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* science/qwalk: Correct the version: it is 1.0.1-300Yuri Victorovich2018-08-212-5/+6
| | | | Notes: svn path=/head/; revision=477706
* New port: science/qwalk: Quantum Monte Carlo package for quantum chemistry ↵Yuri Victorovich2018-08-216-0/+72
| | | | | | | computations Notes: svn path=/head/; revision=477701
* - Update to 1.0.4TAKATSU Tomonari2018-08-202-4/+4
| | | | Notes: svn path=/head/; revision=477639
* - Update to 1.0.3TAKATSU Tomonari2018-08-202-5/+11
| | | | | | | - Update LICENSE Notes: svn path=/head/; revision=477636
* science/qmcpack: Broken on 10Yuri Victorovich2018-08-201-0/+2
| | | | Notes: svn path=/head/; revision=477635
* New port: science/qmcpack: Many-body ab initio Quantum Monte Carlo code for ↵Yuri Victorovich2018-08-205-0/+72
| | | | | | | quantum chemstry Notes: svn path=/head/; revision=477634
* science/py-pymatgen: Update 2018.6.11 -> 2018.8.10Yuri Victorovich2018-08-202-5/+5
| | | | | | | Reported by: repology Notes: svn path=/head/; revision=477633
* New port: science/chrono: C++ library for multi-physics simulationYuri Victorovich2018-08-196-0/+1308
| | | | Notes: svn path=/head/; revision=477607
* Update to 1.9.5Sunpoet Po-Chuan Hsieh2018-08-182-6/+8
| | | | | | | Changes: https://code.mpimet.mpg.de/projects/cdo/news Notes: svn path=/head/; revision=477515
* science/py-spglib: Update 1.10.3.65 -> 1.10.4.1Yuri Victorovich2018-08-182-4/+4
| | | | | | | Reported by: repology Notes: svn path=/head/; revision=477482
* science/rdkit: Update 2018_03_3 -> 2018_03_4Yuri Victorovich2018-08-182-5/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=477479
* - Update to 0.9-27TAKATSU Tomonari2018-08-132-4/+4
| | | | Notes: svn path=/head/; revision=477058
* - Update to 1.7-0TAKATSU Tomonari2018-08-102-5/+4
| | | | Notes: svn path=/head/; revision=476824
* Set MAINTAINER of mine ports to @FreeBSD.org email.Gleb Popov2018-08-092-2/+2
| | | | | | | | Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D16640 Notes: svn path=/head/; revision=476747
* Re-add port: science/xdrawchem: Two-dimensional molecule drawing programYuri Victorovich2018-08-095-0/+220
| | | | Notes: svn path=/head/; revision=476726
* devel/boost-*: update to 1.68.0Jan Beich2018-08-0914-11/+14
| | | | | | | | | | | | - Switch to C++14 for libboost_system to support C++14 consumers Changes: http://www.boost.org/users/history/version_1_68_0.html PR: 229569 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D16165 Notes: svn path=/head/; revision=476723
* science/spglib: Update 1.10.3 -> 1.10.4Yuri Victorovich2018-08-082-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=476693
* Remove broken and expired port which also depends on clang38 (on 10).Brooks Davis2018-08-0810-7766/+0
| | | | Notes: svn path=/head/; revision=476658
* Switch to xorgproto instead of individual packagesNiclas Zeising2018-07-311-2/+2
| | | | | | | | | | | | | | | | | | | | | Upstream used to distribute protocol headers as separate packages, but has decided to merge those to a common package, named xorgproto. This update tracks that change. * Add a new port, x11/xorgproto, with are protocol headers for xorg. * Hook the new protocol port to the build and to infrastructure in bsd.xorg.mk. * Update all ports with a dependency on any of the old *proto packages to instead depend on xorgproto. Bump portrevision. * Delete the old *proto packages, update MOVED. PR: 230023 Submitted by: zeising Approved by: portmgr (antoine) exp-run by: antoine Notes: svn path=/head/; revision=476013
* science/py-scikit-learn: update to 0.19.2Ruslan Makhmatkhanov2018-07-302-5/+4
| | | | | | | | | | | | | This release adds support for python 3.7 Changelog: http://scikit-learn.org/stable/whats_new.html#version-0-19-2 PR: 230180 Approved by: demon (maintainer) Notes: svn path=/head/; revision=475875
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-07-2961-44/+61
| | | | | | | | | | | | | | | | | in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which has now moved from GCC 6 to GCC 7 by default. This includes ports - featuring USE_GCC=yes or USE_GCC=any, - featuring USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and those - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x, c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib. PR: 222542 Notes: svn path=/head/; revision=475857
* Update WWWSunpoet Po-Chuan Hsieh2018-07-291-1/+1
| | | | | | | Approved by: portmgr (blanket) Notes: svn path=/head/; revision=475828
* Update to 1.14.4Sunpoet Po-Chuan Hsieh2018-07-292-5/+4
| | | | | | | Changes: https://github.com/pysal/pysal/releases Notes: svn path=/head/; revision=475761
* science/abinit: Update 8.8.3 -> 8.8.4Yuri Victorovich2018-07-282-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=475613
* science/ALPSCore: Update 2.1.1 -> 2.2.0Yuri Victorovich2018-07-284-16/+50
| | | | | | | | | | Now it is broken on 10. PR: 230010 Submitted by: Michael Danilov <mike.d.ft402@gmail.com> (maintainer) Notes: svn path=/head/; revision=475612
* Update math/libqalculate and math/qalculate to 2.6.1Jason E. Hale2018-07-272-1/+2
| | | | | | | Chase libqalculate shared library version bump Notes: svn path=/head/; revision=475421
* science/xcrysden: Add missing runtime dependenciesYuri Victorovich2018-07-271-1/+6
| | | | Notes: svn path=/head/; revision=475418
* science/libghemical: Fix C++11 errors on 12Yuri Victorovich2018-07-261-0/+1
| | | | | | | Add CXXFLAGS+=-Wno-c++11-narrowing Notes: svn path=/head/; revision=475349
* science/mpqc: Fix buildYuri Victorovich2018-07-243-41/+8
| | | | | | | | | | | Two fixes: * Force some stl-related define values because configured values are wrong * Force the C++-98 standard because of breakage on newer clangs/systems Reported by: fallout Notes: svn path=/head/; revision=475273
* science/psychopy: Update 1.90.2 -> 1.90.3Yuri Victorovich2018-07-222-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=475083
* science/mpqc: Unbreak on CURRENTYuri Victorovich2018-07-222-0/+40
| | | | | | | For some reason, STL's endl fail and need to be std::endl only on CURRENT. Notes: svn path=/head/; revision=475079
* science/paraview: Add patch to fix build with upcomeing cmake-3.12Tobias C. Berner2018-07-202-1/+14
| | | | | | | | | | | | | The behaviour of cmake's copy_directory was changed, so that it now fails if the source directory does not exist. Further add missing dependency on xmlpatterns. PR: 229854 Reported by: antoine Notes: svn path=/head/; revision=475037
* science/rdkit: Update 2018_03_2 -> 2018_03_3Yuri Victorovich2018-07-202-9/+4
| | | | | | | | Changelog: https://github.com/rdkit/rdkit/releases/tag/Release_2018_03_3 Notes: svn path=/head/; revision=474991
* New port: science/xcrysden: Crystalline and molecular structure ↵Yuri Victorovich2018-07-197-0/+530
| | | | | | | visualisation program Notes: svn path=/head/; revision=474971
* science/quantum-espresso: Add pseudo potential files because they are used ↵Yuri Victorovich2018-07-195-19/+273
| | | | | | | | | | | | | | in all calculations Port changes: * Download and install all pseudo potential files that are mentioned in any examples * Remove ALL_TARGET - it had a default value * Merge post-patch target into post-extract target * Add the run-examples target * Add DIST_SUBDIR because there are many distfiles Notes: svn path=/head/; revision=474956
* New port: science/quantum-espresso: Package for research in electronic ↵Yuri Victorovich2018-07-187-0/+181
| | | | | | | structure, simulation, optimization Notes: svn path=/head/; revision=474904
* science/libghemical: Use ${GCC_DEFAULT} in CONFIGURE_ENVYuri Victorovich2018-07-181-1/+1
| | | | | | | Improve the workaround line. Notes: svn path=/head/; revision=474844
* science/ghemical: Remove DEPRECATED/EXPIRATION_DATE labelsYuri Victorovich2018-07-182-5/+3
| | | | | | | | | | | libghemical isn't broken any more. Port changes: * Take maintainership * Add LICENSE_FILE Notes: svn path=/head/; revision=474835
* science/libghemical: Remove BROKEN/DEPRECATED labelsYuri Victorovich2018-07-182-6/+10
| | | | | | | | | | | | | | | The main cause of the breakage was a libary linkage problem in science/mpqc which is now fixed. Other port changes: * Add LICENSE/LICENSE_FILE * Add missing items to LIB_DEPENDS * Add workaround for the problem that configure fails due to the libgcc.so mismatch. By using CONFIGURE_ENV, preload libgcc.so from the gcc package. * Update WWW Notes: svn path=/head/; revision=474834
* science/mpqc: Fix library dependenciesYuri Victorovich2018-07-184-15/+40
| | | | | | | | | | | | | | | | | | | | | | | | Problems in this port caused the science/libghemical breakage (it was labeled as DEPRECATED). Two major fixes: * Fix the unknown 'backtrace' symbol: libexecinfo.so dependency was missing for libSCmisc.so * Fix broken libint.so: -L${LOCALBASE} was missing for libSCcints.so and libint.so was just ignored and effectively missing These two problems were previously attempted to be patched with "-Wl,--as-needed -lexecinfo -Wl,--no-as-needed" but this didn't work. So this line is now removed from Makefile, and proper flags are supplied to the link commands. Other port changes: * Take maintainership * Add missing RUN_DEPENDS for wish:x11-toolkits/tk-wrapper * Add CONFLICTS_BUILD * Fix MPICH_LIB_DEPENDS to point to net/mpich2 * patch the 'wish' path in configure Notes: svn path=/head/; revision=474828
* science/py-OpenFermion: Update 0.7 -> 0.8Yuri Victorovich2018-07-172-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=474816
* science/libghemical: Take maintainership.Yuri Victorovich2018-07-171-1/+1
| | | | | | | It has been labeled DEPRECATED, but I will fix it. Notes: svn path=/head/; revision=474790
* Deprecate ports broken for more than 5 monthsAntoine Brodin2018-07-172-0/+5
| | | | Notes: svn path=/head/; revision=474787
* Update KDE Applications to 18.04.3Tobias C. Berner2018-07-133-7/+6
| | | | Notes: svn path=/head/; revision=474596
* science/openstructure: Add USE_CXXSTD=c++98; Use MASTER_SITES instead of ↵Yuri Victorovich2018-07-132-10/+8
| | | | | | | | | | | | | | USE_GITLAB USE_GITLAB doesn't work in this case because it requires GL_COMMIT while only DISTVERSION should be sufficient. USE_CXXSTD=c++98 is used because -DCMAKE_CXX_FLAGS='-std=c++98' os overridden. Reported by: tobik Notes: svn path=/head/; revision=474569
* science/openstructure: Fix build by using -std=c++98Yuri Victorovich2018-07-132-6/+10
| | | | | | | | | | | The upstream recommended to use -std=c++98 to fix C++ errors on CURRENT. Also switch to USE_GITLAB. Reported by: fallout (build failure) Reported by: mat (USE_GITLAB use) Notes: svn path=/head/; revision=474549
* science/libssm: Fix build: put spaces between quotedstrings and defined ↵Yuri Victorovich2018-07-131-1/+10
| | | | | | | | | values in C Reported by: fallout Notes: svn path=/head/; revision=474548
* science/pulseview: unbreak with boost 1.68 on FreeBSD 10.*Jan Beich2018-07-121-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | After https://github.com/boostorg/multiprecision/commit/3cedeeab3048 building with Clang 3.4.1 fails like the following: In file included from pv/views/trace/view.cpp:26: In file included from /usr/include/c++/v1/algorithm:628: In file included from /usr/include/c++/v1/memory:607: /usr/include/c++/v1/tuple:187:73: error: reference to type 'const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0>' requires an initializer _NOEXCEPT_(is_nothrow_default_constructible<_Hp>::value) : value() ^ /usr/include/c++/v1/type_traits:2359:44: note: in instantiation of member function 'std::__1::__tuple_leaf<1, const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, false>::__tuple_leaf' requested here typename __select_2nd<decltype(_VSTD::move(_Tp(_VSTD::declval<_Args>()...))), true_type>::type ^ /usr/include/c++/v1/type_traits:2360:1: note: while substituting deduced template arguments into function template '__is_constructible_test' [with _Tp = std::__1::__tuple_leaf<1, const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, false>, _Args = <>] __is_constructible_test(_Tp&&, _Args&& ...); ^ /usr/include/c++/v1/type_traits:2419:14: note: in instantiation of template class 'std::__1::__libcpp_is_constructible<false, std::__1::__tuple_leaf<1, const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, false>>' requested here : public __libcpp_is_constructible<is_scalar<_Tp>::value || is_reference<_Tp>::value, ^ /usr/include/c++/v1/type_traits:2445:14: note: in instantiation of template class 'std::__1::__is_constructible_void_check<false, std::__1::__tuple_leaf<1, const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, false>>' requested here : public __is_constructible_void_check<__contains_void<_Tp, _Args...>::value ^ /usr/include/c++/v1/type_traits:2653:14: note: in instantiation of template class 'std::__1::is_constructible<std::__1::__tuple_leaf<1, const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, false>>' requested here : public is_constructible<_Tp> ^ /usr/local/include/boost/multiprecision/number.hpp:645:119: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) template <class T, class = typename boost::disable_if_c<std::is_constructible<T, self_type const&>::value || !std::is_default_constructible<T>::value, T>::type> ^ /usr/include/c++/v1/tuple:882:12: note: in instantiation of function template specialization 'std::__1::tuple<pv::views::trace::View &, const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, QString &&>::tuple<pv::views::trace::View &, const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, QString, false>' requested here return tuple<_Tp&&...>(_VSTD::forward<_Tp>(__t)...); ^ /usr/include/c++/v1/memory:3705:27: note: in instantiation of function template specialization 'std::__1::forward_as_tuple<pv::views::trace::View &, const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, QString>' requested here _VSTD::forward_as_tuple(_VSTD::forward<_Args>(__args)...)) {} ^ /usr/include/c++/v1/memory:4280:26: note: in instantiation of function template specialization 'std::__1::__shared_ptr_emplace<pv::views::trace::Flag, std::__1::allocator<pv::views::trace::Flag> >::__shared_ptr_emplace<pv::views::trace::View &, const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, QString>' requested here ::new(__hold2.get()) _CntrlBlk(__a2, _VSTD::forward<_Args>(__args)...); ^ /usr/include/c++/v1/memory:4644:29: note: in instantiation of function template specialization 'std::__1::shared_ptr<pv::views::trace::Flag>::make_shared<pv::views::trace::View &, const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, QString>' requested here return shared_ptr<_Tp>::make_shared(_VSTD::forward<_Args>(__args)...); ^ pv/views/trace/view.cpp:641:19: note: in instantiation of function template specialization 'std::__1::make_shared<pv::views::trace::Flag, pv::views::trace::View &, const boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, QString>' requested here flags_.push_back(make_shared<Flag>(*this, time, ^ In file included from pv/views/trace/view.cpp:26: In file included from /usr/include/c++/v1/algorithm:628: In file included from /usr/include/c++/v1/memory:607: /usr/include/c++/v1/tuple:188:9: error: static_assert failed "Attempted to default construct a reference element in a tuple" {static_assert(!is_reference<_Hp>::value, ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/tuple:187:73: error: reference to type 'boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0>' requires an initializer _NOEXCEPT_(is_nothrow_default_constructible<_Hp>::value) : value() ^ /usr/include/c++/v1/type_traits:2359:44: note: in instantiation of member function 'std::__1::__tuple_leaf<1, boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, false>::__tuple_leaf' requested here typename __select_2nd<decltype(_VSTD::move(_Tp(_VSTD::declval<_Args>()...))), true_type>::type ^ /usr/include/c++/v1/type_traits:2360:1: note: while substituting deduced template arguments into function template '__is_constructible_test' [with _Tp = std::__1::__tuple_leaf<1, boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, false>, _Args = <>] __is_constructible_test(_Tp&&, _Args&& ...); ^ /usr/include/c++/v1/type_traits:2419:14: note: in instantiation of template class 'std::__1::__libcpp_is_constructible<false, std::__1::__tuple_leaf<1, boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, false>>' requested here : public __libcpp_is_constructible<is_scalar<_Tp>::value || is_reference<_Tp>::value, ^ /usr/include/c++/v1/type_traits:2445:14: note: in instantiation of template class 'std::__1::__is_constructible_void_check<false, std::__1::__tuple_leaf<1, boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, false>>' requested here : public __is_constructible_void_check<__contains_void<_Tp, _Args...>::value ^ /usr/include/c++/v1/type_traits:2653:14: note: in instantiation of template class 'std::__1::is_constructible<std::__1::__tuple_leaf<1, boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &, false>>' requested here : public is_constructible<_Tp> ^ /usr/local/include/boost/multiprecision/number.hpp:645:119: note: (skipping 4 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) template <class T, class = typename boost::disable_if_c<std::is_constructible<T, self_type const&>::value || !std::is_default_constructible<T>::value, T>::type> ^ /usr/include/c++/v1/tuple:882:12: note: in instantiation of member function 'std::__1::tuple<pv::views::trace::View &, boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &>::tuple' requested here return tuple<_Tp&&...>(_VSTD::forward<_Tp>(__t)...); ^ /usr/include/c++/v1/memory:3705:27: note: in instantiation of function template specialization 'std::__1::forward_as_tuple<pv::views::trace::View &, boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &>' requested here _VSTD::forward_as_tuple(_VSTD::forward<_Args>(__args)...)) {} ^ /usr/include/c++/v1/memory:4280:26: note: in instantiation of function template specialization 'std::__1::__shared_ptr_emplace<pv::views::trace::TriggerMarker, std::__1::allocator<pv::views::trace::TriggerMarker> >::__shared_ptr_emplace<pv::views::trace::View &, boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &>' requested here ::new(__hold2.get()) _CntrlBlk(__a2, _VSTD::forward<_Args>(__args)...); ^ /usr/include/c++/v1/memory:4644:29: note: in instantiation of function template specialization 'std::__1::shared_ptr<pv::views::trace::TriggerMarker>::make_shared<pv::views::trace::View &, boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &>' requested here return shared_ptr<_Tp>::make_shared(_VSTD::forward<_Args>(__args)...); ^ pv/views/trace/view.cpp:696:29: note: in instantiation of function template specialization 'std::__1::make_shared<pv::views::trace::TriggerMarker, pv::views::trace::View &, boost::multiprecision::number<boost::multiprecision::backends::cpp_dec_float<24, int, void>, 0> &>' requested here trigger_markers_.push_back(make_shared<TriggerMarker>(*this, location)); ^ In file included from pv/views/trace/view.cpp:26: In file included from /usr/include/c++/v1/algorithm:628: In file included from /usr/include/c++/v1/memory:607: /usr/include/c++/v1/tuple:188:9: error: static_assert failed "Attempted to default construct a reference element in a tuple" {static_assert(!is_reference<_Hp>::value, ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ PR: 229569 Notes: svn path=/head/; revision=474542
* science/rubygem-ruby-dcl: update to 1.8.1Steve Wills2018-07-102-6/+12
| | | | | | | | PR: 225012 Approved by: maintainer timeout (murashin@gfd-dennou.org, >6 months) Notes: svn path=/head/; revision=474375
* science/libssm: Fix build on 12Yuri Victorovich2018-07-101-0/+13
| | | | | | | | | Add spaces between quoted strings and defined values. Reported by: fallout Notes: svn path=/head/; revision=474336
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