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Port details
py-scikit-bio Data structures, algorithms, educational resources for bioinformatics
0.5.7_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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-05-16 02:25:40
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
Also Listed In: education python
License: BSD3CLAUSE
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
There is no configure plist information for this port.
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}scikit-bio>0:biology/py-scikit-bio@${PY_FLAVOR}
Conflicts:
CONFLICTS_INSTALL:
  • py39-ddtrace
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
To install the port:
cd /usr/ports/biology/py-scikit-bio/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/py-scikit-bio
  • pkg install py39-scikit-bio
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-scikit-bio listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-scikit-bio
Package flavors (<flavor>: <package>)
  • py39: py39-scikit-bio
distinfo:

Packages (timestamps in pop-ups are UTC):
py38-scikit-bio
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd640.5.60.5.6
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i3860.5.60.5.6
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-falloutpkg-fallout
FreeBSD:12:amd64pkg-falloutpkg-fallout
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd64pkg-falloutpkg-fallout
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd64pkg-falloutpkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
py39-scikit-bio
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd64pkg-falloutpkg-fallout
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-falloutpkg-fallout
FreeBSD:12:amd640.5.7_20.5.7_2
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i3860.5.7_20.5.7_2
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd640.5.7_20.5.7_2
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-fallout0.5.7_2
FreeBSD:13:i3860.5.7_20.5.7_2
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd640.5.7_2pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv70.5.7_2pkg-fallout
FreeBSD:14:i3860.5.7_2pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py39-numpy>=1.16,1<1.24,1 : math/py-numpy@py39
  2. cython-3.9 : lang/cython@py39
  3. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  4. python3.9 : lang/python39
Runtime dependencies:
  1. py39-numpy>=1.16,1<1.24,1 : math/py-numpy@py39
  2. py39-CacheControl>=0.11.5 : www/py-cachecontrol@py39
  3. py39-decorator>=3.4.2 : devel/py-decorator@py39
  4. py39-h5py>=2.9.0 : science/py-h5py@py39
  5. py39-hdmedians>=0.14.1 : math/py-hdmedians@py39
  6. py39-ipython>=3.2.0 : devel/ipython@py39
  7. py39-lockfile>=0.10.2 : devel/py-lockfile@py39
  8. py39-matplotlib>=1.4.3 : math/py-matplotlib@py39
  9. py39-natsort>=4.0.3 : devel/py-natsort@py39
  10. py39-pandas>=1.0.0 : math/py-pandas@py39
  11. py39-scikit-learn>=0.19.1 : science/py-scikit-learn@py39
  12. py39-scipy>=1.3.0 : science/py-scipy@py39
  13. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  14. python3.9 : lang/python39
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

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/s/scikit-bio/
  2. https://pypi.org/packages/source/s/scikit-bio/
Collapse this list.

Number of commits found: 17

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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)
0.5.7_2
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)
0.5.7_2
03 Jun 2022 22:56:03
commit hash:45c4e1c9f3b0c920267c38538262e4440d3f9eeacommit hash:45c4e1c9f3b0c920267c38538262e4440d3f9eeacommit hash:45c4e1c9f3b0c920267c38538262e4440d3f9eeacommit hash:45c4e1c9f3b0c920267c38538262e4440d3f9eea files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-scikit-bio: Broken on aarch64

Reported by:	fallout
0.5.7_2
21 Apr 2022 17:11:15
commit hash:52e46764cf10f8485f55c2cc71549cf5ca39aedccommit hash:52e46764cf10f8485f55c2cc71549cf5ca39aedccommit hash:52e46764cf10f8485f55c2cc71549cf5ca39aedccommit hash:52e46764cf10f8485f55c2cc71549cf5ca39aedc files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/py-scikit-bio: drop unnecessary USE_GCC on powerpc64
0.5.7_1
19 Apr 2022 12:09:20
commit hash:a3f5e20929cdb8a33ac629e005cc49261472b2dbcommit hash:a3f5e20929cdb8a33ac629e005cc49261472b2dbcommit hash:a3f5e20929cdb8a33ac629e005cc49261472b2dbcommit hash:a3f5e20929cdb8a33ac629e005cc49261472b2db files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/py-scikit-bio: build with clang on powerpc64le
0.5.7
15 Apr 2022 19:09:57
commit hash:1aa4b199504fab66ea1575a27c7280b4b41ee6b4commit hash:1aa4b199504fab66ea1575a27c7280b4b41ee6b4commit hash:1aa4b199504fab66ea1575a27c7280b4b41ee6b4commit hash:1aa4b199504fab66ea1575a27c7280b4b41ee6b4 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-scikit-bio: Update 0.5.6 -> 0.5.7

Reported by:	portscout
0.5.6
06 Feb 2022 18:36:07
commit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9e files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)
0.5.6
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
0.5.6
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.
0.5.6
09 Mar 2021 10:38:33
Revision:567918Original commit files touched by this commit
pkubaj search for other commits by this committer
biology/py-scikit-bio: fix build on powerpc64

GCC is also necessary on powerpc64:
In file included from skbio/alignment/_ssw_wrapper.c:626:
In file included from skbio/alignment/_lib/ssw.h:17:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion
between vector type '__m64' (vector of 1 'long long' value) and integer type
'int' of different size
    return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
0.5.6
09 Mar 2021 01:21:22
Revision:567882Original commit files touched by this commit
pkubaj search for other commits by this committer
biology/py-scikit-bio: fix build on powerpc64le

Use GCC:
In file included from skbio/alignment/_ssw_wrapper.c:626:
In file included from skbio/alignment/_lib/ssw.h:17:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion
between vector type '__m64' (vector of 1 'long long' value) and integer type
'int' of different size
    return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
0.5.6
20 Nov 2020 07:16:06
Revision:555738Original commit files touched by this commit
adamw search for other commits by this committer
Add education virtual category

PR:		248402
Submitted by:	PauAmma
0.5.6
24 Sep 2020 23:16:26
Revision:549974Original commit files touched by this commit
yuri search for other commits by this committer
biology/py-scikit-bio: Fix build on the i386 architecture

Reported by:	fallout
MFH:		2020Q3
0.5.6
15 Aug 2020 12:50:58
Revision:544938Original commit files touched by this commit
dbaio search for other commits by this committer
devel/ipython: Update to 7.17.0

IPython 7.17+ supports Python 3.7 and above, following NEP 29.
Update consumers to use Python >= 3.7 (avoid break bulk -a).

Changelog:	https://ipython.readthedocs.io/en/latest/whatsnew/version7.html?highlight=7.17#ipython-7-17

Approved by:	dbaio (python, maintainer)
0.5.6
16 May 2020 02:29:20
Revision:535346Original commit files touched by this commit
yuri search for other commits by this committer
biology/py-scikit-bio: Fix license
0.5.6
16 May 2020 02:28:14
Revision:535345Original commit files touched by this commit
yuri search for other commits by this committer
biology/py-scikit-bio: Remove bogus lines
0.5.6
16 May 2020 02:25:36
Revision:535344Original commit files touched by this commit
yuri search for other commits by this committer
New port: biology/py-scikit-bio: Data structures, algorithms, educational
resources for bioinformatics

Number of commits found: 17