Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-09-12

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All times shown according to UTC.

Time Nick Message
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07:51 Pyryhyry a totally newbie question: do you know of some place where one can download the 20 amino acids for bioclipse?
07:52 Pyryhyry Im going through the book "introduction to pharmaceutical bioinformatics" and it suggests downloading the file:
07:52 Pyryhyry http://www.oakleaf.com/intro​pharmbio/resources/20aa.zip
07:53 Pyryhyry but that file does not seem to exist on the server
07:54 Pyryhyry ...And if this is off-topic for the channel, i apologize
07:54 zaetnick Pyryhyry: http://oakleafacademic.com​/intropharmbio/resources/
07:54 Pyryhyry ...okay, that works
07:54 zaetnick Pyryhyry: we apologize for the broken link
07:55 zaetnick working hard to release the new edition where those things should be fixed
07:55 Pyryhyry no need, im just glad to get it working :)
07:58 zaetnick and Pyryhyry, we can recommend you to run the latest dev version of Bioclipse from http://pele.farmbio.uu.se/​jenkins/job/Bioclipse_2.6/
07:58 zaetnick it's a beta, but very close to release
08:00 Pyryhyry ok, thanks
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19:07 Pyryhyry assuming i have the package openjdk-6-jdk, have the R packages: rJava and rj installed, have installed the R extension on bioclipse 2.6, and have set the environment variable R_HOME with "export R_HOME=/usr/lib/R"
19:08 Pyryhyry any idea, what could be causing the error message "Incorrect R_HOME path: null" ?
19:12 Pyryhyry ...running linux mint 12 64bit (related to ubuntu 11.10)
20:06 egonw Pyryhyry: did you set the R_HOME value in Bioclipse too?
20:06 egonw should be in the Preferences dialog
20:09 egonw menu: Window -> Preferences ->
20:10 egonw ...
20:11 egonw menu: Window -> Preferences -> R
20:11 egonw there you have to set the R_HOME value too
20:12 egonw the R_HOME environmental property (that you set with "export") is hard to catch in Java
20:29 Pyryhyry i hadn't done that. its working now, thanks!
20:47 egonw cool!
20:50 egonw we have been talking about doing some autodetection
20:50 egonw but that too is hard to implement in a cross-platform environment...
20:50 egonw hard := takes more effort
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