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01/01: Merge branch 'master' into core-updates
|
From: |
Ludovic Courtès |
|
Subject: |
01/01: Merge branch 'master' into core-updates |
|
Date: |
Fri, 30 Sep 2016 10:06:13 +0000 (UTC) |
civodul pushed a commit to branch core-updates
in repository guix.
commit 79355ae3e84359716f5135cc7083e72246bc8bf9
Merge: 39d6b9c 86d8f6d
Author: Ludovic Courtès <address@hidden>
Date: Fri Sep 30 12:01:32 2016 +0200
Merge branch 'master' into core-updates
Makefile.am | 11 +
configure.ac | 21 +-
doc/emacs.texi | 6 +-
doc/guix.texi | 378 ++++++-
etc/completion/bash/guix | 41 +-
etc/completion/zsh/_guix | 456 +++++++++
gnu/build/activation.scm | 3 +
gnu/build/file-systems.scm | 34 +-
gnu/local.mk | 35 +-
gnu/packages.scm | 11 +-
gnu/packages/admin.scm | 103 +-
gnu/packages/adns.scm | 8 +-
gnu/packages/algebra.scm | 30 +-
gnu/packages/animation.scm | 5 +
gnu/packages/astronomy.scm | 9 +-
gnu/packages/audio.scm | 123 ++-
gnu/packages/autotools.scm | 4 +-
gnu/packages/backup.scm | 132 ++-
gnu/packages/bioinformatics.scm | 846 ++++++++++++++--
gnu/packages/bittorrent.scm | 4 +-
gnu/packages/boost.scm | 8 +-
gnu/packages/c.scm | 3 +
gnu/packages/calendar.scm | 55 +-
gnu/packages/ccache.scm | 22 +-
gnu/packages/cdrom.scm | 8 +-
gnu/packages/certs.scm | 4 +-
gnu/packages/ci.scm | 17 +-
gnu/packages/compression.scm | 112 ++-
gnu/packages/crypto.scm | 209 +++-
gnu/packages/curl.scm | 4 +-
gnu/packages/databases.scm | 72 +-
gnu/packages/debug.scm | 20 +-
gnu/packages/dictionaries.scm | 64 +-
gnu/packages/disk.scm | 4 +-
gnu/packages/display-managers.scm | 164 +++-
gnu/packages/django.scm | 195 ++++
gnu/packages/dns.scm | 80 +-
gnu/packages/emacs.scm | 149 ++-
gnu/packages/enlightenment.scm | 149 +--
gnu/packages/finance.scm | 6 +-
gnu/packages/flashing-tools.scm | 11 +-
gnu/packages/fonts.scm | 4 +-
gnu/packages/freedesktop.scm | 75 ++
gnu/packages/game-development.scm | 4 +-
gnu/packages/games.scm | 124 ++-
gnu/packages/gd.scm | 1 +
gnu/packages/gforth.scm | 60 ++
gnu/packages/gl.scm | 31 +-
gnu/packages/glib.scm | 44 +
gnu/packages/gnome.scm | 98 +-
gnu/packages/gnunet.scm | 51 +-
gnu/packages/gnupg.scm | 1 +
gnu/packages/gnuzilla.scm | 4 +-
gnu/packages/gobby.scm | 131 +++
gnu/packages/golang.scm | 18 +-
gnu/packages/graphics.scm | 31 +-
gnu/packages/grub.scm | 8 +-
gnu/packages/gstreamer.scm | 34 +-
gnu/packages/gtk.scm | 71 +-
gnu/packages/guile-wm.scm | 85 +-
gnu/packages/guile.scm | 202 ++--
gnu/packages/haskell.scm | 1028 +++++++++++++++++++-
gnu/packages/image.scm | 176 +++-
gnu/packages/imagemagick.scm | 11 +-
gnu/packages/irc.scm | 8 +-
gnu/packages/java.scm | 27 +
gnu/packages/ldc.scm | 16 +-
gnu/packages/libftdi.scm | 4 +-
gnu/packages/libupnp.scm | 4 +-
gnu/packages/lighting.scm | 75 ++
gnu/packages/links.scm | 40 +-
gnu/packages/linux.scm | 446 +++++----
gnu/packages/lisp.scm | 65 +-
gnu/packages/llvm.scm | 28 +-
gnu/packages/lua.scm | 86 +-
gnu/packages/machine-learning.scm | 39 +-
gnu/packages/mail.scm | 195 +++-
gnu/packages/man.scm | 31 +-
gnu/packages/markdown.scm | 31 +
gnu/packages/maths.scm | 61 +-
gnu/packages/messaging.scm | 300 +++++-
gnu/packages/microcom.scm | 57 ++
gnu/packages/mpd.scm | 54 +-
gnu/packages/music.scm | 218 ++++-
gnu/packages/nano.scm | 5 +-
gnu/packages/ncurses.scm | 48 +-
gnu/packages/networking.scm | 119 ++-
gnu/packages/nfs.scm | 118 +++
gnu/packages/nickle.scm | 54 +
gnu/packages/ocaml.scm | 2 +-
gnu/packages/onc-rpc.scm | 2 +-
gnu/packages/openstack.scm | 49 +
gnu/packages/orpheus.scm | 75 +-
gnu/packages/package-management.scm | 4 +-
gnu/packages/parallel.scm | 4 +-
gnu/packages/password-utils.scm | 35 +
gnu/packages/patches/azr3.patch | 151 +++
.../patches/dtc-add-missing-symbols-to-lds.patch | 59 --
gnu/packages/patches/flashrom-use-libftdi1.patch | 70 --
gnu/packages/patches/gnupg-fix-expired-test.patch | 78 ++
.../gtk2-respect-GUIX_GTK2_IM_MODULE_FILE.patch | 15 +
.../gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch | 15 +
gnu/packages/patches/hydra-automake-1.15.patch | 63 --
.../patches/jbig2dec-ignore-testtest.patch | 24 +-
gnu/packages/patches/llvm-for-extempore.patch | 118 +++
gnu/packages/patches/lua51-pkgconfig.patch | 101 ++
.../patches/mupdf-build-with-openjpeg-2.1.patch | 38 +
gnu/packages/patches/mysql-fix-failing-test.patch | 57 --
.../patches/onionshare-fix-install-paths.patch | 39 +
gnu/packages/patches/openjpeg-CVE-2016-5157.patch | 96 ++
gnu/packages/patches/openjpeg-CVE-2016-7163.patch | 71 ++
.../patches/openssl-1.1.0-c-rehash-in.patch | 19 +
.../patches/p7zip-remove-unused-code.patch | 959 ++++++++++++++++++
gnu/packages/patches/plink-endian-detection.patch | 30 +
.../patches/python-django-fix-testcase.patch | 42 +
gnu/packages/patches/slock-CVE-2016-6866.patch | 51 +
gnu/packages/patches/steghide-fixes.patch | 71 ++
gnu/packages/patches/swish-e-format-security.patch | 33 +
gnu/packages/patches/swish-e-search.patch | 43 +
gnu/packages/pdf.scm | 85 +-
gnu/packages/perl.scm | 171 +++-
gnu/packages/python.scm | 821 +++++++++++++++-
gnu/packages/qemu.scm | 6 +-
gnu/packages/qt.scm | 10 +
gnu/packages/regex.scm | 32 +
gnu/packages/ruby.scm | 3 +-
gnu/packages/scheme.scm | 22 +-
gnu/packages/screen.scm | 2 +
gnu/packages/scribus.scm | 4 +-
gnu/packages/sdcc.scm | 69 ++
gnu/packages/search.scm | 94 +-
gnu/packages/shells.scm | 23 +
gnu/packages/shellutils.scm | 34 +
gnu/packages/ssh.scm | 2 +-
gnu/packages/statistics.scm | 507 ++++++++--
gnu/packages/suckless.scm | 8 +-
gnu/packages/tbb.scm | 75 +-
gnu/packages/telephony.scm | 22 +-
gnu/packages/terminals.scm | 86 +-
gnu/packages/tex.scm | 43 +
gnu/packages/texinfo.scm | 12 +
gnu/packages/tls.scm | 129 ++-
gnu/packages/tor.scm | 117 ++-
gnu/packages/tre.scm | 57 --
gnu/packages/u-boot.scm | 21 +-
gnu/packages/version-control.scm | 48 +-
gnu/packages/video.scm | 94 +-
gnu/packages/vim.scm | 18 +-
gnu/packages/web.scm | 252 ++++-
gnu/packages/webkit.scm | 4 +-
gnu/packages/wm.scm | 77 +-
gnu/packages/xml.scm | 180 +++-
gnu/packages/xorg.scm | 19 +
gnu/packages/zip.scm | 11 +-
gnu/services.scm | 22 +-
gnu/services/avahi.scm | 2 +-
gnu/services/base.scm | 279 ++++--
gnu/services/databases.scm | 4 +-
gnu/services/dbus.scm | 4 +-
gnu/services/desktop.scm | 11 +-
gnu/services/dict.scm | 2 +-
gnu/services/mail.scm | 14 +-
gnu/services/networking.scm | 27 +-
gnu/services/nfs.scm | 54 +
gnu/services/sddm.scm | 318 ++++++
gnu/services/spice.scm | 2 +-
gnu/services/ssh.scm | 133 ++-
gnu/services/web.scm | 6 +-
gnu/services/xorg.scm | 13 +-
gnu/system.scm | 72 +-
gnu/system/examples/lightweight-desktop.tmpl | 2 +-
gnu/system/file-systems.scm | 1 +
gnu/system/grub.scm | 72 +-
gnu/system/install.scm | 16 +-
gnu/system/linux-initrd.scm | 25 +-
gnu/system/mapped-devices.scm | 5 +-
gnu/system/vm.scm | 23 +-
gnu/tests/base.scm | 9 +-
guix/build-system/python.scm | 2 +
guix/build/ant-build-system.scm | 2 +-
guix/build/syscalls.scm | 180 ++--
guix/gexp.scm | 131 ++-
guix/gnupg.scm | 4 +-
guix/import/gem.scm | 13 +-
guix/import/pypi.scm | 13 +-
guix/import/utils.scm | 104 +-
guix/licenses.scm | 12 +-
guix/modules.scm | 155 +++
guix/packages.scm | 18 +-
guix/profiles.scm | 111 ++-
guix/scripts/build.scm | 14 +-
guix/scripts/hash.scm | 27 +-
guix/scripts/import/gnu.scm | 6 +-
guix/scripts/import/nix.scm | 4 +-
guix/scripts/offload.scm | 4 +-
guix/scripts/package.scm | 139 ++-
guix/scripts/refresh.scm | 2 +-
guix/scripts/substitute.scm | 2 +-
guix/scripts/system.scm | 9 +-
guix/ui.scm | 12 +-
tests/gexp.scm | 53 +
tests/guix-build.sh | 6 +
tests/guix-hash.sh | 16 +
tests/import-utils.scm | 5 +
tests/modules.scm | 45 +
tests/packages.scm | 59 ++
tests/profiles.scm | 3 +
207 files changed, 13650 insertions(+), 2226 deletions(-)
diff --cc gnu/local.mk
index f86fc02,b864ea9..7c44196
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@@ -507,8 -517,6 +516,7 @@@ dist_patch_DATA =
%D%/packages/patches/fasthenry-spFactor.patch \
%D%/packages/patches/findutils-localstatedir.patch \
%D%/packages/patches/findutils-test-xargs.patch \
- %D%/packages/patches/flashrom-use-libftdi1.patch \
+ %D%/packages/patches/flex-CVE-2016-6354.patch \
%D%/packages/patches/flint-ldconfig.patch \
%D%/packages/patches/fltk-shared-lib-defines.patch \
%D%/packages/patches/fltk-xfont-on-demand.patch \
@@@ -652,8 -663,8 +662,9 @@@
%D%/packages/patches/libwmf-CVE-2015-4695.patch \
%D%/packages/patches/libwmf-CVE-2015-4696.patch \
%D%/packages/patches/libxslt-generated-ids.patch \
+ %D%/packages/patches/linux-pam-no-setfsuid.patch \
%D%/packages/patches/lirc-localstatedir.patch \
+ %D%/packages/patches/llvm-for-extempore.patch \
%D%/packages/patches/lm-sensors-hwmon-attrs.patch \
%D%/packages/patches/lua-CVE-2014-5461.patch \
%D%/packages/patches/lua-pkgconfig.patch \
@@@ -749,9 -771,9 +767,10 @@@
%D%/packages/patches/python-2.7-source-date-epoch.patch \
%D%/packages/patches/python-3-deterministic-build-info.patch \
%D%/packages/patches/python-3-search-paths.patch \
+ %D%/packages/patches/python-3.4-fix-tests.patch \
+ %D%/packages/patches/python-3.5-fix-tests.patch \
%D%/packages/patches/python-dendropy-exclude-failing-tests.patch \
- %D%/packages/patches/python-disable-ssl-test.patch \
+ %D%/packages/patches/python-django-fix-testcase.patch \
%D%/packages/patches/python-fix-tests.patch \
%D%/packages/patches/python-ipython-inputhook-ctype.patch \
%D%/packages/patches/python-rarfile-fix-tests.patch \
diff --cc gnu/packages/crypto.scm
index 920c346,14084c9..88e9038
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@@ -192,27 -181,26 +181,26 @@@ communication."
version "/encfs-" version ".tar.gz"))
(sha256
(base32
- "1lfmcsk187qr6ahy8c8959p7jrk9d5rd9kcsx572850ca3zmf0la"))))
- (build-system gnu-build-system)
- (arguments
- `(#:configure-flags '("--with-boost-serialization=boost_wserialization"
- "--with-boost-filesystem=boost_filesystem")
- #:phases (modify-phases %standard-phases
- (add-before 'configure 'autoconf
- (lambda _
- (zero? (system* "autoreconf" "-vfi")))))))
+ "1906254dg5hwljh0h4gyrw09ms3b57dlhjfzhfzffv50yzpkl837"))
+ (modules '((guix build utils)))
+ ;; Remove bundled dependencies in favour of proper inputs.
+ (snippet '(for-each delete-file-recursively
+ (find-files "internal" "^tinyxml2-[0-9]"
+ #:directories? #t)))))
+ (build-system cmake-build-system)
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)
- ("gettext" ,gettext-minimal)
- ("libtool" ,libtool)
- ("perl" ,perl)
- ("pkg-config" ,pkg-config)))
- `(("gettext" ,gnu-gettext)
++ `(("gettext" ,gettext-minimal)
+
+ ;; Test dependencies.
+ ("expect" ,expect)
+ ("perl" ,perl)))
(inputs
- `(("boost" ,boost)
+ `(("attr" ,attr)
("fuse" ,fuse)
("openssl" ,openssl)
- ("rlog" ,rlog)))
+ ("tinyxml2" ,tinyxml2)))
+ (arguments
+ `(#:configure-flags (list "-DUSE_INTERNAL_TINYXML=OFF")))
(home-page "https://vgough.github.io/encfs";)
(synopsis "Encrypted virtual file system")
(description
diff --cc gnu/packages/curl.scm
index 0e1badf,5cd8086..b267497
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@@ -40,14 -40,15 +40,14 @@@
(define-public curl
(package
(name "curl")
- (version "7.50.1")
- (replacement curl-7.50.3)
- (version "7.47.0")
++ (version "7.50.3")
(source (origin
(method url-fetch)
(uri (string-append "https://curl.haxx.se/download/curl-";
version ".tar.lzma"))
(sha256
(base32
- "0qc3qp3h18v24irzw7dgg1jf39v4hnz8irv83v9lbn9rxzrpdcdj"))))
- "1n284wdqzwb4bkmv0fnh36zl6lhlzy3clw2b7pn28kpgdy09ly7p"))))
++ "1spmk0345hq0sgpwxs8d410268lmg3wf1x9v23hxff7wxki5fm4c"))))
(build-system gnu-build-system)
(outputs '("out"
"doc")) ;1.2 MiB of man3 pages
diff --cc gnu/packages/gnupg.scm
index 2817f2c,0eaeb45..c15a4af
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@@ -215,9 -243,10 +215,10 @@@ compatible to GNU Pth."
(method url-fetch)
(uri (string-append "mirror://gnupg/gnupg/gnupg-" version
".tar.bz2"))
+ (patches (search-patches "gnupg-fix-expired-test.patch"))
(sha256
(base32
- "0xcn46vcb5x5qx0bc803vpzhzhnn6wfhp7x71w9n1ahx4ak877ag"))))
+ "1pgz02gd84ab94w4xdg67p9z8kvkyr9d523bvcxxd2hviwh1m362"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
diff --cc gnu/packages/gtk.scm
index b7be57c,df79239..569d8d1
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@@ -623,9 -637,9 +637,10 @@@ application suites."
name "-" version ".tar.xz"))
(sha256
(base32
- "05xcwvy68p7f4hdhi4bgdm3aycvqqr4pr5kkkr8ba91l5yx0k9l3"))
- (patches (search-patches "gtk3-respect-GUIX_GTK3_PATH.patch"))))
+ "157nh9gg0p2avw765hrnkvr8lsh2w811397yxgjv6q5j4fzz6d1q"))
+ (patches (search-patches "gtk3-respect-GUIX_GTK3_PATH.patch"
+
"gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch"))))
+ (outputs '("out" "bin" "doc"))
(propagated-inputs
`(("at-spi2-atk" ,at-spi2-atk)
("atk" ,atk)
diff --cc gnu/packages/linux.scm
index fc7d64e,7089af3..64e8bfb
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@@ -159,69 -139,34 +159,13 @@@
(for-each delete-file (find-files out "\\.install"))
#t))))))
- (package
- (name "linux-libre-headers")
- (version version)
- (source (origin
- (method url-fetch)
- (uri (linux-libre-urls version))
- (sha256
- (base32
- "1bddh2rg645lavhjkk9z75vflba5y0g73z2fjwgbfrj5jb44x9i7"))))
- (build-system gnu-build-system)
- (native-inputs `(("perl" ,perl)))
- (arguments
- `(#:modules ((guix build gnu-build-system)
- (guix build utils)
- (srfi srfi-1))
- #:phases (alist-replace
- 'build ,(build-phase (or (%current-target-system)
- (%current-system)))
- (alist-replace
- 'install ,install-phase
- (alist-delete 'configure %standard-phases)))
#:allowed-references ()
#:tests? #f))
+ (home-page "http://www.gnu.org/software/linux-libre";)
(synopsis "GNU Linux-Libre kernel headers")
(description "Headers of the Linux-Libre kernel.")
- (license license:gpl2)
- (home-page "http://www.gnu.org/software/linux-libre/";))))
+ (license license:gpl2)))
- (define-public module-init-tools
- (package
- (name "module-init-tools")
- (version "3.16")
- (source (origin
- (method url-fetch)
- (uri (string-append
-
"mirror://kernel.org/linux/utils/kernel/module-init-tools/module-init-tools-"
- version ".tar.bz2"))
- (sha256
- (base32
- "0jxnz9ahfic79rp93l5wxcbgh4pkv85mwnjlbv1gz3jawv5cvwp1"))
- (patches (search-patches "module-init-tools-moduledir.patch"))))
- (build-system gnu-build-system)
- (arguments
- ;; FIXME: The upstream tarball lacks man pages, and building them would
- ;; require DocBook & co. We used to use Gentoo's pre-built man pages,
- ;; but they vanished. In the meantime, fake it.
- '(#:phases (alist-cons-before
- 'configure 'fake-docbook
- (lambda _
- (substitute* "Makefile.in"
- (("^DOCBOOKTOMAN.*$")
- "DOCBOOKTOMAN = true\n")))
- %standard-phases)))
- (home-page
"http://www.kernel.org/pub/linux/utils/kernel/module-init-tools/";)
- (synopsis "Tools for loading and managing Linux kernel modules")
- (description
- "Tools for loading and managing Linux kernel modules, such as `modprobe',
- `insmod', `lsmod', and more.")
- (license license:gpl2+)))
-
- (define-public libnfsidmap
- (package
- (name "libnfsidmap")
- (version "0.25")
- (source (origin
- (method url-fetch)
- (uri (string-append
- "http://www.citi.umich.edu/projects/nfsv4/linux/";
- name "/" name "-" version ".tar.gz"))
- (sha256
- (base32
- "1kzgwxzh83qi97rblcm9qj80cdvnv8kml2plz0q103j0hifj8vb5"))))
- (build-system gnu-build-system)
- (home-page
-
"http://www.citi.umich.edu/projects/nfsv4/crossrealm/libnfsidmap_config.html";)
- (synopsis
- "NFSv4 support library for name/ID mapping")
- (description "Libnfsidmap is a library holding mulitiple methods of
- mapping names to ids and visa versa, mainly for NFSv4. It provides an
- extensible array of mapping functions, currently consisting of two choices:
- the default @code{nsswitch} and the experimental @code{umich_ldap}.")
- (license (license:non-copyleft "file://COPYING"
- "See COPYING in the distribution."))))
-
(define %boot-logo-patch
;; Linux-Libre boot logo featuring Freedo and a gnu.
(origin
diff --cc gnu/packages/nano.scm
index b297885,3c4c699..01ef5dc
--- a/gnu/packages/nano.scm
+++ b/gnu/packages/nano.scm
@@@ -36,10 -37,10 +37,10 @@@
version ".tar.gz"))
(sha256
(base32
- "1vhjrcydcfxqq1719vcsvqqnbjbq2523m00dhzag5vwzkc961c5j"))))
+ "1hzazcrbwjqiw89jjvlj97q0wf385qqkzcm0870pdrixiv7yklax"))))
(build-system gnu-build-system)
(inputs
- `(("gettext" ,gnu-gettext)
+ `(("gettext" ,gettext-minimal)
("ncurses" ,ncurses)))
(home-page "http://www.nano-editor.org/";)
(synopsis "Small, user-friendly console text editor")
diff --cc gnu/packages/pdf.scm
index b2598af,61fe84e..6f779fe
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@@ -5,8 -5,8 +5,9 @@@
;;; Copyright © 2015 Paul van der Walt <address@hidden>
;;; Copyright © 2016 Roel Janssen <address@hidden>
;;; Coypright © 2016 ng0 <address@hidden>
+;;; Coypright © 2016 Efraim Flashner <address@hidden>
;;; Coypright © 2016 Marius Bakke <address@hidden>
+ ;;; Coypright © 2016 Ludovic Courtès <address@hidden>
;;;
;;; This file is part of GNU Guix.
;;;
diff --cc gnu/packages/tls.scm
index 5578e48,c73131a..5af3e57
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@@ -4,9 -4,10 +4,10 @@@
;;; Copyright © 2014 Ian Denhardt <address@hidden>
;;; Copyright © 2013, 2015 Andreas Enge <address@hidden>
;;; Copyright © 2015 David Thompson <address@hidden>
-;;; Copyright © 2015 Leo Famulari <address@hidden>
+;;; Copyright © 2015, 2016 Leo Famulari <address@hidden>
;;; Copyright © 2016 Efraim Flashner <address@hidden>
;;; Copyright © 2016 ng0 <address@hidden>
+ ;;; Copyright © 2016 Hartmut Goebel <address@hidden>
;;;
;;; This file is part of GNU Guix.
;;;