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Merge branch 'master' into core-updates

gn-latest-20200725
Marius Bakke 2 years ago
parent
commit
bd21acf6c3
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  1. 29
      Makefile.am
  2. 146
      NEWS
  3. 12
      build-aux/compile-all.scm
  4. 5
      doc/guix.texi
  5. 30
      etc/release-manifest.scm
  6. 5
      gnu/installer.scm
  7. 4
      gnu/local.mk
  8. 16
      gnu/packages/bioconductor.scm
  9. 14
      gnu/packages/bioinformatics.scm
  10. 4
      gnu/packages/bootloaders.scm
  11. 8
      gnu/packages/cook.scm
  12. 117
      gnu/packages/cran.scm
  13. 51
      gnu/packages/dlang.scm
  14. 209
      gnu/packages/emacs-xyz.scm
  15. 32
      gnu/packages/engineering.scm
  16. 50
      gnu/packages/games.scm
  17. 3
      gnu/packages/gnome.scm
  18. 2
      gnu/packages/gnuzilla.scm
  19. 6
      gnu/packages/gpodder.scm
  20. 88
      gnu/packages/guile-xyz.scm
  21. 31
      gnu/packages/hardware.scm
  22. 8
      gnu/packages/i2p.scm
  23. 16
      gnu/packages/kawa.scm
  24. 24
      gnu/packages/linux.scm
  25. 81
      gnu/packages/lisp-xyz.scm
  26. 39
      gnu/packages/lisp.scm
  27. 4
      gnu/packages/mail.scm
  28. 4
      gnu/packages/man.scm
  29. 4
      gnu/packages/mpd.scm
  30. 4
      gnu/packages/networking.scm
  31. 8
      gnu/packages/package-management.scm
  32. 91
      gnu/packages/patches/gdm-default-session.patch
  33. 34
      gnu/packages/patches/libvpx-use-after-free-in-postproc.patch
  34. 38
      gnu/packages/patches/python-jedi-deleted-variables.patch
  35. 59
      gnu/packages/patches/txr-shell.patch
  36. 190
      gnu/packages/perl.scm
  37. 42
      gnu/packages/python-xyz.scm
  38. 21
      gnu/packages/radio.scm
  39. 4
      gnu/packages/shells.scm
  40. 81
      gnu/packages/statistics.scm
  41. 10
      gnu/packages/version-control.scm
  42. 23
      gnu/packages/video.scm
  43. 21
      gnu/packages/virtualization.scm
  44. 6
      gnu/packages/webkit.scm
  45. 1
      gnu/services/linux.scm
  46. 7
      gnu/services/shepherd.scm
  47. 43
      gnu/system/install.scm
  48. 5
      guix/scripts/weather.scm
  49. 18793
      po/doc/guix-manual.de.po
  50. 18819
      po/doc/guix-manual.es.po
  51. 502
      po/doc/guix-manual.ru.po
  52. 1262
      po/guix/de.po
  53. 1266
      po/guix/es.po
  54. 1262
      po/guix/fr.po
  55. 1266
      po/guix/pt_BR.po
  56. 9349
      po/packages/de.po
  57. 23311
      po/packages/fr.po

29
Makefile.am

@ -663,11 +663,16 @@ AM_DISTCHECK_CONFIGURE_FLAGS = \
--enable-daemon \
ac_cv_guix_test_root="$(GUIX_TEST_ROOT)"
# Name of the 'guix' package shipped in the binary tarball.
GUIX_FOR_BINARY_TARBALL = guile3.0-guix
# The self-contained tarball.
guix-binary.%.tar.xz:
$(AM_V_GEN)GUIX_PACKAGE_PATH= \
tarball=`$(top_builddir)/pre-inst-env guix pack -K -C xz \
-s "$*" --localstatedir --profile-name=current-guix guix` ; \
--fallback \
-s "$*" --localstatedir --profile-name=current-guix \
$(GUIX_FOR_BINARY_TARBALL)` ; \
cp "$$tarball" "$@.tmp" ; mv "$@.tmp" "$@"
@ -701,6 +706,16 @@ gen-AUTHORS:
"$(top_srcdir)" "$(distdir)/AUTHORS"; \
fi
# Like 'dist', but regenerate 'configure' so we get an up-to-date
# 'PACKAGE_VERSION' string. (In Gnulib, 'GNUmakefile' has a special trick to
# do that whenever a 'dist' target is used.)
dist-with-updated-version:
@echo "Running './bootstrap' for new version string..."
$(top_srcdir)/bootstrap
$(MAKE) $(AM_MAKEFLAGS) $(top_srcdir)/.version dist
.PHONY: dist-with-updated-version
#
# Release management.
@ -756,7 +771,7 @@ system_flags = $(foreach system,$(1),-s $(system))
#
# XXX: Depend on 'dist' rather than 'distcheck' to work around the Gettext
# issue described at <https://savannah.gnu.org/bugs/index.php?51027>.
release: dist
release: dist-with-updated-version
cd po; git checkout .
@if ! git diff-index --quiet HEAD; then \
echo "There are uncommitted changes; stopping." >&2 ; \
@ -770,9 +785,9 @@ release: dist
"`git rev-parse HEAD`" "$(PACKAGE_VERSION)"
git add $(top_srcdir)/gnu/packages/package-management.scm
git commit -m "gnu: guix: Update to $(PACKAGE_VERSION)."
$(top_builddir)/pre-inst-env guix build guix \
$(top_builddir)/pre-inst-env guix build $(GUIX_FOR_BINARY_TARBALL) \
$(call system_flags,$(SUPPORTED_SYSTEMS)) \
-v1 --no-grafts -K
-v1 --no-grafts --fallback
rm -f $(BINARY_TARBALLS)
$(MAKE) $(BINARY_TARBALLS)
for system in $(SUPPORTED_SYSTEMS) ; do \
@ -786,12 +801,12 @@ release: dist
git commit -m "gnu: guix: Update to `git rev-parse HEAD | cut -c1-7`."
$(top_builddir)/pre-inst-env guix build guix \
$(call system_flags,$(GUIX_SYSTEM_SUPPORTED_SYSTEMS)) \
-v1 --no-grafts -K
-v1 --no-grafts --fallback
for system in $(GUIX_SYSTEM_SUPPORTED_SYSTEMS) ; do \
image=`$(top_builddir)/pre-inst-env \
guix system disk-image \
--file-system-type=iso9660 \
--system=$$system \
--system=$$system --fallback \
gnu/system/install.scm` ; \
if [ ! -f "$$image" ] ; then \
echo "failed to produced Guix installation image for $$system" >&2 ; \
@ -804,7 +819,7 @@ release: dist
for system in $(GUIX_SYSTEM_VM_SYSTEMS) ; do \
image=`$(top_builddir)/pre-inst-env \
guix system vm-image $(GUIX_SYSTEM_VM_IMAGE_FLAGS) \
--system=$$system \
--system=$$system --fallback \
gnu/system/examples/vm-image.tmpl` ; \
if [ ! -f "$$image" ] ; then \
echo "failed to produced Guix VM image for $$system" >&2 ; \

146
NEWS

@ -2,7 +2,7 @@
#+TITLE: Guix NEWS – history of user-visible changes
#+STARTUP: content hidestars
Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
Copying and distribution of this file, with or without modification,
@ -11,6 +11,150 @@ Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
Please send Guix bug reports to bug-guix@gnu.org.
* Changes in 1.1.0 (since 1.0.1)
** Package management
*** New ‘guix deploy’ command to deploy several machines at once
*** Channels can now provide news, viewed with ‘guix pull --news’
*** ‘guix system reconfigure’ saves provenance data
*** New ‘guix system describe’ command to view system provenance info
*** New /run/current-system/{channels,configuration}.scm files
*** New ‘guix time-machine’ command
*** ‘guix pack’ has a new ‘--entry-point’ option
*** ‘guix pack’ saves environment variables for ‘docker’ and ‘singularity’
*** ‘guix pack’ provides a meaningful repository name for ‘docker’
*** New ‘--target’ option for ‘guix system’
*** ‘--no-build-hook’ was renamed to ‘--no-offload’
*** ‘--keep-failed’ now implies ‘--no-offload’
*** ‘--dry-run’ no longer implies ‘--no-grafts’
*** ‘guix import crate’ has a new ‘--recursive’ option
*** ‘guix import crate’ can import a specific package version
*** ‘guix pull’ returns Guix on Guile 3.0
*** ‘guix pull’ and ‘--with-git-url’ can clone repositories over SSH
*** ‘--with-commit’ now accepts tags
*** ‘guix challenge’ has a new ‘--diff’ option to show differences
*** ‘guix weather’ has a new ‘--display-missing’ option
*** Guix can now fetch lzip-compressed substitutes in addition to gzip
*** ‘guix publish’ supports lzip compression via ‘-C’
*** ‘guix lint -c archival’ queries Software Heritage
*** ‘guix archive’ has a new ‘-t’ option to list archive contents
*** ‘guix describe’ and similar commands emit terminal hyperlinks
*** ‘guix build’ now attempts to substitute missing .drv files
*** ‘guix package’ etc. now lock the profile they operate on
*** ‘guix pull’ honors /etc/guix/channels.scm when it exists
*** New ‘guix show’ command, synonymous with ‘guix package --show’
*** The ‘--manifest’ option can be repeated to combine manifests
*** Some commands previously lacking ‘--load-path’ now support it
** Distribution
*** The set of pre-built bootstrap “binary seeds” has been halved
*** Graphical installer has better support for non-Latin keyboard layouts
*** Graphical installer allows users to choose an HTTP/HTTPS proxy
*** Graphical installer allows users to edit the system configuration
*** New ‘kernel-loadable-modules’ field in ‘operating-system’
*** rottlog service is now part of ‘%base-services’
*** ‘%base-services’ now includes /usr/bin/env as a “special file”
*** ‘herd set-http-proxy guix-daemon URL’ can be used to set a proxy
*** ‘qemu-binfmt’ service now supports riscv32 and riscv64
*** File system UUIDs and labels are now supported for JFS
*** New services
auditd, fontconfig-file-system, getmail, gnome-keyring, kernel-module-loader,
knot-resolver, mumi, nfs, nftables, nix, pagekite, pam-mount, patchwork,
polkit-wheel, provenance, pulseaudio, sane, singularity, usb-modeswitch
*** 3514 new packages
*** 3368 package updates
Noteworthy updates:
bash 5.0.7, binutils 2.32, cups 2.3.1, emacs 26.3, enlightenment 0.23.1,
gcc-toolchain 9.3.0, gdb 9.1, ghc 8.6.5, gimp 2.10.18, glibc 2.29,
gnome 3.32.2, gnupg 2.2.20, go 1.13.9, guile 2.2.7,
icecat 68.7.0-guix0-preview1, icedtea 3.7.0, julia 1.3.1,
libreoffice 6.4.2.2, linux-libre 5.4.31, mate 1.24.0, ocaml 4.09.0,
octave 5.2.0, openjdk 12.33, perl 5.30.0, python2 2.7.16, python 3.7.4,
racket 7.6, rust 1.39.0, r 3.6.3, sbcl 2.0.3, shepherd 0.7.0, xfce 4.14.0,
xorg-server 1.20.7
** Programming interfaces
*** New build systems
copy-build-system, julia-build-system, node-build-system, qt-build-system
*** New ‘with-build-handler’ and ‘map/accumulate-builds’ in (guix store)
*** (guix gexp) has a new ‘with-parameters’ form
*** New (guix remote) module for remote evaluation of gexps
*** New ‘eval/container’ procedure in (gnu system linux-container)
*** (guix inferior) now reifies exceptions as ‘&inferior-exception’
*** (guix cve) uses the new NIST-provided JSON files instead of XML
*** New (guix json) module to map JSON objects to Scheme records
*** New (gnu installer tests) module to drive the graphical installer
*** New (guix diagnostics) module for consistent diagnostic messages
*** “Checkers” now live in (guix lint)
** Notewothy bug fixes
*** Grafts leads to inefficient substitute info retrieval
(<https://issues.guix.gnu.org/issue/22990>)
*** Grafting prevents build plan from being displayed upfront
(https://issues.guix.gnu.org/issue/28310)
*** Changing the HTTP/FTP proxy used by the daemon is inconvenient
(<https://issues.guix.gnu.org/issue/25569>)
*** ‘guix system disk-image’ successfully builds a bad image
(<https://issues.guix.gnu.org/issue/34276>)
*** Installer cannot be restarted after a failed install
(<https://issues.guix.gnu.org/issue/35543>)
*** Null pointer error when partitioning with the graphical installer
(<https://issues.guix.gnu.org/issue/35858>)
*** 'guix upgrade' misdiagnoses upgrades in the presence of propagated inputs
(<https://issues.guix.gnu.org/issue/35872>)
*** mcron randomly stops running jobs
(<https://issues.guix.gnu.org/issue/37237>)
*** Mistaken warning "guix pull was never run"
(<https://issues.guix.gnu.org/issue/38196>)
*** `guix pack --format=squashfs` fails on CentOS7
(<https://issues.guix.gnu.org/issue/40043>)
*** installer: No way to input Latin characters with non-Latin keyboard layouts
(<https://issues.guix.gnu.org/issue/40273>)
*** installer: Always add '%base-initrd-modules' to 'initrd-modules'
(<https://issues.guix.gnu.org/issue/36099>)
*** [MATE] shutdown and reboot not possible from UI
(<https://issues.guix.gnu.org/issue/40327>)
*** 'guix-daemon' honors %localstatedir, %sysconfdir, and %storedir
(<https://issues.guix.gnu.org/issue/35874>)
*** Fix ‘GUIX_LOCPATH’ quoting in ‘guix-daemon.service’ (systemd)
(<https://issues.guix.gnu.org/issue/36074>)
*** Include USB_ModeSwitch in %desktop-services
(<https://issues.guix.gnu.org/issue/35640>)
*** linux-container: Mount a new /dev/pts instance in the container
(<https://issues.guix.gnu.org/issue/36463>)
*** system: Write the timezone to /etc/timezone
(<https://issues.guix.gnu.org/issue/35746>)
*** linux-modules: Define and use a module name database
(<https://issues.guix.gnu.org/issue/34902>)
*** pack: Create /tmp in Docker images
(<https://issues.guix.gnu.org/issue/37161>)
*** guix system: Reinstalling the bootloader preserves extra menu entries
(<https://issues.guix.gnu.org/issue/36876>)
*** system: Add 'mount' and 'umount' to '%setuid-programs'
(<https://issues.guix.gnu.org/issue/37569>)
*** linux-libre: Try to aggressively gather entropy during boot
(<https://issues.guix.gnu.org/issue/37501>)
*** daemon: Make 'profiles/per-user' non-world-writable
(<https://issues.guix.gnu.org/issue/37744>)
*** linux-boot: Don't ignore options when mounting root file system
(<https://issues.guix.gnu.org/issue/37977>)
*** Files produced by syslogd are no longer world-readable
(<https://issues.guix.gnu.org/issue/40405>)
** Native language support
*** Updated translations of the manual
The manual is fully translated into Spanish, more than 85% complete in French
and German, and has preliminary translations into Russian and Chinese.
*** Updated translations of messages
This version of Guix is fully translated in Brazilian Portuguese, French,
German, and Spanish, and partially translated in 10 other languages.
* Changes in 1.0.1 (since 1.0.0)
** Package management
*** The ‘https_proxy’ environment variable is now honored

12
build-aux/compile-all.scm

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2016, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -79,6 +79,14 @@ to 'make'."
(current-processor-count))))
(loop tail)))))))))
(define (parallel-job-count*)
;; XXX: Work around memory requirements not sustainable on i686 above '-j4'
;; or so: <https://bugs.gnu.org/40522>.
(let ((count (parallel-job-count)))
(if (string-prefix? "i686" %host-type)
(min count 4)
count)))
(define (% completed total)
"Return the completion percentage of COMPLETED over TOTAL as an integer."
(inexact->exact (round (* 100. (/ completed total)))))
@ -95,7 +103,7 @@ to 'make'."
(lambda ()
(compile-files srcdir (getcwd)
(filter file-needs-compilation? files)
#:workers (parallel-job-count)
#:workers (parallel-job-count*)
#:host host
#:report-load (lambda (file total completed)
(when file

5
doc/guix.texi

@ -20919,7 +20919,7 @@ The time in seconds after which a process with no requests is killed.
@end deftp
@deffn {Scheme Procedure} nginx-php-fpm-location @
@deffn {Scheme Procedure} nginx-php-location @
[#:nginx-package nginx] @
[socket (string-append "/var/run/php" @
(version-major (package-version php)) @
@ -27340,7 +27340,8 @@ VM. To enable that you'll also have to pass the following flags to @command{qem
name=com.redhat.spice.0
@end example
You'll also need to add the @pxref{Miscellaneous Services, Spice service}.
You'll also need to add the @code{(spice-vdagent-service)} to your
system definition (@pxref{Miscellaneous Services, Spice service}).
@node Defining Services
@section Defining Services

30
etc/release-manifest.scm

@ -23,6 +23,7 @@
(guix packages)
(guix profiles)
((gnu ci) #:select (%cross-targets))
((gnu services xorg) #:select (%default-xorg-modules))
(guix utils)
(srfi srfi-1)
(srfi srfi-26))
@ -49,16 +50,17 @@ TARGET."
(define %system-packages
;; Key packages proposed by the Guix System installer.
(map specification->package
'("xorg-server" "xfce" "gnome" "mate" "enlightenment"
"openbox" "awesome" "i3-wm" "ratpoison"
"xlockmore" "slock" "libreoffice"
"connman" "network-manager" "network-manager-applet"
"openssh" "ntp" "tor"
"linux-libre" "grub-hybrid"
;; FIXME: Add IceCat when Rust is available on i686.
;;"icecat"
)))
(append (map specification->package
'("xorg-server" "xfce" "gnome" "mate" "enlightenment"
"openbox" "awesome" "i3-wm" "ratpoison"
"xlockmore" "slock" "libreoffice"
"connman" "network-manager" "network-manager-applet"
"openssh" "ntp" "tor"
"linux-libre" "grub-hybrid"
;; FIXME: Add IceCat when Rust is available on i686.
;;"icecat"
))
%default-xorg-modules))
(define %packages-to-cross-build
;; Packages that must be cross-buildable from x86_64-linux.
@ -93,6 +95,13 @@ TARGET."
%base-packages))
%hydra-supported-systems)))
(define %system-manifest
(manifest
(append-map (lambda (system)
(map (cut package->manifest-entry* <> system)
%system-packages))
'("x86_64-linux" "i686-linux")))) ;Guix System
(define %cross-manifest
(manifest
(append-map (lambda (target)
@ -115,5 +124,6 @@ TARGET."
;; Return the union of all three manifests.
(concatenate-manifests (list %base-manifest
%system-manifest
%cross-manifest
%cross-bootstrap-manifest))

5
gnu/installer.scm

@ -118,9 +118,8 @@ version of this file."
;; printed on the console.
(parameterize ((shepherd-message-port
(%make-void-port "w")))
(lambda ()
(stop-service 'term-tty2)
(start-service 'term-tty2 (list locale)))))))
(stop-service 'term-tty2)
(start-service 'term-tty2 (list locale))))))
(define* (compute-locale-step #:key
locales-name

4
gnu/local.mk

@ -943,6 +943,7 @@ dist_patch_DATA = \
%D%/packages/patches/gcc-9-strmov-store-file-names.patch \
%D%/packages/patches/gd-fix-tests-on-i686.patch \
%D%/packages/patches/gd-brect-bounds.patch \
%D%/packages/patches/gdm-default-session.patch \
%D%/packages/patches/geoclue-config.patch \
%D%/packages/patches/ghc-8.0-fall-back-to-madv_dontneed.patch \
%D%/packages/patches/ghc-testsuite-dlopen-pie.patch \
@ -1179,7 +1180,6 @@ dist_patch_DATA = \
%D%/packages/patches/libvnc-CVE-2018-20750.patch \
%D%/packages/patches/libvnc-CVE-2019-15681.patch \
%D%/packages/patches/libvpx-CVE-2016-2818.patch \
%D%/packages/patches/libvpx-use-after-free-in-postproc.patch \
%D%/packages/patches/libxslt-generated-ids.patch \
%D%/packages/patches/libxt-guix-search-paths.patch \
%D%/packages/patches/lierolibre-check-unaligned-access.patch \
@ -1385,7 +1385,6 @@ dist_patch_DATA = \
%D%/packages/patches/python-pep8-stdlib-tokenize-compat.patch \
%D%/packages/patches/python-pyfakefs-remove-bad-test.patch \
%D%/packages/patches/python-flint-includes.patch \
%D%/packages/patches/python-jedi-deleted-variables.patch \
%D%/packages/patches/python-libxml2-utf8.patch \
%D%/packages/patches/python-mox3-python3.6-compat.patch \
%D%/packages/patches/python-testtools.patch \
@ -1506,7 +1505,6 @@ dist_patch_DATA = \
%D%/packages/patches/ttfautohint-source-date-epoch.patch \
%D%/packages/patches/tomb-fix-errors-on-open.patch \
%D%/packages/patches/tuxpaint-stamps-path.patch \
%D%/packages/patches/txr-shell.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 \

16
gnu/packages/bioconductor.scm

@ -1958,14 +1958,14 @@ experiments.")
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
(version "1.20.2")
(version "1.20.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
"0mqb899wah5n7bp2lajhwy2zpqqhi18plza3i3m51rfl9n62smph"))))
"01ps97cs29qvzy5piq2l2k0yyr56rmg5cycfiqhbbvqpjrfvy60g"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
@ -3332,14 +3332,14 @@ peak definition in combination with known profile characteristics.")
(define-public r-varianttools
(package
(name "r-varianttools")
(version "1.28.0")
(version "1.28.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "VariantTools" version))
(sha256
(base32
"0aafcprsqbn1xl8jqnxfl8r2d0lmzhssqpr26lam2cprh3yk0xiv"))))
"1x57shc3slcbnc807ra1nwnjr37sqjh04n2xfwd469m4hkjb0jzh"))))
(properties `((upstream-name . "VariantTools")))
(build-system r-build-system)
(propagated-inputs
@ -3783,14 +3783,14 @@ provides reporting features.")
(define-public r-a4base
(package
(name "r-a4base")
(version "1.34.0")
(version "1.34.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Base" version))
(sha256
(base32
"0dgqyq4dnlcik5qqygnhxlhfr98sh6kmdcj2qllhrwyk0lmsfk01"))))
"1a0yk05ikk1hr1vpxynydrb5xb1hj4hdqlh9zd13n83ir89dss83"))))
(properties `((upstream-name . "a4Base")))
(build-system r-build-system)
(propagated-inputs
@ -4032,14 +4032,14 @@ position-specific scores within R and Bioconductor.")
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
(version "1.10.3")
(version "1.10.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
"18zf90iksglbs13cwr4jjwsv332a19lf4bpdmy69jz8bpwrklv22"))))
"1g07ni134cyl3jd9y19afip39kxddfgpm1jjm0rhrm7jgssp24in"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs

14
gnu/packages/bioinformatics.scm

@ -7502,13 +7502,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
(define-public r-s4vectors
(package
(name "r-s4vectors")
(version "0.24.3")
(version "0.24.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
"01f7dms4kw9ajwqlvh5s47riv748xrrs41na03byhjvn4fbdc44y"))))
"1fzs8j2d3wwfzm2fq63ywf68a4dbggyl5l098f148yn4jw7jd3bc"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
@ -7944,13 +7944,13 @@ tab-delimited (tabix) files.")
(define-public r-delayedarray
(package
(name "r-delayedarray")
(version "0.12.2")
(version "0.12.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
"09lackgix5jpm16k0mz2zkibflfb4wzidbz4q32mlxmklf40037q"))))
"02i88ll2d7r83nk0wdj28akvsz3jq19g6ixpaahfy3jy5av4byv6"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
@ -7961,6 +7961,8 @@ tab-delimited (tabix) files.")
("r-iranges" ,r-iranges)
("r-matrix" ,r-matrix)
("r-matrixstats" ,r-matrixstats)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/DelayedArray")
(synopsis "Delayed operations on array-like objects")
(description
@ -12769,7 +12771,7 @@ expression report comparing samples in an easily configurable manner.")
(define-public pigx-chipseq
(package
(name "pigx-chipseq")
(version "0.0.41")
(version "0.0.42")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
@ -12777,7 +12779,7 @@ expression report comparing samples in an easily configurable manner.")
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
"0akbxdmsjsq5fzbwaap04hqjpsfgv1l6yrc2pwgbya1xgqvcq6vy"))))
"0xbvgqpk32a8iczhvac56cacr46rdkqb0allhhpvmj940idf72bi"))))
(build-system gnu-build-system)
;; parts of the tests rely on access to the network
(arguments '(#:tests? #f))

4
gnu/packages/bootloaders.scm

@ -443,7 +443,7 @@ tree binary files. These are board description files used by Linux and BSD.")
(define u-boot
(package
(name "u-boot")
(version "2020.01")
(version "2020.04")
(source (origin
(method url-fetch)
(uri (string-append
@ -451,7 +451,7 @@ tree binary files. These are board description files used by Linux and BSD.")
"u-boot-" version ".tar.bz2"))
(sha256
(base32
"1w9ml4jl15q6ixpdqzspxjnl7d3rgxd7f99ms1xv5c8869h3qida"))))
"0wjkasnz87q86hx93inspdjfjsinmxi87bcvj30c773x0fpjlwzy"))))
(native-inputs
`(("bc" ,bc)
("bison" ,bison)

8
gnu/packages/cook.scm

@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 John Darrington <jmd@gnu.org>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -60,6 +61,13 @@
(substitute* "test/00/t0077a.sh"
(("ar qc") "ar qcU"))
;; Guix builds have LC_ALL set to "en_US.utf8", which causes
;; `date` to use a 12-hour clock instead of 24h, which in turn
;; makes t0217a.sh fail because of unexpected date output.
(substitute* "test/02/t0217a.sh"
(("export TZ")
"export TZ\nLC_ALL=POSIX\nexport LC_ALL"))
(setenv "SH" (which "sh"))
#t)))))
(native-inputs `(("bison" ,bison)

117
gnu/packages/cran.scm

@ -1559,15 +1559,20 @@ colors are provided.")
(define-public r-glue
(package
(name "r-glue")
(version "1.3.2")
(version "1.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "glue" version))
(sha256
(base32
"0alklqcf68kmccssp4j7a7fv553pyqyy6mkkfslav83inppm4d3g"))))
"1hb9j2519jv9zgkgjb25hnqi22i7zxnaksqd16m4nxa1f6gl0v7a"))))
(build-system r-build-system)
;; knitr depends on glue, so we can't add knitr here to build the
;; vignettes.
#;
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/tidyverse/glue")
(synopsis "Interpreted string literals")
(description
@ -1727,13 +1732,13 @@ you to rapidly iterate while developing a package.")
(define-public r-rcpp
(package
(name "r-rcpp")
(version "1.0.4")
(version "1.0.4.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rcpp" version))
(sha256
(base32 "1m80pdhzi2p82db5xkbwc2m3fzv6df59955yj03nlq40fj7zx4nr"))))
(base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
(build-system r-build-system)
(home-page "http://www.rcpp.org")
(synopsis "Seamless R and C++ integration")
@ -4042,14 +4047,18 @@ iVAT).")
(define-public r-xfun
(package
(name "r-xfun")
(version "0.12")
(version "0.13")
(source
(origin
(method url-fetch)
(uri (cran-uri "xfun" version))
(sha256
(base32 "0sgh8kafi9x1glmmcp1ly827pm8q7fsfngbplr41fbb4nc9363df"))))
(base32 "03iyqgx9mmdbd3qih70qzijjqcdg7k7ps5r1y6q8praanx9qvnm3"))))
(build-system r-build-system)
;; knitr itself depends on xfun
#;
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/yihui/xfun")
(synopsis "Miscellaneous functions")
(description
@ -5387,14 +5396,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).")
(define-public r-arules
(package
(name "r-arules")
(version "1.6-4")
(version "1.6-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "arules" version))
(sha256
(base32
"003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
"0bcvfn8lvcv74vv9z3kgg7yq5hm7wjqhmzadi55cbm8zxd76g84v"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)))
@ -6500,14 +6509,14 @@ vice versa), or to deal with multiple declared missing values.")
(define-public r-sjmisc
(package
(name "r-sjmisc")
(version "2.8.3")
(version "2.8.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjmisc" version))
(sha256
(base32
"0w8l9grmp4q775jrf4q6rxx36ld5daz9b0gdxyyh42xfihk6m62h"))))
"1ad7ca71w0v9ja4wb47aygczc987zz1lnjljhh2n497nzrpzzv64"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@ -6517,6 +6526,8 @@ vice versa), or to deal with multiple declared missing values.")
("r-rlang" ,r-rlang)
("r-sjlabelled" ,r-sjlabelled)
("r-tidyselect" ,r-tidyselect)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/strengejacke/sjmisc")
(synopsis "Data and variable transformation functions")
(description
@ -7905,14 +7916,14 @@ console, resulting in an interactive editing environment.")
(define-public r-survey
(package
(name "r-survey")
(version "3.37")
(version "4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "survey" version))
(sha256
(base32
"1f31dvh48gzzan13pdrwh84ls35x9116095i7mdrcbrhz809r8dy"))))
"1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)
@ -8285,14 +8296,14 @@ packages maintained by Torsten Hothorn.")
(define-public r-multcomp
(package
(name "r-multcomp")
(version "1.4-12")
(version "1.4-13")
(source
(origin
(method url-fetch)
(uri (cran-uri "multcomp" version))
(sha256
(base32
"14c2f10rz546w7ly5f4r6wnd07yj5gic38an17gxny1vf2nsff0b"))))
"1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-codetools" ,r-codetools)
@ -8630,20 +8641,22 @@ results using @code{ggplot2}.")
(define-public r-effectsize
(package
(name "r-effectsize")
(version "0.2.0")
(version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "effectsize" version))
(sha256
(base32
"1liix8rf8xq3hzi7684bl0s20iflsq6g5mxr5k59wp2qwn1i6aww"))))
"0kijp4wamkidaxysc11dd4vhvnm4wnbi87871wcbwn27k5b6i5dg"))))
(properties `((upstream-name . "effectsize")))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
("r-insight" ,r-insight)
("r-parameters" ,r-parameters)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/easystats/effectsize")
(synopsis "Indices of effect size and standardized parameters")
(description
@ -8744,14 +8757,14 @@ back to file after modifications.")
(define-public r-fs
(package
(name "r-fs")
(version "1.4.0")
(version "1.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "fs" version))
(sha256
(base32
"1ishdxrxy88w1lrn657a573wdra5v7xf1yfa1c4kss07rlynwrj7"))))
"0kksig9pk8aid9l6r250na8z8j9919jvs20lj0s6m9bcybgh74df"))))
(build-system r-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
@ -8786,18 +8799,18 @@ terminals that do not support Unicode.")
(define-public r-usethis
(package
(name "r-usethis")
(version "1.5.1")
(version "1.6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "usethis" version))
(sha256
(base32
"07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
"12iyimqyza752anj29wpfisl8nz5r25kfcqbssybg24nb4wyy146"))))
(build-system r-build-system)
(propagated-inputs
`(("r-clipr" ,r-clipr)
("r-clisymbols" ,r-clisymbols)
`(("r-cli" ,r-cli)
("r-clipr" ,r-clipr)
("r-crayon" ,r-crayon)
("r-curl" ,r-curl)
("r-desc" ,r-desc)
@ -8806,6 +8819,7 @@ terminals that do not support Unicode.")
("r-git2r" ,r-git2r)
("r-glue" ,r-glue)
("r-purrr" ,r-purrr)
("r-rematch2" ,r-rematch2)
("r-rlang" ,r-rlang)
("r-rprojroot" ,r-rprojroot)
("r-rstudioapi" ,r-rstudioapi)
@ -9175,14 +9189,14 @@ experiments using ANOVA or mixed models.")
(define-public r-lmertest
(package
(name "r-lmertest")
(version "3.1-1")
(version "3.1-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "lmerTest" version))
(sha256
(base32
"0r2vvs3nl6p8xla3gd943khb4ixp0alvspqpnz2y6n3wk8zgh3jj"))))
"1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
(properties `((upstream-name . "lmerTest")))
(build-system r-build-system)
(propagated-inputs
@ -12067,14 +12081,14 @@ users of rARPACK are advised to switch to the RSpectra package.")
(define-public r-compositions
(package
(name "r-compositions")
(version "1.40-4")
(version "1.40-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "compositions" version))
(sha256
(base32
"0z40llyij3cc80ac1vzzrpykk6ysp89bn6dyyh40fbnc4anwx69a"))))
"0l9ayz2nb2wqhl7v9hkfl7pd950ba0h6hma8zqncbcxh6xh2k7l7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayesm" ,r-bayesm)
@ -12817,14 +12831,14 @@ can be used with function approximation, eligibility traces (Singh & Sutton,
(define-public r-lemon
(package
(name "r-lemon")
(version "0.4.3")
(version "0.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "lemon" version))
(sha256
(base32
"0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
"0m9hqwi709j9iwsxn8jh63741jiyr7ppwgqaw2zkv285p3m5wvd5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@ -12833,6 +12847,7 @@ can be used with function approximation, eligibility traces (Singh & Sutton,
("r-knitr" ,r-knitr)
("r-lattice" ,r-lattice)
("r-plyr" ,r-plyr)
("r-rlang" ,r-rlang)
("r-scales" ,r-scales)))
(home-page "https://github.com/stefanedwards/lemon")
(synopsis "Freshen up your ggplot2 plots")
@ -13113,21 +13128,23 @@ classes.")
(define-public r-classint
(package
(name "r-classint")
(version "0.4-2")
(version "0.4-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "classInt" version))
(sha256
(base32
"0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv"))))
"1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
(properties `((upstream-name . "classInt")))
(build-system r-build-system)
(propagated-inputs
`(("r-class" ,r-class)
("r-e1071" ,r-e1071)
("r-kernsmooth" ,r-kernsmooth)))
(native-inputs `(("gfortran" ,gfortran)))
(native-inputs
`(("gfortran" ,gfortran)
("r-knitr" ,r-knitr)))
(home-page "https://github.com/r-spatial/classInt/")
(synopsis "Choose univariate class intervals")
(description
@ -13138,14 +13155,14 @@ univariate class intervals for mapping or other graphics purposes.")
(define-public r-spdata
(package
(name "r-spdata")
(version "0.3.3")
(version "0.3.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "spData" version))
(sha256
(base32
"1v66qkvsx77hvv5c78v760yp0hknf7xzcjir2ri3ha456mz79yl5"))))
"09l9j1vjbfyc8mikb8kliqmdjkg4xigq3zhdx98mv51flh5q87lh"))))
(properties `((upstream-name . "spData")))
(build-system r-build-system)
(propagated-inputs
@ -13215,14 +13232,14 @@ tessellation.")
(define-public r-sf
(package
(name "r-sf")
(version "0.9-0")
(version "0.9-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "sf" version))
(sha256
(base32
"117r9l3v7nkdj9bfy6qr0yz0gd5bv0pwnkc9vk2gv3xqj0h1fpf6"))))
"1qghrskqwwlwxmmvkv7knhlr1a32ngyimycasy5gfazgviljsfn4"))))
(build-system r-build-system)
(inputs
`(("gdal" ,gdal)
@ -15960,14 +15977,14 @@ in pipelines.")
(define-public r-parameters
(package
(name "r-parameters")
(version "0.6.0")
(version "0.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "parameters" version))
(sha256
(base32
"0zin3ikc013hc713n5zs0dbhc3m4nfw1vhc3924z0mrww8r241xn"))))
"0mylxkf1y6mk4kf6c57x102sf4c800pfasjcfbf1hnsh6ya0m6dy"))))
(properties `((upstream-name . "parameters")))
(build-system r-build-system)
(propagated-inputs
@ -16191,14 +16208,14 @@ are noisy or are discontinuous at the solution.")
(define-public r-txtplot
(package
(name "r-txtplot")
(version "1.0-3")
(version "1.0-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "txtplot" version))
(sha256
(base32
"1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
"00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/txtplot/")
(synopsis "Text-based plotting")
@ -17112,17 +17129,19 @@ See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
(define-public r-lhs
(package
(name "r-lhs")
(version "1.0.1")
(version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "lhs" version))
(sha256
(base32
"0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4"))))
"0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
(properties `((upstream-name . "lhs")))
(build-system r-build-system)
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/bertcarnell/lhs")
(synopsis "Latin Hypercube Samples")
(description
@ -18790,14 +18809,14 @@ Edition), John Wiley and Sons.")
(define-public r-anthropometry
(package
(name "r-anthropometry")
(version "1.13")
(version "1.14")
(source
(origin
(method url-fetch)
(uri (cran-uri "Anthropometry" version))
(sha256
(base32
"1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8"))))
"0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
(properties `((upstream-name . "Anthropometry")))
(build-system r-build-system)
(propagated-inputs
@ -18810,6 +18829,8 @@ Edition), John Wiley and Sons.")
("r-nnls" ,r-nnls)
("r-rgl" ,r-rgl)
("r-shapes" ,r-shapes)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/Anthropometry/")
(synopsis "Statistical methods for anthropometric data")
(description
@ -20804,19 +20825,21 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
(define-public r-isoband
(package
(name "r-isoband")
(version "0.2.0")
(version "0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "isoband" version))
(sha256
(base32
"1r023s73qypnvpx18znr9ymylr022m90v65mz2jasn0a1kjrfcbq"))))
"1ndlnv4g9pbd02y50sx4ffg2ccwqbi7fm2v1lh22wdd8pq33d20q"))))
(properties `((upstream-name . "isoband")))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
("r-testthat" ,r-testthat)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/wilkelab/isoband")
(synopsis "Generate isolines and isobands from regularly spaced elevation grids")
(description
@ -20924,13 +20947,13 @@ carrying out convergence diagnostics and statistical and graphical analysis of
(define-public r-httpcode
(package
(name "r-httpcode")
(version "0.2.0")
(version "0.3.0")
(source (origin
(method url-fetch)
(uri (cran-uri "httpcode" version))
(sha256
(base32
"06k853ihwzkcx4z3jzazpb03p91frqkwz18jy4fwr8j2nwyqbhgv"))))
"0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
(build-system r-build-system)
(home-page "https://github.com/sckott/httpcode")
(synopsis "HTTP status code helper")

51
gnu/packages/dlang.scm

@ -4,6 +4,7 @@
;;; Copyright © 2017 Frederick Muriithi <fredmanglis@gmail.com>
;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020 Guy Fleury Iteriteka <gfleury@disroot.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -35,9 +36,11 @@
#:use-module (gnu packages gdb)
#:use-module (gnu packages libedit)
#:use-module (gnu packages llvm)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages textutils))
#:use-module (gnu packages textutils)
#:use-module (gnu packages xorg))
(define-public rdmd
(package
@ -348,3 +351,49 @@ The design emphasis is on maximum simplicity for simple projects,
while providing the opportunity to customize things when
needed.")
(license license:expat)))
(define-public gtkd
(package
(name "gtkd")
(version "3.9.0")
(source
(origin
(method url-fetch/zipbomb)
(uri (string-append "https://gtkd.org/Downloads/sources/GtkD-"
version ".zip"))
(sha256
(base32 "0qv8qlpwwb1d078pnrf0a59vpbkziyf53cf9p6m8ms542wbcxllp"))))
(build-system gnu-build-system)
(native-inputs
`(("unzip" ,unzip)
("ldc" ,ldc)
("pkg-config" ,pkg-config)
("xorg-server-for-tests" ,xorg-server-for-tests)))
(arguments
`(#:test-target "test"
#:make-flags
`("DC=ldc2"
,(string-append "prefix=" (assoc-ref %outputs "out"))
,(string-append "libdir=" (assoc-ref %outputs "out")
"/lib"))
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'patch-makefile
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "GNUmakefile"
;; We do the tests ourselves.
(("default-goal: libs test") "default-goal: libs")
(("all: libs shared-libs test") "all: libs shared-libs")
;; Work around upstream bug.
(("\\$\\(prefix\\)\\/\\$\\(libdir\\)") "$(libdir)"))
#t))
(add-before 'check 'prepare-x
(lambda _
(system "Xvfb :1 &")
(setenv "DISPLAY" ":1")
#t)))))
(home-page "https://gtkd.org/")
(synopsis "D binding and OO wrapper of GTK+")
(description "This package provides bindings to GTK+ for D.")
(license license:lgpl2.1)))

209
gnu/packages/emacs-xyz.scm

@ -67,6 +67,7 @@
;;; Copyright © 2020 6033fe7de85d <6033fe7de85d@airmail.cc>
;;; Copyright © 2020 John Soo <jsoo1@asu.edu>
;;; Copyright © 2020 Jérémy Korwin-Zmijowski <jeremy@korwin-zmijowski.fr>
;;; Copyright © 2020 Alberto Eleuterio Flores Guerrero <barbanegra+guix@posteo.mx>
;;;
;;; This file is part of GNU Guix.
;;;
@ -596,6 +597,45 @@ Gitea, Gogs and Bitbucket. It abstracts access to API resources using only a
handful of functions that are not resource-specific.")
(license license:gpl3+))))
(define-public emacs-typit
;; Last release is from 2017.
(let ((commit "231cb7df43253b84323520b8ed70f128d37003af")
(revision "1"))
(package
(name "emacs-typit")
(version (git-version "0.2.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mrkkrp/typit.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1savrxs7xl92ifyxpxkkzv2didr7lb405h0dwz1bs1wldr5fb53f"))))
(build-system emacs-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'install 'install-dictionaries
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(site-lisp
(string-append
out "/share/emacs/site-lisp/dict")))
(mkdir-p site-lisp)
(copy-recursively "dict" site-lisp)
#t))))))
(propagated-inputs
`(("emacs-f" ,emacs-f)
("emacs-mmt" ,emacs-mmt)))
(home-page "https://github.com/mrkkrp/typit")
(synopsis "Typing game for Emacs with two difficulties")
(description "Emacs Typit is a typing game for Emacs. Words that are
picked randomly from the most frequent words in language you're practicing,
until time is up.")
(license license:gpl3+))))
(define-public emacs-scribble-mode
(let ((commit "217945d54de5e4bb207033f2116baa28f5c5ecf2")
(revision "2"))
@ -2122,6 +2162,26 @@ window).")
single buffer.")
(license license:gpl3+)))
(define-public emacs-mmt
(package
(name "emacs-mmt")
(version "0.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mrkkrp/mmt.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "13vbfc5597v0gd87qyhn10f93nb477vjpg3jlpphbax9fvkf4gav"))))
(build-system emacs-build-system)
(home-page "https://github.com/mrkkrp/mmt")
(synopsis "Classic tools to write Emacs Lisp macros")
(description "Emacs MMT is a package that contains classic tools for Emacs
Lisp developers who want to write macros with convenience.")
(license license:gpl3+)))
(define-public emacs-tablist
(package
(name "emacs-tablist")
@ -7424,29 +7484,27 @@ for search-based navigation of buffers.")
(license license:gpl2+)))
(define-public emacs-helm-ag
(let ((commit "2fc02c4ead29bf0db06fd70740cc7c364cb650ac")
(revision "1"))
(package
(name "emacs-helm-ag")
(version (git-version "0.58" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/syohex/emacs-helm-ag.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1gnn0byywbld6afcq1vp92cjvy4wlag9d1wgymnqn86c3b1bcf21"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-helm" ,emacs-helm)))
(home-page "https://github.com/syohex/emacs-helm-ag")
(synopsis "Helm interface to the Silver Searcher")
(description
"This package provides a frontend for grepping tools like ag and ack,
(package
(name "emacs-helm-ag")
(version "0.59")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/syohex/emacs-helm-ag.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0vsz2b5qw4qahlf74059z4p1grinhfz28f0psw4c3qf4jasv3b9j"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-helm" ,emacs-helm)))
(home-page "https://github.com/syohex/emacs-helm-ag")
(synopsis "Helm interface to the Silver Searcher")
(description
"This package provides a frontend for grepping tools like ag and ack,
as well as features for editing search results.")
(license license:gpl3+))))
(license license:gpl3+)))
;; There hasn't been a tag or release since 2016, so we take the latest
;; commit.
@ -12864,7 +12922,7 @@ into sections while preserving the structure imposed by any timestamps.")
(define-public emacs-org-make-toc
(package
(name "emacs-org-make-toc")
(version "0.4")
(version "0.5")
(source (origin
(method git-fetch)
(uri (git-reference
@ -12873,7 +12931,7 @@ into sections while preserving the structure imposed by any timestamps.")
(file-name (git-file-name name version))
(sha256
(base32
"0348iq3bc3rxs5bqdvskyly4agqxiapamqkfm0323620kxl70agw"))))
"180ji6nnj6qj0rs1rdp1zlcrfsqf7ikb44ym8icbp5d6al2s4hnr"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-org" ,emacs-org)
@ -14158,12 +14216,12 @@ their meaning for the current Emacs major-mode.")
(license license:gpl3+)))
(define-public emacs-org-ref
(let ((commit "8c9b5d7efb9f0c1ad5186b8203bdd017f4249129")
(revision "1"))
;; No release since June 2017.
(let ((commit "5bb9be2232db72b04754d7e4c02a3976ad422f6f")
(revision "2"))
(package
(name "emacs-org-ref")
(version (string-append "1.1.1" "-" revision "."
(string-take commit 7)))
(version (git-version "1.1.1" revision commit))
(source
(origin
(method git-fetch)
@ -14172,29 +14230,40 @@ their meaning for the current Emacs major-mode.")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1rxz0bjdsayk0slv23i07d9xhj2m7s4hsc81wc2d1cs52dkr5zmz"))))
(base32 "15gcvbfj19kyv4nxa632b261dwhb26m99plq230qhv9ssfwfgxbx"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-dash" ,emacs-dash)
("emacs-f" ,emacs-f)
("emacs-helm" ,emacs-helm)
("emacs-helm-bibtex" ,emacs-helm-bibtex)
("emacs-ivy" ,emacs-ivy)
("emacs-htmlize" ,emacs-htmlize)
("emacs-hydra" ,emacs-hydra)
("emacs-ivy" ,emacs-ivy)
("emacs-key-chord" ,emacs-key-chord)
("emacs-s" ,emacs-s)
("emacs-f" ,emacs-f)
("emacs-pdf-tools" ,emacs-pdf-tools)))
("emacs-pdf-tools" ,emacs-pdf-tools)
("emacs-s" ,emacs-s)))
(home-page "https://github.com/jkitchin/org-ref")
(synopsis "Citations, cross-references and bibliographies in org-mode")
(synopsis "Citations, cross-references and bibliographies in Org mode")
(description
"Lisp code to setup bibliography, cite, ref and label org-mode links.
Also sets up reftex and helm for org-mode citations. The links are
clickable and do things that are useful.
The default setup uses helm-bibtex.
You should really read org-ref.org in this package for details.")
"Org Ref is an Emacs library that provides rich support for citations,
labels and cross-references in Org mode.
The basic idea of Org Ref is that it defines a convenient interface to insert
citations from a reference database (e.g., from BibTeX files), and a set of
functional Org links for citations, cross-references and labels that export
properly to LaTeX, and that provide clickable functionality to the user. Org
Ref interfaces with Helm BibTeX to facilitate citation entry, and it can also
use RefTeX.
It also provides a fairly large number of utilities for finding bad citations,
extracting BibTeX entries from citations in an Org file, and functions to
create and modify BibTeX entries from a variety of sources, most notably from
a DOI.
Org Ref is especially suitable for Org documents destined for LaTeX export and
scientific publication. Org Ref is also useful for research documents and
notes.")
(license license:gpl3+))))
;; This project is unmaintained. Please use emacs-org-re-reveal instead.
@ -22407,3 +22476,59 @@ conventions.")
(description "Haskell-Snippets is a collection of YASnippet Haskell
snippets for Emacs.")
(license license:expat))))
(define-public emacs-org-roam
(package
(name "emacs-org-roam")
(version "1.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jethrokuan/org-roam.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "08pfa63k194dpk0y2gfa0nzn5lig81q0l9axkq5j4ibj6ifaap4a"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-company" ,emacs-company)
("emacs-dash" ,emacs-dash)
("emacs-emacsql-sqlite" ,emacs-emacsql)
("emacs-f" ,emacs-f)
("emacs-org-ref" ,emacs-org-ref)
("emacs-s" ,emacs-s)))
(home-page "https://github.com/jethrokuan/org-roam/")
(synopsis "Non-hierarchical note-taking with Org mode")
(description "Emacs Org Roam is a solution for taking non-hierarchical
notes with Org mode. Notes are captured without hierarchy and are connected
by tags. Notes can be found and created quickly. Org Roam should also work
as a plug-and-play solution for anyone already using Org mode for their
personal wiki.")
(license license:gpl3+)))
(define-public emacs-uml-mode
;; Package has no release. Version is extracted from "Version:" keyword in
;; main file.
(let ((commit "4c37ac1c4424b2313cd8f16ba48a98a4cc214200")
(revision "1"))
(package
(name "emacs-uml-mode")
(version (git-version "0.0.4" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ianxm/emacs-uml.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "145i4srnfvd1vyibri2a1l6p9mbjvkkwlrpi41134pbarqffcnka"))))
(build-system emacs-build-system)
(home-page "https://github.com/ianxm/emacs-uml")
(synopsis "Minor mode for editing ASCII UML sequence diagrams")
(description "Emacs UML mode is a minor mode that makes it easy to build
ASCII UML sequence diagrams in Emacs, which can be embedded in source code,
comments or emails.")
(license license:gpl3+))))

32
gnu/packages/engineering.scm