[Debichem-devel] [Avogadro-devel] Pre-releases for Avogadro 1.2

Fri Aug 12 10:12:22 UTC 2016

Hi Anton,

you worked on the Eigen3 support in Avogadro I believe.  The last time I
had a look (see below), it failed to build, could you maybe take another
look?

The only thing I changed in the packaging was disabled all or most of
the patches.

Michael

On Tue, Jun 07, 2016 at 12:25:39AM +0200, Michael Banck wrote:
> Hi,
> 
> Sorry it took a while, I had less time on the weekend than I thought I
> would have.
> 
> On Fri, Jun 03, 2016 at 05:55:53PM -0400, Geoffrey Hutchison wrote:
> > > I'm happy to test-package it for Debian/Ubuntu, if you can point me at a
> > > tarball.
> > 
> > https://github.com/cryos/avogadro/archive/master.tar.gz
> > 
> > I have not yet created a 1.2 branch.
> 
> OK, I gave it a shot on Debian stable and unstable. Most patches we had
> or 1.0.3 seem to no longer apply, except for the first three hunk of
> this one:
> 
> http://anonscm.debian.org/viewvc/debichem/unstable/avogadro/debian/patches/boost148.patch?revision=3743&view=markup
> 
> Not sure that is still useful/needed.
> 
> About building:
> 
> Debian unstable has eigen-3.3beta, and it fails to build with that:
> 
> |make[3]: Entering directory '/«PKGBUILDDIR»/obj-x86_64-linux-gnu'
> |[  0%] Building CXX object libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o
> |cd /«PKGBUILDDIR»/obj-x86_64-linux-gnu/libavogadro/src/colors && /usr/bin/c++   -DENABLE_GLSL -DENABLE_PYTHON -DHAVE_GCC_VISIBILITY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_PLUGIN -DQT_SHARED -D_BSD_SOURCE -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/libavogadro/include -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/libavogadro/src -I/usr/include/openbabel-2.0 -I/usr/include/eigen3 -I/usr/include/python2.7 -I/«PKGBUILDDIR»/obj-x86_64-linux-gnu/libavogadro/src/colors  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive   -DQT_STATICPLUGIN -fPIC -o CMakeFiles/elementcolor.dir/elementcolor.cpp.o -c /«PKGBUILDDIR»/libavogadro/src/colors/elementcolor.cpp
> |In file included from /usr/include/x86_64-linux-gnu/c++/5/bits/os_defines.h:39:0,
> |                 from /usr/include/x86_64-linux-gnu/c++/5/bits/c++config.h:482,
> |                 from /usr/include/c++/5/utility:68,
> |                 from /usr/include/c++/5/algorithm:60,
> |                 from /usr/include/qt4/QtCore/qglobal.h:68,
> |                 from /usr/include/qt4/QtCore/qnamespace.h:45,
> |                 from /usr/include/qt4/QtCore/qobjectdefs.h:45,
> |                 from /usr/include/qt4/QtCore/qobject.h:47,
> |                 from /usr/include/qt4/QtCore/qtranslator.h:45,
> |                 from /usr/include/qt4/QtCore/QTranslator:1,
> |                 from /«PKGBUILDDIR»/obj-x86_64-linux-gnu/libavogadro/include/avogadro/global.h:29,
> |                 from /«PKGBUILDDIR»/libavogadro/src/colors/elementcolor.h:29,
> |                 from /«PKGBUILDDIR»/libavogadro/src/colors/elementcolor.cpp:25:
> |/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
> | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
> |   ^
> |In file included from /«PKGBUILDDIR»/obj-x86_64-linux-gnu/libavogadro/include/avogadro/primitive.h:36:0,
> |                 from /«PKGBUILDDIR»/libavogadro/src/colors/elementcolor.cpp:27:
> |/usr/include/eigen3/Eigen/Core:275:2: error: #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information
> | #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information
> |  ^
> |make[3]: *** [libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o] Error 1
> 
> The include chain might indicate that is an issue with Debian unstable's
> Qt/Eigen packages maybe, not sure.
> 
> Also, I see the following warnings when running CMake:
> 
> |-- Configuring done
> |CMake Warning (dev) in libavogadro/src/CMakeLists.txt:
> |  Policy CMP0022 is not set: INTERFACE_LINK_LIBRARIES defines the link
> |  interface.  Run "cmake --help-policy CMP0022" for policy details.  Use the
> |  cmake_policy command to set the policy and suppress this warning.
> |
> |  Target "avogadro" has an INTERFACE_LINK_LIBRARIES property which differs
> |  from its LINK_INTERFACE_LIBRARIES properties.
> |
> |  INTERFACE_LINK_LIBRARIES:
> |
> |    openbabel;/usr/lib/x86_64-linux-gnu/libQtOpenGL.so;/usr/lib/x86_64-linux-gnu/libQtGui.so;/usr/lib/x86_64-linux-gnu/libQtCore.so;/usr/lib/x86_64-linux-gnu/libGLU.so;/usr/lib/x86_64-linux-gnu/libGL.so;/usr/lib/x86_64-linux-gnu/libGLEW.so;/usr/lib/x86_64-linux-gnu/libpython2.7.so;/usr/lib/x86_64-linux-gnu/libboost_python.so;bsdyengine;navigatetool;elementcolor
> |
> |  LINK_INTERFACE_LIBRARIES:
> |
> |
> |
> |This warning is for project developers.  Use -Wno-dev to suppress it.
> |
> |CMake Warning (dev) in libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt:
> |  Policy CMP0022 is not set: INTERFACE_LINK_LIBRARIES defines the link
> |  interface.  Run "cmake --help-policy CMP0022" for policy details.  Use the
> |  cmake_policy command to set the policy and suppress this warning.
> |
> |  Target "OpenQube" has an INTERFACE_LINK_LIBRARIES property which differs
> |  from its LINK_INTERFACE_LIBRARIES properties.
> |
> |  INTERFACE_LINK_LIBRARIES:
> |
> |    $<$<NOT:$<CONFIG:DEBUG>>:/usr/lib/x86_64-linux-gnu/libQtCore.so>;$<$<CONFIG:DEBUG>:/usr/lib/x86_64-linux-gnu/libQtCore.so>;$<$<NOT:$<CONFIG:DEBUG>>:/usr/lib/x86_64-linux-gnu/libQtGui.so>;$<$<CONFIG:DEBUG>:/usr/lib/x86_64-linux-gnu/libQtGui.so>
> |
> |  LINK_INTERFACE_LIBRARIES:
> |
> |
> |
> |This warning is for project developers.  Use -Wno-dev to suppress it.
> |
> |-- Generating done
> |CMake Warning:
> |  Manually-specified variables were not used by the project:
> |
> |    CMAKE_INSTALL_LOCALSTATEDIR
> |    CMAKE_INSTALL_SYSCONFDIR
> |
> |
> |-- Build files have been written to: /«PKGBUILDDIR»/obj-x86_64-linux-gnu
> 
> Debian stable built fine as it has eigen-3.2, but there are a lot of
> deprecation warnings about Eigen2:
> 
> |/usr/include/eigen3/Eigen/Eigen2Support:20:2: warning: #warning "Eigen2
> |support is deprecated in Eigen 3.2.x and it will be removed in Eigen
> |3.3. (Define EIGEN_NO_EIGEN2_DEPRECATED_WARNING to disable this
> |warning)" [-Wcpp]
> 
> A quick some test did not bring any serious bugs, but I really only
> opened the program, loaded 2 files and clicked a bit.
> 
> Minor things I've noticed:
> 
> 1. The menu bar in the german translation is busted - there's the
> equivalent to "Select" twice (with different parts of the menu), and the
> equivalent to the "Build" menu is empty. I didn't check the others.
> 
> The empty Build menu seems to be present in 1.0.3 as well, just
> checked.
> 
> 2. The View -> Properties -> Atom Properties window has no obvious
> button to close it, ctrl-w doesn't work either (this is with Gnome3).
> 
> This behaviour is also already present in 1.0.3.
> 
> 
> Michael
> 
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