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The cause of the slowdown was a change to the ZFS dataset. In conjunction with the database server, very little caching was being done. This combination resulted in increased disk I/O as the system churned through the database. Details in the blog post which outlines the various things which changed. Many graphs.

Port details
pycogent Toolkit for statistical analysis of biological sequences
1.9_3 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 1.9Version of this port present on the latest quarterly branch.
Deprecated DEPRECATED: Unmaintained, uses EOLed python27
Expired This port expired on: 2020-01-27
Maintainer: python@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-06-22 12:47:26
Last Update: 2020-01-27 15:34:18
SVN Revision: 524263
Also Listed In: python
License: GPLv2
Description:
SVNWeb : Homepage

There is no configure plist information for this port.

Dependency lines:
  • pycogent>0:biology/pycogent
No installation instructions: this port has been deleted.
The package name of this deleted port was:
PKGNAME: pycogent
Package flavors (<flavor>: <package>)
  • py27: pycogent
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py27-numpy>0 : math/py-numpy@py27
  2. py27-sphinx>=0 : textproc/py-sphinx@py27
  3. py27-sqlalchemy10>=1.0.13 : databases/py-sqlalchemy10@py27
  4. cython-2.7 : lang/cython@py27
  5. py27-setuptools>0 : devel/py-setuptools@py27
  6. python2.7 : lang/python27
Runtime dependencies:
  1. py27-numpy>0 : math/py-numpy@py27
  2. py27-sphinx>=0 : textproc/py-sphinx@py27
  3. py27-sqlalchemy10>=1.0.13 : databases/py-sqlalchemy10@py27
  4. py27-setuptools>0 : devel/py-setuptools@py27
  5. python2.7 : lang/python27
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/pycogent/pycogent/tar.gz/1.9?dummy=/
Port Moves
  • port deleted on 2020-01-27
    REASON: Has expired: Unmaintained, uses EOLed python27

Number of commits found: 25

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  1.9_3
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)
26 Dec 2019 07:54:29
Original commit files touched by this commit  1.9_3
Revision:520894
antoine search for other commits by this committer
Deprecate a few ports

With hat:	portmgr
26 Jul 2019 20:46:57
Original commit files touched by this commit  1.9_3
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
12 Dec 2018 01:35:36
Original commit files touched by this commit  1.9_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
20 Jun 2018 17:05:44
Original commit files touched by this commit  1.9_1
Revision:472884
mat search for other commits by this committer
Use PY_FLAVOR for dependencies.

FLAVOR is the current port's flavor, it should not be used outside of
this scope.

Sponsored by:	Absolight
10 Mar 2018 17:46:06
Original commit files touched by this commit  1.9_1
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).
11 Dec 2017 16:54:20
Original commit files touched by this commit  1.9
Revision:456050
antoine search for other commits by this committer
- Those ports fail to build with python3
- Add some explicit FLAVOR to dependencies where needed
30 Nov 2017 15:50:34
Original commit files touched by this commit  1.9
Revision:455210  Sanity Test Failure
mat search for other commits by this committer
Convert Python ports to FLAVORS.

  Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
08 Aug 2016 11:21:04
Original commit files touched by this commit  1.9
Revision:419818
wen search for other commits by this committer
- Update to 1.9 [1]
- Moved to github [1]
- Depend on newer sqlalchemy10 [1]
- Update pkg-descr and WWW [1]
- Limit python to -2.7 [2]
- Reset maintainer to python@ for better maintain

PR:		211621
Submitted by:	pi@ [1], koobs@ [2]
01 Apr 2016 13:29:17
Original commit files touched by this commit  1.5.3_3
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
19 Oct 2014 07:38:12
Original commit files touched by this commit  1.5.3_3
Revision:371171
mva search for other commits by this committer
- Convert ports from benchmarks/ and biology/ to new USES=python

Approved by:	portmgr (implicit)
10 Sep 2014 20:50:37
Original commit files touched by this commit  1.5.3_3
Revision:367888
gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
02 May 2014 14:00:13
Original commit files touched by this commit  1.5.3_2
Revision:352814
wen search for other commits by this committer
- Stage support [1]
- Pet portlint [1]
- Add LICENSE
- Convert to PYDISTUTILS_AUTOPLIST

PR:		188819 [1]
Submitted by:	Bartek Rutkowski <ports@robakdesign.com> [1]
10 Mar 2014 20:55:22
Original commit files touched by this commit  1.5.3_2
Revision:347809
gerald search for other commits by this committer
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
26 Oct 2013 00:52:36
Original commit files touched by this commit  1.5.3_1
Revision:331644
gerald search for other commits by this committer
Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
(Only the first 15 lines of the commit message are shown above View all of this commit message)
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.5.3
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
08 Oct 2012 03:17:03
Original commit files touched by this commit  1.5.3
Revision:305516
wen search for other commits by this committer
- Update to 1.5.3
- Trim Makefile headers
10 Jun 2012 18:42:48
Original commit files touched by this commit  1.5.1

swills search for other commits by this committer
- Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or
  RUN_DEPENDS=${BUILD_DEPENDS} to use := which portlint has warned
  about for a while.

PR:             ports/168208
Approved by:    portmgr (miwi)
11 Aug 2011 11:37:18
Original commit files touched by this commit  1.5.1

wen search for other commits by this committer
- Update to 1.5.1
25 Jun 2011 07:21:20
Original commit files touched by this commit  1.5_1

nivit search for other commits by this committer
- Fix *_DEPENDS after the repocopy of databases/py-sqlalchemy
  (This port doesn't yet support SQLAlchemy 0.7.X)
- Bump PORTREVISION
10 Nov 2010 08:52:26
Original commit files touched by this commit  1.5

wen search for other commits by this committer
- Update to 1.5.0
01 Jun 2010 06:57:30
Original commit files touched by this commit  1.4.1

wen search for other commits by this committer
- Update to 1.4.1
17 Dec 2009 06:51:53
Original commit files touched by this commit  1.4

wen search for other commits by this committer
- Update to 1.4
- Update my mail address to FreeBSD
22 Aug 2009 00:15:15
Original commit files touched by this commit  1.3.1

amdmi3 search for other commits by this committer
- Switch SourceForge ports to the new File Release System: categories starting
with B,C
22 Jun 2009 12:46:56
Original commit files touched by this commit  1.3.1

miwi search for other commits by this committer
PyCogent is a software library for genomic biology. It is a fully integrated
and thoroughly tested framework for: controlling third-party applications;
devising workflows; querying databases; conducting novel probabilistic
analyses of biological sequence evolution; and generating publication quality
graphics. It is distinguished by many unique built-in capabilities (such as
true codon alignment) and the frequent addition of entirely new methods for
the analysis of genomic data.

WWW:    http://pycogent.sourceforge.net/

PR:             ports/135863
Submitted by:   Wen Heping <wenheping at gmail.com>

Number of commits found: 25

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