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Port details
py-orange3-bioinformatics Orange add-on providing common functionality for bioinformatics
3.2.2_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
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-06-14 06:26:12
Last Update: 2019-01-16 11:13:45
SVN Revision: 490472
Also Listed In: python
License: GPLv3
Orange Bioinformatics extends Orange, a data mining software package, with
common functionality for bioinformatics. The provided functionality can be
accessed as a Python library or through a visual programming interface (Orange
Canvas). The latter is also suitable for non-programmers.

Orange Bioinformatics provides access to publicly available data, like GEO data
sets, GO and KEGG. All features can be combined with powerful visualization,
network exploration and data mining techniques from the Orange data mining
framework.

WWW: https://github.com/biolab/orange3-bioinformatics
SVNWeb : Homepage : PortsMon

There is no configure plist information for this port.

Dependency line: py36-orange3-bioinformatics>0:biology/py-orange3-bioinformatics


To install the port: cd /usr/ports/biology/py-orange3-bioinformatics/ && make install clean
To add the package: pkg install py36-orange3-bioinformatics

PKGNAME: py36-orange3-bioinformatics

Package flavors (<flavor>: <package>)
  • py36: py36-orange3-bioinformatics

distinfo:

TIMESTAMP = 1539463729
SHA256 (biolab-orange3-bioinformatics-3.2.2_GH0.tar.gz) = 4654d77e3a4298b49f12289f1ade24cb8c8831753488c516764edef2ce472455
SIZE (biolab-orange3-bioinformatics-3.2.2_GH0.tar.gz) = 1869440


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. py36-setuptools>0 : devel/py-setuptools@py36
  2. python3.6 : lang/python36
Runtime dependencies:
  1. orange3>0 : misc/orange3
  2. py36-Genesis-PyAPI>0 : biology/py-Genesis-PyAPI@py36
  3. py36-requests>0 : www/py-requests@py36
  4. py36-requests-cache>0 : www/py-requests-cache@py36
  5. py36-serverfiles>0 : misc/py-serverfiles@py36
  6. py36-setuptools>0 : devel/py-setuptools@py36
  7. python3.6 : lang/python36

This port is required by:

for Run * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...
Configuration Options
     No options to configure

USES:
python:3.4+

Master Sites:
  1. https://codeload.github.com/biolab/orange3-bioinformatics/tar.gz/3.2.2?dummy=/
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: 6

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
16 Jan 2019 11:13:45
Original commit files touched by this commit  3.2.2_2
Revision:490472
tijl search for other commits by this committer
Fix Qt5 symbol version scripts to put the catch-all clause first.  When
a symbol matches multiple clauses the last one takes precedence.  If the
catch-all is last it captures everything.  In the case of Qt5 libraries
this caused all symbols to have a Qt_5 label while some should have
Qt_5_PRIVATE_API.  This only affects lld because GNU ld always gives the
catch-all lowest priority.

Older versions of Qt5Webengine exported some memory allocation symbols from
the bundled Chromium.  Version 5.9 stopped exporting these [1] but the
symbols were kept as weak wrappers for the standard allocation functions to
maintain binary compatibility. [2][3]  The problem is that the call to the
standard function in these weak wrappers is only resolved to the standard
function if there's a call to this standard function in other parts of
Qt5Webengine, because only then is there a non-weak symbol that takes
precedence over the weak one.  If there's no such non-weak symbol the call
(Only the first 15 lines of the commit message are shown above View all of this commit message)
12 Dec 2018 01:35:36
Original commit files touched by this commit  3.2.2_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
14 Oct 2018 03:22:50
Original commit files touched by this commit  3.2.2
Revision:482019
yuri search for other commits by this committer
biology/py-orange3-bioinformatics: Update 3.2.0 -> 3.2.2

Reported by:	portscout
09 Aug 2018 00:29:50
Original commit files touched by this commit  3.2.0
Revision:476712
yuri search for other commits by this committer
biology/py-orange3-bioinformatics: Update 3.1.1 -> 3.2.0

Reported by:	portscout
12 Jul 2018 20:09:38
Original commit files touched by this commit  3.1.1
Revision:474534
yuri search for other commits by this committer
biology/py-orange3-bioinformatics: Update 3.1.0 -> 3.1.1

Reported by:	portscout
14 Jun 2018 06:25:22
Original commit files touched by this commit  3.1.0
Revision:472358
yuri search for other commits by this committer
New port: biology/py-orange3-bioinformatics: Orange add-on providing common
functionality for bioinformatics

Number of commits found: 6

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