| Port details |
- smoldyn Biochemical simulator for molecular diffusion, surface interactions
- 2.74 science
 =2      2.73_1Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2019-06-09 03:26:30
- Last Update: 2025-01-23 07:40:37
- Commit Hash: 6b4cef0
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: LGPL3
- WWW:
- https://www.smoldyn.org/
- Description:
- Smoldyn is a computer program for cell-scale biochemical simulations. It
simulates each molecule of interest individually to capture natural
stochasticity and to yield nanometer-scale spatial resolution. It treats other
molecules implicitly, enabling it to simulate hundreds of thousands of molecules
over several minutes of real time. Simulated molecules diffuse, react, are
confined by surfaces, and bind to membranes much as they would in a real
biological system.
Smoldyn is easy to use and easy to install. It is more accurate and faster than
other particle-based simulators. Smoldyn's unique features include:
a "virtual experimenter" who can manipulate or measure the simulated system,
support for spatial compartments, molecules with excluded volume, and
simulations in 1, 2, or 3 dimensions.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- smoldyn>0:science/smoldyn
- To install the port:
- cd /usr/ports/science/smoldyn/ && make install clean
- To add the package, run one of these commands:
- pkg install science/smoldyn
- pkg install smoldyn
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: smoldyn
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1737604798
SHA256 (smoldyn-2.74.tgz) = 1abae836ac515092be14e2058af58a25981d7872c3a002fbff67bde0f64fa28a
SIZE (smoldyn-2.74.tgz) = 34348669
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:
-
- cmake : devel/cmake-core
- ninja : devel/ninja
- xorgproto>=0 : x11/xorgproto
- xorgproto>=0 : x11/xorgproto
- xi.pc : x11/libXi
- xmu.pc : x11-toolkits/libXmu
- Test dependencies:
-
- py311-flaky>0 : devel/py-flaky@py311
- py311-matplotlib>0 : math/py-matplotlib@py311
- py311-numpy>=1.16,1<1.27,1 : math/py-numpy@py311
- python3.11 : lang/python311
- Runtime dependencies:
-
- xi.pc : x11/libXi
- xmu.pc : x11-toolkits/libXmu
- Library dependencies:
-
- libtiff.so : graphics/tiff
- libGL.so : graphics/libglvnd
- libGLU.so : graphics/libGLU
- libglut.so : graphics/freeglut
- There are no ports dependent upon this port
Configuration Options:- ===> The following configuration options are available for smoldyn-2.74:
PYTHON=off: Python bindings or support
===> Use 'make config' to modify these settings
- Options name:
- science_smoldyn
- USES:
- cmake:testing compiler:c++11-lang gl localbase:ldflags python:test tar:tgz shebangfix xorg
- 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 |
|---|
2.74
23 Jan 2025 07:40:37
 |
Yuri Victorovich (yuri) |
science/smoldyn: update 2.73 → 2.74
Reported by: portscout |
2.73_1
09 Oct 2024 19:43:26
|
Daniel Engberg (diizzy) |
science/smoldyn: Fix build with tiff 4.7.0
Use TIFF:tiff to define the library instead of ${TIFF_LIBRARY} and
remove custom logic that tried to replace CMake's own.
PR: 281763
Reviewed by: yuri |
2.73_1
27 Apr 2024 12:44:59
|
Tijl Coosemans (tijl) |
graphics/tiff: Update to 4.6.0
PR: 278577
Exp-run by: antoine |
2.73
11 Mar 2024 16:20:40
|
Yuri Victorovich (yuri) |
science/smoldyn: update 2.72 → 2.73
Reported by: portscout |
2.72
19 Aug 2023 07:55:08
|
Yuri Victorovich (yuri) |
science/smoldyn: Update 2.71 → 2.72 |
2.71
18 Jul 2023 00:53:09
|
Charlie Li (vishwin) |
devel/py-setuptools: convert individual consumers to ${PY_SETUPTOOLS}
Currently a no-op, but in the future outputs the correct setuptools
port depending on whether USES_PYTHON=distutils is specified.
With hat: python
PR: 270510, 270358 |
2.71
17 Jul 2023 01:40:07
|
Yuri Victorovich (yuri) |
science/smoldyn: Fix build with clang-16 by adding USE_CXXSTD
Reported by: fallout |
2.71
07 Jun 2023 15:04:51
|
Yuri Victorovich (yuri) |
science/smoldyn: Update 2.69 → 2.71
Reported by: portscout |
2.69
20 Oct 2022 20:31:39
|
Yuri Victorovich (yuri) |
science/smoldyn: Update 2.68 -> 2.69; Fix tests
PYTHON options was added but it is disabled because one dependency
is missing. Tests, however, pass with PYTHON=ON
(and only with PYTHON=ON). |
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) |
2.68
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  ) |
2.68
31 Jul 2022 08:12:49
|
Yuri Victorovich (yuri) |
science/smoldyn: Update 2.67 -> 2.68 |
2.67
06 Nov 2021 23:56:37
|
Yuri Victorovich (yuri) |
science/smoldyn: Update 2.66 -> 2.67
Also
* replace MASTER_SITES and WWW with their https:// counterparts
* add the test target which is broken due to tarballs lacking test code
Reported by: portscout |
2.66
20 Jun 2021 17:58:51
|
Yuri Victorovich (yuri) |
science/smoldyn: Update 2.65 -> 2.66
Reported by: portscout |
2.65_1
10 Jun 2021 00:24:37
|
Yuri Victorovich (yuri) |
science/smoldyn: Fix build - release was rerolled
The upstream has confirmed that they rerolled it.
Reported by: fallout |
2.65
21 May 2021 10:00:48
|
Yuri Victorovich (yuri) |
science/smoldyn: Update 2.64 -> 2.65
Reported by: portscout |
2.64
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.64
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.64
25 Mar 2021 09:57:48
 |
yuri |
science/smoldyn: Update 2.63 -> 2.64
Reported by: portscout |
2.63
20 Dec 2020 06:45:09
|
yuri |
science/smoldyn: Update 2.62 -> 2.63
Reported by: portscout |
2.62
03 Nov 2020 20:46:52
|
pkubaj |
science/smoldyn: fix build on GCC architectures
/wrkdirs/usr/ports/science/smoldyn/work/smoldyn-2.62/source/pybind11/include/pybind11/buffer_info.h:18:
error: 'nullptr' was not declared in this scope |
2.62
19 Oct 2020 03:49:24
|
yuri |
science/smoldyn: Update distinfo after the upstream rerolled the release tarball
The changes only affect the Windows build and not FreeBSD.
Reported by: fallout |
2.62
15 Oct 2020 22:37:53
|
yuri |
science/smoldyn: Update 2.61 -> 2.62
Reported by: portscout |
2.61
07 Nov 2019 17:17:54
|
zeising |
Add USES=xorg USES=gl, ports categories s
Add USES=xorg and USES=gl to ports in categories starting with 's'
While here, try to sprinkle other USES (mostly gnome and sdl) as needed. |
2.61
31 Jul 2019 06:15:13
|
yuri |
science/smoldyn: Update 2.60 -> 2.61
Reported by: portscout |
2.60
09 Jun 2019 03:26:16
|
yuri |
New port: science/smoldyn: Biochemical simulator for molecular diffusion,
surface interactions |
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