Camelia, the Perl 6 bug

IRC log for #cdk, 2011-03-28

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All times shown according to UTC.

Time Nick Message
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10:32 CIA-59 cdk: Egon Willighagen cdk-1.2.x * r5a358fc / build.props : Release 1.2.8 - http://bit.ly/e4UlQP
11:42 maclean joined #cdk
11:46 maclean hi
11:46 zarah hi maclean
11:48 egonw hi maclean
11:48 maclean hi egonw
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12:07 maclean hmmm. cdk's ant target 'dist-pure' doesn't like being called in subant, it see,ms.
12:08 egonw please elaborate
12:09 maclean I'm trying to build cdk from a build.xml that is outside the cdk dir
12:09 maclean in fact, it is in another project. This can be done with the subant task. works fine for the "info" task.
12:11 maclean But I get NullPointerExceptions from within ant classes if I try dist-all or dist-pure
12:18 maclean Aaargh! and "$cdkdir>ant clean; ant" doesn't work anyway...
12:18 egonw huh?
12:18 egonw that normally works
12:19 maclean complains about build/interfaces.javafiles not found
12:20 maclean hmm. well, works in cdk dir, not asad-cdk dir...
12:21 egonw mm... absolute/relative path
12:22 maclean you mean if I rename the "cdk" dir to "mycdk" it won't work?
12:22 egonw I guess it might have trouble finding the build/ directory
12:23 egonw or... you might need to call ... ummm ...
12:23 egonw mom
12:23 egonw ant runDoclet
12:23 maclean nope, works.
12:23 egonw to create the *.javafiles
12:23 maclean well, runDoclet is the one that gives NPE from subant.
12:24 egonw ah...
12:24 egonw ok, can you ran ant in debug mode
12:24 egonw and put the output in a gist?
12:24 maclean ok
12:27 maclean https://gist.github.com/890379
12:27 maclean that's for the subant run, btw.
12:28 maclean damn, no wate.
12:29 maclean I commented out the runDoclet task just now (to avoid NPE).
12:36 egonw ok, wrong gist?
12:36 maclean well, I've just found that cdk/cdk:master works, where asad/cdk:master doesn't.
12:37 maclean It still throws NPE, but it gets past needing the javafiles
12:37 maclean I'm now trying to work out how to diff repositories.
12:43 egonw :)
12:49 maclean hmmm. now works. also works with fresh repository, so it's not that. sigh. lunch.
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13:51 maclean egonw : https://gist.github.com/890488
13:51 maclean this is a  minimal buildfile for triggering the bug.
13:52 maclean Obviously, it needs to be in a sibling directory of cdk
13:52 egonw what about using the ant task instead?
13:53 maclean er, could try that.
13:54 maclean no, that fails too.
13:55 maclean absolute vs relative paths in buildpath (or dir) parameter makes no difference also.
13:56 maclean ant version 1.8.2
14:00 maclean Hmmm. Waiiiit a min. Error thrown in MakeJavafilesFiles - that's cdk code...
14:00 egonw yes
14:01 egonw stacktrace?
14:01 maclean https://gist.github.com/890504
14:02 egonw hang on
14:03 egonw booting eclipse
14:03 maclean Ah, sorry. Didn't mean to make you do that.
14:08 egonw got build.xml open?
14:08 egonw the CDK one?
14:08 egonw look at line 263
14:08 egonw in the runDoclet target
14:09 egonw the first arg passed to MakeJavafilesFiles should be the full path to the META-INF/ folder
14:09 egonw make sure that is correct
14:09 maclean yes, got that far :)
14:09 maclean But it is {$src}/META-INF
14:09 maclean so, assuming that ${src} is correct...
14:09 egonw indeed
14:10 maclean well, that is ${src} == "src"
14:13 s_wolf hi
14:13 zarah hello s_wolf, you fantastic person you
14:14 sneumann :-)
14:14 * egonw needs to run in about 5 minutes...
14:14 egonw hi sneumann, s_wolf
14:14 egonw maclean: does your subant call set it correctly?
14:14 s_wolf just a quick question...ran into problems reading chebi SDF file
14:14 maclean egonw : Ok, will let you know if I find anything.
14:14 s_wolf example:
14:14 s_wolf > <Synonyms>
14:14 s_wolf 16 alpha OHE
14:14 s_wolf 16alpha-Hydroxyestrone
14:15 s_wolf 3,16alpha-Dihydroxyestra-1,3,5(10)-trien-17-one
14:15 s_wolf 3,16alpha-dihydroxy-1,3,5(10)-estratrien-17-one
14:15 s_wolf estra-1,3,5(10)-triene-3,16alpha-diol-17-one
14:15 s_wolf those synonymes are in this SDF file...the CDK reads those individual lines by appending this lines into 1 line without line breaks
14:15 s_wolf ?
14:15 maclean s_wolf : hmmm. a bug in the SDF reader, then?
14:16 sneumann or would that be by design ?
14:16 egonw google for ctfile.pdf
14:16 zarah egonw: http://www.symyx.com/downloa​ds/public/ctfile/ctfile.jsp
14:16 s_wolf I am not sure...or allows the SDF only one line?
14:16 egonw check the specs
14:16 egonw no, multiline is fine...
14:16 egonw it defines when a line is continued on the next...
14:17 s_wolf k thx...i'll have a look
14:19 * egonw would guess that newlines should be preserved in this case... but not sure
14:22 maclean aha! absolute paths in the cdk buildfile 'solves' it...
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14:36 s_wolf mhm i think i found the problem...the iteratingMDL reader does something like this: https://github.com/egonw/cdk/blob/mas​ter/src/main/org/openscience/cdk/io/i​terator/IteratingMDLReader.java#L206
14:36 s_wolf and the MDLV2000 Reader: https://github.com/egonw/cdk/blob/master/src/main​/org/openscience/cdk/io/MDLV2000Reader.java#L310
14:39 s_wolf should I file a bugreport or is this behaviour intended?
14:42 sneumann I'd say yes
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14:47 maclean s_wolf : so the iterating reader is not adding line.separator in between?
14:48 s_wolf yes it seems so
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14:50 maclean well, I would have thought they should do the same thing as each other :) If the specs agree, do file a bug, I think.
14:53 s_wolf k thanks
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18:21 maclean hah! in your face, ant!
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