| Time |
S |
Nick |
Message |
| 05:05 |
|
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thomas_ku joined #bioclipse |
| 06:00 |
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Gpox joined #bioclipse |
| 06:31 |
|
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egonw joined #bioclipse |
| 07:43 |
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egonw joined #bioclipse |
| 07:43 |
|
egonw |
hi stain! |
| 07:43 |
|
zarah |
egonw: You have new messages. Write '@messages' to read them. |
| 07:43 |
|
egonw |
@msg |
| 07:43 |
|
zarah |
egonw: 15 h 51 m 40 s ago, jonalv said is our bugzilla totally open or do I have to get a log in? |
| 07:44 |
|
egonw |
@tell jonalv you need a log in, but you can create one from the website |
| 07:44 |
|
zarah |
Consider it noted. |
| 07:44 |
|
egonw |
zarah: tack |
| 07:44 |
|
zarah |
you're welcome, egonw :) |
| 08:00 |
|
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olaz joined #bioclipse |
| 08:02 |
|
egonw |
http://git.or.cz/gitwiki/EclipsePluginScreenshots |
| 08:02 |
|
zarah |
egonw's link is also http://tinyurl.com/5obdea |
| 08:03 |
|
|
jonalv joined #bioclipse |
| 08:03 |
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olass joined #bioclipse |
| 08:04 |
|
egonw |
jonalv: http://git.or.cz/gitwiki/EclipsePluginScreenshots |
| 08:04 |
|
zarah |
egonw's link is also http://tinyurl.com/5obdea |
| 08:04 |
|
egonw |
you've just missed it by seconds :) |
| 08:04 |
|
egonw |
the plugin is under active development... last commits yesterday |
| 08:07 |
|
|
gilleain joined #bioclipse |
| 08:15 |
|
jonalv |
egonw: missed what with seconds? |
| 08:17 |
|
egonw |
that URL |
| 08:17 |
|
egonw |
I'll look into the email problem for bugzilla |
| 08:18 |
|
jonalv |
egonw: HAve you tried it? |
| 08:19 |
|
egonw |
nej |
| 08:23 |
|
olass |
how is CIA? |
| 08:23 |
|
egonw |
dead again, I think |
| 08:24 |
|
egonw |
umm... Ubuntu intrepid has Bugzilla 3.0.4 |
| 08:24 |
|
olass |
it's dead a lot |
| 08:24 |
|
egonw |
where we now use 2.22 |
| 08:24 |
|
olass |
oh!? |
| 08:24 |
|
egonw |
should we upgrade pele along we go? |
| 08:24 |
|
olass |
why not? |
| 08:24 |
|
egonw |
is it physically accessible? |
| 08:24 |
|
egonw |
in case the reboot fails... |
| 08:25 |
|
egonw |
(kernel upgrade) |
| 08:25 |
|
olass |
well, not really today |
| 08:25 |
|
olass |
(for me at least) |
| 08:25 |
|
egonw |
same here |
| 08:25 |
|
egonw |
but Thu would be ok? |
| 08:25 |
|
olass |
let's do it tomorrow then when we are in uppsala |
| 08:25 |
|
egonw |
right |
| 08:25 |
|
olass |
about cdk.debug |
| 08:25 |
|
olass |
should that go in release? |
| 08:26 |
|
jonalv |
olass: when are you planning to release? |
| 08:26 |
|
egonw |
maybe not |
| 08:26 |
|
egonw |
let's leave it out for now |
| 08:26 |
|
olass |
now |
| 08:26 |
|
olass |
ok |
| 08:26 |
|
olass |
jonalv: about usermanager feature |
| 08:26 |
|
olass |
should we release that too? |
| 08:26 |
|
jonalv |
olass: no news. Still license trouble on that one... |
| 08:26 |
|
olass |
or wait? |
| 08:27 |
|
olass |
ok |
| 08:27 |
|
olass |
no release then |
| 08:27 |
|
jonalv |
olass: besides Idon't think we have anything that needs it... |
| 08:27 |
|
olass |
true |
| 08:27 |
|
olass |
and speclipse? |
| 08:27 |
|
olass |
egonw: did you try it? |
| 08:27 |
|
olass |
is it stable? |
| 08:27 |
|
olass |
are there use cases? |
| 08:27 |
|
olass |
no shk3 here |
| 08:28 |
|
gilleain |
he's here, but not here here. |
| 08:29 |
|
olass |
can you ask him to come here here soon soon? |
| 08:29 |
|
|
edrin joined #bioclipse |
| 08:30 |
|
edrin |
hi |
| 08:30 |
|
zarah |
hi edrin |
| 08:30 |
|
|
shk3 joined #bioclipse |
| 08:30 |
|
jonalv |
hi edrin |
| 08:30 |
|
jonalv |
hi shk3 |
| 08:30 |
|
edrin |
hi jonalv |
| 08:30 |
|
shk3 |
hi jonalv |
| 08:30 |
|
olass |
shk3: is speclipse feature stable? |
| 08:31 |
|
olass |
enough for a release? |
| 08:31 |
|
shk3 |
I think so, yes |
| 08:31 |
|
olass |
sample data exists? |
| 08:31 |
|
olass |
use cases? |
| 08:31 |
|
shk3 |
I would say yes |
| 08:31 |
|
olass |
good |
| 08:31 |
|
shk3 |
sample data in sample data |
| 08:31 |
|
shk3 |
not yet in the xml |
| 08:31 |
|
shk3 |
use cases in wiki |
| 08:33 |
|
egonw |
shk3: I'd say EBI should host the Speclipse feature |
| 08:33 |
|
egonw |
shk3: I'd say EBI should host the Speclipse feature update site |
| 08:34 |
|
shk3 |
hm, what does that mean? |
| 08:35 |
|
edrin |
shk3: what does speclipse do? |
| 08:35 |
|
shk3 |
what do we need to do for the update site? |
| 08:35 |
|
shk3 |
edrin: see use cases on wiki |
| 08:36 |
|
jonalv |
google speclipse bioclipse use cases |
| 08:36 |
|
zarah |
jonalv: No hits. |
| 08:36 |
|
shk3 |
http://wiki.bioclipse.net/inde[…]for_Bioclipse_2.0 |
| 08:37 |
|
zarah |
shk3's link is also http://tinyurl.com/6ew7tl |
| 08:42 |
|
gilleain |
Hmmm. There are quite a few (32) pages on the wiki that are orphans. |
| 08:45 |
|
olass |
wiki needs a serious update |
| 08:45 |
|
olass |
egonw: why? |
| 08:45 |
|
olass |
why not bioclipse.net? |
| 08:45 |
|
olass |
it IS in our svn... |
| 08:46 |
|
olass |
shk3: basically just a web server |
| 08:47 |
|
egonw |
world conquest |
| 08:47 |
|
olass |
shk3: maybe it's better if you hosted anyway... |
| 08:47 |
|
olass |
that way you can update |
| 08:47 |
|
olass |
yourself |
| 08:47 |
|
egonw |
we want to show that EBI is actively working with Bioclipse |
| 08:47 |
|
egonw |
that makes more impact of people download/update from ebi.ac.uk |
| 08:49 |
|
edrin |
egonw: I fully agree |
| 08:49 |
|
olass |
shk3: it's very easy |
| 08:49 |
|
olass |
create a new project "update site" |
| 08:49 |
|
egonw |
(olass: we could still secretly host it too, of course :) |
| 08:49 |
|
olass |
add your feature |
| 08:49 |
|
olass |
build update site |
| 08:50 |
|
olass |
FTP entire content from the update site project to a location on a web server |
| 08:50 |
|
olass |
add update site in bc2 pointing to the server |
| 08:50 |
|
olass |
done |
| 08:50 |
|
olass |
let me know if you run into problems |
| 08:51 |
|
egonw |
olass: jonalv was able to log in on bugzilla pele now |
| 08:51 |
|
egonw |
email problem fixes |
| 08:51 |
|
egonw |
email problem fixed |
| 08:51 |
|
olass |
hmm |
| 08:51 |
|
olass |
I get no email... |
| 08:51 |
|
olass |
i got it |
| 08:52 |
|
egonw |
excellent :) |
| 08:52 |
|
olass |
hmm, link is very broken |
| 08:52 |
|
egonw |
what link? |
| 08:52 |
|
olass |
but I think I understand how to use it |
| 08:52 |
|
egonw |
in the email? |
| 08:52 |
|
olass |
yes |
| 08:52 |
|
egonw |
hahah... indeed |
| 08:52 |
|
egonw |
yeah, just go to the website |
| 08:56 |
|
olass |
egonw: why have you added 1.2? |
| 08:56 |
|
olass |
to bugzilla? |
| 08:56 |
|
shk3 |
olass: need to talk to christoph about webspace |
| 08:56 |
|
olass |
it is totally abandoned |
| 08:56 |
|
egonw |
for the old bugs? |
| 08:56 |
|
olass |
hmm |
| 08:56 |
|
olass |
is it necessary? |
| 08:56 |
|
egonw |
olass: did you close all 1.2 bugs on SF? |
| 08:57 |
|
olass |
no |
| 08:57 |
|
olass |
I have closed none |
| 08:57 |
|
egonw |
anyway, just needed more than on thingy... |
| 08:57 |
|
olass |
but will not solve any of them |
| 08:57 |
|
egonw |
to test things |
| 08:57 |
|
olass |
ok |
| 08:59 |
|
* jonalv |
is exploring bugzilla... |
| 09:03 |
|
egonw |
cool |
| 09:03 |
|
jonalv |
egonw: is voting turned off? |
| 09:03 |
|
egonw |
I just received a popup window on my screen |
| 09:03 |
|
egonw |
olass: something about P2 -> P1 ?? |
| 09:03 |
|
egonw |
:) |
| 09:03 |
|
jonalv |
a popup window? |
| 09:03 |
|
egonw |
mylyn in action :) |
| 09:04 |
|
egonw |
yes, a cool OSD popup :) |
| 09:04 |
|
olass |
how use mylyn with bugzilla? |
| 09:04 |
|
* egonw |
feels a growing open source development grid... |
| 09:04 |
|
egonw |
jonalv: listening too? |
| 09:05 |
|
jonalv |
egonw: you lost me.. |
| 09:05 |
|
egonw |
jonalv: just follow these steps: |
| 09:05 |
|
jonalv |
egonw: oki |
| 09:05 |
|
egonw |
Eclipse -> WIndow -> Show View |
| 09:06 |
|
egonw |
-> Other |
| 09:06 |
|
egonw |
Mylyn -> Task List |
| 09:06 |
|
egonw |
and Mylyn -> Task Repositories |
| 09:06 |
|
olass |
egonw: wiki page? |
| 09:06 |
|
egonw |
we'll use both |
| 09:06 |
|
egonw |
yes, will copy paste later into the wiki |
| 09:06 |
|
olass |
go on |
| 09:07 |
|
egonw |
open the Task Repos view |
| 09:07 |
|
egonw |
hit the add repos icon |
| 09:07 |
|
egonw |
blue battery + '+' signe |
| 09:07 |
|
egonw |
pick Bugzilla |
| 09:07 |
|
egonw |
(well, assuming that you already have mylyn installed...) |
| 09:08 |
|
jonalv |
(or right click choose add task reposistpry...) |
| 09:08 |
|
egonw |
if not, read the Mylyn 2.0 papers in IBM developers network |
| 09:08 |
|
egonw |
OK, that should give a window called: |
| 09:08 |
|
egonw |
Props for Task Repos |
| 09:08 |
|
egonw |
with "Bugzilla Repos Settings" |
| 09:09 |
|
egonw |
Server: http://pele.farmbio.uu.se/bugs |
| 09:09 |
|
zarah |
egonw's link is also http://tinyurl.com/57eu7e |
| 09:09 |
|
egonw |
Label Pele |
| 09:09 |
|
egonw |
No Anom Access |
| 09:09 |
|
egonw |
enter your User ID |
| 09:09 |
|
egonw |
and Password |
| 09:09 |
|
egonw |
(likely you click Save Password too) |
| 09:10 |
|
egonw |
I have Http Auth enabled too, but not sure if that is really needed |
| 09:10 |
|
egonw |
in Additional Settings: |
| 09:10 |
|
egonw |
pick repos Version 2.22 |
| 09:10 |
|
egonw |
for the rest, default did it for me |
| 09:10 |
|
egonw |
make sure to hit the 'Validate Settings' button |
| 09:11 |
|
egonw |
oh... did not notice the 'Create new account' link earlier :) |
| 09:11 |
|
olass |
so how set up query? |
| 09:11 |
|
olass |
using form or URL? |
| 09:11 |
|
olass |
to see all/my bugs |
| 09:12 |
|
jonalv |
wow the dialog for query paramaters looks so cool! :) |
| 09:13 |
|
egonw |
OK, now the query |
| 09:13 |
|
egonw |
open the Task List view |
| 09:13 |
|
egonw |
right click on view -> New -> Query |
| 09:13 |
|
egonw |
and set up your query |
| 09:13 |
|
egonw |
I have: |
| 09:14 |
|
egonw |
Email: egon.willighagen |
| 09:14 |
|
egonw |
with owner, reported, cc, commenter |
| 09:14 |
|
egonw |
to see all related to me |
| 09:14 |
|
egonw |
as one query |
| 09:14 |
|
egonw |
another useful one would be 'unassiged' |
| 09:15 |
|
egonw |
that's it |
| 09:17 |
|
jonalv |
uhm I created a query for pele but it's not showing up in the Task List... :( |
| 09:17 |
|
jonalv |
ah it's becasue it was empty |
| 09:18 |
|
olass |
nice |
| 09:18 |
|
olass |
I se my comment on your bug, egonw |
| 09:18 |
|
* olass |
likes this |
| 09:18 |
|
jonalv |
wow this is so cool! >( |
| 09:18 |
|
jonalv |
|lol |
| 09:18 |
|
jonalv |
:) |
| 09:19 |
|
jonalv |
and you can attach a mylyn context to the bug? |
| 09:20 |
|
egonw |
dunno that yet |
| 09:20 |
|
egonw |
actually, how did I only have the mylyn context show up in my navigator again? |
| 09:21 |
|
egonw |
I guess I just have to do some account clean up :) |
| 09:25 |
|
egonw |
ok, everyone is using there farmbio email? right? |
| 09:25 |
|
egonw |
so I delete all @gmail accounts now |
| 09:26 |
|
jonalv |
oki |
| 09:27 |
|
gilleain |
wait, what? egon's deleting all gmail accounts? |
| 09:28 |
|
egonw |
yeah: ssh rootgmail.com; \rm -Rf /home/* |
| 09:28 |
|
gilleain |
Er, more seriously - is this mylyn thing only going to work for those with farmbio emails? |
| 09:28 |
|
egonw |
no |
| 09:28 |
|
gilleain |
ah, ok. |
| 09:28 |
|
egonw |
but the postfix got time outs from the gmail.com relay |
| 09:29 |
|
gilleain |
hmm. |
| 09:29 |
|
egonw |
[10:41] <egonw> Oct 22 09:33:49 pele postfix/smtp[19874]: connect to alt2.gmail-smtp-in.l.google.com[209.85.163.27]:25: Connection timed out |
| 09:31 |
|
egonw |
ok, 4 registered users left |
| 09:31 |
|
egonw |
olass, jonalv, egonw, Gpox |
| 09:31 |
|
jonalv |
egonw: yea? |
| 09:32 |
|
jonalv |
oh hehe sry |
| 09:32 |
|
jonalv |
olass: what happend to olas? |
| 09:39 |
|
olass |
dunni |
| 09:39 |
|
olass |
early vac? |
| 09:41 |
|
jonalv |
what does the last s stand for? :) |
| 09:41 |
|
egonw |
sad |
| 09:45 |
|
* jonalv |
<- lunch |
| 09:45 |
|
egonw |
Gpox: so, how do I 'open' your context? |
| 09:46 |
|
|
Julio joined #bioclipse |
| 09:46 |
|
|
Julio left #bioclipse |
| 09:46 |
|
egonw |
Gpox: never mind |
| 09:46 |
|
egonw |
I now see the 'retrieve context' |
| 09:48 |
|
egonw |
how did I 'search' for classes in Eclipse again? |
| 09:49 |
|
olass |
ctrl shift T |
| 09:50 |
|
olass |
egonw: have you set our permissions on bugzilla? |
| 09:50 |
|
egonw |
I have not touched any permissions |
| 09:50 |
|
olass |
I'd like to be admin |
| 09:50 |
|
olass |
hmm |
| 09:50 |
|
olass |
how do we assign bugs? |
| 09:50 |
|
olass |
aah |
| 09:50 |
|
olass |
scroll down :-) |
| 09:51 |
|
egonw |
ola.spjuth now has supercow powers |
| 09:52 |
|
olass |
hmm |
| 09:52 |
|
olass |
we assign by email? |
| 09:52 |
|
egonw |
hmm... indeed |
| 09:53 |
|
olass |
no combobox? |
| 09:53 |
|
egonw |
yes, by email |
| 09:53 |
|
olass |
so you must remember everyones email!? |
| 09:54 |
|
egonw |
hahahaha :) |
| 09:54 |
|
egonw |
I hope not |
| 09:54 |
|
egonw |
check the docs |
| 09:54 |
|
egonw |
http://www.bugzilla.org/docs/2.22/html/ |
| 09:54 |
|
zarah |
egonw's link is also http://tinyurl.com/erkcq |
| 09:55 |
|
egonw |
http://www.bugzilla.org/docs/2[…]ml/lifecycle.html |
| 09:55 |
|
zarah |
egonw's link is also http://tinyurl.com/fsua4 |
| 09:55 |
|
egonw |
sounds like one 'takes possesion' of a bug |
| 09:55 |
|
egonw |
instead of getting a bug assigned |
| 09:57 |
|
egonw |
Mylyn has a content assistent for the Assigned |
| 09:57 |
|
egonw |
but it only shows me... |
| 09:57 |
|
egonw |
not sure how that is filled |
| 10:09 |
|
egonw |
how do I get a manager to output a message to the console? |
| 10:09 |
|
egonw |
google Bioclipse Console message |
| 10:09 |
|
zarah |
egonw: http://www.bioclipse.net/doc/1[…]rials_extApp.html |
| 10:09 |
|
egonw |
google Bioclipse 2 Console message |
| 10:09 |
|
zarah |
egonw: http://www.biomedcentral.com/1471-2105/8/59 |
| 10:09 |
|
egonw |
hahaha |
| 10:19 |
|
olass |
egonw: you here? |
| 10:20 |
|
egonw |
ja |
| 10:20 |
|
olass |
priority p5 is most urgent or p1 ? |
| 10:20 |
|
* egonw |
is working on the JChemPaintManager |
| 10:20 |
|
egonw |
olass: no idea :) |
| 10:20 |
|
olass |
P1 right? |
| 10:21 |
|
egonw |
no clue |
| 10:21 |
|
egonw |
trying to find it in the docs |
| 10:22 |
|
egonw |
# |
| 10:22 |
|
egonw |
Priority: The bug assignee uses this field to prioritize his or her bugs. It's a good idea not to change this on other people's bugs. |
| 10:23 |
|
egonw |
really, no clue |
| 10:23 |
|
Gpox |
i would say that mylyn thinks p1 is very high |
| 10:24 |
|
egonw |
ok, good |
| 10:27 |
|
egonw |
olass: ping |
| 10:28 |
|
egonw |
Gpox: ping |
| 10:28 |
|
egonw |
both for lunch? |
| 10:28 |
|
Gpox |
no i am here |
| 10:29 |
|
egonw |
Gpox: how do I open a MDL file in the new JChemPaint editor? |
| 10:29 |
|
egonw |
is that possible already? |
| 10:33 |
|
Gpox |
Open With -> Other... |
| 10:33 |
|
egonw |
ok, that killed my BC2 :) |
| 10:34 |
|
egonw |
and that's reproducable... :( |
| 10:34 |
|
egonw |
and I don't get stacktraces or what |
| 10:38 |
|
olass |
egonw: pong |
| 10:39 |
|
olass |
egonw: I dare say that org.openscience.cdk.atomtype was not created 1.1.0.20080907 |
| 10:39 |
|
olass |
should it not be 1.2.0? |
| 10:39 |
|
olass |
and why that date? |
| 10:40 |
|
olass |
did you not create that plugin just a week ago? |
| 10:40 |
|
egonw |
do you want to me copy in a new snapshot of CDK 1.2.x? |
| 10:40 |
|
olass |
let's have disc over IRC and not via bug reports |
| 10:40 |
|
olass |
hmm |
| 10:40 |
|
egonw |
hope not |
| 10:40 |
|
olass |
maybe not |
| 10:40 |
|
egonw |
because this would not be good at this moment |
| 10:40 |
|
olass |
ok |
| 10:40 |
|
egonw |
better directly *after* a release |
| 10:40 |
|
olass |
then let's stick to your version |
| 10:40 |
|
olass |
thought you used lates for the plugins |
| 10:42 |
|
egonw |
it's not horribly old... |
| 10:42 |
|
egonw |
if you really want to change them... |
| 10:43 |
|
egonw |
I can set the date to when I actually generated them |
| 10:43 |
|
egonw |
whcih I should be able to recover from SVN logs |
| 10:43 |
|
egonw |
tack |
| 10:43 |
|
egonw |
I really like this OSD updates :) |
| 10:44 |
|
egonw |
makes you feel to be in the same office :) |
| 10:45 |
|
egonw |
OK, lunch time now |
| 10:48 |
|
Gpox |
egonw: I think i solved the jchempainteditor crash |
| 10:48 |
|
egonw |
great |
| 11:03 |
|
olass |
egonw: OSD updates? |
| 11:04 |
|
olass |
how are you informed? |
| 11:04 |
|
olass |
egonw: please announce on devel our move to bugzilla |
| 11:04 |
|
olass |
and that people should register there |
| 11:04 |
|
olass |
and that SF will be phased out |
| 11:06 |
|
olass |
hmm |
| 11:06 |
|
olass |
anyone has any notion if I ever checked in a feature patch to SVN? |
| 11:07 |
|
|
gilleain joined #bioclipse |
| 11:10 |
|
olass |
should XOM go with bioclipse-feature? It sems central to many plugins... |
| 11:10 |
|
* olass |
created a new feature patch anyways |
| 11:10 |
|
egonw |
no, would not do that |
| 11:10 |
|
egonw |
would just add it to those features that really need it |
| 11:17 |
|
olass |
OK |
| 11:17 |
|
olass |
egonw: chemoinfo feature requires org.op.cdk.jchempaint |
| 11:17 |
|
olass |
but that is not in svn externals |
| 11:17 |
|
olass |
why? |
| 11:18 |
|
olass |
can I remove it from feature? |
| 11:18 |
|
olass |
(this is for release) |
| 11:18 |
|
egonw |
think so |
| 11:18 |
|
olass |
ok |
| 11:19 |
|
olass |
is that the one you are working on? |
| 11:19 |
|
egonw |
no |
| 11:19 |
|
egonw |
got things in a branch |
| 11:19 |
|
egonw |
in net.bioclipse.cdk.jchempaint.business |
| 11:20 |
|
olass |
ok |
| 11:20 |
|
olass |
feature updated anyway |
| 11:21 |
|
* jonalv |
just found much more work with structuredb business and gui layer... |
| 11:25 |
|
olass |
egonw: chemoinfo feature does not export |
| 11:25 |
|
olass |
can you look at it? |
| 11:25 |
|
olass |
here's how to reproduce: |
| 11:26 |
|
olass |
check out update-site (or create a new one, you just need one for testing purposes) |
| 11:26 |
|
olass |
hmm |
| 11:26 |
|
olass |
will do this in a bug report |
| 11:26 |
|
egonw |
tack |
| 11:30 |
|
olass |
egonw: did you get that? |
| 11:30 |
|
egonw |
yes |
| 11:30 |
|
egonw |
upon a sync |
| 11:31 |
|
egonw |
it does not do that every second :) |
| 11:31 |
|
egonw |
no context?!?! |
| 11:38 |
|
olass |
no |
| 11:38 |
|
olass |
since you can create your own update site |
| 11:47 |
|
egonw |
OK, all trackers on SF are now no longer visible to users... |
| 11:47 |
|
egonw |
bugs and feature requests still have items open (64+29( |
| 11:47 |
|
jonalv |
so how do we do with the porting? |
| 11:47 |
|
egonw |
which need to be closed and transfered to pele |
| 11:48 |
|
egonw |
you port those assigned to you, or reported to you |
| 11:48 |
|
jonalv |
but if I no longer can see them... |
| 11:48 |
|
egonw |
mark them as: |
| 11:48 |
|
egonw |
closed, duplicated |
| 11:48 |
|
egonw |
closed, duplicate |
| 11:48 |
|
egonw |
jonalv: both those two trackes are visible to project members |
| 11:49 |
|
egonw |
but you might need to log in on SF first |
| 11:49 |
|
jonalv |
egonw: oh okey |
| 11:49 |
|
egonw |
I've added a default reply: "Moved to Bugzilla" |
| 11:50 |
|
egonw |
and in Bugzilla I add the link to the SF bug report as URL |
| 11:50 |
|
jonalv |
ah okey |
| 11:52 |
|
egonw |
btw |
| 11:52 |
|
egonw |
olass: 1.2.0 bugs which do not apply to 2.0 we just close with "Out of Date", correct? |
| 11:52 |
|
olass |
yes |
| 12:08 |
|
egonw |
OK, 58 open bugs remaining in SF |
| 12:20 |
|
jonalv |
I will have a look once I have gotten through this readtrue of StrucutredbManagerTest.java :) |
| 12:21 |
|
egonw |
ack |
| 12:21 |
|
* egonw |
will get to this bug report on exporting the chemoinformatics feature |
| 12:22 |
|
|
gilleain joined #bioclipse |
| 12:30 |
|
edrin |
egonw: hi, and did you play with xws ? |
| 12:30 |
|
egonw |
hi edrin, ah, no :( |
| 12:30 |
|
egonw |
but I did play with Mylyn/Bugzilla |
| 12:31 |
|
egonw |
and JChemPaintManager |
| 12:31 |
|
egonw |
it's high on my todo list... |
| 12:31 |
|
egonw |
but it's pretty crowded at the top |
| 12:31 |
|
edrin |
hehe |
| 12:58 |
|
|
charlgren joined #bioclipse |
| 13:06 |
|
|
gilleain joined #bioclipse |
| 13:10 |
|
egonw |
olass: ping |
| 13:10 |
|
olass |
pong |
| 13:10 |
|
egonw |
did you not have this problem last time? |
| 13:10 |
|
egonw |
can you try this: |
| 13:10 |
|
olass |
what prob? |
| 13:10 |
|
egonw |
got to the cdk10 plugin |
| 13:11 |
|
egonw |
and run the ant task javacc |
| 13:12 |
|
olass |
I have no build.xml there |
| 13:13 |
|
egonw |
ok |
| 13:14 |
|
egonw |
hang on |
| 13:14 |
|
egonw |
another exit svn:externals |
| 13:15 |
|
olass |
exit? |
| 13:16 |
|
olass |
did you fix the export problem of chemoinfo-feature?? |
| 13:16 |
|
egonw |
that's what we are talking about |
| 13:16 |
|
olass |
ok |
| 13:16 |
|
olass |
previously I have always removed all tests from cdk10 |
| 13:16 |
|
olass |
just deleted them |
| 13:16 |
|
olass |
maybe not required anymore... |
| 13:16 |
|
egonw |
the problem that the 'export' forgot to autogenerate some .java files with this 'javacc' ant target |
| 13:17 |
|
egonw |
actually, these cannot even be imported with svn:externals |
| 13:17 |
|
egonw |
it never showed up, because I think we had the dependent .java files removed from the build path |
| 13:17 |
|
egonw |
apparently the export does not care about excludes from the build path |
| 13:17 |
|
egonw |
:( |
| 13:18 |
|
egonw |
so, this is what I shall do: |
| 13:18 |
|
egonw |
uploade the CDK pure 1.0.4 jar |
| 13:19 |
|
egonw |
and hope nothing breaks |
| 13:20 |
|
egonw |
jonalv: you have two SF accounts?? |
| 13:20 |
|
jonalv |
egonw: uhm yea... It's not something I am proud about.. |
| 13:20 |
|
egonw |
:) |
| 13:20 |
|
egonw |
miguel howard, of Jmol fame, switch account name too |
| 13:20 |
|
egonw |
so,. you're in a good audience :) |
| 13:21 |
|
egonw |
but, why??? |
| 13:21 |
|
olass |
egonw: eclipse export can NOT have classes not on th classpath |
| 13:21 |
|
egonw |
olass: right |
| 13:21 |
|
olass |
you need to remove all those |
| 13:21 |
|
egonw |
which is why I asked, whether this has ever workde :) |
| 13:21 |
|
egonw |
olass: whcih I can't, because they are in CDK SVN... |
| 13:21 |
|
egonw |
hence, I'll upload the jar |
| 13:21 |
|
egonw |
and be done with that |
| 13:21 |
|
olass |
ok |
| 13:21 |
|
jonalv |
I didn't want to mess up my "play" account with the one I used for Bioclipse + I wanted the same nich on both sourceforge and freenode |
| 13:22 |
|
olass |
egonw: as long as it works I'm fine with it |
| 13:22 |
|
egonw |
:) |
| 13:22 |
|
egonw |
:) |
| 13:22 |
|
olass |
ping me when done |
| 13:22 |
|
olass |
REALLY want this solved today |
| 13:22 |
|
egonw |
mmm... already 306 downloads for CDK 1.0.4 |
| 13:22 |
|
egonw |
not bad |
| 13:23 |
|
egonw |
I had no idea so many people were still using the 1.0.x series |
| 13:29 |
|
egonw |
olass: good news, and bad news |
| 13:29 |
|
egonw |
what do you want first |
| 13:29 |
|
olass |
bad |
| 13:29 |
|
olass |
always bad first |
| 13:29 |
|
egonw |
ok, it will take me another hour or so, to work things out... |
| 13:29 |
|
egonw |
maybe more... |
| 13:29 |
|
olass |
good? |
| 13:29 |
|
egonw |
and things will need some new testing |
| 13:30 |
|
edrin |
that is good? |
| 13:30 |
|
egonw |
he, I'm not done with the bad news yet... :) |
| 13:30 |
|
olass |
right... |
| 13:30 |
|
olass |
go on |
| 13:30 |
|
edrin |
long list |
| 13:30 |
|
egonw |
the good news is, I can reuse the new 3rd party libs |
| 13:30 |
|
egonw |
which will reduce the download size |
| 13:30 |
|
olass |
:-) |
| 13:31 |
|
egonw |
oh, sorry... that's not good news to you :) |
| 13:31 |
|
olass |
working is most important |
| 13:31 |
|
olass |
cdk10 is scheduled for removal anyway |
| 13:32 |
|
olass |
how long? |
| 13:32 |
|
olass |
one hour? |
| 13:32 |
|
jonalv |
okey out of 223 tests in Bioclipse2 110 passes. If anyone is intrested... :) |
| 13:32 |
|
olass |
how many are structuredb out of these 233? |
| 13:33 |
|
olass |
223 |
| 13:33 |
|
jonalv |
I am glad you asked. 122 of them are from structuredb |
| 13:33 |
|
olass |
do you run as junit-plugin-tests or junit-tests? |
| 13:33 |
|
jonalv |
oh right these where the junit-tests ones |
| 13:33 |
|
jonalv |
there are a few more plugin tests |
| 13:33 |
|
jonalv |
forgot about them :) |
| 13:34 |
|
olass |
any crucial that fail? |
| 13:34 |
|
shk3 |
guys, are we moving away from sf for bugtracking? |
| 13:34 |
|
jonalv |
shk3: yup |
| 13:34 |
|
shk3 |
why so? |
| 13:34 |
|
jonalv |
olass: I don't know really. HArd to say... |
| 13:34 |
|
olass |
shk3: there's a mail on devel ML from egon |
| 13:34 |
|
olass |
shk3: REALLY nice with good integration of bugzilla in mylyn |
| 13:35 |
|
olass |
egonw promised to write up a wiki page with screenshots how to set that up |
| 13:35 |
|
olass |
actually not hard at all |
| 13:35 |
|
shk3 |
they always say that |
| 13:35 |
|
egonw |
no screenshot, but the wiki page is mentioned in the emila |
| 13:35 |
|
shk3 |
how do we get accounts in bugzilla? |
| 13:35 |
|
jonalv |
it was easy |
| 13:35 |
|
shk3 |
sure it was easy... |
| 13:35 |
|
gilleain |
I applied for one, but it never arrived. |
| 13:36 |
|
gilleain |
It said to contact some "egon" guy, I dunno. |
| 13:37 |
|
olass |
egon fixed it |
| 13:37 |
|
olass |
try again |
| 13:37 |
|
egonw |
(connect to pihlis.ebi.ac.uk[193.62.195.233]:25: Connection timed out) |
| 13:37 |
|
egonw |
mmm... |
| 13:37 |
|
egonw |
I fixed farmbio email... |
| 13:37 |
|
egonw |
but it seems not just gmail is failing ... |
| 13:38 |
|
egonw |
but ebi email too... |
| 13:38 |
|
* jonalv |
has a bad feeling about this... |
| 13:38 |
|
egonw |
I guess we need to ask permission for pele to use the 25 port? |
| 13:38 |
|
olass |
problem with open ports on server? |
| 13:38 |
|
olass |
right |
| 13:38 |
|
egonw |
weird thing is... |
| 13:38 |
|
egonw |
this is port 25 on the target |
| 13:38 |
|
egonw |
not pele:25 |
| 13:38 |
|
olass |
that might be tricky but not impossible |
| 13:38 |
|
olass |
so port 25 out? |
| 13:39 |
|
egonw |
yes |
| 13:39 |
|
jonalv |
egonw: are you taking over responibility for pele? (that would be awesome...) |
| 13:39 |
|
egonw |
jonalv: nope |
| 13:39 |
|
olass |
seems so :-) |
| 13:39 |
|
egonw |
just making the admins life hell :) |
| 13:39 |
|
olass |
jonalv was admin |
| 13:39 |
|
olass |
is the new egonw? |
| 13:40 |
|
egonw |
no |
| 13:41 |
|
egonw |
but happy to maintain bugzilla |
| 13:42 |
|
gilleain |
woah. I didn't realise the internals of GridLayout were so complex. |
| 13:45 |
|
shk3 |
well, account creation didn't work for me |
| 13:46 |
|
egonw |
gilleain, shk3: I'll email you your pwd |
| 13:46 |
|
gilleain |
ta. |
| 13:47 |
|
egonw |
please change it immediately |
| 13:47 |
|
gilleain |
will do. |
| 13:49 |
|
gilleain |
oh very funny. |
| 13:49 |
|
egonw |
hahahaha |
| 13:50 |
|
egonw |
please let me know if it works |
| 13:50 |
|
egonw |
shk3: you too please |
| 13:51 |
|
gilleain |
Eclipse just crashed. |
| 13:51 |
|
egonw |
a custom ebi version? |
| 13:51 |
|
shk3 |
no |
| 13:51 |
|
shk3 |
i get |
| 13:51 |
|
gilleain |
no |
| 13:51 |
|
egonw |
disallowing certain passwords? |
| 13:51 |
|
shk3 |
Not Found |
| 13:51 |
|
shk3 |
The requested URL /cgi-bin/bugzilla/cgi-bin/bugzilla/index.cgi was not found on this server. |
| 13:51 |
|
egonw |
sure |
| 13:51 |
|
shk3 |
when hitting the login button |
| 13:52 |
|
egonw |
using the webinterface? |
| 13:52 |
|
shk3 |
yes |
| 13:52 |
|
gilleain |
yup. |
| 13:52 |
|
shk3 |
i go to http://pele.farmbio.uu.se/bugzilla/ |
| 13:53 |
|
zarah |
shk3's link is also http://tinyurl.com/5duh93 |
| 13:53 |
|
egonw |
works for me |
| 13:53 |
|
shk3 |
not for me |
| 13:53 |
|
egonw |
where do you log in? |
| 13:53 |
|
gilleain |
not for me, neither. |
| 13:53 |
|
shk3 |
the url it generates has /cgi-bin/bugzilla two times in it |
| 13:53 |
|
egonw |
ah, indeed |
| 13:53 |
|
egonw |
that one does not work for me either... |
| 13:54 |
|
egonw |
try the Log In in the bottom right |
| 13:54 |
|
egonw |
meanwhile, I'll fix that form |
| 13:54 |
|
gilleain |
success. |
| 13:54 |
|
gilleain |
for, me |
| 13:54 |
|
egonw |
feels like I am the first Ubuntu user actually installing Bugzilla :( |
| 13:55 |
|
shk3 |
username or password wrong |
| 13:55 |
|
shk3 |
what is my username? |
| 13:55 |
|
shk3 |
email? |
| 13:55 |
|
egonw |
yes |
| 13:55 |
|
gilleain |
changed pwd. |
| 13:56 |
|
shk3 |
not working |
| 13:56 |
|
shk3 |
username stefan.kuhnebi.uk.ac |
| 13:56 |
|
shk3 |
password the funny one you sent |
| 13:56 |
|
shk3 |
ok, wrong email |
| 13:57 |
|
gilleain |
unless the uk has been taken over by the academic world! :) |
| 13:57 |
|
egonw |
OK, front page login should work again |
| 13:57 |
|
egonw |
dirty hack |
| 13:57 |
|
egonw |
but works :) |
| 13:58 |
|
egonw |
gilleain: hehehehe |
| 13:58 |
|
gilleain |
:). Right, I'm trying mylyn again. better not crash, though *shakes fist* |
| 13:59 |
|
gilleain |
Ok, cool, that seems to do more stuff now. Query form and all that jazz. |
| 14:01 |
|
olass |
egonw: how's progress with cdk10? |
| 14:02 |
|
egonw |
olass: working on it... |
| 14:02 |
|
egonw |
it's compiling CDK |
| 14:03 |
|
olass |
ok |
| 14:06 |
|
egonw |
http://wiki.bioclipse.net/index.php?title=Mylyn |
| 14:06 |
|
zarah |
egonw's link is also http://tinyurl.com/5qp5rl |
| 14:06 |
|
egonw |
now improved, with screenshot |
| 14:06 |
|
egonw |
per popular demand |
| 14:09 |
|
jonalv |
ywy now even better :) |
| 14:16 |
|
egonw |
grpmh... |
| 14:26 |
|
jonalv |
grmph? |
| 14:27 |
|
egonw |
you know... the sounds you make when you do not like something? |
| 14:27 |
|
jonalv |
egonw: ah yea, but what made you do the sound? :) |
| 14:28 |
|
egonw |
oh, sent a jar in the wrong direction |
| 14:28 |
|
olass |
egonw: ETA for cdk10? |
| 14:28 |
|
egonw |
tomorrow |
| 14:28 |
|
olass |
sorry for buggering you but waiting for it... |
| 14:28 |
|
olass |
NO |
| 14:29 |
|
olass |
really? |
| 14:29 |
|
olass |
:-( |
| 14:29 |
|
olass |
:-( |
| 14:29 |
|
olass |
:-( |
| 14:29 |
|
egonw |
working on it... |
| 14:29 |
|
zarah |
:-( |
| 14:29 |
|
jonalv |
:( |
| 14:29 |
|
olass |
was it that hard? |
| 14:29 |
|
olass |
or much I guess |
| 14:29 |
|
egonw |
well, it's back in the SVN world |
| 14:29 |
|
* olass |
is always here |
| 14:30 |
|
* olass |
just moved his car and bought a muskavadobulle |
| 14:30 |
|
olass |
I wonder what it tastes like |
| 14:30 |
|
jonalv |
sounds intresting |
| 14:30 |
|
olass |
will make coffee first |
| 14:31 |
|
* jonalv |
is gonna guy and buy something to eat too. That was a good idea :) |
| 14:31 |
|
olass |
probably muskavado... |
| 14:31 |
|
* jonalv |
afk |
| 14:32 |
|
olass |
http://en.wikipedia.org/wiki/Muscavado |
| 14:32 |
|
zarah |
olass's link is also http://tinyurl.com/6e6sz5 |
| 14:35 |
|
olass |
seriously, egonw, you will not make it today? |
| 14:35 |
|
egonw |
trying... |
| 14:35 |
|
olass |
egonw++ # good job |
| 14:38 |
|
|
gilleain joined #bioclipse |
| 14:39 |
|
egonw |
olass: is the rdfeditor and sdfeditor stuff in the feature too? |
| 14:39 |
|
olass |
sdf, not rdf |
| 14:40 |
|
olass |
cdk10.sdf, not cdk.sdf |
| 14:40 |
|
egonw |
ok |
| 14:40 |
|
egonw |
fixed cdk10 and cdk10.jchempaint |
| 14:40 |
|
egonw |
as least no the compile level |
| 14:40 |
|
egonw |
won't have time to test |
| 14:40 |
|
egonw |
comitting now |
| 14:40 |
|
olass |
thx |
| 14:40 |
|
egonw |
and'd welcome if you cuold test |
| 14:41 |
|
olass |
sure |
| 14:41 |
|
olass |
will jump right on |
| 14:41 |
|
egonw |
ok, that's commited |
| 14:41 |
|
olass |
ok |
| 14:41 |
|
olass |
see you tomorrow |
| 14:42 |
|
olass |
or later :-) |
| 14:42 |
|
egonw |
I'm not gone yet |
| 14:43 |
|
olass |
should I do a fresh checkout? |
| 14:43 |
|
egonw |
what do you mean with fresh? |
| 14:44 |
|
egonw |
oh, you're in the SVN world :) |
| 14:44 |
|
olass |
check out new? |
| 14:44 |
|
egonw |
umm... not sure |
| 14:44 |
|
egonw |
I had too... |
| 14:44 |
|
olass |
update complains about already have a jar folder |
| 14:44 |
|
egonw |
for cdk10 |
| 14:44 |
|
egonw |
that is |
| 14:44 |
|
egonw |
the others should be fine without |
| 14:44 |
|
egonw |
right |
| 14:44 |
|
egonw |
\rm -Rf net.bioclipse.cdk |
| 14:44 |
|
egonw |
oops |
| 14:44 |
|
egonw |
\rm -Rf net.bioclipse.cdk10 |
| 14:44 |
|
egonw |
svn update net.bioclipse.cdk10 |
| 14:48 |
|
olass |
egonw: I get errors in cdk.jcp |
| 14:48 |
|
olass |
import org.openscience.cdk.applications.jchempaint.JChemPaintModel; |
| 14:48 |
|
olass |
missing |
| 14:48 |
|
egonw |
in cdk.jcp? |
| 14:48 |
|
egonw |
or cdk10.jdp |
| 14:48 |
|
olass |
cdk10.jcp |
| 14:48 |
|
egonw |
did you update that one? |
| 14:48 |
|
olass |
hmm |
| 14:49 |
|
olass |
yes |
| 14:49 |
|
olass |
confirmed |
| 14:50 |
|
olass |
hmm that package is not in cdk1.0.jar |
| 14:50 |
|
olass |
egonw? |
| 14:50 |
|
olass |
how can that compile for you? |
| 14:50 |
|
olass |
clean + upsate classpath |
| 14:51 |
|
olass |
has jcp been refactored out of cdk1.0? |
| 14:51 |
|
olass |
in that case we need taht jar too |
| 14:51 |
|
olass |
oh |
| 14:51 |
|
egonw |
yes, the classes for that are in cdk10.jchempaint/jars/cdk-jchempaint.jar |
| 14:51 |
|
olass |
that jar is in cdk10,jcp |
| 14:51 |
|
olass |
just not on CP |
| 14:51 |
|
olass |
mom, fixing |
| 14:51 |
|
egonw |
wait |
| 14:52 |
|
egonw |
just commited some extra fixes |
| 14:52 |
|
egonw |
please try that first |
| 14:52 |
|
egonw |
otherwise we get svn conflicts |
| 14:52 |
|
egonw |
it's almost done |
| 14:52 |
|
olass |
too late :-( |
| 14:52 |
|
olass |
ok |
| 14:52 |
|
olass |
will undo my fixes |
| 14:52 |
|
egonw |
check r7364 |
| 14:53 |
|
olass |
updating |
| 14:53 |
|
olass |
ok, no compile errors |
| 14:53 |
|
olass |
will try export now |
| 14:54 |
|
olass |
building... |
| 14:54 |
|
olass |
that that work with you? |
| 14:54 |
|
olass |
update site -> build? |
| 14:54 |
|
olass |
ah, no errors at least |
| 14:54 |
|
egonw |
trying now |
| 14:54 |
|
olass |
or maybe... |
| 14:55 |
|
egonw |
and do note the download sizes ... |
| 14:55 |
|
egonw |
mmm... I did not get any errors |
| 14:56 |
|
olass |
me neither |
| 14:56 |
|
olass |
good |
| 14:56 |
|
olass |
will test now |
| 14:56 |
|
olass |
wish me luck |
| 14:59 |
|
jonalv |
olass: good luck |
| 14:59 |
|
egonw |
olass: good luck |
| 14:59 |
|
gilleain |
good test-luck. |
| 15:00 |
|
egonw |
olass: you can stop now |
| 15:00 |
|
egonw |
was too good to be true |
| 15:00 |
|
egonw |
export is not good |
| 15:00 |
|
egonw |
JCP does not work |
| 15:00 |
|
egonw |
missing deps |
| 15:00 |
|
egonw |
hang on |
| 15:01 |
|
olass |
ok |
| 15:03 |
|
olass |
I can confirm that jcp does not work :-) |
| 15:04 |
|
egonw |
just learned something about rcp classloading :) |
| 15:05 |
|
olass |
fixed? |
| 15:06 |
|
egonw |
think so |
| 15:07 |
|
olass |
committed? |
| 15:07 |
|
olass |
only cdk10.jcp plugin? |
| 15:07 |
|
olass |
to update I mean? |
| 15:08 |
|
olass |
egonw: let me know |
| 15:08 |
|
egonw |
you know |
| 15:08 |
|
egonw |
just cdk10 |
| 15:08 |
|
olass |
ok |
| 15:08 |
|
egonw |
not cdk10.jcp :) |
| 15:08 |
|
egonw |
that's the thing about classloading |
| 15:08 |
|
egonw |
cdk10.jcp was using something from cdk10 which was missing a class :) |
| 15:09 |
|
egonw |
my first attempt was to add the missing class as depp to cdk10.jcp |
| 15:09 |
|
egonw |
stupid me |
| 15:09 |
|
egonw |
:) |
| 15:09 |
|
egonw |
OK, that's enough for me today |
| 15:09 |
|
egonw |
I even fixed InChI generation missing class on the fly |
| 15:09 |
|
shk3 |
just one question |
| 15:09 |
|
egonw |
that will have to do |
| 15:09 |
|
olass |
DEBUG - java.lang.NoClassDefFoundError: org/xmlcml/cml/element/CMLMolecule |
| 15:09 |
|
egonw |
have to catch the bus home |
| 15:09 |
|
egonw |
hahahah |
| 15:09 |
|
egonw |
oops |
| 15:09 |
|
egonw |
ok, you know the drill |
| 15:09 |
|
olass |
egonw: no |
| 15:10 |
|
egonw |
go to nb.cdk10 |
| 15:10 |
|
shk3 |
i am sure there will be another bus |
| 15:10 |
|
egonw |
add net.bioclipse.cml |
| 15:10 |
|
olass |
ok |
| 15:10 |
|
olass |
ok |
| 15:10 |
|
egonw |
rest will ahve to be tomorrow |
| 15:10 |
|
egonw |
otherwise my kids will beat me up |
| 15:10 |
|
egonw |
(or tonite) |
| 15:10 |
|
egonw |
after dinner |
| 15:11 |
|
olass |
Caused by: org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType C.3 could not be found |
| 15:11 |
|
egonw |
ah, cool |
| 15:11 |
|
olass |
what have you done? |
| 15:11 |
|
egonw |
and not cool |
| 15:11 |
|
egonw |
because that is not cdk10 stuff |
| 15:11 |
|
olass |
I know |
| 15:11 |
|
egonw |
so, sort of scary |
| 15:12 |
|
olass |
m2d depends on cdk for atom typing |
| 15:12 |
|
olass |
and cdk10 for JCP rendering |
| 15:12 |
|
egonw |
ah, nasty... |
| 15:12 |
|
olass |
but what is wrong? |
| 15:12 |
|
egonw |
just rendering? |
| 15:12 |
|
egonw |
then use cdk.jchempaint |
| 15:12 |
|
egonw |
for now |
| 15:12 |
|
egonw |
ok, bye! |
| 15:12 |
|
egonw |
olass: no idea |
| 15:12 |
|
egonw |
let's finish it tomorrow |
| 15:12 |
|
olass |
but you have changed something |
| 15:13 |
|
olass |
it worked before |
| 15:13 |
|
olass |
ok |
| 15:13 |
|
egonw |
yes, I fixed an export bug |
| 15:13 |
|
olass |
I guess we have to... |
| 15:13 |
|
olass |
fixed and fixed... |
| 15:13 |
|
egonw |
yeah, we're bound to find other problems |
| 15:13 |
|
olass |
ok |
| 15:13 |
|
olass |
tomorrow then |
| 15:13 |
|
egonw |
gone now |
| 15:13 |
|
olass |
bye |
| 15:15 |
|
olass |
egonw: I can still see you... |
| 15:20 |
|
jonalv |
zarah: ping |
| 15:20 |
|
zarah |
jonalv: pong |
| 15:20 |
|
jonalv |
zarah: tell zarah hi |
| 15:20 |
|
zarah |
jonalv: You are wasting your time, and mine. |
| 15:20 |
|
jonalv |
zarah: tell me a joke |
| 15:20 |
|
zarah |
jonalv: You have no new messages. |
| 15:21 |
|
jonalv |
zarah: that wasn't funny... |
| 15:21 |
|
zarah |
jonalv: excuse me? |
| 15:21 |
|
jonalv |
zarah: no fun |
| 15:21 |
|
zarah |
jonalv: I see. |
| 15:21 |
|
jonalv |
zarah: good |
| 15:21 |
|
zarah |
jonalv: please rephrase or stop trying to be witty :) |
| 15:21 |
|
jonalv |
zarah: so basically... |
| 15:21 |
|
zarah |
jonalv: excuse me? |
| 15:22 |
|
jonalv |
zarah: okey... |
| 15:22 |
|
zarah |
jonalv: are you making fun of me? |
| 15:22 |
|
jonalv |
zarah: what if I am? |
| 15:22 |
|
zarah |
jonalv: are you making fun of me? |
| 15:23 |
|
jonalv |
zarah: what if I am? |
| 15:23 |
|
zarah |
jonalv: excuse me? |
| 15:23 |
|
jonalv |
zarah: you are excused... |
| 15:23 |
|
zarah |
jonalv: well, yeah. you're excused too. |
| 15:23 |
|
jonalv |
zarah: good |
| 15:23 |
|
zarah |
jonalv: I did not understand that |
| 15:38 |
|
olass |
zarah: tell ME a joke |
| 15:38 |
|
zarah |
Consider it noted. |
| 15:38 |
|
olass |
? |
| 15:39 |
|
olass |
zarah: tell me a joke |
| 15:39 |
|
zarah |
olass: You have no new messages. |
| 15:39 |
|
olass |
@msg |
| 15:39 |
|
zarah |
olass: You have no new messages. |
| 15:55 |
|
|
hello____ joined #bioclipse |
| 15:56 |
|
hello____ |
hii anybody there? |
| 15:57 |
|
gilleain |
hello, hello___ |
| 15:57 |
|
hello____ |
hii gilleain |
| 15:57 |
|
hello____ |
how are u ? |
| 15:57 |
|
jonalv |
hi hello____ who are you_ |
| 15:58 |
|
gilleain |
I am fine, I don't know about this "u" fellow. |
| 15:58 |
|
hello____ |
well i am new in this chat room |
| 15:58 |
|
jonalv |
hello____: yup... :) |
| 15:58 |
|
hello____ |
i am a coputer graduate and started some reacher in bioinformatics |
| 15:59 |
|
hello____ |
research* |
| 15:59 |
|
hello____ |
what abt u ? |
| 16:00 |
|
gilleain |
mostly the same. currently swearing at layout managers. |
| 16:00 |
|
jonalv |
I am a new phd-student in Uppsala. I haven't worked much with Bioclispe 1 but I have been a central part of the development of Bioclispe 2 :) |
| 16:00 |
|
|
charlgren joined #bioclipse |
| 16:00 |
|
jonalv |
charlgren: hi |
| 16:01 |
|
charlgren |
jonalv: hi |
| 16:01 |
|
hello____ |
thts nice |
| 16:02 |
|
hello____ |
well i am basically programmer so trying to do some computation thigns in gene motifs analysis and promoter prediction |
| 16:02 |
|
jonalv |
hello____: ohh bioinformatics :) |
| 16:03 |
|
hello____ |
yes |
| 16:03 |
|
hello____ |
jonalv |
| 16:03 |
|
jonalv |
(much chemoinformatics around here normally...) :) |
| 16:03 |
|
hello____ |
i see jonalv |
| 16:04 |
|
hello____ |
then am i the first person of bioinformatics here ? jonalv |
| 16:04 |
|
jonalv |
but it is _bio_clipse after all :) |
| 16:04 |
|
hello____ |
ya thts true jonalv |
| 16:04 |
|
jonalv |
well since my master program was in Bioinfomatics I am not sure I would go that far... :) |
| 16:04 |
|
hello____ |
basically i search using bioinformatics jonalv |
| 16:08 |
|
hello____ |
so wht do u do jonalv |
| 16:09 |
|
jonalv |
for the moment I am working on a integrated database for storing molecules with annotation in Bioclipse. Spring, iBatis, HSQLDB... |
| 16:09 |
|
jonalv |
hello____: I am also in deep in the core parts of Bioclipse... :) |
| 16:10 |
|
jonalv |
Bioclispe 2 that is... |
| 16:10 |
|
hello____ |
the development of bioclioes ? jonalv or any project dvelopment using bioclipse? |
| 16:11 |
|
gilleain |
heh. whenever I see "bioclispe" I think of some sort of BioLisp (like BioJava, or so :) |
| 16:12 |
|
hello____ |
well yes i also guess so |
| 16:12 |
|
stain |
(((gene 'GATTACCATA))))))))) |
| 16:12 |
|
hello____ |
i generally use c#.net to program for bioinformatics |
| 16:13 |
|
hello____ |
currently i am working on promoter prediction algorithm development |
| 16:13 |
|
jonalv |
hello____: I am sort of responsible for the "manager architecture" as it looks in Bioclipse 2 and then I am doing the structure database and I am also doing the Brunn project. Which is a database for screening data from microtiter plates. |
| 16:15 |
|
hello____ |
tht is good |
| 16:16 |
|
hello____ |
my research is in core level tht is developing algorithm and also testing performance of those |
| 16:16 |
|
jonalv |
hello____: so if you have any Bioclipse 2 related questions I should be able to answer or at least direct you to someone who can answer :) |
| 16:17 |
|
hello____ |
thanks actually i didnt use Bioclipse before but yes i will try it jonalv |
| 16:19 |
|
|
gilleain left #bioclipse |
| 16:20 |
|
hello____ |
well... jonalv can u give me some hints about research funds on bioinformatics ? |
| 16:21 |
|
jonalv |
hello____: uhm no I don't think so... |
| 16:21 |
|
hello____ |
jonalv ok thx |
| 16:25 |
|
hello____ |
ok jonalv nice to chat with u |
| 16:25 |
|
hello____ |
now i am leaving this room |
| 16:25 |
|
jonalv |
hello____: bye |
| 16:25 |
|
|
hello____ left #bioclipse |
| 16:35 |
|
jonalv |
did someone know mister hello____? |
| 16:35 |
|
egonw |
nope |
| 16:35 |
|
egonw |
where is .bd ?!?! |
| 16:37 |
|
jonalv |
bangladesh? |
| 16:37 |
|
egonw |
http://plindenbaum.blogspot.co[…]ugh-java2dia.html |
| 16:37 |
|
zarah |
egonw's link is also http://tinyurl.com/6navjk |
| 16:39 |
|
jonalv |
since javadoc isn't enough we have an annotation that does soet of the same thing. example: http://bioclipse.svn.sourcefor[…].java?view=markup |
| 16:39 |
|
jonalv |
:) |
| 16:39 |
|
zarah |
jonalv's link is also http://tinyurl.com/5n9tlb |
| 16:54 |
|
edrin |
egonw: nice tool. I am curious how xws4j would look like... |
| 16:55 |
|
edrin |
going home, cu later if you still around |
| 16:55 |
|
|
charlgren_ joined #bioclipse |
| 16:55 |
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|
edrin left #bioclipse |
| 19:14 |
|
|
edrin joined #bioclipse |
| 19:38 |
|
|
masak joined #bioclipse |
| 20:27 |
|
edrin |
hi masak |
| 20:27 |
|
masak |
hello edrin |
| 20:28 |
|
masak |
I'm only semi-here tonight |
| 20:28 |
|
edrin |
sure, me, too |
| 20:41 |
|
masak |
@reload |
| 20:42 |
|
|
zarah joined #bioclipse |
| 20:42 |
|
masak |
@fnord |
| 20:57 |
|
masak |
zarah: restart, dear |
| 20:59 |
|
|
zarah joined #bioclipse |
| 21:14 |
|
|
m4r1in joined #bioclipse |
| 21:17 |
|
masak |
zarah: restart again dear. thanks. |
| 21:17 |
|
|
zarah joined #bioclipse |
| 21:40 |
|
masak |
@restart |
| 21:41 |
|
|
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