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Merge branch 'master' into core-updates

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Conflicts:
	gnu/local.mk
	gnu/packages/bioinformatics.scm
	gnu/packages/django.scm
	gnu/packages/gtk.scm
	gnu/packages/llvm.scm
	gnu/packages/python-web.scm
	gnu/packages/python.scm
	gnu/packages/tex.scm
	guix/build-system/asdf.scm
	guix/build/emacs-build-system.scm
	guix/profiles.scm
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Marius Bakke 2021-05-09 21:29:46 +02:00
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2
.gitignore vendored
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@ -146,7 +146,7 @@ tmp
/doc/os-config-lightweight-desktop.texi
/nix/scripts/download
/.version
/doc/stamp-[0-9]
/doc/stamp-[0-9]*
/gnu/packages/bootstrap
/gnu/packages/aux-files/guile-guile-launcher.o
/guile

2
.guix-authorizations
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@ -86,8 +86,6 @@
(;; primary: "4F71 6F9A 8FA2 C80E F1B5 E1BA 5E35 F231 DE1A C5E0"
"B051 5948 F1E7 D3C1 B980 38A0 2646 FA30 BACA 7F08"
(name "lfam"))
("148B CB8B D80B FB16 B1DE 0E91 45A8 B1E8 6BCD 10A6"
(name "lle_bout"))
("8887 84C4 1459 ACCB 83E7 E84C 634C 6E89 79FA BEC2"
(name "m1gu3l"))
("CBF5 9755 CBE7 E7EF EF18 3FB1 DD40 9A15 D822 469D"

2
.mailmap
View File

@ -38,7 +38,7 @@ Joshua Grant <tadni@riseup.net> <gzg@riseup.net>
Joshua Grant <tadni@riseup.net> <jgrant@parenthetical.io>
Joshua Grant <tadni@riseup.net> <tadnimi@gmail.com>
Joshua Grant <tadni@riseup.net> <youlysses@riseup.net>
Kei Kebreau <kei@openmailbox.org> <kkebreau@posteo.net>
Kei Kebreau <kkebreau@posteo.net>
Leo Famulari <leo@famulari.name> <lfamular@gmail.com>
Ludovic Courtès <ludo@gnu.org> <ludovic.courtes@inria.fr>
Marek Benc <dusxmt@gmx.com> <merkur32@gmail.com>

98
Makefile.am
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@ -260,7 +260,6 @@ MODULES = \
guix/import/opam.scm \
guix/import/print.scm \
guix/import/pypi.scm \
guix/import/snix.scm \
guix/import/stackage.scm \
guix/import/texlive.scm \
guix/import/utils.scm \
@ -299,7 +298,6 @@ MODULES = \
guix/scripts/import/go.scm \
guix/scripts/import/hackage.scm \
guix/scripts/import/json.scm \
guix/scripts/import/nix.scm \
guix/scripts/import/opam.scm \
guix/scripts/import/pypi.scm \
guix/scripts/import/stackage.scm \
@ -364,6 +362,10 @@ AUX_FILES = \
gnu/packages/aux-files/chromium/master-preferences.json \
gnu/packages/aux-files/emacs/guix-emacs.el \
gnu/packages/aux-files/guix.vim \
gnu/packages/aux-files/linux-libre/5.12-arm.conf \
gnu/packages/aux-files/linux-libre/5.12-arm64.conf \
gnu/packages/aux-files/linux-libre/5.12-i686.conf \
gnu/packages/aux-files/linux-libre/5.12-x86_64.conf \
gnu/packages/aux-files/linux-libre/5.11-arm.conf \
gnu/packages/aux-files/linux-libre/5.11-arm64.conf \
gnu/packages/aux-files/linux-libre/5.11-i686.conf \
@ -487,10 +489,10 @@ SCM_TESTS = \
tests/search-paths.scm \
tests/services.scm \
tests/services/file-sharing.scm \
tests/services/configuration.scm \
tests/services/linux.scm \
tests/sets.scm \
tests/size.scm \
tests/snix.scm \
tests/status.scm \
tests/store-database.scm \
tests/store-deduplication.scm \
@ -970,76 +972,32 @@ cuirass-jobs: $(GOBJECTS)
# Downloading up-to-date PO files.
# make-download-po-rule DOMAIN DIRECTORY [FILE-NAME-PREFIX]
define make-download-po-rule
WEBLATE_REPO = https://framagit.org/tyreunom/guix-translations
download-po.$(1):
if [ -f "$(top_srcdir)/$(2)/LINGUAS" ]; then \
LINGUAS="`grep -v '^[[:blank:]]*#' < $(top_srcdir)/$(2)/LINGUAS`" ; \
else \
LINGUAS="`(cd $(top_srcdir)/$(2); \
for i in *.po; do echo $$$$i; done) | cut -d . -f 2`" ; \
fi ; \
for lang in $$$$LINGUAS; do \
if wget -nv -O "$(top_srcdir)/$(2)/$(3)$$$$lang.po.tmp" \
"https://translate.fedoraproject.org/api/translations/guix/$(1)/$$$$lang/file/" ; \
then \
msgfilter --no-wrap -i "$(top_srcdir)/$(2)/$(3)$$$$lang.po.tmp" \
cat > "$(top_srcdir)/$(2)/$(3)$$$$lang.po.tmp2" ; \
rm "$(top_srcdir)/$(2)/$(3)$$$$lang.po.tmp" ; \
mv "$(top_srcdir)/$(2)/$(3)$$$$lang.po"{.tmp2,} ; \
else \
rm "$(top_srcdir)/$(2)/$(3)$$$$lang.po.tmp" ; \
fi ; \
done
.PHONY: download-po.$(1)
endef
# Checking po files for issues. This is useful to run after downloading new
# po files.
# make-check-po-rule DOMAIN DIRECTORY [FILE-NAME-PREFIX]
define make-check-po-rule
check-po.$(1):
if [ -f "$(top_srcdir)/$(2)/LINGUAS" ]; then \
LINGUAS="`grep -v '^[[:blank:]]*#' < $(top_srcdir)/$(2)/LINGUAS`" ; \
else \
LINGUAS="`(cd $(top_srcdir)/$(2); \
for i in *.po; do echo $$$$i; done) | cut -d . -f 2`" ; \
fi ; \
for lang in $$$$LINGUAS; do \
if [ -f "$(top_srcdir)/$(2)/$(3)$$$$lang.po" ]; \
then \
if ! msgfmt -c "$(top_srcdir)/$(2)/$(3)$$$$lang.po" ; \
then \
exit 1 ; \
fi ; \
fi ; \
done
.PHONY: check-po.$(1)
endef
$(eval $(call make-download-po-rule,documentation-cookbook,po/doc,guix-cookbook.))
$(eval $(call make-download-po-rule,documentation-manual,po/doc,guix-manual.))
$(eval $(call make-download-po-rule,guix,po/guix))
$(eval $(call make-download-po-rule,packages,po/packages))
$(eval $(call make-check-po-rule,documentation-cookbook,po/doc,guix-cookbook.))
$(eval $(call make-check-po-rule,documentation-manual,po/doc,guix-manual.))
$(eval $(call make-check-po-rule,guix,po/guix))
$(eval $(call make-check-po-rule,packages,po/packages))
download-po: $(foreach domain,guix packages documentation-manual documentation-cookbook,download-po.$(domain))
# Shallow clone the Git repository behind Weblate and copy files from it if
# they contain at least one translation, and they are well-formed (Scheme
# format only), warn otherwise. Copied files are converted to a canonical
# form.
download-po:
dir=$$(mktemp -d); \
git clone --depth 1 "$(WEBLATE_REPO)" "$$dir/translations"; \
for domain in po/doc po/guix po/packages; do \
for po in "$$dir/translations/$$domain"/*.po; do \
translated=$$(LANG=en_US.UTF-8 msgfmt --statistics "$$po" 2>&1 | cut -f1 -d' '); \
target=$$(basename "$$po"); \
target="$$domain/$$target"; \
if msgfmt -c "$$po" && [ "$$translated" != "0" ]; then \
msgfilter --no-wrap -i "$$po" cat > "$$po".tmp; \
mv "$$po".tmp "$$target"; \
echo "copied $$target."; \
else \
echo "WARN: $$target ($$translated translated messages) was not added/updated."; \
fi; \
done; \
done; \
rm -rf "$$dir"
.PHONY: download-po
check-po: $(foreach domain,guix packages documentation-manual documentation-cookbook,check-po.$(domain))
.PHONY: check-po
## -------------- ##
## Silent rules. ##
## -------------- ##

1
build-aux/build-self.scm
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@ -250,6 +250,7 @@ interface (FFI) of Guile.")
(match-lambda
(('guix 'config) #f)
(('guix 'channels) #f)
(('guix 'build 'download) #f) ;autoloaded by (guix download)
(('guix _ ...) #t)
(('gnu _ ...) #t)
(_ #f)))

7
build-aux/test-env.in
View File

@ -1,7 +1,7 @@
#!/bin/sh
# 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, 2021 Ludovic Courtès <ludo@gnu.org>
#
# This file is part of GNU Guix.
#
@ -91,14 +91,11 @@ then
# Place for the substituter's cache.
XDG_CACHE_HOME="$GUIX_STATE_DIRECTORY/cache-$$"
# For the (guix import snix) tests.
NIXPKGS="@NIXPKGS@"
export NIX_IGNORE_SYMLINK_STORE NIX_STORE_DIR \
GUIX_LOG_DIRECTORY GUIX_STATE_DIRECTORY GUIX_DATABASE_DIRECTORY \
GUIX_BINARY_SUBSTITUTE_URL \
GUIX_ALLOW_UNAUTHENTICATED_SUBSTITUTES \
GUIX_CONFIGURATION_DIRECTORY XDG_CACHE_HOME NIXPKGS
GUIX_CONFIGURATION_DIRECTORY XDG_CACHE_HOME
# Launch the daemon without chroot support because is may be
# unavailable, for instance if we're not running as root.

17
configure.ac
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@ -195,23 +195,6 @@ AC_SUBST([GZIP])
AC_SUBST([BZIP2])
AC_SUBST([XZ])
AC_ARG_WITH([nixpkgs],
[AS_HELP_STRING([--with-nixpkgs=DIR],
[search for Nixpkgs in DIR (for testing purposes only)])],
[case "$withval" in
yes|no) AC_MSG_ERROR([Please use `--with-nixpkgs=DIR'.]);;
*) NIXPKGS="$withval";;
esac],
[])
AC_MSG_CHECKING([for Nixpkgs source tree])
if test -f "$NIXPKGS/default.nix"; then
AC_MSG_RESULT([$NIXPKGS])
AC_SUBST([NIXPKGS])
else
AC_MSG_RESULT([not found])
fi
LIBGCRYPT_LIBDIR="no"
LIBGCRYPT_PREFIX="no"

6
doc/build.scm
View File

@ -63,9 +63,9 @@
"guix"))
(define %languages
;; The cookbook is currently only translated into German.
;; The cookbook is not translated in the same languages as the manual
(if (string=? %manual "guix-cookbook")
'("de" "en")
'("de" "en" "fr")
'("de" "en" "es" "fr" "ru" "zh_CN")))
(define (texinfo-manual-images source)
@ -948,7 +948,7 @@ from SOURCE."
(div
(ul
(li (a (@ (href "html_node"))
"HTML, with one page per node"))
"HTML, with a separate page per node"))
(li (a (@ (href
,(string-append
#$manual

270
doc/contributing.texi
View File

@ -29,6 +29,7 @@ choice.
* Tracking Bugs and Patches:: Using Debbugs.
* Commit Access:: Pushing to the official repository.
* Updating the Guix Package:: Updating the Guix package definition.
* Translating Guix:: Make Guix speak your native language.
@end menu
@node Building from Git
@ -1079,12 +1080,14 @@ rebuilding induced, commits go to different branches, along these lines:
@code{staging} branch (non-disruptive changes). This branch is intended
to be merged in @code{master} every 6 weeks or so. Topical changes
(e.g., an update of the GNOME stack) can instead go to a specific branch
(say, @code{gnome-updates}).
(say, @code{gnome-updates}). This branch is not expected to be
buildable or usable until late in its development process.
@item more than 1,800 dependent packages
@code{core-updates} branch (may include major and potentially disruptive
changes). This branch is intended to be merged in @code{master} every
6 months or so.
6 months or so. This branch is not expected to be buildable or usable
until late in its development process.
@end table
All these branches are @uref{@value{SUBSTITUTE-URL},
@ -1429,3 +1432,266 @@ This check can be disabled, @emph{at your own peril}, by setting the
@code{GUIX_ALLOW_ME_TO_USE_PRIVATE_COMMIT} environment variable. When
this variable is set, the updated package source is also added to the
store. This is used as part of the release process of Guix.
@cindex translation
@cindex l10n
@cindex i18n
@cindex native language support
@node Translating Guix
@section Translating Guix
Writing code and packages is not the only way to provide a meaningful
contribution to Guix. Translating to a language you speak is another
example of a valuable contribution you can make. This section is designed
to describe the translation process. It gives you advice on how you can
get involved, what can be translated, what mistakes you should avoid and
what we can do to help you!
Guix is a big project that has multiple components that can be translated.
We coordinate the translation effort on a
@uref{https://translate.fedoraproject.org/projects/guix/,Weblate instance}
hosted by our friends at Fedora. You will need an account to submit
translations.
Some of the software packaged in Guix also contain translations. We do not
host a translation platform for them. If you want to translate a package
provided by Guix, you should contact their developers or find the information
on their website. As an example, you can find the homepage of the
@code{hello} package by typing @code{guix show hello}. On the ``homepage''
line, you will see @url{https://www.gnu.org/software/hello/} as the homepage.
Many GNU and non-GNU packages can be translated on the
@uref{https://translationproject.org,Translation Project}. Some projects
with multiple components have their own platform. For instance, GNOME has
its own platform, @uref{https://l10n.gnome.org/,Damned Lies}.
Guix has five components hosted on Weblate.
@itemize
@item @code{guix} contains all the strings from the Guix software (the
guided system installer, the package manager, etc), excluding packages.
@item @code{packages} contains the synopsis (single-sentence description
of a package) and description (longer description) of packages in Guix.
@item @code{website} contains the official Guix website, except for
blog posts and multimedia content.
@item @code{documentation-manual} corresponds to this manual.
@item @code{documentation-cookbook} is the component for the cookbook.
@end itemize
@subsubheading General Directions
Once you get an account, you should be able to select a component from
@uref{https://translate.fedoraproject.org/projects/guix/,the guix project},
and select a language. If your language does not appear in the list, go
to the bottom and click on the ``Start new translation'' button. Select
the language you want to translate to from the list, to start your new
translation.
Like lots of other free software packages, Guix uses
@uref{https://www.gnu.org/software/gettext,GNU Gettext} for its translations,
with which translatable strings are extracted from the source code to so-called
PO files.
Even though PO files are text files, changes should not be made with a text
editor but with PO editing software. Weblate integrates PO editing
functionality. Alternatively, translators can use any of various
free-software tools for filling in translations, of which
@uref{https://poedit.net/,Poedit} is one example, and (after logging in)
@uref{https://docs.weblate.org/en/latest/user/files.html,upload} the changed
file. There is also a special
@uref{https://www.emacswiki.org/emacs/PoMode,PO editing mode} for users of GNU
Emacs. Over time translators find out what software they are happy with and
what features they need.
On Weblate, you will find various links to the editor, that will show various
subsets (or all) of the strings. Have a look around and at the
@uref{https://docs.weblate.org/en/latest/,documentation} to familiarize
yourself with the platform.
@subsubheading Translation Components
In this section, we provide more detailed guidance on the translation
process, as well as details on what you should or should not do. When in
doubt, please contact us, we will be happy to help!
@table @asis
@item guix
Guix is written in the Guile programming language, and some strings contain
special formating that is interpreted by Guile. These special formating
should be highlighted by Weblate. They start with @code{~} followed by one
or more characters.
When printing the string, Guile replaces the special formating symbols with
actual values. For instance, the string @samp{ambiguous package specification
`~a'} would be substituted to contain said package specification instead of
@code{~a}. To properly translate this string, you must keep the formating
code in your translation, although you can place it where it makes sense in
your language. For instance, the French translation says @samp{spécification
du paquet « ~a » ambiguë} because the adjective needs to be placed in the
end of the sentence.
If there are multiple formating symbols, make sure to respect the order.
Guile does not know in which order you intended the string to be read, so it
will substitute the symbols in the same order as the English sentence.
As an example, you cannot translate @samp{package '~a' has been superseded by
'~a'} by @samp{'~a' superseeds package '~a'}, because the meaning would be
reversed. If @var{foo} is superseded by @var{bar}, the translation would read
@samp{'foo' superseeds package 'bar'}. To work around this problem, it
is possible to use more advanced formating to select a given piece of data,
instead of following the default English order. @xref{Formatted Output,,,
guile, GNU Guile Reference Manual}, for more information on formating in Guile.
@item packages
Package descriptions occasionally contain Texinfo markup (@pxref{Synopses
and Descriptions}). Texinfo markup looks like @samp{@@code@{rm -rf@}},
@samp{@@emph@{important@}}, etc. When translating, please leave markup as is.
The characters after ``@@'' form the name of the markup, and the text between
``@{'' and ``@}'' is its content. In general, you should not translate the
content of markup like @code{@@code}, as it contains literal code that do not
change with language. You can translate the content of formating markup such
as @code{@@emph}, @code{@@i}, @code{@@itemize}, @code{@@item}. However, do
not translate the name of the markup, or it will not be recognized. Do
not translate the word after @code{@@end}, it is the name of the markup that
is closed at this position (e.g.@: @code{@@itemize ... @@end itemize}).
@item documentation-manual and documentation-cookbook
The first step to ensure a successful translation of the manual is to find
and translate the following strings @emph{first}:
@itemize
@item @code{version.texi}: Translate this string as @code{version-xx.texi},
where @code{xx} is your language code (the one shown in the URL on
weblate).
@item @code{contributing.texi}: Translate this string as
@code{contributing.xx.texi}, where @code{xx} is the same language code.
@item @code{Top}: Do not translate this string, it is important for Texinfo.
If you translate it, the document will be empty (missing a Top node).
Please look for it, and register @code{Top} as its translation.
@end itemize
Translating these strings first ensure we can include your translation in
the guix repository without breaking the make process or the
@command{guix pull} machinery.
The manual and the cookbook both use Texinfo. As for @code{packages}, please
keep Texinfo markup as is. There are more possible markup types in the manual
than in the package descriptions. In general, do not translate the content
of @code{@@code}, @code{@@file}, @code{@@var}, @code{@@value}, etc. You
should translate the content of formating markup such as @code{@@emph},
@code{@@i}, etc.
The manual contains sections that can be refered to by name by @code{@@ref},
@code{@@xref} and @code{@@pxref}. We have a mechanism in place so you do
not have to translate their content. If you keep the English title, we will
automatically replace it with your translation of that title. This ensures
that Texinfo will always be able to find the node. If you decide to change
the translation of the title, the references will automatically be updated
and you will not have to update them all yourself.
When translating references from the cookbook to the manual, you need to
replace the name of the manual and the name of the section. For instance,
to translate @code{@@pxref@{Defining Packages,,, guix, GNU Guix Reference
Manual@}}, you would replace @code{Defining Packages} with the title of that
section in the translated manual @emph{only} if that title is translated.
If the title is not translated in your language yet, do not translate it here,
or the link will be broken. Replace @code{guix} with @code{guix.xx} where
@code{xx} is your language code. @code{GNU Guix Reference Manual} is the
text of the link. You can translate it however you wish.
@item website
The website pages are written using SXML, an s-expression version of HTML,
the basic language of the web. We have a process to extract translatable
strings from the source, and replace complex s-expressions with a more familiar
XML markup, where each markup is numbered. Translators can arbitrarily change
the ordering, as in the following example.
@example
#. TRANSLATORS: Defining Packages is a section name
#. in the English (en) manual.
#: apps/base/templates/about.scm:64
msgid "Packages are <1>defined<1.1>en</1.1><1.2>Defining-Packages.html</1.2></1> as native <2>Guile</2> modules."
msgstr "Pakete werden als reine <2>Guile</2>-Module <1>definiert<1.1>de</1.1><1.2>Pakete-definieren.html</1.2></1>."
@end example
Note that you need to include the same markups. You cannot skip any.
@end table
In case you make a mistake, the component might fail to build properly with your
language, or even make guix pull fail. To prevent that, we have a process
in place to check the content of the files before pushing to our repository.
We will not be able to update the translation for your language in Guix, so
we will notify you (through weblate and/or by email) so you get a chance to
fix the issue.
@subsubheading Outside of Weblate
Currently, some parts of Guix cannot be translated on Weblate, help wanted!
@itemize
@item @command{guix pull} news can be translated in @file{news.scm}, but is not
available from Weblate. If you want to provide a translation, you
can prepare a patch as described above, or simply send us your
translation with the name of the news entry you translated and your
language. @xref{Writing Channel News}, for more information about
channel news.
@item Guix blog posts cannot currently be translated.
@item The installer script (for foreign distributions) is entirely in English.
@item Some of the libraries Guix uses cannot be translated or are translated
outside of the Guix project. Guile itself is not internationalized.
@item Other manuals linked from this manual or the cookbook might not be
translated.
@end itemize
@subsubheading Translation Infrastructure
Weblate is backed by a git repository from which it discovers new strings to
translate and pushes new and updated translations. Normally, it would be
enough to give it commit access to our repositories. However, we decided
to use a separate repository for two reasons. First, we would have to give
Weblate commit access and authorize its signing key, but we do not trust it
in the same way we trust guix developers, especially since we do not manage
the instance ourselves. Second, if translators mess something up, it can
break the generation of the website and/or guix pull for all our users,
independently of their language.
For these reasons, we use a dedicated repository to host translations, and we
synchronize it with our guix and artworks repositories after checking no issue
was introduced in the translation.
Developers can download the latest PO files from weblate in the Guix
repository by runnig the @command{make download-po} target. It will
automatically download the latest files from weblate, reformat them to a
canonical form, and check they do not contain issues. The manual needs to be
built again to check for additional issues that might crash Texinfo.
Before pushing new translation files, developers should add them to the
make machinery so the translations are actually available. The process
differs for the various components.
@itemize
@item New po files for the @code{guix} and @code{packages} components must
be registered by adding the new language to @file{po/guix/LINGUAS} or
@file{po/packages/LINGUAS}.
@item New po files for the @code{documentation-manual} component must be
registered by adding the file name to @code{DOC_PO_FILES} in
@file{po/doc/local.mk}, the generated @file{%D%/guix.xx.texi} manual to
@code{info_TEXINFOS} in @file{doc/local.mk} and the generated
@file{%D%/guix.xx.texi} and @file{%D%/contributing.xx.texi} to
@code{TRANSLATED_INFO} also in @file{doc/local.mk}.
@item New po files for the @code{documentation-cookbook} component must be
registered by adding the file name to @code{DOC_COOKBOOK_PO_FILES} in
@file{po/doc/local.mk}, the generated @file{%D%/guix-cookbook.xx.texi}
manual to @code{info_TEXINFOS} in @file{doc/local.mk} and the generated
@file{%D%/guix-cookbook.xx.texi} to @code{TRANSLATED_INFO} also
in @file{doc/local.mk}.
@item New po files for the @code{website} component must be added to the
@code{guix-artwork} repository, in @file{website/po/}.
@file{website/po/LINGUAS} and @file{website/po/ietf-tags.scm} must
be updated accordingly (see @file{website/i18n-howto.txt} for more
information on the process).
@end itemize

189
doc/guix.texi
View File

@ -36,7 +36,7 @@ Copyright @copyright{} 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner@*
Copyright @copyright{} 2016 John Darrington@*
Copyright @copyright{} 2016, 2017 Nikita Gillmann@*
Copyright @copyright{} 2016, 2017, 2018, 2019, 2020 Jan Nieuwenhuizen@*
Copyright @copyright{} 2016, 2017, 2018, 2019, 2020 Julien Lepiller@*
Copyright @copyright{} 2016, 2017, 2018, 2019, 2020, 2021 Julien Lepiller@*
Copyright @copyright{} 2016 Alex ter Weele@*
Copyright @copyright{} 2016, 2017, 2018, 2019, 2020, 2021 Christopher Baines@*
Copyright @copyright{} 2017, 2018, 2019 Clément Lassieur@*
@ -68,7 +68,7 @@ Copyright @copyright{} 2019 Ivan Petkov@*
Copyright @copyright{} 2019 Jakob L. Kreuze@*
Copyright @copyright{} 2019 Kyle Andrews@*
Copyright @copyright{} 2019 Alex Griffin@*
Copyright @copyright{} 2019, 2020 Guillaume Le Vaillant@*
Copyright @copyright{} 2019, 2020, 2021 Guillaume Le Vaillant@*
Copyright @copyright{} 2020 Leo Prikler@*
Copyright @copyright{} 2019, 2020 Simon Tournier@*
Copyright @copyright{} 2020 Wiktor Żelazny@*
@ -88,6 +88,7 @@ Copyright @copyright{} 2020 John Soo@*
Copyright @copyright{} 2020 Jonathan Brielmaier@*
Copyright @copyright{} 2020 Edgar Vincent@*
Copyright @copyright{} 2021 Maxime Devos@*
Copyright @copyright{} 2021 B. Wilson@*
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3 or
@ -146,7 +147,7 @@ Spanish (@pxref{Top,,, guix.es, Manual de referencia de GNU Guix}), and
Russian (@pxref{Top,,, guix.ru, Руководство GNU Guix}). If you
would like to translate it in your native language, consider joining
@uref{https://translate.fedoraproject.org/projects/guix/documentation-manual,
Weblate}.
Weblate} (@pxref{Translating Guix}).
@menu
* Introduction:: What is Guix about?
@ -11427,36 +11428,6 @@ and outputs a package expression:
guix import json hello.json
@end example
@item nix
Import metadata from a local copy of the source of the
@uref{https://nixos.org/nixpkgs/, Nixpkgs distribution}@footnote{This
relies on the @command{nix-instantiate} command of
@uref{https://nixos.org/nix/, Nix}.}. Package definitions in Nixpkgs are
typically written in a mixture of Nix-language and Bash code. This
command only imports the high-level package structure that is written in
the Nix language. It normally includes all the basic fields of a
package definition.
When importing a GNU package, the synopsis and descriptions are replaced
by their canonical upstream variant.
Usually, you will first need to do:
@example
export NIX_REMOTE=daemon
@end example
@noindent
so that @command{nix-instantiate} does not try to open the Nix database.
As an example, the command below imports the package definition of
LibreOffice (more precisely, it imports the definition of the package
bound to the @code{libreoffice} top-level attribute):
@example
guix import nix ~/path/to/nixpkgs libreoffice
@end example
@item hackage
@cindex hackage
Import metadata from the Haskell community's central package archive
@ -19958,6 +19929,9 @@ Socket file to use for local (non-network) connections.
@item @code{extra-content} (default: @code{""})
Additional settings for the @file{my.cnf} configuration file.
@item @code{extra-environment} (default: @code{#~'()})
List of environment variables passed to the @command{mysqld} process.
@item @code{auto-upgrade?} (default: @code{#t})
Whether to automatically run @command{mysql_upgrade} after starting the
service. This is necessary to upgrade the @dfn{system schema} after
@ -20106,6 +20080,38 @@ This is used by imap (for shared users) and lda.
It defaults to @samp{"/var/run/dovecot/auth-userdb"}.
@end deftypevr
@deftypevr {@code{protocol-configuration} parameter} boolean imap-metadata?
Whether to enable the @code{IMAP METADATA} extension as defined in
@uref{https://tools.ietf.org/html/rfc5464,RFC@tie{}5464}, which provides
a means for clients to set and retrieve per-mailbox, per-user metadata
and annotations over IMAP.
If this is @samp{#t}, you must also specify a dictionary @i{via} the
@code{mail-attribute-dict} setting.
Defaults to @samp{#f}.
@end deftypevr
@deftypevr {@code{protocol-configuration} parameter} space-separated-string-list managesieve-notify-capabilities
Which NOTIFY capabilities to report to clients that first connect to
the ManageSieve service, before authentication. These may differ from the
capabilities offered to authenticated users. If this field is left empty,
report what the Sieve interpreter supports by default.
Defaults to @samp{()}.
@end deftypevr
@deftypevr {@code{protocol-configuration} parameter} space-separated-string-list managesieve-sieve-capability
Which SIEVE capabilities to report to clients that first connect to
the ManageSieve service, before authentication. These may differ from the
capabilities offered to authenticated users. If this field is left empty,
report what the Sieve interpreter supports by default.
Defaults to @samp{()}.
@end deftypevr
@deftypevr {@code{protocol-configuration} parameter} space-separated-string-list mail-plugins
Space separated list of plugins to load.
@end deftypevr
@ -20804,6 +20810,17 @@ could allow a user to delete others' mailboxes, or @code{ln -s
@samp{""}.
@end deftypevr
@deftypevr {@code{dovecot-configuration} parameter} string mail-attribute-dict
The location of a dictionary used to store @code{IMAP METADATA}
as defined by @uref{https://tools.ietf.org/html/rfc5464, RFC@tie{}5464}.
The IMAP METADATA commands are available only if the ``imap''
protocol configuration's @code{imap-metadata?} field is @samp{#t}.
Defaults to @samp{""}.
@end deftypevr
@deftypevr {@code{dovecot-configuration} parameter} boolean mail-full-filesystem-access?
Allow full file system access to clients. There's no access checks
other than what the operating system does for the active UID/GID@. It
@ -27039,6 +27056,12 @@ The peer public-key represented as a base64 string.
A list of IP addresses from which incoming traffic for this peer is
allowed and to which incoming traffic for this peer is directed.
@item @code{keep-alive} (default: @code{#f})
An optional time interval in seconds. A packet will be sent to the
server endpoint once per time interval. This helps receiving
incoming connections from this peer when you are behind a NAT or
a firewall.
@end table
@end deftp
@ -29061,10 +29084,11 @@ By default, it produces
@lisp
'("--device" "rtl8139,netdev=net0"
"--netdev" "user,id=net0\
,hostfwd=tcp:127.0.0.1:@var{secrets-port}-:1004\
,hostfwd=tcp:127.0.0.1:@var{ssh-port}-:2222\
,hostfwd=tcp:127.0.0.1:@var{vnc-port}-:5900")
"--netdev" (string-append
"user,id=net0,"
"hostfwd=tcp:127.0.0.1:@var{secrets-port}-:1004,"
"hostfwd=tcp:127.0.0.1:@var{ssh-port}-:2222,"
"hostfwd=tcp:127.0.0.1:@var{vnc-port}-:5900"))
@end lisp
with forwarded ports:
@ -31189,6 +31213,15 @@ will use the current system it's running on as the default.
@item @code{max-parallel-builds} (default: @code{1})
The number of builds to perform in parallel.
@item @code{max-1min-load-average} (default: @code{#f})
Load average value to look at when considering starting new builds, if
the 1 minute load average exceeds this value, the agent will wait before
starting new builds.
This will be unspecified if the value is @code{#f}, and the agent will
use the number of cores reported by the system as the max 1 minute load
average.
@item @code{derivation-substitute-urls} (default: @code{#f})
URLs from which to attempt to fetch substitutes for derivations, if the
derivations aren't already available.
@ -31292,7 +31325,7 @@ The Guix Build Coordinator package to use.
@item @code{user} (default: @code{"guix-build-coordinator-queue-builds"})
The system user to run the service as.
@item @code{coordinator} (default: @code{"http://localhost:8745"})
@item @code{coordinator} (default: @code{"http://localhost:8746"})
The URI to use when connecting to the coordinator.
@item @code{systems} (default: @code{#f})
@ -31467,6 +31500,86 @@ parameters, can be done as follow:
@end lisp
@end deffn
@cindex rasdaemon
@cindex Platform Reliability, Availability and Serviceability daemon
@subsubheading Rasdaemon Service
The Rasdaemon service provides a daemon which monitors platform
@acronym{RAS, Reliability@comma{} Availability@comma{} and Serviceability} reports from
Linux kernel trace events, logging them to syslogd.
Reliability, Availability and Serviceability is a concept used on servers meant
to measure their robustness.
@strong{Relability} is the probability that a system will produce correct
outputs:
@itemize @bullet
@item Generally measured as Mean Time Between Failures (MTBF), and
@item Enhanced by features that help to avoid, detect and repair hardware
faults
@end itemize
@strong{Availability} is the probability that a system is operational at a
given time:
@itemize @bullet
@item Generally measured as a percentage of downtime per a period of time, and
@item Often uses mechanisms to detect and correct hardware faults in runtime.
@end itemize
@strong{Serviceability} is the simplicity and speed with which a system can be
repaired or maintained:
@itemize @bullet
@item Generally measured on Mean Time Between Repair (MTBR).
@end itemize
Among the monitoring measures, the most usual ones include:
@itemize @bullet
@item CPU – detect errors at instruction execution and at L1/L2/L3 caches;
@item Memory – add error correction logic (ECC) to detect and correct errors;
@item I/O – add CRC checksums for transferred data;
@item Storage – RAID, journal file systems, checksums, Self-Monitoring,
Analysis and Reporting Technology (SMART).
@end itemize
By monitoring the number of occurrences of error detections, it is possible to
identify if the probability of hardware errors is increasing, and, on such
case, do a preventive maintenance to replace a degraded component while those
errors are correctable.
For detailed information about the types of error events gathered and how to
make sense of them, see the kernel administrator's guide at
@url{https://www.kernel.org/doc/html/latest/admin-guide/ras.html}.
@defvr {Scheme Variable} rasdaemon-service-type
Service type for the @command{rasdaemon} service. It accepts a
@code{rasdaemon-configuration} object. Instantiating like
@lisp
(service rasdaemon-service-type)
@end lisp
will load with a default configuration, which monitors all events and logs to
syslogd.
@end defvr
@deftp {Data Type} rasdaemon-configuration
The data type representing the configuration of @command{rasdaemon}.
@table @asis
@item @code{record?} (default: @code{#f})
A boolean indicating whether to record the events in an SQLite database. This
provides a more structured access to the information contained in the log file.
The database location is hard-coded to @file{/var/lib/rasdaemon/ras-mc_event.db}.
@end table
@end deftp
@cindex zram
@cindex compressed swap
@cindex Compressed RAM-based block devices

10
doc/htmlxref.cnf
View File

@ -397,15 +397,15 @@ guile-gtk node ${GS}/guile-gtk/docs/guile-gtk/
guile-rpc mono ${GS}/guile-rpc/manual/guile-rpc.html
guile-rpc node ${GS}/guile-rpc/manual/html_node/
guix.de mono ${GS}/guix/manual/de/guix.html
guix.de mono ${GS}/guix/manual/de/guix.de.html
guix.de node ${GS}/guix/manual/de/html_node/
guix.es mono ${GS}/guix/manual/es/guix.html
guix.es mono ${GS}/guix/manual/es/guix.es.html
guix.es node ${GS}/guix/manual/es/html_node/
guix.fr mono ${GS}/guix/manual/fr/guix.html
guix.fr mono ${GS}/guix/manual/fr/guix.fr.html
guix.fr node ${GS}/guix/manual/fr/html_node/
guix.ru mono ${GS}/guix/manual/ru/guix.html
guix.ru mono ${GS}/guix/manual/ru/guix.ru.html
guix.ru node ${GS}/guix/manual/ru/html_node/
guix.zh_CN mono ${GS}/guix/manual/zh-cn/guix.html
guix.zh_CN mono ${GS}/guix/manual/zh-cn/guix.zh_CN.html
guix.zh_CN node ${GS}/guix/manual/zh-cn/html_node/
guix mono ${GS}/guix/manual/en/guix.html
guix node ${GS}/guix/manual/en/html_node/

30
doc/local.mk
View File

@ -24,11 +24,20 @@
info_TEXINFOS = %D%/guix.texi \
%D%/guix.de.texi \
%D%/guix.es.texi \
%D%/guix.fa.texi \
%D%/guix.fr.texi \
%D%/guix.it.texi \
%D%/guix.ko.texi \
%D%/guix.pt_BR.texi \
%D%/guix.ru.texi \
%D%/guix.sk.texi \
%D%/guix.zh_CN.texi \
%D%/guix-cookbook.texi \
%D%/guix-cookbook.de.texi
%D%/guix-cookbook.de.texi \
%D%/guix-cookbook.fa.texi \
%D%/guix-cookbook.fr.texi \
%D%/guix-cookbook.ko.texi \
%D%/guix-cookbook.zh_Hans.texi
%C%_guix_TEXINFOS = \
%D%/contributing.texi \
@ -61,18 +70,33 @@ OS_CONFIG_EXAMPLES_TEXI = \
%D%/os-config-desktop.texi \
%D%/os-config-lightweight-desktop.texi
# Do not forget to update these, when updating info_TEXINFOS
TRANSLATED_INFO = \
%D%/guix.de.texi \
%D%/guix.es.texi \
%D%/guix.fa.texi \
%D%/guix.fr.texi \
%D%/guix.it.texi \
%D%/guix.ko.texi \
%D%/guix.pt_BR.texi \
%D%/guix.ru.texi \
%D%/guix.sk.texi \
%D%/guix.zh_CN.texi \
%D%/contributing.de.texi \
%D%/contributing.es.texi \
%D%/contributing.fa.texi \
%D%/contributing.fr.texi \
%D%/contributing.it.texi \
%D%/contributing.ko.texi \
%D%/contributing.pt_BR.texi \
%D%/contributing.ru.texi \
%D%/contributing.sk.texi \
%D%/contributing.zh_CN.texi \
%D%/guix-cookbook.de.texi
%D%/guix-cookbook.de.texi \
%D%/guix-cookbook.fa.texi \
%D%/guix-cookbook.fr.texi \
%D%/guix-cookbook.ko.texi \
%D%/guix-cookbook.zh_Hans.texi
# Bundle this file so that makeinfo finds it in out-of-source-tree builds.
BUILT_SOURCES += $(OS_CONFIG_EXAMPLES_TEXI) $(TRANSLATED_INFO)
@ -100,7 +124,7 @@ cat "$@.tmp" | egrep '@p?x?ref' -A1 | sed 'N;s|--\n||g;P;D' | sed 's|^| |g' | \
line=$$(grep -n "^msgid \"$$e\"" "$<" | cut -f1 --delimiter=":") ;\
((line++)) ;\
if [ "$$line" != "1" ]; then \
translation=$$(head -n "$$line" "$<" | tail -1 | grep msgstr | sed 's|msgstr "\(.*\)"|\1|') ;\
translation=$$(head -n "$$line" "$<" | tail -1 | grep msgstr | sed 's|msgstr "\([^"]*\)"|\1|') ;\
if [ "$$translation" != "" ]; then \
sed "N;s@\(p\?x\?ref\){$$(echo $$e | sed 's| |[\\n ]|g')\(,\|}\)@\1{$$translation\2@g;P;D" -i "$@.tmp" ;\
fi ;\

52
etc/committer.scm.in
View File

@ -38,6 +38,33 @@
(ice-9 rdelim)
(ice-9 textual-ports))
(define* (break-string str #:optional (max-line-length 70))
"Break the string STR into lines that are no longer than MAX-LINE-LENGTH.
Return a single string."
(define (restore-line words)
(string-join (reverse words) " "))
(if (<= (string-length str) max-line-length)
str
(let ((words+lengths (map (lambda (word)
(cons word (string-length word)))
(string-tokenize str))))
(match (fold (match-lambda*
(((word . length)
(count current lines))
(let ((new-count (+ count length 1)))
(if (< new-count max-line-length)
(list new-count
(cons word current)
lines)
(list length
(list word)
(cons (restore-line current) lines))))))
'(0 () ())
words+lengths)
((_ last-words lines)
(string-join (reverse (cons (restore-line last-words) lines))
"\n"))))))
(define (read-excursion port)
"Read an expression from PORT and reset the port position before returning
the expression."
@ -204,18 +231,19 @@ corresponding to the top-level definition containing the staged changes."
(added (lset-difference equal? new-values old-values)))
(format port
"[~a]: ~a~%" field
(match (list (map symbol->string removed)
(map symbol->string added))
((() added)
(format #f "Add ~a."
(listify added)))
((removed ())
(format #f "Remove ~a."
(listify removed)))
((removed added)
(format #f "Remove ~a; add ~a."
(listify removed)
(listify added)))))))))
(break-string
(match (list (map symbol->string removed)
(map symbol->string added))
((() added)
(format #f "Add ~a."
(listify added)))
((removed ())
(format #f "Remove ~a."
(listify removed)))
((removed added)
(format #f "Remove ~a; add ~a."
(listify removed)
(listify added))))))))))
'(inputs propagated-inputs native-inputs)))
(define* (add-commit-message file-name variable-name #:optional (port (current-output-port)))

2
etc/completion/fish/guix.fish
View File

@ -322,8 +322,6 @@ complete -f -c guix -n '__fish_guix_needs_command' -a import -d 'Run IMPORTER wi
##### import gnu
complete -f -c guix -n '__fish_guix_using_command import; and not __fish_seen_subcommand_from $remotecommands' -a gnu -d 'Return a package declaration template for PACKAGE, a GNU package.'
complete -f -c guix -n '__fish_guix_using_command import; and __fish_seen_subcommand_from gnu' -a "--key-download=" -d 'handle missing OpenPGP keys according to POLICY: "always", "never", and "interactive", which is also used when "key-download" is not specified.'
##### import nix
complete -f -c guix -n '__fish_guix_using_command import; and not __fish_seen_subcommand_from $remotecommands' -a nix -d 'Import and convert the Nix expression ATTRIBUTE of NIXPKGS.'
##### import pypi
complete -f -c guix -n '__fish_guix_using_command import; and not __fish_seen_subcommand_from $remotecommands' -a pypi -d 'Import and convert the PyPI package for PACKAGE-NAME.'
##### import cpan

43
etc/guix-install.sh
View File

@ -64,7 +64,12 @@ INF="[ INFO ] "
DEBUG=0
GNU_URL="https://ftp.gnu.org/gnu/guix/"
#GNU_URL="https://alpha.gnu.org/gnu/guix/"
OPENPGP_SIGNING_KEY_ID="3CE464558A84FDC69DB40CFB090B11993D9AEBB5"
# The following associative array holds set of GPG keys used to sign the
# releases, keyed by their corresponding Savannah user ID.
declare -A GPG_SIGNING_KEYS
GPG_SIGNING_KEYS[15145]=3CE464558A84FDC69DB40CFB090B11993D9AEBB5 # ludo
GPG_SIGNING_KEYS[127547]=27D586A4F8900854329FF09F1260E46482E63562 # maxim
# This script needs to know where root's home directory is. However, we
# cannot simply use the HOME environment variable, since there is no guarantee
@ -113,14 +118,21 @@ chk_require()
chk_gpg_keyring()
{ # Check whether the Guix release signing public key is present.
_debug "--- [ $FUNCNAME ] ---"
local user_id
local gpg_key_id
local exit_flag
# Without --dry-run this command will create a ~/.gnupg owned by root on
# systems where gpg has never been used, causing errors and confusion.
gpg --dry-run --list-keys ${OPENPGP_SIGNING_KEY_ID} >/dev/null 2>&1 || (
_err "${ERR}Missing OpenPGP public key. Fetch it with this command:"
echo " wget 'https://sv.gnu.org/people/viewgpg.php?user_id=15145' -qO - | sudo -i gpg --import -"
exit 1
)
for user_id in "${!GPG_SIGNING_KEYS[@]}"; do
gpg_key_id=${GPG_SIGNING_KEYS[$user_id]}
# Without --dry-run this command will create a ~/.gnupg owned by root on
# systems where gpg has never been used, causing errors and confusion.
if ! gpg --dry-run --list-keys "$gpg_key_id" >/dev/null 2>&1; then
_err "${ERR}Missing OpenPGP public key ($gpg_key_id). Fetch it with this command:"
echo " wget \"https://sv.gnu.org/people/viewgpg.php?user_id=$user_id\" -qO - | sudo -i gpg --import -"
exit_flag=yes
fi
done
test "$exit_flag" = yes && exit 1 || true
}
chk_term()
@ -554,10 +566,19 @@ main()
umask 0022
tmp_path="$(mktemp -t -d guix.XXX)"
guix_get_bin_list "${GNU_URL}"
guix_get_bin "${GNU_URL}" "${BIN_VER}" "$tmp_path"
if [ -z "${GUIX_BINARY_FILE_NAME}" ]; then
guix_get_bin_list "${GNU_URL}"
guix_get_bin "${GNU_URL}" "${BIN_VER}" "$tmp_path"
GUIX_BINARY_FILE_NAME=${BIN_VER}.tar.xz
else
if ! [[ $GUIX_BINARY_FILE_NAME =~ $ARCH_OS ]]; then
_err "$ARCH_OS not in ${GUIX_BINARY_FILE_NAME}; aborting"
fi
_msg "Using manually provided binary ${GUIX_BINARY_FILE_NAME}"
GUIX_BINARY_FILE_NAME=$(realpath "$GUIX_BINARY_FILE_NAME")
fi
sys_create_store "${BIN_VER}.tar.xz" "${tmp_path}"
sys_create_store "${GUIX_BINARY_FILE_NAME}" "${tmp_path}"
sys_create_build_user
sys_enable_guix_daemon
sys_authorize_build_farms

44
gnu/build/file-systems.scm
View File

@ -3,7 +3,7 @@
;;; Copyright © 2016, 2017 David Craven <david@craven.ch>
;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 David C. Trudgian <dave@trudgian.net>
;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
@ -239,15 +239,15 @@ if DEVICE does not contain an linux-swap file system."
(define (read-bcachefs-superblock device)
"Return the raw contents of DEVICE's bcachefs superblock as a bytevector, or #f
if DEVICE does not contain a bcachefs file system."
;; We completely ignore the back-up superblock & any checksum errors.
;; Superblock field names, with offset & length respectively, in bytes:
;; Field offsets & lengths, in bytes. There are more (and the superblock is
;; extensible) but we need only some basic information here:
;; 0 16 bch_csum
;; 16 8 version
;; 24 16 magic
;; 40 16 uuid ← ‘internal UUID’, you probably don't want this
;; 56 16 user_uuid ← ‘external UUID’, the one by which to mount
;; 40 16 uuid ← ‘internal’: you probably don't want this one
;; 56 16 user_uuid ← ‘external’: user-visible one by which to mount
;; 72 32 label
;; … there are more & the superblock is extensible, but we don't care yet.
;; Assume a sane file system: ignore the back-up superblock & checksums.
(read-superblock device 4096 104 bcachefs-superblock?))
(define (bcachefs-superblock-external-uuid sblock)
@ -264,11 +264,12 @@ bytevector."
"Return the health of a bcachefs file system on DEVICE."
(let ((ignored-bits (logior 2)) ; DEVICE was mounted read-only
(status
;; A number, or #f on abnormal termination (e.g., assertion failure).
(status:exit-val
(apply system* "bcachefs" "fsck" "-p" "-v"
;; Make each multi-device member a separate argument.
(string-split device #\:)))))
(match (logand (lognot ignored-bits) status)
(match (and=> status (cut logand <> (lognot ignored-bits)))
(0 'pass)
(1 'errors-corrected)
(_ 'fatal-error))))
@ -644,16 +645,13 @@ if DEVICE does not contain a NTFS file system."
(loop parts))))))))))
(define (ENOENT-safe proc)
"Wrap the one-argument PROC such that ENOENT errors are caught and lead to a
warning and #f as the result."
"Wrap the one-argument PROC such that ENOENT, EIO, and ENOMEDIUM errors are
caught and lead to a warning and #f as the result."
(lambda (device)
(catch 'system-error
(lambda ()
(proc device))
(lambda args
;; When running on the hand-made /dev,
;; 'disk-partitions' could return partitions for which
;; we have no /dev node. Handle that gracefully.
(let ((errno (system-error-errno args)))
(cond ((= ENOENT errno)
(format (current-error-port)
@ -671,11 +669,10 @@ warning and #f as the result."
(define (partition-field-reader read field)
"Return a procedure that takes a device and returns the value of a FIELD in
the partition superblock or #f."
(let ((read (ENOENT-safe read)))
(lambda (device)
(let ((sblock (read device)))
(and sblock
(field sblock))))))
(lambda (device)
(let ((sblock (read device)))
(and sblock
(field sblock)))))
(define (read-partition-field device partition-field-readers)
"Returns the value of a FIELD in the partition superblock of DEVICE or #f. It
@ -742,11 +739,14 @@ partition field reader that returned a value."
(define (partition-predicate reader =)
"Return a predicate that returns true if the FIELD of partition header that
was READ is = to the given value."
(lambda (expected)
(lambda (device)
(let ((actual (reader device)))
(and actual
(= actual expected))))))
;; When running on the hand-made /dev, 'disk-partitions' could return
;; partitions for which we have no /dev node. Handle that gracefully.
(let ((reader (ENOENT-safe reader)))
(lambda (expected)
(lambda (device)
(let ((actual (reader device)))
(and actual
(= actual expected)))))))
(define partition-label-predicate
(partition-predicate read-partition-label string=?))

92
gnu/ci.scm
View File

@ -66,9 +66,14 @@
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-26)
#:use-module (ice-9 match)
#:export (%core-packages
#:export (derivation->job
image->job
%core-packages
%cross-targets
channel-source->package
arguments->systems
cuirass-jobs))
;;; Commentary:
@ -232,43 +237,48 @@ SYSTEM."
(define (hours hours)
(* 3600 hours))
(define* (image->job store image
#:key name system)
"Return the job for IMAGE on SYSTEM. If NAME is passed, use it as job name,
otherwise use the IMAGE name."
(let* ((image-name (or name
(symbol->string (image-name image))))
(name (string-append image-name "." system))
(drv (run-with-store store
(mbegin %store-monad
(set-guile-for-build (default-guile))
(lower-object (system-image image))))))
(parameterize ((%graft? #f))
(derivation->job name drv))))
(define (image-jobs store system)
"Return a list of jobs that build images for SYSTEM."
(define (->job name drv)
(let ((name (string-append name "." system)))
(parameterize ((%graft? #f))
(derivation->job name drv))))
(define (build-image image)
(run-with-store store
(mbegin %store-monad
(set-guile-for-build (default-guile))
(lower-object (system-image image)))))
(define MiB
(expt 2 20))
(if (member system %guix-system-supported-systems)
`(,(->job "usb-image"
(build-image
(image
(inherit efi-disk-image)
(operating-system installation-os))))
,(->job "iso9660-image"
(build-image
(image
(inherit (image-with-label
iso9660-image
(string-append "GUIX_" system "_"
(if (> (string-length %guix-version) 7)
(substring %guix-version 0 7)
%guix-version))))
(operating-system installation-os))))
`(,(image->job store
(image
(inherit efi-disk-image)
(operating-system installation-os))
#:name "usb-image"
#:system system)
,(image->job
store
(image
(inherit (image-with-label
iso9660-image
(string-append "GUIX_" system "_"
(if (> (string-length %guix-version) 7)
(substring %guix-version 0 7)
%guix-version))))
(operating-system installation-os))
#:name "iso9660-image"
#:system system)
;; Only cross-compile Guix System images from x86_64-linux for now.
,@(if (string=? system "x86_64-linux")
(map (lambda (image)
(->job (symbol->string (image-name image))
(build-image image)))
(map (cut image->job store <>
#:system system)
%guix-system-images)
'()))
'()))
@ -354,6 +364,7 @@ SYSTEM."
(>>= (profile-derivation (packages->manifest (list guix)))
(lambda (profile)
(self-contained-tarball "guix-binary" profile
#:profile-name "current-guix"
#:localstatedir? #t
#:compressor
(lookup-compressor "xz")))))
@ -434,6 +445,13 @@ valid."
load-manifest)
manifests))))
(define (arguments->systems arguments)
"Return the systems list from ARGUMENTS."
(match (assoc-ref arguments 'systems)
(#f %cuirass-supported-systems)
((lst ...) lst)
((? string? str) (call-with-input-string str read))))
;;;
;;; Cuirass entry point.
@ -445,10 +463,7 @@ valid."
(assoc-ref arguments 'subset))
(define systems
(match (assoc-ref arguments 'systems)
(#f %cuirass-supported-systems)
((lst ...) lst)
((? string? str) (call-with-input-string str read))))
(arguments->systems arguments))
(define channels
(let ((channels (assq-ref arguments 'channels)))
@ -513,6 +528,15 @@ valid."
('tarball
;; Build Guix tarball only.
(tarball-jobs store system))
(('custom . modules)
;; Build custom modules jobs only.
(append-map
(lambda (module)
(let ((proc (module-ref
(resolve-interface module)
'cuirass-jobs)))
(proc store arguments)))
modules))
(('channels . channels)
;; Build only the packages from CHANNELS.
(let ((all (all-packages)))

17
gnu/installer/newt/partition.scm
View File

@ -95,14 +95,17 @@ DEVICES list."
(define (run-label-page button-text button-callback)
"Run a page asking the user to select a partition table label."
(run-listbox-selection-page
#:info-text (G_ "Select a new partition table type. \
;; Force the GPT label if UEFI is supported.
(if (efi-installation?)
"gpt"
(run-listbox-selection-page
#:info-text (G_ "Select a new partition table type. \
Be careful, all data on the disk will be lost.")
#:title (G_ "Partition table")
#:listbox-items '("msdos" "gpt")
#:listbox-item->text identity
#:button-text button-text
#:button-callback-procedure button-callback))
#:title (G_ "Partition table")
#:listbox-items '("msdos" "gpt")
#:listbox-item->text identity
#:button-text button-text
#:button-callback-procedure button-callback)))
(define (run-type-page partition)
"Run a page asking the user to select a partition type."

45
gnu/installer/parted.scm
View File

@ -70,6 +70,7 @@
small-freespace-partition?
esp-partition?
boot-partition?
efi-installation?
default-esp-mount-point
with-delay-device-in-use?
@ -193,12 +194,8 @@ inferior to MAX-SIZE, #f otherwise."
(define (esp-partition? partition)
"Return #t if partition has the ESP flag, return #f otherwise."
(let* ((disk (partition-disk partition))
(disk-type (disk-disk-type disk))
(has-extended? (disk-type-check-feature
disk-type
DISK-TYPE-FEATURE-EXTENDED)))
(disk-type (disk-disk-type disk)))
(and (data-partition? partition)
(not has-extended?)
(partition-is-flag-available? partition PARTITION-FLAG-ESP)
(partition-get-flag partition PARTITION-FLAG-ESP))))
@ -918,30 +915,26 @@ exists."
;; disk space. Otherwise, set the swap size to 5% of the disk space.
(swap-size (min default-swap-size five-percent-disk)))
(if has-extended?
;; msdos - remove everything.
(disk-remove-all-partitions disk)
;; gpt - remove everything but esp if it exists.
(for-each
(lambda (partition)
(and (data-partition? partition)
(disk-remove-partition* disk partition)))
non-boot-partitions))
;; Remove everything but esp if it exists.
(for-each
(lambda (partition)
(and (data-partition? partition)
(disk-remove-partition* disk partition)))
non-boot-partitions)
(let* ((start-partition
(and (not has-extended?)
(if (efi-installation?)
(and (not esp-partition)
(user-partition
(fs-type 'fat32)
(esp? #t)
(size new-esp-size)
(mount-point (default-esp-mount-point))))
(if (efi-installation?)
(and (not esp-partition)
(user-partition
(fs-type 'ext4)
(bootable? #t)
(bios-grub? #t)
(size bios-grub-size)))))
(fs-type 'fat32)
(esp? #t)
(size new-esp-size)
(mount-point (default-esp-mount-point))))
(user-partition
(fs-type 'ext4)
(bootable? #t)
(bios-grub? #t)
(size bios-grub-size))))
(new-partitions
(cond
((or (eq? scheme 'entire-root)

37
gnu/installer/tests.scm
View File

@ -37,7 +37,8 @@
enter-host-name+passwords
choose-services
choose-partitioning
conclude-installation
start-installation
complete-installation
edit-configuration-file))
@ -281,14 +282,19 @@ instrumented for further testing."
(define* (choose-partitioning port
#:key
(encrypted? #t)
(uefi-support? #f)
(passphrase "thepassphrase")
(edit-configuration-file
edit-configuration-file))
"Converse over PORT to choose the partitioning method. When ENCRYPTED? is
true, choose full-disk encryption with PASSPHRASE as the LUKS passphrase.
When UEFI-SUPPORT? is true, assume that we are running the installation tests
on an UEFI capable machine.
This conversation stops when the user partitions have been formatted, right
before the installer generates the configuration file and shows it in a dialog
box."
box. "
(converse port
((list-selection (title "Partitioning method")
(multiple-choices? #f)
@ -306,11 +312,15 @@ box."
disks))
;; The "Partition table" dialog pops up only if there's not already a
;; partition table.
;; partition table and if the system does not support UEFI.
((list-selection (title "Partition table")
(multiple-choices? #f)
(items _))
;; When UEFI is supported, the partition is forced to GPT by the
;; installer.
(not uefi-support?)
"gpt")
((list-selection (title "Partition scheme")
(multiple-choices? #f)
(items (,one-partition _ ...)))
@ -338,10 +348,10 @@ box."
;; UUIDs before it generates the configuration file.
(values))))
(define (conclude-installation port)
"Conclude the installation by checking over PORT that we get the generated
(define (start-installation port)
"Start the installation by checking over PORT that we get the generated
configuration file, accepting it and starting the installation, and then
receiving the final messages once the 'guix system init' process has
receiving the pause message once the 'guix system init' process has
completed."
;; Assume the previous message received was 'starting-final-step'; here we
;; send the reply to that message, which lets the installer continue.
@ -355,8 +365,19 @@ completed."
(file ,configuration-file))
(edit-configuration-file configuration-file))
((pause) ;"Press Enter to continue."
#t)
((installation-complete) ;congratulations!
(values))))
(define (complete-installation port)
"Complete the installation by replying to the installer pause message and
waiting for the installation-complete message."
;; Assume the previous message received was 'pause'; here we send the reply
;; to that message, which lets the installer continue.
(write #t port)
(newline port)
(force-output port)
(converse port
((installation-complete)
(values))))
;;; Local Variables:

22
gnu/local.mk
View File

@ -1,5 +1,5 @@
# GNU Guix --- Functional package management for GNU
# Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
# Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2021 Ludovic Courtès <ludo@gnu.org>
# Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Andreas Enge <andreas@enge.fr>
# Copyright © 2016 Mathieu Lirzin <mthl@gnu.org>
# Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Mark H Weaver <mhw@netris.org>
@ -421,6 +421,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/openldap.scm \
%D%/packages/openpgp.scm \
%D%/packages/openstack.scm \
%D%/packages/orange.scm \
%D%/packages/orpheus.scm \
%D%/packages/ots.scm \
%D%/packages/package-management.scm \
@ -472,6 +473,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/toys.scm \
%D%/packages/tryton.scm \
%D%/packages/qt.scm \
%D%/packages/racket.scm \
%D%/packages/radio.scm \
%D%/packages/ragel.scm \
%D%/packages/rails.scm \
@ -878,7 +880,6 @@ dist_patch_DATA = \
%D%/packages/patches/blender-2.79-python-3.8-fix.patch \
%D%/packages/patches/boost-fix-transitive-linking.patch \
%D%/packages/patches/bpftrace-disable-bfd-disasm.patch \
%D%/packages/patches/busybox-CVE-2021-28831.patch \
%D%/packages/patches/byobu-writable-status.patch \
%D%/packages/patches/cairo-CVE-2018-19876.patch \
%D%/packages/patches/cairo-CVE-2020-35492.patch \
@ -904,6 +905,7 @@ dist_patch_DATA = \
%D%/packages/patches/clang-9.0-libc-search-path.patch \
%D%/packages/patches/clang-10.0-libc-search-path.patch \
%D%/packages/patches/clang-11.0-libc-search-path.patch \
%D%/packages/patches/clang-12-tools-extra-directory.patch \
%D%/packages/patches/clang-runtime-asan-build-fixes.patch \
%D%/packages/patches/clang-runtime-esan-build-fixes.patch \
%D%/packages/patches/clang-runtime-9-libsanitizer-mode-field.patch \
@ -971,6 +973,8 @@ dist_patch_DATA = \
%D%/packages/patches/emacs-exec-path.patch \
%D%/packages/patches/emacs-exwm-fix-fullscreen-states.patch \
%D%/packages/patches/emacs-fix-scheme-indent-function.patch \
%D%/packages/patches/emacs-geiser-guile-auto-activate.patch \
%D%/packages/patches/emacs-geiser-autoload-activate-implementation.patch \
%D%/packages/patches/emacs-ignore-empty-xim-styles.patch \
%D%/packages/patches/emacs-json-reformat-fix-tests.patch \
%D%/packages/patches/emacs-highlight-stages-add-gexp.patch \
@ -1083,7 +1087,6 @@ dist_patch_DATA = \
%D%/packages/patches/ghostscript-no-header-id.patch \
%D%/packages/patches/ghostscript-no-header-uuid.patch \
%D%/packages/patches/ghostscript-no-header-creationdate.patch \
%D%/packages/patches/gimp-make-gegl-introspect-optional.patch \
%D%/packages/patches/glib-appinfo-watch.patch \
%D%/packages/patches/glib-skip-failing-test.patch \
%D%/packages/patches/glibc-CVE-2018-11236.patch \
@ -1148,7 +1151,13 @@ dist_patch_DATA = \
%D%/packages/patches/grub-setup-root.patch \
%D%/packages/patches/grub-verifiers-Blocklist-fallout-cleanup.patch \
%D%/packages/patches/gspell-dash-test.patch \
%D%/packages/patches/gst-libav-64channels-stack-corruption.patch \
%D%/packages/patches/gst-plugins-bad-fix-overflow.patch \
%D%/packages/patches/gst-plugins-base-fix-id3v2-invalid-read.patch \
%D%/packages/patches/gst-plugins-good-fix-test.patch \
%D%/packages/patches/gst-plugins-good-CVE-2021-3497.patch \
%D%/packages/patches/gst-plugins-good-CVE-2021-3498.patch \
%D%/packages/patches/gst-plugins-ugly-fix-out-of-bound-reads.patch \
%D%/packages/patches/guile-1.8-cpp-4.5.patch \
%D%/packages/patches/guile-2.2-skip-oom-test.patch \
%D%/packages/patches/guile-2.2-skip-so-test.patch \
@ -1342,6 +1351,7 @@ dist_patch_DATA = \
%D%/packages/patches/linkchecker-tests-require-network.patch \
%D%/packages/patches/linphone-desktop-without-sdk.patch \
%D%/packages/patches/linux-libre-support-for-Pinebook-Pro.patch \
%D%/packages/patches/linux-libre-arm64-generic-pinebook-lcd.patch \
%D%/packages/patches/linux-pam-no-setfsuid.patch \
%D%/packages/patches/lirc-localstatedir.patch \
%D%/packages/patches/lirc-reproducible-build.patch \
@ -1487,6 +1497,7 @@ dist_patch_DATA = \
%D%/packages/patches/perl-autosplit-default-time.patch \
%D%/packages/patches/perl-cross.patch \
%D%/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch \
%D%/packages/patches/perl-image-exiftool-CVE-2021-22204.patch \
%D%/packages/patches/perl-net-amazon-s3-moose-warning.patch \
%D%/packages/patches/perl-net-dns-resolver-programmable-fix.patch \
%D%/packages/patches/perl-no-sys-dirs.patch \
@ -1615,7 +1626,6 @@ dist_patch_DATA = \
%D%/packages/patches/rpcbind-CVE-2017-8779.patch \
%D%/packages/patches/rtags-separate-rct.patch \
%D%/packages/patches/racket-sh-via-rktio.patch \
%D%/packages/patches/racket-store-checksum-override.patch \
%D%/packages/patches/remake-impure-dirs.patch \
%D%/packages/patches/retroarch-LIBRETRO_DIRECTORY.patch \
%D%/packages/patches/rnp-add-version.cmake.patch \
@ -1694,18 +1704,18 @@ dist_patch_DATA = \
%D%/packages/patches/tipp10-remove-license-code.patch \
%D%/packages/patches/tipp10-qt5.patch \
%D%/packages/patches/tk-find-library.patch \
%D%/packages/patches/tla2tools-build-xml.patch \
%D%/packages/patches/transcode-ffmpeg.patch \
%D%/packages/patches/transmission-honor-localedir.patch \
%D%/packages/patches/ttf2eot-cstddef.patch \
%D%/packages/patches/tup-unbundle-dependencies.patch \
%D%/packages/patches/tuxpaint-stamps-path.patch \
%D%/packages/patches/twinkle-bcg729.patch \
%D%/packages/patches/u-boot-rockchip-inno-usb.patch \
%D%/packages/patches/u-boot-riscv64-fix-extlinux.patch \
%D%/packages/patches/ucx-tcp-iface-ioctl.patch \
%D%/packages/patches/udiskie-no-appindicator.patch \
%D%/packages/patches/ungoogled-chromium-extension-search-path.patch \
%D%/packages/patches/ungoogled-chromium-system-nspr.patch \
%D%/packages/patches/ungoogled-chromium-system-opus.patch \
%D%/packages/patches/unison-fix-ocaml-4.08.patch \
%D%/packages/patches/unknown-horizons-python-3.8-distro.patch \
%D%/packages/patches/unzip-CVE-2014-8139.patch \

63
gnu/packages/admin.scm
View File

@ -41,6 +41,7 @@
;;; Copyright © 2021 qblade <qblade@protonmail.com>
;;; Copyright © 2021 Hyunseok Kim <lasnesne@lagunposprasihopre.org>
;;; Copyright © 2021 David Larsson <david.larsson@selfhosted.xyz>
;;; Copyright © 2021 WinterHound <winterhound@yandex.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -470,6 +471,34 @@ services.")
(license license:public-domain)
(home-page "https://cr.yp.to/daemontools.html")))
(define-public daemonize
(package
(name "daemonize")
(version "1.7.8")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/bmc/daemonize")
(commit (string-append "release-" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0w4g0iyssyw7dd0061881z8s5czcl01mz6v00znax57zfxjqpvnm"))))
(build-system gnu-build-system)
(arguments '(#:tests? #f)) ; No tests available.
(home-page "http://software.clapper.org/daemonize/")
(synopsis "Command line utility to run a program as a daemon")
(description
"daemonize runs a command as a Unix daemon. It will close all open file
descriptors, change working directory of the process to the root filesystem,
reset its umask, run in the background, ignore I/O signals, handle
@code{SIGCLD}, etc. Most programs that are designed to be run as daemons do
that work for themselves. However, you’ll occasionally run across one that
does not. When you must run a daemon program that does not properly make
itself into a true Unix daemon, you can use daemonize to force it to run as a
true daemon.")
(license license:bsd-3)))
(define-public dfc
(package
(name "dfc")
@ -654,14 +683,13 @@ memory, disks, network and processes.")
(define-public bpytop
(package
(name "bpytop")
(version "1.0.63")
(version "1.0.65")
(source
(origin
(method url-fetch)
(uri (pypi-uri "bpytop" version))
(sha256
(base32
"0ql72s842g56rnzdqja6m53lw5y68c4gb540ihp1bjg7x9ycim11"))))
(base32 "1vq51vg2ygk2p738zi21v5chn908d4bd5zkb8s4fbgf4zqp425ny"))))
(build-system python-build-system)
(inputs
`(("python-psutil" ,python-psutil)))
@ -681,7 +709,7 @@ memory, disks, network and processes.")
"https://github.com/aristocratos/bpytop")
(synopsis "Resource monitor")
(description "Resource monitor that shows usage and stats for processor,
memory, disks, network and processes. It's a Python port of
memory, disks, network and processes. It's a Python port and continuation of
@command{bashtop}.")
(license license:asl2.0)))
@ -1115,7 +1143,7 @@ connection alive.")
(define-public isc-dhcp
(let* ((bind-major-version "9")
(bind-minor-version "11")
(bind-patch-version "29")
(bind-patch-version "31")
(bind-release-type "") ; for patch release, use "-P"
(bind-release-version "") ; for patch release, e.g. "6"
(bind-version (string-append bind-major-version
@ -1252,7 +1280,7 @@ connection alive.")
"/bind-" bind-version ".tar.gz"))
(sha256
(base32
"01vvkvlhsxz4ffz2fw86z0fsf170b93jjnn5710ai6vfri8wgfy7"))))
"0sm3vy5g21isdywxr650442x9r00fpj9cxc81n3qcbibyibl9wpm"))))
("coreutils*" ,coreutils)
("sed*" ,sed)))
@ -3039,7 +3067,7 @@ produce uniform output across heterogeneous networks.")
`(#:tests? #f ; no tests
#:make-flags
(list (string-append "PREFIX=" (assoc-ref %outputs "out"))
"CC=gcc")
,(string-append "CC=" (cc-for-target)))
#:phases
(modify-phases %standard-phases
(delete 'configure)))) ; no configure script
@ -3571,14 +3599,14 @@ information tool.")
(define-public nnn
(package
(name "nnn")
(version "3.6")
(version "4.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/jarun/nnn/releases/download/v"
version "/nnn-v" version ".tar.gz"))
(sha256
(base32 "1dbq16cdipij5ws59ab3alfmxli7n4wx28ip7gsyq8ncxg598l47"))))
(base32 "0m07nh1cdfikn4bkpni29j61hr9jdwbl0n5fmlm53l1xmn7yq6d2"))))
(build-system gnu-build-system)
(inputs
`(("ncurses" ,ncurses)
@ -3594,10 +3622,7 @@ information tool.")
(lambda _
(substitute* "Makefile"
(("pkg-config")
(or (which "pkg-config")
(string-append ,(%current-target-system)
"-pkg-config"))))
#t)))
,(pkg-config-for-target))))))
#:make-flags
(list
(string-append "PREFIX="
@ -3615,7 +3640,7 @@ make it a perfect utility on modern distros.")
(define-public thermald
(package
(name "thermald")
(version "2.4.3")
(version "2.4.4")
(source
(origin
(method git-fetch)
@ -3624,7 +3649,7 @@ make it a perfect utility on modern distros.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1ibihgpmx038xci0k2h471scs5ssn7z5kcvjrfz63qf2ppdf9yh8"))))
(base32 "1k0r2c13fihjndwfh0byw0i8ni4lzsjgwz874pvpj1l1nvjj0ajx"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@ -3813,7 +3838,7 @@ Python loading in HPC environments.")
(let ((real-name "inxi"))
(package
(name "inxi-minimal")
(version "3.3.03-1")
(version "3.3.04-1")
(source
(origin
(method git-fetch)
@ -3822,7 +3847,7 @@ Python loading in HPC environments.")
(commit version)))
(file-name (git-file-name real-name version))
(sha256
(base32 "1pahns10i5farw47v9v8cykrk5arq8218vpsa8c0bmaia0rf2n1q"))))
(base32 "1rrhycp8i43yf9wi80n4pq2hkfhvb2rg1srz8if28bh6fhhasjzw"))))
(build-system trivial-build-system)
(inputs
`(("bash" ,bash-minimal)
@ -4023,7 +4048,7 @@ cache of unix and unix-like systems.")
(define-public solaar
(package
(name "solaar")
(version "1.0.5")
(version "1.0.6")
(source (origin
(method git-fetch)
(uri (git-reference
@ -4032,7 +4057,7 @@ cache of unix and unix-like systems.")
(file-name (git-file-name name version))
(sha256
(base32
"17gkr2lf1kzp1198gcdr30j3c8xd81kg7ly12aar1jrgi6lc7klk"))))
"04zclzfc31l2fj5shcsngnmcvcmmhnc567l3wb9yfhs8k39k9kb2"))))
(build-system python-build-system)
(arguments
`(#:phases

8
gnu/packages/algebra.scm
View File

@ -76,7 +76,7 @@
(define-public mpfrcx
(package
(name "mpfrcx")
(version "0.6")
(version "0.6.1")
(source (origin
(method url-fetch)
(uri (string-append
@ -84,7 +84,7 @@
version ".tar.gz"))
(sha256
(base32
"0gz5rma9al2jrifpknqkcnd9dkf8l05jcxy3s4ghwhd4y3h5dwia"))))
"0gk2l40awp3q1lh828dhcjshcldy3b1l2v51glaq0lj1h7w34sin"))))
(build-system gnu-build-system)
(propagated-inputs
`(("gmp" ,gmp)
@ -341,7 +341,7 @@ precision.")
(define-public giac
(package
(name "giac")
(version "1.7.0-1")
(version "1.7.0-5")
(source
(origin
(method url-fetch)
@ -353,7 +353,7 @@ precision.")
"~parisse/debian/dists/stable/main/source/"
"giac_" version ".tar.gz"))
(sha256
(base32 "0s926aza2larfz02hrhdlpxn77yjlrhjg844b3fhwz11yj942p9q"))))
(base32 "1fg82azzsxgglqq2im60wbqh18inaaf7cmz30aq8v9mdwrfp34x1"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((ice-9 ftw)

13
gnu/packages/aspell.scm
View File

@ -12,6 +12,7 @@
;;; Copyright © 2020 Jonathan Brielmaier <jonathan.brielmaier@web.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2020 Noah Landis <noahlandis@posteo.net>
;;; Copyright © 2021 Sergiu Ivanov <sivanov@colimite.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -202,10 +203,10 @@ dictionaries, including personal ones.")
(define-public aspell-dict-en
(aspell-dictionary "en" "English"
#:version "2019.10.06-0"
#:version "2020.12.07-0"
#:sha256
(base32
"1zai9wrqwgb9z9vfgb22qhrvxvg73jg0ix44j1khm2f6m96lncr4")))
"1cwzqkm8gr1w51rpckwlvb43sb0b5nbwy7s8ns5vi250515773sc")))
(define-public aspell-dict-eo
(aspell-dictionary "eo" "Esperanto"
@ -356,6 +357,14 @@ dictionaries, including personal ones.")
(base32
"137i4njvnslab6l4s291s11xijr5jsy75lbdph32f9y183lagy9m")))
(define-public aspell-dict-ro
(aspell-dictionary "ro" "Romanian"
#:version "3.3-2"
#:prefix "aspell5-"
#:sha256
(base32
"0gb8j9iy1acdl11jq76idgc2lbc1rq3w04favn8cyh55d1v8phsk")))
;;;
;;; Hunspell packages made from the Aspell word lists.

2
gnu/packages/assembly.scm
View File

@ -229,7 +229,7 @@ It has macro abilities and focuses on operating system portability.")
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; They use submakes wrong
#:make-flags (list "CC=gcc"
#:make-flags (list ,(string-append "CC=" (cc-for-target))
(string-append "PREFIX="
(assoc-ref %outputs "out")))
#:system "i686-linux" ; Standalone ld86 had problems otherwise

73
gnu/packages/astronomy.scm
View File

@ -4,7 +4,7 @@
;;; Copyright © 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019 by Amar Singh <nly@disroot.org>
;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2020, 2021 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
;;;
;;; This file is part of GNU Guix.
@ -792,10 +792,43 @@ provide you with detailed information about each pass.")
(home-page "http://gpredict.oz9aec.net/index.php")
(license license:gpl2+)))
(define-public sgp4
;; No tagged releases, use commit directly.
(let ((commit "ca9d4d97af4ee62461de6f13e0c85d1dc6000040")
(revision "1"))
(package
(name "sgp4")
(version (git-version "0.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/dnwrnr/sgp4")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1xwfa6papmd2qz5w0hwzvijmzvp9np8dlw3q3qz4bmsippzjv8p7"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
;; Tests fails, probably because of a few "(e <= -0.001)" errors.
;; Or maybe this is not the right way to run the tests?
;; (invoke "runtest/runtest")
#t)))))
(home-page "https://github.com/dnwrnr/sgp4")
(synopsis "Simplified perturbations models library")
(description
"This is a library implementing the simplified perturbations model.
It can be used to calculate the trajectory of satellites.")
(license license:asl2.0))))
(define-public indi
(package
(name "indi")
(version "1.8.9")
(version "1.9.0")
(source
(origin
(method git-fetch)
@ -804,7 +837,7 @@ provide you with detailed information about each pass.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0nw4b2cdsg244slcm3yf1v11jlxbbjrpvi6ax90svs7rlandz8jv"))))
(base32 "0hxklmf432czfmzsyy3rgahs9nr48k4f8v7jxyv2j6py3k743mb1"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
@ -816,17 +849,15 @@ provide you with detailed information about each pass.")
(string-append "-DUDEVRULES_INSTALL_DIR=" out "/lib/udev/rules.d")))
#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(chdir "test")
(invoke "ctest")
(chdir "..")
#t))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(with-directory-excursion "test"
(invoke "ctest")))))
(add-before 'install 'set-install-directories
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(mkdir-p (string-append out "/lib/udev/rules.d")))
#t)))))
(mkdir-p (string-append out "/lib/udev/rules.d"))))))))
(native-inputs
`(("googletest" ,googletest)))
(inputs
@ -887,13 +918,13 @@ JPL ephemerides use to predict raw (x,y,z) planetary positions.")
(define-public python-pyerfa
(package
(name "python-pyerfa")
(version "1.7.2")
(version "1.7.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyerfa" version))
(sha256
(base32 "1s78mdyrxha2jcckfs0wg5ynkf0pwh1bw9mmh99vprinxh9n4xri"))
(base32 "1jqqrxvrgly4r0br5f6dsy8nab2xmhz915vp6md5f31ysr2sdwvc"))
(modules '((guix build utils)))
(snippet
'(begin
@ -953,13 +984,13 @@ of stand-alone functions and classes.")
(define-public python-asdf
(package
(name "python-asdf")
(version "2.7.2")
(version "2.7.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "asdf" version))
(sha256
(base32 "1y47zhkd90i8wmm2i35amfl0rvjqlb3fcx90xp7n9kr2z0byzyzg"))))
(base32 "1mj52l2m8pbhiqacgjakjpvqi8kyx470yw151lcsswbq5wp0rsc6"))))
(build-system python-build-system)
(arguments
;; TODO: (Sharlatan-20210207T165820+0000): Tests depend on astropy, astropy
@ -1011,23 +1042,23 @@ astronomical images, especially when there is no WCS information available.")
(define-public python-skyfield
(package
(name "python-skyfield")
(version "1.38")
(version "1.39")
(source
(origin
(method url-fetch)
(uri (pypi-uri "skyfield" version))
(sha256
(base32 "1qi1l8qn6irdv6w41qq30s2yjwak7h6ayywr1pry9gwcm2c25bv5"))))
(base32 "1qh3k7g9dm6idppk87hnwxpx9a22xx98vav0zk31p6291drak3as"))))
(build-system python-build-system)
(arguments
;; NOTE: (Sharlatan-20210207T163305+0000): tests depend on custom test
;; framework https://github.com/brandon-rhodes/assay
`(#:tests? #f))
(inputs
`(("certifi" ,python-certifi)
("jplephem" ,python-jplephem)
("numpy" ,python-numpy)
("sgp4" ,python-sgp4)))
`(("python-certifi" ,python-certifi)
("python-jplephem" ,python-jplephem)
("python-numpy" ,python-numpy)
("python-sgp4" ,python-sgp4)))
(home-page "https://rhodesmill.org/skyfield/")
(synopsis "Astronomy for Python")
(description

40
gnu/packages/audio.scm
View File

@ -29,7 +29,7 @@
;;; Copyright © 2019 Hartmt Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2019, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2020, 2021 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2020 Jonathan Frederickson <jonathan@terracrypt.net>
;;; Copyright © 2020 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
@ -302,7 +302,7 @@ Linux kernel.")
(define-public libopenmpt
(package
(name "libopenmpt")
(version "0.5.4")
(version "0.5.8")
(source
(origin
(method url-fetch)
@ -310,7 +310,7 @@ Linux kernel.")
(string-append "https://download.openmpt.org/archive/libopenmpt/src/"
"libopenmpt-" version "+release.autotools.tar.gz"))
(sha256
(base32 "0h7gpjx1221jwsq3k91p8zhf1h77qaxyasakc88s3g57vawhckgk"))))
(base32 "1kca5nc870mfv7i4ww2g1q9jn61gsq46irsypbr6fgxpfh8w5qi9"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@ -407,7 +407,7 @@ by MusicIP.")
(define-public libtimidity
(package
(name "libtimidity")
(version "0.2.6")
(version "0.2.7")
(source
(origin
(method url-fetch)
@ -415,7 +415,7 @@ by MusicIP.")
(string-append "https://sourceforge.net/projects/" name "/files/"
name "/" version "/" name "-" version ".tar.gz"))
(sha256
(base32 "0p2px0m907gi1zpdr0l9adq25jl89j85c11ag9s2g4yc6n1nhgfm"))))
(base32 "0sif6lxa058b1mg19zwjm8rl2sg8cg0443k4dgi65clz0jy7qi16"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f)) ; XXX: LibTiMidity could not be initialised
@ -4466,7 +4466,7 @@ library.")
(define-public faudio
(package
(name "faudio")
(version "21.04")
(version "21.05")
(source
(origin
(method git-fetch)
@ -4475,7 +4475,7 @@ library.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1g3zp7igh4ns31sqnxddxqhgibijngkbcqqsj23i9d1lah6k4747"))))
(base32 "0lzvfx5gg5m6jbdzqwkjl4wq4fdg5n98fxn5x8n65vgvrj95sx6z"))))
(arguments
'(#:tests? #f ; No tests.
#:configure-flags '("-DGSTREAMER=ON")))
@ -5036,6 +5036,32 @@ digital radio.")
(home-page "https://www.rowetel.com/?page_id=452")
(license license:lgpl2.1)))
(define-public mbelib
;; No release since 2016, use commit directly.
(let ((commit "9a04ed5c78176a9965f3d43f7aa1b1f5330e771f")
(revision "1"))
(package
(name "mbelib")
(version (git-version "1.3.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/szechyjs/mbelib")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0a7xmf87xnjzm5b437j2vnwv39x0ascja1j04c5wj6xs1529gw8h"))))
(build-system cmake-build-system)
(home-page "https://github.com/szechyjs/mbelib")
(synopsis "P25 Phase 1 and ProVoice vocoder")
(description
"The mbelib library provides support for the 7200x4400 bit/s codec used
in P25 Phase 1, the 7100x4400 bit/s codec used in ProVoice and the @emph{Half
Rate} 3600x2250 bit/s vocoder used in various radio systems.")
(license (list license:bsd-3 ; test/ framework
license:isc))))) ; the rest
(define-public ableton-link
(package
(name "ableton-link")

35
gnu/packages/authentication.scm
View File

@ -24,6 +24,8 @@
#:use-module (gnu packages linux)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages security-token)
#:use-module (gnu packages tls)
#:use-module (gnu packages xml)
#:use-module (guix build-system gnu)
#:use-module (guix download)
#:use-module (guix git-download)
@ -33,19 +35,21 @@
(define-public oath-toolkit
(package
(name "oath-toolkit")
(version "2.6.6")
(version "2.6.7")
(source
(origin
(method url-fetch)
(uri (string-append "https://download.savannah.nongnu.org/releases/"
name "/" name "-" version ".tar.gz"))
(sha256
(base32 "0v4lrgip08b8xlivsfn3mwql3nv8hmcpzrn6pi3xp88vqwav6s7x"))))
(base32 "1aa620k05lsw3l3slkp2mzma40q3p9wginspn9zk8digiz7dzv9n"))))
(build-system gnu-build-system)
(arguments
;; TODO ‘--enable-pskc’ causes xmlsec-related test suite failures.
`(#:configure-flags
(list "--enable-pam")
(list "--enable-pam"
"--enable-pskc"
"--with-xmlsec-crypto-engine=openssl")
#:phases
(modify-phases %standard-phases
(add-after 'install 'delete-static-libraries
@ -55,16 +59,16 @@
(for-each delete-file (find-files lib "\\.a$"))
#t))))))
(native-inputs
`(("pkg-config" ,pkg-config)))
`(("pkg-config" ,pkg-config)
;; XXX: Perhaps this should be propagated from xmlsec.
("libltdl" ,libltdl)))
(inputs
`(("linux-pam" ,linux-pam))) ; for --enable-pam
`(("linux-pam" ,linux-pam)
("openssl" ,openssl)
("xmlsec-openssl" ,xmlsec-openssl)))
(home-page "https://www.nongnu.org/oath-toolkit/")
(synopsis "One-time password (OTP) components")
;; TODO Add the following items after they've been enabled.
;; @item @command{pskctool}, a command-line tool for manipulating secret key
;; files in the Portable Symmetric Key Container (@dfn{PSKC}) format
;; described in RFC6030.
;; @item @code{libpskc}, a shared and static C library for PSKC handling.
(description
"The @dfn{OATH} (Open AuTHentication) Toolkit provides various components
for building one-time password (@dfn{OTP}) authentication systems:
@ -72,11 +76,18 @@ for building one-time password (@dfn{OTP}) authentication systems:
@itemize
@item @command{oathtool}, a command-line tool for generating & validating OTPs.
@item @code{liboath}, a C library for OATH handling.
@item @command{pskctool}, a command-line tool for manipulating secret key
files in the Portable Symmetric Key Container (@dfn{PSKC}) format
described in RFC6030.
@item @code{libpskc}, a shared and static C library for PSKC handling.
@item @code{pam_oath}, a PAM module for pluggable login authentication.
@end itemize
Supported technologies include the event-based @dfn{HOTP} algorithm (RFC4226)
and the time-based @dfn{TOTP} algorithm (RFC6238).")
Supported technologies include the event-based @acronym{HOTP, Hash-based Message
Authentication Code One-Time Password} algorithm (RFC4226), the time-based
@acronym{TOTP, Time-based One-Time Password} algorithm (RFC6238), and
@acronym{PSKC, Portable Symmetric Key Container} (RFC6030) to manage secret key
data.")
(license (list license:lgpl2.1+ ; the libraries (liboath/ & libpskc/)
license:gpl3+)))) ; the tools (everything else)

4
gnu/packages/aux-files/linux-libre/5.10-arm.conf
View File

@ -648,12 +648,12 @@ CONFIG_CPU_FREQ=y
CONFIG_CPU_FREQ_GOV_ATTR_SET=y
CONFIG_CPU_FREQ_GOV_COMMON=y
CONFIG_CPU_FREQ_STAT=y
CONFIG_CPU_FREQ_DEFAULT_GOV_PERFORMANCE=y
# CONFIG_CPU_FREQ_DEFAULT_GOV_PERFORMANCE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_POWERSAVE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_USERSPACE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_ONDEMAND is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_CONSERVATIVE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_SCHEDUTIL is not set
CONFIG_CPU_FREQ_DEFAULT_GOV_SCHEDUTIL=y
CONFIG_CPU_FREQ_GOV_PERFORMANCE=y
CONFIG_CPU_FREQ_GOV_POWERSAVE=m
CONFIG_CPU_FREQ_GOV_USERSPACE=m

4
gnu/packages/aux-files/linux-libre/5.10-arm64.conf
View File

@ -544,12 +544,12 @@ CONFIG_CPU_FREQ=y
CONFIG_CPU_FREQ_GOV_ATTR_SET=y
CONFIG_CPU_FREQ_GOV_COMMON=y
CONFIG_CPU_FREQ_STAT=y
CONFIG_CPU_FREQ_DEFAULT_GOV_PERFORMANCE=y
# CONFIG_CPU_FREQ_DEFAULT_GOV_PERFORMANCE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_POWERSAVE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_USERSPACE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_ONDEMAND is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_CONSERVATIVE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_SCHEDUTIL is not set
CONFIG_CPU_FREQ_DEFAULT_GOV_SCHEDUTIL=y
CONFIG_CPU_FREQ_GOV_PERFORMANCE=y
CONFIG_CPU_FREQ_GOV_POWERSAVE=m
CONFIG_CPU_FREQ_GOV_USERSPACE=m

4
gnu/packages/aux-files/linux-libre/5.11-arm.conf
View File

@ -646,12 +646,12 @@ CONFIG_CPU_FREQ=y
CONFIG_CPU_FREQ_GOV_ATTR_SET=y
CONFIG_CPU_FREQ_GOV_COMMON=y
CONFIG_CPU_FREQ_STAT=y
CONFIG_CPU_FREQ_DEFAULT_GOV_PERFORMANCE=y
# CONFIG_CPU_FREQ_DEFAULT_GOV_PERFORMANCE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_POWERSAVE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_USERSPACE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_ONDEMAND is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_CONSERVATIVE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_SCHEDUTIL is not set
CONFIG_CPU_FREQ_DEFAULT_GOV_SCHEDUTIL=y
CONFIG_CPU_FREQ_GOV_PERFORMANCE=y
CONFIG_CPU_FREQ_GOV_POWERSAVE=m
CONFIG_CPU_FREQ_GOV_USERSPACE=m

39
gnu/packages/aux-files/linux-libre/5.11-arm64.conf
View File

@ -542,12 +542,12 @@ CONFIG_CPU_FREQ=y
CONFIG_CPU_FREQ_GOV_ATTR_SET=y
CONFIG_CPU_FREQ_GOV_COMMON=y
CONFIG_CPU_FREQ_STAT=y
CONFIG_CPU_FREQ_DEFAULT_GOV_PERFORMANCE=y
# CONFIG_CPU_FREQ_DEFAULT_GOV_PERFORMANCE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_POWERSAVE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_USERSPACE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_ONDEMAND is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_CONSERVATIVE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_SCHEDUTIL is not set
CONFIG_CPU_FREQ_DEFAULT_GOV_SCHEDUTIL=y
CONFIG_CPU_FREQ_GOV_PERFORMANCE=y
CONFIG_CPU_FREQ_GOV_POWERSAVE=m
CONFIG_CPU_FREQ_GOV_USERSPACE=m
@ -4088,7 +4088,7 @@ CONFIG_SPI_MESON_SPIFC=m
# CONFIG_SPI_ORION is not set
# CONFIG_SPI_PL022 is not set
# CONFIG_SPI_PXA2XX is not set
# CONFIG_SPI_ROCKCHIP is not set
CONFIG_SPI_ROCKCHIP=m
# CONFIG_SPI_QCOM_QSPI is not set
CONFIG_SPI_QUP=m
# CONFIG_SPI_QCOM_GENI is not set
@ -4446,7 +4446,7 @@ CONFIG_AXP288_FUEL_GAUGE=m
# CONFIG_CHARGER_ISP1704 is not set
# CONFIG_CHARGER_MAX8903 is not set
# CONFIG_CHARGER_LP8727 is not set
# CONFIG_CHARGER_GPIO is not set
CONFIG_CHARGER_GPIO=m
# CONFIG_CHARGER_MANAGER is not set
# CONFIG_CHARGER_LT3651 is not set
# CONFIG_CHARGER_DETECTOR_MAX14656 is not set
@ -4657,7 +4657,7 @@ CONFIG_IMX8MM_THERMAL=m
# CONFIG_MAX77620_THERMAL is not set
# CONFIG_QORIQ_THERMAL is not set
CONFIG_SUN8I_THERMAL=m
# CONFIG_ROCKCHIP_THERMAL is not set
CONFIG_ROCKCHIP_THERMAL=m
CONFIG_ARMADA_THERMAL=m
CONFIG_AMLOGIC_THERMAL=y
@ -6072,6 +6072,12 @@ CONFIG_DRM_LEGACY=y
CONFIG_DRM_VIA=m
CONFIG_DRM_SAVAGE=m
CONFIG_DRM_PANEL_ORIENTATION_QUIRKS=y
CONFIG_DRM_ROCKCHIP=m
CONFIG_ROCKCHIP_CDN_DP=y
CONFIG_ROCKCHIP_DW_MIPI_DSI=y
CONFIG_ROCKCHIP_ANALOGIX_DP=y
CONFIG_ROCKCHIP_DW_HDMI=y
#
# Frame buffer Devices
@ -6469,7 +6475,11 @@ CONFIG_SND_SOC_QDSP6_ASM_DAI=m
CONFIG_SND_SOC_QDSP6=m
CONFIG_SND_SOC_MSM8996=m
CONFIG_SND_SOC_SC7180=m
# CONFIG_SND_SOC_ROCKCHIP is not set
CONFIG_SND_SOC_ROCKCHIP=m
CONFIG_SND_SOC_ROCKCHIP_I2S=m
CONFIG_SND_SOC_ROCKCHIP_SPDIF=m
CONFIG_SND_SOC_ROCKCHIP_RT5645=m
# CONFIG_SND_SOC_SOF_TOPLEVEL is not set
#
@ -7209,7 +7219,9 @@ CONFIG_USB_G_SERIAL=m
CONFIG_USB_RAW_GADGET=m
# end of USB Gadget precomposed configurations
# CONFIG_TYPEC is not set
CONFIG_TYPEC=m
CONFIG_TYPEC_TCPM=m
CONFIG_TYPEC_FUSB302=m
CONFIG_USB_ROLE_SWITCH=m
CONFIG_MMC=y
CONFIG_PWRSEQ_EMMC=y
@ -8063,7 +8075,7 @@ CONFIG_IOMMU_IO_PGTABLE_LPAE=y
CONFIG_OF_IOMMU=y
CONFIG_IOMMU_DMA=y
CONFIG_IOMMU_SVA_LIB=y
# CONFIG_ROCKCHIP_IOMMU is not set
CONFIG_ROCKCHIP_IOMMU=y
CONFIG_SUN50I_IOMMU=y
CONFIG_TEGRA_IOMMU_SMMU=y
CONFIG_ARM_SMMU=y
@ -8825,15 +8837,16 @@ CONFIG_PHY_QCOM_USB_HSIC=m
CONFIG_PHY_QCOM_USB_HS_28NM=m
CONFIG_PHY_QCOM_USB_SS=m
# CONFIG_PHY_QCOM_IPQ806X_USB is not set
# CONFIG_PHY_ROCKCHIP_DP is not set
CONFIG_PHY_ROCKCHIP_DP=m
CONFIG_PHY_ROCKCHIP_DPHY_RX0=m
CONFIG_PHY_ROCKCHIP_EMMC=m
# CONFIG_PHY_ROCKCHIP_INNO_HDMI is not set
CONFIG_PHY_ROCKCHIP_INNO_HDMI=m
CONFIG_PHY_ROCKCHIP_INNO_USB2=m
# CONFIG_PHY_ROCKCHIP_INNO_DSIDPHY is not set
CONFIG_PHY_ROCKCHIP_PCIE=m
# CONFIG_PHY_ROCKCHIP_TYPEC is not set
# CONFIG_PHY_ROCKCHIP_USB is not set
CONFIG_PHY_ROCKCHIP_TYPEC=m
CONFIG_PHY_ROCKCHIP_USB=m
# CONFIG_PHY_SAMSUNG_USB2 is not set
CONFIG_PHY_TEGRA_XUSB=m
CONFIG_PHY_TEGRA194_P2U=m
@ -8895,7 +8908,7 @@ CONFIG_NVMEM_IMX_OCOTP=m
CONFIG_NVMEM_IMX_OCOTP_SCU=m
CONFIG_QCOM_QFPROM=m
CONFIG_NVMEM_SPMI_SDAM=m
# CONFIG_ROCKCHIP_EFUSE is not set
CONFIG_ROCKCHIP_EFUSE=m
CONFIG_ROCKCHIP_OTP=m
CONFIG_NVMEM_SUNXI_SID=m
# CONFIG_MESON_EFUSE is not set

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19
gnu/packages/backup.scm
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@ -2,7 +2,7 @@
;;; Copyright © 2014, 2015, 2020 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2017 Kei Kebreau <kkebreau@posteo.net>
@ -85,7 +85,7 @@
(define-public duplicity
(package
(name "duplicity")
(version "0.8.17")
(version "0.8.19")
(source
(origin
(method url-fetch)
@ -94,7 +94,7 @@
"-series/" version "/+download/duplicity-"
version ".tar.gz"))
(sha256
(base32 "114rwkf9b3h4fcagrx013sb7krc4hafbwl9gawjph2wd9pkv2wx2"))))
(base32 "1c03rp4gw97gz3dzrbrray3dh4q5an3gdq0cmxbhw3qa1nw8ni4c"))))
(build-system python-build-system)
(native-inputs
`(("gettext" ,gettext-minimal) ; for msgfmt
@ -130,12 +130,15 @@
"testing/overrides/bin/lftp")
(("/bin/sh") (which "sh")))
#t))
(add-before 'check 'check-setup
(add-before 'check 'set-up-tests
(lambda* (#:key inputs #:allow-other-keys)
(setenv "HOME" (getcwd)) ; gpg needs to write to $HOME
(setenv "TZDIR" ; some timestamp checks need TZDIR
(string-append (assoc-ref inputs "tzdata")
"/share/zoneinfo"))
;; Some things respect TMPDIR, others hard-code /tmp, and the
;; defaults don't match up, breaking test_restart. Fix it.
(setenv "TMPDIR" "/tmp")
#t)))))
(home-page "http://duplicity.nongnu.org/index.html")
(synopsis "Encrypted backup using rsync algorithm")
@ -719,14 +722,14 @@ to not fully trusted targets. Borg is a fork of Attic.")
(define-public wimlib
(package
(name "wimlib")
(version "1.13.3")
(version "1.13.4")
(source (origin
(method url-fetch)
(uri (string-append "https://wimlib.net/downloads/"
"wimlib-" version ".tar.gz"))
(sha256
(base32
"0zpsbl9iicc6y81xfl6kf8farwfsyrl63shc0idp654kgp8421wa"))))
"04ny5s5z05gk6davbwkjkraan781k2xzw6kjwp75h6ncv45dv1sb"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
@ -736,7 +739,9 @@ to not fully trusted targets. Borg is a fork of Attic.")
("ntfs-3g" ,ntfs-3g)
("openssl" ,openssl)))
(arguments
`(#:configure-flags (list "--enable-test-support")))
`(#:configure-flags
(list "--disable-static"
"--enable-test-support")))
(home-page "https://wimlib.net/")
(synopsis "WIM file manipulation library and utilities")
(description "wimlib is a C library and set of command-line utilities for

4
gnu/packages/benchmark.scm
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@ -227,7 +227,7 @@ This can give a much better understanding of the command's performance.")
(define-public benchmark
(package
(name "benchmark")
(version "1.5.2")
(version "1.5.3")
(source (origin
(method git-fetch)
(uri (git-reference
@ -236,7 +236,7 @@ This can give a much better understanding of the command's performance.")
(file-name (git-file-name name version))
(sha256
(base32
"13rxagpzw6bal6ajlmrxlh9kgfvcixn6j734b2bvfqz7lch8n0pa"))))
"1hls0aqqj5cfldn9jfpvzjhpxkhrydrz9crp477rwllwjsybdxw7"))))
(build-system cmake-build-system)
(native-inputs
`(("googletest-source" ,(package-source googletest))

163
gnu/packages/bioconductor.scm
View File

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
@ -1185,13 +1185,13 @@ of Bioconductor.")
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
(version "0.36.0")
(version "0.36.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocGenerics" version))
(sha256
(base32
"1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q"))))
"0x8cllriayrs99wd5l003iq6i28rb1mci23qcn13ga85578f5lz5"))))
(properties
`((upstream-name . "BiocGenerics")))
(build-system r-build-system)
@ -2048,13 +2048,13 @@ high-throughput sequencing experiments.")
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
(version "1.26.6")
(version "1.26.7")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
"1wy4dwiv0pgim975var802z565py4a0nakx6zdvbhry4c0dfczd1"))))
"0fp7sp3jmc2a1hk4r624lfavx8gc2ik3lv43ksc2jmspg6cvh516"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
@ -2395,17 +2395,51 @@ purposes. The package also contains legacy support for early single-end,
ungapped alignment formats.")
(license license:artistic2.0)))
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
(version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
"04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-delayedarray" ,r-delayedarray)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-matrix" ,r-matrix)
("r-matrixgenerics" ,r-matrixgenerics)
("r-s4vectors" ,r-s4vectors)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/SummarizedExperiment")
(synopsis "Container for representing genomic ranges by sample")
(description
"The SummarizedExperiment container contains one or more assays, each
represented by a matrix-like object of numeric or other mode. The rows
typically represent genomic ranges of interest and the columns represent
samples.")
(license license:artistic2.0)))
(define-public r-systempiper
(package
(name "r-systempiper")
(version "1.24.3")
(version "1.24.6")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "systemPipeR" version))
(sha256
(base32
"0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
"05qnn105gm423fka4kb84vpgzjmz1py6mxpfa2agwwmc5v012qbp"))))
(properties `((upstream-name . "systemPipeR")))
(build-system r-build-system)
(propagated-inputs
@ -3247,16 +3281,16 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
(license license:gpl3)))
(define-public r-interactionset
(package ;BROKEN
(package
(name "r-interactionset")
(version "1.18.0")
(version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "InteractionSet" version))
(sha256
(base32
"14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31"))))
"0dx6yw6rxgkcidnnyjzv57vzd112nf9n2bj6dkv7r3a2d2wj6xh4"))))
(properties
`((upstream-name . "InteractionSet")))
(build-system r-build-system)
@ -3979,14 +4013,14 @@ independent of the p-value under the null hypothesis.")
(define-public r-icobra
(package
(name "r-icobra")
(version "1.18.0")
(version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "iCOBRA" version))
(sha256
(base32
"0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
"183asczy9v2v1vrzxb7n7pa2yfzym3l24r3737k0jg6hnp2bpw50"))))
(properties `((upstream-name . "iCOBRA")))
(build-system r-build-system)
(propagated-inputs
@ -7528,18 +7562,19 @@ self-organizing map clustering and minimal spanning trees.")
(define-public r-mixomics
(package
(name "r-mixomics")
(version "6.14.0")
(version "6.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
"0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
"07d1z33bc3bym1jwp1qqfhs18w4v9axk0ycnmldmj6piswvp44wk"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
`(("r-corpcor" ,r-corpcor)
`(("r-biocparallel" ,r-biocparallel)
("r-corpcor" ,r-corpcor)
("r-dplyr" ,r-dplyr)
("r-ellipse" ,r-ellipse)
("r-ggrepel" ,r-ggrepel)
@ -7767,7 +7802,7 @@ accessibility data.")
(description
"@code{r-circrnaprofiler} is a computational framework for a comprehensive
in silico analysis of @dfn{circular RNA} (circRNAs). This computational
framework allows to combine and analyze circRNAs previously detected by
framework allows combining and analyzing circRNAs previously detected by
multiple publicly available annotation-based circRNA detection tools. It
covers different aspects of circRNAs analysis from differential expression
analysis, evolutionary conservation, biogenesis to functional analysis.")
@ -8401,14 +8436,14 @@ data.")
(define-public r-universalmotif
(package
(name "r-universalmotif")
(version "1.8.4")
(version "1.8.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "universalmotif" version))
(sha256
(base32
"0pmi5mp5v0srr482vlkfmkp28bywq969fvv9g5kjl5rxki963zmr"))))
"07862bs771xldmdnq0zr8926dr299ach8nrgci14p5bbrc88l3ly"))))
(properties
`((upstream-name . "universalmotif")))
(build-system r-build-system)
@ -8866,14 +8901,14 @@ structures.")
(define-public r-bioassayr
(package
(name "r-bioassayr")
(version "1.28.2")
(version "1.28.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bioassayR" version))
(sha256
(base32
"0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5"))))
"03pdb76j7c28b1h1flb40ahq7i9iha22kblq6mkl3x4xmrdgaw5y"))))
(properties `((upstream-name . "bioassayR")))
(build-system r-build-system)
(propagated-inputs
@ -9168,14 +9203,14 @@ also known as views, in a controlled vocabulary.")
(define-public r-experimenthub
(package
(name "r-experimenthub")
(version "1.16.0")
(version "1.16.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ExperimentHub" version))
(sha256
(base32
"1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
"1iyf052hh2dhlwzwwrj571cwr3hd9wp2j915sqg77x6jn40wjr1g"))))
(properties `((upstream-name . "ExperimentHub")))
(build-system r-build-system)
(propagated-inputs
@ -9338,14 +9373,14 @@ gene selection, testing relationships, and so on.")
(define-public r-biocpkgtools
(package
(name "r-biocpkgtools")
(version "1.8.0")
(version "1.8.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocPkgTools" version))
(sha256
(base32
"12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
"18m816mh1ic0znp38wax8xppai77lkym3w84x4x30x2mf0vriqfw"))))
(properties `((upstream-name . "BiocPkgTools")))
(build-system r-build-system)
(propagated-inputs
@ -10329,14 +10364,14 @@ quality control.")
(define-public r-scran
(package
(name "r-scran")
(version "1.18.5")
(version "1.18.7")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
"0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1"))))
"0hsr58b7xj2cqdkyjdpzyifg5wrl1lbylq2h91zbjh5861qjv2n4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
@ -10550,7 +10585,7 @@ experiments, and visualize de influence of the involved factors.")
"https://bioconductor.org/packages/msmsTests")
(synopsis "Differential LC-MS/MS expression tests")
(description
"This packages provides statistical tests for label-free LC-MS/MS data
"This package provides statistical tests for label-free LC-MS/MS data
by spectral counts, to discover differentially expressed proteins between two
biological conditions. Three tests are available: Poisson GLM regression,
quasi-likelihood GLM regression, and the negative binomial of the edgeR
@ -10563,14 +10598,14 @@ relevant, and the minimum expression of the most abundant condition.")
(define-public r-catalyst
(package
(name "r-catalyst")
(version "1.14.0")
(version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CATALYST" version))
(sha256
(base32
"13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
"04b5kcvkfiw4ina11x3qf5kwrb7056zihm7xp1919bqm8k7nl3mn"))))
(properties `((upstream-name . "CATALYST")))
(build-system r-build-system)
(propagated-inputs
@ -10996,6 +11031,44 @@ optionally include the physical locations or genetic map distances of each SNP
on the plot.")
(license license:gpl3)))
;; This is a CRAN package, but it depends on r-rgraphviz, which is a
;; Bioconductor package.
(define-public r-abn
(package
(name "r-abn")
(version "2.5-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "abn" version))
(sha256
(base32
"1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw"))))
(build-system r-build-system)
(inputs
`(("gsl" ,gsl)))
(propagated-inputs
`(("r-lme4" ,r-lme4)
("r-nnet" ,r-nnet)
("r-rcpp" ,r-rcpp)
("r-rcpparmadillo" ,r-rcpparmadillo)
("r-rgraphviz" ,r-rgraphviz)
("r-rjags" ,r-rjags)))
(home-page "https://r-bayesian-networks.org/")
(synopsis "Modelling multivariate data with additive bayesian networks")
(description
"Bayesian network analysis is a form of probabilistic graphical models
which derives from empirical data a directed acyclic graph, DAG, describing
the dependency structure between random variables. An additive Bayesian
network model consists of a form of a DAG where each node comprises a
@dfn{generalized linear model} (GLM). Additive Bayesian network models are
equivalent to Bayesian multivariate regression using graphical modelling, they
generalises the usual multivariable regression, GLM, to multiple dependent
variables. This package provides routines to help determine optimal Bayesian
network models for a given data set, where these models are used to identify
statistical dependencies in messy, complex data.")
(license license:gpl2+)))
(define-public r-pathview
(package
(name "r-pathview")
@ -11095,6 +11168,38 @@ export to genome browser viewable files, and functions for enrichment
analyses.")
(license license:artistic2.0)))
(define-public r-guitar
(package
(name "r-guitar")
(version "2.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Guitar" version))
(sha256
(base32
"0lvfrpgrvmrz4f4qmsii70hw10h72zh1g1alv2sf6a6ixhndm0mz"))))
(properties `((upstream-name . "Guitar")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-dplyr" ,r-dplyr)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
("r-knitr" ,r-knitr)
("r-magrittr" ,r-magrittr)
("r-rtracklayer" ,r-rtracklayer)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/Guitar")
(synopsis "Visualize genomic features")
(description
"This package is designed for visualization of RNA-related genomic
features with respect to the landmarks of RNA transcripts, i.e., transcription
starting site, start codon, stop codon and transcription ending site.")
(license license:gpl2)))
(define-public r-sushi
(package
(name "r-sushi")

543
gnu/packages/bioinformatics.scm
View File

@ -3,7 +3,7 @@
;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
@ -130,6 +130,7 @@
#:use-module (gnu packages qt)
#:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
#:use-module (gnu packages rsync)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
#:use-module (gnu packages shells)
@ -144,6 +145,7 @@
#:use-module (gnu packages tls)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gnu packages wget)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (srfi srfi-1)
@ -311,7 +313,7 @@ BAM files.")
(define-public bcftools
(package
(name "bcftools")
(version "1.11")
(version "1.12")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/samtools/bcftools/"
@ -319,11 +321,11 @@ BAM files.")
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
"0r508mp15pqzf8r1269kb4v5naw9zsvbwd3cz8s1yj7carsf9viw"))
"1x94l1hy2pi3lbz0sxlbw0g6q5z5apcrhrlcwda94ns9n4r6a3ks"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
(delete-file-recursively "htslib-1.11")
(delete-file-recursively "htslib-1.12")
#t))))
(build-system gnu-build-system)
(arguments
@ -437,7 +439,7 @@ computational cluster.")
(define-public bedtools
(package
(name "bedtools")
(version "2.29.2")
(version "2.30.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/releases/"
@ -445,7 +447,7 @@ computational cluster.")
"bedtools-" version ".tar.gz"))
(sha256
(base32
"0m3hk6548846w83a9s5drsczvy67n2azx41kj71n03klb2gbzwg3"))))
"1f2hh79l7dn147c2xyfgf5wfjvlqfw32kjfnnh2n1qy6rpzx2fik"))))
(build-system gnu-build-system)
(arguments
'(#:test-target "test"
@ -457,7 +459,7 @@ computational cluster.")
(native-inputs
`(("python" ,python-wrapper)))
(inputs
`(("samtools" ,samtools-1.9)
`(("samtools" ,samtools)
("zlib" ,zlib)))
(home-page "https://github.com/arq5x/bedtools2")
(synopsis "Tools for genome analysis and arithmetic")
@ -553,6 +555,40 @@ input and output BAMs must adhere to the PacBio BAM format specification.
Non-PacBio BAMs will cause exceptions to be thrown.")
(license license:bsd-3)))
(define-public pbgzip
(let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974"))
(package
(name "pbgzip")
(version (git-version "0.0.0" "0" commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/nh13/pbgzip")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)))
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/nh13/pbgzip")
(synopsis "Parallel Block GZIP")
(description "This package implements parallel block gzip. For many
formats, in particular genomics data formats, data are compressed in
fixed-length blocks such that they can be easily indexed based on a (genomic)
coordinate order, since typically each block is sorted according to this order.
This allows for each block to be individually compressed (deflated), or more
importantly, decompressed (inflated), with the latter enabling random retrieval
of data in large files (gigabytes to terabytes). @code{pbgzip} is not limited
to any particular format, but certain features are tailored to genomics data
formats when enabled. Parallel decompression is somewhat faster, but the true
speedup comes during compression.")
(license license:expat))))
(define-public blasr-libcpp
(package
(name "blasr-libcpp")
@ -797,13 +833,13 @@ intended to behave exactly the same as the original BWK awk.")
(define-public python-pybedtools
(package
(name "python-pybedtools")
(version "0.8.1")
(version "0.8.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "pybedtools" version))
(sha256
(base32
"14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0"))))
"0wc7z8g8prgdx7n5chjva2fdq03wiwhqisjjxzkjg1j5k5ha7151"))))
(build-system python-build-system)
(arguments
`(#:modules ((srfi srfi-26)
@ -814,13 +850,6 @@ intended to behave exactly the same as the original BWK awk.")
(modify-phases %standard-phases
(add-after 'unpack 'disable-broken-tests
(lambda _
(substitute* "pybedtools/test/test_scripts.py"
;; This test freezes.
(("def test_intron_exon_reads")
"def _do_not_test_intron_exon_reads")
;; This test fails in the Python 2 build.
(("def test_venn_mpl")
"def _do_not_test_venn_mpl"))
(substitute* "pybedtools/test/test_helpers.py"
;; Requires internet access.
(("def test_chromsizes")
@ -1097,6 +1126,31 @@ converted to Alignment objects, and so on. This means that the objects
provide a coordinated and extensible framework to do computational biology.")
(license license:perl-license))))
(define-public perl-bio-db-hts
(package
(name "perl-bio-db-hts")
(version "3.01")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://cpan/authors/id/A/AV/AVULLO/Bio-DB-HTS-"
version ".tar.gz"))
(sha256
(base32
"0hjg0igfkpvh27zdkdr6pa7cqm9n6r7cwz0np74cl4wmawgvr9hj"))))
(build-system perl-build-system)
(native-inputs
`(("perl-module-build" ,perl-module-build)
("pkg-config" ,pkg-config)))
(propagated-inputs
`(("bioperl-minimal" ,bioperl-minimal)
("htslib" ,htslib-1.9)))
(home-page "https://metacpan.org/release/Bio-DB-HTS")
(synopsis "Perl interface to HTS library for DNA sequencing")
(description "This is a Perl interface to the HTS library for DNA
sequencing.")
(license license:asl2.0)))
(define-public python-biopython
(package
(name "python-biopython")
@ -1324,7 +1378,7 @@ package provides command line tools using the Bio++ library.")
(define-public blast+
(package
(name "blast+")
(version "2.10.1")
(version "2.11.0")
(source (origin
(method url-fetch)
(uri (string-append
@ -1332,7 +1386,7 @@ package provides command line tools using the Bio++ library.")
version "/ncbi-blast-" version "+-src.tar.gz"))
(sha256
(base32
"11kvrrl0mcwww6530r55hccpg3x3msmhr3051fwnjbq8rzg2j1qi"))
"0m0r9vkw631ky1za1wilsfk9k9spwqh22nkrb9a57rbwmrc1i3nq"))
(modules '((guix build utils)))
(snippet
'(begin
@ -4421,7 +4475,7 @@ performance.")
(define-public htslib
(package
(name "htslib")
(version "1.11")
(version "1.12")
(source (origin
(method url-fetch)
(uri (string-append
@ -4429,7 +4483,7 @@ performance.")
version "/htslib-" version ".tar.bz2"))
(sha256
(base32
"1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng"))))
"1jplnvizgr0fyyvvmkfmnsywrrpqhid3760vw15bllz98qdi9012"))))
(build-system gnu-build-system)
;; Let htslib translate "gs://" and "s3://" to regular https links with
;; "--enable-gcs" and "--enable-s3". For these options to work, we also
@ -5846,7 +5900,7 @@ to the user's query of interest.")
(define-public samtools
(package
(name "samtools")
(version "1.11")
(version "1.12")
(source
(origin
(method url-fetch)
@ -5855,11 +5909,11 @@ to the user's query of interest.")
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
"1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2"))
"1jrdj2idpma5ja9cg0rr73b565vdbr9wyy6zig54bidicc2pg8vd"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
(delete-file-recursively "htslib-1.11")
(delete-file-recursively "htslib-1.12")
#t))))
(build-system gnu-build-system)
(arguments
@ -7175,6 +7229,43 @@ clustering analysis, differential analysis, motif inference and exploration of
single cell ATAC-seq sequencing data.")
(license license:gpl3)))
(define-public r-shinycell
(let ((commit
"aecbd56e66802f28e397f5ae1f19403aadd12163")
(revision "1"))
(package
(name "r-shinycell")
(version (git-version "2.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/SGDDNB/ShinyCell")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"13jn2ikmvljnzayk485g1mmq5abcp9m1b8n1djdb1agmn83zaki5"))))
(properties `((upstream-name . "ShinyCell")))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
("r-ggplot2" ,r-ggplot2)
("r-glue" ,r-glue)
("r-gridextra" ,r-gridextra)
("r-hdf5r" ,r-hdf5r)
("r-matrix" ,r-matrix)
("r-r-utils" ,r-r-utils)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-readr" ,r-readr)
("r-reticulate" ,r-reticulate)))
(home-page "https://github.com/SGDDNB/ShinyCell")
(synopsis "Shiny interactive web apps for single-cell data")
(description
"This package provides Shiny apps for interactive exploration of
single-cell data.")
(license license:gpl3))))
(define-public r-archr
(let ((commit "46b519ffb6f73edf132497ac31650d19ef055dc1")
(revision "1"))
@ -7489,6 +7580,64 @@ Perl and can be helpful if you want to filter, reformat, or trim your sequence
data. It also generates basic statistics for your sequences.")
(license license:gpl3+)))
(define-public shorah
(package
(name "shorah")
(version "1.99.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/cbg-ethz/shorah"
"/releases/download/v" version
"/shorah-" version ".tar.xz"))
(sha256
(base32
"158dir9qcqspknlnyfr9zwk41x48nrh5wcg10k2grh9cidp9daiq"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-test-wrapper
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(substitute* "examples/run_end2end_test"
(("\\$\\{interpreter\\} ../\\$\\{testscript\\}")
(string-append bin "/${testscript}"))))))
(delete 'check)
(add-after 'install 'wrap-programs
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(site (string-append
out "/lib/python"
,(version-major+minor
(package-version python))
"/site-packages"))
(pythonpath (getenv "PYTHONPATH"))
(script (string-append out "/bin/shorah")))
(chmod script #o555)
(wrap-program script `("PYTHONPATH" ":" prefix (,site ,pythonpath))))))
(add-after 'wrap-programs 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "make" "check")))))))
(inputs
`(("boost" ,boost)
("htslib" ,htslib)
("python" ,python)
("python-biopython" ,python-biopython)
("python-numpy" ,python-numpy)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "")
(synopsis "Short reads assembly into haplotypes")
(description
"ShoRAH is a project for the analysis of next generation sequencing data.
It is designed to analyse genetically heterogeneous samples. Its tools
provide error correction, haplotype reconstruction and estimation of the
frequency of the different genetic variants present in a mixed sample.")
(license license:gpl3+)))
(define-public ruby-bio-kseq
(package
(name "ruby-bio-kseq")
@ -7633,40 +7782,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
(version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
"04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-delayedarray" ,r-delayedarray)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-matrix" ,r-matrix)
("r-matrixgenerics" ,r-matrixgenerics)
("r-s4vectors" ,r-s4vectors)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/SummarizedExperiment")
(synopsis "Container for representing genomic ranges by sample")
(description
"The SummarizedExperiment container contains one or more assays, each
represented by a matrix-like object of numeric or other mode. The rows
typically represent genomic ranges of interest and the columns represent
samples.")
(license license:artistic2.0)))
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
@ -9461,14 +9576,14 @@ Shiny-based display methods for Bioconductor objects.")
(define-public r-annotationhub
(package
(name "r-annotationhub")
(version "2.22.0")
(version "2.22.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationHub" version))
(sha256
(base32
"1950x654ffqx53b154kbph808zdh2xm5vmj9vzmc5nxc28fi2z5g"))))
"08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5"))))
(properties `((upstream-name . "AnnotationHub")))
(build-system r-build-system)
(propagated-inputs
@ -9558,14 +9673,14 @@ microarrays or GRanges for sequencing data.")
(define-public r-gage
(package
(name "r-gage")
(version "2.40.1")
(version "2.40.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gage" version))
(sha256
(base32
"1iawa03dy4bl333my69d4sk7d74cjzfg5dpcxga6q5dglan4sp8r"))))
"1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@ -9691,14 +9806,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
(define-public r-ensembldb
(package
(name "r-ensembldb")
(version "2.14.0")
(version "2.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
"04il99gcrqzakvc0bxchdp9gghkn1sp9lpiian0iz4y7r67z3wpy"))))
"1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@ -11775,7 +11890,7 @@ in an easily configurable manner.")
(define-public pigx-bsseq
(package
(name "pigx-bsseq")
(version "0.1.2")
(version "0.1.3")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
@ -11783,7 +11898,7 @@ in an easily configurable manner.")
"/pigx_bsseq-" version ".tar.gz"))
(sha256
(base32
"0mpzlay2d5cjpmrcp7knff6rg1c2mqszd638n7lw0mc0cycbp9f8"))))
"0blm0bl5z3ng01n7hh2ffk4rkzvf7vb3nm0crgdzrxr5cahxdxql"))))
(build-system gnu-build-system)
(arguments
`(;; TODO: tests currently require 12+GB of RAM. See
@ -11809,8 +11924,11 @@ in an easily configurable manner.")
("r-annotationhub" ,r-annotationhub)
("r-dt" ,r-dt)
("r-genomation" ,r-genomation)
("r-ggbio" ,r-ggbio)
("r-ggrepel" ,r-ggrepel)
("r-matrixstats" ,r-matrixstats)
("r-methylkit" ,r-methylkit)
("r-reshape2" ,r-reshape2)
("r-rtracklayer" ,r-rtracklayer)
("r-rmarkdown" ,r-rmarkdown)
("r-bookdown" ,r-bookdown)
@ -12408,7 +12526,7 @@ in RNA-seq data.")
("python-igraph" ,python-igraph)
("python-joblib" ,python-joblib)
("python-legacy-api-wrap" ,python-legacy-api-wrap)
("python-louvain" ,python-louvain)
("python-louvain" ,python-louvain-0.6)
("python-matplotlib" ,python-matplotlib)
("python-natsort" ,python-natsort)
("python-networkx" ,python-networkx)
@ -14979,6 +15097,299 @@ signaling, and more. It continues to be evolved and expanded by an
international community.")
(license license:lgpl2.1+)))
(define-public kraken2
(package
(name "kraken2")
(version "2.1.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/DerrickWood/kraken2")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0h7a7vygd7y5isbrnc6srwq6xj1rmyd33pm8mmcgfkmlxlg5vkg3"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #false ; there are none
#:make-flags (list "-C" "src"
(string-append "KRAKEN2_DIR="
(assoc-ref %outputs "out") "/bin"))
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'install 'install-scripts
(lambda* (#:key outputs #:allow-other-keys)
(let* ((bin (string-append (assoc-ref outputs "out") "/bin"))
(replacements `(("KRAKEN2_DIR" . ,bin)
("VERSION" . ,,version))))
(mkdir-p bin)
(with-directory-excursion "scripts"
(let ((scripts (find-files "." ".*")))
(substitute* scripts
(("#####=([^=]+)=#####" _ key)
(or (assoc-ref replacements key)
(error (format #false "unknown key: ~a~%" key)))))
(substitute* "kraken2"
(("compression_program = \"bzip2\"")
(string-append "compression_program = \""
(which "bzip2")
"\""))
(("compression_program = \"gzip\"")
(string-append "compression_program = \""
(which "gzip")
"\"")))
(substitute* '("download_genomic_library.sh"
"download_taxonomy.sh"
"16S_gg_installation.sh"
"16S_silva_installation.sh"
"16S_rdp_installation.sh")
(("wget") (which "wget")))
(substitute* '("download_taxonomy.sh"
"download_genomic_library.sh"
"rsync_from_ncbi.pl")
(("rsync -")
(string-append (which "rsync") " -")))
(substitute* "mask_low_complexity.sh"
(("which") (which "which")))
(substitute* '("mask_low_complexity.sh"
"download_genomic_library.sh"
"16S_silva_installation.sh")
(("sed -e ")
(string-append (which "sed") " -e ")))
(substitute* '("rsync_from_ncbi.pl"
"16S_rdp_installation.sh"
"16S_silva_installation.sh"
"16S_gg_installation.sh"
"download_taxonomy.sh"
"download_genomic_library.sh")
(("gunzip") (which "gunzip")))
(for-each (lambda (script)
(chmod script #o555)
(install-file script bin))
scripts)))))))))
(inputs
`(("gzip" ,gzip)
("perl" ,perl)
("rsync" ,rsync)
("sed" ,sed)
("wget" ,wget)
("which" ,which)))
(home-page "https://github.com/DerrickWood/kraken2")
(synopsis "Taxonomic sequence classification system")
(description "Kraken is a taxonomic sequence classifier that assigns
taxonomic labels to DNA sequences. Kraken examines the k-mers within a query
sequence and uses the information within those k-mers to query a
database. That database maps k-mers to the lowest common ancestor (LCA) of all
genomes known to contain a given k-mer.")
(license license:expat)))
(define-public lofreq
(package
(name "lofreq")
(version "2.1.5")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/CSB5/lofreq")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0qssrn3mgjak7df6iqc1rljqd3g3a5syvg0lsv4vds43s3fq23bl"))))
(build-system gnu-build-system)
(arguments
'(#:test-target "bug-tests"
#:tests? #false)) ; test data are not included
(inputs
`(("htslib" ,htslib)
("python" ,python-wrapper)
("zlib" ,zlib)))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("which" ,which)))
(home-page "https://csb5.github.io/lofreq/")
(synopsis "Sensitive variant calling from sequencing data ")
(description "LoFreq is a fast and sensitive variant-caller for inferring
SNVs and indels from next-generation sequencing data. It makes full use of
base-call qualities and other sources of errors inherent in
sequencing (e.g. mapping or base/indel alignment uncertainty), which are
usually ignored by other methods or only used for filtering.")
(license license:expat)))
(define-public python-pyliftover
(package
(name "python-pyliftover")
(version "0.4")
;; The version of pypi does not include test data.
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/konstantint/pyliftover")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1j8jp9iynv2l3jv5pr0pn0p3azlama1bqg233piglzm6bqh3m2m3"))))
(build-system python-build-system)
(arguments `(#:tests? #false)) ; the tests access the web
(native-inputs
`(("python-pytest" ,python-pytest)))
(home-page "https://github.com/konstantint/pyliftover")
(synopsis "Python implementation of UCSC liftOver genome coordinate conversion")
(description
"PyLiftover is a library for quick and easy conversion of genomic (point)
coordinates between different assemblies.")
(license license:expat)))
(define-public ensembl-vep
(let* ((api-version "103")
(api-module
(lambda (name hash)
(origin (method git-fetch)
(uri (git-reference
(url (string-append "https://github.com/Ensembl/"
name ".git"))
(commit (string-append "release/" api-version))))
(file-name (string-append name "-" api-version "-checkout"))
(sha256 (base32 hash))))))
(package
(name "ensembl-vep")
(version (string-append api-version ".1"))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Ensembl/ensembl-vep.git")
(commit (string-append "release/" version))))
(sha256
(base32
"1iq7p72cv9b38jz2v8a4slzy2n8y0md487943180ym9xc8qvw09c"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build gnu-build-system)
(guix build utils)
(ice-9 match))
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
;; Tests need to run after installation
(delete 'check)
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((modules '(("ensembl" "/")
("ensembl-variation" "/Variation")
("ensembl-funcgen" "/Funcgen")
("ensembl-io" "/")))
(scripts '(("convert_cache.pl" "vep_convert_cache.pl")
("INSTALL.pl" "vep_install.pl")
("haplo" #f)
("variant_recoder" #f)
("filter_vep" #f)
("vep" #f)))
(out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(perl (string-append out "/lib/perl5/site_perl")))
(for-each
(match-lambda
((name path)
(let ((dir (string-append perl "/Bio/EnsEMBL" path)))
(mkdir-p dir)
(copy-recursively
(string-append (assoc-ref inputs (string-append "api-module-" name))
"/modules/Bio/EnsEMBL" path)
dir))))
modules)
(copy-recursively "modules/" perl)
(mkdir-p bin)
(for-each
(match-lambda
((script new-name)
(let ((location (string-append bin "/"
(or new-name (basename script)))))
(copy-file script location)
(chmod location #o555)
(wrap-program location
`("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")
,perl))))))
scripts)
;; Fix path to tools
(with-directory-excursion (string-append perl "/Bio/EnsEMBL")
(substitute* '("Funcgen/RunnableDB/ProbeMapping/PrePipelineChecks.pm"
"VEP/BaseRunner.pm"
"VEP/Utils.pm"
"VEP/AnnotationSource/Cache/VariationTabix.pm"
"VEP/AnnotationSource/Cache/BaseSerialized.pm"
"Variation/Utils/BaseVepTabixPlugin.pm"
"Variation/Utils/VEP.pm"
"Variation/Pipeline/ReleaseDataDumps/PreRunChecks.pm")
(("`which")
(string-append "`"
(assoc-ref inputs "which")
"/bin/which")))))))
(add-after 'install 'check
(lambda* (#:key tests? inputs outputs #:allow-other-keys)
(when tests?
(setenv "PERL5LIB"
(string-append (getenv "PERL5LIB")
":"
(assoc-ref outputs "out")
"/lib/perl5/site_perl"))
(copy-recursively (string-append (assoc-ref inputs "source") "/t")
"/tmp/t")
(for-each make-file-writable (find-files "/tmp/t"))
;; TODO: haplo needs Set/IntervalTree.pm
(invoke "perl" "-e" (string-append "
use Test::Harness; use Test::Exception;
my $dirname = \"/tmp\";
opendir TEST, \"$dirname\\/t\";
my @test_files = map {\"$dirname\\/t\\/\".$_} grep {!/^\\./ && /\\.t$/} readdir TEST; closedir TEST;
@test_files = grep {!/Haplo/} @test_files;
runtests(@test_files);
"))))))))
(inputs
`(("bioperl-minimal" ,bioperl-minimal)
("perl-bio-db-hts" ,perl-bio-db-hts)
("perl-dbi" ,perl-dbi)
("perl-dbd-mysql" ,perl-dbd-mysql)
("perl-libwww" ,perl-libwww)
("perl-http-tiny" ,perl-http-tiny)
("perl-json" ,perl-json)
("which" ,which)))
(propagated-inputs
`(("kentutils" ,kentutils)))
(native-inputs
`(("unzip" ,unzip)
("perl" ,perl)
("api-module-ensembl"
,(api-module "ensembl"
"0s59rj905g72hljzfpvnx5nxwz925b917y4jp912i23f5gwxh14v"))
("api-module-ensembl-variation"
,(api-module "ensembl-variation"
"1dvwdzzfjhzymq02b6n4p6j3a9q4jgq0g89hs7hj1apd7zhirgkq"))
("api-module-ensembl-funcgen"
,(api-module "ensembl-funcgen"
"1x23pv38dmv0w0gby6rv3wds50qghb4v3v1mf43vk55msfxzry8n"))
("api-module-ensembl-io"
,(api-module "ensembl-io"
"14adb2x934lzsq20035mazdkhrkcw0qzb0xhz6zps9vk4wixwaix"))
("perl-test-harness" ,perl-test-harness)
("perl-test-exception" ,perl-test-exception)))
(home-page "http://www.ensembl.org/vep")
(synopsis "Predict functional effects of genomic variants")
(description
"This package provides a Variant Effect Predictor, which predicts
the functional effects of genomic variants. It also provides
Haplosaurus, which uses phased genotype data to predict
whole-transcript haplotype sequences, and Variant Recoder, which
translates between different variant encodings.")
(license license:asl2.0))))
(define-public r-signac
(let ((commit "e0512d348adeda4a3f23a2e8f56d1fe09840e03c")
(revision "1"))

43
gnu/packages/bootloaders.scm
View File

@ -475,11 +475,19 @@ menu to select one of the installed operating systems.")
tree binary files. These are board description files used by Linux and BSD.")
(license license:gpl2+)))
(define %u-boot-rockchip-inno-usb-patch
;; Fix regression in 2020.10 causing freezes on boot with USB boot enabled.
;; See https://gitlab.manjaro.org/manjaro-arm/packages/core/uboot-rockpro64/-/issues/4
;; and https://patchwork.ozlabs.org/project/uboot/patch/20210406151059.1187379-1-icenowy@aosc.io
(search-patch "u-boot-rockchip-inno-usb.patch"))
(define u-boot
(package
(name "u-boot")
(version "2021.04")
(source (origin
(patches
(list %u-boot-rockchip-inno-usb-patch))
(method url-fetch)
(uri (string-append
"https://ftp.denx.de/pub/u-boot/"
@ -505,6 +513,21 @@ tree binary files. These are board description files used by Linux and BSD.")
also initializes the boards (RAM etc).")
(license license:gpl2+)))
(define-public u-boot-2021.07
(package
(inherit u-boot)
(version "2021.07-rc1")
(source (origin
(patches
(list %u-boot-rockchip-inno-usb-patch))
(method url-fetch)
(uri (string-append
"https://ftp.denx.de/pub/u-boot/"
"u-boot-" version ".tar.bz2"))
(sha256
(base32
"12krpy85iwy40xlhqb61d0d4bzj0sbn9sdf8brn57m4cjh1svaya"))))))
(define-public u-boot-tools
(package
(inherit u-boot)
@ -889,13 +912,6 @@ to Novena upstream, does not load u-boot.img from the first partition.")
(substitute-keyword-arguments (package-arguments base)
((#:phases phases)
`(modify-phases ,phases
(add-after 'unpack 'patch-rockpro64-config
;; Fix regression in 2020.10 causing freezes on boot with USB boot enabled.
;; See https://gitlab.manjaro.org/manjaro-arm/packages/core/uboot-rockpro64/-/issues/4
(lambda _
(substitute* "configs/rockpro64-rk3399_defconfig"
(("CONFIG_USE_PREBOOT=y") "CONFIG_USE_PREBOOT=n"))
#t))
(add-after 'patch-rockpro64-config 'set-environment
(lambda* (#:key inputs #:allow-other-keys)
(setenv "BL31" (string-append (assoc-ref inputs "firmware")
@ -912,17 +928,12 @@ to Novena upstream, does not load u-boot.img from the first partition.")
(let ((base (make-u-boot-package "pinebook-pro-rk3399" "aarch64-linux-gnu")))
(package
(inherit base)
(version (package-version u-boot-2021.07))
(source (package-source u-boot-2021.07))
(arguments
(substitute-keyword-arguments (package-arguments base)
((#:phases phases)
`(modify-phases ,phases
(add-after 'unpack 'patch-pinebook-pro-config
;; Fix regression in 2020.10 causing freezes on boot with USB boot enabled.
;; See https://gitlab.manjaro.org/manjaro-arm/packages/core/uboot-rockpro64/-/issues/4
(lambda _
(substitute* "configs/pinebook-pro-rk3399_defconfig"
(("CONFIG_USE_PREBOOT=y") "CONFIG_USE_PREBOOT=n"))
#t))
(add-after 'unpack 'set-environment
(lambda* (#:key inputs #:allow-other-keys)
(setenv "BL31" (string-append (assoc-ref inputs "firmware")
@ -1207,8 +1218,8 @@ order to add a suitable bootloader menu entry.")
(description "iPXE is a network boot firmware. It provides a full PXE
implementation enhanced with additional features such as booting from: a web
server via HTTP, an iSCSI SAN, a Fibre Channel SAN via FCoE, an AoE SAN, a
wireless network, a wide-area network, an Infiniband network. It allows to
control the boot process with a script. You can use iPXE to replace the
wireless network, a wide-area network, an Infiniband network. It
controls the boot process with a script. You can use iPXE to replace the
existing PXE ROM on your network card, or you can chainload into iPXE to obtain
the features of iPXE without the hassle of reflashing.")
(license license:gpl2+))))

8
gnu/packages/browser-extensions.scm
View File

@ -49,7 +49,7 @@ supported content to the Kodi media center.")
(make-chromium-extension play-to-kodi))
(define uassets
(let ((commit "61b43044fbe7be0cf4e9c636fe96236dc52e44cf"))
(let ((commit "f521473026f5f60cc753fa4a533af41badfc700e"))
(origin
(method git-fetch)
(uri (git-reference
@ -58,12 +58,12 @@ supported content to the Kodi media center.")
(file-name (git-file-name "uAssets" (string-take commit 9)))
(sha256
(base32
"03ikia0prmzsc34qa3418dc49ss8ari9hj6g3s6nvxrgyd127idi")))))
"0ms0xxj6rcfkib33wjbki631wix17vvzr4m6z0phqmaj49bla4kz")))))
(define ublock-origin
(package
(name "ublock-origin")
(version "1.33.2")
(version "1.35.2")
(home-page "https://github.com/gorhill/uBlock")
(source (origin
(method git-fetch)
@ -71,7 +71,7 @@ supported content to the Kodi media center.")
(file-name (git-file-name name version))
(sha256
(base32
"1pdf3fzc7ld65gr87s1cdy2sb84jbqnyq9lvwg1mgzi9dg8x7639"))))
"0w4rfwgvkjvdfccxi9b4qhp0hylnd946diri19cp3fd72zkjlcky"))))
(build-system gnu-build-system)
(outputs '("xpi" "firefox" "chromium"))
(arguments

5
gnu/packages/busybox.scm
View File

@ -33,7 +33,7 @@
(define-public busybox
(package
(name "busybox")
(version "1.33.0")
(version "1.33.1")
(source (origin
(method url-fetch)
(uri (string-append
@ -41,8 +41,7 @@
version ".tar.bz2"))
(sha256
(base32
"1gcg7ggg79apdlp5qnrh9pbjl10fx30yn33p21kxqpm8j4f6hs6m"))
(patches (search-patches "busybox-CVE-2021-28831.patch"))))
"0a0dcvsh7nxnhxc5y73fky0z30i9p7r30qfidm2akn0n5fywdkhj"))))
(build-system gnu-build-system)
(arguments
'(#:phases

48
gnu/packages/calendar.scm
View File

@ -5,7 +5,7 @@
;;; Copyright © 2016, 2017, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Troy Sankey <sankeytms@gmail.com>
;;; Copyright © 2016, 2021 Stefan Reichoer <stefan@xsteve.at>
;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018, 2019, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com
;;; Copyright © 2020 Brendan Tildesley <mail@brendan.scot>
;;; Copyright © 2020 Tanguy Le Carrour <tanguy@bioneland.org>
@ -35,6 +35,7 @@
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
#:use-module (guix build-system python)
#:use-module (gnu packages admin)
#:use-module (gnu packages base)
#:use-module (gnu packages check)
#:use-module (gnu packages dav)
@ -51,6 +52,7 @@
#:use-module (gnu packages qt)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages tcl)
#:use-module (gnu packages time)
#:use-module (gnu packages xml)
#:use-module (srfi srfi-26))
@ -178,13 +180,13 @@ data units.")
(define-public khal
(package
(name "khal")
(version "0.10.2")
(version "0.10.3")
(source (origin
(method url-fetch)
(uri (pypi-uri "khal" version))
(sha256
(base32
"11qhrga44knlnp88py9p547d4nr5kn041d2nszwa3dqw7mf22ks9"))))
"0cm4xn871w3i99l3qmhv0bnv8q6rd1w3rip9sskyb5z59z0qzp9g"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ; The test suite is unreliable. See <https://bugs.gnu.org/44197>
@ -226,7 +228,7 @@ able to synchronize with CalDAV servers through vdirsyncer.")
(define-public remind
(package
(name "remind")
(version "3.3.5")
(version "3.3.6")
(source
(origin
(method url-fetch)
@ -237,10 +239,44 @@ able to synchronize with CalDAV servers through vdirsyncer.")
".")
".tar.gz"))
(sha256
(base32 "1hbfsq6444abkiws28xqy0k9cwzgzfi1hwfmd1rgm4yydgc1gvb1"))))
(base32 "0nszv62gqyclsvsygqj4b1c5h40rp66s5njgcf1h7iy9f00hr6ln"))))
(build-system gnu-build-system)
(outputs (list "out"
"tcl")) ; more than doubles the closure by >110 MiB
(arguments
'(#:tests? #f)) ; no "check" target
'(#:test-target "test"
#:phases
(modify-phases %standard-phases
(add-after 'install 'split-:tcl
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(tcl (assoc-ref outputs "tcl")))
(for-each
(lambda (file)
(let ((from (string-append out "/" file))
(to (string-append tcl "/" file)))
(mkdir-p (dirname to))
(rename-file from to)
;; For simplicity, wrap all scripts with the same variables
;; even though, e.g., inetutils is not needed by cm2rem.tcl.
;; XXX Using WRAP-SCRIPT currently breaks tkremind.
(wrap-program to
`("PATH" ":" prefix
,(map (lambda (dir)
(string-append dir "/bin"))
(append (list out tcl)
(map (lambda (input)
(assoc-ref inputs input))
(list "tcl" "tk" "inetutils")))))
`("TCLLIBPATH" " " =
(,(getenv "TCLLIBPATH"))))))
(list "bin/cm2rem.tcl"
"bin/tkremind"))))))))
(inputs
`(("inetutils" ,inetutils)
("tcl" ,tcl)
("tcllib" ,tcllib)
("tk" ,tk)))
(home-page "https://dianne.skoll.ca/projects/remind/")
(synopsis "Sophisticated calendar and alarm program")
(description

24
gnu/packages/cdrom.scm
View File

@ -8,7 +8,7 @@
;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017 John Darrington <jmd@gnu.org>
;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Nikita <nikita@n0.is>
;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
@ -599,9 +599,9 @@ the data.")
#t))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
`(#:tests? #f
#:phases (modify-phases %standard-phases (delete 'configure))
#:make-flags (list "CC=gcc"
#:make-flags (list ,(string-append "CC=" (cc-for-target))
(string-append "PREFIX="
(assoc-ref %outputs "out")))))
(synopsis "Get CDDB discid information from an audio CD")
@ -953,15 +953,15 @@ CD data, and more. It's mostly compatible with @code{cdrtools}.")
(define-public libmirage
(package
(name "libmirage")
(version "3.2.4")
(version "3.2.5")
(source (origin
(method url-fetch)
(uri (string-append
"mirror://sourceforge/cdemu/libmirage/libmirage-"
version ".tar.bz2"))
version ".tar.xz"))
(sha256
(base32
"0md3f71x2dbgyw5s254vx1s80slh3f25r9pvjihkrmj0rn53nnzw"))))
"0f8i2ha44rykkk3ac2q8zsw3y1zckw6qnf6zvkyrj3qqbzhrf3fm"))))
(build-system cmake-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
@ -982,15 +982,15 @@ the data stored in various image formats.")
(define-public cdemu-daemon
(package
(name "cdemu-daemon")
(version "3.2.4")
(version "3.2.5")
(source (origin
(method url-fetch)
(uri (string-append
"mirror://sourceforge/cdemu/cdemu-daemon/"
"cdemu-daemon-" version ".tar.bz2"))
"cdemu-daemon-" version ".tar.xz"))
(sha256
(base32
"02yyj8sr7d5briamhzrqh8zdsiiggxmx5y05kx25y7k3g15jvcx6"))))
"16g6fv1lxkdmbsy6zh5sj54dvgwvm900fd18aq609yg8jnqm644d"))))
(build-system cmake-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
@ -1011,15 +1011,15 @@ drive and disc (including CD-ROMs and DVD-ROMs).")
(define-public cdemu-client
(package
(name "cdemu-client")
(version "3.2.4")
(version "3.2.5")
(source (origin
(method url-fetch)
(uri (string-append
"mirror://sourceforge/cdemu/cdemu-client/cdemu-client-"
version ".tar.bz2"))
version ".tar.xz"))
(sha256
(base32
"1swylaja1p1jfjf3s58c9hsk1cyy20i7mrq32kcg6kzp88grs8my"))))
"1prrdhv0ia0axc6b73crszqzh802wlkihz6d100yvg7wbgmqabd7"))))
(build-system cmake-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)

23
gnu/packages/check.scm
View File

@ -2878,3 +2878,26 @@ system. The code under test requires no modification to work with pyfakefs.")
(description "Aiounittest is a library that helps write tests using
asynchronous code in Python (asyncio).")
(license license:expat)))
(define-public python-pytest-dependency
(package
(name "python-pytest-dependency")
(version "0.5.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pytest-dependency" version))
(sha256
(base32
"0swl3mxca7nnjbb5grfzrm3fa2750h9vjsha0f2kyrljc6895a62"))))
(build-system python-build-system)
(propagated-inputs
`(("python-pytest" ,python-pytest)))
(home-page
"https://github.com/RKrahl/pytest-dependency")
(synopsis "Manage dependencies of tests")
(description "This pytest plugin manages dependencies of tests. It allows
to mark some tests as dependent from other tests. These tests will then be
skipped if any of the dependencies did fail or has been skipped.")
(license license:asl2.0)))

77
gnu/packages/chromium.scm
View File

@ -150,9 +150,14 @@
"third_party/devtools-frontend/src/third_party/pyjson5" ;ASL2.0
"third_party/devtools-frontend/src/third_party/typescript" ;ASL2.0
"third_party/dom_distiller_js" ;BSD-3
"third_party/eigen3" ;MPL2.0
"third_party/emoji-segmenter" ;ASL2.0
"third_party/farmhash" ;Expat
"third_party/fdlibm" ;non-copyleft
"third_party/fft2d" ;non-copyleft
"third_party/flatbuffers" ;ASL2.0
"third_party/fusejs" ;ASL2.0
"third_party/gemmlowp" ;ASL2.0
"third_party/google_input_tools" ;ASL2.0
"third_party/google_input_tools/third_party/closure_library" ;ASL2.0
"third_party/google_input_tools/third_party/closure_library/third_party/closure" ;Expat
@ -171,8 +176,10 @@
"third_party/libXNVCtrl" ;Expat
"third_party/libaddressinput" ;ASL2.0
"third_party/libaom" ;BSD-2 or "Alliance for Open Media Patent License 1.0"
"third_party/libaom/source/libaom/third_party/fastfeat" ;BSD-3
"third_party/libaom/source/libaom/third_party/vector" ;Expat
"third_party/libaom/source/libaom/third_party/x86inc" ;ISC
"third_party/libgav1" ;ASL2.0
"third_party/libgifcodec" ;MPL1.1/GPL2+/LGPL2.1+, BSD-3, BSD-2
"third_party/libjingle_xmpp" ;BSD-3
"third_party/libphonenumber" ;ASL2.0
@ -190,6 +197,7 @@
"third_party/libwebm" ;BSD-3
"third_party/libxml/chromium" ;BSD-3
"third_party/libyuv" ;BSD-3
"third_party/libzip" ;BSD-3
"third_party/lottie" ;Expat
"third_party/lss" ;BSD-3
"third_party/mako" ;Expat
@ -211,6 +219,7 @@
"third_party/pdfium/third_party/agg23" ;Expat
"third_party/pdfium/third_party/base" ;BSD-3
"third_party/pdfium/third_party/bigint" ;Public domain, BSD-3
"third_party/pdfium/third_party/libtiff" ;non-copyleft
"third_party/pdfium/third_party/skia_shared" ;BSD-3
"third_party/pdfium/third_party/freetype/include/pstables.h" ;FreeType
"third_party/perfetto" ;ASL2.0
@ -228,6 +237,7 @@
;; ABI relies on libstdc++ internals. See build/linux/unbundle/re2.gn.
"third_party/re2" ;BSD-3
"third_party/rnnoise" ;BSD-3
"third_party/ruy" ;ASL2.0
"third_party/s2cellid" ;ASL2.0
"third_party/schema_org" ;CC-BY-SA3.0
"third_party/securemessage" ;ASL2.0
@ -247,9 +257,15 @@
"third_party/swiftshader/third_party/subzero" ;NCSA
"third_party/swiftshader/third_party/SPIRV-Headers" ;X11-style
"third_party/tcmalloc/chromium" ;BSD-3
"third_party/tensorflow-text" ;ASL2.0
"third_party/tflite" ;ASL2.0
"third_party/tflite/src/third_party/eigen3" ;MPL2.0
"third_party/tflite/src/third_party/fft2d" ;ASL2.0
"third_party/tflite-support" ;ASL2.0
"third_party/ukey2" ;ASL2.0
"third_party/usb_ids" ;BSD-3
"third_party/usrsctp" ;BSD-2
"third_party/utf" ;Expat
"third_party/vulkan-deps" ;ASL2.0, BSD-3, Expat
"third_party/vulkan_memory_allocator" ;Expat
"third_party/wayland/protocol" ;Expat
@ -269,6 +285,7 @@
"third_party/widevine/cdm/widevine_cdm_version.h" ;BSD-3
"third_party/widevine/cdm/widevine_cdm_common.h" ;BSD-3
"third_party/woff2" ;ASL2.0
"third_party/wuffs" ;ASL2.0
"third_party/xcbproto" ;X11
"third_party/xdg-utils" ;Expat
@ -293,7 +310,7 @@
;; run the Blink performance tests, just remove everything to save ~70MiB.
'("third_party/blink/perf_tests"))
(define (debian-patch name revision hash)
(define* (debian-patch name hash #:optional (revision %debian-revision))
(origin
(method url-fetch)
(uri (string-append "https://salsa.debian.org/chromium-team/chromium/-/raw/"
@ -303,36 +320,34 @@
(string-append "ungoogled-chromium-" category "-" name))))
(sha256 (base32 hash))))
(define %ungoogled-revision "89.0.4389.114-1")
(define %debian-revision "debian/84.0.4147.105-1")
(define %chromium-version "90.0.4430.93")
(define %debian-revision "debian/90.0.4430.85-1")
(define %ungoogled-revision "90.0.4430.85-1-11-g3184907")
(define %debian-patches
(list (debian-patch "system/zlib.patch" %debian-revision
"09vqgs37w9ycc7par14wa7rnvmg9bm0z9pqg6fyl3iqvpghyjyr4")
(debian-patch "system/openjpeg.patch" %debian-revision
"0zd6v5njx1pc7i0y6mslxvpx5j4cq01mmyx55qcqx8qzkm0gm48j")))
(list (debian-patch "fixes/missing-includes.patch"
"1f0drxp1cy76g71rkkzxxbwixn03yn9b0q22vb0mb6h2qk6cw92q")
(debian-patch "fixes/nomerge.patch"
"0lybs2b5gk08j8cr6vjrs9d3drd7qfw013z2r0y00by8dnpm74i3")
(debian-patch "system/nspr.patch"
"1gdirn1k1i841l8zp8xgr95kl16b5nx827am9rcxj8sfkm8hgkn3")
(debian-patch "system/zlib.patch"
"0j313bd3q8qc065j60x97dckrfgbwl4qxc8jhz33iihvv4lwziwv")
(debian-patch "system/openjpeg.patch"
"048405xh84pys0kky81vlqhaxjyxvcql4py217z01qxiv991zxaj")))
(define %ungoogled-origin
(origin
(method git-fetch)
(uri (git-reference (url "https://github.com/Eloston/ungoogled-chromium")
(commit %ungoogled-revision)))
(file-name (git-file-name "ungoogled-chromium"
(if (= 40 (string-length %ungoogled-revision))
(string-take %ungoogled-revision 7)
%ungoogled-revision)))
(file-name (git-file-name "ungoogled-chromium" %ungoogled-revision))
(sha256
(base32
"0cr2i51gxhgl55c8f9w0ra3m5q2dk03sf7p2qn4bqq1l1l72hw6s"))))
"18xfwgkw3xarxcgnzvyv70h4icyqh3k8lfx6fvhp7fsr6x20sai0"))))
(define %guix-patches
(list (local-file
(assume-valid-file-name
(search-patch "ungoogled-chromium-system-nspr.patch")))
(local-file
(assume-valid-file-name
(search-patch "ungoogled-chromium-system-opus.patch")))
(local-file
(assume-valid-file-name
(search-patch "ungoogled-chromium-extension-search-path.patch")))))
@ -415,7 +430,7 @@
(define libvpx/chromium
(package
(inherit libvpx)
(version "1.9.0-104-gb5d77a48d")
(version "1.9.0-147-g61edec1ef")
(source (origin
(inherit (package-source libvpx))
(uri (git-reference
@ -424,7 +439,7 @@
(file-name (git-file-name "libvpx" version))
(sha256
(base32
"07nkpx8myw5nd4bkaj6l4wr5ipk2c6lg9cwirz0i5qbr659051rk"))))))
"0mw13y7j2lg8jj3alm9367c3b40b6s218fdz3nn1m2k85c78wzr7"))))))
;; 'make-ld-wrapper' can only work with an 'ld' executable, so we need
;; this trick to make it wrap 'lld'.
@ -454,17 +469,19 @@
(define-public ungoogled-chromium
(package
(name "ungoogled-chromium")
(version %ungoogled-revision)
(version (string-append %chromium-version "-0."
(match (string-split %ungoogled-revision #\-)
((version revision commits g+short)
(string-drop g+short 1)))))
(synopsis "Graphical web browser")
(source (origin
(method url-fetch)
(uri (string-append "https://commondatastorage.googleapis.com"
"/chromium-browser-official/chromium-"
(string-drop-right %ungoogled-revision 2)
".tar.xz"))
%chromium-version ".tar.xz"))
(sha256
(base32
"007df9p78bbmk3iyfi8qn57mmn68qqrdhx6z8n2hl8ksd7lspw7j"))
"0zimr975vp0v12zz1nqjwag3f0q147wrmdhpzgi4yf089rgwfbjk"))
(modules '((guix build utils)))
(snippet (force ungoogled-chromium-snippet))))
(build-system gnu-build-system)
@ -506,6 +523,9 @@
"enable_widevine=false"
;; Disable type-checking for the Web UI to avoid a Java dependency.
"enable_js_type_check=false"
;; Disable code using TensorFlow until it has been scrutinized
;; by the ungoogled project.
"build_with_tflite_lib=false"
;; Define a custom toolchain that simply looks up CC, AR and
;; friends from the environment.
@ -565,7 +585,13 @@
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-stuff
(lambda _
(lambda* (#:key inputs #:allow-other-keys)
(let ((openjpeg (assoc-ref inputs "openjpeg")))
(substitute* "third_party/pdfium/BUILD.gn"
;; This include path is added by Debians openjpeg patch.
(("/usr/include/openjpeg")
(string-append openjpeg "/include/openjpeg"))))
(substitute*
'("base/process/launch_posix.cc"
"base/third_party/dynamic_annotations/dynamic_annotations.c"
@ -735,6 +761,7 @@
"chrome_200_percent.pak"
"resources.pak"
"v8_context_snapshot.bin"
;; Chromium ships its own libGL
;; implementation called ANGLE.
"libEGL.so" "libGLESv2.so"))

26
gnu/packages/ci.scm
View File

@ -54,9 +54,27 @@
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu))
(define-public guile-squee-dev
(let ((commit "e0614273ad4067af82f508db51c8a100131151ea")
(revision "3"))
(package
(inherit guile-squee)
(name "guile-squee")
(version (string-append "0-" revision "." (string-take commit 7)))
(home-page "https://notabug.org/mothacehe/guile-squee.git")
(source (origin
(method git-fetch)
(uri (git-reference
(url home-page)
(commit commit)))
(sha256
(base32
"1jps14z8653ah2kr367iayzyi3ql2s55l77xrafz7gk3mzcvgrrg"))
(file-name (string-append name "-" version "-checkout")))))))
(define-public cuirass
(let ((commit "922cc66089035d4dbc277df06366e41a0806bffb")
(revision "11"))
(let ((commit "31fd4d4fe107d86f5e202510e177726a1f49e828")
(revision "17"))
(package
(name "cuirass")
(version (git-version "1.0.0" revision commit))
@ -69,7 +87,7 @@
(file-name (git-file-name name version))
(sha256
(base32
"1kanag19dvaqpij7j6gznsfzajc5iir9qj6vq016bc4al5x6ggj4"))))
"08phqr0sfi6hkzrqhqsh9ri9434sd41qg1b5vijbadgsj1ql33rw"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build utils)
@ -156,7 +174,7 @@
("guile-gcrypt" ,guile-gcrypt)
("guile-json" ,guile-json-4)
("guile-simple-zmq" ,guile-simple-zmq)
("guile-squee" ,guile-squee)
("guile-squee" ,guile-squee-dev)
("guile-git" ,guile-git)
("guile-zlib" ,guile-zlib)
("guile-mastodon" ,guile-mastodon)

25
gnu/packages/cobol.scm
View File

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017, 2018, 2021 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -25,7 +25,9 @@
#:use-module (gnu packages dbm)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl))
#:use-module (gnu packages perl)
#:use-module (gnu packages web)
#:use-module (gnu packages xml))
(define-public gnucobol
(package
@ -43,7 +45,10 @@
(arguments
'(#:configure-flags (list (string-append "LDFLAGS=-Wl,-rpath="
(assoc-ref %outputs "out")
"/lib"))
"/lib")
(string-append "JSON_C_CFLAGS=-I"
(assoc-ref %build-inputs "json-c")
"/include/json-c"))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'place-cobol85-test-suite
@ -55,19 +60,21 @@
(lambda _ (setenv "TERM" "xterm-256color"))))
#:test-target "checkall"))
(native-inputs
`(("perl" ,perl)))
(inputs
`(("bdb" ,bdb)
("gmp" ,gmp)
("ncurses" ,ncurses)
`(("perl" ,perl)
("newcob" ,(origin
(method url-fetch)
(uri "https://www.itl.nist.gov/div897/ctg/suites/newcob.val.Z")
(sha256
(base32
"1yb1plmv4firfnbb119r2vh1hay221w1ya34nyz0qwsxppfr56hy"))))))
(inputs
`(("bdb" ,bdb)
("gmp" ,gmp)
("json-c" ,json-c)
("libxml2" ,libxml2)
("ncurses" ,ncurses)))
(build-system gnu-build-system)
(home-page "https://savannah.gnu.org/projects/gnucobol/")
(home-page "https://www.gnu.org/software/gnucobol/")
(synopsis "A modern COBOL compiler")
(description "GnuCOBOL is a free, modern COBOL compiler. GnuCOBOL
implements a substantial part of the COBOL 85, COBOL 2002 and COBOL 2014

20
gnu/packages/code.scm
View File

@ -15,6 +15,7 @@
;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
;;; Copyright © 2020 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2021 lu hui <luhuins@163.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -126,16 +127,17 @@ highlighting your own code that seemed comprehensible when you wrote it.")
(define-public global ; a global variable
(package
(name "global")
(version "6.6.5")
(version "6.6.6")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/global/global-"
version ".tar.gz"))
(sha256
(base32
"10vvsgx8v54whb4j9mk5qqyb5h3rdd9da0il3wir8pcpksyk0dww"))))
"0pad5p31rdspyrzqky3ppgx7f6gdlfnwg1c7qm8w1m4qzyppi03m"))))
(build-system gnu-build-system)
(inputs `(("ncurses" ,ncurses)
(inputs `(("coreutils" ,coreutils)
("ncurses" ,ncurses)
("libltdl" ,libltdl)
("sqlite" ,sqlite)
("python-wrapper" ,python-wrapper)))
@ -149,6 +151,12 @@ highlighting your own code that seemed comprehensible when you wrote it.")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-globash
(lambda* (#:key inputs #:allow-other-keys)
(let* ((echo (string-append
(assoc-ref inputs "coreutils") "/bin/echo")))
(substitute* "globash/globash.in"
(("/bin/echo") echo)))))
(add-after 'install 'post-install
(lambda* (#:key outputs #:allow-other-keys)
;; Install the plugin files in the right place.
@ -234,16 +242,16 @@ COCOMO model or user-provided parameters.")
(define-public cloc
(package
(name "cloc")
(version "1.88")
(version "1.90")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/AlDanial/cloc")
(commit version)))
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1ixgswzbzv63bl50gb2kgaqr0jcicjz6w610hi9fal1i7744zraw"))))
(base32 "0ic9q6qqw5f1wafp9lpmhr0miasbdb9zr59c0jlymnzffdmnliyc"))))
(build-system gnu-build-system)
(inputs
`(("coreutils" ,coreutils)

3
gnu/packages/commencement.scm
View File

@ -3814,6 +3814,9 @@ is the GNU Compiler Collection.")
(define-public gcc-toolchain-10
(make-gcc-toolchain gcc-10))
(define-public gcc-toolchain-11
(make-gcc-toolchain gcc-11))
(define-public gcc-toolchain-aka-gcc
;; It's natural for users to try "guix install gcc". This package
;; automatically "redirects" them to 'gcc-toolchain'.

15
gnu/packages/conky.scm
View File

@ -29,6 +29,7 @@
#:use-module (gnu packages curl)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages image)
#:use-module (gnu packages linux)
#:use-module (gnu packages lua)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages pkg-config)
@ -39,7 +40,7 @@
(package
(name "conky")
(home-page "https://github.com/brndnmtthws/conky")
(version "1.11.6")
(version "1.12.2")
(source
(origin
(method git-fetch)
@ -48,13 +49,14 @@
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0y2g66fjqp2hdk0y1h4ijxhnv34j16gizvxpmbigwh4n6zijcm6v"))))
(base32 "1grxapl4q37fzk2rsijwz2rrl0aj520y8daki6bg48jb9vjd39n7"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; there are no tests
#:configure-flags
`(#:configure-flags
(list "-DRELEASE=true"
"-DBUILD_PULSEAUDIO=ON")
"-DBUILD_PULSEAUDIO=ON"
"-DBUILD_WLAN=ON"
"-DBUILD_TESTS=ON")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'add-freetype-to-search-path
@ -82,7 +84,8 @@
("pulseaudio" ,pulseaudio)
("lua" ,lua)
("ncurses" ,ncurses)
("curl" ,curl)))
("curl" ,curl)
("wireless-tools" ,wireless-tools)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(synopsis "Lightweight system monitor for X")

8
gnu/packages/cpp.scm
View File

@ -273,7 +273,7 @@ combination of these streams.")
(define-public xsimd
(package
(name "xsimd")
(version "7.4.10")
(version "7.5.0")
(source
(origin
(method git-fetch)
@ -281,7 +281,7 @@ combination of these streams.")
(url "https://github.com/QuantStack/xsimd")
(commit version)))
(sha256
(base32 "097yvxrxdldi5s5m4nsxv8f4gwv9xj42mqig98a1z3hkjj1j2gn5"))
(base32 "0c9pq5vz43j99z83w3b9qylfi66mn749k1afpv5cwfxggbxvy63f"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(arguments
@ -775,7 +775,7 @@ standard GNU style syntax for options.")
(define-public folly
(package
(name "folly")
(version "2021.01.25.00")
(version "2021.04.26.00")
(source (origin
(method git-fetch)
(uri (git-reference
@ -784,7 +784,7 @@ standard GNU style syntax for options.")
(file-name (git-file-name name version))
(sha256
(base32
"14dl1g6vf7mc90mcync5h2lp14fwcx8n9h91pmiq6rfgv1fjjrwz"))))
"0s3jb02qjl9f4gfj01pa01cilkfpc4p0gbpn6bg5vcicyj76garg"))))
(build-system cmake-build-system)
(arguments
'(;; Tests must be explicitly enabled

749
gnu/packages/cran.scm
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File diff suppressed because it is too large Load Diff

2
gnu/packages/crates-graphics.scm
View File

@ -2532,7 +2532,7 @@ properly display animated cursors.")
(synopsis "Bindings to libwayland-egl")
(description
"This crate provides bindings for OpenGL/Vulkan support for
Wayland client apps. It allows to create an EGLSurface from any
Wayland client apps. It creates an EGLSurface from any
WlSurface, which can then play the role of the base surface for
initializing an OpenGL or Vulkan context.")
(license license:expat)))

14
gnu/packages/crates-io.scm
View File

@ -15832,7 +15832,7 @@ derived from an internal hasher used in FireFox and Rustc.")
(home-page "https://github.com/Stebalien/gag-rs")
(synopsis "Gag, redirect, or hold stdout/stderr output")
(description
"This packages gags, redirects, or holds stdout/stderr output.")
"This package gags, redirects, or holds stdout/stderr output.")
(license license:expat)))
(define-public rust-galil-seiferas-0.1
@ -20379,8 +20379,8 @@ byte slices for sets of ASCII characters or bytes.")
(home-page "https://github.com/jni-rs/jni-rs")
(synopsis "Rust bindings to the JNI")
(description
"This package provides Rust bindings to the JNI. It permits to
implement native Java methods for JVM and Android in Rust, call Java
"This package provides Rust bindings to the JNI. It
implements native Java methods for JVM and Android in Rust, call Java
code from Rust, embed JVM in Rust applications and use any Java
libraries.")
(license (list license:expat license:asl2.0))))
@ -27400,7 +27400,7 @@ deserialization, and interpreter in Rust.")
(("rust-easy-parallel" ,rust-easy-parallel-3))))
(home-page "https://github.com/stjepang/parking")
(synopsis "Thread parking and unparking")
(description "This packages provides methods for thread parking and
(description "This package provides methods for thread parking and
unparking.")
(license (list license:asl2.0 license:expat))))
@ -27708,7 +27708,7 @@ synchronization primitives.")
(home-page "")
(synopsis "Parse zoneinfo files from the IANA database")
(description
"This packages parses zoneinfo files from the IANA database.")
"This package parses zoneinfo files from the IANA database.")
(license license:expat)))
(define-public rust-partial-io-0.3
@ -32079,7 +32079,7 @@ Rust.")
(home-page "https://github.com/jonathandturner/rawkey")
(synopsis "Raw terminal key input")
(description
"This packages provides support for raw key input in terminals.")
"This package provides support for raw key input in terminals.")
(license license:expat)))
(define-public rust-rayon-core-1
@ -42641,7 +42641,7 @@ closures after a delay or at a given timestamp.")
(("rust-lazy-static" ,rust-lazy-static-0.2))))
(home-page "https://github.com/savage13/tint")
(synopsis "Color creation and manipulation")
(description "This packages provides tools for color creation and
(description "This package provides tools for color creation and
manipulation in Rust.")
(license license:expat)))

16
gnu/packages/crypto.scm
View File

@ -7,7 +7,7 @@
;;; Copyright © 2016, 2017 Nikita <nikita@n0.is>
;;; Copyright © 2016, 2017, 2019, 2020 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2017 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2018, 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
@ -214,7 +214,7 @@ communication, encryption, decryption, signatures, etc.")
;; like OpenBSD's pledge().
(arguments
`(#:make-flags
(list "CC=gcc"
(list ,(string-append "CC=" (cc-for-target))
(string-append "PREFIX=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
@ -376,7 +376,7 @@ the wrong hands.")
(arguments
`(#:phases (modify-phases %standard-phases
(delete 'configure)) ; no configure script
#:make-flags (list "CC=gcc"
#:make-flags (list ,(string-append "CC=" (cc-for-target))
"RPATH=-Wl,-rpath,$(DESTDIR)$(LIBDIR)"
(string-append "DESTDIR="
(assoc-ref %outputs "out"))
@ -469,7 +469,7 @@ no man page, refer to the home page for usage details.")
(arguments
`(#:tests? #f ; No test suite
#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
"CC=gcc")
,(string-append "CC=" (cc-for-target)))
#:phases
(modify-phases %standard-phases
(delete 'configure) ; no configuration to be done
@ -629,7 +629,7 @@ attacks than alternative functions such as @code{PBKDF2} or @code{bcrypt}.")
(outputs (list "out" "static"))
(arguments
`(#:make-flags (list (string-append "PREFIX=" %output)
"CC=gcc")
,(string-append "CC=" (cc-for-target)))
#:phases
(modify-phases %standard-phases
(delete 'configure) ; no configure script
@ -782,6 +782,7 @@ data on your platform, so the seed itself will be as random as possible.
(commit
(string-append "CRYPTOPP_"
(string-replace-substring version "." "_")))))
(file-name (git-file-name name version))
(sha256
(base32
"0in7rlazq91vfi519g9wr7bh87hii47cimxv7fmj0f88vhjaidq3"))))
@ -1069,8 +1070,9 @@ cannot sign messages in OpenBSD format yet.")
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ; no check target '
#:make-flags (list "CC=gcc" "PREFIX=$(out)")
`(#:tests? #f ; no check target '
#:make-flags (list ,(string-append "CC=" (cc-for-target))
"PREFIX=$(out)")
#:phases (modify-phases %standard-phases
(delete 'configure)
(add-after 'install 'post-install

10
gnu/packages/cups.scm
View File

@ -850,7 +850,7 @@ HP@tie{}LaserJet, and possibly other printers. See @file{README} for details.")
(define-public epson-inkjet-printer-escpr
(package
(name "epson-inkjet-printer-escpr")
(version "1.7.9")
(version "1.7.10")
;; XXX: This currently works. But it will break as soon as a newer
;; version is available since the URLs for older versions are not
;; preserved. An alternative source will be added as soon as
@ -858,11 +858,11 @@ HP@tie{}LaserJet, and possibly other printers. See @file{README} for details.")
(source
(origin
(method url-fetch)
(uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/12/50/95/"
"322b8d6b915ab85add33d41f04ba5130866aadbe/"
"epson-inkjet-printer-escpr-1.7.9-1lsb3.2.tar.gz"))
(uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/12/68/"
"34/82ca3e84f17410b5ec6818e5698524b1f42862cb/"
"epson-inkjet-printer-escpr-1.7.10-1lsb3.2.tar.gz"))
(sha256
(base32 "136hhvhimxfnrdn3ksbiswjxgsifrwlp3zz8h0v63w4k1vkzpgc0"))))
(base32 "0j31w85gbi2g3ad316vw7azns382m2di6wazdbiyv9vix5gvb60g"))))
(build-system gnu-build-system)
(arguments
`(#:modules

21
gnu/packages/cyrus-sasl.scm
View File

@ -44,8 +44,8 @@
version ".tar.gz")))
(sha256 (base32
"1m85zcpgfdhm43cavpdkhb1s2zq1b31472hq1w1gs3xh94anp1i6"))
(patches (search-patches "cyrus-sasl-ac-try-run-fix.patch"))))
(replacement cyrus-sasl/fixed)
(patches (search-patches "cyrus-sasl-ac-try-run-fix.patch"
"cyrus-sasl-CVE-2019-19906.patch"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
@ -81,20 +81,3 @@ server writers.")
(license (license:non-copyleft "file://COPYING"
"See COPYING in the distribution."))
(home-page "https://cyrusimap.org/sasl/")))
(define cyrus-sasl/fixed
(package
(inherit cyrus-sasl)
(version "2.1.27")
(source (origin
(method url-fetch)
(uri (list (string-append
"https://cyrusimap.org/releases/cyrus-sasl-"
version ".tar.gz")
(string-append
"ftp://ftp.cyrusimap.org/cyrus-sasl/cyrus-sasl-"
version ".tar.gz")))
(sha256 (base32
"1m85zcpgfdhm43cavpdkhb1s2zq1b31472hq1w1gs3xh94anp1i6"))
(patches (search-patches "cyrus-sasl-ac-try-run-fix.patch"
"cyrus-sasl-CVE-2019-19906.patch"))))))

87
gnu/packages/databases.scm
View File

@ -17,7 +17,7 @@
;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2016 Andy Patterson <ajpatter@uwaterloo.ca>
;;; Copyright © 2016 Danny Milosavljevic <dannym+a@scratchpost.org>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke <marius@gnu.org>
;;; Copyright © 2017, 2018 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2017, 2020 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org>
@ -28,7 +28,7 @@
;;; Copyright © 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2017, 2018 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2015, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2017, 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Kristofer Buffington <kristoferbuffington@gmail.com>
;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
@ -49,6 +49,7 @@
;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
;;; Copyright © 2021 David Larsson <david.larsson@selfhosted.xyz>
;;; Copyright © 2021 Pjotr Prins <pjotr.guix@thebird.nl>
;;;
;;; This file is part of GNU Guix.
;;;
@ -2079,6 +2080,36 @@ Driver.")
;; COPYING contains copy of lgpl2.1 - but copyright notices just say "LGPL"
(home-page "http://www.unixodbc.org")))
(define-public nanodbc
(package
(name "nanodbc")
(version "2.13.0")
(source (origin
(method git-fetch)
(uri
(git-reference
(url "https://github.com/nanodbc/nanodbc")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1q80p7yv9mcl4hyvnvcjdr70y8nc940ypf368lp97vpqn5yckkgm"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
;; The tests require ODBC backends to be installed.
(list "-DNANODBC_DISABLE_TESTS=ON"
"-DBUILD_SHARED_LIBS=ON")
#:tests? #false))
(inputs
`(("unixodbc" ,unixodbc)))
(home-page "https://nanodbc.io/")
(synopsis "C++ wrapper for the native C ODBC API")
(description "The goal for nanodbc is to make developers happy by providing
a simpler and less verbose API for working with ODBC. Common tasks should be
easy, requiring concise and simple code.")
(license license:expat)))
(define-public unqlite
(package
(name "unqlite")
@ -2157,6 +2188,27 @@ sets, bitmaps and hyperloglogs.")
(home-page "https://redis.io/")
(license license:bsd-3)))
(define-public ruby-redis
(package
(name "ruby-redis")
(version "4.2.5")
(source
(origin
(method url-fetch)
(uri (rubygems-uri "redis" version))
(sha256
(base32
"15x2sr6h094rjbvg8pkq6m3lcd5abpyx93aifvfdz3wv6x55xa48"))))
(build-system ruby-build-system)
(arguments
`(#:tests? #f)) ; Tests require a running redis server.
(synopsis "Ruby client for Redis' API")
(description
"This package provides a Ruby client that tries to match Redis' API
one-to-one, while still providing an idiomatic interface.")
(home-page "https://github.com/redis/redis-rb")
(license license:expat)))
(define-public kyotocabinet
(package
(name "kyotocabinet")
@ -3458,19 +3510,34 @@ is designed to have a low barrier to entry.")
(define-public python-sqlparse
(package
(name "python-sqlparse")
(version "0.3.1")
(version "0.4.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "sqlparse" version))
(sha256
(base32
"0j652a6z7bdf6c77aczfn8m8b2nsr1bcqq48wzghf8vi6wvj0qp1"))))
"1s2l0jgi1v7rk7smzb99iamasaz22apfkczsphn3ci4wh8pgv48g"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _ (invoke "py.test"))))))
(lambda _
(invoke "py.test")))
;; XXX: The regular wrap phase ends up storing pytest as a runtime
;; dependency. See <https://bugs.gnu.org/25235>.
(replace 'wrap
(lambda* (#:key native-inputs inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(python (assoc-ref (or native-inputs inputs) "python"))
(sitedir (string-append "/lib/python"
(python-version python)
"/site-packages")))
(wrap-program (string-append out "/bin/sqlformat")
`("PYTHONPATH" ":" prefix
,(map (lambda (output)
(string-append output sitedir))
(list python out))))))))))
(native-inputs
`(("python-pytest" ,python-pytest)))
(home-page "https://github.com/andialbrecht/sqlparse")
@ -3803,16 +3870,16 @@ The drivers officially supported by @code{libdbi} are:
(define-public soci
(package
(name "soci")
(version "4.0.1")
(version "4.0.2")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/SOCI/soci/")
(commit version)))
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"14x2gjblkgpflv75wl144cyjp1sis5rbxnr9r2gj3yw16v2av0bp"))))
"0qc6d71lyrfh5zb7pmfihd1hjyazlkgq6p0g06ans77wnnjh0k9l"))))
(build-system cmake-build-system)
(propagated-inputs
;; Headers of soci has include-references to headers of these inputs.
@ -3838,14 +3905,14 @@ PostreSQL, SQLite, ODBC and MySQL.")
(define-public freetds
(package
(name "freetds")
(version "1.2.19")
(version "1.2.20")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.freetds.org/files/stable/"
"freetds-" version ".tar.gz"))
(sha256
(base32 "11xf2w8gh2p9cq4i38jfvdiwgig8wqbg098xjc08kx4iii8lxy3m"))))
(base32 "11fzwcahc1bc8npxbif0448v9cwyf7k04167i7fcspmfw7a0hj0d"))))
(build-system gnu-build-system)
(arguments
;; NOTE: (Sharlatan-20210110213908+0000) some tests require DB connection,

4
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View File

@ -126,7 +126,7 @@ contains the archive keys used for that.")
(define-public debootstrap
(package
(name "debootstrap")
(version "1.0.123")
(version "1.0.124")
(source
(origin
(method git-fetch)
@ -135,7 +135,7 @@ contains the archive keys used for that.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0fr5ir8arzisx71jybbk4xz85waz50lf2y052nfimzh6vv9dx54c"))))
(base32 "0pbvrp7gb87pwmjika5hy97342mdfvm0gmy23ag8xz1nnpmn160j"))))
(build-system gnu-build-system)
(arguments
`(#:phases

9
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@ -1,7 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;;
;;; This file is part of GNU Guix.
@ -39,18 +39,19 @@
(define-public dico
(package
(name "dico")
(version "2.10")
(version "2.11")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/dico/dico-"
version ".tar.xz"))
(sha256
(base32
"0qag47mzs00d53hnrmh381r0jay42766vp5xrffmzmsn2307x8vl"))))
"0nic4mggc0yhms130k7x4qp5k9c42fwg6n8hmk5cmynh6gi9h7xc"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags (list (string-append "--with-guile-site-dir=" %output
"/share/guile/site/2.0"))
"/share/guile/site/2.0")
"--disable-static")
#:make-flags '("V=1")
#:phases (modify-phases %standard-phases
(add-before 'check 'silence-guile

23
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View File

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2017, 2018, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2017, 2018, 2019, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
@ -113,14 +113,14 @@ acronyms distributed as an info document.")
(define-public gcide
(package
(name "gcide")
(version "0.52")
(version "0.53")
(source (origin
(method url-fetch)
(uri (string-append
"mirror://gnu/gcide/gcide-" version ".tar.xz"))
(sha256
(base32
"1n3bp91sik66z3ca7mjqbr9nck3hg5ck0c8g84xc0qnfpx5vznh2"))))
"17rigzfmih5i1z5s5v1hdr1jw8rngf40768kblnh5kp19ncbvb6k"))))
(build-system copy-build-system)
(arguments
'(#:install-plan
@ -277,17 +277,18 @@ and a Python library.")
rlwrap "/bin")))))
#t))
(add-after 'install 'emacs-install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(dest (string-append out "/share/emacs/site-lisp"))
(emacs (string-append (assoc-ref inputs "emacs") "/bin/emacs")))
(install-file "google-translate-mode.el" dest)
(emacs-generate-autoloads ,name dest)))))
(assoc-ref emacs:%standard-phases 'install))
(add-after 'emacs-install 'emacs-make-autoloads
(assoc-ref emacs:%standard-phases 'make-autoloads))
(add-after 'emacs-make-autoloads 'emacs-autoloads-compilation
(assoc-ref emacs:%standard-phases 'enable-autoloads-compilation)))
#:make-flags (list (string-append "PREFIX=" %output)
"NETWORK_ACCESS=no test")
#:imported-modules (,@%gnu-build-system-modules (guix build emacs-utils))
#:imported-modules (,@%gnu-build-system-modules
(guix build emacs-build-system)
(guix build emacs-utils))
#:modules ((guix build gnu-build-system)
(guix build emacs-utils)
((guix build emacs-build-system) #:prefix emacs:)
(guix build utils))
#:test-target "test"))
(inputs

6
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View File

@ -1,7 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018, 2019 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2019 Vagrant Cascadian <vagrant@reproducible-builds.org>
@ -72,7 +72,7 @@
(define-public diffoscope
(package
(name "diffoscope")
(version "172")
(version "174")
(source (origin
(method git-fetch)
(uri (git-reference
@ -81,7 +81,7 @@
(file-name (git-file-name name version))
(sha256
(base32
"1lglxn9h8s7kvmfd2rsyhrcv3y8a4bppbxr9nf2sgnlbdln1vwqq"))))
"16nvcvvps2gxr0b9wbfilrn4397cqkcm716zvhlx5hsbq6w6cx08"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases

43
gnu/packages/disk.scm
View File

@ -13,7 +13,7 @@
;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018, 2019, 2020 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2019 Leo Famulari <leo@famulari.name>
;;; Copyright © 2019, 2021 Leo Famulari <leo@famulari.name>
;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2020 Pkill -9 <pkill9@runbox.com>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
@ -494,14 +494,14 @@ and a @command{fsck.vfat} compatibility symlink for use in an initrd.")
(define-public sdparm
(package
(name "sdparm")
(version "1.11")
(version "1.12")
(source
(origin
(method url-fetch)
(uri (string-append "http://sg.danny.cz/sg/p/"
"sdparm-" version ".tar.xz"))
(sha256
(base32 "1nqjc4w2w47zavcbf5xmm53x1zbwgljaw1lpajcdi537cgy32fa8"))))
(base32 "1gmdxr36allrgap2j4dv238d8awkj327ww0jjwpjwrpbvfpyzjf4"))))
(build-system gnu-build-system)
(home-page "http://sg.danny.cz/sg/sdparm.html")
(synopsis "Provide access to SCSI device parameters")
@ -1216,3 +1216,40 @@ that support this feature).")
built on top of jemalloc which enables control of memory characteristics
and a partitioning of the heap between kinds of memory (for NUMA).")
(license license:bsd-3)))
(define-public mmc-utils
(let ((commit "e9654ebc4a6a48642848822c4a1355a9de4958d1")
(revision "0"))
(package
(name "mmc-utils")
(version (git-version "0.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.kernel.org/pub/scm/linux/kernel/git/cjb/mmc-utils.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1dbsppsmky0r4z6kxwczrw8pih8bhc2pb61gsvs986r4xy6jr17a"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; No test suite
#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))
(string-append "CC=" ,(cc-for-target)))
#:phases
(modify-phases %standard-phases
;; No ./configure script
(delete 'configure)
;; The Makefile's "install-man" target is a no-op.
(add-after 'install 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(man1 (string-append out "/share/man/man1")))
(install-file "man/mmc.1" man1)))))))
(home-page "https://git.kernel.org/pub/scm/linux/kernel/git/cjb/mmc-utils.git/")
(synopsis "Configure MMC storage devices from userspace")
(description "mmc-utils is a command-line tool for configuring and
inspecting MMC storage devices from userspace.")
(license license:gpl2))))

90
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View File

@ -6,7 +6,7 @@
;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
;;; Copyright © 2019 Sam <smbaines8@gmail.com>
;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
;;; Copyright © 2020, 2021 Marius Bakke <marius@gnu.org>
;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
@ -48,13 +48,13 @@
(define-public python-django
(package
(name "python-django")
(version "3.1.8")
(version "3.2.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "Django" version))
(sha256
(base32
"1b0ymqv09b523k3c2jnpb2gjy2fsy6irbfyc2g9x5hjyw41k2fgq"))))
"0gffaabnnpzj0sl3jl7mllvi3gc0jvab6xw2bckvyljwsrd1j78a"))))
(build-system python-build-system)
(arguments
'(#:phases
@ -77,13 +77,21 @@
(string-append " @unittest.skipIf(True, 'Disabled by Guix')\n"
all)))))
(replace 'check
(lambda _
(with-directory-excursion "tests"
(invoke "python" "runtests.py"
;; By default tests run in parallel, which may cause
;; various race conditions. Run sequentially for
;; consistent results.
"--parallel=1")))))))
(lambda* (#:key tests? #:allow-other-keys)
(if tests?
(with-directory-excursion "tests"
(invoke "python" "runtests.py"
;; By default tests run in parallel, which may cause
;; various race conditions. Run sequentially for
;; consistent results.
"--parallel=1"))
(format #t "test suite not run~%"))))
;; XXX: The 'wrap' phase adds native inputs as runtime dependencies,
;; see <https://bugs.gnu.org/25235>. The django-admin script typically
;; runs in an environment that has Django and its dependencies on
;; PYTHONPATH, so just disable the wrapper to reduce the size from
;; ~710 MiB to ~203 MiB.
(delete 'wrap))))
;; TODO: Install extras/django_bash_completion.
(native-inputs
`(("tzdata" ,tzdata-for-tests)
@ -91,7 +99,6 @@
;; tests/requirements/py3.txt
("python-docutils" ,python-docutils)
;; optional for tests: ("python-geoip2" ,python-geoip2)
("python-jinja2" ,python-jinja2) ; >= 2.7
;; optional for tests: ("python-memcached" ,python-memcached)
("python-numpy" ,python-numpy)
("python-pillow" ,python-pillow)
@ -99,14 +106,17 @@
;; optional for tests: ("python-selenium" ,python-selenium)
("python-tblib" ,python-tblib)))
(propagated-inputs
`(("python-argon2-cffi" ,python-argon2-cffi)
("python-asgiref" ,python-asgiref)
("python-bcrypt" ,python-bcrypt)
`(("python-asgiref" ,python-asgiref)
("python-pytz" ,python-pytz)
("python-sqlparse" ,python-sqlparse)
;; Optional dependencies.
("python-argon2-cffi" ,python-argon2-cffi)
("python-bcrypt" ,python-bcrypt)
;; This input is not strictly required, but in practice many Django
;; libraries need it for test suites and similar.
("python-sqlparse" ,python-sqlparse)))
("python-jinja2" ,python-jinja2)))
(home-page "https://www.djangoproject.com/")
(synopsis "High-level Python Web framework")
(description
@ -120,13 +130,13 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
(define-public python-django-2.2
(package
(inherit python-django)
(version "2.2.20")
(version "2.2.22")
(source (origin
(method url-fetch)
(uri (pypi-uri "Django" version))
(sha256
(base32
"0r3a6gbhwngxl172yy6n0sq5knibl2vxc0wbk1g8licfbzfgjs95"))))
"0q30zjcmnvwp1v1syn739wapahs2dx784n0yjyypq0cr3kdi88nv"))))
(native-inputs
`(;; XXX: In 2.2 and 3.0, selenium is required for the test suite.
("python-selenium" ,python-selenium)
@ -452,7 +462,7 @@ account authentication.")
(define-public python-django-debug-toolbar
(package
(name "python-django-debug-toolbar")
(version "2.2")
(version "3.2.1")
(source
(origin
(method git-fetch)
@ -462,7 +472,7 @@ account authentication.")
(file-name (git-file-name name version))
(sha256
(base32
"14069rlgjd5g724iaglai0nc636g9km4ba56r4j3k84chibqzn03"))))
"1m1j2sx7q0blma0miswj3c8hrfi5q4y5cq2b816v8gagy89xgc57"))))
(build-system python-build-system)
(propagated-inputs
`(("python-sqlparse" ,python-sqlparse)))
@ -646,7 +656,10 @@ conn_max_age argument to easily enable Django’s connection pool.")
(lambda _
(invoke "python" "-m" "django" "test" "-v2"
"--settings=tests.settings"))))))
(native-inputs `(("python-django" ,python-django)))
(native-inputs
;; XXX: Picklefield has not been updated in 10+ years and fails tests
;; with Django 3.2.
`(("python-django@2.2" ,python-django-2.2)))
(synopsis "Pickled object field for Django")
(description "Pickled object field for Django")
(license license:expat)))
@ -981,18 +994,36 @@ Django projects, which allows association of a number of tags with any
(define-public python-djangorestframework
(package
(name "python-djangorestframework")
(version "3.12.1")
(version "3.12.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "djangorestframework" version))
(method git-fetch)
(uri (git-reference
(url "https://github.com/encode/django-rest-framework")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0jb22psb823vh5fj9az63p5lgyax9ygjy2faah16ajxvvsp54i6m"))))
"16n17dw35wqv47m8k8fixn0yywrvd6v4r573yr4nx6lbbiyi2cqn"))))
(build-system python-build-system)
(arguments
'(;; No included tests
#:tests? #f))
'(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
;; Add a fix from the master branch for compatibility with Django
;; 3.2: https://github.com/encode/django-rest-framework/pull/7911
;; Remove for versions > 3.12.4.
(substitute* "tests/test_fields.py"
(("class MockTimezone:")
"class MockTimezone(pytz.BaseTzInfo):"))
(if tests?
(invoke "python" "runtests.py" "--nolint")
(format #t "test suite not run~%")))))))
(native-inputs
`(("python-django" ,python-django)
("python-pytest" ,python-pytest)
("python-pytest-django" ,python-pytest-django)))
(home-page "https://www.django-rest-framework.org")
(synopsis "Toolkit for building Web APIs with Django")
(description
@ -1132,13 +1163,13 @@ FileFields during tests.")
(define-public python-django-auth-ldap
(package
(name "python-django-auth-ldap")
(version "2.2.0")
(version "2.4.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "django-auth-ldap" version))
(sha256
(base32
"1gq49l5lv6ar6yf73c8pix8n7md4109yq31s5jfk64w6n1rigbqi"))))
"0xk6cxiqz5j3q79bd54x64f26alrlc8p7k9wkp2c768w2k1vzz30"))))
(build-system python-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
@ -1205,8 +1236,7 @@ to ElasticSearch.")
(native-inputs
`(("python-django" ,python-django)))
(propagated-inputs
`(("python-ipaddress" ,python-ipaddress)
("python-netaddr" ,python-netaddr)
`(("python-netaddr" ,python-netaddr)
("python-six" ,python-six)))
(home-page "https://github.com/jimfunk/django-postgresql-netfields")
(synopsis "PostgreSQL netfields implementation for Django")

8
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View File

@ -320,7 +320,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
;; When updating, check whether isc-dhcp's bundled copy should be as well.
;; The BIND release notes are available here:
;; https://www.isc.org/bind/
(version "9.16.13")
(version "9.16.15")
(source (origin
(method url-fetch)
(uri (string-append
@ -328,7 +328,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
"/bind-" version ".tar.xz"))
(sha256
(base32
"026cliyj570wxvvij96mrzsxyf421xv9a80gc5gv6savza9wfk55"))))
"0fbqisrh84f8wszm94cqp7v8q9r7pql3qyzbay7vz9vqv0rg9dlq"))))
(build-system gnu-build-system)
(outputs `("out" "utils"))
(inputs
@ -943,14 +943,14 @@ synthesis, and on-the-fly re-configuration.")
(define-public knot-resolver
(package
(name "knot-resolver")
(version "5.3.1")
(version "5.3.2")
(source (origin
(method url-fetch)
(uri (string-append "https://secure.nic.cz/files/knot-resolver/"
"knot-resolver-" version ".tar.xz"))
(sha256
(base32
"1j99sz6r1hdvvd8rffx1917r9cyb7z46ivp5934sq57irmxnnkcx"))))
"0dhlq25lig8wmn72ambfmb1njwwp980d98i9q7a24d79bxyl8vwb"))))
(build-system meson-build-system)
(outputs '("out" "doc"))
(arguments

4
gnu/packages/ebook.scm
View File

@ -474,7 +474,7 @@ following formats:
(define-public cozy
(package
(name "cozy")
(version "0.7.8")
(version "0.9.4")
(source
(origin
(method git-fetch)
@ -483,7 +483,7 @@ following formats:
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0z2wj9g32aa5g9pw81q49iv1smb6yvlv9zs0vrzbx6mw8cj3c5d2"))))
(base32 "182y6mkr39qgwk1n33nhfngqjyadrijiyfkzxydx9hfch302i8wz"))))
(build-system meson-build-system)
(arguments
`(#:glib-or-gtk? #t

9
gnu/packages/education.scm
View File

@ -614,14 +614,14 @@ Portuguese, Spanish and Italian.")
(define-public fet
(package
(name "fet")
(version "5.49.1")
(version "6.0.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.lalescu.ro/liviu/fet/download/"
"fet-" version ".tar.bz2"))
(sha256
(base32 "1aa8xnhwvbhvp7yigcdk7qdwqh59yyfknqbpn3ybgjljc22m8w5n"))))
(base32 "08q265i43bnj9syh3xlp11fr47xmzb0nma3nnwm76xq314102f0f"))))
(build-system gnu-build-system)
(arguments
`(#:phases
@ -653,14 +653,14 @@ hours.")
(define-public klavaro
(package
(name "klavaro")
(version "3.11")
(version "3.12")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/klavaro/klavaro-"
version ".tar.bz2"))
(sha256
(base32 "1rkxaqb62w4mv86fcnmr32lq6y0h4hh92wmsy5ddb9a8jnzx6r7w"))))
(base32 "0ymrmgllyjk9wp1f1ayw51xc3myar8ld9a5531wdbrym0xzy4l64"))))
(build-system gnu-build-system)
(native-inputs
`(("intltool" ,intltool)
@ -669,6 +669,7 @@ hours.")
`(("cairo" ,cairo)
("curl" ,curl)
("gtk+" ,gtk+)
("gtkdatabox" ,gtkdatabox)
("pango" ,pango)))
(home-page "https://klavaro.sourceforge.io/en/index.html")
(synopsis "Touch typing tutor")

10
gnu/packages/electronics.scm
View File

@ -43,6 +43,7 @@
#:use-module (gnu packages libftdi)
#:use-module (gnu packages libusb)
#:use-module (gnu packages linux)
#:use-module (gnu packages m4)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages qt))
@ -308,22 +309,23 @@ individual low-level driver modules.")
(define-public xoscope
(package
(name "xoscope")
(version "2.2")
(version "2.3")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/xoscope/xoscope/"
version "/xoscope-" version ".tar.gz"))
(sha256
(base32
"1b9wxnrwz8qy6qyx5icrklb4720rlxnr1c4h3dr6g0dzj6nkc5av"))))
"0a5ycfc1qdmibvagc82r2mhv2i99m6pndy5i6ixas3j2297g6pgq"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
`(("m4" ,m4)
("pkg-config" ,pkg-config)))
(inputs
`(("alsa-lib" ,alsa-lib)
("comedilib" ,comedilib)
("fftw" ,fftw)
("gtk+-2" ,gtk+-2)
("gtk+" ,gtk+)
("gtkdatabox" ,gtkdatabox)))
(synopsis "Digital oscilloscope")
(description "Xoscope is a digital oscilloscope that can acquire signals

896
gnu/packages/emacs-xyz.scm
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File diff suppressed because it is too large Load Diff

50
gnu/packages/emacs.scm
View File

@ -202,6 +202,31 @@
(car (find-files "bin" "^emacs-([0-9]+\\.)+[0-9]+$"))
"bin/emacs")
#t)))
(add-after 'strip-double-wrap 'wrap-emacs-paths
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(lisp-dirs (find-files (string-append out "/share/emacs")
"^lisp$"
#:directories? #t)))
(for-each
(lambda (prog)
(wrap-program prog
;; emacs-next and variants rely on uname being in PATH for
;; Tramp. Tramp paths can't be hardcoded, because they
;; need to be portable.
`("PATH" suffix
,(map (lambda (in) (string-append in "/bin"))
(list (assoc-ref inputs "gzip")
(assoc-ref inputs "coreutils"))))
`("EMACSLOADPATH" suffix ,lisp-dirs)))
(find-files (string-append out "/bin")
;; Matches versioned and unversioned emacs binaries.
;; We don't patch emacsclient, because it takes its
;; environment variables from emacs.
;; Likewise, we don't need to patch helper binaries
;; like etags, ctags or ebrowse.
"^emacs(-[0-9]+(\\.[0-9]+)*)?$"))
#t)))
(add-before 'reset-gzip-timestamps 'make-compressed-files-writable
;; The 'reset-gzip-timestamps phase will throw a permission error
;; if gzip files aren't writable then. This phase is needed when
@ -214,6 +239,10 @@
`(("gnutls" ,gnutls)
("ncurses" ,ncurses)
;; Required for "core" functionality, such as dired and compression.
("coreutils" ,coreutils)
("gzip" ,gzip)
;; Avoid Emacs's limited movemail substitute that retrieves POP3 email
;; only via insecure channels. This is not needed for (modern) IMAP.
("mailutils" ,mailutils)
@ -261,9 +290,7 @@
(native-search-paths
(list (search-path-specification
(variable "EMACSLOADPATH")
;; The versioned entry is for the Emacs' builtin libraries.
(files (list "share/emacs/site-lisp"
(string-append "share/emacs/" version "/lisp"))))
(files '("share/emacs/site-lisp")))
(search-path-specification
(variable "INFOPATH")
(files '("share/info")))))
@ -300,18 +327,7 @@ languages.")
"0igjm9kwiswn2dpiy2k9xikbdfc7njs07ry48fqz70anljj8y7y3"))))
(native-inputs
`(("autoconf" ,autoconf)
,@(package-native-inputs emacs)))
(native-search-paths
(list (search-path-specification
(variable "EMACSLOADPATH")
;; The versioned entry is for the Emacs' builtin libraries.
(files (list "share/emacs/site-lisp"
(string-append "share/emacs/"
(version-major+minor+point version)
"/lisp"))))
(search-path-specification
(variable "INFOPATH")
(files '("share/info"))))))))
,@(package-native-inputs emacs))))))
(define-public emacs-next-pgtk
(let ((commit "ae18c8ec4f0ef37c8c9cda473770ff47e41291e2")
@ -362,7 +378,9 @@ also enabled and works without glitches even on X server."))))
(delete 'strip-double-wrap)))))
(inputs
`(("guix-emacs.el" ,(search-auxiliary-file "emacs/guix-emacs.el"))
("ncurses" ,ncurses)))
("ncurses" ,ncurses)
("coreutils" ,coreutils)
("gzip" ,gzip)))
(native-inputs
`(("pkg-config" ,pkg-config)))))

119
gnu/packages/emulators.scm
View File

@ -13,6 +13,7 @@
;;; Copyright © 2019 David Wilson <david@daviwil.com>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2020 Christopher Howard <christopher@librehacker.com>
;;; Copyright © 2021 Felipe Balbi <balbi@kernel.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -44,6 +45,7 @@
#:use-module (gnu packages autogen)
#:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages backup)
#:use-module (gnu packages cdrom)
@ -53,6 +55,7 @@
#:use-module (gnu packages curl)
#:use-module (gnu packages digest)
#:use-module (gnu packages elf)
#:use-module (gnu packages flex)
#:use-module (gnu packages fonts)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
@ -97,6 +100,45 @@
#:use-module (guix build-system gnu)
#:use-module (guix build-system python))
(define-public vice
(package
(name "vice")
(version "3.5")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/vice-emu/releases/"
"vice-" version ".tar.gz"))
(sha256
(base32
"03nwcldg2h7dxj6aa77ggqc0442hqc1lsq5x69h8kcmqmvx7ifan"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("--disable-pdf-docs")))
(native-inputs
`(("bison" ,bison)
("dos2unix" ,dos2unix)
("flex" ,flex)
("glib" ,glib "bin") ; for glib-genmarshal, etc.
("pkg-config" ,pkg-config)))
(inputs
`(("alsa-lib" ,alsa-lib)
("glew" ,glew)
("glib" ,glib)
("gtk+" ,gtk+)
("pulseaudio" ,pulseaudio)
("sdl" ,sdl)
("sdl-image" ,sdl-image)
("xa" ,xa)))
(home-page "https://vice-emu.sourceforge.io/")
(synopsis "The versatile Commodore emulator")
(description
"VICE is a program that emulates the C64, the C64DTV, the C128, the
VIC20, practically all PET models, the PLUS4 and the CBM-II (aka
C610/C510). An extra emulator is provided for C64 expanded with the CMD
SuperCPU.")
(license license:gpl2+)))
(define-public desmume
(package
(name "desmume")
@ -540,7 +582,7 @@ The following systems are supported:
(define-public mgba
(package
(name "mgba")
(version "0.9.0")
(version "0.9.1")
(source
(origin
(method git-fetch)
@ -549,7 +591,7 @@ The following systems are supported:
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "16v08m9irping65d94vb5skp4m6nc63zj6bfajbzhmf944dswmi5"))
(base32 "163azad5y4zxwzxyrb481rwfc2p86v99pf7nvdr6bavzq98x2z8h"))
(modules '((guix build utils)))
(snippet
;; Make sure we don't use the bundled software.
@ -1233,47 +1275,45 @@ emulation community. It provides highly accurate emulation.")
(license license:gpl2+)))
(define-public libretro-lowresnx
(let ((commit "743ab43a6c4a13e0d5363b0d25ac12c7511c6581")
(revision "1"))
(package
(name "libretro-lowresnx")
(version (git-version "1.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/timoinutilis/lowres-nx")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0r15kb5p5s2jwky6zy4v1j9i95i4rz36p9wxg0g6xdjksf04b5cf"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no tests
#:make-flags (list "-C" "platform/LibRetro"
(string-append "CC=" ,(cc-for-target)))
#:phases
(modify-phases %standard-phases
(delete 'configure) ; no configure script
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(libretrodir (string-append out "/lib/libretro")))
(install-file "platform/LibRetro/lowresnx_libretro.so"
libretrodir)
#t))))))
(home-page "https://lowresnx.inutilis.com/")
(synopsis "Libretro core for LowRES NX")
(description "LowRES NX is a simulated retro game console, which can be
(package
(name "libretro-lowresnx")
(version "1.2")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/timoinutilis/lowres-nx")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0b0vg3iz342dpkffvf7frsnqh8inj8yzi8550bsx8vnbpq5r2ay5"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no tests
#:make-flags (list "-C" "platform/LibRetro"
(string-append "CC=" ,(cc-for-target)))
#:phases
(modify-phases %standard-phases
(delete 'configure) ; no configure script
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(libretrodir (string-append out "/lib/libretro")))
(install-file "platform/LibRetro/lowresnx_libretro.so"
libretrodir)
#t))))))
(home-page "https://lowresnx.inutilis.com/")
(synopsis "Libretro core for LowRES NX")
(description "LowRES NX is a simulated retro game console, which can be
programmed in the classic BASIC language. This package provides a libretro
core allowing the lowRES NX programs to be used with libretro frontends such
as RetroArch.")
(license license:zlib))))
(license license:zlib)))
(define-public retroarch
(package
(name "retroarch")
(version "1.9.0")
(version "1.9.2")
(source
(origin
(method git-fetch)
@ -1282,7 +1322,7 @@ as RetroArch.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1n0dcv85vqrdr79psnf009hi4r2mvsgsjbghrrc9pm5g7ywwwcvp"))
(base32 "0zrry2zwknzsrrz8r6rl1iy9hmiv4dwjmf61aidx3xwxby3g82qg"))
(patches
(search-patches "retroarch-LIBRETRO_DIRECTORY.patch"))))
(build-system gnu-build-system)
@ -1589,7 +1629,7 @@ This is a part of the TiLP project.")
(define-public mame
(package
(name "mame")
(version "0.230")
(version "0.231")
(source
(origin
(method git-fetch)
@ -1598,7 +1638,7 @@ This is a part of the TiLP project.")
(commit (apply string-append "mame" (string-split version #\.)))))
(file-name (git-file-name name version))
(sha256
(base32 "0dk8q2691pycv9mq77h6sdfwjnwdrfwrblf8nwyykrmdawzi56ks"))
(base32 "0rgch8fg8ra48wa4gl5ah70q6191sxs28x39iyalb6ballmz8v1w"))
(modules '((guix build utils)))
(snippet
;; Remove bundled libraries.
@ -1755,6 +1795,7 @@ This is a part of the TiLP project.")
("portaudio" ,portaudio)
("portmidi" ,portmidi)
("pugixml" ,pugixml)
("pulseaudio" ,pulseaudio)
("python-wrapper" ,python-wrapper)
("qtbase" ,qtbase)
("rapidjson" ,rapidjson)

23
gnu/packages/engineering.scm
View File

@ -281,14 +281,14 @@ utilities.")
(package
(inherit geda-gaf)
(name "lepton-eda")
(version "1.9.13-20201211")
(version "1.9.14-20210407")
(home-page "https://github.com/lepton-eda/lepton-eda")
(source (origin
(method git-fetch)
(uri (git-reference (url home-page) (commit version)))
(sha256
(base32
"0xfx6d0pyfrxr1c0nm4pbmb716hng78rgizaa6vsas9347n4kk1n"))
"0kyq0g6271vlwraw98637fn8bq2l6q4rll6748nn8rwsmfz71d0m"))
(file-name (git-file-name name version))))
(native-inputs
`(("autoconf" ,autoconf)
@ -304,7 +304,7 @@ utilities.")
`(("glib" ,glib)
("gtk" ,gtk+)
("gtksheet" ,gtksheet)
("guile" ,guile-2.2)
("guile" ,guile-3.0)
("shared-mime-info" ,shared-mime-info)
("m4" ,m4)
("pcb" ,pcb)))
@ -332,15 +332,19 @@ utilities.")
(string-append (assoc-ref outputs "out")
"/lib/libleptongui.so")))
(substitute* '("libleptongui/scheme/schematic/ffi/gtk.scm.in"
"libleptonattrib/lepton-attrib.scm")
"utils/attrib/lepton-attrib.scm")
(("@LIBGTK@")
(string-append (assoc-ref inputs "gtk")
"/lib/libgtk-3.so")))
(substitute* '("libleptongui/scheme/schematic/ffi/gobject.scm.in")
(("@LIBGOBJECT@")
(string-append (assoc-ref inputs "glib")
"/lib/libgobject-2.0.so")))
(substitute* "liblepton/scheme/lepton/ffi.scm.in"
(("@LIBLEPTON@")
(string-append (assoc-ref outputs "out")
"/lib/liblepton.so")))
(substitute* "libleptonattrib/lepton-attrib.scm"
(substitute* "utils/attrib/lepton-attrib.scm"
(("@LIBLEPTONATTRIB@")
(string-append (assoc-ref outputs "out")
"/lib/libleptonattrib.so")))
@ -2359,7 +2363,7 @@ comments.")))
(define-public freecad
(package
(name "freecad")
(version "0.19.1")
(version "0.19.2")
(source
(origin
(method git-fetch)
@ -2368,8 +2372,7 @@ comments.")))
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0c53q2iawy4yfp11czyc7lbr9ivp3r7v24x4c20myh11wyplffc0"))))
(base32 "0fhjv0x3dix1c7jml91yx63z9xifjlbhjbcdb73lw80smpxrq7mm"))))
(build-system qt-build-system)
(native-inputs
`(("doxygen" ,doxygen)
@ -2734,14 +2737,14 @@ GUI.")
(define-public poke
(package
(name "poke")
(version "1.1")
(version "1.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/poke/poke-" version
".tar.gz"))
(sha256
(base32
"1mkaq19a8d951n9l6d3f8rwq45a7gkr05snb285idd21qxixys6d"))))
"0qnz7lc681nxa16rw9n9q4spy9fas6m2adrpb49imh34bgdgh77n"))))
(build-system gnu-build-system)
;; The GUI, which we elide, requires tcl and tk.
(native-inputs `(("bison" ,bison)

6
gnu/packages/enlightenment.scm
View File

@ -36,6 +36,7 @@
#:use-module (gnu packages code)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#:use-module (gnu packages fonts)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages fribidi)
@ -370,7 +371,10 @@ Libraries with some extra bells and whistles.")
(propagated-inputs
`(("efl" ,efl)
("libxkbcommon" ,libxkbcommon)
("wayland-protocols" ,wayland-protocols)))
("wayland-protocols" ,wayland-protocols)
;; Default font that applications such as IceCat require.
("font-dejavu" ,font-dejavu)))
(home-page "https://www.enlightenment.org/about-enlightenment")
(synopsis "Lightweight desktop environment")
(description

4
gnu/packages/fcitx.scm
View File

@ -50,7 +50,7 @@
(define-public fcitx-qt5
(package
(name "fcitx-qt5")
(version "1.2.5")
(version "1.2.6")
(source
(origin
(method git-fetch)
@ -61,7 +61,7 @@
(file-name
(git-file-name name version))
(sha256
(base32 "1d56bp11jp85b2r4syw1clfg4vqxqfh7gygpwz8wk5sxmfmmdq83"))))
(base32 "13sanrir696fv7s44b7q453s5qi4r7ag0r3iyggyzk8xyf6rw8fk"))))
(build-system qt-build-system)
(arguments
`(#:tests? #f ; No target

13
gnu/packages/file-systems.scm
View File

@ -340,8 +340,8 @@ from a mounted file system.")
(license license:gpl2+)))
(define-public bcachefs-tools
(let ((commit "bb6eccc2ecd4728871bfc70462d3a4a20daa9d68")
(revision "4"))
(let ((commit "7942d5cab4f02bd4db12ee26a792a6012b4d7b07")
(revision "7"))
(package
(name "bcachefs-tools")
(version (git-version "0.1" revision commit))
@ -353,14 +353,15 @@ from a mounted file system.")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0ziqmcxbrak6bjck6s46hqrqx44zc97yaj0kbk3amsxf18rsfs0n"))))
(base32 "0k8cnkjm0v9xs7w02sj5151y6h8bj0gxmc3fq8js1wzx6wip9w96"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(list ,(string-append "VERSION=" version) ; bogus vX.Y-nogit otherwise
(string-append "PREFIX=" (assoc-ref %outputs "out"))
"INITRAMFS_DIR=$(PREFIX)/share/initramfs-tools"
"CC=gcc"
,(string-append "CC=" (cc-for-target))
,(string-append "PKG_CONFIG=" (pkg-config-for-target))
"PYTEST=pytest")
#:phases
(modify-phases %standard-phases
@ -472,7 +473,7 @@ from the bcachefs-tools package. It is meant to be used in initrds.")
(define-public exfatprogs
(package
(name "exfatprogs")
(version "1.1.0")
(version "1.1.1")
(source
(origin
(method git-fetch)
@ -481,7 +482,7 @@ from the bcachefs-tools package. It is meant to be used in initrds.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1ciy28lx7c1vr1f138qi0mkz88pzlkay6nlwmp1yjzd830x48549"))))
(base32 "1zl3w5w2mzyggizc4dsiln0pa013f8sf5dxmm5wflplpfm6k4brk"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags

15
gnu/packages/finance.scm
View File

@ -6,7 +6,7 @@
;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au>
;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
;;; Copyright © 2017 Vasile Dumitrascu <va511e@yahoo.com>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2018 Adriano Peluso <catonano@gmail.com>
;;; Copyright © 2018, 2019, 2020, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
@ -23,6 +23,7 @@
;;; Copyright © 2020 Carlo Holl <carloholl@gmail.com>
;;; Copyright © 2020 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2021 ZmnSCPxj jxPCSnmZ <ZmnSCPxj@protonmail.com>
;;; Copyright © 2021 François J <francois-oss@avalenn.eu>
;;;
;;; This file is part of GNU Guix.
;;;
@ -113,7 +114,7 @@
(define-public bitcoin-core-0.21
(package
(name "bitcoin-core")
(version "0.21.0")
(version "0.21.1")
(source (origin
(method url-fetch)
(uri
@ -121,7 +122,7 @@
version "/bitcoin-" version ".tar.gz"))
(sha256
(base32
"0dszcn4r43w0ffsmgwmyzkzr5lqws3bbhlkssmjgnjgfc8n2148s"))))
"1q51nqv64lhng5wh1cqb01jar7iswpnyyb1i7xslbkr0j9227zya"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
@ -762,7 +763,7 @@ the Monero command line client and daemon.")
(define-public monero-gui
(package
(name "monero-gui")
(version "0.17.2.0")
(version "0.17.2.1")
(source
(origin
(method git-fetch)
@ -779,7 +780,7 @@ the Monero command line client and daemon.")
(delete-file-recursively "monero")
#t))
(sha256
(base32 "17il26gh0g69x7lqkyb461x1712959wajg3iadx0p08djr3m13mf"))))
(base32 "17z4l7xj3zzbkb3fivsam38y5psknc2qbsg6yc72vb6n675khnsa"))))
(build-system qt-build-system)
(native-inputs
`(,@(package-native-inputs monero)
@ -1588,14 +1589,14 @@ that allows you to run services and through them access the Bitcoin Cash network
(define-public beancount
(package
(name "beancount")
(version "2.2.3")
(version "2.3.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "beancount" version))
(sha256
(base32
"0pcfl2rx2ng06i4f9izdpnlnb1k0rdzsckbzzn4cn4ixfzyssm0m"))
"1h465zc7gb0bc5pagm9fsp083sqxrn2mjfbk9l7h162xm7k8rw1b"))
(patches (search-patches "beancount-disable-googleapis-fonts.patch"))))
(build-system python-build-system)
(arguments

29
gnu/packages/fonts.scm
View File

@ -39,6 +39,7 @@
;;; Copyright © 2020 Tim Van den Langenbergh <tmt_vdl@gmx.com>
;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; Copyright © 2021 Antoine Côté <antoine.cote@posteo.net>
;;; Copyright © 2021 Sergiu Ivanov <sivanov@colimite.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -334,15 +335,15 @@ The Lato 2.010 family supports more than 100 Latin-based languages, over
(define-public font-liberation
(package
(name "font-liberation")
(version "2.1.3")
(version "2.1.4")
(source
(origin
(method url-fetch)
(uri (string-append
"https://github.com/liberationfonts/liberation-fonts/"
"files/6060976/liberation-fonts-ttf-" version ".tar.gz"))
"files/6418984/liberation-fonts-ttf-" version ".tar.gz"))
(sha256
(base32 "0bv8i47iq2irxkkjlqwdli4zz01sb1qg2n6vbdqjrqqhx912zji2"))))
(base32 "1vx5q5bif9d1cn5pvm78203sf4may2mch72aa1hx1a8avl959y16"))))
(build-system font-build-system)
(home-page "https://github.com/liberationfonts")
(synopsis "Fonts compatible with Arial, Times New Roman, and Courier New")
@ -2156,3 +2157,25 @@ suitable for a wide range of uses.")
(description "Cozette is a 6x13px (bounding box) bitmap font based on Dina
and heavily inspired by Creep.")
(license license:expat)))
(define-public font-montserrat
(package
(name "font-montserrat")
(version "7.210")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JulietaUla/Montserrat")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0jn1yvfamq5xazw85sfnxgriji60g7mkss9mkf8d0117vdk838bn"))))
(build-system font-build-system)
(home-page "https://github.com/JulietaUla/Montserrat")
(synopsis "The Montserrat font")
(description "The old posters and signs in the traditional Montserrat
neighborhood of Buenos Aires inspired Julieta Ulanovsky to design this
typeface and rescue the beauty of urban typography that emerged in the first
half of the twentieth century.")
(license license:silofl1.1)))

6
gnu/packages/fontutils.scm
View File

@ -6,7 +6,7 @@
;;; Copyright © 2017 Rene Saavedra <rennes@openmailbox.org>
;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2017 Nikita <nikita@n0.is>
;;; Copyright © 2017, 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017, 2018, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2019, 2020 Marius Bakke <mbakke@fastmail.com>
@ -833,7 +833,7 @@ maintain the Noto Fonts project.")
(define-public fcft
(package
(name "fcft")
(version "2.3.2")
(version "2.3.3")
(home-page "https://codeberg.org/dnkl/fcft")
(source (origin
(method git-fetch)
@ -841,7 +841,7 @@ maintain the Noto Fonts project.")
(file-name (git-file-name name version))
(sha256
(base32
"0k2i57rakm4g86f7hbhkby8af0vv7v63a70lk3m58mkycpy5q2rm"))))
"0314r038jl17hrhc9nrbx30jk0pz8ckbdnizws4r46b1rf4h0b1f"))))
(build-system meson-build-system)
(arguments
`(#:meson ,meson-0.55))

4
gnu/packages/fpga.scm
View File

@ -349,7 +349,7 @@ FOSS FPGA place and route tool.")
(define-public gtkwave
(package
(name "gtkwave")
(version "3.3.108")
(version "3.3.109")
(source
(origin
(method url-fetch)
@ -359,7 +359,7 @@ FOSS FPGA place and route tool.")
(string-append "http://gtkwave.sourceforge.net/"
"gtkwave-" version ".tar.gz")))
(sha256
(base32 "0fzbap72zm4ka6n85j0873fpaarrx199ay0kjw1avrs20hs4gr7c"))))
(base32 "0pf0qf40wggn03v3w5hm35vsg5n0src10n769nx8d03jkdg7wj6a"))))
(build-system gnu-build-system)
(native-inputs
`(("gperf" ,gperf)

10
gnu/packages/freedesktop.scm
View File

@ -12,7 +12,7 @@
;;; Copyright © 2017, 2018, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017, 2018, 2019 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2017, 2020 Brendan Tildesley <mail@brendan.scot>
;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2018 Stefan Stefanović <stefanx2ovic@gmail.com>
;;; Copyright © 2019 Reza Alizadeh Majd <r.majd@pantherx.org>
@ -524,7 +524,7 @@ other applications that need to directly deal with input devices.")
(define-public libxdg-basedir
(package
(name "libxdg-basedir")
(version "1.2.0")
(version "1.2.3")
(source (origin
(method git-fetch)
(uri (git-reference
@ -533,10 +533,12 @@ other applications that need to directly deal with input devices.")
(file-name (git-file-name name version))
(sha256
(base32
"12yz53ny5bi2dii3zwcr6b9ay0yy1g1xv13jg097k7gjligcq11m"))))
"0j8fgp41kxipzdnqsdy83d7w6kadbc45n98qyr84zsj46wl582vv"))))
(build-system gnu-build-system)
(arguments
'(#:phases
'(#:configure-flags
(list "--disable-static")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-autogen
(lambda _

10
gnu/packages/ftp.scm
View File

@ -32,6 +32,7 @@
#:use-module (gnu packages cpio)
#:use-module (gnu packages compression)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gettext)
#:use-module (gnu packages glib)
#:use-module (gnu packages gtk)
@ -175,20 +176,21 @@ as required.")
(define-public libfilezilla
(package
(name "libfilezilla")
(version "0.24.1")
(version "0.28.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://download.filezilla-project.org/"
"libfilezilla/libfilezilla-" version ".tar.bz2"))
(sha256
(base32 "1zfnqbn14dx0fl45mfaznr5n5xsxy1kx8z9f80fppbqn37pb9mgx"))))
(base32 "0f0n0kkhclp387glmc758134z4l0qk8935mi523q60b11q3j3h77"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
(list "--disable-static")))
(native-inputs
`(("cppunit" ,cppunit)
("gcc" ,gcc-8) ; XXX remove when it's the default
("gettext" ,gettext-minimal)
("pkg-config" ,pkg-config)))
(inputs
@ -218,14 +220,14 @@ output.
(define-public filezilla
(package
(name "filezilla")
(version "3.50.0")
(version "3.53.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://download.filezilla-project.org/client/"
"FileZilla_" version "_src.tar.bz2"))
(sha256
(base32 "042w2f5cf8g9cr7d3m6294ygx7jggcria9502jnql855khk8gnz0"))))
(base32 "0ygpqfzj5ms1pd46fpfya1y1jl4w2kmaa7plf8n6fm7cxbr78s35"))))
(build-system gnu-build-system)
(arguments
;; Don't let filezilla phone home to check for updates.

4
gnu/packages/game-development.scm
View File

@ -1765,7 +1765,7 @@ scripted in a Python-like language.")
(define-public entt
(package
(name "entt")
(version "3.7.0")
(version "3.7.1")
(source (origin
(method git-fetch)
(uri (git-reference
@ -1774,7 +1774,7 @@ scripted in a Python-like language.")
(file-name (git-file-name name version))
(sha256
(base32
"0nzvnhiw3r6nkmxp749zwxc8kzja09nijyxibdbri3g2i7pysf58"))))
"151jg3m262xwaywl2rqnc90yr6p48rhmgi5mxyv6bwqvmfli2m5p"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list "-DENTT_BUILD_TESTING=ON"

121
gnu/packages/games.scm
View File

@ -59,6 +59,7 @@
;;; Copyright © 2021 Olivier Rojon <o.rojon@posteo.net>
;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
;;; Copyright © 2021 David Pflug <david@pflug.io>
;;;
;;; This file is part of GNU Guix.
;;;
@ -1623,6 +1624,50 @@ destroying an ancient book using a special wand.")
;; license. The whole package is released under GPLv3+.
(license license:gpl3+)))
(define-public gnome-2048
(package
(name "gnome-2048")
(version "3.38.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/gnome-2048/"
(version-major+minor version) "/"
"gnome-2048-" version ".tar.xz"))
(sha256
(base32
"0s5fg4z5in1h39fcr69j1qc5ynmg7a8mfprk3mc3c0csq3snfwz2"))))
(build-system meson-build-system)
(arguments
'(#:glib-or-gtk? #t
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-gtk-update-icon-cache
;; Don't create 'icon-theme.cache'.
(lambda _
(substitute* "meson_post_install.py"
(("gtk-update-icon-cache") "true"))
#t)))))
(inputs
`(("gtk+" ,gtk+)
("clutter" ,clutter)
("clutter-gtk" ,clutter-gtk)
("libgee" ,libgee)
("libgnome-games-support" ,libgnome-games-support)))
(native-inputs
`(("gettext" ,gettext-minimal)
("glib:bin" ,glib "bin") ; for desktop-file-validate and appstream-util
("itstool" ,itstool)
("libxml2" ,libxml2)
("pkg-config" ,pkg-config)
("vala" ,vala)))
(home-page "https://wiki.gnome.org/Apps/2048")
(synopsis "Move the tiles until you obtain the 2048 tile")
(description "GNOME 2048 provides a 2D grid for playing 2048, a
single-player sliding tile puzzle game. The objective of the game is to merge
together adjacent tiles of the same number until the sum of 2048 is achieved
in one tile.")
(license license:gpl3+)))
(define-public gnome-chess
(package
(name "gnome-chess")
@ -3017,7 +3062,7 @@ a C library, so they can easily be integrated into other programs.")
(define-public taisei
(package
(name "taisei")
(version "1.3.1")
(version "1.3.2")
(source
(origin
(method url-fetch)
@ -3025,7 +3070,7 @@ a C library, so they can easily be integrated into other programs.")
"taisei/releases/download/v" version
"/taisei-v" version ".tar.xz"))
(sha256
(base32 "11f9mlqmzy1lszwcc1nsbar9q1hs4ml6pbm52hqfd4q0f4x3ln46"))))
(base32 "1g53fcyrlzmvlsb40pw90gaglysv6n1w42hk263iv61ibhdmzh6v"))))
(build-system meson-build-system)
(arguments
`(#:build-type "release" ;comment out for bug-reporting (and cheats)
@ -3040,7 +3085,8 @@ a C library, so they can easily be integrated into other programs.")
("python-docutils" ,python-docutils)
("python-pygments" ,python-pygments)))
(inputs
`(("freetype" ,freetype)
`(("cglm" ,cglm)
("freetype" ,freetype)
("libpng" ,libpng)
("libwebp" ,libwebp)
("libzip" ,libzip)
@ -3118,6 +3164,16 @@ asynchronously and at a user-defined speed.")
(base32
"0ilq4bfl0lwyzf11q7n2skydjhalfn3bgxhrp5hjxs5bc5d6fdp5"))))
(build-system gnu-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'install 'fix-shell-scripts
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(chdir bin)
(substitute* '("gnuchessx" "gnuchessu")
(("^gnuchess") (string-append bin "/gnuchess")))))))))
(home-page "https://www.gnu.org/software/chess/")
(synopsis "Full chess implementation")
(description "GNU Chess is a chess engine. It allows you to compete
@ -3279,8 +3335,27 @@ exec ~a/bin/freedink -refdir ~a/share/dink\n"
(base32
"1mkh36xnnacnz9r00b5f9ld9309k32jv6mcavklbdnca8bl56bib"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; Fixes https://issues.guix.gnu.org/47195.
(add-after 'unpack 'patch-aplay-path
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "xboard.conf"
(("aplay -q")
(string-append (assoc-ref inputs "alsa-utils") "/bin/aplay -q")))))
;; Fixes https://issues.guix.gnu.org/45236.
(add-after 'unpack 'patch-default-engine
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "xboard.conf"
(("-firstChessProgram fairymax")
(string-append "-firstChessProgram "
(assoc-ref inputs "chess")
"/bin/gnuchessx"))))))))
(inputs
`(("gtk+" ,gtk+-2)
`(("alsa-utils" ,alsa-utils)
("chess" ,chess)
("gtk+" ,gtk+-2)
("librsvg" ,librsvg)))
(native-inputs
`(("texinfo" ,texinfo)
@ -4528,7 +4603,7 @@ Transport Tycoon Deluxe.")
(define-public openrct2
(package
(name "openrct2")
(version "0.3.2")
(version "0.3.3")
(source
(origin
(method git-fetch)
@ -4537,7 +4612,7 @@ Transport Tycoon Deluxe.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1fd32wniiy6qz2046ppqfj2sb3rf2qf086rf9v1bdhyj254d0b1z"))))
(base32 "01nanpbz5ycdhkyd46fjfvj18sw729l4vk7xg12600f9rjngjk76"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list "-DDOWNLOAD_OBJECTS=OFF"
@ -4644,7 +4719,18 @@ are only two levels to play with, but they are very addictive.")
(base32
"07b3xdd81n8ybsb4fzc5lx0813y9crzp1hj69khncf4faj48sdcs"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; Fixes https://issues.guix.gnu.org/47131.
(add-after 'unpack 'patch-beep-path
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "client/gtk/audio.c"
(("\"beep\"")
(string-append "\"" (assoc-ref inputs "beep") "/bin/beep\"")))
#t)))))
(inputs `(("avahi" ,avahi)
("beep" ,beep)
("gtk+" ,gtk+)
("librsvg" ,librsvg)))
(native-inputs `(("intltool" ,intltool)
@ -5498,7 +5584,7 @@ a style similar to the original Super Mario games.")
(define-public tintin++
(package
(name "tintin++")
(version "2.02.05")
(version "2.02.11")
(source
(origin
(method url-fetch)
@ -5506,7 +5592,7 @@ a style similar to the original Super Mario games.")
(string-drop-right version 1)
"/tintin-" version ".tar.gz"))
(sha256
(base32 "18fm9ga08mxqmblahmnlzwnl387i8mbkj4n0gffxc91d299019v3"))))
(base32 "1xdim1ckq1kgjyxmghcnvnahq1llv2y70gz3yyvzbli63vpqk4mk"))))
(inputs
`(("gnutls" ,gnutls)
("pcre" ,pcre)
@ -7416,22 +7502,25 @@ Strife, Chex Quest, and fan-created games like Harmony, Hacx and Freedoom.")
(define-public odamex
(package
(name "odamex")
(version "0.8.3")
(version "0.9.0")
(source
(origin
(method url-fetch)
(uri (string-append
"mirror://sourceforge/odamex/Odamex/" version "/"
"odamex-src-" version ".tar.gz"))
"odamex-src-" version ".tar.bz2"))
(sha256
(base32 "0f887g87bmcq4dpcga7xc2mpxs947dkbc934ir9xs55gz6z13q96"))))
(base32 "0yfrvx8zb3chy47fyz4nik6gbh0y5608yvld4gz4y8l158qk71y1"))))
(build-system cmake-build-system)
(arguments `(#:tests? #f)) ; no tests
(native-inputs
`(("deutex" ,deutex)))
(inputs
`(("sdl" ,sdl)
("sdl-mixer" ,sdl-mixer)
`(("sdl" ,sdl2)
("sdl-mixer" ,sdl2-mixer)
("zlib" ,zlib)
("libpng" ,libpng)
("curl" ,curl-minimal)
("alsa-lib" ,alsa-lib)))
(home-page "https://odamex.net/")
(synopsis "Multiplayer Doom port")
@ -11829,6 +11918,12 @@ and chess engines.")
(lambda _
(setenv "QT_RCC_SOURCE_DATE_OVERRIDE" "1")
#t))
(add-after 'make-qt-deterministic 'disable-versioncheck
(lambda _
(substitute* "src/database/settings.cpp"
(("\"/General/onlineVersionCheck\", true")
"\"/General/onlineVersionCheck\", false"))
#t))
(replace 'configure
(lambda _
(invoke "qmake")

19
gnu/packages/gcc.scm
View File

@ -582,6 +582,20 @@ It also includes runtime support libraries for these languages.")))
(patches (search-patches "gcc-9-strmov-store-file-names.patch"
"gcc-5.0-libvtv-runpath.patch"))))))
(define-public gcc-11
(package
(inherit gcc-8)
(version "11.1.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gcc/gcc-"
version "/gcc-" version ".tar.xz"))
(sha256
(base32
"1pwxrjhsymv90xzh0x42cxfnmhjinf2lnrrf3hj5jq1rm2w6yjjc"))
(patches (search-patches "gcc-9-strmov-store-file-names.patch"
"gcc-5.0-libvtv-runpath.patch"))))))
;; Note: When changing the default gcc version, update
;; the gcc-toolchain-* definitions.
(define-public gcc gcc-8)
@ -734,6 +748,11 @@ as the 'native-search-paths' field."
(custom-gcc gcc-10 "gdc" '("d")
%generic-search-paths)))
(define-public gdc-11
(hidden-package
(custom-gcc gcc-11 "gdc" '("d")
%generic-search-paths)))
(define-public libgccjit
(package
(inherit gcc-9)

6
gnu/packages/gdb.scm
View File

@ -1,7 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2016, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2016, 2019, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
@ -45,14 +45,14 @@
(define-public gdb-10
(package
(name "gdb")
(version "10.1")
(version "10.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gdb/gdb-"
version ".tar.xz"))
(sha256
(base32
"1h32dckz1y8fnyxh22iyw8h3hnhxr79v1ng85px3ljn1xv71wbzq"))))
"0aag1c0fw875pvhjg1qp7x8pf6gf92bjv5gcic5716scacyj58da"))))
(build-system gnu-build-system)
(arguments

9
gnu/packages/gimp.scm
View File

@ -208,7 +208,7 @@ provided, as well as a framework to add new color models and data types.")
(define-public gegl
(package
(name "gegl")
(version "0.4.28")
(version "0.4.30")
(source (origin
(method url-fetch)
(uri (list (string-append "https://download.gimp.org/pub/gegl/"
@ -222,7 +222,7 @@ provided, as well as a framework to add new color models and data types.")
"/gegl-" version ".tar.xz")))
(sha256
(base32
"003ri7yv7lm2fi86ama3vlkwnz656yyib4r36hxwlk6mfy2hs48x"))))
"1pd8xkx70k0fsi1hrzrmaify7112wjmxzk0p6bi6js89yhn7h4n1"))))
(build-system meson-build-system)
(arguments
`(#:meson ,meson-0.55
@ -269,7 +269,7 @@ buffers.")
(define-public gimp
(package
(name "gimp")
(version "2.10.22")
(version "2.10.24")
(source
(origin
(method url-fetch)
@ -277,8 +277,7 @@ buffers.")
(version-major+minor version)
"/gimp-" version ".tar.bz2"))
(sha256
(base32 "1fqqyshakvdarf1jipk2n33ibqr23ni22z3d8srq13bpydblpf1d"))
(patches (search-patches "gimp-make-gegl-introspect-optional.patch"))))
(base32 "17lq6ns5qhspd171zqh76yf98xnn5n0hcl7hbhbx63cc6ribf6xx"))))
(build-system gnu-build-system)
(outputs '("out"
"doc")) ; 9 MiB of gtk-doc HTML

6
gnu/packages/gl.scm
View File

@ -9,7 +9,7 @@
;;; Copyright © 2017, 2018, 2019, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2017, 2018, 2019 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2020 Giacomo Leidi <goodoldpaul@autistici.org>
@ -712,7 +712,7 @@ OpenGL graphics API.")
(define-public libglvnd
(package
(name "libglvnd")
(version "1.3.2")
(version "1.3.3")
(home-page "https://gitlab.freedesktop.org/glvnd/libglvnd")
(source (origin
(method git-fetch)
@ -722,7 +722,7 @@ OpenGL graphics API.")
(file-name (git-file-name name version))
(sha256
(base32
"10x7fgb114r4gikdg6flszl3kwzcb9y5qa7sj9936mk0zxhjaylz"))))
"0gjk6m3gkdm12bmih2jflp0v5s1ibkixk7mrzrk0cj884m3hy1z6"))))
(build-system meson-build-system)
(arguments
'(#:configure-flags '("-Dx11=enabled")

1
gnu/packages/glib.scm
View File

@ -1045,6 +1045,7 @@ Some codes examples can be find at:
(build-system meson-build-system)
(native-inputs
`(("gettext" ,gettext-minimal)
("gsettings" ,gsettings-desktop-schemas) ; for ‘org.gnome.system.proxy’
("glib:bin" ,glib "bin") ; for glib-compile-resources
("pkg-config" ,pkg-config)))
(propagated-inputs

66
gnu/packages/gnome.scm
View File

@ -1331,6 +1331,9 @@ a debugging tool, @command{gssdp-device-sniffer}.")
`(("gssdp" ,gssdp)
("gtk+" ,gtk+)
("libsoup" ,libsoup)))
(propagated-inputs
`(;; For ‘org.gnome.system.proxy’.
("gsettings-desktop-schemas" ,gsettings-desktop-schemas)))
(synopsis "PnP API for GNOME")
(description "This package provides GUPnP, an object-oriented framework
for creating UPnP devices and control points, written in C using
@ -3221,10 +3224,10 @@ the GNOME desktop environment.")
(uri (string-append "mirror://gnome/sources/" name "/"
(version-major+minor version) "/"
name "-" version ".tar.xz"))
(patches (search-patches "libcroco-CVE-2020-12825.patch"))
(sha256
(base32
"1m110rbj5d2raxcdp4iz0qp172284945awrsbdlq99ksmqsc4zkn"))))
(replacement libcroco/fixed)
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
@ -3243,21 +3246,6 @@ XML/CSS rendering engine.")
;; LGPLv2.1-only.
(license license:lgpl2.1)))
(define libcroco/fixed
(package
(inherit libcroco)
(name "libcroco")
(version "0.6.13")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
(version-major+minor version) "/"
name "-" version ".tar.xz"))
(sha256
(base32
"1m110rbj5d2raxcdp4iz0qp172284945awrsbdlq99ksmqsc4zkn"))
(patches (search-patches "libcroco-CVE-2020-12825.patch"))))))
(define-public libgsf
(package
(name "libgsf")
@ -4881,17 +4869,18 @@ libxml to ease remote use of the RESTful API.")
("curl" ,curl)
("httpd" ,httpd)))
(propagated-inputs
;; libsoup-2.4.pc refers to all these.
;; libsoup-2.4.pc refers to all of these (except where otherwise noted)
`(("brotli" ,google-brotli)
("glib" ,glib)
("glib-networking" ,glib-networking) ; for GIO runtime modules
("libpsl" ,libpsl)
("libxml2" ,libxml2)
("sqlite" ,sqlite)
("zlib" ,zlib)))
(inputs
`(("glib-networking" ,glib-networking)
("mit-krb5" ,mit-krb5)))
(home-page "https://live.gnome.org/LibSoup/")
`(("mit-krb5" ,mit-krb5)
("ntlm_auth" ,samba))) ; For ntlm_auth support
(home-page "https://wiki.gnome.org/Projects/libsoup")
(synopsis "GLib-based HTTP Library")
(description
"LibSoup is an HTTP client/server library for GNOME. It uses GObjects
@ -5956,7 +5945,7 @@ queries upon that data.")
(define-public libgnome-games-support
(package
(name "libgnome-games-support")
(version "1.4.4")
(version "1.7.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/libgnome-games-support/"
@ -5964,16 +5953,17 @@ queries upon that data.")
"libgnome-games-support-" version ".tar.xz"))
(sha256
(base32
"1zkbmnrn161p74qg6jhsn9f66yjjzxfm13pl1klv9av8k1bax9pq"))))
(build-system gnu-build-system)
"11g1r3ppb9v8m3anks9gxf7fv1x38vmjiya3lr7zjjv328pb69d6"))))
(build-system meson-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(add-before 'check 'pre-check
(lambda _
;; Tests require a writable HOME.
(setenv "HOME" (getcwd))
#t)))))
'(#:glib-or-gtk? #t
#:phases
(modify-phases %standard-phases
(add-before 'check 'pre-check
(lambda _
;; Tests require a writable HOME.
(setenv "HOME" (getcwd))
#t)))))
(native-inputs
`(("intltool" ,intltool)
("pkg-config" ,pkg-config)
@ -8667,7 +8657,7 @@ core C library, and bindings for Python (PyGTK).")
(define-public gnome-autoar
(package
(name "gnome-autoar")
(version "0.3.1")
(version "0.3.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
@ -8675,7 +8665,7 @@ core C library, and bindings for Python (PyGTK).")
name "-" version ".tar.xz"))
(sha256
(base32
"1y6hh5dldhdq7mpbmd571zl0yadfackvifhnxvykkqqddwz72y0f"))))
"0wkwix44yg126xn1v4f2j60bv9yiyadfpzf8ifx0bvd9x5f4v354"))))
(build-system glib-or-gtk-build-system)
(native-inputs
`(("gobject-introspection" ,gobject-introspection)
@ -10608,7 +10598,7 @@ configurable file renaming. ")
(define-public workrave
(package
(name "workrave")
(version "1.10.42")
(version "1.10.43")
(source
(origin
(method git-fetch)
@ -10619,7 +10609,7 @@ configurable file renaming. ")
version)))))
(file-name (git-file-name name version))
(sha256
(base32 "03i9kk8r1wgrfkkbwikx8wxaw4r4kn62vismr2zdq5g34fkkjh95"))))
(base32 "1baa9qjzd4b3q1zy5vhvyrx0hyz17mk237373ca48647897kw4cr"))))
(build-system glib-or-gtk-build-system)
(arguments
;; The only tests are maintainer tests (in po/), which fail.
@ -10810,7 +10800,7 @@ functionality.")
(define-public gthumb
(package
(name "gthumb")
(version "3.10.2")
(version "3.10.3")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/gthumb/"
@ -10818,7 +10808,7 @@ functionality.")
"gthumb-" version ".tar.xz"))
(sha256
(base32
"14sw8d37g1lkp44dwsgyxjjsgh5pnpp4wq00mcy9p3rp30lf9spx"))))
"04n2sgasc03kiczyzkq362pjilj12hq2r5qj07lynqr9rivkzdys"))))
(build-system meson-build-system)
(arguments
`(#:glib-or-gtk? #t
@ -10932,7 +10922,7 @@ tabs, and it supports drag and drop re-ordering of terminals.")
(define-public libhandy
(package
(name "libhandy")
(version "1.2.0")
(version "1.2.2")
(source
(origin
(method git-fetch)
@ -10941,7 +10931,7 @@ tabs, and it supports drag and drop re-ordering of terminals.")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1a8wfgm2jd3gcbk1nzhq6f2xq7vkxdc9qky8p9k0za9gqi7xfg4v"))))
(base32 "0345x7gif6yjm95y62lww71lj84wfwsr2p32r3iww8shavb8scyk"))))
(build-system meson-build-system)
(arguments
`(#:configure-flags

12
gnu/packages/gnunet.scm
View File

@ -2,7 +2,7 @@
;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2014 Sree Harsha Totakura <sreeharsha@totakura.in>
;;; Copyright © 2015, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015, 2017, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2017, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Nikita <nikita@n0.is>
@ -74,14 +74,14 @@
(define-public libextractor
(package
(name "libextractor")
(version "1.10")
(version "1.11")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/libextractor/libextractor-"
version ".tar.gz"))
(sha256
(base32
"0mr38g7kfn3p050hd3hckbcz2yd3za6dwl1c26x2kjf7vnsi3vcy"))))
"13xxv11mif3m0mpk7i43mljhhaqrj52kznm1qi3qb8s6hymk7xhn"))))
(build-system gnu-build-system)
;; WARNING: Checks require /dev/shm to be in the build chroot, especially
;; not to be a symbolic link to /run/shm.
@ -115,7 +115,7 @@
(native-inputs
`(("pkg-config" ,pkg-config)))
(outputs '("out"
"static")) ; 396 KiB .a files
"static")) ; 420 KiB .a files
(arguments
`(#:configure-flags
(list (string-append "--with-ltdl="
@ -157,14 +157,14 @@ tool to extract metadata from a file and print the results.")
(define-public libmicrohttpd
(package
(name "libmicrohttpd")
(version "0.9.72")
(version "0.9.73")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/libmicrohttpd/libmicrohttpd-"
version ".tar.gz"))
(sha256
(base32
"1y1g9hk608jm4sfdbs8gql5wphalyhfdz824zl0i5x6pw3w2bs0a"))))
"0bh39irwzkv48fkw43skfgkk8ka3793bx1lm21sgw6zxi0djyyx3"))))
(build-system gnu-build-system)
(inputs
`(("curl" ,curl)

3
gnu/packages/gnupg.scm
View File

@ -72,6 +72,7 @@
#:use-module (gnu packages xml)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (guix build-system perl)
@ -996,7 +997,7 @@ them to transform your existing public key into a secret key.")
(arguments
`(#:tests? #f ; no make check
#:configure-flags (list "--prefix=/")
#:make-flags (list "CC=gcc"
#:make-flags (list ,(string-append "CC=" (cc-for-target))
(string-append "DESTDIR=" (assoc-ref %outputs "out")))))
(inputs
`(("zlib" ,zlib)))

14
gnu/packages/gnuzilla.scm
View File

@ -694,8 +694,8 @@ from forcing GEXP-PROMISE."
#:system system
#:guile-for-build guile)))
(define %icecat-version "78.9.0-guix0-preview1")
(define %icecat-build-id "20210323000000") ;must be of the form YYYYMMDDhhmmss
(define %icecat-version "78.10.0-guix0-preview1")
(define %icecat-build-id "20210419000000") ;must be of the form YYYYMMDDhhmmss
;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
@ -717,7 +717,7 @@ from forcing GEXP-PROMISE."
"firefox-" upstream-firefox-version ".source.tar.xz"))
(sha256
(base32
"0r28wrsk2k6pc922zfs5wljh8ziqm4a98lisn7409j2szhfsq0wf"))))
"0h6zl87czbhyhy3597bxqzwy4p1vsaqimkg92lw31gjbv6k434cp"))))
(upstream-icecat-base-version "78.7.0") ; maybe older than base-version
;;(gnuzilla-commit (string-append "v" upstream-icecat-base-version))
@ -1305,11 +1305,11 @@ standards of the IceCat project.")
(cpe-version . ,(first (string-split version #\-)))))))
;; Update this together with icecat!
(define %icedove-build-id "20210323000000") ;must be of the form YYYYMMDDhhmmss
(define %icedove-build-id "20210504000000") ;must be of the form YYYYMMDDhhmmss
(define-public icedove
(package
(name "icedove")
(version "78.9.0")
(version "78.10.1")
(source icecat-source)
(properties
`((cpe-name . "thunderbird_esr")))
@ -1589,7 +1589,7 @@ standards of the IceCat project.")
;; in the Thunderbird release tarball. We don't use the release
;; tarball because it duplicates the Icecat sources and only adds the
;; "comm" directory, which is provided by this repository.
,(let ((changeset "1a5cd2aa11de609116f258b413afcf113ed72f3a"))
,(let ((changeset "14a9afcfb6cc0c466e0d0b8222e85de5b2d8078d"))
(origin
(method hg-fetch)
(uri (hg-reference
@ -1598,7 +1598,7 @@ standards of the IceCat project.")
(file-name (string-append "thunderbird-" version "-checkout"))
(sha256
(base32
"0qgz9qj8gbn2ccmhvk3259ahs9p435ipvkzsysn3xj8a6klbz02w")))))
"18658r4b1f5p8jcz68l31z29ny73lic0br7gc827m72nfc85wqz3")))))
("autoconf" ,autoconf-2.13)
("cargo" ,rust "cargo")
("clang" ,clang)

4
gnu/packages/golang.scm
View File

@ -656,7 +656,7 @@ way of specifying command line options.")
'(#:import-path "gopkg.in/go-playground/assert.v1"))
(synopsis "Basic assertion library used alongside native Go testing")
(description
"This package provides bassic assertions along with building blocks for
"This package provides basic assertions along with building blocks for
custom assertions to be used alongside native Go testing.")
(license license:expat)))
@ -6837,7 +6837,7 @@ sinks and sources.")
(home-page "https://github.com/mesilliac/pulse-simple")
(synopsis "Cgo bindings to PulseAudio's Simple API")
(description
"This packages provides Cgo bindings to PulseAudio's Simple API, to play
"This package provides Cgo bindings to PulseAudio's Simple API, to play
or capture raw audio.")
(license license:expat))))

49
gnu/packages/gpodder.scm
View File

@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019, 2020, 2021 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
;;;
;;; This file is part of GNU Guix.
;;;
@ -21,25 +22,32 @@
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages check)
#:use-module (gnu packages curl)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages glib)
#:use-module (gnu packages gtk)
#:use-module (gnu packages groff)
#:use-module (gnu packages mp3)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages qt)
#:use-module (gnu packages video))
#:use-module (gnu packages video)
#:use-module (gnu packages xml))
(define-public gpodder
(package
(name "gpodder")
(version "3.10.18")
(version "3.10.19")
(source
(origin
(method git-fetch)
@ -47,7 +55,7 @@
(url "https://github.com/gpodder/gpodder")
(commit version)))
(sha256
(base32 "1d73q46sqandzbn74nfw9bzzah99z91wsxq2hcivwdgnsv2g2d8y"))
(base32 "1nx1cdwij9zy01s97aciqbkd63h4alzyvjdzdvr6wrl6hh42amrx"))
(file-name (git-file-name name version))
(patches (search-patches "gpodder-disable-updater.patch"))))
(build-system python-build-system)
@ -200,3 +208,36 @@ downloading episode status changes.")
provide an easy and reliable way of parsing RSS and Atom-based podcast feeds
in Python.")
(license license:isc)))
(define-public castget
(package
(name "castget")
(version "2.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mlj/castget")
(commit (string-append "rel_" (string-replace-substring
version "." "_")))))
(sha256
(base32 "1129x64rw587q3sdpa3lrgs0gni5f0siwbvmfz8ya4zkbhgi2ik7"))
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)
("pkg-config" ,pkg-config)
("ronn-ng" ,ronn-ng)))
(inputs `(("curl" ,curl)
("glib" ,glib)
("id3lib" ,id3lib)
("libxml2" ,libxml2)))
(synopsis "Command line podcast downloader")
(description
"castget is a simple, command-line based RSS enclosure downloader. It is
primarily intended for automatic, unattended downloading of podcasts. It uses
libcurl for the download process.")
(license license:lgpl2.1+)
(home-page "https://castget.johndal.com")))

22
gnu/packages/graph.scm
View File

@ -6,6 +6,7 @@
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru>
;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com>
;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -229,6 +230,27 @@ subplots, multiple-axes, polar charts, and bubble charts. ")
(package-with-python2 python-plotly-2.4.1))
(define-public python-louvain
(package
(name "python-louvain")
(version "0.15")
(source
(origin
(method url-fetch)
(uri (pypi-uri "python-louvain" version))
(sha256
(base32 "1sqp97fwh4asx0jr72x8hil8z8fcg2xq92jklmh2m599pvgnx19a"))))
(build-system python-build-system)
(propagated-inputs
`(("python-networkx" ,python-networkx)
("python-numpy" ,python-numpy)))
(home-page "https://github.com/taynaud/python-louvain")
(synopsis "Louvain algorithm for community detection")
(description
"This package provides a pure Python implementation of the Louvain
algorithm for community detection in large networks.")
(license license:bsd-3)))
(define-public python-louvain-0.6
(package
(name "python-louvain")
(version "0.6.1")

9
gnu/packages/graphics.scm
View File

@ -503,14 +503,14 @@ typically encountered in feature film production.")
(define-public blender
(package
(name "blender")
(version "2.91.0")
(version "2.92.0")
(source (origin
(method url-fetch)
(uri (string-append "https://download.blender.org/source/"
"blender-" version ".tar.xz"))
(sha256
(base32
"0x396lgmk0dq9115yrc36s8zwxzmjr490sr5n2y6w27y17yllyjm"))))
"15a5vffn18a920286x0avbc2rap56k6y531wgibq68r90g2cz4g7"))))
(build-system cmake-build-system)
(arguments
(let ((python-version (version-major+minor (package-version python))))
@ -527,6 +527,7 @@ typically encountered in feature film production.")
"-DWITH_INSTALL_PORTABLE=OFF"
"-DWITH_JACK=ON"
"-DWITH_MOD_OCEANSIM=ON"
"-DWITH_OPENVDB=ON"
"-DWITH_OPENSUBDIV=ON"
"-DWITH_PYTHON_INSTALL=OFF"
(string-append "-DPYTHON_LIBRARY=python" ,python-version)
@ -535,6 +536,9 @@ typically encountered in feature film production.")
(string-append "-DPYTHON_INCLUDE_DIR=" (assoc-ref %build-inputs "python")
"/include/python" ,python-version)
(string-append "-DPYTHON_VERSION=" ,python-version)
(string-append "-DPYTHON_NUMPY_INCLUDE_DIRS="
(assoc-ref %build-inputs "python-numpy")
"/lib/python" ,python-version "/site-packages/numpy/core/include/")
(string-append "-DPYTHON_NUMPY_PATH="
(assoc-ref %build-inputs "python-numpy")
"/lib/python" ,python-version "/site-packages/"))
@ -582,6 +586,7 @@ typically encountered in feature film production.")
("pugixml" ,pugixml)
("python" ,python)
("python-numpy" ,python-numpy)
("openvdb" ,openvdb)
("tbb" ,tbb)
("zlib" ,zlib)
("embree" ,embree)))

8
gnu/packages/gstreamer.scm
View File

@ -527,6 +527,7 @@ This package provides the core library and elements.")
(method url-fetch)
(uri (string-append "https://gstreamer.freedesktop.org/src/" name "/"
name "-" version ".tar.xz"))
(patches (search-patches "gst-plugins-base-fix-id3v2-invalid-read.patch"))
(sha256
(base32
"1b05kg46azrxxvq42c71071lfsnc34pw4vynnkczdqi6g0gzn16x"))))
@ -591,7 +592,9 @@ for the GStreamer multimedia library.")
(string-append
"https://gstreamer.freedesktop.org/src/" name "/"
name "-" version ".tar.xz"))
(patches (search-patches "gst-plugins-good-fix-test.patch"))
(patches (search-patches "gst-plugins-good-fix-test.patch"
"gst-plugins-good-CVE-2021-3497.patch"
"gst-plugins-good-CVE-2021-3498.patch"))
(sha256
(base32 "1929nhjsvbl4bw37nfagnfsnxz737cm2x3ayz9ayrn9lwkfm45zp"))))
(build-system meson-build-system)
@ -679,6 +682,7 @@ model to base your own plug-in on, here it is.")
(method url-fetch)
(uri (string-append "https://gstreamer.freedesktop.org/src/"
name "/" name "-" version ".tar.xz"))
(patches (search-patches "gst-plugins-bad-fix-overflow.patch"))
(sha256
(base32
"06ildd4rl6cynirv3p00d2ddf5is9svj4i7mkahldzhq24pq5mca"))))
@ -789,6 +793,7 @@ par compared to the rest.")
(uri
(string-append "https://gstreamer.freedesktop.org/src/"
name "/" name "-" version ".tar.xz"))
(patches (search-patches "gst-plugins-ugly-fix-out-of-bound-reads.patch"))
(sha256
(base32 "1nwbcv5yaib3d8icvyja3zf6lyjf5zf1hndbijrhj8j7xlia0dx3"))))
(build-system meson-build-system)
@ -849,6 +854,7 @@ think twice about shipping them.")
(string-append
"https://gstreamer.freedesktop.org/src/" name "/"
name "-" version ".tar.xz"))
(patches (search-patches "gst-libav-64channels-stack-corruption.patch"))
(sha256
(base32 "0jbzams9ggk3sq9ywv4gsl9rghyn203l2582m6l5c1sz9ka9m5in"))))
(build-system meson-build-system)

69
gnu/packages/gtk.scm
View File

@ -15,7 +15,7 @@
;;; Copyright © 2016 Patrick Hetu <patrick.hetu@auf.org>
;;; Copyright © 2016 Nikita <nikita@n0.is>
;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2018, 2020 Arun Isaac <arunisaac@systemreboot.net>
@ -26,6 +26,7 @@
;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2021 Leo Famulari <leo@famulari.name>
;;; Copyright © 2021 Simon Streit <simon@netpanic.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -98,6 +99,7 @@
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages pulseaudio)
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-26)
#:use-module (ice-9 match))
@ -2615,19 +2617,19 @@ foreground and background colors, text justification and more.")
(define-public gtkdatabox
(package
(name "gtkdatabox")
(version "0.9.3.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/gtkdatabox/gtkdatabox/"
version "/gtkdatabox-" version ".tar.gz"))
(sha256
(base32
"1rdxnjgh6v3yjqgsfmamyzpfxckzchps4kqvvz88nifmd7ckhjfh"))))
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/gtkdatabox/gtkdatabox-1/"
"gtkdatabox-" version ".tar.gz"))
(sha256
(base32 "1qykm551bx8j8pfgxs60l2vhpi8lv4r8va69zvn2594lchh71vlb"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
(inputs
`(("gtk+-2" ,gtk+-2)))
`(("gtk+" ,gtk+)))
(synopsis "Display widget for dynamic data")
(description "GtkDatabox is a widget for live display of large amounts of
fluctuating numerical data. It enables data presentation (for example, on
@ -2635,3 +2637,50 @@ linear or logarithmic scales, as dots or lines, with markers/labels) as well as
user interaction (e.g. measuring distances).")
(home-page "https://sourceforge.net/projects/gtkdatabox/")
(license license:lgpl2.1+)))
(define-public volctl
(package
(name "volctl")
(version "0.8.2")
(source (origin
(method git-fetch)
(uri (git-reference (url "https://github.com/buzz/volctl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1cx27j83pz2qffnzb85fbl1x6pp3irv1kbw7g1hri7kaw6ky4xiz"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-path
(lambda* (#:key inputs #:allow-other-keys)
(let ((pulse (assoc-ref inputs "pulseaudio"))
(xfixes (assoc-ref inputs "libxfixes")))
(substitute* "volctl/lib/xwrappers.py"
(("libXfixes.so")
(string-append xfixes "/lib/libXfixes.so")))
(substitute* "volctl/lib/pulseaudio.py"
(("libpulse.so.0")
(string-append pulse "/lib/libpulse.so.0")))
#t))))))
(inputs
`(("gtk+" ,gtk+)
("libxfixes" ,libxfixes)
("pulseaudio" ,pulseaudio)))
(propagated-inputs
`(("python-click" ,python-click)
("python-pycairo" ,python-pycairo)
("python-pygobject" ,python-pygobject)
("python-pyyaml" ,python-pyyaml)))
(home-page "https://buzz.github.io/volctl/")
(synopsis "Per-application volume control and on-screen display (OSD) for graphical desktops")
(description "Volctl is a PulseAudio-enabled tray icon volume control and
OSD applet for graphical desktops. It's not meant to be an replacement for a
full-featured mixer application. If you're looking for that check out the
excellent pavucontrol.")
;; XXX: 'setup.py' says "GPLv2" but nothing says "version 2 only". Is
;; GPLv2+ intended?
(license license:gpl2)))

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