 * olass will release 2.2.0 today as RC3 apparantly did work if we just add the linux start script
08:38 olass there are still bugs but we can always release 2.2.1
08:39 olass no blockers IMO
08:39 egonw excellent
08:39 olass egonw: glad you agree
08:39 egonw well, we have to move on
08:39 olass indeed
08:39 egonw release soon, release often
08:39 olass so I will add the linux start script and upload to SF
08:40 egonw thanx
08:40 olass and update the update sites
08:40 olass and write a release blog
08:40 olass :)
08:40 egonw perfect
08:40 * egonw will patiently wait, and advertize the blog in his social network
08:41 egonw btw, the bc2 paper is bookmarked on citeulike by six people (incl me) and in 3 groups
08:41 olass nice
08:41 olass hmm, should we have a new update site for 2.2 and keep the update-site for 2.0?
08:41 olass I always envisioned overwriting th old one..
08:41 egonw that depends
08:41 egonw is 2.0 EOL with the 2.2 release?
08:41 egonw I would say so
08:41 olass what is EOL?
08:41 egonw end-of-life
08:41 egonw meaning...
08:41 egonw we stop supporting it
08:42 olass yes
08:42 egonw not that 2.0 got overly many bug reports
08:42 olass true
08:42 olass but we could have an update site update2-2.bioclipse.net, update2-4.bioclipse.net
08:42 olass etc
08:42 olass if we wanted to
08:42 olass but I think we should move on
08:43 olass and just use update2.bioclipse.net
08:43 olass (liek we had in 2.0.0)
08:43 egonw what is update.bioclipse.net for then?
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08:57 olass egonw: may I request for all your repos you change version from 2.2.0.RC3 to 2.2.0.v20100127 ?
08:57 egonw yes
08:58 egonw I'll fetch breakfast first...
08:58 olass ok, but happy if you do it straightaway
08:58 olass and ping me after
08:58 * olass will start updateing his repos
08:58 * olass will fetch a coffee first too :)
09:03 olass @pz ubuntu
09:03 zarah [1722] Patch boot scripts for platfor... http://tinyurl.com/yafe5c9
09:03 zarah [1559] R Console does not run on Ubun... http://tinyurl.com/yjtltxv
09:03 zarah Entire list at http://tinyurl.com/yeotm44
09:15 jonalv joined #bioclipse
09:15 jonalv oh hai
09:15 zarah hello jonalv, you fantastic person you
09:19 masak joined #bioclipse
09:21 CIA-59 bioclipse.core: Ola Spjuth 2.2.x * r3fe3bc1 / (25 files in 24 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/9lS8yi
09:21 olass hi jonalv
09:21 olass jonalv: I will now release 2.2.0
09:21 olass if you have no objections?
09:22 CIA-59 bioclipse.balloon: Ola Spjuth 2.2.x * r7f82609 / (8 files in 8 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/boPbAu
09:24 egonw jonalv: ping
09:24 CIA-59 bioclipse.ds: Ola Spjuth 2.2.x * r2a771ec / (9 files in 9 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/bfvMfY
09:24 egonw jonalv: what did you want me to pull?
09:24 egonw I only see updates in newWizard-something, and 2.2.x
09:24 egonw but not in master
09:25 jonalv egonw: no from my branch
09:25 jonalv egonw: I thought I made that clear using the github interface... :/
09:26 egonw ah, sorry... my mistake
09:26 CIA-59 bioclipse.qsar: Ola Spjuth 2.2.x * r45f898f / (16 files in 16 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/adEpL6
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09:27 CIA-59 bioclipse.cheminformatics: jonalv master * r67ff65e / (3 files in 3 dirs): MoleculeFromStringBuilder for new from Clipboard - http://bit.ly/9N475Q
09:27 CIA-59 bioclipse.statistics: Ola Spjuth 2.2.x * r4cd7769 / (3 files in 3 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/bOQgu3
09:28 olass jonalv: please set structuredb version to 2.2.0.v20100127
09:29 olass ping me when done
09:29 * olass wonders when masak will arrive
09:29 CIA-59 bioclipse.cheminformatics: Egon Willighagen 2.2.x * rf99c5e1 / (16 files in 16 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/8YcJUP
09:30 masak joined #bioclipse
09:30 olass \o/
09:30 * olass can summon masak
09:31 masak it's not that hard. all you need is a wristwatch and good timing. :)
09:31 * olass does not have a wristwatch
09:31 * olass has good timing apparently
09:32 olass masak: please set bioinformatics version to 2.2.0.v20100127 in branch 2.2-releng
09:32 masak gladly.
09:32 * masak fires up his script
09:32 olass for all plugins and features
09:32 masak nodnod
09:32 * olass should have a script too
09:32 masak here, take mine.
09:32 masak it's right there in the repo.
09:32 masak called 'bump-version'.
09:33 CIA-59 bioclipse.joelib: Egon Willighagen 2.2.x * rd76ac88 / (4 files in 3 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/btHgZY
09:33 masak it's not specific to bioclipse.bioinformatics
09:33 egonw olass: can we do bioclipse.opentox too?
09:34 masak olass: bumped, pushed.
09:35 olass thx
09:35 * masak also notes that jonalv has committed line-ending whitespace into his nice code, grrr...
09:36 jonalv masak: it's white space. It's invisible
09:36 masak oblig: http://www.codinghorror.com​/blog/archives/001310.html
09:36 zarah masak's link is also http://tinyurl.com/yjla56m
09:42 olass egonw: sure, on experimental update site
09:43 egonw ack, will branch and update version number
09:43 olass it is not tested in RC3 so experimental sounds like the place for opentox plugin
09:43 egonw yes, sounds good
09:43 olass hence version number can be arbitrary
09:43 olass (IMHO)
09:43 egonw ack, but then I have to make up something :)
09:43 olass sounds like a good idea
09:43 olass 0.2.0?
09:44 olass egonw: ping me when to pull all stuff
09:44 olass cheminfo, rdf, opentox etc
09:44 CIA-59 bioclipse.rdf: Egon Willighagen 2.2.x * rd00910a / (9 files in 7 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/ck7lnC
09:45 olass egonw: filed bug 1829 for you (wiki poge for opentox)
09:46 egonw tack
09:46 olass de nada
09:47 CIA-59 bioclipse.social: Egon Willighagen 2.2.x * r35e94c2 / (4 files in 3 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/dxkQhr
09:56 egonw does anyone know how to see all existing wiki templates?
09:56 olass templates?
09:56 olass what do you mean?
09:57 egonw like: http://wiki.bioclipse.net/ind​ex.php?title=Template:Project
09:57 zarah egonw's link is also http://tinyurl.com/ya8r3vh
09:57 olass you need to ask samuell
09:57 * olass does not know
09:57 olass http://wiki.bioclipse.net/inde​x.php?title=Category:Projects
09:57 zarah olass's link is also http://tinyurl.com/yh7jqah
09:57 egonw yes, something like that
09:57 egonw but then different :)
09:58 olass egonw: one question
09:58 egonw http://wiki.bioclipse.net/index.php​?title=Special:MostLinkedTemplates
09:59 olass if I push to githib and send a pull request which you deny, how do I remove my commit to github?
09:59 zarah egonw's link is also http://tinyurl.com/yabtav5
09:59 egonw that's close enough
09:59 egonw yeah, tricky one
09:59 olass that last denied commit makes subsequent commits to be rejected...
09:59 egonw remove the commit locally
09:59 olass done that
09:59 olass but cannot push
09:59 egonw then push the updated branch
09:59 olass I get [rejected]
10:00 egonw yeah, different histories
10:00 egonw remove it first
10:00 egonw by adding a colon in front of the branch name
10:00 egonw only works if you have more than one branch on GH
10:00 olass remove the branch?
10:00 egonw yeah, with:
10:00 egonw git push origin :branchToRemove
10:00 egonw assuming origin = GH upstream
10:00 olass and then push it again?
10:00 egonw right
10:00 jonalv ..or just force the push
10:00 * olass is testing
10:01 olass jonalv: what does force the push actually do?
10:01 egonw jonalv: how does that work?
10:01 jonalv --force
10:01 olass jonalv: what does force the push actually do?
10:01 jonalv olass: uhm 'forces the push'?
10:02 jonalv olass: what answer do you expect?
10:02 masak olass: it ignores the (possible) fact that HEAD is not a descendent of upstream.
10:02 masak that answer, perhaps? :)
10:02 olass masak++
10:02 jonalv ah okey
10:02 olass masak: that will leave a zombie commit?
10:02 masak learn git, bitches.
10:02 * jonalv is probably not awake yet
10:03 masak olass: hm, yes it will.
10:03 egonw masak: what language??
10:03 masak one or several.
10:03 olass not good
10:03 olass egonw's solution will not I assume
10:03 masak olass: well, what's worse is that downstream pullers will have to force their pulls, too.
10:03 egonw they should be equivalent
10:04 olass masak: that sounds very bad
10:04 * egonw is making a wiki template for Bioclipse repositories
10:04 masak olass: that's why the man pages warn about it with capital letters.
10:04 olass masak: what solution would you go with in this case then?
10:04 jonalv yea in my oppinion you should only do these to branches starting with your own name so that people know that if they check this out then they mgiht be left behind...
10:04 masak olass: I'm not backlogged yet.
10:04 egonw olass: which is why you work in branches as much as possible
10:04 egonw olass: so that your main branches stay clean
10:05 * jonalv tries to only rebase branches starting with his own name
10:05 olass masak: please backlog and advice
10:05 masak will do.
10:05 masak in general, there's always this tension between pushing-early-pushing-often and how much you can sensibly rebase.
10:05 masak but what egonw/jonalv just said helps to an extent.
10:06 olass but you suggest something different?
10:06 * olass tries --force
10:06 olass seems to work
10:06 masak olass: yeah, --force sounds like the way to go.
10:07 masak olass: why did you end up in this situation?
10:07 masak I couldn't discern from the backlog.
10:07 olass it was strange
10:07 masak three-headed monkey?
10:08 olass I pushed a commit for "set verion 2.2.0.RC3" and sent a pull request, egon did the same thing (he is upstream)
10:08 olass so a conflict
10:08 olass I reset HEAD^1
10:08 olass abd pulled
10:08 masak o_O
10:08 olass problem solved (or so I thought)
10:08 masak no...!
10:08 olass how should I have behaved?
10:09 masak ...merge...?
10:09 * jonalv has often wondered about this situation as ell. egonw will refuse to accept merge commits...
10:09 olass but I just wanted to remove my commit
10:09 olass from github too
10:09 masak I still maintain that merge commits are bettern than pushing with force.
10:09 olass is that not possible?
10:10 masak olass: you can remove a whole branch. don't know if the commit as such goes away.
10:10 jonalv the only solution I seee is to throw away your branch and start oer with egonw's branch
10:10 masak olass: probably not.
10:10 olass hmm, ok
10:10 olass jonalv: I see
10:10 masak olass: it's like this: you've *PUSHED*.
10:10 masak it's out there.
10:10 masak it's published.
10:10 masak it's official.
10:10 olass well, I pushed, I can remove
10:10 masak it's known to the world.
10:10 masak it's shoved out of your front door.
10:10 masak it's made known.
10:11 masak it's public.
10:11 jonalv masak: yea but if egonw refuses to merge with it then the only way is to make it unpublic
10:11 olass if people fork me, you should play by my rules
10:11 olass jonalv: exactly!
10:11 masak I want to make it known that I don't refuse merge commits to my repo.
10:12 masak at least not in this case.
10:12 olass a bit annoying to always remove a branch if a commit is denied...
10:12 jonalv olass: mhm
10:12 olass that does not sound like good practice
10:12 jonalv tell me about it
10:12 jonalv I know
10:12 jonalv I totally agree
10:12 masak nod.
10:12 olass egonw: do you agree with this?
10:12 jonalv I have felt your pain
10:13 masak there's nothing wrong with merge commits as such.
10:13 * olass is severely injured
10:13 * olass is roaring in agony
10:13 masak they are useful for exactly this situation.
10:13 olass ok, next time I will merge
10:14 olass however, for a denied commit, you cannot merge
10:14 olass then you need to delete the branch, right?
10:14 egonw removing branches is not that much work
10:14 egonw I disagree with that being a burden
10:15 olass egonw: so you suggest that a denied commit implies you should remove a branch?
10:15 olass sounds drastic..
10:15 * olass don't disagree, just notes the implications
10:15 egonw no, I suggest that a project which has finished should be closed
10:16 olass ?
10:16 jonalv egonw: now you lost me. What project is it that has been finished?
10:16 olass egonw: how do you suggest I should operate if a pushed commit is denied?
10:17 egonw fix the commit
10:17 egonw or, if it is made redundant by other work, just drop it
10:17 egonw when either is done, and merged, you close that project
10:17 olass how do I drop a commit on ithub?
10:17 egonw hence the branch
10:18 masak olass: you don't. it's published already.
10:18 masak olass: you can drop the whole project.
10:18 olass egonw: the only way I know how to drop a commit on github is to remove the branch
10:18 olass which is fine with me
10:18 masak olass: removing a branch doesn't remove the commit.
10:18 olass no?
10:18 masak olass: no.
10:19 olass where is it then?
10:19 masak it's still there.
10:19 olass on github?
10:19 masak yes.
10:19 masak accessible through its SHA-1 id.
10:19 olass can I not clean that up?
10:19 masak not that I know of.
10:19 masak you can remove the whole project...
10:19 olass like vacuum-db
10:20 masak maybe github has some sort of GC of orphaned commits.
10:20 masak but I doubt it.
10:20 olass hmm
10:20 olass good to know
10:20 masak perhaps you could do it locally and then push with force.
10:20 masak but I don't know if that removes things.
10:20 egonw http://wiki.bioclipse.net/index​.php?title=Category:Repository
10:20 olass right, I think I know how to deal with these situations now, at least more than before
10:20 zarah egonw's link is also http://tinyurl.com/y95k44m
10:21 masak olass: it's like this: branches in git are not long lines of commits. they're moving pointers to the latest commit in a long line of commit. remove a branch and you only remove that pointer. the commits are still there.
10:21 egonw removing a branch removes a pointer to the commit
10:21 egonw the commit is no longer part of a branch history
10:21 * olass thought there was some sort of garbage collection
10:21 egonw called dangling
10:21 egonw upon GC, dangling commit can be removed
10:21 * olass is used to java++
10:21 masak olass: there is.
10:21 egonw but not on the default GC, AFAIK
10:22 olass and GC is?
10:22 masak olass: um. garbage collection.
10:22 egonw which allows you to recover accidentally removed commits
10:22 olass right
10:22 masak well, things still in the 30-day reflog are not GC-ed, for one.
10:22 olass egonw: all done now for 2.2.0 versions?
10:23 olass jonalv: all done now for 2.2.0 versions? structuredb?
10:23 jonalv olass: Uhm, what needs to be done?
10:23 jonalv olass: do you set the version number or do I?
10:23 olass you do
10:23 olass I asked before
10:23 olass please backlog
10:23 jonalv olass: oh, anything else I need to do?
10:24 olass nope
10:24 olass we tag after release
10:24 olass and merge withy master at that time
10:24 jonalv olass: please file buigs for things you want me to do. only expect that I read get things in IRC if I confirm thatI have read them
10:24 jonalv olass: oki so I will set version number,
10:24 jonalv to what btw_
10:24 jonalv :)
10:25 * olass thought jonalv would notice the 30+ commit msgs and be reminded a few times
10:25 olass hmm 30+ was an exaggeration
10:25 olass more like 10+
10:25 olass jonalv: anyway, please ping me when done
10:25 olass and I will export and build update sites
10:26 olass can I also request from all of you no more commits to the 2.2.x branch?
10:26 olass if you do so, please let me know
10:28 olass masak: ping
10:29 olass I get this: error: Entry 'features/net.bioclipse.joe​lib_feature/joelib.product' not uptodate. Cannot merge.
10:29 olass what does this mean and how do I fix it?
10:29 masak olass: pong
10:29 olass "not uptodate"
10:29 masak olass: it means you have a dirty checkout.
10:29 olass what is that?
10:29 olass I have chstuff?
10:30 olass I have changed stuff?
10:30 masak it is a checked-out copy of a repo that contains changes.
10:30 masak 'git status' will tell you more.
10:30 olass but I did "git checkout features/net.bioclipse.joelib_feature/feature.xml"
10:31 olass masak: ok, found a solution
10:31 olass thx
10:31 masak olass: that's a different file? why's it matter that you checked that one out?
10:32 * olass noted only one error was reported and the rest not
10:32 olass a mixup of names
10:32 olass my bad
10:32 * olass expected all update errors would be reported
10:32 masak olass: I suggest you try to solve this locally first :)
10:33 olass already fixed
10:35 egonw annzi: http://wiki.bioclipse.net/in​dex.php?title=Bioclipse.MOSS
10:35 zarah egonw's link is also http://tinyurl.com/yj5vna8
10:35 CIA-59 bioclipse.structuredb: jonalv master * r711f6e4 / bump-version : addded bump-version script - http://bit.ly/c3JCeV
10:35 CIA-59 bioclipse.structuredb: jonalv master * re717e0e / (8 files in 8 dirs): bumped version to 2.2.0.v20100127 - http://bit.ly/95RvCg
10:35 olass egonw: ping
10:35 olass egonw: ping
10:35 egonw pong
10:35 jonalv olass: ping, structuredb version bumped
10:35 olass please look at the deps for bug 1580
10:35 olass jonalv: ack
10:36 masak tbbbp!
10:36 olass egonw: I need your advice
10:36 olass many bugs there
10:36 egonw what's up
10:36 egonw where?
10:36 olass especially 1627
10:36 egonw @pz 1627
10:36 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1627
10:37 olass egonw: and 1549, 1631, 1630, 1628
10:38 egonw wasn't 1627 fixed?
10:38 olass please look at them so we can remove the deps to 1580 (release 2.2.0)
10:38 egonw wasn't that the atom type serialization problem?
10:38 olass egonw: bug is still open
10:38 olass if fixed, mark as fixed and I will verify
10:39 * olass wants to clear out all bug deps in 1580 (release 2.2.0 container)
10:41 olass masak: how can I reset HEAD to a certain commit by SHA? is that possible?
10:41 olass git reset HEAD 2faf22e622ce9c65debc059abb567b727c8e8628
10:41 olass hmm
10:41 masak yes.
10:42 masak olass: most everywhere you write a branch name, you can write a commit id.
10:42 olass ok
10:42 masak branch names are just (moving) aliases for commits.
10:42 masak tag names are just (static) aliases for commits.
10:43 olass I see
10:44 olass jonalv: did you also update version on sdb feature?
10:45 jonalv masak: does your script also update the version on the feature?
10:45 * jonalv guesses no
10:45 egonw olass: please check 1580 now
10:45 * masak guesses yes
10:46 olass jonalv: please fix
10:47 olass egonw: 1627 is till open and assigned to you?
10:47 olass apart from that it looks nice
10:47 egonw yes, will try to look at that this afternoon
10:47 olass ok
10:47 * olass will also look at 1806
10:48 CIA-59 bioclipse.structuredb: jonalv master * rca6fceb / features/net.bioclipse.stru​cturedb_feature/feature.xml : bumped version on feature - http://bit.ly/d0x3Ma
10:48 jonalv olass: okey now I hope everythign is as it should
10:48 olass jonalv: ok
10:50 jonalv git checkout .
10:50 jonalv OSX--
10:50 * egonw invites everyone to register his/hers git repositories in the Bioclipse wiki: http://wiki.bioclipse.net/index​.php?title=Category:Repository
10:51 CIA-59 bioclipse.structuredb: jonalv master * r92f90c1 / bump-version : fix for bump-version script - http://bit.ly/bjPXkE
10:51 jonalv everythign starts with a 'B' :)
10:51 jonalv egonw: okey how do I do htat?
10:51 egonw jonalv: see: http://wiki.bioclipse.net/index​.php?title=Template:Repository
10:51 olass egonw: how?
10:52 egonw olass: see http://wiki.bioclipse.net/index​.php?title=Template:Repository
10:52 zarah egonw's link is also http://tinyurl.com/ygqatno
10:52 olass where do I add that snippet?
10:52 egonw top of the page
10:52 olass of what page?
10:52 olass ok, I need to createa repo page first?
10:52 zarah egonw's link is also http://tinyurl.com/ygqatno
10:52 egonw olass: yes
10:53 egonw I'll ask Samuel how we can link Feature, Project, and Plugin pages to a repository page
10:53 egonw so that we can make statements like:
10:53 egonw FeatureX isPartOf RepositoryY
10:53 egonw of course, everything is expressed in RDF :)
10:54 egonw samuell++
10:54 olass should we really capitalize B and C in http://wiki.bioclipse.net/index.ph​p?title=Bioclipse.Cheminformatics ?
10:54 zarah olass's link is also http://tinyurl.com/yapbtmv
10:54 olass or is that done by mediawiki?
10:54 egonw no clue
10:54 egonw no, my choice...
10:54 egonw but seems mediawiki best-practice
10:54 * olass will use lowercase
10:54 egonw I won't complain about that at all
10:56 masak` joined #bioclipse
11:09 * egonw notes that the template does not nicely translate into RDF yet :(
11:12 olass egonw: is gitorious better than github?
11:12 egonw nope
11:12 egonw GitHub is better
11:12 egonw but was running out of free space
11:13 * masak` is considering signing up on github
11:13 masak` I like them.
11:13 olass masak: I will ask if Jarl can sponsor github
11:13 egonw Template:Repository now correctly maps to RDF triples
11:13 olass for us developers
11:13 masak olass: that would be nice.
11:13 olass if we can get a group coupon
11:14 egonw olass: I'd love a 'bioclipse' account on GitHub
11:14 olass egonw: what for?
11:14 egonw for all bioclipse repositories
11:14 egonw the stable ones, that is
11:14 olass would that not be going back to the SVN world?
11:14 egonw no
11:14 egonw it's like this:
11:14 olass what would you have in this acount and what would you have in your own repos?
11:14 egonw the bioclipse account would own them
11:15 egonw and on a repository level, share with respective maintainers
11:15 egonw e.g.
11:15 egonw bioclipse.core
11:15 olass what do you mean share?
11:15 egonw would be writable for bioclipse and olas
11:15 egonw and bioclipse.cheminformatics would be writable for bioclipse and egonw
11:15 egonw bioclipse.bioinformatics for bioclipse and mask
11:15 egonw masak
11:15 egonw etc
11:16 egonw no one would actually use the bioclipse account to make commits
11:16 jonalv egonw: that sounds liek a good solution actually
11:16 olass ok, I will set this up
11:16 olass just need to clear financing
11:16 jonalv it's cheaper than paying for us all + it collects all repos on one place
11:16 olass yup
11:16 * olass will make it so
11:17 jonalv olass: make it so! :)
11:17 jonalv olass: engage
11:17 olass is github the best choice?
11:17 egonw at this moment: I think so
11:17 * masak thinks so
11:17 olass ok
11:17 jonalv <AOL>me too</AOL>
11:18 egonw me loves the RDF query functionality build into MediaWiki :)
11:18 egonw == My Development Tutorials ==
11:18 egonw {{#ask: [[Category:Development tutorials]] [[has author::User:Egon Willighagen]]
11:18 egonw | ?applies to bioclipse version
11:18 egonw }}
11:18 egonw see http://wiki.bioclipse.net/index.​php?title=User:Egon_Willighagen
11:18 jonalv <AOL>me too</AOL>
11:19 jonalv (I grabbed that code from egonw++)
11:19 * olass is considering the size required
11:19 zarah egonw's link is also http://tinyurl.com/ya729r9
11:19 jonalv olass: what are the sizes?
11:19 olass http://github.com/plans
11:19 * olass thinks Medium would suffice for now
11:19 * egonw is checking
11:20 olass 2.4 Gb
11:20 olass we could always upgrade when need be
11:20 egonw size-wise, small might be enough, not?
11:20 olass let me know and I'll clear this with Jarl
11:20 olass well, let's be proactive :)
11:21 egonw one question would be if we are not in the business area
11:21 egonw olass: I suggest emailing them...
11:21 egonw they are very cooperative to open source projects...
11:21 egonw and there is no bioclipse business yet...
11:21 egonw and ask them what would suite us best
11:22 olass yes, i will do so
11:23 jonalv olass++ oha it was egonws idea, egonw++
12:09 egonw all: please check: http://wiki.bioclipse.net/index.ph​p?title=Bioclipse.Cheminformatics
12:09 egonw and see how you can now link Features to Repositories
12:09 egonw and how to automatically list Features for a particular Repository with a small bit of RDF query
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12:29 egonw ha, finally worked out why the RDF triples were showing out in the HTML output too...
12:30 egonw olass: did you know there is a template for Features too? http://wiki.bioclipse.net/inde​x.php?title=Category:Features
12:31 olass no
12:31 olass well, now I do
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12:50 egonw annzi: ping
12:50 egonw annzi: are you running SPARQL queries on ChEMBL by any chance?
12:50 * egonw notes that Pele is damn slow
12:51 annzi egonw: i'm trying to access it myselff
12:51 annzi but I can't
12:53 egonw can someone at BMC try to SSH into pele?
12:56 jonalv egonw: hm it doesn't seem to answer
12:56 egonw same here...
12:56 egonw can you ping it?
12:56 egonw that works here...
12:56 jonalv egonw: yea
12:56 jonalv ping works fine
12:57 olass ping works here too
12:57 egonw damn
12:57 sneumann memory hogged ?
12:57 jonalv what about bugzilla?
12:57 olass hmm, ssh does not seem to work...
12:57 olass or at least extremely slow..
12:57 sneumann joined #bioclipse
12:58 olass pelezilla seems to be down too
12:58 olass egonw: can you maybe restart pele?
12:58 egonw no
12:58 egonw not at bmc
12:58 egonw and ssh does not work
13:00 olass jonalv: can you ssh into pele?
13:00 jonalv olass: I am tryhing but I am not in yet
13:01 olass jonalv: if nothing works, could you please grab someone at BMC comp dept and restart pele?
13:01 olass it could be a routing problem..
13:01 jonalv olass: I guess so
13:01 olass jonalv++
13:01 jonalv olass: but it responds on ping so routing trouble seems strange
13:01 olass egonw: this looks crappy: http://wiki.bioclipse.net/i​ndex.php?title=MetaPrint2D
13:02 olass if a page is a feature and a project
13:02 egonw yeah, use either, not both
13:02 egonw either Template:Project or Template:Feature
13:03 * olass chose project
13:03 jonalv egonw: isn't it possible to make those boxes line up a bit better?
13:03 olass that would be nice
13:03 egonw probably...
13:03 egonw but /me is not so good as CSS magic
13:03 * jonalv doesn't see a good reason for why a site can't ahve both feature and project
13:04 jonalv masak: you know CSS magic I have heard...
13:04 olass does "git clone xxxx" create a new dir?
13:04 * jonalv tries to find someone who can help with pele
13:04 olass or should I do mkdir first?
13:05 olass man page says: Clones a repository into a newly created directory,
13:05 olass it does not say that the dir is created by git
13:06 olass it did create the dir
13:06 olass bad doc IMHO
13:09 masak egonw: looking at the page, I guess you removed the feature box, because I see only a project box.
13:10 olass I removed it
13:10 olass (my project)
13:12 masak oki, so there's no CSS question anymore :)
13:12 masak the short answer, in this case, would have been "you don't".
13:13 CIA-59 bioclipse: ospjuth * r11747 /bioclipse2/trunk/ (2 files in 2 dirs): Set version to 2.2.0.v20100127
13:22 egonw pele is back
13:23 * masak starts up zarah again
13:23 zarah joined #bioclipse
13:24 masak zarah: welcome back.
13:24 zarah masak: excuse me?
13:24 masak zarah: welcome back!
13:24 zarah masak: I'm just a bot, you expect me to understand that?
13:24 masak guess not.
13:28 jonalv @ping
13:28 zarah jonalv: pong
13:28 * jonalv takes that as pele is back oh and zarah++
13:28 jonalv pele had crashed quite hard it seemed
13:29 egonw so, the did a hard reboot
13:30 jonalv yea hard rebbot
13:30 jonalv 'det blev knappen'
13:30 egonw so, we'll never know what was going on :(
13:31 jonalv egonw: outofmemory
13:31 jonalv egonw: not sure what though...
13:31 jonalv it didn't really respond
13:31 jonalv even to keyboard input
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13:38 dsurdyk hey all - i'm having a problem updating and installing plugins from a newly-cloned version of bioclipse
13:39 dsurdyk when i click Help>SoftwareUpdates... it gives me two sites to upgrade from,
13:40 dsurdyk 1. Bioclipse Update Site
13:40 dsurdyk 2. Bioclipse Experimental Update Site
13:41 dsurdyk and when I select any of the possible upgrades it tells me the following...
13:41 dsurdyk Current configuration contains errors that are not corrected by the requested operation and more errors would be introduced. See details for more information.
13:41 dsurdyk ----- Current configuration problems -----
13:41 dsurdyk Core Patch (2.0.0.B20090417) requires feature "net.bioclipse.core_feature (2.0.0.B20090409)".
13:41 dsurdyk Bioclipse core patch (2.0.0.A20081028) requires feature "net.bioclipse_feature (2.0.0.A20080808)".
13:41 dsurdyk ----- Configuration problems after the operation -----
13:41 dsurdyk Core Patch (2.0.0.B20090417) requires feature "net.bioclipse.core_feature (2.0.0.B20090409)".
13:41 dsurdyk Bioclipse core patch (2.0.0.A20081028) requires feature "net.bioclipse_feature (2.0.0.A20080808)".
13:41 dsurdyk Bioclipse CDK Feature (2.2.0.RC3) requires feature "net.bioclipse.chemoinformatics_feature (2.2.0.RC3)", or later version.
13:41 dsurdyk any ideas?
13:43 olass dsurdyk: are you running from a downloaded version or from a compiled version?
13:44 olass dsurdyk: I am in the process of releasing 2.2.0 as we speak :)
13:45 olass dsurdyk: the core patch you see should not be available, I am thinkg you are trying to install features from the update site from a compiled version (RC3). This is not possible, you need to check out and run the plugins from Eclipse
13:45 olass dsurdyk: The update site can only be used from a binary build of Bioclipse
13:45 olass hope this helps
13:45 olass if not, let me know
13:47 dsurdyk compiled version from src - i'm working on the phylip plugin
13:48 olass dsurdyk: then you cannot use the update site
13:48 dsurdyk so i DL each of the src plugins in eclipse SDK and then set them as a dependancy in which XML file?
13:48 olass in the bioclipse.product
13:48 olass that is easiest
13:49 olass and then click "run product"
13:49 dsurdyk ok - thanks
13:49 dsurdyk that makes sense now
13:49 olass this is how I always start bioclipse
13:49 dsurdyk oh - i thought i we have to set the target machine again?
13:49 olass that is only required once
13:49 dsurdyk oh okay
13:50 dsurdyk i'll do that then
13:50 dsurdyk thanks
13:50 olass glad I could help :)
13:50 dsurdyk left #bioclipse
13:51 CIA-59 bioclipse.social: Egon Willighagen 2.2.x * r1cd7272 / features/net.bioclipse.social_feature/feature.xml : Also depend on the RDF feature - http://bit.ly/asUir2
13:51 CIA-59 bioclipse.social: Egon Willighagen 2.2.x * r93cae36 / plugins/net.bioclipse.myexpe​riment/META-INF/MANIFEST.MF : Removed versions from dependencies - http://bit.ly/cy6Atr
13:51 CIA-59 bioclipse.social: Egon Willighagen 2.2.x * r0da5bb4 / features/net.bioclipse.soc​ial_feature/social.product : Added the RDF feature - http://bit.ly/8ZTOv8
14:21 CIA-59 bioclipse.core: Ola Spjuth 2.2.x * r3858bef / plugins/net.bioclipse.ui/src/net/bi​oclipse/ui/BioclipseConstants.java : Default update site: http://update2.bioclipse.net - http://bit.ly/dobLtP
14:21 jonalv karma blame
14:21 zarah blame has a karma of -4
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15:32 * olass still has not been able to complete an export... :(
15:32 olass will try again now
15:32 olass waiting for workspace to build
15:33 olass afk
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15:43 egonw pondering about a mediawiki Template:BSLScript
15:44 egonw but reminds himself we have MyExperiment for that
15:44 * egonw likes http://wiki.bioclipse.net/inde​x.php?title=Category:Managers
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