ykazakov / cb-reasoner Goto Github PK

Hi,
I'd like to use CB as a reasoner within Protege.

When trying to make all in the src I got an error about missing jni_md.h. Which I fixed by setting the env var:
export JNI_INCLUDE="/usr/lib/jvm/java-8-oracle/include/linux;/usr/lib/jvm/java-8-oracle/include"

But now I receive the following error:
make all
ocamlbuild -build-dir _build main/cb.native jni cwrap/libcb.a
Finished, 1 target (0 cached) in 00:00:00.
Building for host: linux, target: linux, arch: amd64

• /usr/lib/jvm/java-8-oracle/bin/javac -source 5 -d java/. java/org/semanticweb/cb/reasoner/CbObjectInverseOf.java java/org/semanticweb/cb/reasoner/CbClassExpressionVisitor.java java/org/semanticweb/cb/reasoner/Loader.java java/org/semanticweb/cb/reasoner/CbAxiom.java java/org/semanticweb/cb/reasoner/CbException.java java/org/semanticweb/cb/reasoner/CbSubClassOfAxiom.java java/org/semanticweb/cb/reasoner/CbClassAxiomIterator.java java/org/semanticweb/cb/reasoner/CbSubObjectPropertyOfAxiom.java java/org/semanticweb/cb/reasoner/CbObjectPropertyDeclarationAxiom.java java/org/semanticweb/cb/reasoner/CbDeclarationAxiom.java java/org/semanticweb/cb/reasoner/CObject.java java/org/semanticweb/cb/reasoner/CbClassAxiom.java java/org/semanticweb/cb/reasoner/CbInverseObjectPropertiesAxiom.java java/org/semanticweb/cb/reasoner/CbDeclarationAxiomVisitor.java java/org/semanticweb/cb/reasoner/CbInverseFunctionalObjectPropertyAxiom.java java/org/semanticweb/cb/reasoner/CbObjectPropertyAxiom.java java/org/semanticweb/cb/reasoner/CbClassExpression.java java/org/semanticweb/cb/reasoner/CbAxiomVisitor.java java/org/semanticweb/cb/reasoner/CbObjectSomeValuesFrom.java java/org/semanticweb/cb/reasoner/CbClassTaxonomyNode.java java/org/semanticweb/cb/reasoner/CbEquivalentClassesAxiom.java java/org/semanticweb/cb/reasoner/CbObjectProperty.java java/org/semanticweb/cb/reasoner/CbObjectPropertyAxiomVisitor.java java/org/semanticweb/cb/reasoner/ProgressMonitor.java java/org/semanticweb/cb/reasoner/CbObjectPropertyExpression.java java/org/semanticweb/cb/reasoner/CbClassNode.java java/org/semanticweb/cb/reasoner/CbObjectPropertyExpressionVisitor.java java/org/semanticweb/cb/reasoner/CbObjectVisitor.java java/org/semanticweb/cb/reasoner/DummyProgressMonitor.java java/org/semanticweb/cb/reasoner/CbObjectIntersectionOf.java java/org/semanticweb/cb/reasoner/CbClassDeclarationAxiom.java java/org/semanticweb/cb/reasoner/CbProgressMonitorStdErr.java java/org/semanticweb/cb/reasoner/CbFunctionalObjectPropertyAxiom.java java/org/semanticweb/cb/reasoner/CbProgressMonitor.java java/org/semanticweb/cb/reasoner/CbClassAxiomVisitor.java java/org/semanticweb/cb/reasoner/CbTransitiveObjectPropertyAxiom.java java/org/semanticweb/cb/reasoner/CbObject.java java/org/semanticweb/cb/reasoner/CbClassAxiomIteratable.java java/org/semanticweb/cb/reasoner/CbOntology.java java/org/semanticweb/cb/reasoner/CbClass.java
  warning: [options] bootstrap class path not set in conjunction with -source 1.5
  warning: [options] source value 1.5 is obsolete and will be removed in a future release
  warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
  3 warnings
• /usr/bin/ocamlopt unix.cmxa -ccopt -shared cwrap/cb.o java/jni/cbce.o java/jni/cbdax.o java/jni/cbont.o java/jni/cbcax.o java/jni/cbcn.o java/jni/cbopax.o java/jni/cbcaxi.o java/jni/cbope.o java/jni/config.o java/jni/cbpm.o libs/consed.cmx libs/chashsetlp.cmx libs/chashtbllp.cmx libs/cset.cmx libs/cmap.cmx libs/hashsetlp.cmx libs/hashtbllp.cmx libs/intset.cmx main/chashset.cmx main/chashmap.cmx main/owl.cmx main/brole.cmx main/polarity.cmx main/ontology.cmx main/index_op.cmx main/saturation_op.cmx main/index.cmx main/progress_monitor.cmx main/progress_tracker.cmx main/saturation.cmx main/class_taxonomy.cmx main/owl_fs_parser.cmx main/owl_fs_lexer.cmx main/owl_io.cmx cwrap/cbclib.cmx -o java/nativelib/linux/amd64/libjcb.so
  /usr/bin/ld: cwrap/cb.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
  cwrap/cb.o: error adding symbols: Bad value
  collect2: error: ld returned 1 exit status
  File "caml_startup", line 1:
  Error: Error during linking
  Command exited with code 2.
  Compilation unsuccessful after building 153 targets (0 cached) in 00:00:19.
  make: *** [all] Error 10

As I do not necessarily require a binary -in principle I would only need a working jar I can copy into my plugin folder... How can I generate that?

Any help would be greatly appreciated.

Thanks,
Daniel

Found this while investigating the cause of a parse error that turned out to be 
unrelated (caused by an incorrectly generated input file). Verified with 
http://www.w3.org/TR/owl2-syntax/#Keys

Original issue reported on code.google.com by [email protected] on 18 Oct 2011 at 3:41

Attachments:

• owl_fs_parser.mly.patch

i am trying to compile the project however upon running make, it is giving the following error.

descending to src
make[1]: Entering directory '/home/shah/Desktop/reasoners/cb-reasoner-master/src'
ocamlbuild -build-dir _build main/cb.native
+ ocamlopt.opt unix.cmxa -I /home/shah/.opam/default/lib/ocamlbuild /home/shah/.opam/default/lib/ocamlbuild/ocamlbuildlib.cmxa myocamlbuild.ml /home/shah/.opam/default/lib/ocamlbuild/ocamlbuild.cmx -o myocamlbuild
File "myocamlbuild.ml", line 13, characters 11-64:
Error: Unbound module Ocamlbuild_pack.Ocamlbuild_Myocamlbuild_config
Command exited with code 2.
Compilation unsuccessful after building 1 target (0 cached) in 00:00:00.
Makefile:8: recipe for target 'main' failed
make[1]: *** [main] Error 10
make[1]: Leaving directory '/home/shah/Desktop/reasoners/cb-reasoner-master/src'
Makefile:14: recipe for target 'src' failed
make: *** [src] Error 2

It has problem when it runs myocamlbuild.ml file.. i guess there is some compability issues with the newer ocambuild.

Here is the comments i got from ocamlbuild github

OCamlbuild exports a stable interface for plugin users as the Ocamlbuild_plugin module. Using Ocamlbuild_pack directly accesses ocamlbuild's internal definitions, and is recommended against as there are no guarantees of backward-compatibility.

In your specific case, a module is used by this code that indeed was removed in more recent ocamlbuild versions (its presence was an artifact of the specific way ocamlbuild's build system was integrated into the compiler distribution). I could correctly build this software with OCaml 3.12.1, 4.00.1 and 4.01.0, but not any more recent version of OCaml and ocamlbuild.

Using opam makes it easy to install old OCaml versions:

opam install 4.01.0
eval $(opam env --switch=4.01.0)
make # if in the project's directoyr

If you are interested in patching this software to make it compatible with more recent OCaml versions, we could discuss how to get the corresponding information in a more robust way.

In any case, I'm closing this as it is not a problem of ocamlbuild, but rather a maintenance question for cb-reasoner. (Of course, feel free to post further comments.)