notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Port details
pyfasta Fast, memory-efficient, pythonic access to fasta sequence files
0.5.2_4 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 0.5.2Version of this port present on the latest quarterly branch.
Maintainer: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-11-18 05:53:48
Last Update: 2019-07-26 21:46:57
SVN Revision: 507372
Also Listed In: python
License: MIT
Description:
SVNWeb : Homepage

There is no configure plist information for this port.

Dependency lines:
  • py36-pyfasta>0:biology/pyfasta
To install the port: cd /usr/ports/biology/pyfasta/ && make install clean
To add the package: pkg install py36-pyfasta
PKGNAME: py36-pyfasta
Package flavors (<flavor>: <package>)
  • py36: py36-pyfasta
  • py27: py27-pyfasta
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py36-numpy>0 : math/py-numpy@py36
  2. py36-setuptools>0 : devel/py-setuptools@py36
  3. python3.6 : lang/python36
Runtime dependencies:
  1. py36-numpy>0 : math/py-numpy@py36
  2. py36-setuptools>0 : devel/py-setuptools@py36
  3. python3.6 : lang/python36
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://files.pythonhosted.org/packages/source/p/pyfasta/
  2. https://pypi.org/packages/source/p/pyfasta/
Notes from UPDATING
These upgrade notes are taken from /usr/ports/UPDATING
  • 2017-11-30
    Affects: */py*
    Author: mat@FreeBSD.org
    Reason: 
      Ports using Python via USES=python are now flavored.  All the py3-* ports
      have been removed and folded into their py-* master ports.
    
      People using Poudriere 3.2+ and binary packages do not have to do anything.
    
      For other people, to build the Python 3.6 version of, for example,
      databases/py-gdbm, you need to run:
    
        # make FLAVOR=py36 install
    
    

Number of commits found: 29

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  0.5.2_4
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
07 Feb 2019 09:30:41
Original commit files touched by this commit  0.5.2_3
Revision:492353
amdmi3 search for other commits by this committer
- Update WWW

Approved by:	portmgr blanket
12 Dec 2018 01:35:36
Original commit files touched by this commit  0.5.2_3
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
10 Mar 2018 17:46:06
Original commit files touched by this commit  0.5.2_2
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).
30 Nov 2017 15:50:34
Original commit files touched by this commit  0.5.2_1
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)
19 May 2016 10:21:25
Original commit files touched by this commit  0.5.2_1
Revision:415498
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket
19 Oct 2014 07:38:12
Original commit files touched by this commit  0.5.2_1
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  0.5.2_1
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)
06 Apr 2014 04:05:43
Original commit files touched by this commit  0.5.2
Revision:350289
wen search for other commits by this committer
- Update to 0.5.2
- Add LICENSE
10 Mar 2014 20:55:22
Original commit files touched by this commit  0.5.1_3
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)
31 Jan 2014 12:31:24
Original commit files touched by this commit  0.5.1_2
Revision:341984
miwi search for other commits by this committer
- Convert to PYDISTUTILS_AUTOPLIST
- Stage support
- Bump PORTREV
13 Jan 2014 21:00:04
Original commit files touched by this commit  0.5.1_1
Revision:339634
rene search for other commits by this committer
Python cleanup:
- USE_PYTHON* = 2.X -> USE_PYTHON* = 2
- USE_PYTHON* = 2.X+ -> USE_PYTHON* = yes
Reviewed by:	python (mva, rm)
Approved by:	portmgr-lurkers (mat)
26 Oct 2013 00:52:36
Original commit files touched by this commit  0.5.1_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)
04 Oct 2013 08:09:02
Original commit files touched by this commit  0.5.1
Revision:329270
wen search for other commits by this committer
- Update to 0.5.1
20 Sep 2013 15:55:44
Original commit files touched by this commit  0.4.5
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)
01 Jun 2013 14:22:36
Original commit files touched by this commit  0.4.5
Revision:319570
wen search for other commits by this committer
- Trim Makefile headers
23 Feb 2012 13:43:25
Original commit files touched by this commit  0.4.5

wen search for other commits by this committer
- Update to 0.4.5
13 Oct 2011 06:27:34
Original commit files touched by this commit  0.4.4

wen search for other commits by this committer
- Update to 0.44
02 Jun 2011 01:38:55
Original commit files touched by this commit  0.4.3

wen search for other commits by this committer
- Update to 0.4.3
13 Apr 2011 09:11:20
Original commit files touched by this commit  0.4.2

wen search for other commits by this committer
- Update to 0.4.2
02 Dec 2010 13:42:09
Original commit files touched by this commit  0.4.1

wen search for other commits by this committer
- Update to 0.4.1
26 Oct 2010 00:34:36
Original commit files touched by this commit  0.4.0

wen search for other commits by this committer
- Update to 0.4.0
18 Aug 2010 14:09:35
Original commit files touched by this commit  0.3.9

glarkin search for other commits by this committer
- Update USE_PYTHON in Makefile to reflect upstream Python
  dependency version requirement

PR:             ports/149251
Submitted by:   glarkin
Approved by:    wen (via email)
19 Mar 2010 08:32:48
Original commit files touched by this commit  0.3.9

wen search for other commits by this committer
- Update to 0.3.9
24 Dec 2009 03:14:34
Original commit files touched by this commit  0.3.7

wen search for other commits by this committer
- Update to 0.3.7
21 Dec 2009 03:29:55
Original commit files touched by this commit  0.3.5

wen search for other commits by this committer
- Update to 0.3.5
16 Dec 2009 12:48:04
Original commit files touched by this commit  0.3.4

wen search for other commits by this committer
- Update to 0.3.4
06 Dec 2009 08:47:36
Original commit files touched by this commit  0.3.3

wen search for other commits by this committer
- Update to 0.3.3
18 Nov 2009 05:53:17
Original commit files touched by this commit  0.3.1

wen search for other commits by this committer
pyfasta is a python module for fast, memory-efficient, pythonic
access to fasta sequence files.

WWW:    http://bitbucket.org/brentp/biostuff/src/

Number of commits found: 29

Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
The latest upgrade!
Privacy
Forums
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
libmadNov 13
chromiumNov 12
wordpressNov 12
wordpressNov 12
wordpressNov 12
wordpressNov 12
wordpressNov 12
nexus2-ossNov 07
php71Nov 06
php72Nov 06
php73Nov 06
php74Nov 06
fileNov 02
mariadb101-serverNov 02
mariadb102-serverNov 02

8 vulnerabilities affecting 177 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last updated:
2019-11-14 00:15:05


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 38061
Broken 787
Deprecated 87
Ignore 1066
Forbidden 3
Restricted 156
No CDROM 72
Vulnerable 33
Expired 7
Set to expire 57
Interactive 0
new 24 hours 3
new 48 hours13
new 7 days37
new fortnight63
new month124

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2019 Dan Langille. All rights reserved.