Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-02-15

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All times shown according to UTC.

Time Nick Message
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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
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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
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09:37 sneumann evening' ;-)
09:40 egonw_ :)
09:40 egonw_ http://chem-bla-ics.blogspot.com/2012/02​/bridgedb-and-semantic-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
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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
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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
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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.brid​gedb/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
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