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01/02: Merge branch 'master' into core-updates
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From: |
guix-commits |
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Subject: |
01/02: Merge branch 'master' into core-updates |
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Date: |
Wed, 18 Mar 2020 14:46:17 -0400 (EDT) |
mbakke pushed a commit to branch core-updates
in repository guix.
commit c4d769d359c67680fe55c3b71e659cd31837f3ec
Merge: de2871c 4de63cf
Author: Marius Bakke <address@hidden>
AuthorDate: Wed Mar 18 19:41:08 2020 +0100
Merge branch 'master' into core-updates
doc/guix.texi | 39 +-
gnu/bootloader/grub.scm | 53 +--
gnu/local.mk | 6 +
gnu/packages/admin.scm | 6 +-
gnu/packages/agda.scm | 2 +-
gnu/packages/algebra.scm | 7 +-
gnu/packages/audio.scm | 86 ++--
gnu/packages/benchmark.scm | 6 +-
gnu/packages/bioconductor.scm | 3 +-
gnu/packages/bioinformatics.scm | 10 +-
gnu/packages/check.scm | 8 +-
gnu/packages/cook.scm | 3 +-
gnu/packages/cran.scm | 46 +-
gnu/packages/crates-io.scm | 25 +-
gnu/packages/databases.scm | 22 +-
gnu/packages/debug.scm | 54 ++-
gnu/packages/emacs-xyz.scm | 40 +-
gnu/packages/embedded.scm | 2 +-
gnu/packages/engineering.scm | 4 +-
gnu/packages/finance.scm | 11 +-
gnu/packages/fribidi.scm | 54 ++-
gnu/packages/game-development.scm | 40 +-
gnu/packages/games.scm | 17 +-
gnu/packages/gcc.scm | 33 +-
gnu/packages/geo.scm | 76 ++++
gnu/packages/gl.scm | 27 +-
gnu/packages/gnome-xyz.scm | 4 +-
gnu/packages/gnome.scm | 126 +++++-
gnu/packages/gnunet.scm | 36 +-
gnu/packages/golang.scm | 96 ++--
gnu/packages/gps.scm | 94 ++--
gnu/packages/graphics.scm | 39 +-
gnu/packages/gtk.scm | 2 +-
gnu/packages/guile-xyz.scm | 59 +++
gnu/packages/haskell-apps.scm | 35 ++
gnu/packages/image.scm | 15 +-
gnu/packages/java.scm | 100 ++---
gnu/packages/libreoffice.scm | 4 +-
gnu/packages/linux.scm | 39 +-
gnu/packages/machine-learning.scm | 21 +-
gnu/packages/mail.scm | 9 +-
gnu/packages/maths.scm | 92 ++--
gnu/packages/monitoring.scm | 6 +-
gnu/packages/music.scm | 1 +
gnu/packages/networking.scm | 10 +-
gnu/packages/opencog.scm | 12 +-
gnu/packages/openstack.scm | 49 --
gnu/packages/patches/beets-werkzeug-compat.patch | 18 +
gnu/packages/patches/bidiv-update-fribidi.patch | 50 +++
.../patches/eigen-stabilise-sparseqr-test.patch | 74 +++
.../patches/python-alembic-exceptions-cause.patch | 69 +++
.../python-flask-restful-werkzeug-compat.patch | 36 ++
.../patches/python-jedi-deleted-variables.patch | 38 ++
gnu/packages/perl-check.scm | 6 +-
gnu/packages/photo.scm | 94 ++++
gnu/packages/profiling.scm | 2 +-
gnu/packages/python-check.scm | 34 +-
gnu/packages/python-crypto.scm | 34 ++
gnu/packages/python-science.scm | 29 +-
gnu/packages/python-web.scm | 185 ++++----
gnu/packages/python-xyz.scm | 495 ++++++++++++++++-----
gnu/packages/qt.scm | 301 ++++++-------
gnu/packages/sawfish.scm | 6 +-
gnu/packages/scheme.scm | 2 +-
gnu/packages/sdl.scm | 10 +-
gnu/packages/ssh.scm | 2 +-
gnu/packages/statistics.scm | 10 +-
gnu/packages/syncthing.scm | 5 +-
gnu/packages/text-editors.scm | 4 +-
gnu/packages/tor.scm | 6 +-
gnu/packages/version-control.scm | 93 ++--
gnu/packages/video.scm | 87 +++-
gnu/packages/web.scm | 2 +-
gnu/packages/wxwidgets.scm | 16 +-
gnu/packages/xml.scm | 5 +-
gnu/services/mail.scm | 4 +-
gnu/services/networking.scm | 4 +-
gnu/services/nfs.scm | 38 +-
gnu/services/web.scm | 16 +-
gnu/system.scm | 1 +
gnu/tests/mail.scm | 29 +-
gnu/tests/networking.scm | 4 +-
gnu/tests/nfs.scm | 36 +-
gnu/tests/rsync.scm | 4 +
guix/build-system/linux-module.scm | 9 +-
guix/import/opam.scm | 2 +-
guix/store.scm | 32 +-
87 files changed, 2469 insertions(+), 952 deletions(-)
diff --cc gnu/local.mk
index 1d3d6ff,caa73d4..25f017b
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@@ -752,10 -754,9 +752,11 @@@ dist_patch_DATA =
%D%/packages/patches/azr3.patch \
%D%/packages/patches/bash-reproducible-linux-pgrp-pipe.patch \
%D%/packages/patches/bash-completion-directories.patch \
+ %D%/packages/patches/bash-linux-pgrp-pipe.patch \
%D%/packages/patches/bastet-change-source-of-unordered_set.patch \
%D%/packages/patches/bazaar-CVE-2017-14176.patch \
+ %D%/packages/patches/bc-fix-cross-compilation.patch \
+ %D%/packages/patches/beets-werkzeug-compat.patch \
%D%/packages/patches/beignet-correct-file-names.patch \
%D%/packages/patches/benchmark-unbundle-googletest.patch \
%D%/packages/patches/biber-fix-encoding-write.patch \
@@@ -1325,11 -1319,13 +1328,12 @@@
%D%/packages/patches/python-3-deterministic-build-info.patch \
%D%/packages/patches/python-3-search-paths.patch \
%D%/packages/patches/python-3-fix-tests.patch \
- %D%/packages/patches/python-3.8-search-paths.patch \
%D%/packages/patches/python-3.8-fix-tests.patch \
%D%/packages/patches/python-CVE-2018-14647.patch \
+ %D%/packages/patches/python-alembic-exceptions-cause.patch \
%D%/packages/patches/python-axolotl-AES-fix.patch \
%D%/packages/patches/python-cairocffi-dlopen-path.patch \
- %D%/packages/patches/python-cffi-x87-stack-clean.patch \
+ %D%/packages/patches/python-cross-compile.patch \
%D%/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch \
%D%/packages/patches/python-configobj-setuptools.patch \
%D%/packages/patches/python-faker-fix-build-32bit.patch \
diff --cc gnu/packages/algebra.scm
index a0f31d1,8682ecd..e2e26c8
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@@ -5,10 -5,9 +5,10 @@@
;;; Copyright © 2014, 2018 Mark H Weaver <address@hidden>
;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus <address@hidden>
;;; Copyright © 2017 Efraim Flashner <address@hidden>
- ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <address@hidden>
+ ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <address@hidden>
;;; Copyright © 2017 Marius Bakke <address@hidden>
;;; Copyright © 2017, 2019 Eric Bavier <address@hidden>
+;;; Copyright © 2019 Mathieu Othacehe <address@hidden>
;;; Copyright © 2020 Björn Höfling <address@hidden>
;;;
;;; This file is part of GNU Guix.
diff --cc gnu/packages/cran.scm
index ea7a390,565fef8..8426285
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@@ -1350,8 -1350,8 +1350,8 @@@ applications. That is, compute distanc
(base32
"1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
(build-system r-build-system)
- (inputs `(("libjpeg" ,libjpeg)))
+ (inputs `(("libjpeg" ,libjpeg-turbo)))
- (home-page "http://www.rforge.net/jpeg/";)
+ (home-page "https://www.rforge.net/jpeg/";)
(synopsis "Read and write JPEG images with R")
(description "This package provides a way to read, write and display
bitmap images stored in the JPEG format with R. It can read and write both
@@@ -9696,9 -9696,9 +9696,9 @@@ redundant complex conjugate when the in
(build-system r-build-system)
(inputs
`(("libtiff" ,libtiff)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("zlib" ,zlib)))
- (home-page "http://www.rforge.net/tiff/";)
+ (home-page "https://www.rforge.net/tiff/";)
(synopsis "Read and write TIFF images")
(description
"This package provides an easy and simple way to read, write and display
diff --cc gnu/packages/fribidi.scm
index 3eff6b1,345529b..e213192
--- a/gnu/packages/fribidi.scm
+++ b/gnu/packages/fribidi.scm
@@@ -46,3 -47,62 +46,55 @@@ Algorithm. This algorithm is used to p
or right-to-left ordering as necessary.")
(home-page "https://github.com/fribidi/fribidi";)
(license lgpl2.1+)))
+
-(define fribidi/fixed
- (package
- (inherit fribidi)
- (source
- (origin (inherit (package-source fribidi))
- (patches (search-patches "fribidi-CVE-2019-18397.patch"))))))
-
+ (define-public bidiv
+ (package
+ (name "bidiv")
+ (version "1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://debian/pool/main/b/bidiv/bidiv_"
+ version ".orig.tar.gz"))
+ (sha256
+ (base32
+ "05p5m2ihxbmc1qsgs8rjlww08fy9859fhl7xf196p8g5qygqd7cv"))
+ (patches (search-patches "bidiv-update-fribidi.patch"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; no configure
+ (add-after 'unpack 'misc-fixes
+ (lambda _
+ (substitute* "bidiv.c"
+ (("FriBidiCharType") "FriBidiParType")
+ (("&c") "(char *)&c"))
+ #t))
+ ;; We don't want to use the handwritten makefile
+ (replace 'build
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((fribidi (assoc-ref inputs "fribidi")))
+ (invoke "gcc" "-o" "bidiv" "bidiv.c"
+ ;; pkg-config --cflags fribidi
+ (string-append "-I" fribidi "/include/fribidi")
+ ;; pkg-config --libs fribidi
+ (string-append "-L" fribidi "/lib") "-lfribidi"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (man (string-append out "/share/man/man1")))
+ (install-file "bidiv" bin)
+ (install-file "bidiv.1" man))
+ #t)))
+ #:tests? #f)) ; no tests
+ (inputs
+ `(("fribidi" ,fribidi)))
+ (home-page "https://tracker.debian.org/pkg/bidiv";)
+ (synopsis "BiDi viewer - command-line tool displaying logical
Hebrew/Arabic")
+ (description "bidiv is a simple utility for converting logical-Hebrew
input
+ to visual-Hebrew output. This is useful for reading Hebrew mail messages,
+ viewing Hebrew texts, etc. It was written for Hebrew but Arabic (or other
BiDi
+ languages) should work equally well.")
+ (license gpl2+)))
diff --cc gnu/packages/gcc.scm
index 0b203d5,08afd80..09367d8
--- a/gnu/packages/gcc.scm
+++ b/gnu/packages/gcc.scm
@@@ -6,7 -6,8 +6,8 @@@
;;; Copyright © 2015, 2016, 2017, 2018, 2020 Efraim Flashner <address@hidden>
;;; Copyright © 2016 Carlos Sánchez de La Lama <address@hidden>
;;; Copyright © 2018 Tobias Geerinckx-Rice <address@hidden>
-;;; Copyright © 2018 Marius Bakke <address@hidden>
+;;; Copyright © 2018, 2020 Marius Bakke <address@hidden>
+ ;;; Copyright © 2020 Joseph LaFreniere <address@hidden>
;;;
;;; This file is part of GNU Guix.
;;;
@@@ -557,9 -531,8 +558,9 @@@ It also includes runtime support librar
version "/gcc-" version ".tar.xz"))
(sha256
(base32
- "01mj3yk7z49i49168hg2cg7qs4bsccrrnv7pjmbdlf8j2a7z0vpa"))
+ "1la2yy27ziasyf0jvzk58y1i5b5bq2h176qil550bxhifs39gqbi"))
(patches (search-patches "gcc-9-strmov-store-file-names.patch"
+ "gcc-9-libsanitizer-mode-size.patch"
"gcc-9-asan-fix-limits-include.patch"
"gcc-5.0-libvtv-runpath.patch"))))))
diff --cc gnu/packages/gnunet.scm
index 775d1f5,8ad2576..1961e6b
--- a/gnu/packages/gnunet.scm
+++ b/gnu/packages/gnunet.scm
@@@ -269,6 -270,7 +270,7 @@@ supports HTTP, HTTPS and GnuTLS."
("libextractor" ,libextractor)
("libidn" ,libidn2)
("libgcrypt" ,libgcrypt)
- ("libjpeg" ,libjpeg)
++ ("libjpeg" ,libjpeg-turbo)
("libltdl" ,libltdl)
("libmicrohttpd" ,libmicrohttpd)
("libogg" ,libogg)
diff --cc gnu/packages/image.scm
index 3850e7f,ad288b8..46ad22d
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@@ -1186,9 -1169,9 +1191,9 @@@ channels."
(propagated-inputs
;; These are all in the 'Libs.private' field of libmng.pc.
`(("lcms" ,lcms)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("zlib" ,zlib)))
- (home-page "http://www.libmng.com/";)
+ (home-page "https://www.libmng.com/";)
(synopsis "Library for handling MNG files")
(description
"Libmng is the MNG (Multiple-image Network Graphics) reference library.")
diff --cc gnu/packages/python-xyz.scm
index 6a191f6,c6d3e2c..945b89f
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@@ -67,9 -67,9 +67,10 @@@
;;; Copyright © 2019 Wiktor Żelazny <address@hidden>
;;; Copyright © 2019 Tanguy Le Carrour <address@hidden>
;;; Copyright © 2019 Mădălin Ionel Patrașcu <address@hidden>
+;;; Copyright © 2020 Riku Viitanen <address@hidden>
;;; Copyright © 2020 Jakub Kądziołka <address@hidden>
;;; Copyright © 2020 sirgazil <address@hidden>
+ ;;; Copyright © 2020 Sebastian Schott <address@hidden>
;;;
;;; This file is part of GNU Guix.
;;;