Package Details: rdkit 2019_09_3-1

Git Clone URL: https://aur.archlinux.org/rdkit.git (read-only, click to copy)
Package Base: rdkit
Description: RDKit - A collection of cheminformatics and machine-learning software written in C++ and Python.
Upstream URL: http://rdkit.org/
Licenses: BSD
Conflicts: rdkit-git, rdkit-python2
Provides: rdkit
Submitter: None
Maintainer: Athemis
Last Packager: Athemis
Votes: 6
Popularity: 0.000040
First Submitted: 2011-03-26 18:34
Last Updated: 2020-02-20 09:36

Latest Comments

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riteme commented on 2020-06-06 03:30

Consider adding -DRDK_BUILD_CPP_TESTS=OFF to cmake. Some tests got compile errors on my system (Manjaro, GCC 10.1.0). Meanwhile, CMakeLists.txt says "disabling (it) can speed up builds".

dviktor commented on 2020-02-19 17:18

Please update PKGBUILD:

--- PKGBUILD.old    2020-02-19 20:17:30.912687743 +0300
+++ PKGBUILD    2020-02-19 20:16:58.946353419 +0300
@@ -1,31 +1,38 @@
 # Maintainer: Samo Turk <samo.turk@gmail.com> 
+
 pkgname=rdkit
-_pkgname=RDKit
-pkgver=2019_09_1
+pkgver=2019_09_3
 pkgrel=1
 pkgdesc="RDKit - A collection of cheminformatics and machine-learning software written in C++ and Python."
 arch=("i686" "x86_64" "armv7h")
 url="http://rdkit.org/"
-license=('New BSD License')
-depends=( 'bison' 'boost' 'boost-libs' 'cmake' 'flex' 'python' 'python-numpy' 'sqlite3' 'python-cairocffi' 'python-pillow' 'eigen3' )
+license=(custom)
+depends=(python python-numpy boost boost-libs sqlite cairo eigen)
+makedepends=('gcc>=4.8' 'clang>=3.9' 'cmake>=3.1')
 source=("https://github.com/rdkit/rdkit/archive/Release_${pkgver}.tar.gz")
-sha256sums=('bfcb3c094cd0e7ec6fbebacde71f29f61df71601eb3d577eb295fd45771513eb')
-conflicts=('rdkit-python2' 'rdkit-git')
+sha256sums=('88bbc298eb6c17584471b17a34e202b1da3d59d92ea5b6b6dcda635b739f76f2')
+conflicts=(rdkit-git)
+provides=(rdkit)

 build() {
   cd ${srcdir}/${pkgname}-Release_${pkgver}
-  cmake . \
+
+  mkdir -p build
+  cd build
+
+  cmake .. \
     -DCMAKE_BUILD_TYPE=Release \
-    -DRDK_INSTALL_INTREE=0 \
+    -DRDK_INSTALL_INTREE=OFF \
     -DCMAKE_INSTALL_PREFIX=/usr \
-    -DPYTHON_LIBRARY=/usr/lib/libpython3.7m.so \
-    -DPYTHON_INCLUDE_DIR=/usr/include/python3.7m/ \
-    -DPYTHON_EXECUTABLE=/usr/bin/python \
-    -DRDK_BUILD_INCHI_SUPPORT=OFF
+    -DBoost_NO_BOOST_CMAKE=ON \
+    -DRDK_BUILD_INCHI_SUPPORT=OFF \
+    -DRDK_BUILD_CAIRO_SUPPORT=ON
+
   make
 }

 package() {
-  cd ${srcdir}/${pkgname}-Release_${pkgver}
+  cd ${srcdir}/${pkgname}-Release_${pkgver}/build
+
   make DESTDIR=${pkgdir} install 
 }

tyaur27182 commented on 2018-08-06 17:12

Arch updated the Python3 upstream to version 3.7, breaking the RDKit build. I got it to rebuild by changing the -DPYTHON_LIBRARY and -DPYTHON_INCLUDE_DIR to 3.7 instead of 3.6 in the PKGBUILD. This seems to have fixed it.

Athemis commented on 2018-06-06 12:24

@yoowul: Thanks, this has been fixed + bump to current release (2018_03_2)

yoowul commented on 2018-06-05 13:39

This fails to build:

:: Checking rdkit integrity...
==> ERROR: conflicts contains invalid characters: ','
:: failed to verify rdkit integrity

samoturk commented on 2016-02-01 13:13

Weird inchi support works fine for me.. But you are right should be with src. I will rebuild rdkit and rdkit-git packages today and report back.

UPDATE:
rdkit and rdkit-git compile and have working inchi support. Though there some boost related bugs: https://github.com/rdkit/rdkit/issues/738 and an issue with Jupyter: https://github.com/rdkit/rdkit/issues/666

davvelsan commented on 2016-01-27 11:45

Just tried and it does not seem to work yet. Looking at the PKGBUILD, I believe the cause may be this command:

cp INCHI-1-API/INCHI_API/inchi_dll/* ${pkgname}-Release_${pkgver}/External/INCHI-API/

which according to the github docs (https://github.com/rdkit/rdkit/tree/master/External/INCHI-API) should be:

cp INCHI-1-API/INCHI_API/inchi_dll/* ${pkgname}-Release_${pkgver}/External/INCHI-API/src

I'll try modifying the build later when I get the chance, see if that works.

Alternatively, it seems we can now use the included script "$ bash download-inchi.sh" to do this for us prior to compilation. However, I rather prefer the manual solution that you used as well.


------------ EDIT

Yep, that seems to be it. I had to create the src/ dir as well, though, since it wasn't there like the docs say.

Now I am having a different problem, which I believe might be related to the 1.6.x version of lib-boost. I'm leaving it here for future reference, but this is something to be reported elsewhere I'm afraid.

"No to_python (by-value) converter found for C++ type: boost::shared_ptr<RDKit::ROMol>"

Thanks for your efforts to add InChi support, hopefully I'll get it to work eventually.

samoturk commented on 2016-01-07 13:06

I added InChi support.

davvelsan commented on 2016-01-04 14:09

Any chance to compile this with InChI support?

From the install page (http://www.rdkit.org/docs/Install.html):
"If you would like to install the RDKit InChI support (first available in the Q2 2011 release), follow the instructions in $RDBASE/External/INCHI-API to get a copy of the InChI source and put it in the appropriate place."

More info here:
https://github.com/rdkit/rdkit/tree/master/External/INCHI-API

samoturk commented on 2014-11-04 14:28

PKGBUILD for python 2.7:
https://gist.github.com/samoturk/32e36597f0b4aac51ba0

and for python 3.4:
https://gist.github.com/samoturk/4af7b0695c9b9bb937bc