| Time |
Nick |
Message |
| 05:14 |
|
sneumann__ joined #bioclipse |
| 05:42 |
|
egonw_ joined #bioclipse |
| 05:48 |
|
annzi joined #bioclipse |
| 07:01 |
|
olass joined #bioclipse |
| 07:01 |
olass |
moin |
| 07:02 |
* olass |
is back from a nice holiday |
| 07:03 |
|
Gpox joined #bioclipse |
| 07:04 |
egonw |
Gpox: when are you going on holiday again? |
| 07:06 |
Gpox |
haven't set a date yet |
| 07:08 |
* egonw |
is leaving at the end of this month, for three weeks |
| 07:10 |
* olass |
has just come back |
| 07:11 |
egonw |
no further holidays then? |
| 07:13 |
* egonw |
is still working on the book chapters |
| 07:13 |
egonw |
singular really... |
| 07:14 |
egonw |
still working on Chapter 3: Representing Molecules in Computers |
| 07:14 |
|
s_wolf joined #bioclipse |
| 07:18 |
|
mgerlich joined #bioclipse |
| 07:22 |
|
sneumann__ joined #bioclipse |
| 07:22 |
egonw |
when jonalv gets in, we should have a 2.4 status meeting, I guess |
| 07:23 |
egonw |
olass: Standard InChi + OS/X is commited, but sometimes seems to fail with class loading problems... |
| 07:23 |
olass |
damn |
| 07:23 |
egonw |
Gpox: is InChI generation still working on your machine? |
| 07:23 |
olass |
egonw: status meeting < Yes, would be nice |
| 07:24 |
Gpox |
I belive so |
| 07:24 |
egonw |
olass: yeah, the cause is unclear |
| 07:24 |
egonw |
Gpox: on jonalv's machine it was not... |
| 07:24 |
egonw |
Gpox: did you also test the exported version? |
| 07:25 |
Gpox |
Yes it works |
| 07:26 |
egonw |
good |
| 08:27 |
|
jonalv joined #bioclipse |
| 08:28 |
jonalv |
moin |
| 08:28 |
jonalv |
or something |
| 08:28 |
* jonalv |
misses zarah |
| 08:31 |
egonw |
http://github.com/bioscala/bioscala |
| 08:34 |
|
Gpox joined #bioclipse |
| 08:38 |
egonw |
@pz 1647 |
| 08:39 |
sneumann__ |
I miss zarah too, but what do you expect on a monday morning ? |
| 08:44 |
jonalv |
ah true |
| 09:00 |
|
zarah joined #bioclipse |
| 09:02 |
egonw |
hi zarah |
| 09:07 |
jonalv |
zarah: welcome back |
| 09:07 |
zarah |
jonalv: are you making fun of me? |
| 09:07 |
jonalv |
it sure is monday morning... |
| 10:00 |
olass |
hi zarah |
| 10:00 |
olass |
zarah: hi |
| 10:00 |
zarah |
hello olass :) |
| 10:22 |
|
mgerlich joined #bioclipse |
| 10:26 |
|
sneumann joined #bioclipse |
| 10:55 |
|
sneumann joined #bioclipse |
| 11:09 |
|
egonw joined #bioclipse |
| 11:20 |
* egonw |
is heading to his TV and tunes in on NL-DK |
| 11:24 |
|
masak joined #bioclipse |
| 11:24 |
|
ice9 joined #bioclipse |
| 11:25 |
ice9 |
hi! Are there any "development from scratch" instructions for 2.4? |
| 11:26 |
egonw |
mmm... no |
| 11:26 |
egonw |
closest match: http://wiki.bioclipse.net/index.php?title=Checking_out_Bioclipse_2.2 |
| 11:26 |
zarah |
egonw's link is also http://tinyurl.com/yaxkhfy |
| 11:27 |
ice9 |
yeah. I'm kind of stuck at the "Apache Commons Codec" feature. Can't see it in Galileo. Maybe I'm looking at the wrong update site? |
| 11:27 |
egonw |
Gpox: do you have time to copy/paste from this 2.2 page to describe the new target_platform approach? |
| 11:27 |
egonw |
ice9: forget that... |
| 11:28 |
egonw |
the 'new' way to do this, it is the target platform that will download the dependencies... |
| 11:28 |
egonw |
but that is not explained in the wiki yet... |
| 11:28 |
ice9 |
aha. So when I set the target platform all those nasty red flags will go away? |
| 11:39 |
egonw |
yeah, it should |
| 11:51 |
ice9 |
indeed they did go away :) |
| 11:52 |
jonalv |
masak: didn't you work on a wiki page for 2.4? |
| 11:53 |
jonalv |
masak: or did I dream that? |
| 11:53 |
masak |
you dreamt that. |
| 11:53 |
jonalv |
:( |
| 11:56 |
ice9 |
do I need to set target platform again after importing cdk and chemoinformatics? |
| 11:57 |
ice9 |
a bunch of bundles are unresolved after importing them |
| 12:06 |
jonalv |
ice9: hm I don't think you should have to do that. Which ones? |
| 12:10 |
egonw |
resetting target platform will seldomly hurt... |
| 12:20 |
ice9 |
egonw: i showed the errors to janalv and was directed to you |
| 12:20 |
ice9 |
do you have some sort of pastebin you prefer? |
| 12:21 |
ice9 |
(resetting target platform made no difference) |
| 12:32 |
egonw |
@google pastebin |
| 12:32 |
zarah |
egonw: http://pastebin.com/ |
| 12:33 |
egonw |
http://bioclipse.pastebin.com/ |
| 12:33 |
zarah |
egonw's link is also http://tinyurl.com/7ckm92 |
| 12:38 |
ice9 |
http://bioclipse.pastebin.com/YR6ARUqg |
| 12:38 |
zarah |
ice9's link is also http://tinyurl.com/327vnhh |
| 12:40 |
ice9 |
put up the list of problems, let me know if you need more |
| 12:41 |
ice9 |
(didn't include the type resolution issues) |
| 13:00 |
egonw |
ice9: did you import the plugins from org.openscience.cdk/externals too? |
| 13:00 |
egonw |
sorry for the delay... I'm hacking on book chapters for the pharmbio.org course |
| 13:04 |
ice9 |
nah, probably not |
| 13:04 |
ice9 |
not used to eclipse devel |
| 13:05 |
ice9 |
actually, they seem to be imported |
| 13:06 |
ice9 |
but if I remember correctly, when switching to 2.4.x in another workspace of mine, we had to remove them first and then import then |
| 13:06 |
ice9 |
is there an order dependency for importing core, chemoinformatics and cdk? |
| 13:07 |
egonw |
don't think it matters, but the order would be: core, cdk, chemoinformatics |
| 13:08 |
ice9 |
ok. That's actually the order I imported them in |
| 13:09 |
ice9 |
pulled core today from git, anything in chem and cdk I should catch up with perhaps? |
| 13:09 |
egonw |
do you have 2.4.x branches for bioclipse.* all of them |
| 13:09 |
egonw |
and the bioclipse2.4.x for org.openscience.cdk ? |
| 13:09 |
ice9 |
should have, jonalv helped me set it up |
| 13:10 |
ice9 |
yup |
| 13:13 |
ice9 |
pulled/refresh/clean, problems remain |
| 13:18 |
ice9 |
aha. this is starting to look familiar. |
| 13:18 |
ice9 |
javax.vecmath was "empty" |
| 13:19 |
ice9 |
removed and imported again from cdk/external -- _that_ problem went away |
| 13:19 |
egonw |
ah... |
| 13:23 |
ice9 |
same thing with cdk.core, and I'm guessing the rest as well. |
| 13:23 |
ice9 |
I'll add the rest of them.. |
| 13:24 |
ice9 |
(brilliant feature of Eclipse showing the expansion arrow even if it's empty) |
| 13:31 |
ice9 |
something is terribly wrong with my import. Most of org.openscience.cdk.* is empty |
| 13:31 |
ice9 |
*sigh* |
| 13:52 |
ice9 |
thanks for the input, I'm giving up for today now |
| 13:59 |
egonw |
jonalv: ping |
| 14:00 |
egonw |
jonalv: did you finish the bioclipse.requiresVersion() method? |
| 14:00 |
jonalv |
egonw: oh right no |
| 14:00 |
jonalv |
oops |
| 14:00 |
jonalv |
there was something with that |
| 14:00 |
egonw |
tests? |
| 14:00 |
jonalv |
I needed something |
| 14:00 |
egonw |
I think I said I would try the SDK |
| 14:00 |
jonalv |
yea tests |
| 14:00 |
jonalv |
that was it |
| 14:00 |
egonw |
ok, I'm on it... |
| 14:00 |
egonw |
Chapter 3 is done for now... |
| 14:01 |
jonalv |
sounds good |
| 14:01 |
egonw |
a whopping 28 pages... |
| 14:01 |
egonw |
bit several Bioclipse Excursions |
| 14:01 |
jonalv |
ah nice |
| 14:10 |
CIA-71 |
bioclipse.core: jonalv 2.4.x * r14d543f / plugins/net.bioclipse.logback/src/logback.xml : Merge branch '2.4.x' of github.com:olas/bioclipse.core into 2.4.x - http://bit.ly/b1aVYO |
| 14:11 |
CIA-71 |
bioclipse.core: jonalv 2.4.x * r1dd3aba / plugins/net.bioclipse.scripting/src/net/bioclipse/scripting/JsEnvironment.java : removed old leftovers - http://bit.ly/ahtLHe |
| 14:11 |
CIA-71 |
bioclipse.core: jonalv 2.4.x * r08e07b5 / plugins/net.bioclipse.scripting/src/net/bioclipse/scripting/JsEnvironment.java : indentation and whitespace - http://bit.ly/9ImOR4 |
| 14:17 |
egonw |
masak-- (for messing with my agenda :) |
| 14:20 |
jonalv |
masak: what did you do now? |
| 14:20 |
masak |
I have not the slightest idea. |
| 14:20 |
masak |
but some people enjoy randomly removing others' karma... :( |
| 14:21 |
egonw |
blame jonalv... he pointed at you |
| 14:21 |
jonalv |
blame blame blame |
| 14:21 |
jonalv |
It's always my fault |
| 14:21 |
egonw |
hehehehe |
| 14:21 |
egonw |
no, only when we cannot blame someone else :) |
| 14:21 |
masak |
egonw: I don't know what jonalv has said. so I can't defend myself. |
| 14:22 |
masak |
in any case, probably not a topic for #farmbio. |
| 14:22 |
* egonw |
feels jonalv is not self-confident enough |
| 14:22 |
jonalv |
masak: this is #bioclipse |
| 14:22 |
masak |
probably not a topic for #bioclipse either :) |
| 14:22 |
masak |
jonalv-- # picky, picky, picky! :P |
| 14:22 |
masak |
this won't end well... :) |
| 14:22 |
* egonw |
noticed that ibg.uu.se was down |
| 14:23 |
egonw |
that's where it started... |
| 14:23 |
masak |
it's down, yes. |
| 14:23 |
masak |
not by my making. |
| 14:24 |
jonalv |
yea and that was masak-- fault. Or maybe not fault but.. uhm osmething I don't know. I think pwople expect masak++ to solve it. Anyway I think masak-- could have done it duirng the weekd, and after all so tdoes he it appears |
| 14:25 |
masak |
I'm being accused for something by a person who can't spell. great. |
| 14:25 |
jonalv |
lol +1 |
| 14:26 |
* jonalv |
can splel ist' jsut taht his figners hist the kyes in the worng odrer |
| 14:27 |
jonalv |
masak: at leas my keyboard is silent |
| 14:28 |
masak |
jonalv: yes, and see what good that does you. :P |
| 14:32 |
egonw |
masak++ (just randomly) |
| 14:32 |
jonalv |
masak++ |
| 14:33 |
masak |
:P |
| 14:35 |
* egonw |
is installing the Bioclipse SDK |
| 14:35 |
egonw |
1.1.10 |
| 14:37 |
* egonw |
is restarting eclipse |
| 14:39 |
* olass |
is restarting his brain |
| 14:40 |
* jonalv |
wonder if his brain has a restart button somehwere |
| 14:40 |
jonalv |
or perhaps a start button? |
| 14:44 |
masak |
for those who are interested, it seems the IBG server had a failed hard drive, which was causing database corruption, causing some pages to produce internal server errors. |
| 14:44 |
jonalv |
oh |
| 14:44 |
jonalv |
really? |
| 14:44 |
masak |
YA RLY |
| 14:45 |
jonalv |
so when can we haz it again? |
| 14:45 |
masak |
I feel it's no longer my domain. I'm not a hardware guy. :) |
| 14:45 |
jonalv |
good point |
| 14:46 |
jonalv |
who is? |
| 14:46 |
masak |
jonalv: Olle. I'd send you an URL, but... you know... :) |
| 14:46 |
jonalv |
*lol* |
| 14:46 |
masak |
...it's on the site, which is down... |
| 14:47 |
jonalv |
@pz SMARTS |
| 14:48 |
zarah |
[1333] 70 source files without copyri... http://tinyurl.com/nz9aff |
| 14:48 |
zarah |
[1326] Fix serialization/deserializat... http://tinyurl.com/msm3ak |
| 14:48 |
zarah |
[1787] Cancel SMARTS file editing thr... http://tinyurl.com/38se9eo |
| 14:48 |
zarah |
[1788] Add individual smarts always i... http://tinyurl.com/2wals8v |
| 14:48 |
zarah |
[680] Run SmartsMatching on files fro... http://tinyurl.com/2udxxup |
| 14:48 |
zarah |
Entire list (13) at http://tinyurl.com/33dyuwz |
| 15:11 |
jonalv |
egonw: do we have a SMARTS object of some kind? |
| 15:12 |
egonw |
olass: do we? |
| 15:12 |
olass |
no |
| 15:12 |
olass |
just a String |
| 15:13 |
olass |
wel.. |
| 15:13 |
olass |
maybe there is an internal object in SMARTS plugin for showing it in the UI |
| 15:13 |
* jonalv |
found bug 1197 |
| 15:13 |
jonalv |
@pz 1197 |
| 15:13 |
olass |
don't remember |
| 15:13 |
zarah |
http://pele.farmbio.uu.se/cgi-bin/bugzilla/show_bug.cgi?id=1197 |
| 15:13 |
jonalv |
I was just wondering if we had something like cdk.newSMARTS or so |
| 15:14 |
olass |
nope |
| 15:14 |
olass |
that does not exist |
| 15:19 |
CIA-71 |
bioclipse.ds: Arvid Berg 2.4.x * rb576445 / (7 files in 5 dirs): Fix for changes of RendererParameters and builders in cdk - http://bit.ly/arzToJ |
| 15:20 |
CIA-71 |
bioclipse.ds: Arvid Berg 2.4.x * rdc42d09 / (2 files): Changes for renderer parameters form cdk - http://bit.ly/dx3CSA |
| 15:20 |
CIA-71 |
bioclipse.ds: jonalv 2.4.x * ra5867f5 / (2 files in 2 dirs): Set version to 2.4.0.RC2 - http://bit.ly/bbuRRq |
| 15:23 |
CIA-71 |
bioclipse.balloon: jonalv 2.4.x * re956f68 / features/net.bioclipse.balloon_feature/feature.xml : Set version to 2.4.0.RC2 - http://bit.ly/clDpBR |
| 15:25 |
CIA-71 |
bioclipse.balloon: Ola Spjuth 2.4.x * r7f53b3c / plugins/net.bioclipse.balloon.business/src/net/bioclipse/balloon/business/Activator.java : Set timeout for manager to 30 secs instead of 10. - http://bit.ly/9Azosh |
| 15:27 |
olass |
egonw: ping |
| 15:28 |
egonw |
pong |
| 15:28 |
olass |
please have a look at my bioclipse.experimental git repo fork queue: |
| 15:28 |
olass |
http://github.com/olas/bioclipse.statistics/forkqueue |
| 15:28 |
olass |
it seems many commits by you are not applied |
| 15:29 |
olass |
no idea how I have missed that |
| 15:29 |
olass |
but you have write access now to stats repo |
| 15:29 |
olass |
can you maybe look at sorting this out? |
| 15:29 |
egonw |
[06/14/10 17:28] <olass> please have a look at my bioclipse.experimental git repo fork queue: |
| 15:29 |
egonw |
[06/14/10 17:28] <olass> http://github.com/olas/bioclipse.statistics/forkqueue |
| 15:29 |
egonw |
stats, not experimental, right? |
| 15:29 |
olass |
yes |
| 15:29 |
olass |
sry |
| 15:29 |
olass |
link is correct |
| 15:30 |
egonw |
sorry, I might have pushed to the wrong upstream perhaps |
| 15:30 |
CIA-71 |
bioclipse.statistics: jonalv 2.4.x * rfea3dcd / features/net.bioclipse.statistics_feature/feature.xml : Set version to 2.4.0.RC2 - http://bit.ly/d4TYAL |
| 15:30 |
olass |
no idea what problem is |
| 15:30 |
olass |
but please confirm fixes are in 2.4.x and master please |
| 15:30 |
egonw |
olass: these are really old |
| 15:30 |
egonw |
are you sure they are not yet in your copy too? |
| 15:31 |
olass |
mom |
| 15:31 |
egonw |
olass: as far as I can see, they are |
| 15:31 |
egonw |
I see quite a few commits in your branch dated Dec 16 |
| 15:31 |
olass |
yes, looks like it |
| 15:31 |
egonw |
merged in on 02-07 |
| 15:31 |
olass |
ok, then I will delete the pull requests |
| 15:32 |
olass |
no idea why they are still here |
| 15:32 |
olass |
done |
| 15:32 |
egonw |
ok, good |
| 15:32 |
egonw |
I love it when a plans comes together |
| 15:32 |
olass |
a plans? |
| 15:33 |
egonw |
yes, that's the problem with cheap rip offs |
| 15:33 |
egonw |
they are never quite right :) |
| 15:33 |
egonw |
oh no... |
| 15:33 |
egonw |
can you access pele? |
| 15:33 |
olass |
yes |
| 15:34 |
olass |
well |
| 15:34 |
egonw |
mmm... |
| 15:34 |
olass |
? |
| 15:34 |
olass |
no |
| 15:34 |
olass |
seems down |
| 15:34 |
olass |
damn |
| 15:34 |
egonw |
damn |
| 15:34 |
egonw |
cannot log in either |
| 15:34 |
egonw |
yes, pele is down |
| 15:34 |
egonw |
bugger |
| 15:35 |
egonw |
and only barely... |
| 15:35 |
egonw |
[06/14/10 17:31] <-- zarah has left this server (Ping timeout: 252 seconds). |
| 15:35 |
olass |
egonw: will you be at bmc tomorrow? Someone at BMC data need to push the rest button... |
| 15:35 |
* olass |
will be in italy |
| 15:35 |
egonw |
yes, I will be at BMC tomorrow |
| 15:35 |
olass |
maybe ask Anders at BMC data? |
| 15:36 |
olass |
tomorrow= |
| 15:36 |
olass |
? |
| 15:36 |
egonw |
or Magnus? |
| 15:36 |
CIA-71 |
bioclipse.qsar: jonalv 2.4.x * r1cea025 / (2 files in 2 dirs): Set version to 2.4.0.RC2 (+5 more commits...) - http://bit.ly/c8chz9 |
| 15:38 |
olass |
@tell jonalv please send pull requests for RDF and cheminfo repo to egonw and not to me |
| 15:39 |
olass |
Magnus might not have key to that server room |
| 15:39 |
olass |
but feel free to ask |
| 15:39 |
olass |
BMC data hosts that server |
| 15:40 |
egonw |
olass: no worries about those... jonalv send them to everyone :) |
| 15:40 |
olass |
why? |
| 15:40 |
olass |
ok, good to know.. |
| 15:41 |
egonw |
ok, will email anders lovgren |
| 15:43 |
egonw |
dinner, bbl |
| 15:46 |
|
egonw_ joined #bioclipse |
| 15:53 |
|
egonw_ joined #bioclipse |
| 15:59 |
|
egonw__ joined #bioclipse |
| 16:28 |
egonw |
pele is back online |
| 16:29 |
egonw |
and has not been down either: |
| 16:29 |
egonw |
$ uptime |
| 16:29 |
egonw |
17:25:45 up 138 days, 3:12, 2 users, load average: 0.08, 0.13, 0.16 |
| 16:29 |
egonw |
so, must have been a network problem |
| 16:31 |
olass |
I see |
| 16:31 |
olass |
good |
| 16:55 |
CIA-71 |
bioclipse.sdk: Egon Willighagen master * rc48fcd4 / (2 files in 2 dirs): Removed code that created a scripting contribution for the test plugin (fixes #1737) - http://bit.ly/9nqVQQ |
| 16:55 |
CIA-71 |
bioclipse.sdk: Egon Willighagen master * r9d9ba13 / (3 files in 3 dirs): Release Bioclipse SDK 1.1.10 (available from the update site) - http://bit.ly/dCBFFo |
| 16:55 |
egonw |
@tell jonalv the Bioclipse SDK is working for me... |
| 16:56 |
egonw |
@tell jonalv use the New Plug-In Project wizard |
| 16:56 |
egonw |
@tell jonalv a new Bioclipse SDK 1.1.10 is released and online on the update site |
| 17:17 |
CIA-71 |
bioclipse.core: Egon Willighagen 2.4.x * r54ba504 / (13 files in 3 dirs): Added a missing test plugin - http://bit.ly/94IpMB |
| 18:52 |
|
sneumann joined #bioclipse |
| 20:07 |
|
sneumann joined #bioclipse |
