| Port details |
- py-scikit-bio Data structures, algorithms, educational resources for bioinformatics
- 0.6.2 biology
 =2      0.6.1Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2020-05-16 02:25:40
- Last Update: 2024-07-13 05:17:53
- Commit Hash: e9af328
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: education python
- License: BSD3CLAUSE
- WWW:
- http://scikit-bio.org/
- Description:
- scikit-bio is an open-source python package providing data structures,
algorithms, and educational resources for bioinformatics.
  ¦  ¦  ¦  ¦ 
- 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:
-
- ${PYTHON_PKGNAMEPREFIX}scikit-bio>0:biology/py-scikit-bio@${PY_FLAVOR}
- Conflicts:
- CONFLICTS_INSTALL:
- 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 py311-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 py311-scikit-bio listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py311-scikit-bio
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1720838021
SHA256 (scikit-bio-0.6.2.tar.gz) = af217ad12243cdaeef74a8f3bebe0d04aefda2a22d963d634201a36318b1a404
SIZE (scikit-bio-0.6.2.tar.gz) = 2699488
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:
-
- py311-numpy>=1.16,1<1.27,1 : math/py-numpy@py311
- py311-setuptools>0 : devel/py-setuptools@py311
- py311-wheel>0 : devel/py-wheel@py311
- cython-3.11 : lang/cython@py311
- python3.11 : lang/python311
- py311-build>=0 : devel/py-build@py311
- py311-installer>=0 : devel/py-installer@py311
- Test dependencies:
-
- py311-pytest>=7,1 : devel/py-pytest@py311
- python3.11 : lang/python311
- Runtime dependencies:
-
- py311-biom-format>0 : biology/py-biom-format@py311
- py311-decorator>=3.4.2 : devel/py-decorator@py311
- py311-h5py>=3.6.0 : science/py-h5py@py311
- py311-hdmedians>=0.14.1 : math/py-hdmedians@py311
- py311-ipython>=3.2.0 : devel/ipython@py311
- py311-matplotlib>=1.4.3 : math/py-matplotlib@py311
- py311-natsort>=4.0.3 : devel/py-natsort@py311
- py311-numpy>=1.16,1<1.27,1 : math/py-numpy@py311
- py311-pandas>=1.5.0 : math/py-pandas@py311
- py311-requests>=2.20.0 : www/py-requests@py311
- py311-scikit-learn>=0.19.1 : science/py-scikit-learn@py311
- py311-scipy>=1.9.0 : science/py-scipy@py311
- py311-statsmodels>=0.14.0 : math/py-statsmodels@py311
- python3.11 : lang/python311
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_py-scikit-bio
- USES:
- python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.6.2
13 Jul 2024 05:17:53
 |
Yuri Victorovich (yuri) |
biology/py-scikit-bio: update 0.6.1 → 0.6.2
Reported by: portscout |
0.6.1
19 Jun 2024 09:56:10
|
Yuri Victorovich (yuri) |
biology/py-scikit-bio: update 0.6.0 → 0.6.1
Reported by: portscout |
0.6.0
06 Apr 2024 01:04:46
|
Yuri Victorovich (yuri) |
biology/py-scikit-bio: update 0.5.9 → 0.6.0
Reported by: portscout |
0.5.9
03 Aug 2023 07:02:05
|
Yuri Victorovich (yuri) |
biology/py-scikit-bio: Update 0.5.8 → 0.5.9
Reported by: portscout |
0.5.8_1
27 Jun 2023 19:34:34
|
Rene Ladan (rene) |
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> |
0.5.8_1
07 May 2023 23:55:57
|
Po-Chuan Hsieh (sunpoet) |
www/py-cachecontrol: Fix port
- Use lowercase PORTNAME
- Fix WWW
- Fix LICENSE
- Fix FILECACHE and REDIS options: add missing RUN_DEPENDS
- Bump PORTREVISION for package change
PR: 266640
Approved by: maintainer (timeout, 3+ months) |
0.5.8_1
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
0.5.8
20 Mar 2023 15:30:16
|
Yuri Victorovich (yuri) |
biology/py-scikit-bio: Update 0.5.7 → 0.5.8
Reported by: portscout |
0.5.7
20 Mar 2023 06:05:44
|
Yuri Victorovich (yuri) |
biology/py-scikit-bio: Update 0.5.7 → 0.5.7
Reported by: portscout |
0.5.7_2
11 Jan 2023 15:58:34
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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
|
Stefan Eßer (se) |
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  ) |
0.5.7_2
03 Jun 2022 22:56:03
|
Yuri Victorovich (yuri) |
biology/py-scikit-bio: Broken on aarch64
Reported by: fallout |
0.5.7_2
21 Apr 2022 17:11:15
|
Piotr Kubaj (pkubaj) |
biology/py-scikit-bio: drop unnecessary USE_GCC on powerpc64 |
0.5.7_1
19 Apr 2022 12:09:20
|
Piotr Kubaj (pkubaj) |
biology/py-scikit-bio: build with clang on powerpc64le |
0.5.7
15 Apr 2022 19:09:57
|
Yuri Victorovich (yuri) |
biology/py-scikit-bio: Update 0.5.6 -> 0.5.7
Reported by: portscout |
0.5.6
06 Feb 2022 18:36:07
|
Stefan Eßer (se) |
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
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.5.6
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.5.6
09 Mar 2021 10:38:33
 |
pkubaj |
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
|
pkubaj |
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
|
adamw |
Add education virtual category
PR: 248402
Submitted by: PauAmma |
0.5.6
24 Sep 2020 23:16:26
|
yuri |
biology/py-scikit-bio: Fix build on the i386 architecture
Reported by: fallout
MFH: 2020Q3 |
0.5.6
15 Aug 2020 12:50:58
|
dbaio |
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
|
yuri |
biology/py-scikit-bio: Fix license |
0.5.6
16 May 2020 02:28:14
|
yuri |
biology/py-scikit-bio: Remove bogus lines |
0.5.6
16 May 2020 02:25:36
|
yuri |
New port: biology/py-scikit-bio: Data structures, algorithms, educational
resources for bioinformatics |
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