Groups > linux.debian.maint.java > #11570

Re: Help needed for calling Java class from R

From	Andreas Tille <andreas@an3as.eu>
Newsgroups	linux.debian.maint.java
Subject	Re: Help needed for calling Java class from R
Date	2020-04-15 12:20 +0200
Message-ID	<zVNjb-8nq-3@gated-at.bofh.it> (permalink)
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Hi again,

On Tue, Apr 14, 2020 at 10:50:28PM +0200, Andreas Tille wrote:
> 1 Test Suite : 
> rcdk rcdk Unit Tests - 31 test functions, 31 errors, 0 failures
> ERROR in test.charges: Error in .jnew("org/openscience/cdk/smiles/SmilesParser", get.chem.object.builder()) : 
>   java.lang.NoClassDefFoundError: com/google/common/collect/Multimap

I inspected the cdk-2.3.jar from upstream and found out that it is
bundling way more classes.  It also contains the missing

    com/google/common/collect/Multimap

which happens to be in the Debian packaged guava.jar.  I went forward
with checking what else is in cdk-2.3.jar and added several other missing
JARs as symlink to the dir where r-cran-rcdk is building its CLASSPATH from.

I'm a bit concerned since in META-INF/DEPENDENCIES is

   Apache Jena, including the Jena IRI library

which is not packaged yet.  But so far I was successful with bringing
down the number of test suite errors.  However, there are some remaining
ones I can not directly attach to missing classes.  Here is the output
of the test suite:

Running unit tests
$pkg
[1] "rcdk"

$getwd
[1] "/tmp/autopkgtest.4IabgP/autopkgtest_tmp"

$pathToUnitTests
[1] "/usr/lib/R/site-library/rcdk/unitTests"

Loading required package: rcdklibs

Executing test function test.charges  ...  done successfully.

Executing test function test.get.hcount  ...  done successfully.

Executing test function test.is.aromatic  ...  done successfully.

Executing test function test.depictiongenerator  ... Timing stopped at: 0.005 0.004 0.004
Error in .jnew("org.openscience.cdk.depict.DepictionGenerator") : 
  java.lang.ClassNotFoundException
 done successfully.

Executing test function test.fp  ... Timing stopped at: 1.429 0.016 0.403
Error in .jnew("org/openscience/cdk/fingerprint/ShortestPathFingerprinter",  : 
  java.lang.NoClassDefFoundError: org/apache/commons/math3/random/RandomGenerator
 done successfully.

Executing test function test.fp.substructures.binary  ...  done successfully.

Executing test function test.fp.substructures.count  ...  done successfully.

Executing test function test.frag1  ...  done successfully.

Executing test function test.frag2  ...  done successfully.

Executing test function test.frag3  ...  done successfully.

Executing test function test.aromaticity.match  ... Timing stopped at: 0.013 0 0.004
Error in .jfindClass(as.character(class)) : 
  java.lang.ClassNotFoundException
 done successfully.

Executing test function test.match1  ... Timing stopped at: 0.012 0 0.004
Error in .jfindClass(as.character(class)) : 
  java.lang.ClassNotFoundException
 done successfully.

Executing test function test.match2  ... Timing stopped at: 0.004 0 0.003
Error in .jfindClass(as.character(class)) : 
  java.lang.ClassNotFoundException
 done successfully.

Executing test function test.match3  ... Timing stopped at: 0.018 0 0.005
Error in .jfindClass(as.character(class)) : 
  java.lang.ClassNotFoundException
 done successfully.

Executing test function test.match4  ... Timing stopped at: 0.02 0.004 0.006
Error in .jfindClass(as.character(class)) : 
  java.lang.ClassNotFoundException
 done successfully.

Executing test function test.mcs1  ... Timing stopped at: 0.028 0 0.008
Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;",  : 
  java.lang.NoClassDefFoundError: org/openscience/cdk/smsd/Isomorphism
 done successfully.

Executing test function test.mcs2  ... Timing stopped at: 0.024 0 0.006
Error in .jcall("org.guha.rcdk.util.Misc", "[[I", "getMcsAsAtomIndexMapping",  : 
  java.lang.NoClassDefFoundError: org/openscience/cdk/smsd/Isomorphism
 done successfully.

Executing test function test.mcs3  ... Timing stopped at: 0.024 0 0.007
Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;",  : 
  java.lang.NoClassDefFoundError: org/openscience/cdk/smsd/Isomorphism
 done successfully.

Executing test function test.get.properties  ... WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by RJavaTools to method java.util.Collections$UnmodifiableCollection$1.next()
WARNING: Please consider reporting this to the maintainers of RJavaTools
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
 done successfully.

Executing test function test.set.props  ...  done successfully.

Executing test function test.atom.count  ...  done successfully.

Executing test function test.desc.calc  ... org.openscience.cdk.io.cml.CMLHandler WARN: Detected unknown convention: cdk:substructureList
 done successfully.

Executing test function test.desc.cats  ... [1] "protein"        "hybrid"         "constitutional" "topological"   
[5] "electronic"     "geometrical"   
Timing stopped at: 0.078 0.004 0.029
Error in checkEquals(5, length(cats)) : Mean relative difference: 0.2

 done successfully.

Executing test function test.desc.names  ...  done successfully.

Executing test function test.exact.natural.mass  ...  done successfully.

Executing test function test.formula  ... Timing stopped at: 0.161 0.012 0.067
Error in load.molecules(formula_file) : 
  java.lang.NoClassDefFoundError: org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector
 done successfully.

Executing test function test.get.largest  ...  done successfully.

Executing test function test.is.connected  ...  done successfully.

Executing test function test.is.neutral  ...  done successfully.

Executing test function test.get.smiles  ...  done successfully.

Executing test function test.get.smiles2  ... Timing stopped at: 0.003 0 0.003
Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;",  : 
  java.lang.NoClassDefFoundError: org/openscience/cdk/smsd/Isomorphism
 done successfully.

------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Wed Apr 15 09:40:11 2020 
*********************************************** 
Number of test functions: 31 
Number of errors: 12 
Number of failures: 1 

1 Test Suite : 
rcdk rcdk Unit Tests - 31 test functions, 12 errors, 1 failure
ERROR in test.depictiongenerator: Error in .jnew("org.openscience.cdk.depict.DepictionGenerator") : 
  java.lang.ClassNotFoundException
ERROR in test.fp: Error in .jnew("org/openscience/cdk/fingerprint/ShortestPathFingerprinter",  : 
  java.lang.NoClassDefFoundError: org/apache/commons/math3/random/RandomGenerator
ERROR in test.aromaticity.match: Error in .jfindClass(as.character(class)) : 
  java.lang.ClassNotFoundException
ERROR in test.match1: Error in .jfindClass(as.character(class)) : 
  java.lang.ClassNotFoundException
ERROR in test.match2: Error in .jfindClass(as.character(class)) : 
  java.lang.ClassNotFoundException
ERROR in test.match3: Error in .jfindClass(as.character(class)) : 
  java.lang.ClassNotFoundException
ERROR in test.match4: Error in .jfindClass(as.character(class)) : 
  java.lang.ClassNotFoundException
ERROR in test.mcs1: Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;",  : 
  java.lang.NoClassDefFoundError: org/openscience/cdk/smsd/Isomorphism
ERROR in test.mcs2: Error in .jcall("org.guha.rcdk.util.Misc", "[[I", "getMcsAsAtomIndexMapping",  : 
  java.lang.NoClassDefFoundError: org/openscience/cdk/smsd/Isomorphism
ERROR in test.mcs3: Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;",  : 
  java.lang.NoClassDefFoundError: org/openscience/cdk/smsd/Isomorphism
FAILURE in test.desc.cats: Error in checkEquals(5, length(cats)) : Mean relative difference: 0.2

ERROR in test.formula: Error in load.molecules(formula_file) : 
  java.lang.NoClassDefFoundError: org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector
ERROR in test.get.smiles2: Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;",  : 
  java.lang.NoClassDefFoundError: org/openscience/cdk/smsd/Isomorphism
Error: 

unit testing failed (#test failures: 1, #R errors: 12)

Execution halted

Since there are several NoClassDefFoundError concerning cdk itself I'd
like to re-ask here again.  In vain I also tried to simply symlink
everything that is in /usr/share/java due to given Build-Depends and
tried the test suite again.  This leads to *more* errors than I have
with the hand crafted list in

   https://salsa.debian.org/r-pkg-team/r-cran-rcdklibs/-/blob/master/debian/rules

and the errors are slightly different.  I wonder whether there might be
some light of inspiration enhance my poking in the dark a bit.

Thanks for any help so far

      Andreas.

-- 
http://fam-tille.de

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Thread

Help needed for calling Java class from R Andreas Tille <andreas@an3as.eu> - 2020-04-14 18:20 +0200
  Re: Help needed for calling Java class from R Florian Weimer <fw@deneb.enyo.de> - 2020-04-14 19:00 +0200
    Re: Help needed for calling Java class from R Andreas Tille <andreas@an3as.eu> - 2020-04-14 20:00 +0200
      Re: Help needed for calling Java class from R Florian Weimer <fw@deneb.enyo.de> - 2020-04-14 20:50 +0200
        Re: Help needed for calling Java class from R Andreas Tille <andreas@an3as.eu> - 2020-04-14 23:00 +0200
          Re: Help needed for calling Java class from R Andreas Tille <andreas@an3as.eu> - 2020-04-15 12:20 +0200

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