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Port details
py-orange3-bioinformatics Orange add-on providing common functionality for bioinformatics
4.3.1_3 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 View this port on Repology. pkg-fallout 4.3.1_3Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-06-14 06:26:12
Last Update: 2024-02-29 07:18:32
Commit Hash: 5d4139f
Also Listed In: python
License: GPLv3
WWW:
https://github.com/biolab/orange3-bioinformatics
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
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 py39-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 py39-orange3-bioinformatics listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-orange3-bioinformatics
Package flavors (<flavor>: <package>)
  • py39: py39-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):
py39-orange3-bioinformatics
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--------
FreeBSD:13:quarterly--------
FreeBSD:14:latest4.3.1_34.3.1_3--4.3.1_3---
FreeBSD:14:quarterly4.3.1_34.3.1_3--4.3.1_3---
FreeBSD:15:latest4.3.1_34.3.1_3n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py39-setuptools-scm>0 : devel/py-setuptools-scm@py39
  2. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  3. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. orange3>0 : misc/orange3
  2. py39-Genesis-PyAPI>0 : biology/py-Genesis-PyAPI@py39
  3. py39-point-annotator>=2.0 : math/py-point-annotator@py39
  4. py39-pyclipper>=1.2.0 : math/py-pyclipper@py39
  5. py39-requests>0 : www/py-requests@py39
  6. py39-requests-cache0>0 : www/py-requests-cache0@py39
  7. py39-resdk>0 : biology/py-resdk@py39
  8. py39-scipy>=1.5.0 : science/py-scipy@py39
  9. py39-serverfiles>0 : misc/py-serverfiles@py39
  10. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  11. python3.9 : lang/python39
This port is required by:
for Run
  1. biology/py-orange3-single-cell

Configuration Options:
No options to configure
Options name:
biology_py-orange3-bioinformatics
USES:
python
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (2 items)
Collapse this list.
  1. https://files.pythonhosted.org/packages/source/O/Orange3-Bioinformatics/
  2. https://pypi.org/packages/source/O/Orange3-Bioinformatics/
Collapse this list.

Number of commits found: 22

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
4.3.1_3
29 Feb 2024 07:18:32
commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454 files touched by this commit
Charlie Li (vishwin) search for other commits by this committer
devel/py-setuptools-scm: update to 8.0.4

Directory and PORTNAME changed to match normalised name in release
tarball; consumers updated to match.

Although setuptools itself is specified as a run dependency in the
Python package metadata, it is currently left out here to prevent
environment pollution until at least PR 270510 is committed.
Additionally, this version of setuptools-scm requires setuptools>=61,
which means this version is only meant for USE_PYTHON=pep517 ports
as all USE_PYTHON=distutils ports will switch to devel/py-setuptools58
also after PR 270510. science/py-emmet-core is switched to
devel/py-setuptools_scm7 accordingly, as it specifies setuptools-scm<8.
devel/py-{flit-scm,hatch-vcs} have ${PY_SETUPTOOLS} added to
RUN_DEPENDS to compensate.

Further details: https://wiki.freebsd.org/Python/setuptools

Reported by: yuri
Co-authored by: matthew
Exp-run by: antoine (earlier iteration)
Approved by: yuri (science/py-emmet-core, previous iteration)
PR: 272134
Differential Revision: https://reviews.freebsd.org/D39288
4.3.1_3
31 Jul 2023 16:42:07
commit hash: 2724b9eb680c15502228fb4ebeb34cc2f691f9eacommit hash: 2724b9eb680c15502228fb4ebeb34cc2f691f9eacommit hash: 2724b9eb680c15502228fb4ebeb34cc2f691f9eacommit hash: 2724b9eb680c15502228fb4ebeb34cc2f691f9ea files touched by this commit
Po-Chuan Hsieh (sunpoet) search for other commits by this committer
biology/py-orange3-bioinformatics: Change RUN_DEPENDS from py-requests-cache to
py-requests-cache0

- Bump PORTREVISION for dependency change
4.3.1_2
27 Jun 2023 19:34:34
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb files touched by this commit
Rene Ladan (rene) search for other commits by this committer
all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>
4.3.1_2
25 Apr 2023 15:17:15
commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96 files touched by this commit
Christian Weisgerber (naddy) search for other commits by this committer
audio/opus: bump consumers after update to 1.4
4.3.1_1
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
4.3.1
11 Jan 2023 15:58:34
commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656 files touched by this commit
Dmitry Marakasov (amdmi3) search for other commits by this committer
*/*: rename CHEESESHOP to PYPI in MASTER_SITES

PR:			267994
Differential revision:	D37518
Approved by:		bapt
4.3.1
06 Dec 2022 11:12:04
commit hash: c37c0138b3b8b870856b2fae6277fcb9d6dcd3cdcommit hash: c37c0138b3b8b870856b2fae6277fcb9d6dcd3cdcommit hash: c37c0138b3b8b870856b2fae6277fcb9d6dcd3cdcommit hash: c37c0138b3b8b870856b2fae6277fcb9d6dcd3cd files touched by this commit
Rene Ladan (rene) search for other commits by this committer
Revert: "all: deprecate ports depending on expired security/py-keyrings.alt"

This reverts commit f9f811816c9a50a19570ef4ee66dc6e3f43baec5.

security/py-keyrings.alt was updated to use supported dependencies in
commit a16d8f14ce3bbcae7b17b690069593b5b0c7fb9e
4.3.1
30 Sep 2022 20:06:28
commit hash: f9f811816c9a50a19570ef4ee66dc6e3f43baec5commit hash: f9f811816c9a50a19570ef4ee66dc6e3f43baec5commit hash: f9f811816c9a50a19570ef4ee66dc6e3f43baec5commit hash: f9f811816c9a50a19570ef4ee66dc6e3f43baec5 files touched by this commit
Rene Ladan (rene) search for other commits by this committer
all: deprecate ports depending on expired security/py-keyrings.alt
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
4.3.1
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
4.3.1
23 Jan 2022 20:56:25
commit hash: 48d98ef9181e828b575f37e1841ad53e5def5987commit hash: 48d98ef9181e828b575f37e1841ad53e5def5987commit hash: 48d98ef9181e828b575f37e1841ad53e5def5987commit hash: 48d98ef9181e828b575f37e1841ad53e5def5987 files touched by this commit
Rene Ladan (rene) search for other commits by this committer
cleanup: remove transitive py27 deprecation (www/qt5-webengine)
4.3.1
27 Apr 2021 08:56:19
commit hash: ce04d9a5ee35cb5f34a91762172aaebd31a8c10fcommit hash: ce04d9a5ee35cb5f34a91762172aaebd31a8c10fcommit hash: ce04d9a5ee35cb5f34a91762172aaebd31a8c10fcommit hash: ce04d9a5ee35cb5f34a91762172aaebd31a8c10f files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1

Reported by:	portscout
3.2.2_3
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
3.2.2_3
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
3.2.2_3
24 Mar 2021 13:34:36
Revision:569118Original commit files touched by this commit
rene search for other commits by this committer
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
3.2.2_3
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
3.2.2_2
16 Jan 2019 11:13:45
Revision:490472Original commit files touched by this commit
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)
3.2.2_1
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
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
3.2.2
14 Oct 2018 03:22:50
Revision:482019Original commit files touched by this commit
yuri search for other commits by this committer
biology/py-orange3-bioinformatics: Update 3.2.0 -> 3.2.2

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

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

Reported by:	portscout
3.1.0
14 Jun 2018 06:25:22
Revision:472358Original commit files touched by this commit
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: 22