Install with Java doesn't work

[tdudgeon]

Installing with the --with-java option does not work for me: https://gist.github.com/tdudgeon/5213f4b4342b298c26ad23296dd0871e With plain: brew install rdkit it works fine. This is on El Capitan 10.11.5

[UnixJunkie]

The gist file no longer exists, so this could be closed. Also, the issue is so old that I guess the user managed to make it work.

[UnixJunkie]

brew install homebrew/cask/java
brew install rdkit --with-inchi --with-java

[UnixJunkie]

There might be a broken build of the java wrappers on Mac:

Last 15 lines from /Users/berenger/Library/Logs/Homebrew/rdkit/02.make:
                            ^
src/org/RDKit/StringMolMap.java:98: error: incompatible types: Iterator cannot be converted to SWIGTYPE_p_std__mapT_std__string_boost__shared_ptrT_RDKit__ROMol_t_std__lessT_std__string_t_t__iterator
    while (itr.isNot(end)) {
                     ^
src/org/RDKit/StringMolMap.java:121: error: incompatible types: SWIGTYPE_p_std__mapT_std__string_boost__shared_ptrT_RDKit__ROMol_t_std__lessT_std__string_t_t__iterator cannot be converted to Iterator
      itr = itr.getNextUnchecked();
                                ^
src/org/RDKit/SubstructLibrary.java:43: error: incompatible types: byte cannot be converted to Short
       vec.add(b[size]);
                ^
Note: Some messages have been simplified; recompile with -Xdiags:verbose to get full output
22 errors
make[2]: *** [Code/JavaWrappers/gmwrapper/org.RDKit.jar] Error 1
make[1]: *** [Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrapJar.dir/all] Error 2
make: *** [all] Error 2

[UnixJunkie]

# java --version
openjdk 12.0.2 2019-07-16
OpenJDK Runtime Environment (build 12.0.2+10)
OpenJDK 64-Bit Server VM (build 12.0.2+10, mixed mode, sharing)

[UnixJunkie]

# brew list swig
/usr/local/Cellar/swig/4.0.1/

Maybe the SWIG version is the problem?

[UnixJunkie]

Tim Dudgeon uses those cmake lines on Linux:

RUN cmake -Wno-dev\
  -DPYTHON_EXECUTABLE=/usr/bin/python3\
  -DRDK_INSTALL_INTREE=OFF\
  -DRDK_BUILD_INCHI_SUPPORT=ON\
  -DRDK_BUILD_AVALON_SUPPORT=ON\
  -DRDK_BUILD_PYTHON_WRAPPERS=ON\
  -DRDK_BUILD_SWIG_WRAPPERS=ON\
  -DRDK_BUILD_PGSQL=ON\
  -DPostgreSQL_ROOT=/usr/lib/postgresql/$POSTGRES_VERSION\
  -DPostgreSQL_TYPE_INCLUDE_DIR=/usr/include/postgresql/$POSTGRES_VERSION/server\
  -DCMAKE_INSTALL_PREFIX=/usr\
  -DCPACK_PACKAGE_RELOCATABLE=OFF

[xrfinbupt]

There might be a broken build of the java wrappers on Mac:

Last 15 lines from /Users/berenger/Library/Logs/Homebrew/rdkit/02.make:
                            ^
src/org/RDKit/StringMolMap.java:98: error: incompatible types: Iterator cannot be converted to SWIGTYPE_p_std__mapT_std__string_boost__shared_ptrT_RDKit__ROMol_t_std__lessT_std__string_t_t__iterator
    while (itr.isNot(end)) {
                     ^
src/org/RDKit/StringMolMap.java:121: error: incompatible types: SWIGTYPE_p_std__mapT_std__string_boost__shared_ptrT_RDKit__ROMol_t_std__lessT_std__string_t_t__iterator cannot be converted to Iterator
      itr = itr.getNextUnchecked();
                                ^
src/org/RDKit/SubstructLibrary.java:43: error: incompatible types: byte cannot be converted to Short
       vec.add(b[size]);
                ^
Note: Some messages have been simplified; recompile with -Xdiags:verbose to get full output
22 errors
make[2]: *** [Code/JavaWrappers/gmwrapper/org.RDKit.jar] Error 1
make[1]: *** [Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrapJar.dir/all] Error 2
make: *** [all] Error 2

meet the same problem

[UnixJunkie]

@tdudgeon @xrfinbupt you should ask the rdkit mailing list or open an issue in rdkit https://github.com/rdkit/rdkit/issues