| Port details |
- checkm Quality assessment tool for the microbial genomes
- 1.2.0_1 biology
 =0      1.2.0_1Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2018-12-07 00:26:14
- Last Update: 2023-06-27 19:34:34
- Commit Hash: 3d9a815
- Also Listed In: python
- License: GPLv3
- WWW:
- https://ecogenomics.github.io/CheckM/
- Description:
- CheckM provides a set of tools for assessing the quality of genomes recovered
from isolates, single cells, or metagenomes. It provides robust estimates of
genome completeness and contamination by using collocated sets of genes that
are ubiquitous and single-copy within a phylogenetic lineage. Assessment of
genome quality can also be examined using plots depicting key genomic
characteristics (e.g., GC, coding density) which highlight sequences outside
the expected distributions of a typical genome. CheckM also provides tools for
identifying genome bins that are likely candidates for merging based on marker
set compatibility, similarity in genomic characteristics, and proximity within
a reference genome tree.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/checkm/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/checkm
- pkg install CheckM
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: CheckM
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1651427292
SHA256 (Ecogenomics-CheckM-v1.2.0_GH0.tar.gz) = 9d2f51409a72e90f1b59c811fa4d8b430051683ca0f3001aa770003f9201cd71
SIZE (Ecogenomics-CheckM-v1.2.0_GH0.tar.gz) = 1017160
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:
-
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
- py39-DendroPy>0 : science/py-DendroPy@py39
- py39-matplotlib>0 : math/py-matplotlib@py39
- py39-pysam>0 : biology/py-pysam@py39
- py39-scipy>0 : science/py-scipy@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_checkm
- USES:
- dos2unix 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 |
|---|
1.2.0_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> |
1.2.0_1
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
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) |
1.2.0
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  ) |
1.2.0
01 May 2022 18:14:09
|
Yuri Victorovich (yuri) |
biology/checkm: Update 1.1.11 -> 1.2.0
Reported by: portscout |
1.1.11
25 Apr 2022 20:50:10
|
Yuri Victorovich (yuri) |
biology/checkm: Update 1.1.10 -> 1.1.11
Reported by: portscout |
1.1.10
22 Apr 2022 18:04:37
|
Yuri Victorovich (yuri) |
biology/checkm: Update 1.1.9 -> 1.1.10
Reported by: portscout |
1.1.9
15 Apr 2022 19:09:58
|
Yuri Victorovich (yuri) |
biology/checkm: Update 1.1.8 -> 1.1.9
Reported by: portscout |
1.1.8
12 Apr 2022 03:22:30
|
Yuri Victorovich (yuri) |
biology/checkm: Update 1.0.18 -> 1.1.8
Reported by: portscout |
1.0.18
25 Mar 2022 13:38:04
|
Po-Chuan Hsieh (sunpoet) |
biology/checkm: Fix build with setuptools 58.0.0+
With hat: python |
1.0.18
10 May 2021 20:13:20
|
Thierry Thomas (thierry) |
math/py-matplotlib: chase minimum Python version in dependent ports
Since the previous update changed USES=python from 3.6+ to 3.7+, all
dependent ports must have USES=python:3.7+ as well, otherwise it breaks
the @py36 flavor.
PR: 255347
Reported by: sunpoet |
1.0.18
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
1.0.18
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
1.0.18
24 Dec 2020 09:03:39
 |
antoine |
scipy 1.5.4 is only compatible with python 3.6+
Reported by: pkg-fallout |
1.0.18
19 Aug 2019 08:25:29
|
yuri |
biology/checkm: Update 1.0.17 -> 1.0.18
Reported by: portscout |
1.0.17
11 Aug 2019 19:16:49
|
yuri |
biology/checkm: Update 1.0.16 -> 1.0.17
Reported by: portscout |
1.0.16
09 Aug 2019 07:22:48
|
yuri |
biology/checkm: Update 1.0.13 -> 1.0.16
Reported by: portscout |
1.0.13_2
26 Jul 2019 20:46:57
|
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 |
1.0.13_1
10 Apr 2019 06:18:32
|
antoine |
Bump a few PORTREVISIONs after r498529
With hat: portmgr |
1.0.13
09 Feb 2019 22:58:10
|
yuri |
biology/checkm: Update 1.0.12 -> 1.0.13
Reported by: portscout |
1.0.12_1
12 Dec 2018 01:35:36
|
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 |
1.0.12
07 Dec 2018 00:26:04
|
yuri |
New port: math/checkm: Quality assessment tool for the microbial genomes |
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