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/
Keywords:	chemistry modeling science
Licenses:	BSD
Conflicts:	rdkit-git, rdkit-python2
Provides:	rdkit
Submitter:	None
Maintainer:	hseara (vedranmiletic)
Last Packager:	vedranmiletic
Votes:	7
Popularity:	0.000000
First Submitted:	2011-03-26 18:34 (UTC)
Last Updated:	2024-04-08 05:02 (UTC)

Latest Comments

lllf commented on 2024-04-02 00:13 (UTC)

Update to 2024_03_01 fixes any hash check problems during build.

# Maintainer: Hector Mtz-Seara <hseara # gmail.com>
# Maintainer: Vedran Miletic <vedran AT miletic DOT net>
# Contributor: Samo Turk <samo.turk@gmail.com>
pkgname=rdkit
pkgver=2024_03_1
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=(
    '5afe78c3d3358fec83f891eb822c0ad07a40ce3709da58071892bce1ea56585b'
)
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 
}

lllf commented on 2024-03-08 01:10 (UTC)

prepare() {
  sed -i 's/850b0df852f1cda4970887b540f8f333/b7fd0df73ad4637504432d72a0accb8f/g' ${srcdir}/${pkgname}-Release_${pkgver}/Code/GraphMol/MolDraw2D/CMakeLists.txt
}

Fixes the font checksum issue

AlexBocken commented on 2024-02-29 09:05 (UTC)

The package currently doesn't build due to an incorrect checksum for Comic Neue. Could you please manually patch this in prepare()?

CMake Warning (dev) at Code/GraphMol/FilterCatalog/CMakeLists.txt:8 (find_package):
  Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
  are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
  the cmake_policy command to set the policy and suppress this warning.

This warning is for project developers.  Use -Wno-dev to suppress it.

Downloading https://fonts.google.com/download?family=Comic%20Neue...
CMake Error at Code/cmake/Modules/RDKitUtils.cmake:257 (MESSAGE):
  The md5 checksum for
  /home/alex/.cache/paru/clone/rdkit/src/rdkit-Release_2023_09_2/Code/GraphMol/MolDraw2D/Comic_Neue.zip
  is incorrect; expected: 850b0df852f1cda4970887b540f8f333, found:
  b7fd0df73ad4637504432d72a0accb8f
Call Stack (most recent call first):
  Code/GraphMol/MolDraw2D/CMakeLists.txt:21 (downloadAndCheckMD5)


-- Configuring incomplete, errors occurred!
==> ERROR: A failure occurred in build().
    Aborting...

Package builds fine if you just swap these md5sums.

vedranmiletic commented on 2023-05-22 11:59 (UTC)

Based on my experience with GCC 13.1 on Arch, RDKit likely needs the patch from this pull request: https://github.com/rdkit/rdkit/pull/6338

diff --git a/Code/RDGeneral/RDLog.h b/Code/RDGeneral/RDLog.h
index 83b04d29a..89ef38cce 100644
--- a/Code/RDGeneral/RDLog.h
+++ b/Code/RDGeneral/RDLog.h
@@ -20,6 +20,7 @@
 #include <iostream>
 #include <fstream>
 #include <vector>
+#include <cstdint>

 namespace boost {
 namespace logging {

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

1 2 3 Next › Last »

Arch Linux User Repository

Search Criteria

Package Details: rdkit 2024_03_1-1

Package Actions

Dependencies (10)

Required by (1)

Sources (1)