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rdkit / homebrew-rdkit

Homebrew formula for rdkit
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Installation Error on Mac 10.15.2 #84

Closed jinserk closed 3 years ago

jinserk commented 4 years ago

I tried to install rdkit with brew and got an error:

$ brew install rdkit --with-python3 --with-inchi --with-avalon --with-postgresql --with-pycairo
==> Installing rdkit from rdkit/rdkit
Warning: A newer Command Line Tools release is available.
Update them from Software Update in System Preferences or
https://developer.apple.com/download/more/.

==> Installing dependencies for rdkit/rdkit/rdkit: py3cairo
==> Installing rdkit/rdkit/rdkit dependency: py3cairo
==> Downloading https://homebrew.bintray.com/bottles/py3cairo-1.18.2.catalina.bottle.tar.gz
######################################################################## 100.0%
==> Pouring py3cairo-1.18.2.catalina.bottle.tar.gz
�  /usr/local/Cellar/py3cairo/1.18.2: 16 files, 321.2KB
==> Installing rdkit/rdkit/rdkit --with-inchi --with-postgresql --with-avalon --with-pycairo --with-python3
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2019_09_1.tar.gz
Already downloaded: /Users/jinserk/Library/Caches/Homebrew/downloads/dbc78c6529381ce39a1c4765d1b16ec83572d3c1ad3cfde3d65efc15a6bfc66f--rdkit-Release_2019_09_1.tar.gz
==> cmake -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/rdkit/2019.09.1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-dev -DRDK_INSTA
==> make -j8
==> make install
Error: An exception occurred within a child process:
  Errno::ENOENT: No such file or directory @ rb_file_s_rename - (Code/PgSQL/rdkit/rdkit.sql91.in, Code/PgSQL/rdkit/rdkit--3.4.sql)

It's the same even though I don't give --with-postgresql option.

UnixJunkie commented 4 years ago

I am only sure about those two flags:

brew install rdkit --with-python3 --with-inchi

For --with-avalon --with-postgresql --with-pycairo, I have no idea of what they do and what they need as external dependencies.

jinserk commented 4 years ago

@UnixJunkie , the options are stated in the README.md.

UnixJunkie commented 4 years ago

Does the standard recipe that I provided just before works for you? Try inserting the exotic options one by one to figure which one is causing trouble.

UnixJunkie commented 3 years ago

You might try the new rdkit formula in brew master, they turn ON PGSQL by default.