Hello community, here is the log from the commit of package avogadro for openSUSE:Factory checked in at 2013-03-14 16:52:55 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/avogadro (Old) and /work/SRC/openSUSE:Factory/.avogadro.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "avogadro", Maintainer is "" Changes: -------- --- /work/SRC/openSUSE:Factory/avogadro/avogadro.changes 2013-03-08 09:07:44.000000000 +0100 +++ /work/SRC/openSUSE:Factory/.avogadro.new/avogadro.changes 2013-03-14 16:52:57.000000000 +0100 @@ -1,0 +2,8 @@ +Tue Feb 5 01:12:27 UTC 2013 - [email protected] + +- added MopacAuxReaderFix.patch to avoid crash when loading aux. +- fixed build on SLES +- split off python package + (also use sitearch for arch-dependent files) + +------------------------------------------------------------------- New: ---- MopacAuxReaderFix.patch ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ avogadro.spec ++++++ --- /var/tmp/diff_new_pack.qJ8i5T/_old 2013-03-14 16:52:59.000000000 +0100 +++ /var/tmp/diff_new_pack.qJ8i5T/_new 2013-03-14 16:52:59.000000000 +0100 @@ -28,14 +28,19 @@ Source2: baselibs.conf # PATCH-FIX-UPSTREAM return at least some value in a bool function Patch0: avogadro-1.1.0-no-return-in-nonvoid-function.patch +# PATCH-FIX-UPSTREAM avoid crash when loading aux - see https://github.com/cryos/avogadro/commit/a4050e8a3f70ddc2bcc75a5b00d26416964b7275.patch +Patch1: MopacAuxReaderFix.patch BuildRequires: boost-devel BuildRequires: cmake BuildRequires: docbook-utils BuildRequires: fdupes BuildRequires: gcc-c++ BuildRequires: glew-devel +%if 0%{?suse_version} > 1220 +BuildRequires: glu-devel +%endif BuildRequires: libeigen2-devel -BuildRequires: libopenbabel-devel >= 2.2.3 +BuildRequires: libopenbabel-devel >= 2.3.1 BuildRequires: libqt4-devel >= 4.5.1 BuildRequires: python-devel BuildRequires: python-numpy-devel @@ -82,18 +87,31 @@ This package contains files to develop applications using Avogadros libraries. +%package -n python-avogadro +Summary: A python wrapper to avogadro +Group: Development/Languages/Python +Requires: python-numpy +Requires: python-sip + +%description -n python-avogadro +This package contains the python wrapper to Avogadro. + +Avogadro is an advanced molecular editor designed +for cross-platform use in computational chemistry, +molecular modeling, bioinformatics, materials science, +and related areas. It offers flexible rendering and +a powerful plugin architecture. + %prep %setup -q %patch0 -p1 +%patch1 -p1 %build mkdir -p build cd build export SUSE_ASNEEDED=0 cmake -DCMAKE_INSTALL_PREFIX=%{_prefix} \ - -DCMAKE_C_FLAGS="%{optflags}" \ - -DCMAKE_CXX_FLAGS="%{optflags}" \ - -DCMAKE_VERBOSE_MAKEFILE=TRUE \ -DENABLE_GLSL=ON \ %if "%{_lib}" == "lib64" -DLIB_SUFFIX=64 \ @@ -108,7 +126,7 @@ %install cd build -%make_install +%makeinstall mkdir -p %{buildroot}/%{_datadir}/qt4/mkspecs/ mv %{buildroot}%{_prefix}/features %{buildroot}/%{_datadir}/qt4/mkspecs/ @@ -130,8 +148,10 @@ # icon install -D -m644 %{SOURCE1} %{buildroot}%{_datadir}/pixmaps/%{name}.png %if "%{_lib}" == "lib64" - mkdir -p %{buildroot}%{python_sitelib} - find %{buildroot} -name 'Avogadro.so' | xargs mv -t %{buildroot}%{python_sitelib}/ + mkdir -p %{buildroot}%{python_sitearch} + if [ ! -e %{buildroot}%{python_sitearch}/Avogadro.so ]; then + find %{buildroot} -name 'Avogadro.so' | xargs mv -t %{buildroot}%{python_sitearch}/ + fi find %{buildroot}%{_lib} -name "python*" |xargs rm -rf %endif %fdupes %{buildroot}%{_datadir}/libavogadro/shaders/ @@ -161,8 +181,6 @@ %dir %{_libdir}/avogadro/1_1/extensions %dir %{_libdir}/avogadro/1_1/tools %{_libdir}/avogadro/1_1/*/*.so -# installed with python support -%{python_sitelib}/Avogadro.so %dir %{_datadir}/libavogadro/engineScripts %dir %{_datadir}/libavogadro/extensionScripts %{_datadir}/libavogadro/engineScripts/wireframe.py @@ -175,15 +193,20 @@ %dir %{_libdir}/avogadro/1_1/cmake %{_libdir}/libavogadro.so %{_libdir}/libavogadro_OpenQube.so -%{_libdir}/pkgconfig/avogadro.pc %{_libdir}/avogadro/1_1/cmake/* %{_libdir}/avogadro/1_1/*.cmake %{_libdir}/avogadro/*.cmake +%{_libdir}/pkgconfig/*.pc %{_datadir}/qt4/mkspecs/features/avogadro.prf %files -n libavogadro1 %defattr(-,root,root,-) %{_libdir}/*.so.* +%files -n python-avogadro +%defattr(-,root,root,-) +# installed with python support +%{python_sitearch}/Avogadro.so + %changelog ++++++ MopacAuxReaderFix.patch ++++++ >From 933ae95d4e759cd83387fc16596fe6bb8df69dd2 Mon Sep 17 00:00:00 2001 From: "David C. Lonie" <[email protected]> Date: Sun, 3 Feb 2013 11:17:05 -0500 Subject: [PATCH] Mark basis set as invalid if no atoms parsed from MOPAC .aux file. Change-Id: I6cfcf6cb65aa8f4ac4457e25ce7d36b2bcc46c12 --- libavogadro/src/extensions/surfaces/openqube/mopacaux.cpp | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/libavogadro/src/extensions/surfaces/openqube/mopacaux.cpp b/libavogadro/src/extensions/surfaces/openqube/mopacaux.cpp index 275428a..a7f8f4d 100644 --- a/libavogadro/src/extensions/surfaces/openqube/mopacaux.cpp +++ b/libavogadro/src/extensions/surfaces/openqube/mopacaux.cpp @@ -122,6 +122,11 @@ void MopacAux::processLine() void MopacAux::load(SlaterSet* basis) { + if (m_atomPos.size() == 0) { + qWarning() << "No atoms found in .aux file. Bailing out."; + basis->setIsValid(false); + return; + } // Now load up our basis set basis->addAtoms(m_atomPos); basis->addSlaterIndices(m_atomIndex); @@ -140,10 +145,12 @@ void MopacAux::load(SlaterSet* basis) mol.addAtom(m_atomPos[i], m_atomNums[i]); } } - else + else { qWarning() << "Number of atomic numbers (" << m_atomNums.size() << ") does not equal the number of atomic positions (" << m_atomPos.size() << "). Not populating molecule."; + basis->setIsValid(false); + } } vector<int> MopacAux::readArrayI(unsigned int n) -- 1.7.10 -- To unsubscribe, e-mail: [email protected] For additional commands, e-mail: [email protected]
