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01/01: Merge branch 'master' into core-updates
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From: |
Mark H. Weaver |
|
Subject: |
01/01: Merge branch 'master' into core-updates |
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Date: |
Mon, 30 Apr 2018 04:06:23 -0400 (EDT) |
mhw pushed a commit to branch core-updates
in repository guix.
commit 3d5ad159b336a9903b31d0be7ae052dbc8d5bfcc
Merge: c77835d 8c21c64
Author: Mark H Weaver <address@hidden>
Date: Mon Apr 30 04:03:54 2018 -0400
Merge branch 'master' into core-updates
Makefile.am | 5 +
build-aux/test-env.in | 14 +-
doc/contributing.texi | 7 +
doc/guix.texi | 67 +
doc/local.mk | 12 +-
gnu/local.mk | 15 +-
gnu/packages/admin.scm | 81 +-
gnu/packages/android.scm | 4 +-
gnu/packages/audio.scm | 15 +-
gnu/packages/benchmark.scm | 9 +-
gnu/packages/bioconductor.scm | 259 +
gnu/packages/bioinformatics.scm | 102 +-
gnu/packages/bittorrent.scm | 2 -
gnu/packages/bootloaders.scm | 25 +-
gnu/packages/cdrom.scm | 2 +-
gnu/packages/commencement.scm | 8 +-
gnu/packages/cran.scm | 353 +-
gnu/packages/cups.scm | 10 +-
gnu/packages/databases.scm | 4 +-
gnu/packages/debug.scm | 3 +-
gnu/packages/dictionaries.scm | 17 +-
gnu/packages/disk.scm | 28 +
gnu/packages/education.scm | 43 +-
gnu/packages/emacs.scm | 115 +-
gnu/packages/emulators.scm | 6 +-
gnu/packages/engineering.scm | 6 +-
gnu/packages/enlightenment.scm | 24 +-
gnu/packages/freedesktop.scm | 4 +-
gnu/packages/game-development.scm | 27 +-
gnu/packages/games.scm | 3 +-
gnu/packages/geo.scm | 8 +-
gnu/packages/gnome.scm | 48 +-
gnu/packages/gnunet.scm | 2 +-
gnu/packages/gnupg.scm | 4 +-
gnu/packages/golang.scm | 12 +-
gnu/packages/graph.scm | 11 +-
gnu/packages/gstreamer.scm | 2 +-
gnu/packages/guile.scm | 2 +-
gnu/packages/image-viewers.scm | 4 +-
gnu/packages/image.scm | 32 +-
gnu/packages/irc.scm | 9 +-
gnu/packages/java.scm | 303 +-
gnu/packages/julia.scm | 2 +-
gnu/packages/libreoffice.scm | 8 +-
gnu/packages/linux.scm | 127 +-
gnu/packages/lxde.scm | 13 +-
gnu/packages/machine-learning.scm | 44 +
gnu/packages/mail.scm | 4 +-
gnu/packages/maths.scm | 16 +-
gnu/packages/mes.scm | 9 +-
gnu/packages/messaging.scm | 36 +-
gnu/packages/mpd.scm | 4 +-
gnu/packages/music.scm | 35 +-
gnu/packages/node.scm | 4 +-
gnu/packages/package-management.scm | 11 +-
gnu/packages/parallel.scm | 6 +-
.../patches/bcftools-regidx-unsigned-char.patch | 16 -
.../patches/ceph-skip-collect-sys-info-test.patch | 11 +-
gnu/packages/patches/freeimage-unbundle.patch | 18 +-
...va-apache-ivy-port-to-latest-bouncycastle.patch | 81 +
gnu/packages/patches/pcmanfm-CVE-2017-8934.patch | 56 -
.../patches/pt-scotch-build-parallelism.patch | 13 -
gnu/packages/patches/qemu-CVE-2018-7550.patch | 66 -
gnu/packages/patches/quassel-fix-tls-check.patch | 25 -
.../patches/scotch-build-parallelism.patch | 39 +
gnu/packages/patches/scotch-graph-diam-64.patch | 27 +
.../patches/scotch-graph-induce-type-64.patch | 19 +
gnu/packages/patches/zsh-CVE-2018-7548.patch | 48 -
gnu/packages/patches/zsh-CVE-2018-7549.patch | 56 -
gnu/packages/perl-check.scm | 24 +-
gnu/packages/perl.scm | 84 +-
gnu/packages/photo.scm | 8 +-
gnu/packages/python-crypto.scm | 13 +-
gnu/packages/python-web.scm | 13 +-
gnu/packages/python.scm | 62 +-
gnu/packages/ruby.scm | 8 +-
gnu/packages/scheme.scm | 4 +-
gnu/packages/sdl.scm | 2 +-
gnu/packages/shells.scm | 10 +-
gnu/packages/spice.scm | 4 +-
gnu/packages/ssh.scm | 16 +-
gnu/packages/statistics.scm | 105 +-
gnu/packages/storage.scm | 4 +-
gnu/packages/syncthing.scm | 2 -
gnu/packages/text-editors.scm | 19 +-
gnu/packages/textutils.scm | 8 +-
gnu/packages/version-control.scm | 50 +
gnu/packages/video.scm | 91 +-
gnu/packages/virtualization.scm | 111 +-
gnu/packages/vpn.scm | 40 +-
gnu/packages/vulkan.scm | 5 +-
gnu/packages/web.scm | 16 +-
gnu/packages/xdisorg.scm | 8 +-
gnu/services/base.scm | 160 +-
gnu/services/networking.scm | 275 +-
gnu/system/file-systems.scm | 9 +-
gnu/tests/networking.scm | 98 +-
guix/download.scm | 8 +-
guix/scripts/system.scm | 24 +-
guix/ui.scm | 1 +
po/doc/contributing.fr.po | 1220 -
po/doc/contributing.pot | 962 -
po/doc/{guix.fr.po => guix-manual.fr.po} | 27043 +++++++++++--------
po/doc/{guix.pot => guix-manual.pot} | 12129 +++++----
po/doc/local.mk | 42 +-
105 files changed, 25373 insertions(+), 19806 deletions(-)
diff --cc gnu/local.mk
index 114dfca,ec11b26..e2dc64b
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@@ -575,11 -575,9 +575,10 @@@ dist_patch_DATA =
%D%/packages/patches/azr3.patch \
%D%/packages/patches/bash-completion-directories.patch \
%D%/packages/patches/bazaar-CVE-2017-14176.patch \
- %D%/packages/patches/bcftools-regidx-unsigned-char.patch \
- %D%/packages/patches/binutils-ld-new-dtags.patch \
%D%/packages/patches/binutils-loongson-workaround.patch \
%D%/packages/patches/blast+-fix-makefile.patch \
+ %D%/packages/patches/boost-fix-icu-build.patch \
+ %D%/packages/patches/btrfs-progs-e-value-block.patch \
%D%/packages/patches/byobu-writable-status.patch \
%D%/packages/patches/cairo-CVE-2016-9082.patch \
%D%/packages/patches/calibre-no-updates-dialog.patch \
@@@ -976,7 -978,8 +976,6 @@@
%D%/packages/patches/patchelf-rework-for-arm.patch \
%D%/packages/patches/patchutils-xfail-gendiff-tests.patch \
%D%/packages/patches/patch-hurd-path-max.patch \
- %D%/packages/patches/pcmanfm-CVE-2017-8934.patch \
- %D%/packages/patches/pcre2-CVE-2017-7186.patch \
- %D%/packages/patches/pcre2-CVE-2017-8786.patch \
%D%/packages/patches/perl-file-path-CVE-2017-6512.patch \
%D%/packages/patches/perl-autosplit-default-time.patch \
%D%/packages/patches/perl-dbd-mysql-CVE-2017-10788.patch \
@@@ -1012,10 -1015,9 +1011,9 @@@
%D%/packages/patches/psm-arch.patch \
%D%/packages/patches/psm-ldflags.patch \
%D%/packages/patches/psm-repro.patch \
- %D%/packages/patches/pt-scotch-build-parallelism.patch \
- %D%/packages/patches/pulseaudio-glibc-2.27.patch \
%D%/packages/patches/pulseaudio-fix-mult-test.patch \
++ %D%/packages/patches/pulseaudio-glibc-2.27.patch \
%D%/packages/patches/pulseaudio-longer-test-timeout.patch \
- %D%/packages/patches/pycairo-wscript.patch \
%D%/packages/patches/pybugz-encode-error.patch \
%D%/packages/patches/pybugz-stty.patch \
%D%/packages/patches/pygpgme-disable-problematic-tests.patch \
@@@ -1057,8 -1059,6 +1055,7 @@@
%D%/packages/patches/python-unittest2-python3-compat.patch \
%D%/packages/patches/python-unittest2-remove-argparse.patch \
%D%/packages/patches/python-waitress-fix-tests.patch \
- %D%/packages/patches/qemu-CVE-2018-7550.patch \
+ %D%/packages/patches/qemu-glibc-2.27.patch \
%D%/packages/patches/qt4-ldflags.patch \
%D%/packages/patches/qtbase-use-TZDIR.patch \
%D%/packages/patches/qtscript-disable-tests.patch \
diff --cc gnu/packages/bioinformatics.scm
index 5af4947,019c46a..61e5d8b
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@@ -293,13 -293,11 +293,12 @@@ BAM files."
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
- "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
- (patches (search-patches "bcftools-regidx-unsigned-char.patch"))
+ "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"))
(modules '((guix build utils)))
- (snippet
- ;; Delete bundled htslib.
- '(delete-file-recursively "htslib-1.8"))))
+ (snippet '(begin
+ ;; Delete bundled htslib.
- (delete-file-recursively "htslib-1.5")
++ (delete-file-recursively "htslib-1.8")
+ #t))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
diff --cc gnu/packages/commencement.scm
index 057ee16,1026ee8..9f85781
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@@ -1024,7 -1027,9 +1024,10 @@@ COREUTILS-FINAL vs. COREUTILS, etc.
(union-build (assoc-ref %outputs "debug")
(list (assoc-ref %build-inputs
"libc-debug")))
+ (union-build (assoc-ref %outputs "static")
+ (list (assoc-ref %build-inputs
- "libc-static")))))))
++ "libc-static")))
+ #t))))
(native-search-paths (package-native-search-paths gcc))
(search-paths (package-search-paths gcc))
diff --cc gnu/packages/linux.scm
index a3b3ab2,196cc77..b92b146
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@@ -3303,10 -3306,10 +3304,11 @@@ disks and SD cards. This package provi
;; The default of 2 seconds is too low: it assumes an
;; open lid and AC power without actually checking.
(substitute* "freefall.c"
- (("alarm\\(2\\)") "alarm(5)")))))
+ (("alarm\\(2\\)") "alarm(5)"))
+ #t)))
#:make-flags (list (string-append "PREFIX="
- (assoc-ref %outputs "out")))
+ (assoc-ref %outputs "out"))
+ "CC=gcc")
#:tests? #f)) ;no tests
(home-page (package-home-page linux-libre))
(synopsis "Free-fall protection for spinning laptop hard drives")
diff --cc gnu/packages/text-editors.scm
index 06e8e47,d12e3d7..2536754
--- a/gnu/packages/text-editors.scm
+++ b/gnu/packages/text-editors.scm
@@@ -239,19 -237,21 +239,21 @@@ Wordstar-, EMACS-, Pico, Nedit or vi-li
(define-public mg
(package
(name "mg")
- (version "20171014")
+ (version "20180408")
(source (origin
- (method url-fetch)
- (uri (string-append
"https://homepage.boetes.org/software/mg/mg-";
- version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/hboetes/mg";)
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0hakfikzsml7z0hja8m8mcahrmfy2piy81bq9nccsjplyfc9clai"))
+ "06w86xk7sjl2x2h3z6msn8kpmwj05qdimcym77wzhz5s94dzh1bl"))
(modules '((guix build utils)))
- (snippet
- '(begin
- (substitute* "GNUmakefile"
- (("/usr/bin/") ""))))))
+ (snippet '(begin
+ (substitute* "GNUmakefile"
+ (("/usr/bin/") ""))
+ #t))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
diff --cc gnu/packages/virtualization.scm
index 0b373b1,b73287c..9dd8bb8
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@@ -38,8 -38,8 +39,9 @@@
#:use-module (gnu packages dns)
#:use-module (gnu packages docbook)
#:use-module (gnu packages documentation)
+ #:use-module (gnu packages flex)
#:use-module (gnu packages fontutils)
+ #:use-module (gnu packages gettext)
#:use-module (gnu packages gl)
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
@@@ -194,12 -196,11 +198,13 @@@ exec smbd $@"))
;; ("vde2" ,vde2)
("virglrenderer" ,virglrenderer)
("zlib" ,zlib)))
- (native-inputs `(("glib:bin" ,glib "bin") ; gtester, etc.
+ (native-inputs `(("gettext" ,gettext-minimal)
+ ("glib:bin" ,glib "bin") ; gtester, etc.
("perl" ,perl)
+ ("flex" ,flex)
+ ("bison" ,bison)
("pkg-config" ,pkg-config)
- ("python" ,python-2) ; incompatible with Python 3
according to error message
+ ("python-wrapper" ,python-wrapper)
("texinfo" ,texinfo)))
(home-page "https://www.qemu.org";)
(synopsis "Machine emulator and virtualizer")
@@@ -234,10 -235,33 +239,35 @@@ server and embedded PowerPC, and S390 g
''("--target-list=i386-softmmu,x86_64-softmmu,mips64el-softmmu,arm-softmmu,aarch64-softmmu"))))
;; Remove dependencies on optional libraries, notably GUI libraries.
+ (native-inputs (fold alist-delete (package-native-inputs qemu)
+ '("gettext")))
(inputs (fold alist-delete (package-inputs qemu)
- '("libusb" "mesa" "sdl" "spice" "virglrenderer"
+ '("libusb" "mesa" "sdl2" "spice" "virglrenderer" "gtk+"
"usbredir" "libdrm" "libepoxy" "pulseaudio")))))
+ ;; The GRUB test suite fails with later versions of Qemu, so we
+ ;; keep it at 2.10 for now. See
+ ;; <https://lists.gnu.org/archive/html/bug-grub/2018-02/msg00004.html>.
+ ;; This package is hidden since we do not backport updates to it.
+ (define-public qemu-minimal-2.10
+ (hidden-package
+ (package
+ (inherit qemu-minimal)
+ (version "2.10.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://download.qemu.org/qemu-";
+ version ".tar.xz"))
+ (sha256
+ (base32
- "17w21spvaxaidi2am5lpsln8yjpyp2zi3s3gc6nsxj5arlgamzgw"))))
++ "17w21spvaxaidi2am5lpsln8yjpyp2zi3s3gc6nsxj5arlgamzgw"))
++ (patches
++ (search-patches "qemu-glibc-2.27.patch"))))
+ ;; qemu-minimal-2.10 needs Python 2. Remove below once no longer
necessary.
+ (native-inputs `(("python-2" ,python-2)
+ ,@(fold alist-delete (package-native-inputs qemu)
+ '("python-wrapper")))))))
+
(define-public libosinfo
(package
(name "libosinfo")
diff --cc guix/download.scm
index 377e8186,7aa6c03..66d97ee
--- a/guix/download.scm
+++ b/guix/download.scm
@@@ -509,15 -509,16 +509,18 @@@ own. This helper makes it easier to de
#:system system
#:guile guile)))
;; Take the tar bomb, and simply unpack it as a directory.
+ ;; Use ungrafted tar/gzip so that the resulting tarball doesn't depend on
+ ;; whether grafts are enabled.
(gexp->derivation (or name file-name)
- #~(begin
- (mkdir #$output)
- (setenv "PATH" (string-append #$gzip "/bin"))
- (chdir #$output)
- (zero? (system* (string-append #$tar "/bin/tar")
- "xf" #$drv)))
+ (with-imported-modules '((guix build utils))
+ #~(begin
+ (use-modules (guix build utils))
+ (mkdir #$output)
+ (setenv "PATH" (string-append #$gzip "/bin"))
+ (chdir #$output)
+ (invoke (string-append #$tar "/bin/tar")
+ "xf" #$drv)))
+ #:graft? #f
#:local-build? #t)))
(define* (url-fetch/zipbomb url hash-algo hash
@@@ -541,14 -542,15 +544,17 @@@ own. This helper makes it easier to de
#:system system
#:guile guile)))
;; Take the zip bomb, and simply unpack it as a directory.
+ ;; Use ungrafted unzip so that the resulting tarball doesn't depend on
+ ;; whether grafts are enabled.
(gexp->derivation (or name file-name)
- #~(begin
- (mkdir #$output)
- (chdir #$output)
- (zero? (system* (string-append #$unzip "/bin/unzip")
- #$drv)))
+ (with-imported-modules '((guix build utils))
+ #~(begin
+ (use-modules (guix build utils))
+ (mkdir #$output)
+ (chdir #$output)
+ (invoke (string-append #$unzip "/bin/unzip")
+ #$drv)))
+ #:graft? #f
#:local-build? #t)))
(define* (download-to-store store url #:optional (name (basename url))