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rdkit / homebrew-rdkit

Homebrew formula for rdkit
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Install fails #28

Closed rscottrowland closed 4 years ago

rscottrowland commented 8 years ago

Hi,

I'm getting a failed install with Mac OS X 10.10.5, brew 0.9.5, and Xcode7.0.1. Error messages below:

==> Installing rdkit/rdkit/rdkit ==> Downloading https://github.com/rdkit/rdkit/archive/Release_2015_03_1.tar.gz ==> Downloading from https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2015_03_1

100.0%

==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2015.03.1' -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DRDK_INSTALL_I ==> make Last 15 lines from /Users/scottrowland/Library/Logs/Homebrew/rdkit/02.make:

include 

     ^

1 error generated. make[2]: * [Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o] Error 1 make[2]: * Waiting for unfinished jobs.... 1 error generated. make[2]: * [Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o] Error 1 make[1]: * [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error 2 1 error generated. make[2]: * [Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o] Error 1 make[1]: * [Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/all] Error 2 1 error generated. make[2]: * [Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o] Error 1 make[1]: * [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2 make: *\ [all] Error 2

djinnome commented 7 years ago

I am also having trouble installing rdkit from homebrew 1.2.6 Homebrew/homebrew-core (git revision 941ca; last commit 2017-07-28), Mac OS X 10.12.5, and Xcode 8.3.3 (8E3004b)

I followed the directions in https://github.com/rdkit/homebrew-rdkit

(anaconda3-4.4.0) bash-3.2$ brew tap rdkit/rdkit
brew tap rdkit/rdkit
==> Tapping rdkit/rdkit
Cloning into '/usr/local/Homebrew/Library/Taps/rdkit/homebrew-rdkit'...
remote: Counting objects: 5, done.        
remote: Compressing objects: 100% (4/4), done.        
remote: Total 5 (delta 0), reused 3 (delta 0), pack-reused 0        
Unpacking objects: 100% (5/5), done.
Tapped 1 formula (29 files, 29.5KB)

But when I attempted to install, I got the following error:

(anaconda3-4.4.0) bash-3.2$ brew install rdkit
brew install rdkit
==> Installing rdkit from rdkit/rdkit
==> Installing dependencies for rdkit/rdkit/rdkit: sqlite, gdbm, python, cmake, boost, eigen, boost-python, numpy
==> Installing rdkit/rdkit/rdkit dependency: sqlite
==> Downloading https://homebrew.bintray.com/bottles/sqlite-3.19.3.sierra.bottle
######################################################################### 100.0%
==> Pouring sqlite-3.19.3.sierra.bottle.tar.gz
==> Using the sandbox
==> Caveats
This formula is keg-only, which means it was not symlinked into /usr/local,
because macOS provides an older sqlite3.

If you need to have this software first in your PATH run:
  echo 'export PATH="/usr/local/opt/sqlite/bin:$PATH"' >> ~/.bash_profile

For compilers to find this software you may need to set:
    LDFLAGS:  -L/usr/local/opt/sqlite/lib
    CPPFLAGS: -I/usr/local/opt/sqlite/include
For pkg-config to find this software you may need to set:
    PKG_CONFIG_PATH: /usr/local/opt/sqlite/lib/pkgconfig

==> Summary
🍺  /usr/local/Cellar/sqlite/3.19.3: 12 files, 2.9MB
==> Installing rdkit/rdkit/rdkit dependency: gdbm
==> Downloading https://homebrew.bintray.com/bottles/gdbm-1.13.sierra.bottle.tar
######################################################################### 100.0%
==> Pouring gdbm-1.13.sierra.bottle.tar.gz
🍺  /usr/local/Cellar/gdbm/1.13: 19 files, 554.4KB
==> Installing rdkit/rdkit/rdkit dependency: python
==> Downloading https://homebrew.bintray.com/bottles/python-2.7.13_1.sierra.bott
######################################################################### 100.0%
==> Pouring python-2.7.13_1.sierra.bottle.tar.gz
==> /usr/local/Cellar/python/2.7.13_1/bin/python2 -s setup.py --no-user-cfg inst
==> /usr/local/Cellar/python/2.7.13_1/bin/python2 -s setup.py --no-user-cfg inst
==> /usr/local/Cellar/python/2.7.13_1/bin/python2 -s setup.py --no-user-cfg inst
==> Caveats
This formula installs a python2 executable to /usr/local/bin.
If you wish to have this formula's python executable in your PATH then add
the following to ~/.bash_profile:
  export PATH="/usr/local/opt/python/libexec/bin:$PATH"

Pip and setuptools have been installed. To update them
  pip2 install --upgrade pip setuptools

You can install Python packages with
  pip2 install <package>

They will install into the site-package directory
  /usr/local/lib/python2.7/site-packages

See: http://docs.brew.sh/Homebrew-and-Python.html
==> Summary
🍺  /usr/local/Cellar/python/2.7.13_1: 3,528 files, 48MB
==> Installing rdkit/rdkit/rdkit dependency: cmake
==> Downloading https://homebrew.bintray.com/bottles/cmake-3.9.0.sierra.bottle.t
######################################################################### 100.0%
==> Pouring cmake-3.9.0.sierra.bottle.tar.gz
==> Caveats
Emacs Lisp files have been installed to:
  /usr/local/share/emacs/site-lisp/cmake
==> Summary
🍺  /usr/local/Cellar/cmake/3.9.0: 2,267 files, 29.6MB
==> Installing rdkit/rdkit/rdkit dependency: boost
==> Downloading https://homebrew.bintray.com/bottles/boost-1.64.0_1.sierra.bottl
######################################################################### 100.0%
==> Pouring boost-1.64.0_1.sierra.bottle.tar.gz
🍺  /usr/local/Cellar/boost/1.64.0_1: 12,628 files, 395.7MB
==> Installing rdkit/rdkit/rdkit dependency: eigen
==> Downloading https://homebrew.bintray.com/bottles/eigen-3.3.4.sierra.bottle.t
######################################################################### 100.0%
==> Pouring eigen-3.3.4.sierra.bottle.tar.gz
🍺  /usr/local/Cellar/eigen/3.3.4: 486 files, 6.5MB
==> Installing rdkit/rdkit/rdkit dependency: boost-python
==> Downloading https://homebrew.bintray.com/bottles/boost-python-1.64.0.sierra.
######################################################################### 100.0%
==> Pouring boost-python-1.64.0.sierra.bottle.tar.gz
🍺  /usr/local/Cellar/boost-python/1.64.0: 458 files, 16.7MB
==> Installing rdkit/rdkit/rdkit dependency: numpy
==> Downloading https://homebrew.bintray.com/bottles/numpy-1.13.1.sierra.bottle.
######################################################################### 100.0%
==> Pouring numpy-1.13.1.sierra.bottle.tar.gz
==> Caveats
Python modules have been installed and Homebrew's site-packages is not
in your Python sys.path, so you will not be able to import the modules
this formula installed. If you plan to develop with these modules,
please run:
  mkdir -p /Users/zuck016/.local/lib/python3.6/site-packages
  echo 'import site; site.addsitedir("/usr/local/lib/python2.7/site-packages")' >> /Users/zuck016/.local/lib/python3.6/site-packages/homebrew.pth
==> Summary
🍺  /usr/local/Cellar/numpy/1.13.1: 449 files, 9.9MB
==> Installing rdkit/rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2017_03_3.tar.gz
==> Downloading from https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2017
######################################################################### 100.0%
==> cmake -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -D
==> make
Last 15 lines from /Users/zuck016/Library/Logs/Homebrew/rdkit/02.make:
cd /tmp/rdkit-20170728-16798-1i2b96u/rdkit-Release_2017_03_3/Code/DataStructs && /usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -isystem /usr/local/include -I/tmp/rdkit-20170728-16798-1i2b96u/rdkit-Release_2017_03_3/Code -I/usr/local/include/eigen3  -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.12 -fPIC   -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /tmp/rdkit-20170728-16798-1i2b96u/rdkit-Release_2017_03_3/Code/DataStructs/FPBReader.cpp
cd /tmp/rdkit-20170728-16798-1i2b96u/rdkit-Release_2017_03_3/Code/Catalogs && /usr/local/Cellar/cmake/3.9.0/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.2017.03.3.dylib ../../lib/libRDKitCatalogs.1.dylib ../../lib/libRDKitCatalogs.dylib
[ 10%] Built target Catalogs
[ 10%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o
cd /tmp/rdkit-20170728-16798-1i2b96u/rdkit-Release_2017_03_3/Code/DataStructs && /usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -isystem /usr/local/include -I/tmp/rdkit-20170728-16798-1i2b96u/rdkit-Release_2017_03_3/Code -I/usr/local/include/eigen3  -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.12 -fPIC   -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /tmp/rdkit-20170728-16798-1i2b96u/rdkit-Release_2017_03_3/Code/DataStructs/MultiFPBReader.cpp
1 error generated.
make[2]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o] Error 1
make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 10%] Linking CXX shared library ../../lib/libRDKitDataStructs.dylib
cd /tmp/rdkit-20170728-16798-1i2b96u/rdkit-Release_2017_03_3/Code/DataStructs && /usr/local/Cellar/cmake/3.9.0/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.12 -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2017.3.3 -o ../../lib/libRDKitDataStructs.2017.03.3.dylib -install_name /tmp/rdkit-20170728-16798-1i2b96u/rdkit-Release_2017_03_3/lib/libRDKitDataStructs.1.dylib CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.2017.03.3.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib 
cd /tmp/rdkit-20170728-16798-1i2b96u/rdkit-Release_2017_03_3/Code/DataStructs && /usr/local/Cellar/cmake/3.9.0/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.2017.03.3.dylib ../../lib/libRDKitDataStructs.1.dylib ../../lib/libRDKitDataStructs.dylib
[ 10%] Built target DataStructs
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/rdkit/homebrew-rdkit/issues

These open issues may also help:
Installing RDKit on Mac OSX 10.10.2 with java and inchi https://github.com/rdkit/homebrew-rdkit/issues/25
greglandrum commented 7 years ago

Just out of curiosity: It looks you're using anaconda python; is there some reason that you don't install the RDKit using conda install -c rdkit rdkit?

djinnome commented 7 years ago

Yay, thanks, that worked!

After sending the bug report, I was trying to follow the instructions in https://github.com/rdkit/conda-rdkit but that also seems to be the wrong way to do it. I was getting hung up with the following error:

ld: library not found for -lpython3.6

But just doing the simple conda install -c rdkit rdkit

worked just fine. Forgive my ignorance, but this simple installation wasn't well documented on the rdkit.org web page, or the rdkit github page. I finally found it by going here:

http://rdkit.readthedocs.io/en/latest/Install.html#cross-platform-under-anaconda-python-fastest-install

From: Greg Landrum notifications@github.com<mailto:notifications@github.com> Reply-To: rdkit/homebrew-rdkit reply@reply.github.com<mailto:reply@reply.github.com> Date: Friday, July 28, 2017 at 12:09 PM To: rdkit/homebrew-rdkit homebrew-rdkit@noreply.github.com<mailto:homebrew-rdkit@noreply.github.com> Cc: "Zucker, Jeremy D" jeremy.zucker@pnnl.gov<mailto:jeremy.zucker@pnnl.gov>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [rdkit/homebrew-rdkit] Install fails (#28)

Just out of curiosity: It looks you're using anaconda python; is there some reason that you don't install the RDKit using conda install -c rdkit rdkit?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/rdkit/homebrew-rdkit/issues/28#issuecomment-318724540, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AAIzUhBS25MrtN2juc08lw-GjeUok_q5ks5sSiPEgaJpZM4GP8-L.

UnixJunkie commented 5 years ago

this can be closed