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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 0.5.6Version 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: 2022-06-03 22:56:03
Commit Hash: 45c4e1c
Also Listed In: education python
License: BSD3CLAUSE
Description:
SVNWeb : git : Homepage
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:
  • py38-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 py38-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 py38-scikit-bio listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py38-scikit-bio
Package flavors (<flavor>: <package>)
  • py38: py38-scikit-bio
distinfo:
Packages (timestamps in pop-ups are UTC):
py38-scikit-bio
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd640.5.60.5.6
FreeBSD:11:armv6--
FreeBSD:11:i3860.5.60.5.6
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd640.5.7_20.5.6
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3860.5.7_20.5.6
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd640.5.7_20.5.6
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3860.5.7_20.5.6
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd640.5.7_2-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3860.5.7_2-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py38-numpy>=1.16,1<1.23,1 : math/py-numpy@py38
  2. cython-3.8 : lang/cython@py38
  3. py38-setuptools>0 : devel/py-setuptools@py38
  4. python3.8 : lang/python38
Runtime dependencies:
  1. py38-numpy>=1.16,1<1.23,1 : math/py-numpy@py38
  2. py38-CacheControl>=0.11.5 : www/py-cachecontrol@py38
  3. py38-decorator>=3.4.2 : devel/py-decorator@py38
  4. py38-h5py>=2.9.0 : science/py-h5py@py38
  5. py38-hdmedians>=0.14.1 : math/py-hdmedians@py38
  6. py38-ipython>=3.2.0 : devel/ipython@py38
  7. py38-lockfile>=0.10.2 : devel/py-lockfile@py38
  8. py38-matplotlib>=1.4.3 : math/py-matplotlib@py38
  9. py38-natsort>=4.0.3 : devel/py-natsort@py38
  10. py38-pandas>=1.0.0 : math/py-pandas@py38
  11. py38-scikit-learn>=0.19.1 : science/py-scikit-learn@py38
  12. py38-scipy>=1.3.0 : science/py-scipy@py38
  13. py38-setuptools>0 : devel/py-setuptools@py38
  14. python3.8 : lang/python38
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: 15

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
03 Jun 2022 22:56:03
 files touched by this commit commit hash:45c4e1c9f3b0c920267c38538262e4440d3f9eea  0.5.7_2
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-scikit-bio: Broken on aarch64

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

Reported by:	portscout
06 Feb 2022 18:36:07
 files touched by this commit commit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9e  0.5.6
Stefan E├čer (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)
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  0.5.6
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  0.5.6
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
09 Mar 2021 10:38:33
Original commit files touched by this commit Revision:567918  0.5.6
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);
09 Mar 2021 01:21:22
Original commit files touched by this commit Revision:567882  0.5.6
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);
20 Nov 2020 07:16:06
Original commit files touched by this commit Revision:555738  0.5.6
adamw search for other commits by this committer
Add education virtual category

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

Reported by:	fallout
MFH:		2020Q3
15 Aug 2020 12:50:58
Original commit files touched by this commit Revision:544938  0.5.6
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)
16 May 2020 02:29:20
Original commit files touched by this commit Revision:535346  0.5.6
yuri search for other commits by this committer
biology/py-scikit-bio: Fix license
16 May 2020 02:28:14
Original commit files touched by this commit Revision:535345  0.5.6
yuri search for other commits by this committer
biology/py-scikit-bio: Remove bogus lines
16 May 2020 02:25:36
Original commit files touched by this commit Revision:535344  0.5.6
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: 15