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Port details
unanimity Pacific Biosciences consensus library and applications
3.4.1_4 biology Deleted 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. 3.4.1_4Version of this port present on the latest quarterly branch.
Broken BROKEN: unfetchable
Deprecated DEPRECATED: Unmaintained, uses EOLed python27
Expired This port expired on: 2020-01-27
Ignore IGNORE: is marked as broken: unfetchable
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
search for ports maintained by this maintainer
Port Added: 2018-04-24 14:17:02
Last Update: 2020-01-27 15:34:18
SVN Revision: 524263
License: BSD3CLAUSE
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (86 items)
  1. @ldconfig
  2. /usr/local/share/licenses/unanimity-3.4.1_4/catalog.mk
  3. /usr/local/share/licenses/unanimity-3.4.1_4/LICENSE
  4. /usr/local/share/licenses/unanimity-3.4.1_4/BSD3CLAUSE
  5. bin/ChimeraLabeler
  6. bin/arrow
  7. bin/ccs
  8. bin/ccs_sim
  9. bin/gcpp
  10. bin/genomic_sim
  11. bin/variantCaller
  12. include/pacbio/UnanimityConfig.h
  13. include/pacbio/UnanimityVersion.h
  14. include/pacbio/align/AffineAlignment.h
  15. include/pacbio/align/AlignConfig.h
  16. include/pacbio/align/BandedAligner.h
  17. include/pacbio/align/BandedChainAlignment.h
  18. include/pacbio/align/ChainScorer.h
  19. include/pacbio/align/ChainSeeds.h
  20. include/pacbio/align/ChainSeedsConfig.h
  21. include/pacbio/align/FilterSeeds.h
  22. include/pacbio/align/FindSeeds.h
  23. include/pacbio/align/FindSeedsConfig.h
  24. include/pacbio/align/HomopolymerHasher.h
  25. include/pacbio/align/LinearAlignment.h
  26. include/pacbio/align/LocalAlignment.h
  27. include/pacbio/align/PairwiseAlignment.h
  28. include/pacbio/align/SeedScorer.h
  29. include/pacbio/align/SparseAlignment.h
  30. include/pacbio/align/internal/BCAlignBlocks.h
  31. include/pacbio/align/internal/BCAlignImpl.h
  32. include/pacbio/ccs/Consensus.h
  33. include/pacbio/ccs/ConsensusSettings.h
  34. include/pacbio/ccs/SparseAlignment.h
  35. include/pacbio/ccs/Whitelist.h
  36. include/pacbio/chimera/ChimeraLabel.h
  37. include/pacbio/chimera/ChimeraLabeler.h
  38. include/pacbio/chimera/ChimeraResultWriter.h
  39. include/pacbio/consensus/AbstractMatrix.h
  40. include/pacbio/consensus/Coverage.h
  41. include/pacbio/consensus/EasyReadScorer.h
  42. include/pacbio/consensus/Evaluator.h
  43. include/pacbio/consensus/Integrator.h
  44. include/pacbio/consensus/IntervalMask.h
  45. include/pacbio/consensus/MatrixViewConvention.h
  46. include/pacbio/consensus/ModelConfig.h
  47. include/pacbio/consensus/ModelSelection.h
  48. include/pacbio/consensus/Mutation.h
  49. include/pacbio/consensus/Polish.h
  50. include/pacbio/consensus/PolishResult.h
  51. include/pacbio/consensus/Template.h
  52. include/pacbio/consensus/internal/ModelInternalInitializer.h
  53. include/pacbio/data/ChemistryMapping.h
  54. include/pacbio/data/ChemistryTriple.h
  55. include/pacbio/data/Interval.h
  56. include/pacbio/data/IntervalTree.h
  57. include/pacbio/data/PlainOption.h
  58. include/pacbio/data/Read.h
  59. include/pacbio/data/ReadId.h
  60. include/pacbio/data/Sequence.h
  61. include/pacbio/data/State.h
  62. include/pacbio/data/StrandType.h
  63. include/pacbio/data/SubreadResultCounter.h
  64. include/pacbio/data/internal/BaseEncoding.h
  65. include/pacbio/data/internal/ConversionFunctions.h
  66. include/pacbio/denovo/PoaConsensus.h
  67. include/pacbio/denovo/PoaGraph.h
  68. include/pacbio/denovo/RangeFinder.h
  69. include/pacbio/denovo/SparsePoa.h
  70. include/pacbio/exception/CCSExceptions.h
  71. include/pacbio/exception/InvalidEvaluatorException.h
  72. include/pacbio/exception/ModelError.h
  73. include/pacbio/exception/StateError.h
  74. include/pacbio/io/Utility.h
  75. include/pacbio/parallel/WorkQueue.h
  76. include/pacbio/util/ExecUtils.h
  77. include/pacbio/util/Timer.h
  78. lib/libunanimity.so
  79. lib/libunanimity.so.3
  80. lib/libunanimity.so.3.0
  81. lib/libunanimity.so.3.0.0
  82. lib/python2.7/site-packages/ConsensusCore2.py
  83. lib/python2.7/site-packages/ConsensusCore2.pyc
  84. lib/python2.7/site-packages/ConsensusCore2.pyo
  85. lib/python2.7/site-packages/_ConsensusCore2.so
  86. libdata/pkgconfig/unanimity.pc
Collapse this list.
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}>0:biology/unanimity
No installation instructions: this port has been deleted.
The package name of this deleted port was:
PKGNAME: unanimity
Flavors: there is no flavor information for this port.
distinfo:
Packages: (move your mouse over the cells for more information)
No package information in database for this port.

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. seqan>=2.4.0 : biology/seqan
  2. swig30>=3.0 : devel/swig30
  3. py27-numpy>0 : math/py-numpy@py27
  4. meson : devel/meson
  5. ninja : devel/ninja
  6. pkgconf>=1.3.0_1 : devel/pkgconf
  7. python2.7 : lang/python27
Runtime dependencies:
  1. py27-numpy>0 : math/py-numpy@py27
  2. python2.7 : lang/python27
Library dependencies:
  1. libhts.so : biology/htslib
  2. libboost_regex.so : devel/boost-libs
  3. libpbbam.so.0.18.0 : biology/pbbam
  4. libpbcopper.so.0.4.1 : biology/pbcopper
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/v3.4.1?dummy=/
Port Moves
  • port deleted on 2020-01-27
    REASON: Has expired: Unmaintained, uses EOLed python27

Number of commits found: 22

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
27 Jan 2020 15:34:18
Original commit files touched by this commit  3.4.1_4
Revision:524263
rene search for other commits by this committer
Remove expired ports:

2020-01-27 accessibility/py-papi: Unmaintained, uses EOLed python27
2020-01-27 archivers/py-czipfile: Unmaintained, uses EOLed python27
2020-01-27 audio/boodler: Unmaintained, uses EOLed python27
2020-01-27 audio/dir2ogg: Unmaintained, uses EOLed python27
2020-01-27 audio/jokosher: Unmaintained, uses EOLed python27
2020-01-27 audio/mpdbrowser: Unmaintained, uses EOLed python27
2020-01-27 audio/nekobee: Unmaintained, uses EOLed python27
2020-01-27 audio/patchage: Unmaintained, uses EOLed python27
2020-01-27 audio/py-ao: Unmaintained, uses EOLed python27
2020-01-27 audio/py-id3: Unmaintained, uses EOLed python27
2020-01-27 audio/py-shout: Unmaintained, uses EOLed python27
2020-01-27 audio/py-speex: Unmaintained, uses EOLed python27
2020-01-27 audio/pytone: Unmaintained, uses EOLed python27
(Only the first 15 lines of the commit message are shown above View all of this commit message)
05 Jan 2020 10:26:04
Original commit files touched by this commit  3.4.1_4
Revision:522132
antoine search for other commits by this committer
Mark a few ports broken (unfetchable)
26 Dec 2019 07:54:29
Original commit files touched by this commit  3.4.1_4
Revision:520894
antoine search for other commits by this committer
Deprecate a few ports

With hat:	portmgr
11 Dec 2019 17:53:49
Original commit files touched by this commit  3.4.1_4
Revision:519824
jbeich search for other commits by this committer
devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136
28 Nov 2019 05:46:05
Original commit files touched by this commit  3.4.1_3
Revision:518557
jwb search for other commits by this committer
biology/unanimity: Remove erroneous BROKEN

Unsure why this was marked unfetchable.  Fetch works fine and the port is
still useful, though it cannot be upgraded to newer releases, which are
closed-source.
24 Nov 2019 15:53:01
Original commit files touched by this commit  3.4.1_3
Revision:518334
jwb search for other commits by this committer
biology/unanimity and dependencies: Flag as no longer open source

PacBio now provides unanimity only as a binary package through bioconda.
See https://github.com/PacificBiosciences/ccs.
06 Nov 2019 12:48:32
Original commit files touched by this commit  3.4.1_3
Revision:516880  Sanity Test Failure
antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
19 Aug 2019 15:35:28
Original commit files touched by this commit  3.4.1_3
Revision:509290
jbeich search for other commits by this committer
devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774
26 Jul 2019 20:46:57
Original commit files touched by this commit  3.4.1_2
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
25 Apr 2019 13:25:50
Original commit files touched by this commit  3.4.1_1
Revision:499993
antoine search for other commits by this committer
Clean up plist
12 Apr 2019 06:36:31
Original commit files touched by this commit  3.4.1_1
Revision:498698
jbeich search for other commits by this committer
devel/boost-*: update to 1.70.0

Changes:	http://www.boost.org/users/history/version_1_70_0.html
PR:		235956
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D19303
24 Feb 2019 16:04:58
Original commit files touched by this commit  3.4.1
Revision:493769
jwb search for other commits by this committer
biology/unanimity: Upgrade to 3.4.1

Minor fixes and enhancements upstream.
22 Feb 2019 23:26:02
Original commit files touched by this commit  3.4.0
Revision:493621
antoine search for other commits by this committer
biology/unanimity is not compatible with python 3.x

PR:		234633
20 Feb 2019 01:36:51
Original commit files touched by this commit  3.4.0
Revision:493402
jwb search for other commits by this committer
biology/unanimity: Upgrade to 3.4.0

Switch from cmake to new meson build system
Tests disabled for now pending work on unbundling googletest
25 Dec 2018 20:25:40
Original commit files touched by this commit  3.1.0_2
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  3.1.0_2
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
12 Dec 2018 00:15:50
Original commit files touched by this commit  3.1.0_1
Revision:487266
jbeich search for other commits by this committer
devel/boost-*: update to 1.69.0

Changes:	http://www.boost.org/users/history/version_1_69_0.html
PR:		232525
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D17645
18 Sep 2018 08:14:23
Original commit files touched by this commit  3.1.0
Revision:479990
linimon search for other commits by this committer
More precisely specify USES=compiler to fix build on gcc-based
platforms such as powerpc64.

Tested on powerpc64, amd64.

Approved by:	portmgr (tier-2 blanket)
25 Aug 2018 22:54:54
Original commit files touched by this commit  3.1.0
Revision:478089
jwb search for other commits by this committer
biology/unanimity: Upgrade to latest release, soften dep version requirements

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D16902
09 Aug 2018 06:58:31
Original commit files touched by this commit  g20180307_1
Revision:476723
jbeich search for other commits by this committer
devel/boost-*: update to 1.68.0

- Switch to C++14 for libboost_system to support C++14 consumers

Changes:	http://www.boost.org/users/history/version_1_68_0.html
PR:		229569
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D16165
22 Jun 2018 00:03:08
Original commit files touched by this commit  g20180307
Revision:473010
linimon search for other commits by this committer
Mark these ports as broken on aarch64.

Approved by:	portmgr (tier-2 blanket)
24 Apr 2018 14:16:46
Original commit files touched by this commit  g20180307
Revision:468214
jwb search for other commits by this committer
biology/unanimity: Pacific Biosciences consensus library and applications

Reviewed by:    jrm
Differential Revision:  https://reviews.freebsd.org/D15172

Number of commits found: 22

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