| Time |
S |
Nick |
Message |
| 02:49 |
|
|
sneumann joined #bioclipse |
| 04:35 |
|
|
sneumann joined #bioclipse |
| 05:49 |
|
|
egonw joined #bioclipse |
| 06:33 |
|
|
zaetnick joined #bioclipse |
| 07:53 |
|
|
mgerlich joined #bioclipse |
| 08:07 |
|
|
Gpox joined #bioclipse |
| 08:29 |
|
|
egonw joined #bioclipse |
| 08:31 |
|
|
zaetnick joined #bioclipse |
| 08:32 |
|
|
egonw joined #bioclipse |
| 08:33 |
|
egonw |
zaetnick: I ran the R manager from my dev environment now... I have some feedback, if you like |
| 08:36 |
|
zaetnick |
egonw: yes |
| 08:36 |
|
egonw |
got time later today then? |
| 08:37 |
|
egonw |
I got a telcon in 20 minutes, and want to scan through my email before that |
| 08:38 |
|
zaetnick |
ok, I have a meeting from 14:00 to … 15:00 I guess |
| 08:38 |
|
zaetnick |
the rest of the day I'll be available |
| 08:38 |
|
egonw |
well, let's do it now then, but quickly |
| 08:38 |
|
egonw |
I don't have that much anyway |
| 08:39 |
|
zaetnick |
good |
| 08:39 |
|
egonw |
https://gist.github.com/1834483 |
| 08:39 |
|
egonw |
context: I worked on the train, so no internet |
| 08:39 |
|
egonw |
use case: r.eval("1+1") |
| 08:40 |
|
egonw |
first problem was that I did not have R_HOME set yet... |
| 08:40 |
|
egonw |
error message was clear |
| 08:40 |
|
egonw |
the pref page is OK, but minimal |
| 08:41 |
|
egonw |
e.g. you could provide suggestions, or test some common locations for various platforms... like a 'Search' button on the pref page, perhaps |
| 08:41 |
|
egonw |
that's optional, just nice to have |
| 08:41 |
|
egonw |
what would be more useful, is a test functionality... e.g. some feedback that the R_HOME is properly set... |
| 08:42 |
|
egonw |
in that pref page, so that users don't have to go back and forth between pref page, and r manager, etc, to test it |
| 08:42 |
|
egonw |
it would also be great if one could set the $RHOME with script commands too, updating the prefs page too |
| 08:42 |
|
egonw |
such is used by some other managers, like jcpprops |
| 08:43 |
|
zaetnick |
ok |
| 08:43 |
|
egonw |
so, once that was set up, the manager discovered that is could not load still |
| 08:43 |
|
egonw |
which the stacktrace showed 'rj' |
| 08:43 |
|
egonw |
to be not present yet |
| 08:43 |
|
egonw |
the error did not say I had to install 'rj' first |
| 08:44 |
|
egonw |
neither did it install rj itself, which may be because I had not internet connection :) |
| 08:44 |
|
egonw |
so, that's where I ended up :) |
| 08:44 |
|
egonw |
the gist has the summary |
| 08:45 |
|
zaetnick |
good, everything up to rj should be probably submitted at Pelezilla |
| 08:46 |
|
|
jonalv joined #bioclipse |
| 08:47 |
|
zaetnick |
I'm aware of most of those issues, but on linux there are different kinds of workarounds for the different distress |
| 08:47 |
|
zaetnick |
distros, I ment |
| 08:48 |
|
zaetnick |
but your suggestions are useful |
| 08:48 |
|
zaetnick |
as for the rj package, it was not installed because you were offline |
| 08:49 |
|
egonw |
ok, so some better error reporting would be good there... |
| 08:49 |
|
zaetnick |
indeed |
| 08:49 |
|
egonw |
e.g. test with bioclipse.isOnline() or so if you are online, and fail specifically on that then |
| 08:49 |
|
egonw |
see the bioclipse manager |
| 08:50 |
|
|
sneumann joined #bioclipse |
| 08:51 |
|
zaetnick |
ok |
| 08:52 |
|
zaetnick |
you still use debian, don't you |
| 08:52 |
|
egonw |
still?!?! |
| 08:52 |
|
egonw |
hi sneumann |
| 08:52 |
|
egonw |
sneumann: still awake then? |
| 08:53 |
|
egonw |
sneumann: how's Japan this time at night? |
| 08:53 |
|
zaetnick |
just asking, maybe you switched to sure, now that you're closer to Germany :) |
| 08:53 |
|
egonw |
hahahah |
| 08:53 |
|
egonw |
no, never liked Suse |
| 08:54 |
|
egonw |
really bad package manager |
| 08:54 |
|
egonw |
I'm sure it improved |
| 08:54 |
|
zaetnick |
I'm not so sure :) |
| 08:55 |
|
jonalv |
could it be worse than yum? |
| 08:55 |
|
egonw |
yum? |
| 08:55 |
|
zaetnick |
I tested BC a little bit on sure and it's not nice |
| 08:55 |
|
jonalv |
egonw: yea the one in fedora |
| 08:56 |
|
zaetnick |
but anyway, I guess on your debian you set R_LIBS_USER to a dir in your home |
| 08:57 |
|
zaetnick |
…before installing packages like rj |
| 08:59 |
|
egonw |
zaetnick: I'll check later |
| 08:59 |
|
zaetnick |
sure, thanks for the feedback |
| 08:59 |
|
zaetnick |
egonw++ |
| 09:07 |
|
olass |
egonw: ping |
| 09:07 |
|
olass |
egonw: are there some enzyme databases around that you know of? |
| 09:08 |
|
olass |
like Brenda? |
| 09:08 |
|
olass |
is this project still alive? |
| 09:08 |
|
egonw |
pathway databases,you mean? |
| 09:08 |
|
zaetnick |
olass: he's on a telcon now |
| 09:08 |
|
egonw |
zaetnick: was delayed 30min :) |
| 09:08 |
|
olass |
egonw: no, more structural databases |
| 09:09 |
|
olass |
and with annotations |
| 09:09 |
|
egonw |
uniprot, PDB? |
| 09:09 |
|
egonw |
CATH, PFAM? |
| 09:09 |
|
egonw |
brenda is a pathway database |
| 09:09 |
|
olass |
do they link to substrates? |
| 09:09 |
|
egonw |
then you need PDB |
| 09:09 |
|
olass |
hmm, not so rich then I guess... |
| 09:10 |
|
egonw |
or http://www.ebi.ac.uk/pdbe-srv/pdbechem/ |
| 09:10 |
|
zaetnick |
egonw: a quick question about the mail server on pele then |
| 09:11 |
|
zaetnick |
egonw: I just installed postfix and took the old pele config, is that all |
| 09:11 |
|
egonw |
sounds good |
| 09:11 |
|
egonw |
well, as said, I'm getting tons of email :) |
| 09:13 |
|
zaetnick |
ok |
| 09:28 |
|
|
egonw_ joined #bioclipse |
| 09:36 |
|
|
sneumann joined #bioclipse |
| 09:37 |
|
sneumann |
evening' ;-) |
| 09:40 |
|
egonw_ |
:) |
| 09:40 |
|
egonw_ |
http://chem-bla-ics.blogspot.c[…]web-for-life.html |
| 09:40 |
|
zarah |
egonw_'s link is also http://tinyurl.com/83wwnqx |
| 09:40 |
|
egonw |
sneumann: maybe that manager is useful to you too... |
| 09:41 |
|
egonw |
sneumann: I am exploring the exact metabolite content in BridgeDB... at least HMDB is in there |
| 09:44 |
|
sneumann |
Thanks, looks interesting |
| 10:38 |
|
|
egonw joined #bioclipse |
| 11:43 |
|
egonw |
zaetnick: |
| 11:43 |
|
egonw |
> r.eval("1+1") |
| 11:43 |
|
egonw |
[1] 2 |
| 11:43 |
|
egonw |
so, it seems it now managed to install the packages correctly :) |
| 11:43 |
|
zaetnick |
egonw: the only diff being the internet connection? |
| 11:44 |
|
egonw |
plotting works fine |
| 11:44 |
|
egonw |
zaetnick: yes, I think so |
| 11:44 |
|
egonw |
I *did* hack on the bridgedb plugin, but cannot imagine how that would have ever any effect :) |
| 11:45 |
|
zaetnick |
egonw: good, so I have to handle the error as you suggested |
| 11:45 |
|
egonw |
yeah, just check first if there is a connection, before you try to install rj |
| 11:46 |
|
egonw |
if not, crash on no internet with something like: "I need to install the rj package, but you need to be connected to the internet for that" |
| 11:46 |
|
egonw |
(or, ship the rj package with Bioclipse itself, but we've discussed that in the past, and had downsides, I think?) |
| 11:47 |
|
zaetnick |
yes, we can re-think it, but thanks for the hints |
| 11:47 |
|
zaetnick |
egonw++ |
| 11:48 |
|
egonw |
> r.eval("library(rrdf)") |
| 11:48 |
|
egonw |
[1] "rrdf" "rrdflibs" "rJava" "bc2r" "rj" "stats" |
| 11:48 |
|
egonw |
[7] "graphics" "grDevices" "utils" "datasets" "methods" "base" |
| 11:48 |
|
egonw |
that seems to work fine too |
| 11:48 |
|
egonw |
so, that bug report can be closed |
| 12:27 |
|
CIA-98 |
bioclipse.statistics: Valentin Georgiev 2.5.x * rbf59949 / (2 files in 2 dirs): |
| 12:27 |
|
CIA-98 |
bioclipse.statistics: Add license info to the walware feature |
| 12:27 |
|
CIA-98 |
bioclipse.statistics: Fix the bioclipse.statistics feature license info - http://git.io/LwbWqg |
| 12:46 |
|
|
zaetnick_ joined #bioclipse |
| 12:54 |
|
CIA-98 |
bioclipse.balloon: Arvid Berg 2.5.x * rb78b8ec / features/net.bioclipse.balloon_feature/feature.xml : fixed jnati-proc version - http://git.io/sIbMbw |
| 13:06 |
|
|
zaetnick joined #bioclipse |
| 13:13 |
|
|
zaetnick joined #bioclipse |
| 14:00 |
|
|
zaetnick_ joined #bioclipse |
| 14:30 |
|
|
zaetnick joined #bioclipse |
| 14:30 |
|
|
zaetnick joined #bioclipse |
| 14:55 |
|
egonw |
ok, more bridgedb/bioclipse fun: |
| 14:55 |
|
egonw |
database = bridgedb.loadRelationalDatabase("/home/egonw/tmp/metabolites_111203.bridge") |
| 14:55 |
|
egonw |
bridgedb.search(database, "aspirin", 5) |
| 14:56 |
|
egonw |
> bridgedb.search(database, "phenyl", 5) |
| 14:56 |
|
egonw |
[Wi:1-phenylethylamine, Wi:Phenylpropanolamine, Wi:Phenylacetic_acid, Wi:L-Phenylalanine, Wi:Hydroxyphenylpyruvic+acid] |
| 15:10 |
|
CIA-98 |
bioclipse.bridgedb: Egon Willighagen master * r0bd8895 / (7 files in 4 dirs): Added support for loading local Derby databases - http://git.io/MaMfdA |
| 15:11 |
|
CIA-98 |
bioclipse.bridgedb: Egon Willighagen master * ra1c97b9 / plugins/net.bioclipse.bridgedb/jar/derby_license.txt : Derby is Apache License 2.0 too - http://git.io/-uTf3A |
| 15:50 |
|
egonw |
Q: do we have code to do regexp in BSL? |
| 15:50 |
|
egonw |
that is, I want to pull out the HMDB\d+ from "CDKMolecule:Beginning of SDF File of HMDB000011-Methylhistidine" |
| 15:51 |
|
egonw |
or do I need to move to Groovy? |
| 15:51 |
|
egonw |
which is just as fine :) |
| 15:52 |
|
jonalv |
egonw: are you bujilding a molecule databse for Bioclipse now? :) |
| 15:53 |
|
egonw |
not yet :) |
| 15:53 |
|
egonw |
but, yes, I do have a need for structuredb too :) |
| 15:53 |
|
egonw |
oh, wow... |
| 15:53 |
|
egonw |
my userscripts paper has been read more than 11k times! |
| 15:53 |
|
jonalv |
w00t |
| 15:56 |
|
egonw |
mind you, the most accessed paper is 10x more accessed :) |
| 15:57 |
|
egonw |
this paper does not even make the top 100 :) |
| 15:57 |
|
jonalv |
okey |
| 16:16 |
|
egonw |
mmm.... not a good idea: |
| 16:16 |
|
egonw |
mols = cdk.loadMolecules("/Open PHACTS/mcard_sdf_all.sdf") |
| 16:16 |
|
egonw |
cdk.getProperty(mols.get(0), "CDKTitle") |
| 16:17 |
|
jonalv |
uhm are you skurping a big file into memory? |
| 16:17 |
|
jonalv |
*slurping |
| 16:17 |
|
egonw |
no, not that large... |
| 16:17 |
|
egonw |
it's the property getting that is not working |
| 16:18 |
|
egonw |
for a sec I though it had crashed |
| 16:18 |
|
egonw |
but it just returned nothing |
| 16:18 |
|
jonalv |
okey |
| 16:18 |
|
egonw |
cdk.getProperty(mols.get(0), "cdk:Title") |
| 16:18 |
|
egonw |
that works fine |
| 16:18 |
|
egonw |
egonw-- |
| 16:18 |
|
jonalv |
aha |
| 19:04 |
|
|
egonw joined #bioclipse |
| 19:28 |
|
|
zaetnick joined #bioclipse |
| 19:59 |
|
|
sneumann joined #bioclipse |
| 23:36 |
|
|
sneumann joined #bioclipse |
