Package: libcdk-java Version: 1:1.2.8-1 Severity: normal Cinfony (http://code.google.com/p/cinfony/) is a python wrapper which presents a common api for several chemimformatics toolkits. Only two of those toolkits are packaged for debian: OpenBabel and CDK.
So I tried to use it with the debian packaged CDK, but it seems to be different from the upstream. Also, upstream CDK consists of a single jar file, while in debian I can see it split in a bunch of them. I tried too repackaging the contents of all those jars into a single one, but the error I get is the same (which means that the CDK is found but something goes wrong when loading it...). Also, while I was repacking it into a single jar, I noticed that there where some missing directories from upstream in the directory structure. How to reproduce it: ssorgatem:/tmp$ export JPYPE_JVM=/usr/lib/jvm/java-6-openjdk/jre/lib/ amd64/server/libjvm.so ssorgatem:/tmp$ python Python 2.6.6 (r266:84292, Apr 20 2011, 09:34:38) [GCC 4.5.2] on linux2 Type "help", "copyright", "credits" or "license" for more information . >>> import os, glob >>> classpath = ":".join(glob.glob('/usr/share/java/cdk*.jar')) >>> classpath '/usr/share/java/cdk-structgen.jar:/usr/share/java/cdk- structgen-1.2.8.jar:/usr/share/java/cdk-libiocml-1.2.8.jar:/usr/share/java/cdk- core.jar:/usr/share/java/cdk-standard-1.2.8.jar:/usr/share/java/cdk- io-1.2.8.jar:/usr/share/java/cdk-builder3dtools-1.2.8.jar:/usr/share/java/cdk- reaction-1.2.8.jar:/usr/share/java/cdk-smiles.jar:/usr/share/java/cdk- smarts-1.2.8.jar:/usr/share/java/cdk-control-1.2.8.jar:/usr/share/java/cdk- pdbcml.jar:/usr/share/java/cdk-sdg.jar:/usr/share/java/cdk- builder3dtools.jar:/usr/share/java/cdk-builder3d-1.2.8.jar:/usr/share/java/cdk- pdbcml-1.2.8.jar:/usr/share/java/cdk-qsarprotein.jar:/usr/share/java/cdk- forcefield-1.2.8.jar:/usr/share/java/cdk-data.jar:/usr/share/java/cdk- charges-1.2.8.jar:/usr/share/java/cdk-qsaratomic.jar:/usr/share/java/cdk- annotation.jar:/usr/share/java/cdk-qm-1.2.8.jar:/usr/share/java/cdk- ionpot-1.2.8.jar:/usr/share/java/cdk-nonotify.jar:/usr/share/java/cdk- smarts.jar:/usr/share/java/cdk-core-1.2.8.jar:/usr/share/java/cdk- ioformats.jar:/usr/share/java/cdk-diff.jar:/usr/share/java/cdk- pcore.jar:/usr/share/java/cdk-valencycheck-1.2.8.jar:/usr/share/java/cdk- control.jar:/usr/share/java/cdk-standard.jar:/usr/share/java/cdk- builder3d.jar:/usr/share/java/cdk-annotation-1.2.8.jar:/usr/share/java/cdk- valencycheck.jar:/usr/share/java/cdk-libiocml.jar:/usr/share/java/cdk- qsarmolecular.jar:/usr/share/java/cdk-qsarionpot.jar:/usr/share/java/cdk- dict.jar:/usr/share/java/cdk-charges.jar:/usr/share/java/cdk- qsarionpot-1.2.8.jar:/usr/share/java/cdk-nonotify-1.2.8.jar:/usr/share/java /cdk-forcefield.jar:/usr/share/java/cdk-inchi.jar:/usr/share/java/cdk- render-1.2.8.jar:/usr/share/java/cdk-pdb-1.2.8.jar:/usr/share/java/cdk- extra-1.2.8.jar:/usr/share/java/cdk-formula-1.2.8.jar:/usr/share/java/cdk- atomtype-1.2.8.jar:/usr/share/java/cdk-extra.jar:/usr/share/java/cdk- io.jar:/usr/share/java/cdk-render.jar:/usr/share/java/cdk- libiomd-1.2.8.jar:/usr/share/java/cdk-qsar-1.2.8.jar:/usr/share/java/cdk- dict-1.2.8.jar:/usr/share/java/cdk-pcore-1.2.8.jar:/usr/share/java/cdk- data-1.2.8.jar:/usr/share/java/cdk-qsarbond.jar:/usr/share/java/cdk- interfaces.jar:/usr/share/java/cdk-reaction.jar:/usr/share/java/cdk- atomtype.jar:/usr/share/java/cdk-ionpot.jar:/usr/share/java/cdk- isomorphism-1.2.8.jar:/usr/share/java/cdk-formula.jar:/usr/share/java/cdk- fingerprint.jar:/usr/share/java/cdk-diff-1.2.8.jar:/usr/share/java/cdk- isomorphism.jar:/usr/share/java/cdk-libiomd.jar:/usr/share/java/cdk- smiles-1.2.8.jar:/usr/share/java/cdk-ioformats-1.2.8.jar:/usr/share/java/cdk- qsarmolecular-1.2.8.jar:/usr/share/java/cdk-qsarcml-1.2.8.jar:/usr/share/java /cdk-sdg-1.2.8.jar:/usr/share/java/cdk-fingerprint-1.2.8.jar:/usr/share/java /cdk-inchi-1.2.8.jar:/usr/share/java/cdk-qsarprotein-1.2.8.jar:/usr/share/java /cdk-qsar.jar:/usr/share/java/cdk-pdb.jar:/usr/share/java/cdk- qsarcml.jar:/usr/share/java/cdk-qm.jar:/usr/share/java/cdk- qsarbond-1.2.8.jar:/usr/share/java/cdk-interfaces-1.2.8.jar:/usr/share/java /cdk-qsaratomic-1.2.8.jar' >>> os.environ['CLASSPATH'] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.6/UserDict.py", line 22, in __getitem__ raise KeyError(key) KeyError: 'CLASSPATH' >>> os.environ['CLASSPATH'] = classpath >>> from cinfony import cdk /usr/lib/pymodules/python2.6/jpype/_pykeywords.py:18: DeprecationWarning: the sets module is deprecated import sets Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/lib/python2.6/dist-packages/cinfony/cdk.py", line 13, in <module> from cdkjpype import * File "/usr/local/lib/python2.6/dist-packages/cinfony/cdkjpype.py", line 59, in <module> _descdict = _getdescdict() File "/usr/local/lib/python2.6/dist-packages/cinfony/cdkjpype.py", line 48, in _getdescdict de = cdk.qsar.DescriptorEngine(cdk.qsar.DescriptorEngine.MOLECULAR) File "/usr/lib/pymodules/python2.6/jpype/_jclass.py", line 79, in _javaInit self.__javaobject__ = self.__class__.__javaclass__.newClassInstance(*args) jpype._jexception.LinkageErrorPyRaisable: java.lang.NoClassDefFoundError: nu/xom/ParsingException >>> However, it works if I use the cdk-1.2.8.jar from http://sourceforge.net/projects/cdk/ as the only item in the classpath. It doesn't work from jython, either: ssorgatem:/tmp$ jython Jython 2.5.1+ (Release_2_5_1, Aug 4 2010, 07:18:19) [Java HotSpot(TM) 64-Bit Server VM (Sun Microsystems Inc.)] on java1.6.0_24 Type "help", "copyright", "credits" or "license" for more information. >>> from cinfony import cdk Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/share/jython/Lib/site-packages/cinfony/cdk.py", line 11, in <module> from cdkjython import * File "/usr/share/jython/Lib/site-packages/cinfony/cdkjython.py", line 17, in <module> import org.openscience.cdk as cdk ImportError: No module named openscience >>> -- System Information: Debian Release: wheezy/sid APT prefers testing APT policy: (900, 'testing'), (899, 'unstable'), (798, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 2.6.38-2-amd64 (SMP w/2 CPU cores) Locale: LANG=ca_ES.UTF-8, LC_CTYPE=ca_ES.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages libcdk-java depends on: ii default-jre-headless [java5 1:1.6-40 Standard Java or Java compatible R ii gcj-4.4-jre-headless [java5 4.4.6-2 Java runtime environment using GIJ ii gcj-jre-headless [java5-run 4:4.4.5-4 Java runtime environment using GIJ ii openjdk-6-jre-headless [jav 6b18-1.8.7-2 OpenJDK Java runtime, using Hotspo ii sun-java6-jre [java5-runtim 6.24-2 Sun Java(TM) Runtime Environment ( libcdk-java recommends no packages. Versions of packages libcdk-java suggests: pn jchempaint <none> (no description available) ii jmol 12.1.42-1 Molecular Viewer -- Adrià Cereto Massagué Biotechnology student Universitat Rovira i Virgili Languages: Català, Español, English, Français, Deutsch, Português, Esperanto -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org