Camelia, the Perl 6 bug

IRC log for #cdk, 2012-01-23

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All times shown according to UTC.

Time Nick Message
05:38 egonw joined #cdk
08:00 Gpox joined #cdk
08:29 egonw joined #cdk
09:02 jonalv joined #cdk
09:15 CIA-66 cdk: Egon Willighagen cdk-1.4.x * r03ef86b / (build.xml javadoc.xml): Ensure the OpenJavaDocCheck plugins are compiled - http://git.io/n2cVJw
09:46 egonw jonalv: java.lang.NoClassDefFoundError: org/openscience/cdk/signature/AtomSignature
09:46 egonw jonalv: that is caused by a missing dependency
09:46 jonalv yea
09:46 jonalv it works in Eclipse... :)
09:46 egonw check src/META_INF/fingerprint.cdkdepends
09:46 egonw sure, Eclipse doesn't know about the modules
09:47 jonalv hang on
09:47 jonalv need to switch workspace and branch
09:47 egonw from the command line, after 'ant clean runDoclet', you can check build/*.javafiles to see in what module a class is, or look for the @cdk.module JavaDoc class doc tag in the source code
09:47 egonw np
09:48 jonalv egonw: but how do I find out what I need to hadd to the dep file?
09:48 egonw what I just typed
09:49 jonalv how do you remember that?
09:49 egonw because I have done that 100 million times by now :)
09:49 egonw jonalv: use a lab note book of some kind
09:49 egonw that's how scientists do it
09:50 jonalv so, now I need to search in these files for my class=
09:50 egonw they do not remember anything, they write down what they do, and look up what they did later
09:50 jonalv ?
09:50 egonw e.g. 'grep AtomSignature build/*.javafiles'
09:52 jonalv so I need to add signatures
09:52 jonalv or is that cdk-signatures?
09:53 egonw cdk-signatures.jar to be precise
09:53 jonalv not cdk-signature.jar?
09:53 egonw depends on the exact spelling of the module name
09:54 egonw @cdk.module signature
09:54 egonw so, yes, cdk-signature.jar
09:54 egonw without the 's' at the end
09:54 jonalv yep
09:54 jonalv how do I try that this made a difference?
09:54 egonw on the command line:
09:54 egonw ant clean dist-all test-dist-all
09:54 egonw (that recompiles everything)
09:55 egonw ant -Dmodule=fingerprint qa-module
09:55 egonw now, the second thing I note on this Nightly report page, is that many methods do not have test method
09:55 egonw as found in this section: ------------- Standard Output ---------------
09:56 egonw check if in that section there is any class mentioned which you hacked on
09:56 jonalv what did that second thing do?
09:57 egonw if not, leave it as is, or fix it in a separate branch, for further git commits
09:57 egonw qa := quality assurance
09:57 egonw that runs JUnit, PMD, OJDC testing
09:57 jonalv or the and -Dmodule=
09:57 egonw that says on which module you want to run it
09:58 jonalv so the first thing did not do that even thogu hthe paramater test-dist-all
09:58 egonw yeah, bad name...
09:58 egonw test-all tests all
09:59 egonw but test-dist-all compiles all the test modules
09:59 egonw like dist-all is make a distribution (jar) for all modules
09:59 egonw likewise there is a test-dist-all to make distributions for all test modules
10:00 egonw also, test-all only runs the unit tests...
10:00 egonw not the pmd, nor ojdc
10:00 jonalv but how do I look to see if I have fewer errors now? (this is quite a bit new things btw)
10:00 egonw check the output in the reports/ folder
10:00 egonw various files are created there
10:01 jonalv hm confused
10:01 jonalv now I have 28 erros
10:01 egonw ah, right, yes...
10:01 egonw run this before the qa-module
10:01 egonw jarTestFiles or so... mom, checking
10:02 egonw ant jarTestdata
10:03 jonalv and what did that do?
10:03 egonw create a .jar file with all the test files
10:03 egonw so, without that all unit tests that require a test file would fail
10:04 jonalv tell you what. This is a bit of a mess
10:04 jonalv now I have 5 erros
10:04 egonw it just requires you to write down what you typed before
10:04 egonw good, good
10:04 egonw that
10:04 egonw that's the same as in master
10:04 egonw (relatively, good, that is :)
10:04 egonw jonalv++
10:04 jonalv no same as what I had before
10:05 jonalv master had 1 error
10:05 egonw it has 5 for me: http://pele.farmbio.uu.se/night​ly/test/result-fingerprint.html
10:05 jonalv egonw: I still get: java.lang.NoClassDefFoundError: signature/AbstractVertexSignature
10:06 egonw yes, same in master
10:06 egonw that's another depenency missing, in fact
10:06 jonalv I see: Failures: 4, Errors: 1
10:06 jonalv in that link
10:06 egonw oh, sorry... yes, you're right
10:06 egonw I tend to take them together... apologies
10:07 egonw problem is...
10:07 egonw things that show up on my machine as error, can be fails on Nightly
10:07 jonalv that dep fix had no effect
10:07 egonw and other way around... not sure why
10:07 egonw right...
10:07 egonw because I should have told you to add the dependency to the cdk-test-fingerprint.cdkdepends
10:08 egonw because it's a dependency when running the tests
10:08 egonw you'll probably find that you have two lines in META-INF/fingerprint.cdkdepends with cdk-signature.jar
10:08 jonalv no
10:08 egonw interesting ...
10:12 jonalv egonw: no effect
10:12 jonalv still java.lang.NoClassDefFoundError: signature/AbstractVertexSignature
10:14 egonw yes, that a different dep anyway
10:14 egonw that's jar/signature[s?].jar
10:14 egonw the AtomSignature was a cdk class
10:14 egonw this is a third party lib class
10:14 jonalv uhm, I still had 5 errors
10:14 egonw that dep, .jar file name again, should go into src/META-INF/test-fingerprint.libdepends
10:15 jonalv uhm what's the diff between that and cdkdpeends then?
10:16 egonw cdkdepends is for cdk dependencies
10:16 jonalv egonw: okey, I am adding 'cdk-signature.jar' to test+fingerpint.libdepends instead
10:16 egonw libdepends is for 3rd party deps
10:16 egonw no, that would be wrong
10:16 jonalv I fail to understand why cdk-signatur.jar goes into thris party file though
10:16 egonw wrong := have not impact whatsoever
10:17 jonalv egonw: but you just said...
10:17 egonw AtomSignature != AbstractVertexSignature
10:17 egonw the first is a cdk class, the latter a signature[s?].jar class
10:17 jonalv so you mean it's not the same five erros I am getting?
10:18 egonw which confusingly has a name remarkingly like cdk-signature.jar
10:18 egonw indeed
10:18 egonw four are for a missing cdk dep
10:18 egonw the AbstractVertexSignature is for the missing 3rd party lib dep
10:18 jonalv Well I don't seem to be able to fix either
10:18 egonw (which I know because the class name does not start with org.openscience.cdk :)
10:19 jonalv egonw: let's take this from the top
10:19 egonw ok
10:19 jonalv in what file should the line: 'cdk-signature.jar' go, and how do you know that?
10:20 egonw src/META-INF/test-signature.cdkdepends
10:20 egonw you know that because cdk-*.jar is a CDK module, and thus a .cdkdepends
10:20 egonw crap, surely not that .cdkdepends file
10:20 egonw sorry, from the top :)
10:20 egonw src/META-INF/test-fingerprint.cdkdepends
10:20 egonw you know that because cdk-*.jar is a CDK module, and thus a .cdkdepends
10:21 egonw and you put it in test-fingerprint.cdkdepends because it was missing class when running the unit tests
10:21 jonalv and how do we know the error is in test?
10:21 egonw and in particular the tests for the fingerprint module
10:21 egonw because it's the reporting by junit you were looking at
10:22 jonalv but doesn't it report when the actual module bwing tested is missing things as well?
10:22 jonalv how do you tell the difference?
10:22 egonw that will show up when you compile the module
10:22 jonalv okey
10:22 egonw so, once 'ant clean dist-all test-dist-all' worked, all META-INF/$module.cdkdepend files are OK
10:26 CIA-66 cdk: Egon Willighagen master * rdb6b021 / .classpath : In Eclipse, use the Eclipse way to find JUnit - http://git.io/XotipA
10:27 jonalv egonw: okey, this would be good if it actually changed the number of erros but it does not
10:27 jonalv egonw: I still have those 5 errors
10:28 CIA-66 cdk: Egon Willighagen master * r03ef86b / (build.xml javadoc.xml): Ensure the OpenJavaDocCheck plugins are compiled - http://git.io/n2cVJw
10:28 CIA-66 cdk: Egon Willighagen master * redddc48 / (10 files in 5 dirs): Merged cdk-1.4.x - http://git.io/_cB_wg
10:28 CIA-66 cdk: Egon Willighagen master * rf878785 / README : Updated the copyright range - http://git.io/QvLL5Q
10:28 egonw can you pastebin the 'git diff' output?
10:29 jonalv http://pastebin.com/hWa9rKXx
10:30 egonw that looks good to me
10:31 jonalv egonw: http://pastebin.com/rLJZLTN2
10:32 egonw you did rerun the qa-module task, right?
10:32 egonw (I cannot think of anything better to say...)
10:32 egonw puzzling...
10:32 egonw oh...
10:32 jonalv I ran:
10:32 jonalv ant clean dist-all test-dist-all && ant jarTestdata && ant -Dmodule=fingerprint qa-module
10:32 egonw yes, that's good
10:32 egonw though when editing dependency files
10:33 egonw you do not need to recompile all the source code
10:33 egonw but, this can be going on...
10:33 egonw if it still cannot find the 3rd party signatures library, it can prob still not load the AtomSignature class either
10:33 jonalv okey
10:34 jonalv what to do then?
10:34 egonw so, add the signatures-1.0.jar to src/META-INF/test-fingerprint.libdepends
10:34 jonalv recompiling
10:36 jonalv egonw: okey that seems to have helped indeed
10:37 jonalv egonw: btw, which branch are you running on nighlty?
10:37 egonw various
10:37 jonalv egonw: I mean which of my branches?
10:37 egonw oh... ummm...
10:38 egonw ok, can you file a cdk 'bug' report to ask that Nightly reports which branch it is compiling?
10:39 egonw signFP-rebaseprone
10:39 jonalv egonw: can you change that?
10:39 egonw yes
10:40 jonalv egonw: to the one called: REBASED
10:40 egonw all caps?
10:40 jonalv it's a mess but I don't wanna break my fingerprint prjoect code by rebasing it right bow...
10:41 egonw I always test-drive a rebase, and merges often too
10:41 jonalv egonw: correct
10:41 egonw ok ,nightly is rerunning, now for the REBASED branch
10:41 egonw Latest commit = e9dfbb097b97d114ad196ba5e862750694e233fd
10:42 jonalv yea
10:44 jonalv egonw: okey pushed, can you trigger a rebuild?
10:46 egonw done:
10:46 egonw Latest commit = 6d58c6680c14ecf66d1fd16fdc5b212d6ca0e943
10:46 egonw will take a while to finish
10:53 egonw wanna continue with the next report?
10:53 egonw e.g. http://pele.farmbio.uu.se/nightly​-jonalv/ojdcheck/fingerprint.html
10:54 jonalv egonw: that file is rather obvious, no?
10:54 * egonw is happy jonalv agrees
10:54 jonalv egonw: how did you find it?
10:54 egonw http://pele.farmbio.uu.se/nightly-jonalv/
10:55 egonw in the OJDC block
10:55 egonw or via the matching Summary
10:55 jonalv egonw: I can't find it
10:55 egonw where are you looking?
10:55 jonalv http://pele.farmbio.uu.se/nightly-jonalv/
10:56 jonalv searching for OJDC
10:56 jonalv oh
10:56 jonalv found it :)
10:57 jonalv egonw: is this all?
10:57 egonw yes
10:58 jonalv egonw: oki
10:58 egonw compared to other modules, it's pretty clean indeed :) http://pele.farmbio.uu.se/night​ly-jonalv/ojdcheckSummary.html
10:58 jonalv egonw: okey, I will look at it later
10:59 jonalv egonw: then comes the problems with my actual api choices... :)
10:59 egonw that
10:59 egonw that's up to the reviewers to look at :)
10:59 jonalv gonna grab some lunch now I think, later
11:01 egonw ack
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21:02 CIA-66 cdk: Rajarshi Guha cdk-1.4.x * r652b5e2 / (9 files in 4 dirs): Merge branch 'cdk-1.4.x' of git@github.com:cdk/cdk into cdk-1.4.x - http://git.io/S5JXDA
21:47 CIA-66 cdk: Egon Willighagen master * r1cdd680 / (19 files in 5 dirs):
21:47 CIA-66 cdk: Use an enum, instead of ints
21:47 CIA-66 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/abGZVA
21:47 CIA-66 cdk: Egon Willighagen master * r3cc4232 / src/test/org/openscience/cdk/​io/ChemObjectWriterTest.java :
21:47 CIA-66 cdk: Very basic tests for the setWriter() methods (it cannot test if something is really written, as we do not know what objects are supported by a random reader; therefore, we just expect that no exception is thrown)
21:47 CIA-66 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/1NORxg

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