notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
This referral link gives you 10% off a Fastmail.com account and gives me a discount on my Fastmail account.

Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

Finally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combination for a given watch list. This is what FreshPorts will look for.

Port details
rubygem-bio-shell Command-line interface on BioRuby
1.0.1 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 1.0.1Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-07-24 07:11:01
Last Update: 2023-01-14 23:08:33
Commit Hash: 18c6e18
Also Listed In: rubygems
License: BSD2CLAUSE RUBY
WWW:
https://github.com/bioruby/bioruby-shell
Description:
bio-shell, providing BioRuby Shell, is a command-line interface for BioRuby, an open source bioinformatics library for Ruby. This code has historically been part of the BioRuby gem, but has been split into its own gem as part of an effort to modularize BioRuby. bio-shell and many more plugins are available at biogems.info.
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 (5 items)
Collapse this list.
  1. bin/bioruby
  2. /usr/local/share/licenses/rubygem-bio-shell-1.0.1/catalog.mk
  3. /usr/local/share/licenses/rubygem-bio-shell-1.0.1/LICENSE
  4. /usr/local/share/licenses/rubygem-bio-shell-1.0.1/BSD2CLAUSE
  5. /usr/local/share/licenses/rubygem-bio-shell-1.0.1/RUBY
Collapse this list.
Dependency lines:
  • rubygem-bio-shell>0:biology/rubygem-bio-shell
Conflicts:
CONFLICTS_INSTALL:
  • ruby??-bio
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
To install the port:
cd /usr/ports/biology/rubygem-bio-shell/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/rubygem-bio-shell
  • pkg install rubygem-bio-shell
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: rubygem-bio-shell
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1637073044 SHA256 (rubygem/bio-shell-1.0.1.gem) = 0adddaab0e1579940820829b777d0f567859e914c2bb2feca3d6c9b12dfbe390 SIZE (rubygem/bio-shell-1.0.1.gem) = 46592

Packages (timestamps in pop-ups are UTC):
rubygem-bio-shell
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.0.11.0.11.0.01.0.11.0.1-1.0.0-
FreeBSD:13:quarterly1.0.11.0.11.0.11.0.11.0.11.0.11.0.11.0.1
FreeBSD:14:latest1.0.11.0.11.0.11.0.11.0.11.0.1-1.0.1
FreeBSD:14:quarterly1.0.11.0.1-1.0.11.0.11.0.11.0.11.0.1
FreeBSD:15:latest1.0.11.0.1n/a1.0.1n/a1.0.11.0.11.0.1
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. ruby30 : lang/ruby30
  2. gem : devel/ruby-gems
Runtime dependencies:
  1. rubygem-bio>=2.0.0 : biology/rubygem-bio
  2. ruby30 : lang/ruby30
  3. gem : devel/ruby-gems
Patch dependencies:
  1. ruby30 : lang/ruby30
  2. gem : devel/ruby-gems
Extract dependencies:
  1. ruby30 : lang/ruby30
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_rubygem-bio-shell
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: 8

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.0.1
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
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)
1.0.1
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)
1.0.1
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)
1.0.1
10 Jan 2022 15:15:39
commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Fix CONFLICTS entries of multiple ports

There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.

This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.

Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.0.1
21 Nov 2021 18:21:58
commit hash: 0d7b8a0b12dc07603350031cba9ad758bbe54408commit hash: 0d7b8a0b12dc07603350031cba9ad758bbe54408commit hash: 0d7b8a0b12dc07603350031cba9ad758bbe54408commit hash: 0d7b8a0b12dc07603350031cba9ad758bbe54408 files touched by this commit
Po-Chuan Hsieh (sunpoet) search for other commits by this committer
biology/rubygem-bio-shell: Update to 1.0.1

Changes:	https://github.com/bioruby/bioruby-shell/commits/master
1.0.0
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.
1.0.0
24 Jul 2020 07:08:11
Revision:543012Original commit files touched by this commit
sunpoet search for other commits by this committer
Add rubygem-bio-shell 1.0.0

bio-shell, providing BioRuby Shell, is a command-line interface for BioRuby, an
open source bioinformatics library for Ruby.

This code has historically been part of the BioRuby gem, but has been split into
its own gem as part of an effort to modularize BioRuby. bio-shell and many more
plugins are available at biogems.info.

WWW: https://github.com/bioruby/bioruby-shell

Number of commits found: 8