AUR (en) - rdkit

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:	hseara
Last Packager:	hseara
Votes:	7
Popularity:	0.000000
First Submitted:	2011-03-26 18:34 (UTC)
Last Updated:	2022-12-14 16:08 (UTC)

Latest Comments

zsurnz commented on 2022-05-29 18:05 (UTC)

This version fails to compile with the current PKGBUILD. However, it does work if -DRDK_BUILD_CPP_TESTS=OFF is reintroduced.

lllf commented on 2022-03-15 23:45 (UTC)

Based on the solution from the ticket: https://github.com/rdkit/rdkit/issues/5089

Add a new file patch-catch2.diff

diff --git a/External/catch/CMakeLists.txt b/External/catch/CMakeLists.txt
index c3cad01993..5a7ed5c1b7 100644
--- a/External/catch/CMakeLists.txt
+++ b/External/catch/CMakeLists.txt
@@ -12,10 +12,10 @@ elseif(EXISTS "${CATCH_DIR}/single_include/catch2/catch.hpp")
 else()
   message("-- Catch not found in ${CATCH_DIR}")
   include(RDKitUtils)
-  set(RELEASE_NO "2.12.4")
+  set(RELEASE_NO "2.13.8")
   downloadAndCheckMD5("https://github.com/catchorg/Catch2/archive/v${RELEASE_NO}.tar.gz"
         "${CMAKE_CURRENT_SOURCE_DIR}/v${RELEASE_NO}.tar.gz"
-        "dbe4fa691e37dd51256876641a821ec8")
+        "3639fb4cb8020de0dcf1fd5addb39418")
   execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
     ${CMAKE_CURRENT_SOURCE_DIR}/v${RELEASE_NO}.tar.gz
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})

Update PKGBUILD

# Old Maintainer: Samo Turk <samo.turk@gmail.com>
# Maintainer: Hector Mtz-Seara <hseara # gmail.com>
pkgname=rdkit
pkgver=2021_09_4
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=('BSD')
depends=(python python-numpy python-cairocffi python-pillow boost boost-libs sqlite cairo eigen)
makedepends=('cmake>=3.1')
source=("https://github.com/rdkit/rdkit/archive/Release_${pkgver}.tar.gz" "patch-catch2.diff")
sha256sums=('ce192e85bbdc1dcf24d327197229099c8625ee20ef022fcbd980791fdbfc7203' 'SKIP')
conflicts=('rdkit-python2' 'rdkit-git')
provides=(rdkit)

build() {
  cd ${srcdir}/${pkgname}-Release_${pkgver}
  sed -i 's/23ed3f833c1ae0adb141a26b4a30d73e/850b0df852f1cda4970887b540f8f333/' ${srcdir}/${pkgname}-Release_${pkgver}/Code/GraphMol/MolDraw2D/CMakeLists.txt

  patch -p1 < ../../patch-catch2.diff
  rm -rf External/catch/*.tar.gz External/catch/catch

  mkdir -p build
  cd build

  cmake .. \
    -DCMAKE_BUILD_TYPE=Release \
    -DRDK_INSTALL_INTREE=OFF \
    -DCMAKE_INSTALL_PREFIX=/usr \
    -DRDK_BUILD_INCHI_SUPPORT=OFF \
    -DBoost_NO_BOOST_CMAKE=ON \
    -DRDK_BUILD_CAIRO_SUPPORT=ON
  make
}

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

hseara commented on 2022-03-13 13:00 (UTC)

@viniavila I submitted a bug report upstream (https://github.com/rdkit/rdkit/issues/5089)

viniavila commented on 2022-03-01 20:26 (UTC) (edited on 2022-03-01 20:28 (UTC) by viniavila)

/home/vinicius/Downloads/rdkit/src/rdkit-Release_2021_09_4/External/catch/catch/single_include/catch2/catch.hpp:10874:45: 
error: size of array ‘altStackMem’ is not an integral constant-expression
    10874 |     char FatalConditionHandler::altStackMem[sigStackSize] = {};
          |                                             ^~~~~~~~~~~~
    make[2]: *** 
[Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make:76: 
Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o] Erro 1
    make[1]: *** [CMakeFiles/Makefile2:4283: Code/Geometry/CMakeFiles/geometryTestsCatch.dir/all] Erro 2
    make: *** [Makefile:166: all] Erro 2
    ==> ERRO: Uma falha ocorreu em build().
        Abortando...

Any ideas???

hseara commented on 2022-01-28 11:00 (UTC)

Working new version:

pkgname=rdkit
pkgver=2021_09_4
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=('BSD')
depends=(python python-numpy python-cairocffi python-pillow boost boost-libs sqlite cairo eigen)
makedepends=('cmake>=3.1')
source=("https://github.com/rdkit/rdkit/archive/Release_${pkgver}.tar.gz")
sha256sums=('ce192e85bbdc1dcf24d327197229099c8625ee20ef022fcbd980791fdbfc7203')
conflicts=('rdkit-python2' 'rdkit-git')
provides=(rdkit)



build() {
  cd ${srcdir}/${pkgname}-Release_${pkgver}
  sed -i 's/23ed3f833c1ae0adb141a26b4a30d73e/850b0df852f1cda4970887b540f8f333/' ${srcdir}/${pkgname}-Release_${pkgver}/Code/GraphMol/MolDraw2D/CMakeLists.txt
  mkdir -p build
  cd build

  cmake .. \
    -DCMAKE_BUILD_TYPE=Release \
    -DRDK_INSTALL_INTREE=OFF \
    -DCMAKE_INSTALL_PREFIX=/usr \
    -DRDK_BUILD_INCHI_SUPPORT=OFF \
    -DBoost_NO_BOOST_CMAKE=ON \
    -DRDK_BUILD_CAIRO_SUPPORT=ON
  make
}

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

Please update

maximtrp commented on 2021-06-27 15:59 (UTC)

Here is PKGBUILD file for the new version (2021_03_3):

pkgname=rdkit
pkgver=2021_03_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=('BSD')
depends=(python python-numpy python-cairocffi python-pillow boost boost-libs sqlite cairo eigen)
makedepends=('cmake>=3.1')
source=("https://github.com/rdkit/rdkit/archive/Release_${pkgver}.tar.gz")
sha256sums=('e95f07adaee9280df077cb147210ee75e16957d81687ab0836d62ebf1f6f715f')
conflicts=('rdkit-python2' 'rdkit-git')
provides=(rdkit)

build() {
  cd ${srcdir}/${pkgname}-Release_${pkgver}

  mkdir -p build
  cd build

  cmake .. \
    -DCMAKE_BUILD_TYPE=Release \
    -DRDK_INSTALL_INTREE=OFF \
    -DCMAKE_INSTALL_PREFIX=/usr \
    -DRDK_BUILD_INCHI_SUPPORT=OFF \
    -DBoost_NO_BOOST_CMAKE=ON \
    -DRDK_BUILD_CAIRO_SUPPORT=ON
  make
}

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

ptrxyz commented on 2021-05-11 16:10 (UTC)

I'd also be interested in a new release/an update. Is this still maintained?

joanmanel commented on 2021-05-10 10:57 (UTC)

The installation seems to be OK, but I don't have rdkit.chem, is this normal? otherwise how can I get rdkit.chem?

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