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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. pkg-fallout Version 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:
HomepagecgitGitHubGitLabSVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (86 items)
Collapse this list.
  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:
  • unanimity>0:biology/unanimity
No installation instructions:
This port has been deleted.
PKGNAME: unanimity
Flavors: there is no flavor information for this port.
distinfo:

No package information for this port in our database
Sometimes this happens. Not all ports have packages.

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:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/v3.4.1?dummy=/
Collapse this list.
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: for full details, see links to repositories near top of page)
CommitCreditsLog message
3.4.1_4
27 Jan 2020 15:34:18
Revision:524263Original commit files touched by this commit
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)
3.4.1_4
05 Jan 2020 10:26:04
Revision:522132Original commit files touched by this commit
antoine search for other commits by this committer
Mark a few ports broken (unfetchable)
3.4.1_4
26 Dec 2019 07:54:29
Revision:520894Original commit files touched by this commit
antoine search for other commits by this committer
Deprecate a few ports

With hat:	portmgr
3.4.1_4
11 Dec 2019 17:53:49
Revision:519824Original commit files touched by this commit
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
3.4.1_3
28 Nov 2019 05:46:05
Revision:518557Original commit files touched by this commit
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.
3.4.1_3
24 Nov 2019 15:53:01
Revision:518334Original commit files touched by this commit
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.
3.4.1_3
06 Nov 2019 12:48:32
Revision:516880Original commit files touched by this commit Sanity Test Failure
antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
3.4.1_3
19 Aug 2019 15:35:28
Revision:509290Original commit files touched by this commit
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
3.4.1_2
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
3.4.1_1
25 Apr 2019 13:25:50
Revision:499993Original commit files touched by this commit
antoine search for other commits by this committer
Clean up plist
3.4.1_1
12 Apr 2019 06:36:31
Revision:498698Original commit files touched by this commit
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
3.4.1
24 Feb 2019 16:04:58
Revision:493769Original commit files touched by this commit
jwb search for other commits by this committer
biology/unanimity: Upgrade to 3.4.1

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

PR:		234633
3.4.0
20 Feb 2019 01:36:51
Revision:493402Original commit files touched by this commit
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
3.1.0_2
25 Dec 2018 20:25:40
Revision:488341Original commit files touched by this commit
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
3.1.0_2
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
3.1.0_1
12 Dec 2018 00:15:50
Revision:487266Original commit files touched by this commit
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
3.1.0
18 Sep 2018 08:14:23
Revision:479990Original commit files touched by this commit
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)
3.1.0
25 Aug 2018 22:54:54
Revision:478089Original commit files touched by this commit
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
g20180307_1
09 Aug 2018 06:58:31
Revision:476723Original commit files touched by this commit
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
g20180307
22 Jun 2018 00:03:08
Revision:473010Original commit files touched by this commit
linimon search for other commits by this committer
Mark these ports as broken on aarch64.

Approved by:	portmgr (tier-2 blanket)
g20180307
24 Apr 2018 14:16:46
Revision:468214Original commit files touched by this commit
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