greglandrum
commented
9 years ago Just to be sure that this isn't something that has "accidentally" been fixed, can you please try installing the dev version of the rdkit with "brew install --HEAD rdkit"?
Closed ChristopherFowler closed 4 years ago
greglandrum
commented
9 years ago Just to be sure that this isn't something that has "accidentally" been fixed, can you please try installing the dev version of the rdkit with "brew install --HEAD rdkit"?
ChristopherFowler
commented
9 years ago Hi Greg. Thanks for the quick reply. I have tried both --HEAD and without when compiling rdkit --with-java and I got the same error both times.
Does this mean that the --with-java functionality is indeed not working right now?
Best, Chris
On Apr 28, 2015, at 12:04 AM, Greg Landrum notifications@github.com wrote:
Just to be sure that this isn't something that has "accidentally" been fixed, can you please try installing the dev version of the rdkit with "brew install --HEAD rdkit"?
— Reply to this email directly or view it on GitHub.
ChristopherFowler
commented
9 years ago Oh and one other thing. We will need Java working for Mac OSX 10.8.5 to current (I'm on 10.10.2 currently). Some of our machines aren't allowed to be upgraded here yet for security purposes.
In general, we really need the Java bindings for windows 7, 8, RHEL 5, 6, and the aforementioned Mac versions. There may be other architectures in the future but we know of these for now.
If all you can do for the moment is the Mac versions that's enough for a start.
Just to give you a heads up, my group is at the National Center for Computational Toxicology at the EPA in Research Triangle Park, NC. We are working on developing a public web application that extensively used rdkit which is why we are needing these architectures.
The cheminformatics community is small, so I figured I would introduce myself and let you know where our group is.
Best, Chris Fowler
On Apr 28, 2015, at 12:04 AM, Greg Landrum notifications@github.com wrote:
Just to be sure that this isn't something that has "accidentally" been fixed, can you please try installing the dev version of the rdkit with "brew install --HEAD rdkit"?
— Reply to this email directly or view it on GitHub.
greglandrum
commented
8 years ago @Grenix apologies that this has taken me so long to track down/reproduce, but I finally managed to reproduce the problem (accidentally, of course), and then, after some struggling, reproduce it.
The problem seems to be a bad interaction between SWIG, boost, and recent versions of clang on the Mac. I was able to solve the problem by reverting to an older version of boost. I was able to get the rdkit java wrappers to build with an up-to-date XCode by using boost 1.48. I can confirm that neither 1.55 nor 1.56 work.
Is it possible to install boost 1.48 using homebrew?
-greg
greglandrum
commented
8 years ago hmm, looks like I spoke too soon.
The wrappers build, but the tests are failing to build for me. It looks like there may be an incompatibility with Java8 that is causing problems. <sigh>
ChristopherFowler
commented
8 years ago Can you try it on Java 7 and 6 just to see if you get the same result?
On Nov 18, 2015, at 9:41 AM, Greg Landrum notifications@github.com wrote:
hmm, looks like I spoke too soon.
The wrappers build, but the tests are failing to build for me. It looks like there may be an incompatibility with Java8 that is causing problems.
— Reply to this email directly or view it on GitHub.
greglandrum
commented
8 years ago Easier said that done. I found a way to patch it so that the docs build under java8, but I will need to spend a bit more time to confirm that this also works back to java 6.
diff --git a/Code/JavaWrappers/gmwrapper/CMakeLists.txt b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
index 461bce4..d099215 100644
--- a/Code/JavaWrappers/gmwrapper/CMakeLists.txt
+++ b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
@@ -140,7 +140,7 @@ endif()
ADD_CUSTOM_COMMAND(
OUTPUT ${CMAKE_JAVA_TEST_OUTDIR}/org/RDKit/WrapperTests.class
- COMMAND ${JAVA_COMPILE} -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" ${JAVA_TEST_FILES}
+ COMMAND ${JAVA_COMPILE} -Xdoclint:none -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" ${JAVA_TEST_FILES}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar ${JAVA_TEST_FILES}
)Thanks for looking into this. I appreciate it.
Chris Fowler
On Wed, Nov 18, 2015 at 9:57 AM, Greg Landrum notifications@github.com wrote:
Easier said that done. I found a way to patch it so that the docs build under java8, but I will need to spend a bit more time to confirm that this also works back to java 6.
diff --git a/Code/JavaWrappers/gmwrapper/CMakeLists.txt b/Code/JavaWrappers/gmwrapper/CMakeLists.txt index 461bce4..d099215 100644 --- a/Code/JavaWrappers/gmwrapper/CMakeLists.txt +++ b/Code/JavaWrappers/gmwrapper/CMakeLists.txt @@ -140,7 +140,7 @@ endif() ADD_CUSTOM_COMMAND( OUTPUT ${CMAKE_JAVA_TEST_OUTDIR}/org/RDKit/WrapperTests.class
- COMMAND ${JAVA_COMPILE} -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" ${JAVA_TEST_FILES}
- COMMAND ${JAVA_COMPILE} -Xdoclint:none -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" ${JAVA_TEST_FILES} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar ${JAVA_TEST_FILES} )
— Reply to this email directly or view it on GitHub https://github.com/rdkit/homebrew-rdkit/issues/25#issuecomment-157739664 .
nbateshaus
commented
8 years ago I've been looking into this. I have compile working with boost 1.60 and Java 1.8.0_77, but still no javadoc. I got this far via:
diff --git a/Code/JavaWrappers/gmwrapper/CMakeLists.txt b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
index 2095d8e..ab55cce 100644
--- a/Code/JavaWrappers/gmwrapper/CMakeLists.txt
+++ b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
@@ -48,6 +48,9 @@ endif()
# Coax SWIG into playing nicely with Apple environments
if(APPLE)
SET(CMAKE_SIZEOF_VOID_P 4)
+ # Invocation of the compiler on swig-generated files somehow 'forgets' that
+ # we use a modern dialect of C++
+ ADD_COMPILE_OPTIONS(-std=c++14)
endif(APPLE)
if(CMAKE_SIZEOF_VOID_P MATCHES 4)*\ Edit: After updating RDKit to HEAD, I can now build all the way through. W00t!
greglandrum
commented
8 years ago The problem that Nik is fixing with the --std=c++14 flag is a tricky one.
Recent versions of the OS X include at least two different versions of the C++ libraries: one for older flavors of C++ and one for modern C++ (=C++11/14). You pick which one to use at compile/link time with the -std and/or -stdlib arguments.
For the RDKit it doesn't matter (yet) which standard you pick, but I believe you can only use one at a time. So you cannot, for example, combine libraries that have been linked against stdc++ and libc++.
@bp-kelley posted some code to test for library versions on OS X here: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05322.html
Here's the test:
if otool -L "$PYROOT/lib/libboost_python.dylib" | grep libc++ ; then
FLAGS="-std=c++11 -stdlib=libc++"
else
FLAGS="-stdlib=libstdc++"
fi
bp-kelley
commented
8 years ago I just make a pull request for CMake to pick the right version of libc++ on OSX. You may want to try it out and see if it works for you:
https://github.com/rdkit/rdkit/pull/845
This was hair-pulling for a while until we figured it out. The problem isn't really that libc++ and stdlibc++ can't work together, they were designed not to collide (except on osx 10.8), the problem is that boost was compiled with libc++ and the symbols can't be found.
Cheers, Brian
On Tue, Apr 5, 2016 at 12:16 AM, Greg Landrum notifications@github.com wrote:
The problem that Nik is fixing with the --std=c++14 flag is a tricky one. Recent versions of the OS X include at least two different versions of the C++ libraries: one for older flavors of C++ and one for modern C++ (=C++11/14). You pick which one to use at compile/link time with the -std and/or -stdlib arguments. For the RDKit it doesn't matter (yet) which standard you pick, but I believe you can only use one at a time. So you cannot, for example, combine libraries that have been linked against stdc++ and libc++.
@bp-kelley https://github.com/bp-kelley posted some code to test for library versions on OS X here: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05322.html
Here's the test:
if otool -L "$PYROOT/lib/libboost_python.dylib" | grep libc++ ; then FLAGS="-std=c++11 -stdlib=libc++" else FLAGS="-stdlib=libstdc++" fi
— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/rdkit/homebrew-rdkit/issues/25#issuecomment-205635577
nbateshaus
commented
8 years ago I just tried that fix instead of mine, and can confirm that it works! Thanks!
bp-kelley
commented
8 years ago Great! Thanks for trying the build.
ChristopherFowler
commented
8 years ago RDKit folks,
So I really appreciate your diligence on this. I've actually left the EPA for graduate school so I won't be needing any more correspondence. Thank you guys very much for all of your hard work!
Best, Chris Fowler
On Tue, Apr 5, 2016 at 12:24 PM, Brian Kelley notifications@github.com wrote:
I just make a pull request for CMake to pick the right version of libc++ on OSX. You may want to try it out and see if it works for you:
https://github.com/rdkit/rdkit/pull/845
This was hair-pulling for a while until we figured it out. The problem isn't really that libc++ and stdlibc++ can't work together, they were designed not to collide (except on osx 10.8), the problem is that boost was compiled with libc++ and the symbols can't be found.
Cheers, Brian
On Tue, Apr 5, 2016 at 12:16 AM, Greg Landrum notifications@github.com wrote:
The problem that Nik is fixing with the --std=c++14 flag is a tricky one. Recent versions of the OS X include at least two different versions of the C++ libraries: one for older flavors of C++ and one for modern C++ (=C++11/14). You pick which one to use at compile/link time with the -std and/or -stdlib arguments. For the RDKit it doesn't matter (yet) which standard you pick, but I believe you can only use one at a time. So you cannot, for example, combine libraries that have been linked against stdc++ and libc++.
@bp-kelley https://github.com/bp-kelley posted some code to test for library versions on OS X here:
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05322.html
Here's the test:
if otool -L "$PYROOT/lib/libboost_python.dylib" | grep libc++ ; then FLAGS="-std=c++11 -stdlib=libc++" else FLAGS="-stdlib=libstdc++" fi
— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub < https://github.com/rdkit/homebrew-rdkit/issues/25#issuecomment-205635577>
— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/rdkit/homebrew-rdkit/issues/25#issuecomment-205882947
UnixJunkie
commented
5 years ago this is so old, I guess it can be closed
This issue may have already been brought up in issue #23 but I wanted to post it here since I've had no luck fixing the problem. I can compile RDKit just fine without using --with-java but I need the java wrappers for my work. Below is the full console print-out with --debug and --verbose.
The familiar error statement is this:
[ 40%] Built target cDataStructs Linking CXX shared library ../../lib/libGraphMol.dylib [ 40%] Built target GraphMol make: *\ [all] Error 2
I'm not exactly sure how to resolve this issue. There has been mention around the web about adding some command to the cmake call but I'm not sure how to do that.
Here's the full story:
$ brew install rdkit --with-java --with-inchi --debug --verbose /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb ==> Installing rdkit from rdkit/homebrew-rdkit /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/cmake.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/wget.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/xz.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/openssl.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/makedepend.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pkg-config.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/swig.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pcre.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost-python.rb /usr/bin/env python -c import numpy /usr/local/Library/Homebrew/build.rb (Formulary::FromPathLoader): loading /usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost-python.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/cmake.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/wget.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/xz.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/openssl.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/makedepend.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pkg-config.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/swig.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pcre.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/python.rb /usr/bin/env python -c import numpy ==> Downloading https://github.com/rdkit/rdkit/archive/Release_2014_09_2.tar.gz Already downloaded: /Library/Caches/Homebrew/rdkit-2014.09.2.tar.gz ==> Verifying rdkit-2014.09.2.tar.gz checksum tar xf /Library/Caches/Homebrew/rdkit-2014.09.2.tar.gz ==> mkdir External/java_lib ==> curl http://search.maven.org/remotecontent?filepath=junit/junit/4.11/junit-4.11.jar -o External/java_lib/junit.jar % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 161 100 161 0 0 401 0 --:--:-- --:--:-- --:--:-- 401
==> cd External/INCHI-API; bash download-inchi.sh
Downloading InChI software distribution version 1.04 http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/INCHI-1-API.zip ====>
/var/folders/rt/s9lnxk2x2jv81c2_6f8ll6rw0000gn/T/rdkit-inchi-XXX.tmQVIw8g
--2015-04-27 13:13:22-- http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/INCHI-1-API.zip Resolving www.inchi-trust.org... 91.151.214.89 Connecting to www.inchi-trust.org|91.151.214.89|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 2701930 (2.6M) [application/zip] Saving to: 'INCHI-1-API.zip'
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2015-04-27 13:13:29 (354 KB/s) - 'INCHI-1-API.zip' saved [2701930/2701930]
Unarchiving
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Make sure you (re)run cmake before running make
==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2014.09.2' -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DRDK_INSTALL_INTREE=OFF -DJAVA_AWT_INCLUDE_DIRECTORIES=/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/include -DRDK_BUILD_SWIG_WRAPPERS=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_CPP_TESTS=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DPYTHON_EXECUTABLE='/usr/bin/python' -DPYTHON_INCLUDE_DIR='/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7' -DPYTHON_LIBRARY='/System/Library/Frameworks/Python.framework/Versions/2.7/Python' -DPYTHON_NUMPY_INCLUDE_PATH='/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include' . -- The C compiler identification is AppleClang 6.1.0.6020049 -- The CXX compiler identification is AppleClang 6.1.0.6020049 -- Check for working C compiler: /usr/local/Library/ENV/4.3/clang -- Check for working C compiler: /usr/local/Library/ENV/4.3/clang -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++ -- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- Found PythonInterp: /usr/bin/python (found version "2.7.6") -- Found PythonLibs: /System/Library/Frameworks/Python.framework/Versions/2.7/Python (found version "2.7.6") -- Boost version: 1.57.0 -- Found the following Boost libraries: -- python Python Install directory /usr/local/Cellar/rdkit/2014.09.2/lib/python2.7/site-packages -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE
-- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR) -- Found InChI software locally -- Found SWIG: /usr/local/bin/swig (found version "3.0.5") -- Found Java: /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/bin/java (found version "1.8.0.25") -- Found JNI: /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre/lib/libjawt.dylib
-- Configuring done -- Generating done -- Build files have been written to: /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2 ==> make [ 0%] Scanning dependencies of target inchi_support Swig source Scanning dependencies of target hc [ 0%] Built target inchi_support [ 0%] [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o Scanning dependencies of target Inchi [ 0%] [ 0%] [ 1%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichicans.c.o Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichican2.c.o Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichicano.c.o Linking C shared library ../../../../lib/libhc.dylib [ 1%] Built target hc [ 1%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiisot.c.o [ 1%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichilnct.c.o [ 2%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimak2.c.o [ 2%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimake.c.o ../BitOps.i:47: Warning 302: Identifier 'AllProbeBitsMatch' redefined (ignored) (Renamed from 'AllProbeBitsMatch< ExplicitBitVect >'), /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/DataStructs/BitOps.h:72: Warning 302: previous definition of 'AllProbeBitsMatch'. ../BitOps.i:48: Warning 302: Identifier 'AllProbeBitsMatch' redefined (ignored) (Renamed from 'AllProbeBitsMatch< ExplicitBitVect >'), /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/DataStructs/BitOps.h:72: Warning 302: previous definition of 'AllProbeBitsMatch'. ../BitOps.i:60: Warning 302: Identifier 'NumBitsInCommon' redefined (ignored) (Renamed from 'NumBitsInCommon< ExplicitBitVect,ExplicitBitVect >'), /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/DataStructs/BitOps.h:219: Warning 302: previous definition of 'NumBitsInCommon'. [ 3%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimap1.c.o /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDBoost/Exceptions.h:18: Warning 401: Nothing known about base class 'std::runtime_error'. Ignored. /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDBoost/Exceptions.h:31: Warning 401: Nothing known about base class 'std::runtime_error'. Ignored. /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDBoost/Exceptions.h:46: Warning 401: Nothing known about base class 'std::runtime_error'. Ignored. /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/QueryOps.h:375: Warning 401: Nothing known about base class 'Queries::EqualityQuery< int,ConstAtomPtr,true >'. Ignored. /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/QueryOps.h:375: Warning 401: Maybe you forgot to instantiate 'Queries::EqualityQuery< int,ConstAtomPtr,true >' using %template. /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/QueryOps.h:415: Warning 401: Nothing known about base class 'Queries::SetQuery< int,Atom const ,true >'. Ignored. /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/QueryOps.h:415: Warning 401: Maybe you forgot to instantiate 'Queries::SetQuery< int,Atom const ,true >' using %template. /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/SanitException.h:26: Warning 520: Base class 'std::exception' of 'MolSanitizeException' is not similarly marked as a smart pointer. /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/SmilesParse/SmilesParse.h:58: Warning 520: Base class 'std::exception' of 'SmilesParseException' is not similarly marked as a smart pointer. [ 3%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimap2.c.o [ 3%] [ 4%] [ 4%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimap4.c.o Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichinorm.c.o Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiparm.c.o [ 4%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiprt1.c.o [ 5%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiprt2.c.o [ 5%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiprt3.c.o [ 5%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiqueu.c.o [ 6%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiring.c.o [ 6%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichisort.c.o [ 6%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichister.c.o [ 7%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichitaut.c.o [ 7%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichi_bns.c.o [ 7%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/inchi_dll.c.o [ 8%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiread.c.o [ 8%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr1.c.o [ 8%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr2.c.o [ 9%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr3.c.o [ 9%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr4.c.o Scanning dependencies of target ChemicalFeatures [ 10%] Scanning dependencies of target RDGeneral Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o [ 10%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o Scanning dependencies of target RDBoost [ 10%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o [ 11%] Building CXX object 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External/INCHI-API/CMakeFiles/Inchi.dir/src/ikey_dll.c.o [ 15%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ikey_base26.c.o [ 16%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichi_io.c.o [ 16%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/sha2.c.o [ 16%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/strutil.c.o [ 17%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/util.c.o Linking C shared library ../../lib/libInchi.dylib [ 17%] Built target Inchi Linking CXX shared library ../../lib/libRDBoost.dylib [ 17%] Built target RDBoost Linking CXX shared library ../../lib/libRDGeneral.dylib [ 17%] Built target RDGeneral Scanning dependencies of target EigenSolvers Scanning dependencies of target SimDivPickers [ 17%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o [ 18%] [ 18%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o 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[ 23%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o Scanning dependencies of target RDGeometryLib Scanning dependencies of target rdMetricMatrixCalc [ 23%] [ 23%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o [ 23%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o Scanning dependencies of target rdSimDivPickers Scanning dependencies of target cDataStructs [ 23%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o [ 23%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDGeneral/versions.h:8: Warning 451: Setting a const char * variable may leak memory. /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDGeneral/versions.h:13: Warning 451: Setting a const char * variable may leak memory. [ 23%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o [ 24%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o Linking CXX shared library ../../../lib/libInfoTheory.dylib Scanning dependencies of target GraphMolWrap [ 24%] Built target InfoTheory [ 25%] Building CXX object Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx.o Scanning dependencies of target rdInfoTheory [ 25%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o [ 25%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o [ 25%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so [ 25%] Built target rdMetricMatrixCalc [ 26%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o [ 26%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o Scanning dependencies of target cQuantize [ 27%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o [ 28%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o Linking CXX shared library ../../lib/libRDGeometryLib.dylib [ 28%] Built target RDGeometryLib [ 28%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138655:31: error: use of undeclared identifier 'arg1'; did you mean 'jarg1'? boost::detail::sp_nullptr_t arg1 ; ^~~~ jarg1 /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138653:121: note: 'jarg1' declared here SWIGEXPORT jlong JNICALL Java_org_RDKit_RDKFuncsJNI_new_1Shared_1Int_1Array_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) { ^ /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138655:18: error: no member named 'sp_nullptr_t' in namespace 'boost::detail' boost::detail::sp_nullptr_t arg1 ;