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Port details
avogadrolibs Avogadro2 libraries for chemical editor and visualization applications
1.93.0_1 science on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.93.0_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-10-17 01:02:48
Last Update: 2020-12-12 17:04:37
SVN Revision: 557839
License: GPLv2
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (223 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/avogadrolibs-1.93.0_1/catalog.mk
  3. /usr/local/share/licenses/avogadrolibs-1.93.0_1/LICENSE
  4. /usr/local/share/licenses/avogadrolibs-1.93.0_1/GPLv2
  5. include/avogadro/core/array.h
  6. include/avogadro/core/atom.h
  7. include/avogadro/core/atomtyper-inline.h
  8. include/avogadro/core/atomtyper.h
  9. include/avogadro/core/avogadrocore.h
  10. include/avogadro/core/avogadrocoreexport.h
  11. include/avogadro/core/avospglib.h
  12. include/avogadro/core/basisset.h
  13. include/avogadro/core/bond.h
  14. include/avogadro/core/color3f.h
  15. include/avogadro/core/coordinateblockgenerator.h
  16. include/avogadro/core/coordinateset.h
  17. include/avogadro/core/crystaltools.h
  18. include/avogadro/core/cube.h
  19. include/avogadro/core/elements.h
  20. include/avogadro/core/gaussianset.h
  21. include/avogadro/core/gaussiansettools.h
  22. include/avogadro/core/graph.h
  23. include/avogadro/core/matrix.h
  24. include/avogadro/core/mesh.h
  25. include/avogadro/core/molecule.h
  26. include/avogadro/core/mutex.h
  27. include/avogadro/core/nameatomtyper.h
  28. include/avogadro/core/residue.h
  29. include/avogadro/core/ringperceiver.h
  30. include/avogadro/core/slaterset.h
  31. include/avogadro/core/slatersettools.h
  32. include/avogadro/core/spacegroups.h
  33. include/avogadro/core/symbolatomtyper.h
  34. include/avogadro/core/types.h
  35. include/avogadro/core/unitcell.h
  36. include/avogadro/core/utilities.h
  37. include/avogadro/core/variant-inline.h
  38. include/avogadro/core/variant.h
  39. include/avogadro/core/variantmap.h
  40. include/avogadro/core/vector.h
  41. include/avogadro/core/version.h
  42. include/avogadro/io/avogadroioexport.h
  43. include/avogadro/io/cjsonformat.h
  44. include/avogadro/io/cmlformat.h
  45. include/avogadro/io/dcdformat.h
  46. include/avogadro/io/fileformat.h
  47. include/avogadro/io/fileformatmanager.h
  48. include/avogadro/io/gromacsformat.h
  49. @comment include/avogadro/io/hdf5dataformat.h
  50. include/avogadro/io/lammpsformat.h
  51. include/avogadro/io/mdlformat.h
  52. include/avogadro/io/mmtfformat.h
  53. include/avogadro/io/pdbformat.h
  54. include/avogadro/io/trrformat.h
  55. include/avogadro/io/vaspformat.h
  56. include/avogadro/io/xyzformat.h
  57. include/avogadro/molequeue/avogadromolequeueexport.h
  58. include/avogadro/molequeue/batchjob.h
  59. include/avogadro/molequeue/inputgenerator.h
  60. include/avogadro/molequeue/inputgeneratordialog.h
  61. include/avogadro/molequeue/inputgeneratorwidget.h
  62. include/avogadro/molequeue/molequeuedialog.h
  63. include/avogadro/molequeue/molequeuemanager.h
  64. include/avogadro/molequeue/molequeuequeuelistmodel.h
  65. include/avogadro/molequeue/molequeuewidget.h
  66. include/avogadro/qtgui/avogadroqtguiexport.h
  67. include/avogadro/qtgui/backgroundfileformat.h
  68. include/avogadro/qtgui/containerwidget.h
  69. include/avogadro/qtgui/customelementdialog.h
  70. include/avogadro/qtgui/elementtranslator.h
  71. include/avogadro/qtgui/extensionplugin.h
  72. include/avogadro/qtgui/filebrowsewidget.h
  73. include/avogadro/qtgui/fileformatdialog.h
  74. include/avogadro/qtgui/generichighlighter.h
  75. include/avogadro/qtgui/hydrogentools.h
  76. include/avogadro/qtgui/interfacescript.h
  77. include/avogadro/qtgui/interfacewidget.h
  78. include/avogadro/qtgui/meshgenerator.h
  79. include/avogadro/qtgui/molecule.h
  80. include/avogadro/qtgui/moleculemodel.h
  81. include/avogadro/qtgui/multiviewwidget.h
  82. include/avogadro/qtgui/periodictableview.h
  83. include/avogadro/qtgui/persistentatom.h
  84. include/avogadro/qtgui/persistentbond.h
  85. include/avogadro/qtgui/pythonscript.h
  86. include/avogadro/qtgui/rwmolecule.h
  87. include/avogadro/qtgui/sceneplugin.h
  88. include/avogadro/qtgui/scenepluginmodel.h
  89. include/avogadro/qtgui/scriptloader.h
  90. include/avogadro/qtgui/toolplugin.h
  91. include/avogadro/qtgui/utilities.h
  92. include/avogadro/qtgui/viewfactory.h
  93. include/avogadro/qtopengl/activeobjects.h
  94. include/avogadro/qtopengl/avogadroqtopenglexport.h
  95. include/avogadro/qtopengl/glwidget.h
  96. include/avogadro/qtopengl/qttextrenderstrategy.h
  97. include/avogadro/qtplugins/avogadroqtpluginsexport.h
  98. include/avogadro/qtplugins/avogadrostaticqtplugins.h
  99. include/avogadro/qtplugins/pluginfactory.h
  100. include/avogadro/qtplugins/pluginmanager.h
  101. include/avogadro/quantumio/avogadroquantumioexport.h
  102. include/avogadro/quantumio/gamessus.h
  103. include/avogadro/quantumio/gaussiancube.h
  104. include/avogadro/quantumio/gaussianfchk.h
  105. include/avogadro/quantumio/molden.h
  106. include/avogadro/quantumio/mopacaux.h
  107. include/avogadro/quantumio/nwchemjson.h
  108. include/avogadro/quantumio/nwchemlog.h
  109. include/avogadro/rendering/arrowgeometry.h
  110. include/avogadro/rendering/avogadrogl.h
  111. include/avogadro/rendering/avogadrorendering.h
  112. include/avogadro/rendering/avogadrorenderingexport.h
  113. include/avogadro/rendering/bufferobject.h
  114. include/avogadro/rendering/camera.h
  115. include/avogadro/rendering/cylindergeometry.h
  116. include/avogadro/rendering/drawable.h
  117. include/avogadro/rendering/geometrynode.h
  118. include/avogadro/rendering/geometryvisitor.h
  119. include/avogadro/rendering/glrenderer.h
  120. include/avogadro/rendering/glrendervisitor.h
  121. include/avogadro/rendering/groupnode.h
  122. include/avogadro/rendering/linestripgeometry.h
  123. include/avogadro/rendering/meshgeometry.h
  124. include/avogadro/rendering/node.h
  125. include/avogadro/rendering/povrayvisitor.h
  126. include/avogadro/rendering/primitive.h
  127. include/avogadro/rendering/scene.h
  128. include/avogadro/rendering/shader.h
  129. include/avogadro/rendering/shaderprogram.h
  130. include/avogadro/rendering/spheregeometry.h
  131. include/avogadro/rendering/textlabel2d.h
  132. include/avogadro/rendering/textlabel3d.h
  133. include/avogadro/rendering/textlabelbase.h
  134. include/avogadro/rendering/textproperties.h
  135. include/avogadro/rendering/textrenderstrategy.h
  136. include/avogadro/rendering/texture2d.h
  137. include/avogadro/rendering/transformnode.h
  138. include/avogadro/rendering/visitor.h
  139. include/avogadro/rendering/volumegeometry.h
  140. include/avogadro/rendering/vrmlvisitor.h
  141. lib/avogadro2/scripts/commands/scale.py
  142. lib/avogadro2/scripts/formatScripts/cclibScript.py
  143. lib/avogadro2/scripts/formatScripts/zyx.py
  144. lib/avogadro2/staticplugins/BallStick.a
  145. lib/avogadro2/staticplugins/BondCentric.a
  146. lib/avogadro2/staticplugins/Bonding.a
  147. lib/avogadro2/staticplugins/CoordinateEditor.a
  148. lib/avogadro2/staticplugins/CopyPaste.a
  149. lib/avogadro2/staticplugins/Crystal.a
  150. lib/avogadro2/staticplugins/CrystalScene.a
  151. lib/avogadro2/staticplugins/CustomElements.a
  152. lib/avogadro2/staticplugins/Editor.a
  153. lib/avogadro2/staticplugins/Force.a
  154. lib/avogadro2/staticplugins/GamessInput.a
  155. lib/avogadro2/staticplugins/Hydrogens.a
  156. lib/avogadro2/staticplugins/ImportPQR.a
  157. lib/avogadro2/staticplugins/LammpsInput.a
  158. lib/avogadro2/staticplugins/Licorice.a
  159. lib/avogadro2/staticplugins/LineFormatInput.a
  160. lib/avogadro2/staticplugins/Manipulator.a
  161. lib/avogadro2/staticplugins/MeasureTool.a
  162. lib/avogadro2/staticplugins/Meshes.a
  163. lib/avogadro2/staticplugins/MolecularProperties.a
  164. lib/avogadro2/staticplugins/MongoChem.a
  165. lib/avogadro2/staticplugins/Navigator.a
  166. lib/avogadro2/staticplugins/NetworkDatabases.a
  167. lib/avogadro2/staticplugins/OpenBabel.a
  168. lib/avogadro2/staticplugins/OverlayAxes.a
  169. lib/avogadro2/staticplugins/POVRay.a
  170. lib/avogadro2/staticplugins/PlayerTool.a
  171. lib/avogadro2/staticplugins/PluginDownloader.a
  172. lib/avogadro2/staticplugins/QuantumInput.a
  173. lib/avogadro2/staticplugins/ScriptFileFormats.a
  174. lib/avogadro2/staticplugins/Select.a
  175. lib/avogadro2/staticplugins/Selection.a
  176. lib/avogadro2/staticplugins/SpaceGroup.a
  177. lib/avogadro2/staticplugins/Spectra.a
  178. lib/avogadro2/staticplugins/Surfaces.a
  179. lib/avogadro2/staticplugins/Symmetry.a
  180. lib/avogadro2/staticplugins/SymmetryScene.a
  181. lib/avogadro2/staticplugins/ThreeDMol.a
  182. lib/avogadro2/staticplugins/VRML.a
  183. lib/avogadro2/staticplugins/VanDerWaals.a
  184. lib/avogadro2/staticplugins/VanDerWaalsAO.a
  185. lib/avogadro2/staticplugins/Wireframe.a
  186. lib/avogadro2/staticplugins/apbs.a
  187. lib/avogadro2/staticplugins/commands.a
  188. lib/cmake/avogadrolibs/AvogadroLibsConfig.cmake
  189. lib/cmake/avogadrolibs/AvogadroLibsConfigVersion.cmake
  190. lib/cmake/avogadrolibs/AvogadroLibsTargets-release.cmake
  191. lib/cmake/avogadrolibs/AvogadroLibsTargets.cmake
  192. lib/cmake/avogadrolibs/FindEigen3.cmake
  193. lib/cmake/avogadrolibs/FindGLEW.cmake
  194. lib/cmake/avogadrolibs/FindLibArchive.cmake
  195. lib/cmake/avogadrolibs/Findlibmsym.cmake
  196. lib/libAvogadroCore.so
  197. lib/libAvogadroCore.so.1
  198. lib/libAvogadroCore.so.1.93.0
  199. lib/libAvogadroIO.so
  200. lib/libAvogadroIO.so.1
  201. lib/libAvogadroIO.so.1.93.0
  202. lib/libAvogadroMoleQueue.so
  203. lib/libAvogadroMoleQueue.so.1
  204. lib/libAvogadroMoleQueue.so.1.93.0
  205. lib/libAvogadroQtGui.so
  206. lib/libAvogadroQtGui.so.1
  207. lib/libAvogadroQtGui.so.1.93.0
  208. lib/libAvogadroQtOpenGL.so
  209. lib/libAvogadroQtOpenGL.so.1
  210. lib/libAvogadroQtOpenGL.so.1.93.0
  211. lib/libAvogadroQtPlugins.so
  212. lib/libAvogadroQtPlugins.so.1
  213. lib/libAvogadroQtPlugins.so.1.93.0
  214. lib/libAvogadroQuantumIO.so
  215. lib/libAvogadroQuantumIO.so.1
  216. lib/libAvogadroQuantumIO.so.1.93.0
  217. lib/libAvogadroRendering.so
  218. lib/libAvogadroRendering.so.1
  219. lib/libAvogadroRendering.so.1.93.0
  220. lib/liblibgwavi.a
  221. @owner
  222. @group
  223. @mode
Collapse this list.
Dependency lines:
  • avogadrolibs>0:science/avogadrolibs
To install the port: cd /usr/ports/science/avogadrolibs/ && make install clean
To add the package: pkg install avogadrolibs
PKGNAME: avogadrolibs
Flavors: there is no flavor information for this port.
distinfo:
Packages: (move your mouse over the cells for more information)
avogadrolibs
ABIlatestquarterly
FreeBSD:11:aarch64-1.93.0
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-1.93.0_1
FreeBSD:12:amd641.93.0_11.93.0_1
FreeBSD:12:armv6-1.93.0
FreeBSD:12:armv7-1.93.0
FreeBSD:12:i3861.93.0_11.93.0_1
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-1.93.0_1
FreeBSD:13:aarch641.93.0_11.93.0_1
FreeBSD:13:amd641.93.0_11.93.0_1
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3861.93.0_11.93.0_1
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64-1.93.0_1
FreeBSD:14:aarch641.93.0_1-
FreeBSD:14:amd641.93.0_1-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3861.93.0_1-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc641.93.0_1-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. mmtf.hpp : science/mmtf-cpp
  2. cmake : devel/cmake
  3. ninja : devel/ninja
  4. eigen3.pc : math/eigen3
  5. xorgproto>=0 : x11/xorgproto
  6. xorgproto>=0 : x11/xorgproto
  7. moc : devel/qt5-buildtools
  8. qmake : devel/qt5-qmake
Runtime dependencies:
  1. eigen3.pc : math/eigen3
Library dependencies:
  1. libmsym.so : science/libmsym
  2. libMoleQueueClient.so : misc/molequeue
  3. libsymspg.so : science/spglib
  4. libarchive.so.13 : archivers/libarchive
  5. libGL.so : graphics/mesa-libs
  6. libGLEW.so : graphics/glew
  7. libGLU.so : graphics/libGLU
  8. libQt5Concurrent.so : devel/qt5-concurrent
  9. libQt5Core.so : devel/qt5-core
  10. libQt5Gui.so : x11-toolkits/qt5-gui
  11. libQt5Network.so : net/qt5-network
  12. libQt5Widgets.so : x11-toolkits/qt5-widgets
This port is required by:
for Libraries
  1. science/avogadro2
  2. science/kalzium
  3. science/py-avogadrolibs

Configuration Options

USES:

Master Sites:
Expand this list (1 items)
    Collapse this list.
  1. https://codeload.github.com/OpenChemistry/avogadrolibs/tar.gz/1.93.0?dummy=/
  2. Collapse this list.

Number of commits found: 17

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
12 Dec 2020 17:04:37
Original commit files touched by this commit  1.93.0_1
Revision:557839
thierry search for other commits by this committer
- Upgrade math/eigen3 to 3.3.8;

- Add some dependencies which might be detected by Find_Package but not
registered;

- Bump PORTREVISION of consumers.

PR:		250833
Submitted by:	/me
Approved by:	tcberner@ (KDE / maintainer) + exp-run
27 Apr 2020 16:09:57
Original commit files touched by this commit  1.93.0
Revision:533149
yuri search for other commits by this committer
science/avogadrolibs: Remove a broken option VTK set to default by mistake

Reported by:	cmt
26 Apr 2020 22:04:10
Original commit files touched by this commit  1.93.0
Revision:533086
yuri search for other commits by this committer
math/vtk8: Update 8.1.2 -> 8.2.0

science/liggght is updated 3.8.0 -> 3.8.0-26 because only later revisions
support vtk8-8.2.0
3 dependent ports bumped.
06 Feb 2020 05:09:44
Original commit files touched by this commit  1.93.0
Revision:525363
yuri search for other commits by this committer
science/avogadrolibs: Update 1.92.1 -> 1.93.0

Reported by:	portscout
26 Jul 2019 20:46:57
Original commit files touched by this commit  1.92.1_1
Revision:507372
gerald search for other commits by this committer
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
11 May 2019 18:10:31
Original commit files touched by this commit  1.92.1
Revision:501276
yuri search for other commits by this committer
science/avogadrolibs: Update 1.92.0 -> 1.92.1
16 Feb 2019 08:02:02
Original commit files touched by this commit  1.92.0_5
Revision:493031
yuri search for other commits by this committer
Move: science/mmtf -> science/mmtf-cpp

Also update its COMMENT to be more descriptive
12 Feb 2019 06:18:06
Original commit files touched by this commit  1.92.0_5
Revision:492755
yuri search for other commits by this committer
science/mmtf: Update g20180730 -> 1.0.0

Bump science/avogadrolibs since it uses this headers-only library.
16 Jan 2019 11:13:45
Original commit files touched by this commit  1.92.0_4
Revision:490472
tijl search for other commits by this committer
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
(Only the first 15 lines of the commit message are shown above View all of this commit message)
05 Jan 2019 22:46:54
Original commit files touched by this commit  1.92.0_3
Revision:489412
sunpoet search for other commits by this committer
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
26 Dec 2018 09:06:35
Original commit files touched by this commit  1.92.0_2
Revision:488363
tcberner search for other commits by this committer
Update math/eigen3 to 3.3.7

- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.6
- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.7
25 Dec 2018 20:25:40
Original commit files touched by this commit  1.92.0_1
Revision:488341
tcberner search for other commits by this committer
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
12 Dec 2018 01:35:36
Original commit files touched by this commit  1.92.0_1
Revision:487272
gerald search for other commits by this committer
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
09 Nov 2018 06:25:39
Original commit files touched by this commit  1.92.0
Revision:484502
yuri search for other commits by this committer
science/avogadrolibs: Update 1.91.0-107 -> 1.92.0

Also add 2 pull requests that fix obvious problems.
18 Oct 2018 22:31:27
Original commit files touched by this commit  1.91.0.107
Revision:482387
yuri search for other commits by this committer
science/avogadrolibs: Update 1.91.0 -> 1.91.0-107

jsoncpp isn't used any more, mmtf is now used.
17 Oct 2018 07:04:19
Original commit files touched by this commit  1.91.0_1
Revision:482273
yuri search for other commits by this committer
science/avogadrolibs: Add options
17 Oct 2018 01:02:16
Original commit files touched by this commit  1.91.0
Revision:482265
yuri search for other commits by this committer
New port: science/avogadrolibs: Avogadro2 libraries for chemical editor and
visualization applications

Number of commits found: 17

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py-saltMar 03
vaultFeb 27
redisFeb 23
redis-develFeb 23
redis5Feb 23
zeekFeb 22
jenkinsFeb 20
raptor2Feb 20
asterisk13Feb 18
asterisk13Feb 18

10 vulnerabilities affecting 79 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last updated:
2021-03-05 21:21:29


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Calculated hourly:
Port count 42676
Broken 75
Deprecated 167
Ignore 313
Forbidden 4
Restricted 139
No CDROM 71
Vulnerable 19
Expired 37
Set to expire 143
Interactive 0
new 24 hours 2
new 48 hours5
new 7 days43
new fortnight87
new month153

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