Arch Linux User Repository

catch2 is missing in makedepends

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 
}

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

Fixes the font checksum issue

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.

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 {

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

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 
}

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

/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???