Port details |
- py-orange3-bioinformatics Orange add-on providing common functionality for bioinformatics
- 4.3.1 biology
=0 4.3.1Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
 - Port Added: 2018-06-14 06:26:12
- Last Update: 2022-01-23 20:56:25
- Commit Hash: 48d98ef
- Also Listed In: python
- License: GPLv3
- Description:
- 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 : git : Homepage
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}orange3-bioinformatics>0:biology/py-orange3-bioinformatics@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-orange3-bioinformatics/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-orange3-bioinformatics
- pkg install py38-orange3-bioinformatics
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.NOTE: This is a Python port. Instead of py38-orange3-bioinformatics listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py38-orange3-bioinformatics
- Package flavors (<flavor>: <package>)
- py38: py38-orange3-bioinformatics
- distinfo:
- TIMESTAMP = 1619513096
SHA256 (Orange3-Bioinformatics-4.3.1.tar.gz) = 4017518f9eeef0e8a9016a3e1c19b362f9f4d7f3e9dd07da0d8615a96a3b8447
SIZE (Orange3-Bioinformatics-4.3.1.tar.gz) = 2943722
- Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py38-setuptools_scm>0 : devel/py-setuptools_scm@py38
- py38-setuptools>0 : devel/py-setuptools@py38
- python3.8 : lang/python38
- Runtime dependencies:
-
- orange3>0 : misc/orange3
- py38-Genesis-PyAPI>0 : biology/py-Genesis-PyAPI@py38
- py38-point-annotator>=2.0 : math/py-point-annotator@py38
- py38-pyclipper>=1.2.0 : math/py-pyclipper@py38
- py38-requests>0 : www/py-requests@py38
- py38-requests-cache>0 : www/py-requests-cache@py38
- py38-resdk>0 : biology/py-resdk@py38
- py38-scipy>=1.5.0 : science/py-scipy@py38
- py38-serverfiles>0 : misc/py-serverfiles@py38
- py38-setuptools>0 : devel/py-setuptools@py38
- python3.8 : lang/python38
- This port is required by:
- for Run
-
- biology/py-orange3-single-cell
- Configuration Options:
- No options to configure
- Options name:
- biology_py-orange3-bioinformatics
- USES:
- python:3.4+
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Commit History - (may be incomplete: see SVNWeb link above for full details) |
Date | By | Description |
23 Jan 2022 20:56:25 4.3.1
|
Rene Ladan (rene)  |
cleanup: remove transitive py27 deprecation (www/qt5-webengine) |
27 Apr 2021 08:56:19 4.3.1
|
Yuri Victorovich (yuri)  |
biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1
Reported by: portscout |
07 Apr 2021 08:09:01 3.2.2_3
|
Mathieu Arnold (mat)  |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
06 Apr 2021 14:31:07 3.2.2_3
|
Mathieu Arnold (mat)  |
Remove # $FreeBSD$ from Makefiles. |
24 Mar 2021 13:34:36
3.2.2_3
|
rene  |
Mark ports recursively depending on Python 2.7 for expiration on June 23.
For ports optionally dependending on Python 2.7, just mark those options
as expired. Remove konquerer from the x11/kde-baseapps metaport and bump
its PORTREVISION.
Submitted by: rene
Reviewed by: portmgr, adridg, ehaupt, lme, madpilot, pizzamig, se, sunpoet, yuri
Approved by: portmgr
Differential Revision: https://reviews.freebsd.org/D28665 |
26 Jul 2019 20:46:57
3.2.2_3
|
gerald  |
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 |
16 Jan 2019 11:13:45
3.2.2_2
|
tijl  |
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 ) |
12 Dec 2018 01:35:36
3.2.2_1
|
gerald  |
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
3.2.2
|
yuri  |
biology/py-orange3-bioinformatics: Update 3.2.0 -> 3.2.2
Reported by: portscout |
09 Aug 2018 00:29:50
3.2.0
|
yuri  |
biology/py-orange3-bioinformatics: Update 3.1.1 -> 3.2.0
Reported by: portscout |
12 Jul 2018 20:09:38
3.1.1
|
yuri  |
biology/py-orange3-bioinformatics: Update 3.1.0 -> 3.1.1
Reported by: portscout |
14 Jun 2018 06:25:22
3.1.0
|
yuri  |
New port: biology/py-orange3-bioinformatics: Orange add-on providing common
functionality for bioinformatics |