Merge branch 'master' into staging

diff --cc gnu/local.mk
index 571df53,af25477..c8b42d1
--- 1/gnu/local.mk
--- 2/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/audio.scm
Simple merge

diff --cc gnu/packages/databases.scm
index c285d2f,1433ca5..cbc5ffc
--- 1/gnu/packages/databases.scm
--- 2/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 root@hostname == root@localhost 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)

diff --cc gnu/packages/freedesktop.scm
Simple merge

diff --cc gnu/packages/gnome.scm
Simple merge

diff --cc gnu/packages/java.scm
Simple merge

diff --cc gnu/packages/maths.scm
Simple merge

diff --cc gnu/packages/pdf.scm
Simple merge

diff --cc gnu/packages/python.scm
Simple merge

diff --cc gnu/packages/video.scm
Simple merge

diff --cc gnu/packages/web.scm
Simple merge

diff --cc gnu/packages/xorg.scm
Simple merge