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Port details
clipper Libraries for the organisation of crystallographic data
2.1.20180802_4 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 2.1.20180802_4Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-07-08 01:30:02
Last Update: 2023-04-23 09:09:58
Commit Hash: 8d3e020
License: LGPL3
WWW:
http://www.ysbl.york.ac.uk/~cowtan/clipper/
Description:
The aim of the project is to produce a set of object-oriented libraries for the organisation of crystallographic data and the performance of crystallographic computation. The libraries are designed as a framework for new crystallographic software, which will allow the full power of modern programming techniques to be exploited by the developer. This will lead to greater functionality from simpler code which will be easier to develop and debug.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (114 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/clipper-2.1.20180802_4/catalog.mk
  3. /usr/local/share/licenses/clipper-2.1.20180802_4/LICENSE
  4. /usr/local/share/licenses/clipper-2.1.20180802_4/LGPL3
  5. include/clipper/ccp4/ccp4_map_io.h
  6. include/clipper/ccp4/ccp4_mtz_io.h
  7. include/clipper/ccp4/ccp4_mtz_types.h
  8. include/clipper/ccp4/ccp4_utils.h
  9. include/clipper/cif/cif_data_io.h
  10. include/clipper/clipper-ccp4.h
  11. include/clipper/clipper-cctbx.h
  12. include/clipper/clipper-cif.h
  13. include/clipper/clipper-cns.h
  14. include/clipper/clipper-contrib.h
  15. include/clipper/clipper-minimol.h
  16. include/clipper/clipper-mmdb.h
  17. include/clipper/clipper-phs.h
  18. include/clipper/clipper.h
  19. include/clipper/cns/cns_hkl_io.h
  20. include/clipper/cns/cns_map_io.h
  21. include/clipper/contrib/convolution_search.h
  22. include/clipper/contrib/edcalc.h
  23. include/clipper/contrib/fffear.h
  24. include/clipper/contrib/function_object_bases.h
  25. include/clipper/contrib/mapfilter.h
  26. include/clipper/contrib/originmatch.h
  27. include/clipper/contrib/sfcalc.h
  28. include/clipper/contrib/sfcalc_obs.h
  29. include/clipper/contrib/sfscale.h
  30. include/clipper/contrib/sfweight.h
  31. include/clipper/contrib/skeleton.h
  32. include/clipper/contrib/test_contrib.h
  33. include/clipper/core/atomsf.h
  34. include/clipper/core/cell.h
  35. include/clipper/core/clipper_instance.h
  36. include/clipper/core/clipper_memory.h
  37. include/clipper/core/clipper_message.h
  38. include/clipper/core/clipper_precision.h
  39. include/clipper/core/clipper_stats.h
  40. include/clipper/core/clipper_sysdep.h
  41. include/clipper/core/clipper_test.h
  42. include/clipper/core/clipper_thread.h
  43. include/clipper/core/clipper_types.h
  44. include/clipper/core/clipper_util.h
  45. include/clipper/core/container.h
  46. include/clipper/core/container_hkl.h
  47. include/clipper/core/container_map.h
  48. include/clipper/core/container_types.h
  49. include/clipper/core/coords.h
  50. include/clipper/core/derivs.h
  51. include/clipper/core/fftmap.h
  52. include/clipper/core/fftmap_sparse.h
  53. include/clipper/core/hkl_compute.h
  54. include/clipper/core/hkl_data.h
  55. include/clipper/core/hkl_datatypes.h
  56. include/clipper/core/hkl_info.h
  57. include/clipper/core/hkl_lookup.h
  58. include/clipper/core/hkl_operators.h
  59. include/clipper/core/map_interp.h
  60. include/clipper/core/map_utils.h
  61. include/clipper/core/nxmap.h
  62. include/clipper/core/nxmap_operator.h
  63. include/clipper/core/ramachandran.h
  64. include/clipper/core/resol_basisfn.h
  65. include/clipper/core/resol_fn.h
  66. include/clipper/core/resol_targetfn.h
  67. include/clipper/core/rotation.h
  68. include/clipper/core/spacegroup.h
  69. include/clipper/core/spacegroup_data.h
  70. include/clipper/core/symop.h
  71. include/clipper/core/test_core.h
  72. include/clipper/core/test_data.h
  73. include/clipper/core/xmap.h
  74. include/clipper/minimal-clipper-hkl.h
  75. include/clipper/minimal-clipper-map.h
  76. include/clipper/minimol/container_minimol.h
  77. include/clipper/minimol/minimol.h
  78. include/clipper/minimol/minimol_data.h
  79. include/clipper/minimol/minimol_io.h
  80. include/clipper/minimol/minimol_seq.h
  81. include/clipper/minimol/minimol_utils.h
  82. include/clipper/mmdb/clipper_mmdb.h
  83. include/clipper/phs/phs_io.h
  84. lib/libclipper-ccp4.so
  85. lib/libclipper-ccp4.so.2
  86. lib/libclipper-ccp4.so.2.0.1
  87. lib/libclipper-cif.so
  88. lib/libclipper-cif.so.2
  89. lib/libclipper-cif.so.2.0.1
  90. lib/libclipper-cns.so
  91. lib/libclipper-cns.so.2
  92. lib/libclipper-cns.so.2.0.1
  93. lib/libclipper-contrib.so
  94. lib/libclipper-contrib.so.2
  95. lib/libclipper-contrib.so.2.0.1
  96. lib/libclipper-core.so
  97. lib/libclipper-core.so.2
  98. lib/libclipper-core.so.2.0.1
  99. lib/libclipper-fortran.so
  100. lib/libclipper-fortran.so.2
  101. lib/libclipper-fortran.so.2.0.1
  102. lib/libclipper-minimol.so
  103. lib/libclipper-minimol.so.2
  104. lib/libclipper-minimol.so.2.0.1
  105. lib/libclipper-mmdb.so
  106. lib/libclipper-mmdb.so.2
  107. lib/libclipper-mmdb.so.2.0.1
  108. lib/libclipper-phs.so
  109. lib/libclipper-phs.so.2
  110. lib/libclipper-phs.so.2.0.1
  111. libdata/pkgconfig/clipper.pc
  112. @owner
  113. @group
  114. @mode
Collapse this list.
Dependency lines:
  • clipper>0:science/clipper
To install the port:
cd /usr/ports/science/clipper/ && make install clean
To add the package, run one of these commands:
  • pkg install science/clipper
  • pkg install clipper
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: clipper
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1538018135 SHA256 (clipper-2.1.20180802.tar.gz) = 7c7774f224b59458e0faa104d209da906c129523fa737e81eb3b99ec772b81e0 SIZE (clipper-2.1.20180802.tar.gz) = 4238748

Packages (timestamps in pop-ups are UTC):
clipper
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-2.1.20180802_4-2.1.20180802_42.1.20180802_4-2.1.20180802_3-
FreeBSD:13:quarterly-2.1.20180802_4-2.1.20180802_42.1.20180802_4-2.1.20180802_42.1.20180802_4
FreeBSD:14:latest-2.1.20180802_4-2.1.20180802_42.1.20180802_4---
FreeBSD:14:quarterly-2.1.20180802_4-2.1.20180802_42.1.20180802_4-2.1.20180802_42.1.20180802_4
FreeBSD:15:latest-2.1.20180802_4n/a2.1.20180802_4n/a-2.1.20180802_42.1.20180802_4
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gfortran12 : lang/gcc12
  2. gmake>=4.3 : devel/gmake
  3. as : devel/binutils
Runtime dependencies:
  1. gfortran12 : lang/gcc12
Library dependencies:
  1. libccp4c.so : science/libccp4
  2. libmmdb2.so : science/mmdb2
  3. libsfftw.so : math/fftw-float
This port is required by:
for Libraries

Deleted ports which required this port:

Expand this list of 1 deleted port
  1. science/coot*
  2. Collapse this list of deleted ports.
* - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

Configuration Options:
No options to configure
Options name:
science_clipper
USES:
compiler:c++11-lang fortran gmake libtool localbase:ldflags
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/
Collapse this list.

Number of commits found: 12

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.1.20180802_4
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.1.20180802_3
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.1.20180802_3
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.1.20180802_3
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.1.20180802_3
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
2.1.20180802_2
11 May 2019 20:30:19
Revision:501304Original commit files touched by this commit
pkubaj search for other commits by this committer
science/clipper: add USES=compiler:c++11-lang

This is needed to build science/coot.

Approved by:	mentors (implicit approval)
2.1.20180802_2
22 Apr 2019 13:16:34
Revision:499638Original commit files touched by this commit
gerald search for other commits by this committer
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
2.1.20180802_1
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
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
2.1.20180802
27 Sep 2018 03:50:56
Revision:480774Original commit files touched by this commit
yuri search for other commits by this committer
science/clipper: Update 2.1.20180526 -> 2.1.20180802

Reported by:	portscout
2.1.20180526_1
29 Jul 2018 22:18:46
Revision:475857Original commit files touched by this commit
gerald search for other commits by this committer
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
2.1.20180526
08 Jul 2018 01:27:11
Revision:474150Original commit files touched by this commit
yuri search for other commits by this committer
New port: science/clipper: Libraries for the organisation of crystallographic
data

Number of commits found: 12