commit: bf5dd7c748cd41b6fa540780d668045d1836db0b Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in> AuthorDate: Tue Jan 9 10:19:33 2024 +0000 Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in> CommitDate: Tue Jan 9 10:19:50 2024 +0000 URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=bf5dd7c7
sci-biology/cmdock: fix build Closes: https://bugs.gentoo.org/901345 Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in> sci-biology/cmdock/cmdock-0.2.0-r1.ebuild | 119 ++++++++++++++++++++ .../cmdock/files/cmdock-0.2.0-cxxopts.patch | 122 +++++++++++++++++++++ .../cmdock/files/cmdock-0.2.0-include.patch | 19 ++++ 3 files changed, 260 insertions(+) diff --git a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild new file mode 100644 index 0000000000..e01a7ecf70 --- /dev/null +++ b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild @@ -0,0 +1,119 @@ +# Copyright 2021-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +BOINC_APP_OPTIONAL="true" +inherit boinc-app flag-o-matic meson optfeature python-any-r1 + +DESCRIPTION="Program for docking ligands to proteins and nucleic acids" +HOMEPAGE="https://gitlab.com/Jukic/cmdock"; +SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.bz2"; +S="${WORKDIR}/${PN}-v${PV}" + +LICENSE="LGPL-3 ZLIB" +SLOT="0/${PV}" +KEYWORDS="~amd64" +IUSE="apidoc boinc cpu_flags_x86_sse2 doc test" + +# Flaky tests +RESTRICT="test" + +RDEPEND=" + boinc? ( sci-misc/boinc-wrapper ) +" +DEPEND=" + dev-cpp/eigen:3 + >=dev-cpp/indicators-2.3-r1 + >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1 + >=dev-libs/cxxopts-3 +" +BDEPEND=" + apidoc? ( + app-doc/doxygen + dev-texlive/texlive-fontutils + ) + doc? ( + $(python_gen_any_dep ' + dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}] + dev-python/sphinx[${PYTHON_USEDEP}] + ') + ) + test? ( ${PYTHON_DEPS} ) +" + +PATCHES=( + "${FILESDIR}"/${P}-include.patch + "${FILESDIR}"/${P}-cxxopts.patch +) + +DOCS=( README.md changelog.md ) + +BOINC_MASTER_URL="https://www.sidock.si/sidock/"; +BOINC_INVITATION_CODE="Crunch_4Science" +BOINC_APP_HELPTEXT=\ +"The easiest way to do something useful with this application +is to attach it to SiDock@home BOINC project." + +INSTALL_PREFIX="${EPREFIX}/opt/${P}" + +python_check_deps() { + use doc || return 0 + + python_has_version "dev-python/sphinx[${PYTHON_USEDEP}]" && + python_has_version "dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]" +} + +foreach_wrapper_job() { + sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die +} + +src_prepare() { + default + python_fix_shebang "${S}"/bin +} + +src_configure() { + # very weird directory layout + local emesonargs=( + --prefix="${INSTALL_PREFIX}" + $(meson_use apidoc) + $(meson_use doc) + $(meson_use test tests) + -Ddocdir="${EPREFIX}"/usr/share/doc/${PF} + ) + meson_src_configure + + use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE" +} + +src_install() { + meson_src_install + python_optimize "${D}${INSTALL_PREFIX}"/bin + + if use boinc; then + doappinfo "${FILESDIR}"/app_info_${PV}.xml + dowrapper cmdock-l + + # install cmdock executable + exeinto "$(get_project_root)" + exeopts --owner root --group boinc + newexe "${D}${INSTALL_PREFIX}"/bin/cmdock cmdock-${PV} + + # install a blank file + touch "${T}"/docking_out || die + insinto "$(get_project_root)" + insopts --owner root --group boinc + doins "${T}"/docking_out + fi +} + +pkg_postinst() { + optfeature "sdtether.py and sdrmsd.py scripts" "dev-python/numpy sci-chemistry/openbabel[python]" + use boinc && boinc-app_pkg_postinst +} + +pkg_postrm() { + use boinc && boinc-app_pkg_postrm +} diff --git a/sci-biology/cmdock/files/cmdock-0.2.0-cxxopts.patch b/sci-biology/cmdock/files/cmdock-0.2.0-cxxopts.patch new file mode 100644 index 0000000000..4d7f227957 --- /dev/null +++ b/sci-biology/cmdock/files/cmdock-0.2.0-cxxopts.patch @@ -0,0 +1,122 @@ +Update to cxxopts 3.0 + +--- a/meson.build ++++ b/meson.build +@@ -40,7 +40,7 @@ if cpp_compiler.get_id() == 'msvc' + message('Applying workaround for MSVC by adding flag /Zc:twoPhase-: https://stackoverflow.com/questions/56782470/why-do-i-have-warning-c4199-two-phase-name-lookup-is-not-supported-for-c-cli') + endif + +-cxxopts_dep = dependency('cxxopts', fallback : ['cxxopts', 'cxxopts_dep']) ++cxxopts_dep = dependency('cxxopts', version : '>=3.0', fallback : ['cxxopts', 'cxxopts_dep']) + eigen3_dep = dependency('eigen3', fallback : ['eigen', 'eigen_dep']) + openmp_dep = dependency('openmp', required : false) + +diff --git a/src/exe/cmcavity.cxx b/src/exe/cmcavity.cxx +index 427d3c0..3a5c747 100644 +--- a/src/exe/cmcavity.cxx ++++ b/src/exe/cmcavity.cxx +@@ -41,7 +41,7 @@ void PrintHeaderAddon(std::ostream &outputStream) { + // MAIN PROGRAM STARTS HERE + ///////////////////////////////////////////////////////////////////// + +-int main(int argc, char *argv[]) { ++int main(const int argc, const char *argv[]) { + // Handle obsolete arguments, if any + for (int i = 0; i < argc; i++) { + std::string opt = argv[i]; +@@ -451,7 +451,7 @@ int main(int argc, char *argv[]) { + + logFile.close(); + } +- } catch (const cxxopts::OptionException &e) { ++ } catch (const cxxopts::exceptions::exception &e) { + std::cout << "Error parsing options: " << e.what() << std::endl; + return 1; + } catch (RbtError &e) { +@@ -463,4 +463,4 @@ int main(int argc, char *argv[]) { + _RBTOBJECTCOUNTER_DUMP_(std::cout) + + return 0; +-} +\ No newline at end of file ++} +diff --git a/src/exe/cmdock.cxx b/src/exe/cmdock.cxx +index 10e18ca..86bbff1 100644 +--- a/src/exe/cmdock.cxx ++++ b/src/exe/cmdock.cxx +@@ -80,7 +80,7 @@ void printHelpFooter() { + // MAIN PROGRAM STARTS HERE + ///////////////////////////////////////////////////////////////////// + +-int main(int argc, char *argv[]) { ++int main(const int argc, const char *argv[]) { + // Handle premature termination + signal (SIGINT, terminator); + +@@ -941,7 +941,7 @@ int main(int argc, char *argv[]) { + log << "Thank you for using " << Rbt::GetProgramName() << " " + << Rbt::GetVersion() << "." << std::endl; + logFile.close(); +- } catch (const cxxopts::OptionException &e) { ++ } catch (const cxxopts::exceptions::exception &e) { + std::cout << "Error parsing options: " << e.what() << std::endl; + return 1; + } catch (RbtError &e) { +@@ -953,4 +953,4 @@ int main(int argc, char *argv[]) { + _RBTOBJECTCOUNTER_DUMP_(std::cout) + + return 0; +-} +\ No newline at end of file ++} +diff --git a/src/exe/cmmoegrid.cxx b/src/exe/cmmoegrid.cxx +index 4bff8f3..bf74b52 100644 +--- a/src/exe/cmmoegrid.cxx ++++ b/src/exe/cmmoegrid.cxx +@@ -57,7 +57,7 @@ RbtModelList CreateProbes(std::string anAtomTypeStr) { + // MAIN PROGRAM STARTS HERE + ///////////////////////////////////////////////////////////////////// + +-int main(int argc, char *argv[]) { ++int main(const int argc, const char *argv[]) { + std::cout.setf(std::ios_base::left, std::ios_base::adjustfield); + + // Strip off the path to the executable, leaving just the file name +@@ -268,7 +268,7 @@ int main(int argc, char *argv[]) { + } + std::cout << "done." << std::endl; + } +- } catch (const cxxopts::OptionException &e) { ++ } catch (const cxxopts::exceptions::exception &e) { + std::cout << "Error parsing options: " << e.what() << std::endl; + return 1; + } catch (RbtError &e) { +diff --git a/src/exe/cmzip.cxx b/src/exe/cmzip.cxx +index 1d1f69a..043d7be 100644 +--- a/src/exe/cmzip.cxx ++++ b/src/exe/cmzip.cxx +@@ -504,7 +504,7 @@ void rescue(cxxopts::ParseResult result){ + } + + // ENTRY POINT +-int main(int argc, char *argv[]) { ++int main(const int argc, const char *argv[]) { + // Handle premature termination + signal (SIGINT, terminator); + +@@ -580,7 +580,7 @@ Use this if CmDock terminates prematurely. CmZIP will search for records in the + return 0; + } + +- } catch (const cxxopts::OptionException &e) { ++ } catch (const cxxopts::exceptions::exception &e) { + std::cout << "Error parsing options: " << e.what() << std::endl; + return 1; + } catch (const std::exception &exc) { +@@ -589,4 +589,4 @@ Use this if CmDock terminates prematurely. CmZIP will search for records in the + /*} catch (...) { + std::cout << "Unknown exception" << std::endl; + }*/ +-} +\ No newline at end of file ++} diff --git a/sci-biology/cmdock/files/cmdock-0.2.0-include.patch b/sci-biology/cmdock/files/cmdock-0.2.0-include.patch new file mode 100644 index 0000000000..b4a6e80bb0 --- /dev/null +++ b/sci-biology/cmdock/files/cmdock-0.2.0-include.patch @@ -0,0 +1,19 @@ +Rbt.cxx: Add missing include + +--- a/src/lib/Rbt.cxx ++++ b/src/lib/Rbt.cxx +@@ -15,6 +15,7 @@ + #include <algorithm> //For sort + #include <climits> //For PATH_MAX + #include <cstdlib> //For getenv ++#include <cstdint> //For int types + #include <ctime> //For time functions + #include <dirent.h> //For directory handling + #include <fstream> //For ifstream +@@ -581,4 +582,4 @@ bool Rbt::endsWith (std::string const &fullString, std::string const &ending) { + } else { + return false; + } +-} +\ No newline at end of file ++}
