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Things are slow!

Some of the pages ont the website are slow. I know diskio is way up. I don't know what it is but it's been going on for about three weeks. It might have been a change to the zpool recordsize on the PostgreSQL database dataset.

One way to know: copy the dataset to another dataset with the original recordsize and use that. I hope can get to that later this week.

I have not tackled the issue yet because I've been concentrating on the BSDCan and PGCon calls for papers.

Port details
cd-hit Clustering and comparing protein or nucleotide sequences
4.8.1_1 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 4.8.1Version 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: 2019-07-26 21:46:57
SVN Revision: 507372
License: GPLv2
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (40 items)
  1. /usr/local/share/licenses/cd-hit-4.8.1_1/catalog.mk
  2. /usr/local/share/licenses/cd-hit-4.8.1_1/LICENSE
  3. /usr/local/share/licenses/cd-hit-4.8.1_1/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
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: pkg install cd-hit
PKGNAME: cd-hit
Flavors: there is no flavor information for this port.
distinfo:

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

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/weizhongli/cdhit/tar.gz/V4.8.1?dummy=/

Number of commits found: 14

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
26 Jul 2019 20:46:57
Original commit files touched by this commit  4.8.1_1
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
14 Mar 2019 23:59:48
Original commit files touched by this commit  4.8.1
Revision:495746
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  4.6.6_5
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
29 Jul 2018 22:18:46
Original commit files touched by this commit  4.6.6_4
Revision:475857
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  4.6.6_3
Revision:464084
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  4.6.6_2
Revision:460452
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  4.6.6_2
Revision:449591
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  4.6.6_1
Revision:437439
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  4.6.6
Revision:429002
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  4.6.4_1
Revision:427552
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  4.6.4_1
Revision:426566
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  4.6.4
Revision:403506
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  4.6.4
Revision:397322
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  4.6.4
Revision:397318
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: 14

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