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Ricardo Wurmus b0190a7d5c
gnu: r-bionet: Update to 1.62.0.
* gnu/packages/bioconductor.scm (r-bionet): Update to 1.62.0.

Change-Id: I0712a4ba67c27b32d6666e91d9515f0299e61848
2023-11-03 22:49:27 +01:00
.mumi Add mumi config. 2023-04-24 15:32:54 +01:00
build-aux maint: Add 'etc/hurd-manifest.scm'. 2023-08-21 10:45:45 +02:00
doc doc: contributiong: Fix ref usage. 2023-11-01 17:20:17 +01:00
etc teams.scm: Add file-local variable prop line for the mode. 2023-11-01 12:24:29 -04:00
gnu gnu: r-bionet: Update to 1.62.0. 2023-11-03 22:49:27 +01:00
guix guix: Upgrade to Bioconductor 3.18. 2023-11-03 22:49:10 +01:00
m4 build: Correct guix_system on musl libc distros. 2023-03-16 12:37:03 +01:00
nix Revert "build: Add missing guix-gc.timer file to binary tarball." 2023-09-24 02:00:00 +02:00
po nls: Update translations. 2023-10-31 23:01:37 +01:00
scripts
tests tests: Adjust to cope with glibc graft. 2023-10-28 01:30:37 +02:00
.dir-locals.el .dir-locals.el: Adjust indentation rule for ‘test-assertm’. 2023-10-20 00:33:26 +02:00
.editorconfig Add EditorConfig specification. 2022-11-05 11:26:55 +01:00
.gitattributes Add git configuration templates to improve diff hunk header detection. 2021-10-14 00:24:34 +02:00
.gitignore teams: Adjust shebang to use 'guix repl'. 2023-10-22 20:35:15 -04:00
.guix-authorizations .guix-authorizations: Authorise Hilton Chain. 2023-08-13 02:00:00 +02:00
.guix-channel
.mailmap Update email addresses for Juliana Sims. 2023-08-16 22:22:06 +02:00
.patman gnu: patman: Apply patch for new Change-Id setting. 2023-10-22 16:09:04 -04:00
AUTHORS
bootstrap bootstrap: Simplify search for translation languages. 2021-06-13 20:46:01 +02:00
ChangeLog build: Generate a ChangeLog file upon "make dist". 2013-05-12 16:35:17 +02:00
CODE-OF-CONDUCT CODE-OF-CONDUCT: Add a top notice. 2022-03-01 13:18:01 -05:00
config-daemon.ac daemon: Do not deduplicate files smaller than 8 KiB. 2021-11-16 14:34:28 +01:00
configure.ac teams: Adjust shebang to use 'guix repl'. 2023-10-22 20:35:15 -04:00
COPYING
gnu.scm
guix.scm guix: Really export 'define-public'. 2022-07-12 01:17:45 +02:00
HACKING
Makefile.am build: Fix it. 2023-10-23 12:50:26 +02:00
manifest.scm maint: Support `guix shell' in Guix's git archive with manifest.scm. 2023-09-18 22:12:39 +02:00
NEWS NEWS: Mention new rpm format. 2023-04-14 15:11:35 -04:00
README The #guix channel is hosted by Libera Chat. 2021-05-20 01:58:04 +02:00
ROADMAP
THANKS
TODO

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-*- mode: org -*-

[[https://www.gnu.org/software/guix/][GNU Guix]] (IPA: /ɡiːks/) is a purely functional package manager, and
associated free software distribution, for the [[https://www.gnu.org/gnu/gnu.html][GNU system]].  In addition
to standard package management features, Guix supports transactional
upgrades and roll-backs, unprivileged package management, per-user
profiles, and garbage collection.

It provides [[https://www.gnu.org/software/guile/][Guile]] Scheme APIs, including a high-level embedded
domain-specific languages (EDSLs) to describe how packages are to be
built and composed.

GNU Guix can be used on top of an already-installed GNU/Linux distribution, or
it can be used standalone (we call that “Guix System”).

Guix is based on the [[https://nixos.org/nix/][Nix]] package manager.


* Requirements

If you are building Guix from source, please see the manual for build
instructions and requirements, either by running:

  info -f doc/guix.info "Requirements"

or by checking the [[https://guix.gnu.org/manual/en/html_node/Requirements.html][web copy of the manual]].

* Installation

See the manual for the installation instructions, either by running

  info -f doc/guix.info "Installation"

or by checking the [[https://guix.gnu.org/manual/en/html_node/Installation.html][web copy of the manual]].

* Building from Git

For information on building Guix from a Git checkout, please see the relevant
section in the manual, either by running

  info -f doc/guix.info "Building from Git"

or by checking the [[https://guix.gnu.org/manual/en/html_node/Building-from-Git.html][web_copy of the manual]].

* How It Works

Guix does the high-level preparation of a /derivation/.  A derivation is
the promise of a build; it is stored as a text file under
=/gnu/store/xxx.drv=.  The (guix derivations) module provides the
`derivation' primitive, as well as higher-level wrappers such as
`build-expression->derivation'.

Guix does remote procedure calls (RPCs) to the build daemon (the =guix-daemon=
command), which in turn performs builds and accesses to the store on its
behalf.  The RPCs are implemented in the (guix store) module.

* Contact

GNU Guix is hosted at https://savannah.gnu.org/projects/guix/.

Please email <help-guix@gnu.org> for questions and <bug-guix@gnu.org> for bug
reports; email <gnu-system-discuss@gnu.org> for general issues regarding the
GNU system.

Join #guix on irc.libera.chat.

* Guix & Nix

GNU Guix is based on [[https://nixos.org/nix/][the Nix package manager]].  It implements the same
package deployment paradigm, and in fact it reuses some of its code.
Yet, different engineering decisions were made for Guix, as described
below.

Nix is really two things: a package build tool, implemented by a library
and daemon, and a special-purpose programming language.  GNU Guix relies
on the former, but uses Scheme as a replacement for the latter.

Using Scheme instead of a specific language allows us to get all the
features and tooling that come with Guile (compiler, debugger, REPL,
Unicode, libraries, etc.)  And it means that we have a general-purpose
language, on top of which we can have embedded domain-specific languages
(EDSLs), such as the one used to define packages.  This broadens what
can be done in package recipes themselves, and what can be done around them.

Technically, Guix makes remote procedure calls to the nix-worker
daemon to perform operations on the store.  At the lowest level, Nix
“derivations” represent promises of a build, stored in .drv files in
the store.  Guix produces such derivations, which are then interpreted
by the daemon to perform the build.  Thus, Guix derivations can use
derivations produced by Nix (and vice versa).

With Nix and the [[https://nixos.org/nixpkgs][Nixpkgs]] distribution, package composition happens at
the Nix language level, but builders are usually written in Bash.
Conversely, Guix encourages the use of Scheme for both package
composition and builders.  Likewise, the core functionality of Nix is
written in C++ and Perl; Guix relies on some of the original C++ code,
but exposes all the API as Scheme.

* Related software

  - [[https://nixos.org][Nix, Nixpkgs, and NixOS]], functional package manager and associated
    software distribution, are the inspiration of Guix
  - [[https://www.gnu.org/software/stow/][GNU Stow]] builds around the idea of one directory per prefix, and a
    symlink tree to create user environments
  - [[https://www.pvv.ntnu.no/~arnej/store/storedoc_6.html][STORE]] shares the same idea
  - [[https://live.gnome.org/OSTree/][GNOME's OSTree]] allows bootable system images to be built from a
    specified set of packages
  - The [[https://www.gnu.org/s/gsrc/][GNU Source Release Collection]] (GSRC) is a user-land software
    distribution; unlike Guix, it relies on core tools available on the
    host system