From: Christoph S. <er...@do...> - 2007-10-15 15:07:50
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Hi, a recent question from Miriame Allouche caused me to look at the API docu for UniversalIsomorphismTester, which contains a warning regarding a special problem of this class with C1CC1 and CC(C)C See: http://cdk.svn.sourceforge.net/viewvc/*checkout*/cdk/trunk/cdk/src/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java?revision=8299 Strangely, this warning does not not show up in the compiled API on http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.html Any idea why that happens? Cheers, Chris |
From: Rajarshi G. <rg...@in...> - 2007-10-15 16:35:25
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On Oct 15, 2007, at 10:10 AM, Christoph Steinbeck wrote: > Hi, > > a recent question from Miriame Allouche caused me to look at the API > docu for UniversalIsomorphismTester, which contains a warning > regarding a special problem of this class with C1CC1 and CC(C)C > See: > http://cdk.svn.sourceforge.net/viewvc/*checkout*/cdk/trunk/cdk/src/ > org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java? > revision=8299 > > Strangely, this warning does not not show up in the compiled API on > > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/ > api/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.html > > Any idea why that happens? I'll take a look at it this week ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- A motion to adjourn is always in order. |
From: Egon W. <ego...@gm...> - 2007-10-15 18:14:06
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On 10/15/07, Christoph Steinbeck <er...@do...> wrote: > Any idea why that happens? Mmmm.... very weird... and disturbing... Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Rajarshi G. <rg...@in...> - 2007-10-15 19:01:35
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On Oct 15, 2007, at 2:14 PM, Egon Willighagen wrote: > On 10/15/07, Christoph Steinbeck <er...@do...> wrote: >> Any idea why that happens? > > Mmmm.... very weird... and disturbing... I just ran the javadoc.xml ant target by hand (using latest SVN) and I get the same result as on the nightly page. But when I ran it by hand on another machine, it generates the docs fine. I'm thinking that it would be fixed by rebuilding the custom javadoc classes - I have never roperly understood this part of the build system. Any pointers? ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Q: What's polite and works for the phone company? A: A deferential operator. |
From: Rajarshi G. <rg...@in...> - 2007-10-19 21:23:45
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On Oct 15, 2007, at 10:10 AM, Christoph Steinbeck wrote: > Hi, > > a recent question from Miriame Allouche caused me to look at the API > docu for UniversalIsomorphismTester, which contains a warning > regarding a special problem of this class with C1CC1 and CC(C)C > See: > http://cdk.svn.sourceforge.net/viewvc/*checkout*/cdk/trunk/cdk/src/ > org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java? > revision=8299 > > Strangely, this warning does not not show up in the compiled API on > > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/ > api/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.html It's all fixed now ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- A computer lets you make more mistakes faster than any other invention, with the possible exceptions of handguns and Tequilla. -- Mitch Ratcliffe |
From: Egon W. <ego...@gm...> - 2007-10-21 17:41:27
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Rajarshi, On 10/19/07, Rajarshi Guha <rg...@in...> wrote: > > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/ > > api/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.html > > It's all fixed now What was the problem? I found another instance of the same problem... please let me know how to fix it: http://cdk.svn.sourceforge.net/viewvc/cdk/trunk/cdk/src/org/openscience/cdk/templates/MoleculeFactory.java?revision=9133&view=markup makeAzulene() method, which has JavaDoc which does not show up on http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/templates/MoleculeFactory.html#makeAzulene() Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Rajarshi G. <rg...@in...> - 2007-10-21 18:44:09
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On Oct 21, 2007, at 1:41 PM, Egon Willighagen wrote: > Rajarshi, > > On 10/19/07, Rajarshi Guha <rg...@in...> wrote: >>> http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/ >>> api/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.html >> >> It's all fixed now > > What was the problem? I found another instance of the same problem... > please let me know how to fix it: The problem was that the Javadoc generation were failing due to bad XML in the XML bibliography file. After fixing it, it worked > http://cdk.svn.sourceforge.net/viewvc/cdk/trunk/cdk/src/org/ > openscience/cdk/templates/MoleculeFactory.java? > revision=9133&view=markup > > makeAzulene() method, which has JavaDoc which does not show up on > > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/ > api/org/openscience/cdk/templates/MoleculeFactory.html#makeAzulene() What is meant to show up? The javadocs you indicate are: /** 527 * Returns azulene without explicit hydrogens. 528 * 529 * @cdk.inchi InChI=1/C10H8/c1-2-5-9-7-4-8-10(9)6-3-1/h1-8H 530 */ Should the nightly javadocs show the Inchi? ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Regular naps prevent old age.... especially if you take them while driving |
From: Rajarshi G. <rg...@in...> - 2007-10-21 18:45:42
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BTW, would it be possible to make the Javadocs have a link from the class description into the SVN repository for that class? Could this be done per method? On Oct 21, 2007, at 1:41 PM, Egon Willighagen wrote: > Rajarshi, > > On 10/19/07, Rajarshi Guha <rg...@in...> wrote: >>> http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/ >>> api/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.html >> >> It's all fixed now > > What was the problem? I found another instance of the same problem... > please let me know how to fix it: > > http://cdk.svn.sourceforge.net/viewvc/cdk/trunk/cdk/src/org/ > openscience/cdk/templates/MoleculeFactory.java? > revision=9133&view=markup > > makeAzulene() method, which has JavaDoc which does not show up on > > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/ > api/org/openscience/cdk/templates/MoleculeFactory.html#makeAzulene() > > Egon > > -- > ---- > http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- I live in my own little world... but it's OK, they like me there |
From: Rajarshi G. <rg...@in...> - 2007-10-21 18:55:13
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On Oct 21, 2007, at 1:41 PM, Egon Willighagen wrote: > Rajarshi, > > On 10/19/07, Rajarshi Guha <rg...@in...> wrote: >>> http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/ >>> api/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.html >> >> It's all fixed now > > What was the problem? I found another instance of the same problem... > please let me know how to fix it: When I do ant clean ant -f javadoc.xml I get the following output [javadoc] javadoc: error - Error - Exception java.lang.ClassNotFoundException thrown while trying to register Taglet net.sf.cdk.tools.doclets.CDKInChIRefTaglet... I thought that maybe ant clean was not removing old taglet classes so I deleted the build dir by hand and reran it, but no change. I assume that if this error is fixed, Inchi's will show up in the Javadocs ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Do radioactive cats have 18 half-lives? |
From: Egon W. <ego...@gm...> - 2007-10-21 19:25:28
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On 10/21/07, Rajarshi Guha <rg...@in...> wrote: > When I do > > ant clean > ant -f javadoc.xml > > I get the following output > > [javadoc] javadoc: error - Error - Exception > java.lang.ClassNotFoundException thrown while trying to register > Taglet net.sf.cdk.tools.doclets.CDKInChIRefTaglet... That's my mistake... will commit fix. > I thought that maybe ant clean was not removing old taglet classes so > I deleted the build dir by hand and reran it, but no change. No, the class name was wrong. The classes are in src/net/sf/cdk/doclets/ > I assume that if this error is fixed, Inchi's will show up in the > Javadocs OK. Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Egon W. <ego...@gm...> - 2007-10-21 19:09:56
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On 10/21/07, Rajarshi Guha <rg...@in...> wrote: > BTW, would it be possible to make the Javadocs have a link from the > class description into the SVN repository for that class? Could this > be done per method? I was just thinking the same thing... yes, it's possible... OK, will need to add some bits to the class JavaDocs to trigger the linking... hang on... Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Egon W. <ego...@gm...> - 2007-10-21 20:28:38
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On 10/21/07, Egon Willighagen <ego...@gm...> wrote: > On 10/21/07, Rajarshi Guha <rg...@in...> wrote: > > BTW, would it be possible to make the Javadocs have a link from the > > class description into the SVN repository for that class? Could this > > be done per method? > > I was just thinking the same thing... yes, it's possible... OK, will > need to add some bits to the class JavaDocs to trigger the linking... > hang on... Working on it... but discovered that the javadoc.jar in develjars/ does not contain the method Tag.position() which would make this possible... that jar comes from gjdoc, which apparently does not do JavaDoc5, but 1.1 which did not have that method yet. :( Bug report filed: https://bugs.launchpad.net/ubuntu/+source/gjdoc/+bug/155519 TBC Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Rajarshi G. <rg...@in...> - 2007-10-21 20:27:14
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The API docs are now generated. However the build is broken [javac] Compiling 23 source files to /home/rguha/src/java/cdk- nightly/cdk/build [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/org/ openscience/cdk/atomtype/CDKAtomTypeMatcher.java:31: package org.openscience.cdk.graph does not exist [javac] import org.openscience.cdk.graph.SpanningTree; [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/org/ openscience/cdk/atomtype/CDKAtomTypeMatcher.java:290: cannot find symbol [javac] symbol : class SpanningTree [javac] location: class org.openscience.cdk.atomtype.CDKAtomTypeMatcher [javac] SpanningTree st = new SpanningTree (atomContainer); [javac] ^ [javac] /home/rguha/src/java/cdk-nightly/cdk/build/src/org/ openscience/cdk/atomtype/CDKAtomTypeMatcher.java:290: cannot find symbol [javac] symbol : class SpanningTree [javac] location: class org.openscience.cdk.atomtype.CDKAtomTypeMatcher [javac] SpanningTree st = new SpanningTree (atomContainer); [javac] ^ [javac] 3 errors On Oct 21, 2007, at 2:45 PM, Rajarshi Guha wrote: > > On Oct 21, 2007, at 1:41 PM, Egon Willighagen wrote: > >> Rajarshi, >> >> On 10/19/07, Rajarshi Guha <rg...@in...> wrote: >>>> http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/ >>>> api/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.html >>> >>> It's all fixed now >> >> What was the problem? I found another instance of the same problem... >> please let me know how to fix it: >> >> http://cdk.svn.sourceforge.net/viewvc/cdk/trunk/cdk/src/org/ >> openscience/cdk/templates/MoleculeFactory.java? >> revision=9133&view=markup >> >> makeAzulene() method, which has JavaDoc which does not show up on >> >> http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/ >> api/org/openscience/cdk/templates/MoleculeFactory.html#makeAzulene() ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Disembowelling takes guts. |
From: Egon W. <ego...@gm...> - 2007-10-21 20:31:32
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On 10/21/07, Rajarshi Guha <rg...@in...> wrote: > The API docs are now generated. However the build is broken Grpmphh..... OK, SpanningTree is in standard while CDKAtomTypeMatcher is on core... SpanningTree should really go to core too, but does not have the full testing yet, IIRC... but then again, it's trunk... so we have some time to get that nicely tested... Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Egon W. <ego...@gm...> - 2007-10-21 20:44:16
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On 10/21/07, Egon Willighagen <ego...@gm...> wrote: > On 10/21/07, Rajarshi Guha <rg...@in...> wrote: > > The API docs are now generated. However the build is broken > > Grpmphh..... OK, SpanningTree is in standard while CDKAtomTypeMatcher > is on core... SpanningTree should really go to core too, but does not > have the full testing yet, IIRC... but then again, it's trunk... so we > have some time to get that nicely tested... Now I remember why it isn't... it depends on PathTools... which is even much further from 'stable' then SpanningTree is... :( Moving CDKAtomTypeMatcher to standard then... Egon -- ---- http://chem-bla-ics.blogspot.com/ |