avogadro2 Chemical editor and visualization application

1.93.0 science =0 1.91.0Version of this port present on the latest quarterly branch.

Maintainer: yuri@FreeBSD.org

Port Added: 2018-10-17 01:04:52

Last Update: 2020-02-06 07:09:42

SVN Revision: 525365

License: BSD3CLAUSE

Description:

Avogadro 2 is a chemical editor and visualization application, it is also a set of reusable software libraries written in C++ using principles of modularity for maximum reuse. The development of the first generation Avogadro application and library is documented in our paper, and this remains the preferred method of citation at present. The motivation for rewriting Avogadro, along with improvements and changes made in Avogadro 2 are summarized in our Source article. We provide a set of permissively licensed, open source, cross platform software components in the Avogadro 2 libraries, along with an end-user application with full source code, and binaries. The library features updated and improved rendering, where we built upon the abstraction provided by previous API, but implemented a simple scene graph. This makes use of features such as impostor sphere rendering, resulting in significant rendering speed improvements while improving the quality of the visualization. The core is built for scalability, looking to enable the analysis of larger chemical structures and simulations being produced by computational chemistry codes today. Emphasis has also been placed on making it even easier to extend, using simple Python scripts to add simulation input capabilities, and data input/output along with access to full-blown C++ plugin APIs where more control is required. WWW: https://www.openchemistry.org/projects/avogadro2/

SVNWeb : Homepage

pkg-plist: as obtained via: make generate-plist

Expand this list (8 items)

1. bin/avogadro2
2. share/applications/avogadro2.desktop
3. share/pixmaps/avogadro2.png
4. @desktop-file-utils
5. @ldconfig
6. /usr/local/share/licenses/avogadro2-1.93.0/catalog.mk
7. /usr/local/share/licenses/avogadro2-1.93.0/LICENSE
8. /usr/local/share/licenses/avogadro2-1.93.0/BSD3CLAUSE

Collapse this list.

Dependency lines:

• avogadro2>0:science/avogadro2

To install the port: cd /usr/ports/science/avogadro2/ && make install clean

To add the package: pkg install avogadro2

PKGNAME: avogadro2

Flavors: there is no flavor information for this port.

distinfo:

TIMESTAMP = 1580972413 SHA256 (OpenChemistry-avogadroapp-1.93.0_GH0.tar.gz) = 8cf913058aff58fe588531618a680d82401fbfe3f21e4783a44979f4a2dd5586 SIZE (OpenChemistry-avogadroapp-1.93.0_GH0.tar.gz) = 2905461

Dependencies

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:

1. hdf5>0 : science/hdf5
2. cmake : devel/cmake
3. ninja : devel/ninja
4. update-desktop-database : devel/desktop-file-utils
5. xorgproto>=0 : x11/xorgproto
6. xorgproto>=0 : x11/xorgproto
7. moc : devel/qt5-buildtools
8. qmake : devel/qt5-qmake

Runtime dependencies:

1. update-desktop-database : devel/desktop-file-utils

Library dependencies:

1. libAvogadroCore.so : science/avogadrolibs
2. libMoleQueueClient.so : misc/molequeue
3. libGL.so : graphics/mesa-libs
4. libGLEW.so : graphics/glew
5. libGLU.so : graphics/libGLU
6. libarchive.so.13 : archivers/libarchive
7. libQt5Concurrent.so : devel/qt5-concurrent
8. libQt5Core.so : devel/qt5-core
9. libQt5Gui.so : x11-toolkits/qt5-gui
10. libQt5Network.so : net/qt5-network
11. libQt5Widgets.so : x11-toolkits/qt5-widgets

There are no ports dependent upon this port

Configuration Options

No options to configure

USES:

cmake compiler:c++11-lang desktop-file-utils gl libarchive qt:5 xorg

Master Sites:

1. https://codeload.github.com/OpenChemistry/avogadroapp/tar.gz/1.93.0?dummy=/

• port moved here from science/avogadro on 2019-03-16
  REASON: Has expired: Qt4 has been EOL since december 2015, the new generation, avogadro2, should be used
  

science/avogadro2: Update 1.91.0 -> 1.93.0

Reported by:	portscout

Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330

Fix Qt5 symbol version scripts to put the catch-all clause first.  When
a symbol matches multiple clauses the last one takes precedence.  If the
catch-all is last it captures everything.  In the case of Qt5 libraries
this caused all symbols to have a Qt_5 label while some should have
Qt_5_PRIVATE_API.  This only affects lld because GNU ld always gives the
catch-all lowest priority.

Older versions of Qt5Webengine exported some memory allocation symbols from
the bundled Chromium.  Version 5.9 stopped exporting these [1] but the
symbols were kept as weak wrappers for the standard allocation functions to
maintain binary compatibility. [2][3]  The problem is that the call to the
standard function in these weak wrappers is only resolved to the standard
function if there's a call to this standard function in other parts of
Qt5Webengine, because only then is there a non-weak symbol that takes
precedence over the weak one.  If there's no such non-weak symbol the call

Update science/hdf5 to 1.10.4

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://portal.hdfgroup.org/display/support/HDF5%201.10.4#releasenotes
PR:		233070
Submitted by:	wen

Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine

Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590

science/avogadrolibs: Update 1.91.0 -> 1.91.0-107

jsoncpp isn't used any more, mmtf is now used.

New port: science/avogadro2: Chemical editor and visualization application

12 vulnerabilities affecting 52 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2020-02-25 03:07:51