{"action":"created","issue":{"url":"https://api.github.com/repos/rdkit/homebrew-rdkit/issues/25","repository_url":"https://api.github.com/repos/rdkit/homebrew-rdkit","labels_url":"https://api.github.com/repos/rdkit/homebrew-rdkit/issues/25/labels{/name}","comments_url":"https://api.github.com/repos/rdkit/homebrew-rdkit/issues/25/comments","events_url":"https://api.github.com/repos/rdkit/homebrew-rdkit/issues/25/events","html_url":"https://github.com/rdkit/homebrew-rdkit/issues/25","id":71351962,"number":25,"title":"Installing RDKit on Mac OSX 10.10.2 with java and inchi","user":{"login":"ChristopherFowler","id":5312716,"avatar_url":"https://avatars.githubusercontent.com/u/5312716?v=3","gravatar_id":"","url":"https://api.github.com/users/ChristopherFowler","html_url":"https://github.com/ChristopherFowler","followers_url":"https://api.github.com/users/ChristopherFowler/followers","following_url":"https://api.github.com/users/ChristopherFowler/following{/other_user}","gists_url":"https://api.github.com/users/ChristopherFowler/gists{/gist_id}","starred_url":"https://api.github.com/users/ChristopherFowler/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ChristopherFowler/subscriptions","organizations_url":"https://api.github.com/users/ChristopherFowler/orgs","repos_url":"https://api.github.com/users/ChristopherFowler/repos","events_url":"https://api.github.com/users/ChristopherFowler/events{/privacy}","received_events_url":"https://api.github.com/users/ChristopherFowler/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":11,"created_at":"2015-04-27T17:33:49Z","updated_at":"2016-04-05T16:24:52Z","closed_at":null,"body":"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.   \r\n\r\nThe familiar error statement is this:\r\n\r\n[ 40%] Built target cDataStructs\r\nLinking CXX shared library ../../lib/libGraphMol.dylib\r\n[ 40%] Built target GraphMol\r\nmake: *** [all] Error 2\r\n\r\nI'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.\r\n\r\nHere's the full story:\r\n\r\n$ brew install rdkit --with-java --with-inchi --debug --verbose\r\n/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb\r\n==> Installing rdkit from rdkit/homebrew-rdkit\r\n/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/cmake.rb\r\n/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/wget.rb\r\n/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/xz.rb\r\n/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/openssl.rb\r\n/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/makedepend.rb\r\n/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pkg-config.rb\r\n/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/swig.rb\r\n/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pcre.rb\r\n/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost.rb\r\n/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost-python.rb\r\n/usr/bin/env python -c import numpy\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FromPathLoader): loading /usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost.rb\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost-python.rb\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/cmake.rb\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/wget.rb\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/xz.rb\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/openssl.rb\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/makedepend.rb\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pkg-config.rb\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/swig.rb\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pcre.rb\r\n/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/python.rb\r\n/usr/bin/env python -c import numpy\r\n==> Downloading https://github.com/rdkit/rdkit/archive/Release_2014_09_2.tar.gz\r\nAlready downloaded: /Library/Caches/Homebrew/rdkit-2014.09.2.tar.gz\r\n==> Verifying rdkit-2014.09.2.tar.gz checksum\r\ntar xf /Library/Caches/Homebrew/rdkit-2014.09.2.tar.gz\r\n==> mkdir External/java_lib\r\n==> curl http://search.maven.org/remotecontent?filepath=junit/junit/4.11/junit-4.11.jar -o External/java_lib/junit.jar\r\n  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\r\n                                 Dload  Upload   Total   Spent    Left  Speed\r\n100   161  100   161    0     0    401      0 --:--:-- --:--:-- --:--:--   401\r\n==> cd External/INCHI-API; bash download-inchi.sh\r\n================================================================\r\nDownloading InChI software distribution version 1.04\r\n  http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/INCHI-1-API.zip\r\n  ====>\r\n  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INCHI-1-API/INCHI_API/vc9/inchi_main/INCHI_MAIN.rc  \r\n  inflating: INCHI-1-API/INCHI_API/vc9/inchi_main/inchi_main.sln  \r\n  inflating: INCHI-1-API/INCHI_API/vc9/inchi_main/inchi_main.vcproj  \r\n  inflating: INCHI-1-API/INCHI_API/vc9/inchi_main/inchi_main1.aps  \r\n  inflating: INCHI-1-API/INCHI_API/vc9/inchi_main/inchi_main1.rc  \r\n   creating: INCHI-1-API/INCHI_API/vc9/inchi_main/Release/\r\n  inflating: INCHI-1-API/INCHI_API/vc9/inchi_main/resource.h  \r\n   creating: INCHI-1-API/INCHI_API/vc9/inchi_main/x64/\r\n   creating: INCHI-1-API/INCHI_API/vc9/inchi_main/x64/Debug/\r\n   creating: INCHI-1-API/INCHI_API/vc9/inchi_main/x64/Release/\r\n  inflating: INCHI-1-API/LICENCE     \r\n  inflating: INCHI-1-API/readme.txt  \r\n  inflating: INCHI-1-API/readme2.txt  \r\n================================================================\r\nCopying files\r\n================================================================\r\n================================================================\r\nRemoving temporary files\r\n================================================================\r\n================================================================\r\nDone!\r\nMake sure you (re)run cmake before running make\r\n================================================================\r\n==> 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' .\r\n-- The C compiler identification is AppleClang 6.1.0.6020049\r\n-- The CXX compiler identification is AppleClang 6.1.0.6020049\r\n-- Check for working C compiler: /usr/local/Library/ENV/4.3/clang\r\n-- Check for working C compiler: /usr/local/Library/ENV/4.3/clang -- works\r\n-- Detecting C compiler ABI info\r\n-- Detecting C compiler ABI info - done\r\n-- Detecting C compile features\r\n-- Detecting C compile features - done\r\n-- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++\r\n-- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++ -- works\r\n-- Detecting CXX compiler ABI info\r\n-- Detecting CXX compiler ABI info - done\r\n-- Detecting CXX compile features\r\n-- Detecting CXX compile features - done\r\n-- Check if the system is big endian\r\n-- Searching 16 bit integer\r\n-- Looking for sys/types.h\r\n-- Looking for sys/types.h - found\r\n-- Looking for stdint.h\r\n-- Looking for stdint.h - found\r\n-- Looking for stddef.h\r\n-- Looking for stddef.h - found\r\n-- Check size of unsigned short\r\n-- Check size of unsigned short - done\r\n-- Using unsigned short\r\n-- Check if the system is big endian - little endian\r\n-- Found PythonInterp: /usr/bin/python (found version \"2.7.6\") \r\n-- Found PythonLibs: /System/Library/Frameworks/Python.framework/Versions/2.7/Python (found version \"2.7.6\") \r\n-- Boost version: 1.57.0\r\n-- Found the following Boost libraries:\r\n--   python\r\nPython Install directory /usr/local/Cellar/rdkit/2014.09.2/lib/python2.7/site-packages\r\n-- Looking for include file pthread.h\r\n-- Looking for include file pthread.h - found\r\n-- Looking for pthread_create\r\n-- Looking for pthread_create - found\r\n-- Found Threads: TRUE  \r\n-- Could NOT find InChI in system locations (missing:  INCHI_LIBRARY INCHI_INCLUDE_DIR) \r\n-- Found InChI software locally\r\n-- Found SWIG: /usr/local/bin/swig (found version \"3.0.5\") \r\n-- Found Java: /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/bin/java (found version \"1.8.0.25\") \r\n-- Found JNI: /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre/lib/libjawt.dylib  \r\n-- Configuring done\r\n-- Generating done\r\n-- Build files have been written to: /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2\r\n==> make\r\n[  0%] Scanning dependencies of target inchi_support\r\nSwig source\r\nScanning dependencies of target hc\r\n[  0%] Built target inchi_support\r\n[  0%] [  0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o\r\nBuilding C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o\r\nScanning dependencies of target Inchi\r\n[  0%] [  0%] [  1%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichicans.c.o\r\nBuilding C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichican2.c.o\r\nBuilding C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichicano.c.o\r\nLinking C shared library ../../../../lib/libhc.dylib\r\n[  1%] Built target hc\r\n[  1%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiisot.c.o\r\n[  1%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichilnct.c.o\r\n[  2%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimak2.c.o\r\n[  2%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimake.c.o\r\n../BitOps.i:47: Warning 302: Identifier 'AllProbeBitsMatch' redefined (ignored) (Renamed from 'AllProbeBitsMatch< ExplicitBitVect >'),\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/DataStructs/BitOps.h:72: Warning 302: previous definition of 'AllProbeBitsMatch'.\r\n../BitOps.i:48: Warning 302: Identifier 'AllProbeBitsMatch' redefined (ignored) (Renamed from 'AllProbeBitsMatch< ExplicitBitVect >'),\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/DataStructs/BitOps.h:72: Warning 302: previous definition of 'AllProbeBitsMatch'.\r\n../BitOps.i:60: Warning 302: Identifier 'NumBitsInCommon' redefined (ignored) (Renamed from 'NumBitsInCommon< ExplicitBitVect,ExplicitBitVect >'),\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/DataStructs/BitOps.h:219: Warning 302: previous definition of 'NumBitsInCommon'.\r\n[  3%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimap1.c.o\r\n/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.\r\n/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.\r\n/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.\r\n/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.\r\n/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.\r\n/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.\r\n/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.\r\n/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.\r\n/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.\r\n[  3%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimap2.c.o\r\n[  3%] [  4%] [  4%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimap4.c.o\r\nBuilding C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichinorm.c.o\r\nBuilding C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiparm.c.o\r\n[  4%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiprt1.c.o\r\n[  5%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiprt2.c.o\r\n[  5%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiprt3.c.o\r\n[  5%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiqueu.c.o\r\n[  6%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiring.c.o\r\n[  6%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichisort.c.o\r\n[  6%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichister.c.o\r\n[  7%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichitaut.c.o\r\n[  7%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichi_bns.c.o\r\n[  7%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/inchi_dll.c.o\r\n[  8%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiread.c.o\r\n[  8%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr1.c.o\r\n[  8%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr2.c.o\r\n[  9%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr3.c.o\r\n[  9%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr4.c.o\r\nScanning dependencies of target ChemicalFeatures\r\n[ 10%] Scanning dependencies of target RDGeneral\r\nBuilding CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o\r\n[ 10%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o\r\nScanning dependencies of target RDBoost\r\n[ 10%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o\r\n[ 11%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o\r\n[ 11%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o\r\n[ 11%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o\r\n[ 12%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.o\r\n[ 12%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr5.c.o\r\n[ 13%] [ 13%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr6.c.o\r\nBuilding C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr7.c.o\r\n[ 14%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/inchi_dll_main.c.o\r\nLinking CXX shared library ../../lib/libChemicalFeatures.dylib\r\n[ 14%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/runichi.c.o\r\n[ 14%] Built target ChemicalFeatures\r\n[ 14%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/inchi_dll_a.c.o\r\n[ 15%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/inchi_dll_a2.c.o\r\n[ 15%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ikey_dll.c.o\r\n[ 15%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ikey_base26.c.o\r\n[ 16%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichi_io.c.o\r\n[ 16%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/sha2.c.o\r\n[ 16%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/strutil.c.o\r\n[ 17%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/util.c.o\r\nLinking C shared library ../../lib/libInchi.dylib\r\n[ 17%] Built target Inchi\r\nLinking CXX shared library ../../lib/libRDBoost.dylib\r\n[ 17%] Built target RDBoost\r\nLinking CXX shared library ../../lib/libRDGeneral.dylib\r\n[ 17%] Built target RDGeneral\r\nScanning dependencies of target EigenSolvers\r\nScanning dependencies of target SimDivPickers\r\n[ 17%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o\r\n[ 18%] [ 18%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o\r\nBuilding CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o\r\nScanning dependencies of target Clustering\r\n[ 18%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o\r\nScanning dependencies of target DataStructs\r\nScanning dependencies of target rdBase\r\n[ 19%] [ 19%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o\r\nBuilding CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o\r\nScanning dependencies of target Catalogs\r\n[ 20%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o\r\n[ 20%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o\r\n[ 21%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o\r\nLinking CXX shared library ../../../lib/libEigenSolvers.dylib\r\n[ 21%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o\r\n[ 21%] Built target EigenSolvers\r\n[ 21%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o\r\n[ 22%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o\r\n[ 22%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o\r\nLinking CXX shared library ../../lib/libSimDivPickers.dylib\r\n[ 22%] [ 22%] Built target SimDivPickers\r\nBuilding CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o\r\n[ 22%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o\r\n[ 23%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o\r\nLinking CXX shared library ../../lib/libCatalogs.dylib\r\n[ 23%] Built target Catalogs\r\n[ 23%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o\r\nLinking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so\r\n[ 23%] Built target Clustering\r\nLinking CXX shared library ../../lib/libDataStructs.dylib\r\n[ 23%] Built target DataStructs\r\nScanning dependencies of target InfoTheory\r\n[ 23%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o\r\nScanning dependencies of target RDGeometryLib\r\nScanning dependencies of target rdMetricMatrixCalc\r\n[ 23%] [ 23%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o\r\nBuilding CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o\r\n[ 23%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o\r\nScanning dependencies of target rdSimDivPickers\r\nScanning dependencies of target cDataStructs\r\n[ 23%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o\r\n[ 23%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDGeneral/versions.h:8: Warning 451: Setting a const char * variable may leak memory.\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDGeneral/versions.h:13: Warning 451: Setting a const char * variable may leak memory.\r\n[ 23%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o\r\n[ 24%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o\r\nLinking CXX shared library ../../../lib/libInfoTheory.dylib\r\nScanning dependencies of target GraphMolWrap\r\n[ 24%] Built target InfoTheory\r\n[ 25%] Building CXX object Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx.o\r\nScanning dependencies of target rdInfoTheory\r\n[ 25%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o\r\n[ 25%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o\r\n[ 25%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o\r\nLinking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so\r\n[ 25%] Built target rdMetricMatrixCalc\r\n[ 26%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o\r\n[ 26%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o\r\nScanning dependencies of target cQuantize\r\n[ 27%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o\r\n[ 28%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o\r\nLinking CXX shared library ../../lib/libRDGeometryLib.dylib\r\n[ 28%] Built target RDGeometryLib\r\n[ 28%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o\r\nLinking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so\r\n/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'?\r\n  boost::detail::sp_nullptr_t arg1 ;\r\n                              ^~~~\r\n                              jarg1\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138653:121: note: 'jarg1' declared here\r\nSWIGEXPORT jlong JNICALL Java_org_RDKit_RDKFuncsJNI_new_1Shared_1Int_1Array_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) {\r\n                                                                                                                        ^\r\n/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'\r\n  boost::detail::sp_nullptr_t arg1 ;\r\n  ~~~~~~~~~~~~~~~^\r\n[ 28%] Built target rdSimDivPickers\r\n[ 29%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138656:18: error: no type named 'sp_nullptr_t' in namespace 'boost::detail'\r\n  boost::detail::sp_nullptr_t *argp1 ;\r\n  ~~~~~~~~~~~~~~~^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138661:28: error: no member named 'sp_nullptr_t' in namespace 'boost::detail'\r\n  argp1 = *(boost::detail::sp_nullptr_t **)&jarg1; \r\n            ~~~~~~~~~~~~~~~^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138661:43: error: expected expression\r\n  argp1 = *(boost::detail::sp_nullptr_t **)&jarg1; \r\n                                          ^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138666:3: error: use of undeclared identifier 'arg1'\r\n  arg1 = *argp1; \r\n  ^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138669:77: error: use of undeclared identifier 'arg1'\r\n      result = (boost::shared_array< int > *)new boost::shared_array< int >(arg1);\r\n                                                                            ^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139268:31: error: use of undeclared identifier 'arg1'; did you mean 'jarg1'?\r\n  boost::detail::sp_nullptr_t arg1 ;\r\n                              ^~~~\r\n                              jarg1\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138653:121: note: 'jarg1' declared here\r\nSWIGEXPORT jlong JNICALL Java_org_RDKit_RDKFuncsJNI_new_1Shared_1Int_1Array_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) {\r\n                                                                                                                        ^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139268:31: error: reference to local variable 'jarg1' declared in enclosing function 'Java_org_RDKit_RDKFuncsJNI_new_1Shared_1Int_1Array_1_1SWIG_11'\r\n  boost::detail::sp_nullptr_t arg1 ;\r\n                              ^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138653:121: note: 'jarg1' declared here\r\nSWIGEXPORT jlong JNICALL Java_org_RDKit_RDKFuncsJNI_new_1Shared_1Int_1Array_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) {\r\n                                                                                                                        ^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139268:18: error: no member named 'sp_nullptr_t' in namespace 'boost::detail'\r\n  boost::detail::sp_nullptr_t arg1 ;\r\n  ~~~~~~~~~~~~~~~^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139269:18: error: no type named 'sp_nullptr_t' in namespace 'boost::detail'\r\n  boost::detail::sp_nullptr_t *argp1 ;\r\n  ~~~~~~~~~~~~~~~^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139274:28: error: no member named 'sp_nullptr_t' in namespace 'boost::detail'\r\n  argp1 = *(boost::detail::sp_nullptr_t **)&jarg1; \r\n            ~~~~~~~~~~~~~~~^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139274:43: error: expected expression\r\n  argp1 = *(boost::detail::sp_nullptr_t **)&jarg1; \r\n                                          ^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139279:3: error: use of undeclared identifier 'arg1'\r\n  arg1 = *argp1; \r\n  ^\r\n/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139282:83: error: use of undeclared identifier 'arg1'\r\n      result = (boost::shared_array< double > *)new boost::shared_array< double >(arg1);\r\n                                                                                  ^\r\nLinking CXX shared module ../../../rdkit/rdBase.so\r\n[ 29%] Built target rdBase\r\nScanning dependencies of target Alignment\r\n[ 29%] Scanning dependencies of target rdGeometry\r\nBuilding CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o\r\n[ 29%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o\r\n15 errors generated.\r\nmake[2]: *** [Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx.o] Error 1\r\nmake[1]: *** [Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/all] Error 2\r\nmake[1]: *** Waiting for unfinished jobs....\r\n[ 29%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o\r\nScanning dependencies of target GraphMol\r\n[ 29%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o\r\nLinking CXX shared module ../../../rdkit/ML/Data/cQuantize.so\r\n[ 29%] Built target cQuantize\r\n[ 29%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o\r\nLinking CXX shared library ../../../lib/libAlignment.dylib\r\n[ 29%] Built target Alignment\r\n[ 29%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o\r\n[ 30%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o\r\nLinking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so\r\n[ 30%] Built target rdInfoTheory\r\n[ 31%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o\r\n[ 31%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o\r\n[ 31%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o\r\n[ 32%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o\r\n[ 33%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o\r\n[ 33%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o\r\n[ 33%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o\r\nLinking CXX shared module ../../../rdkit/Geometry/rdGeometry.so\r\n[ 33%] Built target rdGeometry\r\n[ 33%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o\r\n[ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o\r\n[ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o\r\n[ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o\r\n[ 35%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o\r\n[ 35%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o\r\n[ 35%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o\r\n[ 36%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o\r\n[ 36%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o\r\n[ 36%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o\r\n[ 37%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o\r\n[ 37%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o\r\n[ 38%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o\r\n[ 38%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o\r\n[ 38%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RankAtoms.cpp.o\r\n[ 39%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o\r\n[ 39%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o\r\n[ 39%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o\r\n[ 40%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o\r\n[ 40%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o\r\nLinking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so\r\n[ 40%] Built target cDataStructs\r\nLinking CXX shared library ../../lib/libGraphMol.dylib\r\n[ 40%] Built target GraphMol\r\nmake: *** [all] Error 2\r\n/usr/local/Library/Homebrew/debrew.rb:11:in `raise'\r\nBuildError: Failed executing: make \r\n1. raise\r\n2. ignore\r\n3. backtrace\r\n4. irb\r\n5. shell\r\nChoose an action: 1\r\n==> Formula\r\nTap: rdkit/homebrew-rdkit\r\nPath: /usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb\r\n==> Configuration\r\nHOMEBREW_VERSION: 0.9.5\r\nORIGIN: https://github.com/Homebrew/homebrew\r\nHEAD: 7731e73cc532a4c9919c019c697e443b1cf70334\r\nLast commit: 4 hours ago\r\nHOMEBREW_PREFIX: /usr/local\r\nHOMEBREW_CELLAR: /usr/local/Cellar\r\nCPU: 8-core 64-bit sandybridge\r\nOS X: 10.10.2-x86_64\r\nXcode: 6.3.1\r\nCLT: 6.2.0.0.1.1424975374\r\nClang: 6.1 build 602\r\nX11: 2.7.7 => /opt/X11\r\nSystem Ruby: 2.0.0-p481\r\nPerl: /usr/bin/perl\r\nPython: /usr/bin/python\r\nRuby: /usr/bin/ruby\r\nJava: 1.8.0_25\r\n==> ENV\r\nHOMEBREW_CC: clang\r\nHOMEBREW_CXX: clang++\r\nMAKEFLAGS: -j8\r\nCMAKE_PREFIX_PATH: /usr/local\r\nCMAKE_INCLUDE_PATH: /usr/include/libxml2:/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers\r\nCMAKE_LIBRARY_PATH: /System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries\r\nPKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Library/ENV/pkgconfig/10.10\r\nACLOCAL_PATH: /usr/local/share/aclocal\r\nPATH: /usr/local/Library/ENV/4.3:/usr/local/opt/cmake/bin:/usr/local/opt/wget/bin:/usr/local/opt/swig/bin:/usr/bin:/bin:/usr/sbin:/sbin\r\n\r\nError: rdkit 2014.09.2 did not build\r\nLogs:\r\n     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/01.java_lib\r\n     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/02.junit.jar\r\n     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/03.INCHI-API;\r\n     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/04.cmake\r\n     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/04.cmake.cc\r\n     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/05.make\r\n     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/05.make.cc\r\n     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/CMakeCache.txt"},"comment":{"url":"https://api.github.com/repos/rdkit/homebrew-rdkit/issues/comments/205882947","html_url":"https://github.com/rdkit/homebrew-rdkit/issues/25#issuecomment-205882947","issue_url":"https://api.github.com/repos/rdkit/homebrew-rdkit/issues/25","id":205882947,"user":{"login":"bp-kelley","id":9888416,"avatar_url":"https://avatars.githubusercontent.com/u/9888416?v=3","gravatar_id":"","url":"https://api.github.com/users/bp-kelley","html_url":"https://github.com/bp-kelley","followers_url":"https://api.github.com/users/bp-kelley/followers","following_url":"https://api.github.com/users/bp-kelley/following{/other_user}","gists_url":"https://api.github.com/users/bp-kelley/gists{/gist_id}","starred_url":"https://api.github.com/users/bp-kelley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bp-kelley/subscriptions","organizations_url":"https://api.github.com/users/bp-kelley/orgs","repos_url":"https://api.github.com/users/bp-kelley/repos","events_url":"https://api.github.com/users/bp-kelley/events{/privacy}","received_events_url":"https://api.github.com/users/bp-kelley/received_events","type":"User","site_admin":false},"created_at":"2016-04-05T16:24:51Z","updated_at":"2016-04-05T16:24:51Z","body":"I just make a pull request for CMake to pick the right version of libc++ on\nOSX.  You may want to try it out and see if it works for you:\n\nhttps://github.com/rdkit/rdkit/pull/845\n\nThis was hair-pulling for a while until we figured it out.  The problem\nisn't really that libc++ and stdlibc++ can't work together, they were\ndesigned not to collide (except on osx 10.8), the problem is that boost was\ncompiled with libc++ and the symbols can't be found.\n\nCheers,\n Brian\n\nOn Tue, Apr 5, 2016 at 12:16 AM, Greg Landrum <notifications@github.com>\nwrote:\n\n> The problem that Nik is fixing with the --std=c++14 flag is a tricky one.\n> Recent versions of the OS X include at least two different versions of the\n> C++ libraries: one for older flavors of C++ and one for modern C++\n> (=C++11/14). You pick which one to use at compile/link time with the -std\n> and/or -stdlib arguments.\n> For the RDKit it doesn't matter (yet) which standard you pick, but I\n> believe you can only use one at a time. So you cannot, for example, combine\n> libraries that have been linked against stdc++ and libc++.\n>\n> @bp-kelley <https://github.com/bp-kelley> posted some code to test for\n> library versions on OS X here:\n> http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05322.html\n>\n> Here's the test:\n>\n> if otool -L \"$PYROOT/lib/libboost_python.dylib\"  | grep libc++ ; then\n>     FLAGS=\"-std=c++11 -stdlib=libc++\"\n> else\n>     FLAGS=\"-stdlib=libstdc++\"\n> fi\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly or view it on GitHub\n> <https://github.com/rdkit/homebrew-rdkit/issues/25#issuecomment-205635577>\n>\n"}}