notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)

/commits.php is going away

I'm proposing to take /commits.php away - it mainly duplicates the home page. Details in this GitHub issue.
Port details
cd-hit Clustering and comparing protein or nucleotide sequences
4.8.1_2 biology 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 4.8.1_2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-09-19 11:17:00
Last Update: 2021-06-10 00:35:36
Commit Hash: 8aae744
License: GPLv2
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (43 items)
Collapse this list.
  1. /usr/local/share/licenses/cd-hit-4.8.1_2/catalog.mk
  2. /usr/local/share/licenses/cd-hit-4.8.1_2/LICENSE
  3. /usr/local/share/licenses/cd-hit-4.8.1_2/GPLv2
  4. bin/FET.pl
  5. bin/cd-hit
  6. bin/cd-hit-2d
  7. bin/cd-hit-2d-para.pl
  8. bin/cd-hit-454
  9. bin/cd-hit-clstr_2_blm8.pl
  10. bin/cd-hit-div
  11. bin/cd-hit-div.pl
  12. bin/cd-hit-est
  13. bin/cd-hit-est-2d
  14. bin/cd-hit-para.pl
  15. bin/clstr2tree.pl
  16. bin/clstr2txt.pl
  17. bin/clstr2xml.pl
  18. bin/clstr_cut.pl
  19. bin/clstr_list.pl
  20. bin/clstr_list_sort.pl
  21. bin/clstr_merge.pl
  22. bin/clstr_merge_noorder.pl
  23. bin/clstr_quality_eval.pl
  24. bin/clstr_quality_eval_by_link.pl
  25. bin/clstr_reduce.pl
  26. bin/clstr_renumber.pl
  27. bin/clstr_rep.pl
  28. bin/clstr_reps_faa_rev.pl
  29. bin/clstr_rev.pl
  30. bin/clstr_select.pl
  31. bin/clstr_select_rep.pl
  32. bin/clstr_size_histogram.pl
  33. bin/clstr_size_stat.pl
  34. bin/clstr_sort_by.pl
  35. bin/clstr_sort_prot_by.pl
  36. bin/clstr_sql_tbl.pl
  37. bin/clstr_sql_tbl_sort.pl
  38. bin/make_multi_seq.pl
  39. bin/plot_2d.pl
  40. bin/plot_len1.pl
  41. @owner
  42. @group
  43. @mode
Collapse this list.
Dependency lines:
  • cd-hit>0:biology/cd-hit
To install the port: cd /usr/ports/biology/cd-hit/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/cd-hit
  • pkg install cd-hit
PKGNAME: cd-hit
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
cd-hit
ABIlatestquarterly
FreeBSD:11:aarch644.6.6_44.8.1_1
FreeBSD:11:amd644.8.1_24.8.1_2
FreeBSD:11:armv64.6.44.8.1_1
FreeBSD:11:i3864.8.1_24.8.1_2
FreeBSD:11:mips--
FreeBSD:11:mips644.6.44.8.1_1
FreeBSD:12:aarch644.6.6_44.8.1_2
FreeBSD:12:amd644.8.1_24.8.1_2
FreeBSD:12:armv64.6.6_44.8.1_1
FreeBSD:12:armv74.6.6_44.8.1_1
FreeBSD:12:i3864.8.1_24.8.1_2
FreeBSD:12:mips--
FreeBSD:12:mips644.6.6_44.8.1_1
FreeBSD:12:powerpc64-4.8.1_2
FreeBSD:13:aarch644.8.1_24.8.1_2
FreeBSD:13:amd644.8.1_24.8.1_2
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3864.8.1_24.8.1_2
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc644.8.1_14.8.1_2
FreeBSD:14:aarch644.8.1_2-
FreeBSD:14:amd644.8.1_2-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3864.8.1_2-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc644.8.1_2-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
This port is required by:
for Run
  1. biology/biostar-tools
  2. biology/ddocent
  3. biology/p5-transdecoder

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/weizhongli/cdhit/tar.gz/V4.8.1?dummy=/
Collapse this list.

Number of commits found: 18

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
10 Jun 2021 00:35:36
 files touched by this commit commit hash:8aae744d04920573ee2c3c34390c268a05beff39  4.8.1_2
pkubaj search for other commits by this committer
biology/cd-hit: fix build on powerpc

LLVM on powerpc doesn't have libomp:
cdhit-common.c++:36:9: fatal error: 'omp.h' file not found
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  4.8.1_2
mat search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  4.8.1_2
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
11 Jan 2021 16:55:15
Original commit files touched by this commit Revision:561228  4.8.1_2
jwb search for other commits by this committer
biology/cd-hit: Drop dependency on gcc

Simply remove compiler:openmp
Builds with base compiler on amd64, i386, and powerpc64

PR:             port/247753, ports/252379
26 Jul 2019 20:46:57
Original commit files touched by this commit Revision:507372  4.8.1_1
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
14 Mar 2019 23:59:48
Original commit files touched by this commit Revision:495746  4.8.1
jwb search for other commits by this committer
biology/cd-hit: Upgrade to 4.8.1

Convert Makefile REINPLACE to patch for sending upstream
12 Dec 2018 01:35:36
Original commit files touched by this commit Revision:487272  4.6.6_5
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
29 Jul 2018 22:18:46
Original commit files touched by this commit Revision:475857  4.6.6_4
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
10 Mar 2018 17:46:06
Original commit files touched by this commit Revision:464084  4.6.6_3
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
31 Jan 2018 01:07:08
Original commit files touched by this commit Revision:460452  4.6.6_2
jwb search for other commits by this committer
Multiple ports:
Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org
Remove Created by comments for same user

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14128
10 Sep 2017 20:55:39
Original commit files touched by this commit Revision:449591  4.6.6_2
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 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, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275
01 Apr 2017 15:23:32
Original commit files touched by this commit Revision:437439  4.6.6_1
gerald search for other commits by this committer
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707
20 Dec 2016 16:48:12
Original commit files touched by this commit Revision:429002  4.6.6
jrm search for other commits by this committer
biology/cd-hit: Update to bug-fix release 4.6.6

Changes in version 4.6.6:
Bug fix for cd-hit-dup in variable length input when write out R1 reads

Changes in version 4.6.5:
Add filter for -aL option so that short sequences will be skipped if not
satisfy representative sequences' -aL requirement. This will make compute
faster in clustering settings where sequences in the same cluster are
required to have similar length using -aL -AL option (e.g. -aL 0.9).

Approved by:	AMDmi3 (mentor) swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8186
02 Dec 2016 11:58:22
Original commit files touched by this commit Revision:427552  4.6.4_1
mat search for other commits by this committer
Do not use post-stage.  Use post-install instead.

The only reason to use post-stage is because the port needs to do
"things" at a later time, like some plist manipulation.
While there, fold post-install in do-install targets when they are
defined.

PR:		214780
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
20 Nov 2016 09:38:09
Original commit files touched by this commit Revision:426566  4.6.4_1
gerald search for other commits by this committer
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

In particular that is ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.
11 Dec 2015 08:48:57
Original commit files touched by this commit Revision:403506  4.6.4
miwi search for other commits by this committer
- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493
19 Sep 2015 13:12:44
Original commit files touched by this commit Revision:397322  4.6.4
wen search for other commits by this committer
- Use compiler:openmp instead of gcc
- Minor cleanup

Reported by:	danfe@
19 Sep 2015 11:16:52
Original commit files touched by this commit Revision:397318  4.6.4
wen search for other commits by this committer
CD-HIT is a very widely used program for clustering and comparing protein or
nucleotide sequences.

WWW: http://weizhong-lab.ucsd.edu/cd-hit/

PR:		203183
Submitted by:	jwbacon@tds.net

Number of commits found: 18