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01/02: Merge branch 'master' into staging
|
From: |
Marius Bakke |
|
Subject: |
01/02: Merge branch 'master' into staging |
|
Date: |
Sat, 28 Jul 2018 15:22:33 -0400 (EDT) |
mbakke pushed a commit to branch staging
in repository guix.
commit 1af575f04df6cfb6e5e3f3273271383b6ee355a8
Merge: 3b6f8a4 48d7ac1
Author: Marius Bakke <address@hidden>
Date: Sat Jul 28 18:34:59 2018 +0200
Merge branch 'master' into staging
.mailmap | 2 +
HACKING | 2 +-
Makefile.am | 10 +-
doc/contributing.texi | 3 +-
doc/guix.texi | 247 ++++-
etc/snippets/scheme-mode/guix-package | 4 +-
.../guix-commit-message-use-https-home-page | 9 +
gnu/local.mk | 26 +-
gnu/packages/admin.scm | 49 +-
gnu/packages/algebra.scm | 19 +-
gnu/packages/aspell.scm | 18 +-
gnu/packages/audio.scm | 4 +-
gnu/packages/bioinformatics.scm | 20 +-
gnu/packages/bittorrent.scm | 4 +-
gnu/packages/bootloaders.scm | 31 +-
gnu/packages/busybox.scm | 13 +-
gnu/packages/cdrom.scm | 6 +-
gnu/packages/chemistry.scm | 125 +++
gnu/packages/ci.scm | 7 +-
gnu/packages/compression.scm | 69 +-
gnu/packages/crypto.scm | 88 +-
gnu/packages/cups.scm | 35 +-
gnu/packages/curl.scm | 8 +-
gnu/packages/databases.scm | 27 +-
gnu/packages/dav.scm | 40 +-
gnu/packages/debian.scm | 15 +-
gnu/packages/dictionaries.scm | 3 +-
gnu/packages/display-managers.scm | 10 +-
gnu/packages/dns.scm | 101 +-
gnu/packages/dunst.scm | 2 +-
gnu/packages/ebook.scm | 4 +-
gnu/packages/elixir.scm | 6 +-
gnu/packages/emacs.scm | 446 +++++++--
gnu/packages/embedded.scm | 11 +-
gnu/packages/erlang.scm | 7 +-
gnu/packages/finance.scm | 96 +-
gnu/packages/fltk.scm | 26 +-
gnu/packages/fonts.scm | 31 +-
gnu/packages/fontutils.scm | 9 +-
gnu/packages/freedesktop.scm | 13 +-
gnu/packages/game-development.scm | 95 +-
gnu/packages/games.scm | 200 +++-
gnu/packages/gcc.scm | 4 +-
gnu/packages/geo.scm | 2 +-
gnu/packages/ghostscript.scm | 11 +
gnu/packages/gimp.scm | 6 +-
gnu/packages/glib.scm | 4 +-
gnu/packages/gnome.scm | 83 +-
gnu/packages/gnu-pw-mgr.scm | 4 +-
gnu/packages/gnunet.scm | 4 +-
gnu/packages/gnupg.scm | 4 +-
gnu/packages/golang.scm | 518 ++++++++++
gnu/packages/graphics.scm | 51 +-
gnu/packages/guile.scm | 585 ++++-------
gnu/packages/haskell.scm | 44 +
gnu/packages/image-viewers.scm | 4 +-
gnu/packages/image.scm | 18 +-
gnu/packages/imagemagick.scm | 4 +-
gnu/packages/irc.scm | 1 -
gnu/packages/iso-codes.scm | 2 +-
gnu/packages/java.scm | 54 +-
gnu/packages/julia.scm | 2 +-
gnu/packages/kodi.scm | 2 +-
gnu/packages/libreoffice.scm | 4 +-
gnu/packages/libusb.scm | 4 +-
gnu/packages/linux.scm | 77 +-
gnu/packages/lsof.scm | 10 +-
gnu/packages/lua.scm | 4 +-
gnu/packages/mail.scm | 12 +-
gnu/packages/maths.scm | 46 +-
gnu/packages/maven.scm | 2 +-
gnu/packages/mes.scm | 10 +-
gnu/packages/messaging.scm | 91 +-
gnu/packages/monitoring.scm | 1 +
gnu/packages/music.scm | 89 ++
gnu/packages/networking.scm | 34 +-
gnu/packages/package-management.scm | 13 +-
gnu/packages/patches/bind-CVE-2018-5738.patch | 100 --
gnu/packages/patches/file-CVE-2017-1000249.patch | 27 -
gnu/packages/patches/fltk-shared-lib-defines.patch | 51 -
gnu/packages/patches/fltk-xfont-on-demand.patch | 45 -
.../patches/ghostscript-CVE-2018-10194.patch | 52 +
gnu/packages/patches/mariadb-gcc-ice.patch | 24 +
.../patches/monero-use-system-miniupnpc.patch | 111 +++
.../openbabel-fix-crash-on-nwchem-output.patch | 34 +
gnu/packages/patches/openscenegraph-ffmpeg3.patch | 156 ---
gnu/packages/patches/pyqt-public-sip.patch | 55 ++
.../patches/python-cairocffi-dlopen-path.patch | 10 +
gnu/packages/patches/quassel-qt-5.11.patch | 72 --
.../patches/rust-bootstrap-stage0-test.patch | 55 ++
gnu/packages/patches/rust-coresimd-doctest.patch | 21 +
.../patches/sddm-fix-build-with-qt-5.11-1024.patch | 28 -
.../patches/twinkle-include-qregexpvalidator.patch | 123 +++
gnu/packages/patches/x265-arm-asm-primitives.patch | 360 +++++++
gnu/packages/patches/xapian-revert-5489fb2f8.patch | 23 +
gnu/packages/patches/xorg-server-rotate-fb.patch | 35 +
gnu/packages/pdf.scm | 56 +-
gnu/packages/photo.scm | 4 +-
gnu/packages/php.scm | 14 +-
gnu/packages/python-crypto.scm | 15 +-
gnu/packages/python.scm | 118 ++-
gnu/packages/qt.scm | 353 ++++---
gnu/packages/ruby.scm | 77 +-
gnu/packages/rust.scm | 207 ++--
gnu/packages/samba.scm | 22 +-
gnu/packages/scanner.scm | 3 +-
gnu/packages/sdl.scm | 19 +-
gnu/packages/search.scm | 7 +-
gnu/packages/statistics.scm | 20 +
gnu/packages/stb.scm | 103 ++
gnu/packages/sync.scm | 36 +-
gnu/packages/syncthing.scm | 18 +-
gnu/packages/telephony.scm | 2 +
gnu/packages/textutils.scm | 18 +-
gnu/packages/tls.scm | 10 +-
gnu/packages/tor.scm | 6 +-
gnu/packages/upnp.scm | 46 +
gnu/packages/version-control.scm | 4 +-
gnu/packages/video.scm | 71 +-
gnu/packages/web-browsers.scm | 68 ++
gnu/packages/web.scm | 51 +-
gnu/packages/wine.scm | 6 +-
gnu/packages/xml.scm | 9 -
gnu/packages/xorg.scm | 73 +-
gnu/services/cuirass.scm | 12 +-
gnu/services/herd.scm | 3 +
gnu/services/mcron.scm | 76 +-
gnu/services/monitoring.scm | 38 +-
gnu/services/shepherd.scm | 23 +-
gnu/services/ssh.scm | 2 +-
gnu/services/virtualization.scm | 1 +
gnu/system/install.scm | 7 +
gnu/system/shadow.scm | 12 +-
gnu/tests/base.scm | 7 +
gnu/tests/monitoring.scm | 97 ++
guix/build-system/guile.scm | 202 ++++
guix/build/go-build-system.scm | 38 +-
guix/build/guile-build-system.scm | 153 +++
guix/build/haskell-build-system.scm | 5 +-
guix/build/profiles.scm | 2 +-
guix/build/ruby-build-system.scm | 111 ++-
guix/gexp.scm | 155 ++-
guix/git.scm | 26 +-
guix/gnu-maintenance.scm | 26 +-
guix/hash.scm | 7 +-
guix/import/cabal.scm | 85 +-
guix/import/gem.scm | 48 +-
guix/import/hackage.scm | 53 +-
guix/import/opam.scm | 193 ++++
guix/import/pypi.scm | 10 +-
guix/inferior.scm | 197 ++++
guix/packages.scm | 3 +
guix/profiles.scm | 28 +-
guix/scripts/environment.scm | 210 ++--
guix/scripts/import.scm | 2 +-
guix/scripts/import/gem.scm | 27 +-
guix/scripts/import/{gem.scm => opam.scm} | 18 +-
guix/scripts/pack.scm | 5 +-
guix/scripts/package.scm | 2 +-
guix/scripts/pull.scm | 140 ++-
guix/scripts/repl.scm | 199 ++++
guix/self.scm | 57 +-
guix/serialization.scm | 140 ++-
guix/store.scm | 115 ++-
guix/store/database.scm | 8 +-
guix/store/deduplication.scm | 54 +-
guix/ui.scm | 2 +-
guix/utils.scm | 12 +-
srfi/srfi-64.scm | 41 -
srfi/srfi-64.upstream.scm | 1040 --------------------
tests/gem.scm | 108 +-
tests/gexp.scm | 87 +-
tests/guix-package.sh | 12 +-
tests/hackage.scm | 71 ++
tests/hash.scm | 4 +-
tests/inferior.scm | 69 ++
tests/nar.scm | 62 +-
tests/opam.scm | 118 +++
tests/pypi.scm | 6 +-
tests/store-database.scm | 7 +-
tests/store.scm | 46 +
181 files changed, 7340 insertions(+), 3505 deletions(-)
diff --cc gnu/local.mk
index 571df53,af25477..c8b42d1
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@@ -979,7 -981,9 +981,8 @@@ dist_patch_DATA =
%D%/packages/patches/ocaml-graph-honor-source-date-epoch.patch \
%D%/packages/patches/omake-fix-non-determinism.patch \
%D%/packages/patches/ola-readdir-r.patch \
+ %D%/packages/patches/openbabel-fix-crash-on-nwchem-output.patch \
%D%/packages/patches/opencascade-oce-glibc-2.26.patch \
- %D%/packages/patches/openblas-fix-tests-i686.patch \
%D%/packages/patches/openexr-missing-samples.patch \
%D%/packages/patches/openfoam-4.1-cleanup.patch \
%D%/packages/patches/openldap-CVE-2017-9287.patch \
diff --cc gnu/packages/databases.scm
index c285d2f,1433ca5..cbc5ffc
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@@ -635,23 -635,10 +635,23 @@@ Language."
name "-" version ".tar.gz"))
(sha256
(base32
- "0bax748j4srsyhw5cs5jvwigndh0zwmf4r2cjvhja31ckx8jqccl"))))
+ "0j2mdpyvj41vkq2rwrzky88b7170hzz6gy2vb2bc1447s2gp3q67"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete bundled snappy and xz.
+ (delete-file-recursively
"storage/tokudb/PerconaFT/third_party")
+
+ ;; Preserve CMakeLists.txt for these.
+ (for-each (lambda (file)
+ (unless (string-suffix? "CMakeLists.txt" file)
+ (delete-file file)))
+ (append (find-files "extra/yassl")
+ (find-files "pcre") (find-files "zlib")))
+ #t))))
(build-system cmake-build-system)
(arguments
- '(#:configure-flags
+ `(#:configure-flags
'("-DBUILD_CONFIG=mysql_release"
;; Linking with libarchive fails, like this:
@@@ -681,76 -662,26 +681,87 @@@
"-DINSTALL_SUPPORTFILESDIR=share/mysql/support-files"
"-DINSTALL_MYSQLSHAREDIR=share/mysql"
"-DINSTALL_DOCDIR=share/mysql/docs"
- "-DINSTALL_SHAREDIR=share/mysql")
+ "-DINSTALL_SHAREDIR=share")
#:phases
(modify-phases %standard-phases
-
+ ;; Apply this patch that's only needed on ARM.
+ ,@(if (and (not (%current-target-system))
+ (string=? "armhf-linux" (%current-system)))
+ `((add-after 'unpack 'apply-patch
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((patch (assoc-ref inputs "gcc-ice-patch")))
+ (invoke "patch" "-p1" "--force"
+ "--input" patch)
+ #t))))
+ '())
+
- (add-before
- 'configure 'pre-configure
- (lambda _
- (setenv "CONFIG_SHELL" (which "sh"))
- #t))
+ (add-after 'unpack 'unbundle
+ (lambda _
+ ;; The bundled PCRE in MariaDB has a patch that was upstreamed
+ ;; in version 8.34. Unfortunately the upstream patch behaves
+ ;; slightly differently and the build system fails to detect it.
+ ;; See <https://bugs.exim.org/show_bug.cgi?id=2173>.
+ ;; XXX: Consider patching PCRE instead.
+ (substitute* "cmake/pcre.cmake"
+ ((" OR NOT PCRE_STACK_SIZE_OK") ""))
+
+ (substitute* "storage/tokudb/PerconaFT/ft/CMakeLists.txt"
+ ;; Remove dependency on these CMake targets.
+ ((" build_lzma build_snappy") ""))
+
+ (substitute* "storage/tokudb/PerconaFT/CMakeLists.txt"
+ ;; This file checks that the bundled sources are present and
+ ;; declares build procedures for them. We don't need that.
+ (("^include\\(TokuThirdParty\\)") ""))
+
+ #t))
+ (add-after 'unpack 'adjust-tests
+ (lambda _
+ (let ((disabled-tests
+ '(;; These fail because address@hidden == address@hidden
in
+ ;; the build environment, causing a user count mismatch.
+ ;; See <https://jira.mariadb.org/browse/MDEV-7761>.
+ "main.join_cache"
+ "main.explain_non_select"
+ "roles.acl_statistics"))
+
+ ;; This file contains a list of known-flaky tests for this
+ ;; release. Append our own items.
+ (unstable-tests (open-file "mysql-test/unstable-tests"
"a")))
+ (for-each (lambda (test)
+ (format unstable-tests "~a : ~a\n"
+ test "Disabled in Guix"))
+ disabled-tests)
+ (close-port unstable-tests)
+
+ (substitute* "mysql-test/mysql-test-run.pl"
+ (("/bin/ls") (which "ls"))
+ (("/bin/sh") (which "sh")))
+ #t)))
+ (add-before 'configure 'disable-plugins
+ (lambda _
+ (let ((disable-plugin (lambda (name)
+ (call-with-output-file
+ (string-append "plugin/" name
+ "/CMakeLists.txt")
+ (lambda (port)
+ (format port "\n")))))
+ (disabled-plugins '(;; FIXME: On armhf-linux, this plugin
+ ;; triggers a GCC ICE. Disable for
now.
+ "semisync"
+ ;; XXX: Causes a test failure.
+ "disks")))
+ (for-each disable-plugin disabled-plugins)
+ #t)))
+ (replace 'check
+ (lambda* (#:key (tests? #t) #:allow-other-keys)
+ (if tests?
+ (with-directory-excursion "mysql-test"
+ (invoke "./mtr" "--verbose"
+ "--parallel" (number->string (parallel-job-count))
+ "--skip-test-list=unstable-tests"))
+ (format #t "test suite not run~%"))
+ #t))
(add-after
'install 'post-install
(lambda* (#:key outputs #:allow-other-keys)