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Port details
py-biom-format Biological Observation Matrix (BIOM) Format Project
2.1.7_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
2.1.7Version of this port present on the latest quarterly branch.
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-05-09 16:37:53
Last Update: 2019-04-10 07:18:32
SVN Revision: 498530
Also Listed In: python
License: BSD3CLAUSE
The BIOM file format (canonically pronounced biome) is designed to be a
general-use format for representing biological sample by observation contingency
tables. BIOM is a recognized standard for the Earth Microbiome Project and is a
Genomics Standards Consortium supported project.

The BIOM format is designed for general use in broad areas of comparative
-omics. For example, in marker-gene surveys, the primary use of this format is
to represent OTU tables: the observations in this case are OTUs and the matrix
contains counts corresponding to the number of times each OTU is observed in
each sample. With respect to metagenome data, this format would be used to
represent metagenome tables: the observations in this case might correspond to
SEED subsystems, and the matrix would contain counts corresponding to the number
of times each subsystem is observed in each metagenome. Similarly, with respect
to genome data, this format may be used to represent a set of genomes: the
observations in this case again might correspond to SEED subsystems, and the
counts would correspond to the number of times each subsystem is observed in
each genome.

WWW: http://biom-format.org/
SVNWeb : Homepage

There is no configure plist information for this port.

Dependency lines:
  • py36-biom-format>0:biology/py-biom-format

To install the port: cd /usr/ports/biology/py-biom-format/ && make install clean
To add the package: pkg install py36-biom-format

PKGNAME: py36-biom-format

Package flavors (<flavor>: <package>)
  • py36: py36-biom-format
  • py27: py27-biom-format

distinfo:

TIMESTAMP = 1538769748
SHA256 (biom-format-2.1.7.tar.gz) = b47e54282ef13cddffdb00aea9183a87175a2372c91a915259086a3f444c42f4
SIZE (biom-format-2.1.7.tar.gz) = 11820666


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-click>0 : devel/py-click@py36
  2. py36-numpy>0 : math/py-numpy@py36
  3. py36-future>=0.16.0 : devel/py-future@py36
  4. py36-scipy>=0.13.0 : science/py-scipy@py36
  5. py36-pandas>=0.20.0 : math/py-pandas@py36
  6. py36-h5py>=2.2.0 : science/py-h5py@py36
  7. py36-six>=1.10.0 : devel/py-six@py36
  8. py36-setuptools>0 : devel/py-setuptools@py36
  9. python3.6 : lang/python36
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
python

Master Sites:
  1. https://files.pythonhosted.org/packages/source/b/biom-format/
  2. https://pypi.org/packages/source/b/biom-format/
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: 12

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
10 Apr 2019 06:18:32
Original commit files touched by this commit  2.1.7_2
Revision:498530
antoine search for other commits by this committer
Bump a few PORTREVISIONs after r498529

With hat:	portmgr
12 Dec 2018 01:35:36
Original commit files touched by this commit  2.1.7_1
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
06 Oct 2018 15:28:02
Original commit files touched by this commit  2.1.7
Revision:481369
jrm search for other commits by this committer
biology/py-biom-format: Update to version 2.1.7

Reported by:	portscout
20 Jun 2018 17:05:44
Original commit files touched by this commit  2.1.6_2
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  2.1.6_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).
10 Dec 2017 03:33:04
Original commit files touched by this commit  2.1.6_1
Revision:455879
jrm search for other commits by this committer
biology/py-biom-format: Add required dependency on math/py-pandas and do
not install tests.
30 Nov 2017 15:50:34
Original commit files touched by this commit  2.1.6
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)
29 Apr 2017 13:59:15
Original commit files touched by this commit  2.1.6
Revision:439751
jrm search for other commits by this committer
biology/py-biom-format: Update to version 2.1.6

Upstream changes: https://github.com/biocore/biom-format/releases/tag/2.1.6

Approved by:	swills (mentor, implicit)
23 Sep 2016 21:42:02
Original commit files touched by this commit  2.1.5_1
Revision:422697
jrm search for other commits by this committer
Update email address to jrm@FreeBSD.org for ports that I maintain

Reviewed by:	mat, swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D7995
11 Jun 2016 09:25:04
Original commit files touched by this commit  2.1.5_1
Revision:416710
olivierd search for other commits by this committer
- Fix run-time dependency issues
- Bump PORTREVISION

PR:		209767
Submitted by:	Joseph Mingrone (maintainer)
09 May 2016 16:42:17
Original commit files touched by this commit  2.1.5
Revision:414866
olivierd search for other commits by this committer
Add final slash in WWW entry
09 May 2016 16:37:44
Original commit files touched by this commit  2.1.5
Revision:414865
olivierd search for other commits by this committer
The BIOM file format (canonically pronounced biome) is designed to be a
general-use format for representing biological sample by observation contingency
tables. BIOM is a recognized standard for the Earth Microbiome Project and is a
Genomics Standards Consortium supported project.

The BIOM format is designed for general use in broad areas of comparative
-omics. For example, in marker-gene surveys, the primary use of this format is
to represent OTU tables: the observations in this case are OTUs and the matrix
contains counts corresponding to the number of times each OTU is observed in
each sample. With respect to metagenome data, this format would be used to
represent metagenome tables: the observations in this case might correspond to
SEED subsystems, and the matrix would contain counts corresponding to the number
of times each subsystem is observed in each metagenome. Similarly, with respect
to genome data, this format may be used to represent a set of genomes: the
observations in this case again might correspond to SEED subsystems, and the
counts would correspond to the number of times each subsystem is observed in
each genome.

WWW: http://biom-format.org/

PR:		209193
Submitted by:	Joseph Mingrone

Number of commits found: 12

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