From f5eb9fb50199f25597cdc08f078962698c49dfc4 Mon Sep 17 00:00:00 2001 From: Carlos Bederián Date: Wed, 4 May 2022 01:24:15 -0300 Subject: autodock-vina: add versions up to v1.2.3, fixes (#30443) * C++ package, use spack_cxx * download from github, add 1.2.x versions * remove patches already present in 1.1.2-boost-new release * specify boost dependencies --- .../builtin/packages/autodock-vina/main.patch | 29 ---------------------- .../builtin/packages/autodock-vina/package.py | 26 ++++++++----------- .../builtin/packages/autodock-vina/split.patch | 29 ---------------------- 3 files changed, 10 insertions(+), 74 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/autodock-vina/main.patch delete mode 100644 var/spack/repos/builtin/packages/autodock-vina/split.patch diff --git a/var/spack/repos/builtin/packages/autodock-vina/main.patch b/var/spack/repos/builtin/packages/autodock-vina/main.patch deleted file mode 100644 index aafd780f64..0000000000 --- a/var/spack/repos/builtin/packages/autodock-vina/main.patch +++ /dev/null @@ -1,29 +0,0 @@ ---- autodock_vina_1_1_2/src/main/main.cpp 2011-05-11 15:35:00.000000000 -0500 -+++ autodock_vina_1_1_2/src/main/main.cpp 2017-09-11 10:06:44.939452217 -0500 -@@ -47,7 +47,7 @@ - using boost::filesystem::path; - - path make_path(const std::string& str) { -- return path(str, boost::filesystem::native); -+ return path(str); - } - - void doing(int verbosity, const std::string& str, tee& log) { -@@ -661,7 +661,7 @@ - cpu, seed, verbosity, max_modes_sz, energy_range, log); - } - catch(file_error& e) { -- std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n"; -+ std::cerr << "\n\nError: could not open \"" << e.name.filename() << "\" for " << (e.in ? "reading" : "writing") << ".\n"; - return 1; - } - catch(boost::filesystem::filesystem_error& e) { -@@ -673,7 +673,7 @@ - return 1; - } - catch(parse_error& e) { -- std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n'; -+ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.filename() << "\": " << e.reason << '\n'; - return 1; - } - catch(std::bad_alloc&) { diff --git a/var/spack/repos/builtin/packages/autodock-vina/package.py b/var/spack/repos/builtin/packages/autodock-vina/package.py index e2f29465e6..bc0a2b9ac5 100644 --- a/var/spack/repos/builtin/packages/autodock-vina/package.py +++ b/var/spack/repos/builtin/packages/autodock-vina/package.py @@ -7,27 +7,23 @@ import sys from spack import * -from spack.pkg.builtin.boost import Boost class AutodockVina(MakefilePackage): """AutoDock Vina is an open-source program for doing molecular docking""" homepage = "http://vina.scripps.edu/" - url = "http://vina.scripps.edu/download/autodock_vina_1_1_2.tgz" + url = "https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v1.2.3.tar.gz" - version('1_1_2', sha256='b86412d316960b1e4e319401719daf57ff009229d91654d623c3cf09339f6776') + version('1.2.3', sha256='22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0') + version('1.2.2', sha256='b9c28df478f90d64dbbb5f4a53972bddffffb017b7bb58581a1a0034fff1b400') + version('1.2.1', sha256='2d8d9871a5a95265c03c621c0584d9f06b202303116e6c87e23c935f7b694f74') + version('1.2.0', sha256='9c9a85766b4d124d7c1d92e767aa8b4580c6175836b8aa2c28f88a9c40a5b90e') + version('1.1.2', sha256='65422b2240c75d40417872a48e98043e7a7c435300dc8490af0c1f752f1ca4a2', + url='https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v1.1.2-boost-new.tar.gz') - depends_on('boost@1.65.0') - - # TODO: replace this with an explicit list of components of Boost, - # for instance depends_on('boost +filesystem') - # See https://github.com/spack/spack/pull/22303 for reference - depends_on(Boost.with_default_variants) - - # Replacing depecrated function call of boost with current function call - patch('main.patch') - patch('split.patch') + depends_on('boost@1.50.0:1.75.0 +filesystem +program_options +serialization +system +thread', when='@1.1.2') + depends_on('boost@1.54.0: +filesystem +program_options +serialization +system +thread', when='@1.2.0:') @property def build_directory(self): @@ -42,9 +38,7 @@ class AutodockVina(MakefilePackage): makefile.filter('BOOST_INCLUDE = .*', 'BOOST_INCLUDE = %s' % self.spec['boost'].prefix.include) makefile.filter('C_PLATFORM=.*', 'C_PLATFORM=-pthread') - makefile.filter('GPP=.*', 'GPP=%s' % spack_cc) - mcp = FileFilter('../../makefile_common') - mcp.filter('LIBS = ', 'LIBS = -l stdc++ -lm ') + makefile.filter('GPP=.*', 'GPP=%s' % spack_cxx) def build(self, spec, prefix): with working_dir(self.build_directory): diff --git a/var/spack/repos/builtin/packages/autodock-vina/split.patch b/var/spack/repos/builtin/packages/autodock-vina/split.patch deleted file mode 100644 index e369d62216..0000000000 --- a/var/spack/repos/builtin/packages/autodock-vina/split.patch +++ /dev/null @@ -1,29 +0,0 @@ ---- autodock_vina_1_1_2/src/split/split.cpp 2011-05-11 15:35:00.000000000 -0500 -+++ autodock_vina_1_1_2/src/split/split.cpp 2017-09-11 10:06:44.933452243 -0500 -@@ -38,7 +38,7 @@ - using boost::filesystem::path; - - path make_path(const std::string& str) { -- return path(str, boost::filesystem::native); -+ return path(str); - } - - std::string default_prefix(const std::string& input_name, const std::string& add) { -@@ -208,7 +208,7 @@ - write_multimodel_pdbqt(tmp, ligand_prefix, flex_prefix); - } - catch(file_error& e) { -- std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n"; -+ std::cerr << "\n\nError: could not open \"" << e.name.filename() << "\" for " << (e.in ? "reading" : "writing") << ".\n"; - return 1; - } - catch(boost::filesystem::filesystem_error& e) { -@@ -220,7 +220,7 @@ - return 1; - } - catch(parse_error& e) { -- std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n'; -+ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.filename() << "\": " << e.reason << '\n'; - return 1; - } - catch(std::bad_alloc&) { -- cgit v1.2.3-70-g09d2