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Port details
rubygem-bio Integrated environment for Bioinformatics written in Ruby
2.0.5 biology on this many watch lists=2 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 2.0.5Version of this port present on the latest quarterly branch.
Maintainer: ruby@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-02-05 04:27:03
Last Update: 2023-09-30 00:46:30
Commit Hash: df6a298
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
Also Listed In: rubygems
License: BSD2CLAUSE RUBY
WWW:
http://bioruby.org/
Description:
BioRuby project aims to implement integrated environment for Bioinformatics by using Ruby.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (4 items)
Collapse this list.
  1. /usr/local/share/licenses/rubygem-bio-2.0.5/catalog.mk
  2. /usr/local/share/licenses/rubygem-bio-2.0.5/LICENSE
  3. /usr/local/share/licenses/rubygem-bio-2.0.5/BSD2CLAUSE
  4. /usr/local/share/licenses/rubygem-bio-2.0.5/RUBY
Collapse this list.
Dependency lines:
  • rubygem-bio>0:biology/rubygem-bio
To install the port:
cd /usr/ports/biology/rubygem-bio/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/rubygem-bio
  • pkg install rubygem-bio
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: rubygem-bio
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1696002174 SHA256 (rubygem/bio-2.0.5.gem) = 36001f30e792ba3e8b0b9ad4ed15941ac5b12a16835c02dc99f3ab34c7455a6b SIZE (rubygem/bio-2.0.5.gem) = 1378816
Packages (timestamps in pop-ups are UTC):
rubygem-bio
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.0.52.0.52.0.12.0.52.0.5-2.0.1-
FreeBSD:13:quarterly2.0.52.0.52.0.42.0.52.0.52.0.52.0.52.0.5
FreeBSD:14:latest2.0.52.0.52.0.42.0.52.0.52.0.4-2.0.4
FreeBSD:14:quarterly2.0.52.0.5-2.0.52.0.52.0.52.0.52.0.5
FreeBSD:15:latest2.0.52.0.5n/a2.0.5n/a2.0.52.0.52.0.5
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. ruby31 : lang/ruby31
  2. gem : devel/ruby-gems
Runtime dependencies:
  1. ruby31 : lang/ruby31
  2. gem : devel/ruby-gems
Patch dependencies:
  1. ruby31 : lang/ruby31
  2. gem : devel/ruby-gems
Extract dependencies:
  1. ruby31 : lang/ruby31
This port is required by:
for Run
  1. biology/rubygem-bio-executables
  2. biology/rubygem-bio-old-biofetch-emulator
  3. biology/rubygem-bio-shell
Configuration Options:
No options to configure
Options name:
biology_rubygem-bio
USES:
gem
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://rubygems.org/downloads/
Collapse this list.

Number of commits found: 13

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.0.5
30 Sep 2023 00:46:30
commit hash: df6a298fb0a2a585f6bd1ebeaa92695026189791commit hash: df6a298fb0a2a585f6bd1ebeaa92695026189791commit hash: df6a298fb0a2a585f6bd1ebeaa92695026189791commit hash: df6a298fb0a2a585f6bd1ebeaa92695026189791 files touched by this commit		 Po-Chuan Hsieh (sunpoet) search for other commits by this committer 
biology/rubygem-bio: Update to 2.0.5

Changes:	https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
2.0.4
14 Jan 2023 23:08:33
commit hash: 18c6e18276691edf5274406bf82a3b06792ff9aecommit hash: 18c6e18276691edf5274406bf82a3b06792ff9aecommit hash: 18c6e18276691edf5274406bf82a3b06792ff9aecommit hash: 18c6e18276691edf5274406bf82a3b06792ff9ae files touched by this commit		 Muhammad Moinur Rahman (bofh) search for other commits by this committer 
Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby

Switch from Mk/bsd.ruby.mk to Mk/Uses/ruby.mk

Notable changes are.

- Mk/bsd.ruby.mk is moved to Mk/Uses/ruby.mk.
- USE_RUBY=yes is replaced with USES=ruby.
- USE_RUBY_EXTCONF is replaced with USES=ruby:extconf.
- USE_RUBY_RDOC is replaced with USES=ruby:rdoc.
- USE_RUBY_SETUP is replaces with USES=ruby:setup.
- RUBY_NO_BUILD_DEPENDS and RUBY_NO_RUN_DEPENDS are replaced with
  USES=ruby:{build,none,run}.
- RUBY_REQUIRE isn't used anywhere, so removed.
- USES=gem now implies USES=ruby.

This is mainly the work of yasu@ at https://reviews.freebsd.org/D27863

I have just made some cosmetic changes and ran exp-run to test that the
tree is not in a BROKEN state.

Approved by:	portmgr
Differential Revision:	https://reviews.freebsd.org/D37925
2.0.4
03 Oct 2022 02:17:49
commit hash: 6df64aaff123f0e3f8393113e228118c6ea81fd6commit hash: 6df64aaff123f0e3f8393113e228118c6ea81fd6commit hash: 6df64aaff123f0e3f8393113e228118c6ea81fd6commit hash: 6df64aaff123f0e3f8393113e228118c6ea81fd6 files touched by this commit		 Po-Chuan Hsieh (sunpoet) search for other commits by this committer 
biology/rubygem-bio: Update to 2.0.4

Changes:	https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
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)
2.0.3
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)
2.0.3
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit		 Tobias C. Berner (tcberner) search for other commits by this committer 
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.0.3
11 Jan 2022 18:47:28
commit hash: 89eb3690b203c14cbcbda745cb7015fccb8c65adcommit hash: 89eb3690b203c14cbcbda745cb7015fccb8c65adcommit hash: 89eb3690b203c14cbcbda745cb7015fccb8c65adcommit hash: 89eb3690b203c14cbcbda745cb7015fccb8c65ad files touched by this commit		 Po-Chuan Hsieh (sunpoet) search for other commits by this committer 
biology/rubygem-bio: Update to 2.0.3

Changes:	https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
2.0.2
30 Jun 2021 20:44:06
commit hash: 10f3f241dd86fd7bb36130b589df0e750b21710bcommit hash: 10f3f241dd86fd7bb36130b589df0e750b21710bcommit hash: 10f3f241dd86fd7bb36130b589df0e750b21710bcommit hash: 10f3f241dd86fd7bb36130b589df0e750b21710b files touched by this commit		 Po-Chuan Hsieh (sunpoet) search for other commits by this committer 
biology/rubygem-bio: Update to 2.0.2

Changes:	https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
2.0.1
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.
2.0.1
24 Jul 2020 07:49:43
Revision:543176Original commit files touched by this commit		 sunpoet search for other commits by this committer 
Update to 2.0.1

Changes:	https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
1.5.2
21 Sep 2018 18:08:24
Revision:480295Original commit files touched by this commit		 sunpoet search for other commits by this committer 
Update to 1.5.2

Changes:	https://github.com/bioruby/bioruby/blob/bioruby-1.5/RELEASE_NOTES.rdoc
1.5.1
06 Feb 2017 23:03:17
Revision:433528Original commit files touched by this commit		 sunpoet search for other commits by this committer 
Update to 1.5.1

- Update LICENSE
- Add LICENSE_FILE

Changes:	https://github.com/bioruby/bioruby/blob/bioruby-1.5/RELEASE_NOTES.rdoc
		https://github.com/bioruby/bioruby/blob/master/doc/RELEASE_NOTES-1.5.0.rdoc
1.4.3.0001_1
05 Feb 2017 04:26:56
Revision:433348Original commit files touched by this commit		 sunpoet search for other commits by this committer 
Move devel/rubygem-bio to biology/rubygem-bio

Number of commits found: 13
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