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Merge branch 'master' into staging

version-1.1.0
Marius Bakke 2 years ago
parent
commit
3941af527d
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  1. 2
      Makefile.am
  2. 2
      bootstrap
  3. 3
      build-aux/build-self.scm
  4. 3
      build-aux/git-authenticate.scm
  5. 62
      doc/contributing.texi
  6. 127
      doc/guix.texi
  7. 6
      doc/local.mk
  8. 34
      etc/copyright.el
  9. 8
      gnu/build/marionette.scm
  10. 5
      gnu/installer.scm
  11. 7
      gnu/installer/parted.scm
  12. 1
      gnu/installer/steps.scm
  13. 47
      gnu/installer/utils.scm
  14. 7
      gnu/local.mk
  15. 49
      gnu/packages/admin.scm
  16. 4
      gnu/packages/algebra.scm
  17. 21
      gnu/packages/android.scm
  18. 5
      gnu/packages/aspell.scm
  19. 6
      gnu/packages/assembly.scm
  20. 20
      gnu/packages/audio.scm
  21. 3
      gnu/packages/autotools.scm
  22. 2
      gnu/packages/backup.scm
  23. 4
      gnu/packages/benchmark.scm
  24. 104
      gnu/packages/bioconductor.scm
  25. 45
      gnu/packages/bioinformatics.scm
  26. 4
      gnu/packages/bittorrent.scm
  27. 6
      gnu/packages/build-tools.scm
  28. 6
      gnu/packages/c.scm
  29. 4
      gnu/packages/cedille.scm
  30. 6
      gnu/packages/certs.scm
  31. 34
      gnu/packages/compression.scm
  32. 7
      gnu/packages/connman.scm
  33. 29
      gnu/packages/cpp.scm
  34. 1341
      gnu/packages/cran.scm
  35. 3081
      gnu/packages/crates-io.scm
  36. 28
      gnu/packages/crypto.scm
  37. 39
      gnu/packages/databases.scm
  38. 2
      gnu/packages/dav.scm
  39. 4
      gnu/packages/debian.scm
  40. 59
      gnu/packages/dictionaries.scm
  41. 6
      gnu/packages/diffoscope.scm
  42. 8
      gnu/packages/distributed.scm
  43. 126
      gnu/packages/dns.scm
  44. 6
      gnu/packages/docker.scm
  45. 2
      gnu/packages/ebook.scm
  46. 6
      gnu/packages/education.scm
  47. 7
      gnu/packages/efi.scm
  48. 4
      gnu/packages/elixir.scm
  49. 119
      gnu/packages/emacs-xyz.scm
  50. 2
      gnu/packages/embedded.scm
  51. 123
      gnu/packages/emulators.scm
  52. 23
      gnu/packages/engineering.scm
  53. 8
      gnu/packages/finance.scm
  54. 4
      gnu/packages/firmware.scm
  55. 10
      gnu/packages/flashing-tools.scm
  56. 2
      gnu/packages/fltk.scm
  57. 42
      gnu/packages/fonts.scm
  58. 14
      gnu/packages/fpga.scm
  59. 163
      gnu/packages/freedesktop.scm
  60. 28
      gnu/packages/game-development.scm
  61. 121
      gnu/packages/games.scm
  62. 2
      gnu/packages/geo.scm
  63. 4
      gnu/packages/gl.scm
  64. 40
      gnu/packages/gnome-xyz.scm
  65. 53
      gnu/packages/gnome.scm
  66. 6
      gnu/packages/gnunet.scm
  67. 16
      gnu/packages/gnupg.scm
  68. 6
      gnu/packages/gnustep.scm
  69. 33
      gnu/packages/graph.scm
  70. 116
      gnu/packages/graphics.scm
  71. 2
      gnu/packages/gtk.scm
  72. 79
      gnu/packages/guile-xyz.scm
  73. 4
      gnu/packages/guile.scm
  74. 9
      gnu/packages/haskell-apps.scm
  75. 2
      gnu/packages/haskell-crypto.scm
  76. 4
      gnu/packages/haskell-web.scm
  77. 50
      gnu/packages/haskell-xyz.scm
  78. 10
      gnu/packages/image-viewers.scm
  79. 3
      gnu/packages/image.scm
  80. 4
      gnu/packages/ipfs.scm
  81. 38
      gnu/packages/irc.scm
  82. 6
      gnu/packages/java.scm
  83. 2
      gnu/packages/javascript.scm
  84. 7
      gnu/packages/kde-internet.scm
  85. 2
      gnu/packages/key-mon.scm
  86. 1
      gnu/packages/libevent.scm
  87. 86
      gnu/packages/libreoffice.scm
  88. 195
      gnu/packages/linux.scm
  89. 388
      gnu/packages/lisp-xyz.scm
  90. 343
      gnu/packages/llvm.scm
  91. 2
      gnu/packages/machine-learning.scm
  92. 8
      gnu/packages/mail.scm
  93. 59
      gnu/packages/maths.scm
  94. 132
      gnu/packages/messaging.scm
  95. 49
      gnu/packages/mono.scm
  96. 12
      gnu/packages/mpd.scm
  97. 88
      gnu/packages/mpi.scm
  98. 2
      gnu/packages/multiprecision.scm
  99. 19
      gnu/packages/music.scm
  100. 6
      gnu/packages/ncdu.scm

2
Makefile.am

@ -122,6 +122,7 @@ MODULES = \
guix/build-system/meson.scm \
guix/build-system/minify.scm \
guix/build-system/asdf.scm \
guix/build-system/copy.scm \
guix/build-system/glib-or-gtk.scm \
guix/build-system/gnu.scm \
guix/build-system/guile.scm \
@ -169,6 +170,7 @@ MODULES = \
guix/build/go-build-system.scm \
guix/build/asdf-build-system.scm \
guix/build/bzr.scm \
guix/build/copy-build-system.scm \
guix/build/git.scm \
guix/build/hg.scm \
guix/build/glib-or-gtk-build-system.scm \

2
bootstrap

@ -16,7 +16,7 @@ for lang in ${langs}; do
fi
done
langs=`find po/doc -type f -name 'guix-cookbook*.po' \
| sed -e 's,guix-manual\.,,' \
| sed -e 's,guix-cookbook\.,,' \
| xargs -n 1 -I{} basename {} .po`
for lang in ${langs}; do
if [ ! -e "doc/guix-cookbook.${lang}.texi" ]; then

3
build-aux/build-self.scm

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -420,6 +420,7 @@ files."
;; $GUILE_LOAD_PATH & co.
(with-clean-environment
(setenv "GUILE_WARN_DEPRECATED" "no") ;be quiet and drive
(setenv "COLUMNS" "120") ;show wider backtraces
(when home
;; Inherit HOME so that 'xdg-directory' works.
(setenv "HOME" home))

3
build-aux/git-authenticate.scm

@ -134,7 +134,8 @@
("lsl88"
"2AE3 1395 932B E642 FC0E D99C 9BED 6EDA 32E5 B0BC")
("mab"
"BE62 7373 8E61 6D6D 1B3A 08E8 A21A 0202 4881 6103")
;; primary: "BE62 7373 8E61 6D6D 1B3A 08E8 A21A 0202 4881 6103"
"39B3 3C8D 9448 0D2D DCC2 A498 8B44 A0CD C7B9 56F2")
("marusich"
"CBF5 9755 CBE7 E7EF EF18 3FB1 DD40 9A15 D822 469D")
("mbakke"

62
doc/contributing.texi

@ -274,6 +274,33 @@ trigger string @code{origin...}, which can be expanded further. The
@code{origin} snippet in turn may insert other trigger strings ending on
@code{...}, which also can be expanded further.
@cindex insert or update copyright
@cindex @code{M-x guix-copyright}
@cindex @code{M-x copyright-update}
Additionaly we provide insertion and automatic update of a copyright in
@file{etc/copyright.el}. You may want to set your full name, mail, and
load a file.
@lisp
(setq user-full-name "Alice Doe")
(setq user-mail-address "alice@@mail.org")
;; @r{Assuming the Guix checkout is in ~/src/guix.}
(load-file "~/src/guix/etc/copyright.el")
@end lisp
To insert a copyright at the current line invoke @code{M-x guix-copyright}.
To update a copyright you need to specify a @code{copyright-names-regexp}.
@lisp
(setq copyright-names-regexp
(format "%s <%s>" user-full-name user-mail-address))
@end lisp
You can check if your copyright is up to date by evaluating @code{M-x
copyright-update}. If you want to do it automatically after each buffer
save then add @code{(add-hook 'after-save-hook 'copyright-update)} in
Emacs.
@node Packaging Guidelines
@section Packaging Guidelines
@ -347,6 +374,7 @@ needed is to review and apply the patch.
* Python Modules:: A touch of British comedy.
* Perl Modules:: Little pearls.
* Java Packages:: Coffee break.
* Rust Crates:: Beware of oxidation.
* Fonts:: Fond of fonts.
@end menu
@ -685,6 +713,40 @@ dashes and prepend the prefix @code{java-}. So the class
@code{java-apache-commons-cli}.
@node Rust Crates
@subsection Rust Crates
@cindex rust
Rust programs standing for themselves are named as any other package, using the
lowercase upstream name.
To prevent namespace collisions we prefix all other Rust packages with the
@code{rust-} prefix. The name should be changed to lowercase as appropriate and
dashes should remain in place.
In the rust ecosystem it is common for multiple incompatible versions of a
package to be used at any given time, so all packages should have a versioned
suffix. If a package has passed version 1.0.0 then just the major version
number is sufficient (e.g.@: @code{rust-clap-2}), otherwise the version suffix
should contain both the major and minor version (e.g.@: @code{rust-rand-0.6}).
Because of the difficulty in reusing rust packages as pre-compiled inputs for
other packages the Cargo build system (@pxref{Build Systems,
@code{cargo-build-system}}) presents the @code{#:cargo-inputs} and
@code{cargo-development-inputs} keywords as build system arguments. It would be
helpful to think of these as similar to @code{propagated-inputs} and
@code{native-inputs}. Rust @code{dependencies} and @code{build-dependencies}
should go in @code{#:cargo-inputs}, and @code{dev-dependencies} should go in
@code{#:cargo-development-inputs}. If a Rust package links to other libraries
then the standard placement in @code{inputs} and the like should be used.
Care should be taken to ensure the correct version of dependencies are used; to
this end we try to refrain from skipping the tests or using @code{#:skip-build?}
when possible. Of course this is not always possible, as the package may be
developed for a different Operating System, depend on features from the Nightly
Rust compiler, or the test suite may have atrophied since it was released.
@node Fonts
@subsection Fonts

127
doc/guix.texi

@ -73,6 +73,7 @@ Copyright @copyright{} 2020 Leo Prikler@*
Copyright @copyright{} 2019, 2020 Simon Tournier@*
Copyright @copyright{} 2020 Wiktor Żelazny@*
Copyright @copyright{} 2020 Damien Cassou@*
Copyright @copyright{} 2020 Jakub Kądziołka@*
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3 or
@ -771,11 +772,11 @@ The following dependencies are optional:
@itemize
@item
@c Note: We need at least 0.10.2 for 'channel-send-eof'.
@c Note: We need at least 0.12.0 for 'userauth-gssapi!'.
Support for build offloading (@pxref{Daemon Offload Setup}) and
@command{guix copy} (@pxref{Invoking guix copy}) depends on
@uref{https://github.com/artyom-poptsov/guile-ssh, Guile-SSH},
version 0.10.2 or later.
version 0.12.0 or later.
@item
When @url{https://www.nongnu.org/lzip/lzlib.html, lzlib} is available, lzlib
@ -2440,6 +2441,11 @@ your system includes the latest security updates (@pxref{Security Updates}).
Note that @command{sudo guix} runs your user's @command{guix} command and
@emph{not} root's, because @command{sudo} leaves @code{PATH} unchanged. To
explicitly run root's @command{guix}, type @command{sudo -i guix @dots{}}.
The difference matters here, because @command{guix pull} updates
the @command{guix} command and package definitions only for the user it is ran
as. This means that if you choose to use @command{guix system reconfigure} in
root's login shell, you'll need to @command{guix pull} separately.
@end quotation
Join us on @code{#guix} on the Freenode IRC network or on
@ -4958,8 +4964,10 @@ shared and will change to the user's home directory within the container
instead. See also @code{--user}.
@item --expose=@var{source}[=@var{target}]
For containers, expose the file system @var{source} from the host system
as the read-only file system @var{target} within the container. If
@itemx --share=@var{source}[=@var{target}]
For containers, @code{--expose} (resp. @code{--share}) exposes the file
system @var{source} from the host system as the read-only
(resp. writable) file system @var{target} within the container. If
@var{target} is not specified, @var{source} is used as the target mount
point in the container.
@ -4971,19 +4979,6 @@ directory:
guix environment --container --expose=$HOME=/exchange --ad-hoc guile -- guile
@end example
@item --share=@var{source}[=@var{target}]
For containers, share the file system @var{source} from the host system
as the writable file system @var{target} within the container. If
@var{target} is not specified, @var{source} is used as the target mount
point in the container.
The example below spawns a Guile REPL in a container in which the user's
home directory is accessible for both reading and writing via the
@file{/exchange} directory:
@example
guix environment --container --share=$HOME=/exchange --ad-hoc guile -- guile
@end example
@end table
@command{guix environment}
@ -6159,6 +6154,70 @@ parameters available to cargo. It will also remove an included
if they are defined by the crate.
@end defvr
@defvr {Scheme Variable} copy-build-system
@cindex (copy build system)
This variable is exported by @code{(guix build-system copy)}. It
supports builds of simple packages that don't require much compiling,
mostly just moving files around.
It adds much of the @code{gnu-build-system} packages to the set of
inputs. Because of this, the @code{copy-build-system} does not require
all the boilerplate code often needed for the
@code{trivial-build-system}.
To further simplify the file installation process, an
@code{#:install-plan} argument is exposed to let the packager specify
which files go where. The install plan is a list of @code{(@var{source}
@var{target} [@var{filters}])}. @var{filters} are optional.
@itemize
@item When @var{source} matches a file or directory without trailing slash, install it to @var{target}.
@itemize
@item If @var{target} has a trailing slash, install @var{source} basename beneath @var{target}.
@item Otherwise install @var{source} as @var{target}.
@end itemize
@item When @var{source} is a directory with a trailing slash, or when @var{filters} are used,
the trailing slash of @var{target} is implied with the same meaning
as above.
@itemize
@item Without @var{filters}, install the full @var{source} @emph{content} to @var{target}.
@item With @var{filters} among @code{#:include}, @code{#:include-regexp}, @code{#:exclude},
@code{#:exclude-regexp}, only select files are installed depending on
the filters. Each filters is specified by a list of strings.
@itemize
@item With @code{#:include}, install all the files which the path suffix matches
at least one of the elements in the given list.
@item With @code{#:include-regexp}, install all the files which the
subpaths match at least one of the regular expressions in the given
list.
@item The @code{#:exclude} and @code{#:exclude-regexp} filters
are the complement of their inclusion counterpart. Without @code{#:include} flags,
install all files but those matching the exclusion filters.
If both inclusions and exclusions are specified, the exclusions are done
on top of the inclusions.
@end itemize
@end itemize
In all cases, the paths relative to @var{source} are preserved within
@var{target}.
@end itemize
Examples:
@itemize
@item @code{("foo/bar" "share/my-app/")}: Install @file{bar} to @file{share/my-app/bar}.
@item @code{("foo/bar" "share/my-app/baz")}: Install @file{bar} to @file{share/my-app/baz}.
@item @code{("foo/" "share/my-app")}: Install the content of @file{foo} inside @file{share/my-app},
e.g., install @file{foo/sub/file} to @file{share/my-app/sub/file}.
@item @code{("foo/" "share/my-app" #:include ("sub/file"))}: Install only @file{foo/sub/file} to
@file{share/my-app/sub/file}.
@item @code{("foo/sub" "share/my-app" #:include ("file"))}: Install @file{foo/sub/file} to
@file{share/my-app/file}.
@end itemize
@end defvr
@cindex Clojure (programming language)
@cindex simple Clojure build system
@defvr {Scheme Variable} clojure-build-system
@ -6815,9 +6874,11 @@ instruct it to listen for TCP connections (@pxref{Invoking guix-daemon,
@item ssh
@cindex SSH access to build daemons
These URIs allow you to connect to a remote daemon over
SSH@footnote{This feature requires Guile-SSH (@pxref{Requirements}).}.
A typical URL might look like this:
These URIs allow you to connect to a remote daemon over SSH. This
feature requires Guile-SSH (@pxref{Requirements}) and a working
@code{guile} binary in @code{PATH} on the destination machine. It
supports public key and GSSAPI authentication. A typical URL might look
like this:
@example
ssh://charlie@@guix.example.org:22
@ -14463,7 +14524,7 @@ Command to run when halting.
Command to run when rebooting.
@item @code{theme} (default "maldives")
Theme to use. Default themes provided by SDDM are "elarun" or "maldives".
Theme to use. Default themes provided by SDDM are "elarun", "maldives" or "maya".
@item @code{themes-directory} (default "/run/current-system/profile/share/sddm/themes")
Directory to look for themes.
@ -14538,7 +14599,7 @@ Relogin after logout.
@cindex X11 login
@defvr {Scheme Variable} sddm-service-type
This is the type of the service to run the
@uref{https://github.com/sddm/sddm,SSDM display manager}. Its value
@uref{https://github.com/sddm/sddm,SDDM display manager}. Its value
must be a @code{sddm-configuration} record (see below).
Here's an example use:
@ -21799,6 +21860,13 @@ Defaults to @samp{#t}.
@end deftypevr
@deftypevr {@code{openvpn-client-configuration} parameter} boolean fast-io?
(Experimental) Optimize TUN/TAP/UDP I/O writes by avoiding a call to
poll/epoll/select prior to the write operation.
Defaults to @samp{#f}.
@end deftypevr
@deftypevr {@code{openvpn-client-configuration} parameter} number verbosity
Verbosity level.
@ -21814,6 +21882,14 @@ Defaults to @samp{#f}.
@end deftypevr
@deftypevr {@code{openvpn-client-configuration} parameter} maybe-string auth-user-pass
Authenticate with server using username/password. The option is a file
containing username/password on 2 lines. Do not use a file-like object as it
would be added to the store and readable by any user.
Defaults to @samp{'disabled}.
@end deftypevr
@deftypevr {@code{openvpn-client-configuration} parameter} key-usage verify-key-usage?
Whether to check the server certificate has server usage extension.
@ -21935,6 +22011,13 @@ Defaults to @samp{#t}.
@end deftypevr
@deftypevr {@code{openvpn-server-configuration} parameter} boolean fast-io?
(Experimental) Optimize TUN/TAP/UDP I/O writes by avoiding a call to
poll/epoll/select prior to the write operation.
Defaults to @samp{#f}.
@end deftypevr
@deftypevr {@code{openvpn-server-configuration} parameter} number verbosity
Verbosity level.

6
doc/local.mk

@ -27,7 +27,8 @@ info_TEXINFOS = %D%/guix.texi \
%D%/guix.fr.texi \
%D%/guix.ru.texi \
%D%/guix.zh_CN.texi \
%D%/guix-cookbook.texi
%D%/guix-cookbook.texi \
%D%/guix-cookbook.de.texi
%C%_guix_TEXINFOS = \
%D%/contributing.texi \
@ -69,7 +70,8 @@ TRANSLATED_INFO = \
%D%/contributing.es.texi \
%D%/contributing.fr.texi \
%D%/contributing.ru.texi \
%D%/contributing.zh_CN.texi
%D%/contributing.zh_CN.texi \
%D%/guix-cookbook.de.texi
# Bundle this file so that makeinfo finds it in out-of-source-tree builds.
BUILT_SOURCES += $(OS_CONFIG_EXAMPLES_TEXI) $(TRANSLATED_INFO)

34
etc/copyright.el

@ -0,0 +1,34 @@
;;; copyright.el --- Insert a Guix copyright.
;; Copyright © 2020 Oleg Pykhalov <go.wigust@gmail.com>
;; This file is part of GNU Guix.
;; GNU Guix is free software; you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation, either version 3 of the License, or
;; (at your option) any later version.
;; GNU Guix is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;; GNU General Public License for more details.
;; You should have received a copy of the GNU General Public License
;; along with this program. If not, see <http://www.gnu.org/licenses/>.
;;; Commentary:
;; This package provides skeleton to insert a copyright with `guix-copyright'.
;;; Code:
(define-skeleton guix-copyright
"Insert a copyright by $USER notice at cursor."
"FULL_NAME <MAIL_ADDRESS>: "
comment-start
";; Copyright © " `(format-time-string "%Y") " "
(or (format "%s <%s>" user-full-name user-mail-address) str)
comment-end)
;;; copyright.el ends here

8
gnu/build/marionette.scm

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2018 Chris Marusich <cmmarusich@gmail.com>
;;;
;;; This file is part of GNU Guix.
@ -204,6 +204,7 @@ MARIONETTE. Raise an error on failure."
(catch 'system-error
(lambda ()
(connect sock AF_INET INADDR_LOOPBACK ,port)
(close-port sock)
'success)
(lambda args
(if (< i ,timeout)
@ -227,6 +228,7 @@ accept connections in MARIONETTE. Raise an error on failure."
(catch 'system-error
(lambda ()
(connect sock AF_UNIX ,file-name)
(close-port sock)
'success)
(lambda args
(if (< i ,timeout)
@ -315,8 +317,8 @@ PREDICATE, whichever comes first. Raise an error when TIMEOUT is exceeded."
(#\( . "shift-9")
(#\) . "shift-0")
(#\/ . "slash")
(#\< . "less")
(#\> . "shift-less")
(#\< . "shift-comma")
(#\> . "shift-dot")
(#\. . "dot")
(#\, . "comma")
(#\; . "semicolon")

5
gnu/installer.scm

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018, 2020 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
@ -26,6 +26,7 @@
#:use-module (guix utils)
#:use-module (guix ui)
#:use-module ((guix self) #:select (make-config.scm))
#:use-module (gnu installer utils)
#:use-module (gnu packages admin)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
@ -395,6 +396,8 @@ selected keymap."
#f)))
(const #f)
(lambda (key . args)
(syslog "crashing due to uncaught exception: ~s ~s~%"
key args)
(let ((error-file "/tmp/last-installer-error"))
(call-with-output-file error-file
(lambda (port)

7
gnu/installer/parted.scm

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018, 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
@ -1070,6 +1070,8 @@ USER-PARTITION if it is encrypted, or the plain file-name otherwise."
(call-with-luks-key-file
password
(lambda (key-file)
(syslog "formatting and opening LUKS entry ~s at ~s~%"
label file-name)
(system* "cryptsetup" "-q" "luksFormat" file-name key-file)
(system* "cryptsetup" "open" "--type" "luks"
"--key-file" key-file file-name label)))))
@ -1077,6 +1079,7 @@ USER-PARTITION if it is encrypted, or the plain file-name otherwise."
(define (luks-close user-partition)
"Close the encrypted partition pointed by USER-PARTITION."
(let ((label (user-partition-crypt-label user-partition)))
(syslog "closing LUKS entry ~s~%" label)
(system* "cryptsetup" "close" label)))
(define (format-user-partitions user-partitions)
@ -1150,6 +1153,7 @@ respective mount-points."
(file-name
(user-partition-upper-file-name user-partition)))
(mkdir-p target)
(syslog "mounting ~s on ~s~%" file-name target)
(mount file-name target mount-type)))
sorted-partitions)))
@ -1165,6 +1169,7 @@ respective mount-points."
(target
(string-append (%installer-target-dir)
mount-point)))
(syslog "unmounting ~s~%" target)
(umount target)
(when crypt-label
(luks-close user-partition))))

1
gnu/installer/steps.scm

@ -177,6 +177,7 @@ return the accumalated result so far."
#:done-steps '())))))
((installer-step-break? c)
(reverse result)))
(syslog "running step '~a'~%" (installer-step-id step))
(let* ((id (installer-step-id step))
(compute (installer-step-compute step))
(res (compute result done-steps)))

47
gnu/installer/utils.scm

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -24,12 +24,16 @@
#:use-module (srfi srfi-34)
#:use-module (ice-9 rdelim)
#:use-module (ice-9 regex)
#:use-module (ice-9 format)
#:use-module (ice-9 textual-ports)
#:export (read-lines
read-all
nearest-exact-integer
read-percentage
run-shell-command))
run-shell-command
syslog-port
syslog))
(define* (read-lines #:optional (port (current-input-port)))
"Read lines from PORT and return them as a list."
@ -85,9 +89,48 @@ COMMAND exited successfully, #f otherwise."
(format (current-error-port)
(G_ "Command failed with exit code ~a.~%")
(invoke-error-exit-status c))
(syslog "command ~s failed with exit code ~a"
command (invoke-error-exit-status c))
(pause)
#f))
(syslog "running command ~s~%" command)
(invoke "bash" "--init-file" file)
(syslog "command ~s succeeded~%" command)
(newline)
(pause)
#t))))
;;;
;;; Logging.
;;;
(define (open-syslog-port)
"Return an open port (a socket) to /dev/log or #f if that wasn't possible."
(let ((sock (socket AF_UNIX SOCK_DGRAM 0)))
(catch 'system-error
(lambda ()
(connect sock AF_UNIX "/dev/log")
(setvbuf sock 'line)
sock)
(lambda args
(close-port sock)
#f))))
(define syslog-port
(let ((port #f))
(lambda ()
"Return an output port to syslog."
(unless port
(set! port (open-syslog-port)))
(or port (%make-void-port "w")))))
(define-syntax syslog
(lambda (s)
"Like 'format', but write to syslog."
(syntax-case s ()
((_ fmt args ...)
(string? (syntax->datum #'fmt))
(with-syntax ((fmt (string-append "installer[~d]: "
(syntax->datum #'fmt))))
#'(format (syslog-port) fmt (getpid) args ...))))))

7
gnu/local.mk

@ -774,7 +774,6 @@ dist_patch_DATA = \
%D%/packages/patches/ceph-disable-cpu-optimizations.patch \
%D%/packages/patches/ceph-volume-respect-PATH.patch \
%D%/packages/patches/chmlib-inttypes.patch \
%D%/packages/patches/choqok-Fix-building-under-Qt-5.13.patch \
%D%/packages/patches/clamav-config-llvm-libs.patch \
%D%/packages/patches/clamav-system-tomsfastmath.patch \
%D%/packages/patches/clang-3.5-libc-search-path.patch \
@ -782,6 +781,7 @@ dist_patch_DATA = \
%D%/packages/patches/clang-3.8-libc-search-path.patch \
%D%/packages/patches/clang-6.0-libc-search-path.patch \
%D%/packages/patches/clang-7.0-libc-search-path.patch \
%D%/packages/patches/clang-9.0-libc-search-path.patch \
%D%/packages/patches/clang-runtime-asan-build-fixes.patch \
%D%/packages/patches/clang-runtime-esan-build-fixes.patch \
%D%/packages/patches/classpath-aarch64-support.patch \
@ -794,6 +794,7 @@ dist_patch_DATA = \
%D%/packages/patches/coda-use-system-libs.patch \
%D%/packages/patches/combinatorial-blas-awpm.patch \
%D%/packages/patches/combinatorial-blas-io-fix.patch \
%D%/packages/patches/containerd-test-with-go1.13.patch \
%D%/packages/patches/cpufrequtils-fix-aclocal.patch \
%D%/packages/patches/crawl-upgrade-saves.patch \
%D%/packages/patches/crda-optional-gcrypt.patch \
@ -809,6 +810,8 @@ dist_patch_DATA = \
%D%/packages/patches/debops-constants-for-external-program-names.patch \
%D%/packages/patches/debops-debops-defaults-fall-back-to-less.patch \
%D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \
%D%/packages/patches/desmume-gcc6-fixes.patch \
%D%/packages/patches/desmume-gcc7-fixes.patch \
%D%/packages/patches/dfu-programmer-fix-libusb.patch \
%D%/packages/patches/diffutils-gets-undeclared.patch \
%D%/packages/patches/dkimproxy-add-ipv6-support.patch \
@ -1351,6 +1354,7 @@ dist_patch_DATA = \
%D%/packages/patches/qrcodegen-cpp-make-install.patch \
%D%/packages/patches/qt4-ldflags.patch \
%D%/packages/patches/qtbase-use-TZDIR.patch \
%D%/packages/patches/qtbase-QTBUG-81715.patch \
%D%/packages/patches/qtscript-disable-tests.patch \
%D%/packages/patches/quagga-reproducible-build.patch \
%D%/packages/patches/quickswitch-fix-dmenu-check.patch \
@ -1463,7 +1467,6 @@ dist_patch_DATA = \
%D%/packages/patches/ustr-fix-build-with-gcc-5.patch \
%D%/packages/patches/util-linux-tests.patch \
%D%/packages/patches/upower-builddir.patch \
%D%/packages/patches/upx-fix-CVE-2017-15056.patch \
%D%/packages/patches/valgrind-enable-arm.patch \
%D%/packages/patches/vboot-utils-fix-format-load-address.patch \
%D%/packages/patches/vboot-utils-fix-tests-show-contents.patch \

49
gnu/packages/admin.scm

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
;;; Copyright © 2014, 2015, 2016, 2018, 2019 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
@ -196,14 +196,14 @@ and provides a \"top-like\" mode (monitoring).")
(define-public shepherd
(package
(name "shepherd")
(version "0.6.1")
(version "0.7.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/shepherd/shepherd-"
version ".tar.gz"))
(sha256
(base32
"1xn6mb5bh8bpfgdrh09ja31jk0ln7bmxbbf0vjcqxkkixs2wl6sk"))))
"07j3vd0y8zab2nwbrwj0ahrfif1ldm5sjssn7m3dw4s307fsrfzx"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags '("--localstatedir=/var")))
@ -228,6 +228,16 @@ interface and is based on GNU Guile.")
(license license:gpl3+)
(home-page "https://www.gnu.org/software/shepherd/")))
(define-public guile3.0-shepherd
(package
(inherit shepherd)
(name "guile3.0-shepherd")
(native-inputs
`(("pkg-config" ,pkg-config)
("guile" ,guile-next)))
(inputs
`(("guile" ,guile-next)))))
(define-public cloud-utils
(package
(name "cloud-utils")
@ -2226,7 +2236,7 @@ displays a table of current bandwidth usage by pairs of hosts.")
(define-public munge
(package
(name "munge")
(version "0.5.13")
(version "0.5.14")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/dun/munge/releases/"
@ -2234,20 +2244,45 @@ displays a table of current bandwidth usage by pairs of hosts.")
version ".tar.xz"))
(sha256
(base32
"1nj486bbg1adfg298zck96vgx57kchcypc1zdz1n7w540vyksxcr"))
"0h06sghb4rqvv1ywyd6mzsmbcgh712v6ygrff0gzm440y4ca41k6"))
(modules '((guix build utils)))
(snippet
'(begin
;; Don't insist on write access to /var.
(substitute* "src/etc/Makefile.in"
(("\\$\\(INSTALL\\)(.*)localstatedir" _ middle)
(string-append "-$(INSTALL)" middle "localstatedir")))
(string-append "-$(INSTALL)" middle "localstatedir"))
(("\\$\\(MKDIR_P\\) .*(local|run)statedir.*")
""))
#t))))
(inputs
`(("openssl" ,openssl)
("libgcrypt" ,libgcrypt)))
(build-system gnu-build-system)
(arguments '(#:configure-flags '("--localstatedir=/var")))
(arguments
'(#:configure-flags
(list "--localstatedir=/var"
(string-append "--with-pkgconfigdir="
(assoc-ref %outputs "out") "/lib/pkgconfig"))
#:phases
(modify-phases %standard-phases
;; XXX Many test series fail. Some might be fixable, others do no-no
;; things like invoking ‘sudo’.
(add-after 'unpack 'skip-failing-tests
(lambda _
(for-each (lambda (test)
(substitute* "t/Makefile.in"
(((string-append test "\\.t ")) "")))
(list "0100-munged-lock"
"0010-basic"
"0011-munged-cmdline"
"0012-munge-cmdline"
"0013-unmunge-cmdline"
"0101-munged-security-socket"
"0102-munged-security-keyfile"
"0103-munged-security-logfile"
"0110-munged-origin-addr"))
#t)))))
(home-page "https://dun.github.io/munge/")
(synopsis "Cluster computing authentication service")
(description

4
gnu/packages/algebra.scm

@ -91,7 +91,7 @@ implement the floating point approach to complex multiplication are
implemented. On the other hand, these comprise asymptotically fast
multiplication routines such as ToomCook and the FFT.")
(license license:lgpl3+)
(home-page "http://mpfrcx.multiprecision.org/")))
(home-page "http://www.multiprecision.org/mpfrcx/")))
(define-public gf2x
(package
@ -140,7 +140,7 @@ multiplication via floating point approximations. It consists of libraries
that can be called from within a C program and of executable command
line applications.")
(license license:gpl3+)
(home-page "http://cm.multiprecision.org/")))
(home-page "http://www.multiprecision.org/cm/")))
(define-public fplll
(package

21
gnu/packages/android.scm

@ -9,6 +9,7 @@
;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -716,7 +717,7 @@ to be passed to the @code{udev} service.")
(define-public git-repo
(package
(name "git-repo")
(version "1.12.37")
(version "2.3")
(source
(origin
(method git-fetch)
@ -725,11 +726,10 @@ to be passed to the @code{udev} service.")
(commit (string-append "v" version))))
(file-name (string-append "git-repo-" version "-checkout"))
(sha256
(base32 "0qp7jqhblv7xblfgpcq4n18dyjdv8shz7r60c3vnjxx2fngkj2jd"))))
(base32 "0jrll0mjfwakyjvlhbxwsdi32jhgss9mwz8c8h24n1qbqqxysrk4"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; code says: "Python 3 support is … experimental."
#:phases
`(#:phases
(modify-phases %standard-phases
(add-before 'build 'set-executable-paths
(lambda* (#:key inputs outputs #:allow-other-keys)
@ -738,8 +738,8 @@ to be passed to the @code{udev} service.")
(gpg (assoc-ref inputs "gnupg"))
(ssh (assoc-ref inputs "ssh")))
(substitute* '("repo" "git_command.py")
(("^GIT = 'git' ")
(string-append "GIT = '" git "/bin/git' ")))
(("^GIT = 'git'")
(string-append "GIT = '" git "/bin/git'")))
(substitute* "repo"
((" cmd = \\['gpg',")
(string-append " cmd = ['" gpg "/bin/gpg',")))
@ -777,9 +777,14 @@ def _FindRepo():
((" rev = _Verify\\(.*\\)") " rev = None"))
#t)))
(delete 'build) ; nothing to build
(add-before 'check 'configure-git
(lambda _
(setenv "HOME" (getcwd))
(invoke "git" "config" "--global" "user.email" "you@example.com")
(invoke "git" "config" "--global" "user.name" "Your Name")))
(replace 'check
(lambda _
(invoke "python" "-m" "nose")))
(invoke "./run_tests")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -798,7 +803,7 @@ def _FindRepo():
("gnupg" ,gnupg)
("ssh" ,openssh)))
(native-inputs
`(("nose" ,python2-nose)))
`(("pytest" ,python-pytest)))
(home-page "https://code.google.com/p/git-repo/")
(synopsis "Helps to manage many Git repositories.")
(description "Repo is a tool built on top of Git. Repo helps manage many

5
gnu/packages/aspell.scm

@ -183,11 +183,10 @@ dictionaries, including personal ones.")
(define-public aspell-dict-da
(aspell-dictionary "da" "Danish"
#:version "1.4.42-1"
#:prefix "aspell5-"
#:version "1.6.36-11-0"
#:sha256
(base32
"1hfkmiyhgrx5lgrb2mffjbdn1hivrm73wcg7x0iid74p2yb0fjpp")))
"1xz2haayvwlxgss9jf1x2311a1ixbk75q2vgfprjhibsmb7cpinv")))
(define-public aspell-dict-el
(aspell-dictionary "el" "Greek"

6
gnu/packages/assembly.scm

@ -148,14 +148,14 @@ to the clients.")
(define-public fasm
(package
(name "fasm")
(version "1.73.21")
(version "1.73.22")
(source
(origin
(method url-fetch)
(uri (string-append "https://flatassembler.net/fasm-"
version ".tgz"))
(sha256
(base32 "143zh7x3q0r2kclshh8n5w4i5pw4lh60si7rspvc725xxjpjkvcv"))))
(base32 "1pb0rcfdsb0h89khjjrbikz5wjdllavj3ajim0rcyh7x12xr1hw5"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no tests exist
@ -232,7 +232,7 @@ assembler, a C compiler and a linker. The assembler uses Intel syntax
(uri (git-reference
(url "https://git.savannah.gnu.org/r/libjit.git")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(file-name (git-file-name name version))
(sha256
(base32
"0p6wklslkkp3s4aisj3w5a53bagqn5fy4m6088ppd4fcfxgqkrcd"))))

20
gnu/packages/audio.scm

@ -1988,7 +1988,7 @@ software.")
(list (search-path-specification
(variable "LV2_PATH")
(files '("lib/lv2")))))
(home-page "http://elephly.net/lv2/mdapiano.html")
(home-page "https://elephly.net/lv2/mdapiano.html")
(synopsis "LV2 port of the mda Piano plugin")
(description "An LV2 port of the mda Piano VSTi.")
(license license:gpl3+)))
@ -2002,7 +2002,7 @@ software.")
(string-append "PREFIX=" (assoc-ref %outputs "out")))
#:tests? #f ; no check target
#:phases (modify-phases %standard-phases (delete 'configure))))
(home-page "http://elephly.net/lv2/mdaepiano.html")
(home-page "https://elephly.net/lv2/mdaepiano.html")
(synopsis "LV2 port of the mda EPiano plugin")
(description "An LV2 port of the mda EPiano VSTi.")))
@ -3523,7 +3523,7 @@ the Snd sources), Ruby, or Forth.")
(define-public noise-repellent
(package
(name "noise-repellent")
(version "0.1.4")
(version "0.1.5")
(source (origin
(method git-fetch)
(uri (git-reference
@ -3532,16 +3532,12 @@ the Snd sources), Ruby, or Forth.")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0rd3dlmk3vivjmcr6x2x860y0j1d49c2j95j6ny50v184mwvn11j"))))
(build-system gnu-build-system)
"0hb89x9i2knzan46q4nwscf5zmnb2nwf4w13xl2c0y1mx1ls1mwl"))))
(build-system meson-build-system)
(arguments
`(#:make-flags
(list "CC=gcc"
(string-append "PREFIX=" (assoc-ref %outputs "out")))
#:tests? #f ; there are none
#:phases
(modify-phases %standard-phases
(delete 'configure))))
`(#:configure-flags
(list (string-append "--prefix=" (assoc-ref %outputs "out")
"/lib/lv2"))))
(inputs
`(("lv2" ,lv2)
("fftwf" ,fftwf)))

3
gnu/packages/autotools.scm

@ -60,8 +60,7 @@
;; XXX: testsuite: 209 and 279 failed. The latter is an impurity. It
;; should use our own "cpp" instead of "/lib/cpp".
(arguments `(#:tests? #f))
(home-page
"http://www.gnu.org/software/autoconf/")
(home-page "https://www.gnu.org/software/autoconf/")
(synopsis "Create source code configuration scripts")
(description
"Autoconf offers the developer a robust set of M4 macros which expand

2
gnu/packages/backup.scm

@ -451,7 +451,7 @@ rdiff-backup is easy to use and settings have sensible defaults.")
(inputs
`(("perl" ,perl)
("rsync" ,rsync)))
(home-page "http://rsnapshot.org")
(home-page "https://rsnapshot.org")
(synopsis "Deduplicating snapshot backup utility based on rsync")
(description "rsnapshot is a file system snapshot utility based on rsync.
rsnapshot makes it easy to make periodic snapshots of local machines, and

4
gnu/packages/benchmark.scm

@ -44,14 +44,14 @@
(define-public fio
(package
(name "fio")
(version "3.17")
(version "3.18")
(source (origin
(method url-fetch)
(uri (string-append "https://brick.kernel.dk/snaps/"
"fio-" version ".tar.bz2"))
(sha256
(base32
"1hvh8syjz6l0q9bm5p7rf0yrmpkfcx5zj5d47mf6335w1i0h5gqf"))))
"12wzi40hn0ylkdiqwjjljdjmiq78nhwsv3qqa0fad7h3x08w6w6b"))))
(build-system gnu-build-system)
(arguments
'(#:test-target "test"

104
gnu/packages/bioconductor.scm

@ -722,6 +722,49 @@ the weighted combination of published signatures that, when summed, most
closely reconstructs the mutational profile.")
(license license:gpl2+)))
;; This is a CRAN package, but it depends on Bioconductor packages.
(define-public r-nmf
(package
(name "r-nmf")
(version "0.22.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "NMF" version))
(sha256
(base32
"0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq"))))
(properties `((upstream-name . "NMF")))
(build-system r-build-system)
(propagated-inputs
`(("r-cluster" ,r-cluster)
("r-biobase" ,r-biobase)
("r-biocmanager" ,r-biocmanager)
("r-bigmemory" ,r-bigmemory) ; suggested
("r-synchronicity" ,r-synchronicity) ; suggested
("r-colorspace" ,r-colorspace)
("r-digest" ,r-digest)
("r-doparallel" ,r-doparallel)
("r-foreach" ,r-foreach)
("r-ggplot2" ,r-ggplot2)
("r-gridbase" ,r-gridbase)
("r-pkgmaker" ,r-pkgmaker)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-registry" ,r-registry)
("r-reshape2" ,r-reshape2)
("r-rngtools" ,r-rngtools)
("r-stringr" ,r-stringr)))
(home-page "http://renozao.github.io/NMF")
(synopsis "Algorithms and framework for nonnegative matrix factorization")
(description
"This package provides a framework to perform Non-negative Matrix
Factorization (NMF). The package implements a set of already published
algorithms and seeding methods, and provides a framework to test, develop and
plug new or custom algorithms. Most of the built-in algorithms have been
optimized in C++, and the main interface function provides an easy way of
performing parallel computations on multicore machines.")
(license license:gpl2+)))
(define-public r-do-db
(package
(name "r-do-db")
@ -1526,6 +1569,30 @@ expressed genes in DNA microarray experiments.")
"This package implements some simple graph handling capabilities for R.")
(license license:artistic2.0)))
;; This is a CRAN package, but it depends on a Bioconductor package.
(define-public r-ggm
(package
(name "r-ggm")
(version "2.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggm" version))
(sha256
(base32
"11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
(properties `((upstream-name . "ggm")))
(build-system r-build-system)
(propagated-inputs
`(("r-graph" ,r-graph)
("r-igraph" ,r-igraph)))
(home-page "https://cran.r-project.org/package=ggm")
(synopsis "Functions for graphical Markov models")
(description
"This package provides functions and datasets for maximum likelihood
fitting of some classes of graphical Markov models.")
(license license:gpl2+)))
(define-public r-codedepends
(package
(name "r-codedepends")
@ -1867,14 +1934,14 @@ experiments.")
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
(version "1.20.0")
(version "1.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
"10kwb70c9aq0bfqpq48h186lsbwgrg18m14r9z8x6n8l7cds5azc"))))
"140bp7c8p079xh5wwxmrq3a73pm6mdc9czq5w2gzjml7dgrca38a"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
@ -2028,14 +2095,14 @@ genes or proteins in these datasets.")
(define-public r-inspect
(package
(name "r-inspect")
(version "1.16.2")
(version "1.16.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "INSPEcT" version))
(sha256
(base32
"1g8la7k4pnyr2hvk4yjd1bwvjy6nqbbb0fwxrrh2ifgqf4h21x2p"))))
"0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp"))))
(properties `((upstream-name . "INSPEcT")))
(build-system r-build-system)
(propagated-inputs
@ -2156,14 +2223,14 @@ achieved for all methods using the BiocParallel framework.")
(define-public r-biocsingular
(package
(name "r-biocsingular")
(version "1.2.1")
(version "1.2.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocSingular" version))
(sha256
(base32
"0fjfmmpda7pszsck2hm7bp4509pl3xaz02q2q03d5vla62h1h81k"))))
"1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407"))))
(properties `((upstream-name . "BiocSingular")))
(build-system r-build-system)
(propagated-inputs
@ -3284,14 +3351,14 @@ gmapR.")
(define-public r-heatplus
(package
(name "r-heatplus")
(version "2.32.0")
(version "2.32.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Heatplus" version))
(sha256
(base32
"0hx5gqgh4xrkx37ccprq7azj9jziff137bdk0gvrixcx52ws6h89"))))
"1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1"))))
(properties `((upstream-name . "Heatplus")))
(build-system r-build-system)
(propagated-inputs
@ -3942,14 +4009,14 @@ position-specific scores within R and Bioconductor.")
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
(version "1.10.1")
(version "1.10.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
"12ix0bvwk50d48z85f3453k7szm1j27gk4qgw56az4fxra472rlh"))))
"0dzrizacy3br8fiy1vnsl5zf242lg1hqv9dyv5ayqh2n480is57f"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
@ -5305,14 +5372,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
(version "2.0.0")
(version "2.0.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
"0l8q9y2a4m1di0w5nlxhq9jgliinhgr2fwjpm5ixnqx5j3iprlwd"))))
"0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@ -5817,14 +5884,14 @@ self-organizing map clustering and minimal spanning trees.")
(define-public r-mixomics
(package
(name "r-mixomics")
(version "6.10.6")
(version "6.10.8")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
"18jwrdyc4pnx917y1kskxz3fqvlrkyy4ny0xqrfcidz0j7p0b7wr"))))
"0307vhx9ck24rxqbvq15815ssxcc226sl2la060n204b51wi9jaa"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
@ -5859,14 +5926,14 @@ delete entire rows with missing data.")
(define-public r-depecher
(package
(name "r-depecher")
(version "1.2.0")
(version "1.2.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DepecheR" version))
(sha256
(base32
"1f6zbc0fq7xjflh3mkjx1n83mpppw663dj22rlpxzwp1kpmf6wm5"))))
"08ja6ayvbax9m3x9w3xzi72z97miiha2nbsild1gp77n6sgn5i35"))))
(properties `((upstream-name . "DepecheR")))
(build-system r-build-system)
(propagated-inputs
@ -5937,14 +6004,14 @@ genes in the gene-set that are ranked above the leading edge).")
(define-public r-cicero
(package
(name "r-cicero")
(version "1.4.0")
(version "1.4.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cicero" version))
(sha256
(base32
"0mmm7vvzq50b5fayid0bw82b5lar3xm9fwl2ya30q0p4db2y6wnz"))))
"07g6r335zqqy3r5v4x4glxdrcsq9bjhs9jmgvppiggv1h630a22w"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@ -5966,6 +6033,7 @@ genes in the gene-set that are ranked above the leading edge).")
("r-s4vectors" ,r-s4vectors)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)
("r-vgam" ,r-vgam)))
(home-page "https://bioconductor.org/packages/cicero/")
(synopsis "Predict cis-co-accessibility from single-cell data")

45
gnu/packages/bioinformatics.scm

@ -2744,7 +2744,7 @@ quantitative phenotypes.")
(define-public edirect
(package
(name "edirect")
(version "12.1.20190819")
(version "12.1.20190829")
(source (origin
(method url-fetch)
(uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
@ -2752,7 +2752,7 @@ quantitative phenotypes.")
"/edirect-" version ".tar.gz"))
(sha256
(base32
"1i9s9mppcfqd60pfywpm8vdyz5vpnyslw22nd7dv0bhykrdnkz9g"))))
"1xb330z28dgp7slrvp8r7rgncsasv9lpcpqim571yg728dq7xdik"))))
(build-system perl-build-system)
(arguments
`(#:phases
@ -6935,14 +6935,14 @@ testing and other simple calculations.")
(define-public r-shortread
(package
(name "r-shortread")
(version "1.44.1")
(version "1.44.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
"1dh3q83hmi4l72vpif6dn51dzbi9ljrjgkq2zxg4sqy2jxv4vwza"))))
"0ykyrj4g6vc67d5s46sp4659qvar2iavflzhggm79w4p50hxia4s"))))
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
@ -7532,13 +7532,13 @@ coding changes and predict coding outcomes.")
(define-public r-limma
(package
(name "r-limma")
(version "3.42.0")
(version "3.42.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
"0cfynv6qbnar5rl7vjh5lvddd381g9wqx1zd6a7l130hf59mwswn"))))
"1nd01r7rd7jb5qz84vbgfnyrmgm9wiq7fsdji68537kjgvrzmm9z"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
@ -7751,13 +7751,13 @@ biological sequences or sets of sequences.")
(define-public r-rsamtools
(package
(name "r-rsamtools")
(version "2.2.1")
(version "2.2.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
"0hpdc88prpq1gcja89n5s1ndcg81523qrkbkm9gbhm7rm8wmi8cl"))))
"1larx1a9cngmcsm2n7yyxrlnk69zi8m9dp3b90jva0ynspyi76v7"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
@ -7939,13 +7939,13 @@ as well as query and modify the browser state, such as the current viewport.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
(version "1.38.1")
(version "1.38.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
"1c1x29f447dv0i1wi88paji645lfsgmg4ckn19hyhlra72smhzqc"))))
"0dd226kgks50jdx5w35f3wmg95hy8aibi4kcn8p5kmqp5i8j580b"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@ -8236,7 +8236,7 @@ throughput genetic sequencing data sets using regression methods.")
(define-public r-qtl
(package
(name "r-qtl")
(version "1.44-9")
(version "1.45-11")
(source
(origin
(method url-fetch)
@ -8244,7 +8244,7 @@ throughput genetic sequencing data sets using regression methods.")
version ".tar.gz"))
(sha256
(base32
"03lmvydln8b7666b6w46qbryhf83vsd11d4y2v95rfgvqgq66l1i"))))
"1d6qgj602fm6zia3djl4hmca0ri4v57ffp3g93p2yc3cabx2hq90"))))
(build-system r-build-system)
(home-page "https://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics")
@ -8332,14 +8332,14 @@ secondary structure and comparative analysis in R.")
(define-public r-rhtslib
(package
(name "r-rhtslib")
(version "1.18.0")
(version "1.18.1")
(source
(origin
(method url-fetch)