| Port details |
- coot Crystallographic Object-Oriented Toolkit
- 0.8.9.2_3 science
 =0      0.8.9.2_3Version of this port present on the latest quarterly branch.  BROKEN: unfetchable
 DEPRECATED: Broken, uses EOLed python27
 This port expired on: 2020-02-19
 IGNORE: is marked as broken: unfetchable
- Maintainer: yuri@FreeBSD.org
- Port Added: 2018-07-08 04:45:42
- Last Update: 2020-02-22 19:08:36
- SVN Revision: 526852
- License: LGPL3
- WWW:
- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
- Description:
- Coot is for macromolecular model building, model completion and validation,
particularly suitable for protein modelling using X-ray data.
Coot displays maps and models and allows model manipulations such as
idealization, real space refinement, manual rotation/translation, rigid-body
fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots,
skeletonization, non-crystallographic symmetry and more.
WWW: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
 cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ 
- Manual pages:
-
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- No installation instructions:
- This port has been deleted.
- PKGNAME: coot
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1554259683
SHA256 (coot/coot-0.8.9.2.tar.gz) = f24ed258e43ea31452b54c62649c071aa15f356d077dce0dab94eb04f27a6625
SIZE (coot/coot-0.8.9.2.tar.gz) = 19635513
No package information for this port in our database- Sometimes this happens. Not all ports have packages. Perhaps there is a build error. Check the fallout link:
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- fftw>0 : math/fftw
- update-desktop-database : devel/desktop-file-utils
- gfortran9 : lang/gcc9
- gmake : devel/gmake
- gtk-update-icon-cache : graphics/gtk-update-icon-cache
- pkgconf>=1.3.0_1 : devel/pkgconf
- python2.7 : lang/python27
- as : devel/binutils
- xorgproto>=0 : x11/xorgproto
- xorgproto>=0 : x11/xorgproto
- ice.pc : x11/libICE
- sm.pc : x11/libSM
- x11.pc : x11/libX11
- xmu.pc : x11-toolkits/libXmu
- xt.pc : x11-toolkits/libXt
- Runtime dependencies:
-
- bash : shells/bash
- update-desktop-database : devel/desktop-file-utils
- gfortran9 : lang/gcc9
- gtk-update-icon-cache : graphics/gtk-update-icon-cache
- python2.7 : lang/python27
- ice.pc : x11/libICE
- sm.pc : x11/libSM
- x11.pc : x11/libX11
- xmu.pc : x11-toolkits/libXmu
- xt.pc : x11-toolkits/libXt
- Library dependencies:
-
- libccp4c.so : science/libccp4
- libclipper-core.so : science/clipper
- libcurl.so : ftp/curl
- libfontconfig.so : x11-fonts/fontconfig
- libfreetype.so : print/freetype2
- libgoocanvas.so : graphics/goocanvas
- libgtkglext-x11-1.0.so : x11-toolkits/gtkglext
- libgsl.so : math/gsl
- libmmdb2.so : science/mmdb2
- libpng.so : graphics/png
- libsfftw.so : math/fftw-float
- libssm.so : science/libssm
- libintl.so : devel/gettext-runtime
- libGL.so : graphics/mesa-libs
- libGLU.so : graphics/libGLU
- libglut.so : graphics/freeglut
- libatk-1.0.so : accessibility/atk
- libcairo.so : graphics/cairo
- libgdk_pixbuf-2.0.so : graphics/gdk-pixbuf2
- libglib-2.0.so : devel/glib20
- libintl.so : devel/gettext-runtime
- libgtk-x11-2.0.so : x11-toolkits/gtk20
- libart_lgpl_2.so : graphics/libart_lgpl
- libglade-2.0.so : devel/libglade2
- libgnomecanvas-2.so : graphics/libgnomecanvas
- libxml2.so : textproc/libxml2
- libpango-1.0.so : x11-toolkits/pango
- libpangox-1.0.so : x11-toolkits/pangox-compat
- libsqlite3.so : databases/sqlite3
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- N/A
- USES:
- compiler:c++11-lang desktop-file-utils fortran gettext-runtime gl gmake gnome libtool localbase:ldflags pkgconfig python:2.7 shebangfix sqlite xorg xorg
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.8.9.2_3
22 Feb 2020 19:08:36
  |
rene |
Remove expired ports, all Python-2.7-only:
2020-02-17 audio/decibel-audio-player: Old, uses EOLed python27
2020-02-17 audio/soundconverter: Old, uses EOLed python27
2020-02-19 cad/linuxcnc-devel: Broken, uses EOLed python27
2020-02-19 databases/monetdb: Broken, uses EOLed python27
2020-02-19 databases/py-cql: Broken, uses EOLed python27
2020-02-18 databases/zodb3: Old, uses EOLed python27
2020-02-17 deskutils/gourmet: Old, uses EOLed python27
2020-02-18 devel/py-Products.PlacelessTranslationService: Old, uses EOLed
python27
2020-02-18 devel/py-Products.ZopeVersionControl: Old, uses EOLed python27
2020-02-18 devel/py-Products.statusmessages: Old, uses EOLed python27
2020-02-18 devel/py-collective.z3cform.datetimewidget: Old, uses EOLed python27
2020-02-20 devel/py-five.formlib: Old, uses EOLed python27
2020-02-18 devel/py-five.localsitemanager: Old, uses EOLed python27 (Only the first 15 lines of the commit message are shown above  ) |
0.8.9.2_3
14 Jan 2020 12:36:37
|
antoine |
Deprecate a few broken ports
With hat: portmgr |
0.8.9.2_3
07 Nov 2019 17:17:54
|
zeising |
Add USES=xorg USES=gl, ports categories s
Add USES=xorg and USES=gl to ports in categories starting with 's'
While here, try to sprinkle other USES (mostly gnome and sdl) as needed. |
0.8.9.2_3
06 Nov 2019 16:26:35
|
antoine |
Mark a few ports BROKEN (unfetchable) |
0.8.9.2_3
25 Oct 2019 23:41:34
|
tcberner |
math/gsl: update to 2.6
- math/p5-Math-GSL does not seem to have any upstream activity to make it work
with this version -> mark it broken
- this also breaks the two consumers of this port
- biology/gemma: has a conflict with cblas, and is makred broken.
PR: 241363
Exp-run by: antoine |
0.8.9.2_2
26 Jul 2019 20:46:57
|
gerald |
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 |
0.8.9.2_1
16 Jun 2019 16:05:29
|
antoine |
Clean up LIB_DEPENDS |
0.8.9.2_1
11 May 2019 20:40:34
|
yuri |
science/coot: Fix build with GCC-based architectures
PR: 237842
Submitted by: pkubaj |
0.8.9.2_1
22 Apr 2019 13:16:34
|
gerald |
Related to revision 499061 bump ports with USES=fortran to have them
benefit from the improved situation where libgcc_s is only used when
absolutely necessary.
Suggested by: tijl |
0.8.9.2
03 Apr 2019 05:01:11
|
yuri |
science/coot: Update 0.8.9.1 -> 0.8.9.2
* Add goocanvas dependency
* Add fftw dependency
Reported by: portscout |
0.8.9.1_2
17 Jan 2019 05:59:38
|
yuri |
science/coot: Remove the unused CONFIGURE_ARGS line
PR: 234737
Reported by: tobik |
0.8.9.1_2
12 Dec 2018 01:35:36
|
gerald |
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 |
0.8.9.1_1
01 Oct 2018 09:36:38
|
antoine |
Cleanup plists |
0.8.9.1_1
29 Jul 2018 22:18:46
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
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 |
0.8.9.1
08 Jul 2018 04:45:25
|
yuri |
New port: science/coot: Crystallographic Object-Oriented Toolkit |
As an Amazon Associate I earn from qualifying purchases.