| Time |
Nick |
Message |
| 04:04 |
|
egonw joined #bioclipse |
| 06:23 |
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thomas_ku_ joined #bioclipse |
| 06:51 |
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rojasm joined #bioclipse |
| 06:55 |
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Gpox joined #bioclipse |
| 07:07 |
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jonalv joined #bioclipse |
| 07:07 |
CIA-47 |
bioclipse: miguelrojasch * r5830 /bioclipse2/trunk/plugins/.classpath: removed file which was commit rev 5809 in the incorrect directory |
| 07:08 |
CIA-47 |
bioclipse: miguelrojasch * r5831 /bioclipse2/trunk/plugins/.project: removed file which was commit rev 5809 in the incorrect directory |
| 07:08 |
CIA-47 |
bioclipse: miguelrojasch * r5832 /bioclipse2/trunk/plugins/plugin.xml: removed file which was commit rev 5809 in the incorrect directory |
| 07:09 |
CIA-47 |
bioclipse: miguelrojasch * r5833 /bioclipse2/trunk/plugins/build.properties: removed file which was commit rev 5809 in the incorrect directory |
| 07:40 |
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olas joined #bioclipse |
| 08:01 |
CIA-47 |
bioclipse: ospjuth * r5834 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.jchempaint/src/net/bioclipse/cdk10/jchempaint/ui/editor/JCPPage.java: Do not set default tooltip to AtomType, that was just for testing. |
| 08:02 |
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edrin joined #bioclipse |
| 08:02 |
edrin |
hi |
| 08:03 |
edrin |
http://xkcd.com/435/ |
| 08:12 |
olas |
hi edrin |
| 08:17 |
|
egonw joined #bioclipse |
| 08:18 |
egonw |
moin |
| 08:18 |
jonalv |
hi egonw |
| 08:21 |
jonalv |
eclipse crasc number 3 today :/ |
| 08:21 |
egonw |
not good |
| 08:21 |
jonalv |
nope |
| 08:21 |
jonalv |
but I am moving to a Mac real soon now. Leaving Ubuntu. |
| 08:21 |
jonalv |
That should work beter |
| 08:21 |
egonw |
hahahaha |
| 08:22 |
jonalv |
egonw, just laughs. What's the secret? |
| 08:22 |
jonalv |
:) |
| 08:27 |
jonalv |
eclipse crash number 4 today :( |
| 08:29 |
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olas_ joined #bioclipse |
| 08:29 |
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olas_ left #bioclipse |
| 08:29 |
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olas joined #bioclipse |
| 08:29 |
olas |
right |
| 08:29 |
olas |
hi egonw |
| 08:30 |
egonw |
jonalv: the trouble with Eclipse here is that it si difficult to get a good stacktrace |
| 08:30 |
egonw |
allowing one to file good bug reports |
| 08:30 |
egonw |
hi olas |
| 08:30 |
olas |
that is a major concern |
| 08:30 |
olas |
we should try to sort that out asap |
| 08:31 |
jonalv |
olas: We where talking about Eclipse in general but yea I guess the problem transfers to Bioclipse as well... |
| 08:36 |
olas |
it does |
| 08:36 |
olas |
and is something which is really annoying |
| 08:37 |
olas |
if we can describe the problem accurately we could email the Eclipse platform or RCP newsgroup |
| 08:38 |
jonalv |
uhm my problem is_: Eclipse crashes wihtout any pattern at all. I ahve seen complaints about permgenspace |
| 08:38 |
jonalv |
that's all |
| 08:38 |
jonalv |
something is leaking somewhere... |
| 08:38 |
jonalv |
not easy to know what and where... |
| 08:38 |
olas |
jonalv: you need to start with -Xmx512m |
| 08:39 |
jonalv |
I think eclipse takes care about that because I have seen it using 700MB |
| 08:40 |
olas |
strange |
| 08:42 |
stain |
set permgen space in eclipse.ini |
| 08:43 |
stain |
I have |
| 08:43 |
stain |
-Xms40m |
| 08:43 |
stain |
-Xmx512m |
| 08:43 |
stain |
-XX:MaxPermSize=256m |
| 08:43 |
jonalv |
what's the las one? |
| 08:48 |
jonalv |
eclipse crash number 5 today :( // I don't think this one was memory related actually |
| 08:49 |
egonw |
brb |
| 08:50 |
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egonw joined #bioclipse |
| 09:00 |
jonalv |
eclipse crash number 6 today |
| 09:05 |
olas |
jonalv: you using new mac? |
| 09:05 |
jonalv |
not yet |
| 09:07 |
stain |
jonalv: the last one is the permgen space, which is basically the space used for Class and ClassLoader instances if I understand correctly.. which could happen easily if you use the Maven plugin or the J2ee modes |
| 09:35 |
|
steinbeck joined #bioclipse |
| 09:42 |
olas |
hi steinbeck |
| 09:43 |
* olas |
is on lunch now |
| 09:44 |
steinbeck |
Cheers olas |
| 11:25 |
jonalv |
eclipse crash number 7 today |
| 11:41 |
olas |
jonalv: get a mac |
| 11:43 |
jonalv |
olas: I was working on that yesterday but I ran out of time... |
| 11:43 |
edrin |
... and become a puppet |
| 11:43 |
edrin |
:) |
| 11:43 |
olas |
MOHAHAHA |
| 11:43 |
olas |
puppet on a mac |
| 11:50 |
egonw |
yeah, ubuntu hardy must be the most unstable release in ages... |
| 11:50 |
* egonw |
has a bloody annoying cold |
| 11:50 |
egonw |
:( |
| 12:02 |
jonalv |
egonw, I think I am running feisty :) |
| 12:25 |
olas |
egonw: get some sleep |
| 13:38 |
jonalv |
eclipse crash number 8 today. //First time it actually was permgen space |
| 13:38 |
olas |
get a mac |
| 13:42 |
CIA-47 |
bioclipse: jonalv * r5835 /bioclipse/trunk/playground/plugins/net.bioclipse.expression.tests/ (.classpath META-INF/MANIFEST.MF): Added dependency to junit4 |
| 13:59 |
* olas |
is away for a meeting |
| 14:34 |
jonalv |
eclipse crash number 9 today. //Second time it actually was permgen space |
| 14:35 |
jonalv |
maybe I should ahck eclipe.ini file :) |
| 14:36 |
jonalv |
hm I already have -Xmx512m |
| 14:36 |
egonw |
also add those other two lines |
| 14:36 |
jonalv |
I had the first too |
| 14:37 |
jonalv |
two |
| 14:37 |
jonalv |
added the third now. Let's see if it makes any difference |
| 16:14 |
CIA-47 |
bioclipse: ospjuth * r5836 /bioclipse2/trunk/plugins/net.bioclipse.pcore/: Initial import. |
| 16:14 |
|
olas joined #bioclipse |
| 16:16 |
CIA-47 |
bioclipse: ospjuth * r5837 /bioclipse2/trunk/plugins/net.bioclipse.pcore/ (20 files in 8 dirs): Initial import of a plugin to query a set of molecules for pharmacophore queries and visualize results in Jmol. More information: http://wiki.bioclipse.net/index.php?title=Pharmacophore_visualization |
| 16:18 |
|
olas left #bioclipse |
| 16:27 |
CIA-47 |
bioclipse: jonalv * r5838 /bioclipse/trunk/playground/plugins/net.bioclipse.expression/src/net/bioclipse/expression/Calculator.java: don't throw SuppressedVariableException return Double.NaN instead |
| 17:23 |
edrin |
anyone has access to this article: http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2005/280/pe18 ? |
| 17:30 |
edrin |
stain? |
| 17:30 |
edrin |
rojasm: ? |
| 17:38 |
|
berry_ joined #bioclipse |
| 17:43 |
rojasm |
yes edrin |
| 17:43 |
edrin |
do you have access to this article? |
| 17:44 |
edrin |
rojasm: can you send me this article as pdf via mail? |
| 17:44 |
edrin |
rojasm: i cannot receive dcc |
| 17:45 |
edrin |
johannes.wagener at med.uni-muenchen.de |
| 17:45 |
rojasm |
ok! your email? |
| 17:45 |
rojasm |
ok |
| 17:45 |
rojasm |
one moment |
| 17:45 |
edrin |
:) |
| 17:45 |
edrin |
great |
| 17:46 |
rojasm |
done |
| 17:47 |
edrin |
thanks very much |
| 17:48 |
rojasm |
not problem |
| 17:49 |
edrin |
rojasm: sorry to bug you, but my uni server removed the file 21386.0.pe18.pdf because of the filename... can you rename it to something else and maybe send again |
| 17:49 |
edrin |
? |
| 17:49 |
rojasm |
yes |
| 17:51 |
rojasm |
done |
| 18:09 |
stain |
edrin: ? |
| 19:09 |
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edrin left #bioclipse |
| 19:29 |
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| 19:52 |
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rojasm joined #bioclipse |
| 20:06 |
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