Merge branch 'master' into core-updates

diff --cc gnu/local.mk
Simple merge

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

diff --cc gnu/packages/cmake.scm
index e9fa866,258ea9c..06b1cab
--- 1/gnu/packages/cmake.scm
--- 2/gnu/packages/cmake.scm
+++ b/gnu/packages/cmake.scm
@@@ -154,3 -151,76 +155,20 @@@ and workspaces that can be used in the 
                     license:bsd-2             ; cmlibarchive
                     license:expat             ; cmjsoncpp is dual MIT/public domain
                     license:public-domain)))) ; cmlibarchive/archive_getdate.c
 -;; Recent Ceph requires Boost 1.66, which in turn requires CMake 3.11 for
 -;; its updated "FindBoost.cmake" facility.
 -(define-public cmake-3.11
 -  (package
 -    (inherit cmake)
 -    (version "3.11.0-rc2")
 -    (source (origin
 -              (inherit (package-source cmake))
 -              (uri (string-append "https://www.cmake.org/files/v"
 -                                  (version-major+minor version)
 -                                  "/cmake-" version ".tar.gz"))
 -              (sha256
 -               (base32
 -                "14p6ais19nfcwl914n4n5rbzaqwafv3qkg6nd8jw54ykn6lz6mf3"))
 -              (snippet
 -               '(begin
 -                  ;; Drop bundled software.
 -                  (with-directory-excursion "Utilities"
 -                    (for-each delete-file-recursively
 -                              '("cmbzip2"
 -                                "cmcurl"
 -                                "cmexpat"
 -                                "cmliblzma"
 -                                "cmzlib"))
 -                    #t)))))
 -    (build-system gnu-build-system)
 -    (arguments
 -     (substitute-keyword-arguments (package-arguments cmake)
 -       ((#:make-flags flags ''()) `(cons (string-append
 -                                          "ARGS=-j "
 -                                          (number->string (parallel-job-count))
 -                                          " --output-on-failure")
 -                                         ,flags))
 -       ((#:phases phases)
 -        `(modify-phases ,phases
 -           (replace 'patch-bin-sh
 -             (lambda _
 -               (substitute*
 -                   '("Modules/CompilerId/Xcode-3.pbxproj.in"
 -                     "Modules/CPack.RuntimeScript.in"
 -                     "Source/cmakexbuild.cxx"
 -                     "Source/cmGlobalXCodeGenerator.cxx"
 -                     "Source/cmLocalUnixMakefileGenerator3.cxx"
 -                     "Source/cmExecProgramCommand.cxx"
 -                     "Utilities/Release/release_cmake.cmake"
 -                     "Utilities/cmlibarchive/libarchive/archive_write_set_format_shar.c"
 -                     "Tests/CMakeLists.txt"
 -                     "Tests/RunCMake/File_Generate/RunCMakeTest.cmake")
 -                 (("/bin/sh") (which "sh")))
 -               #t))
 -           ;; This is now passed through #:make-flags.
 -           (delete 'set-test-environment)))))
 -    (inputs
 -     `(("rhash" ,rhash)
 -       ,@(package-inputs cmake)))))
 -
+ 
+ (define-public emacs-cmake-mode
+   (package
+     (inherit cmake)
+     (name "emacs-cmake-mode")
+     (build-system emacs-build-system)
+     (arguments
+      `(#:phases
+        (modify-phases %standard-phases
+          (add-after 'unpack 'chdir-elisp
+            ;; Elisp directory is not in root of the source.
+            (lambda _
+              (chdir "Auxiliary"))))))
+     (synopsis "Emacs major mode for editing Cmake expressions")
+     (description "@code{cmakeos-mode} provides an Emacs major mode for editing
+ Cmake files.  It supports syntax highlighting, indenting and refilling of
+ comments.")))

diff --cc gnu/packages/code.scm
index d636945,fc1c000..edf0f98
--- 1/gnu/packages/code.scm
--- 2/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@@ -529,3 -531,117 +533,118 @@@ produce colored output."
  output is a graphviz-dot file, a Gexf-XML file or a list of the deepest
  independent targets.")
      (license license:expat)))
 -    `(#:phases (alist-cons-after
 -                'unpack 'fix-docdir
 -                (lambda _
 -                  ;; Although indent uses a modern autoconf in which docdir
 -                  ;; defaults to PREFIX/share/doc, the doc/Makefile.am
 -                  ;; overrides this to be in PREFIX/doc.  Fix this.
 -                  (substitute* "doc/Makefile.in"
 -                    (("^docdir = .*$") "docdir = @docdir@\n")))
 -                %standard-phases)))
+ 
+ (define-public uncrustify
+   (package
+     (name "uncrustify")
+     (version "0.67")
+     (source (origin
+               (method url-fetch)
+               (uri (string-append
+                     "https://github.com/uncrustify/uncrustify/archive/"
+                     "uncrustify-" version ".zip"))
+               (sha256
+                (base32
+                 "0n13kq0nsm35fxhdp0f275n4x0w88hdv3bdjy0hgvv42x0dx5zyp"))))
+     (build-system cmake-build-system)
+     (native-inputs
+      `(("unzip" ,unzip)))
+     (arguments
+      `(#:phases
+        (modify-phases %standard-phases
+          (add-after 'unpack 'unpack-etc
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              ;; Configuration samples are not installed by default.
+              (let* ((output (assoc-ref outputs "out"))
+                     (etcdir (string-append output "/etc")))
+                (for-each (lambda (l)
+                            (install-file l etcdir))
+                          (find-files "etc" "\\.cfg$")))
+              #t)))))
+     (home-page "http://uncrustify.sourceforge.net/")
+     (synopsis "Code formatter for C and other related languages")
+     (description
+      "Beautify source code in many languages of the C family (C, C++, C#,
+ Objective@tie{}C, D, Java, Pawn, and Vala).  Features:
+ @itemize
+ @item Indent and align code.
+ @item Reformat comments (a little bit).
+ @item Fix inter-character spacing.
+ @item Add or remove parens / braces.
+ @item Supports embedded SQL @code{EXEC SQL} stuff.
+ @item Highly configurable - More than 600 configurable options.
+ @end itemize\n")
+     (license license:gpl2+)))
+ 
+ (define-public astyle
+   (package
+     (name "astyle")
+     (version "2.05")
+     (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "mirror://sourceforge/astyle/astyle/astyle%20"
+                            version "/astyle_"  version "_linux.tar.gz"))
+        (sha256
+         (base32
+          "0f9sh9kq5ajp1yz133h00fr9235p1m698x7n3h7zbrhjiwgynd6s"))))
+     (build-system gnu-build-system)
+     (arguments
+      `(#:tests? #f                      ;no tests
+        #:make-flags (list (string-append "prefix=" %output)
+                           "INSTALL=install"
+                           "all")
+        #:phases
+        (modify-phases %standard-phases
+          (replace 'configure
+            (lambda _ (chdir "build/gcc") #t))
+          (add-after 'install 'install-libs
+            (lambda* (#:key outputs #:allow-other-keys)
+              ;; Libraries are not installed by default
+              (let* ((output (assoc-ref outputs "out"))
+                     (libdir (string-append output "/lib")))
+                (begin
+                  (mkdir-p libdir)
+                  (for-each (lambda (l)
+                              (copy-file
+                               l (string-append libdir "/" (basename l))))
+                            (find-files "bin" "lib*"))))
+              #t)))))
+     (home-page "http://astyle.sourceforge.net/")
+     (synopsis "Source code indenter, formatter, and beautifier")
+     (description
+      "Artistic Style is a source code indenter, formatter, and beautifier for
+ the C, C++, C++/CLI, Objective‑C, C#, and Java programming languages.")
+     (license license:lgpl3+)))
+ 
+ (define-public indent
+   (package
+    (name "indent")
+    (version "2.2.10")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "mirror://gnu/indent/indent-" version
+                                 ".tar.gz"))
+             (sha256 (base32
+                      "0f9655vqdvfwbxvs1gpa7py8k1z71aqh8hp73f65vazwbfz436wa"))))
+    (build-system gnu-build-system)
+    (arguments
++    `(#:phases
++      (modify-phases %standard-phases
++        (add-after 'unpack 'fix-docdir
++          (lambda _
++            ;; Although indent uses a modern autoconf in which docdir
++            ;; defaults to PREFIX/share/doc, the doc/Makefile.am
++            ;; overrides this to be in PREFIX/doc.  Fix this.
++            (substitute* "doc/Makefile.in"
++              (("^docdir = .*$") "docdir = @docdir@\n"))
++            #t)))))
+    (synopsis "Code reformatter")
+    (description
+     "Indent is a program that makes source code easier to read by
+ reformatting it in a consistent style.  It can change the style to one of
+ several different styles such as GNU, BSD or K&R.  It has some flexibility to
+ deal with incomplete or malformed syntax.  GNU indent offers several
+ extensions over the standard utility.")
+    (license license:gpl3+)
+    (home-page "https://www.gnu.org/software/indent/")))

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

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

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

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

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

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

diff --cc gnu/packages/pretty-print.scm
Simple merge

diff --cc gnu/packages/version-control.scm
Simple merge

diff --cc gnu/packages/video.scm
index 0477793,7df318e..52003ce
--- 1/gnu/packages/video.scm
--- 2/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@@ -387,11 -388,12 +387,11 @@@ and creating Matroska files from other 
                              "x265_" version ".tar.gz"))
          (sha256
           (base32
-           "1gyd94jkwdii9308m07nymsbxrmrcl81c0j8i10zhslr2mj07w0v"))
+           "18llni1m8kfvdwy5bp950z6gyd0nijmvi3hzd6gd8vpy5yk5zrym"))
          (modules '((guix build utils)))
 -        (snippet
 -         '(begin
 -            (delete-file-recursively "source/compat/getopt")
 -            #t))))
 +        (snippet '(begin
 +                    (delete-file-recursively "source/compat/getopt")
 +                    #t))))
      (build-system cmake-build-system)
      (arguments
       `(#:tests? #f ; tests are skipped if cpu-optimized code isn't built

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

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