Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-09-24

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All times shown according to UTC.

Time Nick Message
04:00 sneumann joined #bioclipse
04:14 sneumann left #bioclipse
05:24 sneumann joined #bioclipse
06:48 egonw joined #bioclipse
06:57 s_wolf joined #bioclipse
07:02 jonalv joined #bioclipse
07:02 jonalv oh hai
07:02 zarah ni hao jonalv
07:02 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
07:02 egonw moin all
07:02 zarah privet egonw
07:02 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
07:02 egonw today is the day that we get Pelezilla back
07:02 egonw I hope...
07:03 jonalv sneumann, egonw: What sort of upgrade problems? Have they resolved themselves?
07:03 egonw no, samuell++ solved them
07:03 egonw it turned out that the problems were not that bad...
07:03 egonw reshuffling of columns
07:03 jonalv okey sounds good
07:03 egonw and we we added a field
07:03 egonw 'Needs more info'
07:03 egonw that one
07:03 sneumann moin
07:03 zarah ni hao sneumann
07:04 egonw hi sneumann
07:04 egonw sneumann: please talk to Gpox about the xerces plugin in the repos
07:04 jonalv hang on, egonw you werent talking to me were you?
07:04 sneumann egonw++ pelezilla++
07:04 egonw jonalv: I was
07:04 jonalv so what did the Bioclipse update have to do with pelezilla database columns?
07:05 jonalv oh
07:05 jonalv aha
07:05 sneumann egonw: xerces problem is solved : http://colabti.org/irclogger/irclogg​er_log/bioclipse?date=2010-09-22#l67
07:05 egonw ok, good
07:05 jonalv egonw: I was refering to what zarah told me. 3 days ago you said that sneumann had trouble with updates
07:05 sneumann jonalv: update problem was solved by updating individual features instead of all at once
07:06 jonalv strange
07:06 jonalv I think the web hotel hosting our update site has some serious problems
07:06 * egonw thinks we need to either release 2.6 asap, or backport p2 to 2.4
07:07 egonw it seems that 2.4 is a bit of a waisted release right now...
07:07 sneumann you mean it has put on weight around the waist :-)
07:07 egonw no, we did not include the RDF feature in the core platform yet :)
07:07 egonw wasted?
07:08 * egonw wishes masak was around
07:08 egonw waysted? :)
07:08 jonalv so it has not enough weight around it's waist?
07:08 Gpox joined #bioclipse
07:08 jonalv ah hi gpox
07:08 egonw moin Gpox
07:08 egonw btw, meeting at AZ was great
07:08 jonalv Gpox: when do you estimate hudson will be able to build bioclipse 2.6 for us?
07:09 jonalv egonw: youve been to AZ?
07:10 egonw yeah, which is why I was not online the past two days
07:10 egonw talking about RDF and the CDK
07:10 * jonalv hasnt noticed, he has not been online either
07:10 jonalv students take a lot of time...
07:10 egonw and Bioclipse too, of course
07:11 jonalv yea
07:24 Gpox egonw: It shouldn't be far off, next step would be installing it which would be like bioclipse but without the brandin stuff
07:25 Gpox egonw: to install hudson I need to chagen some config files for tomcat and stuff that requiers sudo rights
07:26 egonw Gpox: try now please
07:27 Gpox egonw: it works, thanks
07:43 egonw bugger
07:43 egonw pelezilla import still doesn't work :(
08:10 egonw arghhhh.....
08:10 egonw stupid ubuntu
08:10 egonw ubuntu--
08:10 egonw ubuntu--
08:10 egonw ubuntu--
08:10 zarah ubuntu--
08:10 egonw ubuntu--
08:10 egonw ubuntu--
08:10 egonw ubuntu--
08:11 egonw egonw: relax... just one more week... then you're done with pele...
08:21 Gpox egonw: you got the hudson backup file?
08:21 egonw mom
08:23 olass joined #bioclipse
08:33 egonw brilliant: http://www.phdcomics.com/comics.php?f=1373
08:34 egonw omg... lucid is soo broken...
08:55 jonalv oh hai
08:55 zarah hi jonalv
09:06 * egonw gives up on the Ubuntu bugzilla3 package
09:06 egonw and downloaded 3.2.8 from bugzilla.org
10:00 egonw olass: import with file that samuel pointed me too just doesn't work
10:00 egonw stopping on pelezilla now
10:31 olass egonw: how should we continue with bugzilla?
10:31 egonw samuel apparently had it fixed
10:31 olass do you think samuell can help?
10:31 egonw but he did not keep a lab notebook
10:32 egonw so cannot follow the steps he took
10:32 egonw yes, think so
10:32 olass let us ask him on monday then
10:32 egonw but he will not be available today
10:32 egonw indeed
10:32 egonw sent him an email about that already
11:39 sneumann you could hook up that laptop to the inet :-)
11:46 egonw yes, perhaps best...
11:56 mgerlich left #bioclipse
12:08 samuell joined #bioclipse
12:09 samuell egonw: ping
12:10 egonw pong
12:10 egonw hi!
12:10 zarah privet egonw
12:10 egonw hi zarah
12:12 samuell hello
12:12 zarah ni hao samuell
12:12 samuell It seems I'm able to be online for a while
12:13 egonw ack
12:13 samuell Btw I realize I should have exported the db tablewise
12:13 egonw samuell: so, I tried both the bugzilla3 of lucid and 3.2.8 from bugzilla.org
12:13 egonw but both give errors when I try to import the SQL
12:13 samuell Ok ... (will check what my version was)
12:14 sneumann left #bioclipse
12:15 samuell Well, I used bugzilla 3.2.5, which should be the lucid version.
12:16 egonw do you want to give it a try on the bugzilla install on pele?
12:16 samuell Sure
12:16 egonw well, you know the details...
12:16 egonw mom
12:16 samuell I don't know if I can access the mysql executable thous
12:20 masak joined #bioclipse
12:34 egonw olass: ping
12:34 olass egonw: I am sitting with jonalv
12:35 egonw ack... can you update later bugs.bioclipse.net/index.html to point to:
12:35 egonw http://pele.farmbio.uu.se/bugzilla3/
12:35 olass will do
12:35 egonw (with a stress on 'later'...)
12:35 olass will do asap :)
12:51 masak will that make all old URLs still work?
12:54 egonw with cgi-bin/ ?
13:00 s_wolf left #bioclipse
13:49 masak I suoppse so. I actually don't know if we have a lot of old URLs laying around.
13:49 masak probably a bit on wiki pages and in emails.
14:05 samuell left #bioclipse
14:15 egonw argghhh
14:21 samuell joined #bioclipse
14:23 egonw samuell: no, no, no
14:23 egonw it keeps looking for fields in bugs that just don't exist
14:23 egonw and checksetup.pl is just useless
14:23 egonw olass: I really give up now... this is one big piece of crapware
14:24 olass egonw: what is?
14:24 olass Bugzilla?
14:24 egonw yes
14:25 egonw samuell: if you like, you can start from scratch
14:25 egonw but upgrading is not helping...
14:25 samuell egonw: Ok ...
14:25 egonw and neither did you install allow searching bugs...
14:25 samuell No, that's true
14:25 egonw and after adding 6-7 missing fields, it still does not work:
14:25 egonw http://pele.farmbio.uu.se/b​ugzilla3/show_bug.cgi?id=1
14:25 samuell But I wonder if there's a search table that needs to be regenerated...
14:26 egonw yeah, I think it might
14:26 egonw but checksetup.pl should do that
14:26 egonw instead of complaining about adding fields that already exists
14:26 egonw and not adding tables that do not...
14:26 egonw crapware
14:27 samuell one option we have not tried, is to go back to 3.2.5 and try to run with the current dump
14:27 egonw please try if you like
14:27 egonw olass: my advice: start with a fresh install
14:27 egonw I will now stop wasting time on trying to get the upgrade going...
14:28 samuell egonw: I guess we could try this quickly (3.2.5), just to have tried it
14:28 samuell Should the 3.2.5. version be installed with apt-get?
14:29 olass can we start from scratch but at least import the old bugs?
14:29 egonw olass: nope
14:29 egonw it's the import which just doesn't work
14:29 egonw samuell: OK, let's give that a last try
14:30 egonw samuell: please drop the bugzilla3 db from mysql
14:30 olass I did see some bugs on pelezilla...?
14:30 samuell egonw: ok, 1 mom
14:31 samuell Well, I don't have permissions to drop, but dropping tables should do equally fine, AFAIK
14:31 egonw yeah, probably
14:31 samuell done
14:31 egonw ok, running checksetup.pl
14:34 egonw ok, empty BZ set up
14:34 egonw samuell: now it's your turn
14:35 samuell Ok
14:35 samuell same folder, right?
14:35 samuell (sorry for the stupid questions ... :p )
14:35 egonw /var/www/bugzilla3/
14:36 samuell right
14:39 samuell search works
14:39 egonw not here:
14:39 egonw http://pele.farmbio.uu.se/bu​gzilla3/show_bug.cgi?id=2086
14:40 egonw DBD::mysql::db selectrow_hashref failed: Unknown column 'blocked' in 'field list'
14:40 samuell :(
14:40 egonw where does the search work?
14:40 egonw for you, that is... ?
14:40 samuell http://pele.farmbio.uu.se/bugzil​la3/buglist.cgi?quicksearch=cdk
14:41 egonw ok, good
14:42 egonw so, the problem is localized to show_bug.cgi
14:42 egonw ok, hacking ...
14:42 egonw mom
14:44 samuell Maybe I should try to copy the exact code I'm using locally (which seems to work)
14:44 egonw nope
14:44 egonw wait
14:44 egonw we need to see where the code is different first
14:44 egonw it's not the .cgi file...
14:45 samuell (now it does not)
14:45 egonw but the failing query is somewhere else
14:45 samuell its broken locally as well
14:45 egonw ack
14:45 egonw the thing is...
14:45 egonw bz creates the scripts depending on the schema
14:45 egonw we changed the pelezilla schema
14:45 egonw which changed the GUI
14:45 egonw but the checksetup.pl is doing it wrong
14:46 egonw making bits work, and others not
14:46 egonw and the whole thing pretty painful
14:46 egonw but with show_bug.cgi not working, the installation is pretty broken
14:48 egonw all in all.. it's just crapware
14:48 samuell But what is strange is that the schema seems broken, although the dump I'm using is created (locally) from a proper schema (just emptyed tables after bz install), into which I imported the data
14:48 egonw don't offer the option for people to change the schema if your software cannot handle it
14:50 samuell true
14:53 samuell If we put a deadline on the fix ... there is still the option to try to go down to nuts and bolts and curate column for column (at least the bugs table... the other ones doesn't seem that troublesome)
14:54 egonw those missing fields are retrieved from the DB content :(
14:54 egonw nothing to be fixed in the code
14:55 samuell Yeah, was thinking about fixing the db
14:55 samuell I think I should try again with the bugs table at least, locally
14:55 samuell I might have missed something
14:56 samuell ... going back to a working schema (by reinstalling bz) and trying to import again ...
14:56 samuell Will see If I can get through the show_bug.cgi error ...
15:02 egonw masak: ping
15:04 jonalv left #bioclipse
15:06 samuell Seems checksetup.pl is VERY picky
15:06 samuell ... about file system right etc ... and stops prematurely without giving an appropriate message
15:13 samuell Well, I get show_bug.cgi?id=2086 to work locally ... hmm
15:16 samuell Ah ... I have been importing the table in a bad way before
15:16 samuell violating foreign key checks by deleting the tables first
15:16 samuell ... it seems
15:17 egonw I found where the non-existing custom fields are defined...
15:17 egonw shall I delete those?
15:18 egonw ok, I will
15:19 egonw dependson, classification, cc, blocked, component
15:19 egonw product
15:20 egonw http://pele.farmbio.uu.se/b​ugzilla3/show_bug.cgi?id=1
15:20 egonw that helps
15:23 egonw ok, we got a winner
15:23 egonw olass: things are not entirely OK yet...
15:23 egonw but this is workable
15:23 olass aaaah!
15:23 olass egonw++ samuell++
15:24 olass so, let me hear what you have to say about Bugzilla:
15:24 olass crapware?
15:24 olass great job both of you
15:24 egonw no, not great job
15:24 egonw nasty habit of persistence
15:24 egonw and not being willing to give up or give in
15:24 * olass never expected an upgrade of bugzilla to be such a horrible process
15:25 egonw bugzilla--
15:25 egonw bugzilla--
15:25 egonw bugzilla--
15:25 zarah bugzilla--
15:25 egonw all together now
15:25 egonw still cannot file a new bug report
15:25 olass bugzilla--
15:25 egonw but that is less important
15:26 masak egonw++ samuell++
15:29 egonw ok, dinner now...
15:33 egonw wild idea, input please
15:33 samuell I also have a rather good version locally now
15:34 egonw this works now, except for new bugs
15:34 samuell After doing some things right which were done wrong before
15:34 egonw make this available as pele/bugzilla3.2/
15:34 samuell Is it the "No bug status is available on bug creation. Please report the problem to THE MAINTAINER HAS NOT YET BEEN SET. "
15:34 samuell ?
15:34 egonw and a new 3.6 install for all new bugs?
15:34 egonw samuell: no, way past that :)
15:34 samuell egonw: ok, how did you fix?
15:34 samuell :)
15:35 samuell Cause, I think my setup might be better working than yours :)
15:35 samuell (except for that one)
15:35 samuell (since it is quite much in its original state)
15:35 samuell (but that's just what I believe of course :) )
15:36 egonw got to Administration
15:36 egonw required fields
15:36 samuell Ok, have no admin account :(
15:36 samuell crap
15:37 samuell Maybe possible to make myself one in db
15:38 samuell but really has to go now ... but I could maybe create a separate installation of the version I have .. in case you want to try it, in case entering new bugs works?
15:38 samuell (later)
15:38 samuell (on pele, I mean)
15:38 samuell bugzilla3alt
15:38 olass left #bioclipse
15:39 samuell (since I cant enter admin panel ...
15:39 samuell ok, gotta go. Tell me per e-mail what you think about that
15:39 samuell left #bioclipse
16:28 egonw an empty Trac for Bioclipse -> http://pele.farmbio.uu.se/projects/bioclipse/
16:42 masak left #bioclipse
17:42 zarah left #bioclipse
18:50 Gpox left #bioclipse
19:01 sneumann joined #bioclipse
19:05 sneumann hi egonw, found this one recently:
19:05 sneumann http://failblog.org/2010/09/21/epic-fai​l-photos-comcast-customer-service-win/
19:19 egonw :)
19:32 sneumann what I don't like about trac is that there is a lot of stuff which is usually/too often not used,
19:32 sneumann such as timeline, wiki etc
19:32 sneumann which makes it look underused, or content not well-maintained
19:33 sneumann if one used it, the irrelevant stuff should be hidden, focussing on e.g. the bug tracker
19:52 egonw yeah, fully agreed...
21:04 edrin joined #bioclipse
21:05 edrin hi egonw
21:05 edrin How was your presentation at AstraZeneca?
21:07 sneumann bye
21:12 sneumann left #bioclipse
21:51 edrin good night
21:53 edrin left #bioclipse
22:32 samuell joined #bioclipse
22:42 samuell left #bioclipse

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