Merge branch 'master' into core-updates

14 files changed, 800 insertions, 26 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 91355f24e2..2c8dc8f399 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6370,7 +6370,7 @@ SELECT or UPDATE queries to an end-point.")
 (define-public vsearch
   (package
     (name "vsearch")
-    (version "2.7.0")
+    (version "2.7.1")
     (source
      (origin
        (method url-fetch)
@@ -6380,7 +6380,7 @@ SELECT or UPDATE queries to an end-point.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0523b8xq5fw60ayl0k5m1fm6yrh1932ljrsz1ys67xnki7p7f1d5"))
+         "0jlzfgh79fzmb4g7sngzdjjsjyc37icvs1k7vmc2ksxglj6x5i7f"))
        (patches (search-patches "vsearch-unbundle-cityhash.patch"))
        (snippet
         '(begin
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index f2117fb8b9..af1158b214 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -7098,6 +7098,78 @@ scratch buffer, and, by virtue of this extension, do so using the Emacs
 formatting rules for that language.")
       (license license:bsd-2))))
 
+(define-public emacs-esxml
+  (package
+    (name "emacs-esxml")
+    (version "0.3.4")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/tali713/esxml.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "00vv8a75wdklygdyr4km9mc2ismxak69c45jmcny41xl44rp9x8m"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/tali713/esxml/")
+    (synopsis "SXML for EmacsLisp")
+    (description "This is XML/XHTML done with S-Expressions in EmacsLisp.
+Simply, this is the easiest way to write HTML or XML in Lisp.  This library
+uses the native form of XML representation as used by many libraries already
+included within Emacs.  See @code{esxml-to-xml} for a concise description of
+the format.")
+    (license license:gpl3+)))
+
+(define-public emacs-nov-el
+  (package
+    (name "emacs-nov-el")
+    (version "0.2.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/wasamasa/nov.el.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "03s0qjvwk1f7y3i4wh2p5y3z4hdv00adgz8za3vphzc0q8i1kjzb"))))
+    (build-system emacs-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'embed-path-to-unzip
+           (lambda _
+             (substitute* "nov.el"
+               (("\\(executable-find \"unzip\"\\)")
+                (string-append "\"" (which "unzip") "\"")))
+             #t)))))
+    (propagated-inputs
+     `(("emacs-dash" ,emacs-dash)
+       ("emacs-esxml" ,emacs-esxml)))
+    (inputs
+     `(("unzip" ,unzip)))
+    (home-page "https://github.com/wasamasa/nov.el/")
+    (synopsis "Major mode for reading EPUBs in Emacs")
+    (description "@code{nov.el} provides a major mode for reading EPUB
+documents.
+
+Features:
+
+@itemize
+@item Basic navigation (jump to TOC, previous/next chapter)
+@item Remembering and restoring the last read position
+@item Jump to next chapter when scrolling beyond end
+@item Renders EPUB2 (@code{.ncx}) and EPUB3 (@code{<nav>}) TOCs
+@item Hyperlinks to internal and external targets
+@item Supports textual and image documents
+@item View source of document files
+@item Metadata display
+@item Image rescaling
+@end itemize
+")
+    (license license:gpl3+)))
+
 (define-public epipe
   (package
     (name "epipe")
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index e94aeedf54..449584f57e 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
@@ -178,6 +178,13 @@ plans and designs.")
          (add-before 'check 'set-home
            (lambda _
              (setenv "HOME" (getenv "TMPDIR"))
+             #t))
+         ;; FIXME: These two tests fail for unknown reasons.  They return "2"
+         ;; when they should return "1".
+         (add-after 'unpack 'disable-failing-tests
+           (lambda _
+             (substitute* "utils/tests/gxyrs/tests.list"
+               (("^do_nothing.*") ""))
              #t)))
        #:configure-flags
        (let ((pcb (assoc-ref %build-inputs "pcb")))
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 51f158d939..a53d3ed406 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -32,7 +32,7 @@
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2017 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2017, 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -5598,3 +5598,83 @@ hacking the gamification of contribution graphs on platforms such as
 Github or Gitlab.")
     (home-page "https://github.com/umayr/badass")
     (license license:expat))))
+
+(define-public colobot
+  (package
+    (name "colobot")
+    (version "0.1.11-alpha")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/colobot/colobot/archive/"
+                           "colobot-gold-" version ".tar.gz"))
+       (sha256
+        (base32
+         "160rq9fp5vd0qaqr3jvzvzrcxk9cac532y8vx4cvq0a8hgylrbad"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f                      ;no test
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'unpack-data
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((data (assoc-ref inputs "colobot-data")))
+               (invoke "tar" "-xvf" data "-Cdata" "--strip-components=1")
+               #t)))
+         (add-after 'unpack-data 'install-music
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Installation process tries to download music files using
+             ;; "wget" if not already present.  Since we are going to install
+             ;; them, skip "wget" command check.
+             (substitute* "data/music/CMakeLists.txt"
+               (("find_program\\(WGET wget\\)") ""))
+             ;; Effectively install music.
+             (let ((data (assoc-ref inputs "colobot-music")))
+               (invoke "tar" "-xvf" data "-Cdata/music")
+               #t)))
+         (add-after 'install 'fix-install-directory
+           ;; Move binary from "games/" to "bin/".
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (rename-file (string-append out "/games")
+                            (string-append out "/bin"))
+               #t))))))
+    (native-inputs
+     `(("colobot-data"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append
+                 "https://github.com/colobot/colobot-data/archive/"
+                 "colobot-gold-" version ".tar.gz"))
+           (sha256
+            (base32
+             "1pdpsyr41g7xmk03k2g76l214f53ahk04qnkzmsv1fdbbaq7p109"))))
+       ("colobot-music"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append "https://colobot.info/files/music/"
+                               "colobot-music_ogg_" version ".tar.gz"))
+           (sha256
+            (base32
+             "1s86cd36rwkff329mb1ay1wi5qqyi35564ppgr3f4qqz9wj9vs2m"))))
+       ("gettext" ,gettext-minimal)
+       ("librsvg" ,librsvg)
+       ("po4a" ,po4a)
+       ("python" ,python-wrapper)))
+    (inputs
+     `(("boost" ,boost)
+       ("glew" ,glew)
+       ("libogg" ,libogg)
+       ("libpng" ,libpng)
+       ("libsndfile" ,libsndfile)
+       ("libvorbis" ,libvorbis)
+       ("openal" ,openal)
+       ("physfs" ,physfs)
+       ("sdl" ,(sdl-union (list sdl2 sdl2-image sdl2-ttf)))))
+    (synopsis "Educational programming strategy game")
+    (description "Colobot: Gold Edition is a real-time strategy game, where
+you can program your units (bots) in a language called CBOT, which is similar
+to C++ and Java.  Your mission is to find a new planet to live and survive.
+You can save humanity and get programming skills!")
+    (home-page "https://colobot.info")
+    (license license:gpl3+)))
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index e82958cee3..2939e4f648 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -1254,7 +1254,7 @@ write GNOME applications.")
                      ("check" ,check)
                      ("gettext" ,gettext-minimal)
                      ("glib:bin" ,glib "bin")
-                     ("xorg-server" ,xorg-server)))
+                     ("xorg-server" ,xorg-server-1.19.3)))
     ;; Listed in 'Requires.private' of 'girara.pc'.
     (propagated-inputs `(("gtk+" ,gtk+)))
     (arguments
@@ -1262,6 +1262,7 @@ write GNOME applications.")
        `(,(string-append "PREFIX=" (assoc-ref %outputs "out"))
          "COLOR=0" "CC=gcc")
        #:test-target "test"
+       #:disallowed-references (,xorg-server-1.19.3)
        #:phases (modify-phases %standard-phases
                   (delete 'configure)
                   (add-before 'check 'start-xserver
@@ -1270,6 +1271,11 @@ write GNOME applications.")
                       (let ((xorg-server (assoc-ref inputs "xorg-server"))
                             (display ":1"))
                         (setenv "DISPLAY" display)
+
+                        ;; On busy machines, tests may take longer than
+                        ;; the default of four seconds.
+                        (setenv "CK_DEFAULT_TIMEOUT" "20")
+
                         ;; Don't fail due to missing '/etc/machine-id'.
                         (setenv "DBUS_FATAL_WARNINGS" "0")
                         (zero? (system (string-append xorg-server "/bin/Xvfb "
diff --git a/gnu/packages/libffcall.scm b/gnu/packages/libffcall.scm
index 84fd1a833f..3a231f30a0 100644
--- a/gnu/packages/libffcall.scm
+++ b/gnu/packages/libffcall.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Joshua S. Grant <jgrant@parenthetical.io>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,7 +27,7 @@
 (define-public libffcall
    (package
     (name "libffcall")
-    (version "2.0")
+    (version "2.1")
     (source
      (origin
        (method url-fetch)
@@ -35,7 +35,7 @@
              "mirror://gnu/libffcall/libffcall-" version ".tar.gz"))
        (sha256
         (base32
-         "0v0rh3vawb8z5q40fs3kr2f9zp06n2fq4rr2ww4562nr96sd5aj1"))))
+         "0iwcad6w78jp84vd6xaz5fwqm84n3cb42bdf5m5cj5xzpa5zp4d0"))))
     (build-system gnu-build-system)
     (arguments `(#:parallel-build? #f))
     (synopsis "Foreign function calls from interpreters")
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 78d23b4f6a..aebbfccdbf 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3153,10 +3153,12 @@ and copy/paste text in the console and in xterm.")
                    (lambda _ (zero? (system* "make" "static"))))
                  (add-after 'install 'install-bash-completion
                    (lambda* (#:key outputs #:allow-other-keys)
-                     (install-file "btrfs-completion"
-                                   (string-append (assoc-ref outputs "out")
-                                                  "/etc/bash_completion.d"))
-                     #t))
+                     (let* ((out (assoc-ref outputs "out"))
+                            (bashcomp (string-append out "/etc/bash_completion.d")))
+                       (mkdir-p bashcomp)
+                       (copy-file "btrfs-completion"
+                                  (string-append bashcomp "/btrfs"))
+                       #t)))
                  (add-after 'install 'install-static
                    (let ((staticbin (string-append (assoc-ref %outputs "static")
                                                   "/bin")))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 13b9fe5786..0f87346ea9 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -339,7 +339,7 @@ the OCaml language.")
 (define-public glpk
   (package
     (name "glpk")
-    (version "4.64")
+    (version "4.65")
     (source
      (origin
       (method url-fetch)
@@ -347,7 +347,7 @@ the OCaml language.")
                           version ".tar.gz"))
       (sha256
        (base32
-        "096cqgjc7vkq6wd8znhcxjbs1s2rym3qf753fqxrrq531vs6g4jk"))))
+        "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
     (build-system gnu-build-system)
     (inputs
      `(("gmp" ,gmp)))
diff --git a/gnu/packages/patches/ruby-rubygems-276-for-ruby24.patch b/gnu/packages/patches/ruby-rubygems-276-for-ruby24.patch
new file mode 100644
index 0000000000..0d0ed6b204
--- /dev/null
+++ b/gnu/packages/patches/ruby-rubygems-276-for-ruby24.patch
@@ -0,0 +1,605 @@
+diff --git lib/rubygems.rb lib/rubygems.rb
+index 0685bcb3c6..a5a9202e56 100644
+--- ruby-2.4.3/lib/rubygems.rb
++++ ruby-2.4.3/lib/rubygems.rb
+@@ -10,7 +10,7 @@
+ require 'thread'
+ 
+ module Gem
+-  VERSION = "2.6.14"
++  VERSION = "2.6.14.1"
+ end
+ 
+ # Must be first since it unloads the prelude from 1.9.2
+diff --git lib/rubygems/commands/owner_command.rb lib/rubygems/commands/owner_command.rb
+index 4b99434e87..2ee7f84462 100644
+--- ruby-2.4.3/lib/rubygems/commands/owner_command.rb
++++ ruby-2.4.3/lib/rubygems/commands/owner_command.rb
+@@ -62,7 +62,7 @@ def show_owners name
+     end
+ 
+     with_response response do |resp|
+-      owners = YAML.load resp.body
++      owners = Gem::SafeYAML.load resp.body
+ 
+       say "Owners for gem: #{name}"
+       owners.each do |owner|
+diff --git lib/rubygems/package.rb lib/rubygems/package.rb
+index 77811ed5ec..b5a5fe2a26 100644
+--- ruby-2.4.3/lib/rubygems/package.rb
++++ ruby-2.4.3/lib/rubygems/package.rb
+@@ -378,7 +378,7 @@ def extract_tar_gz io, destination_dir, pattern = "*" # :nodoc:
+             File.dirname destination
+           end
+ 
+-        FileUtils.mkdir_p mkdir, mkdir_options
++        mkdir_p_safe mkdir, mkdir_options, destination_dir, entry.full_name
+ 
+         open destination, 'wb' do |out|
+           out.write entry.read
+@@ -416,20 +416,35 @@ def install_location filename, destination_dir # :nodoc:
+     raise Gem::Package::PathError.new(filename, destination_dir) if
+       filename.start_with? '/'
+ 
+-    destination_dir = File.realpath destination_dir if
+-      File.respond_to? :realpath
++    destination_dir = realpath destination_dir
+     destination_dir = File.expand_path destination_dir
+ 
+     destination = File.join destination_dir, filename
+     destination = File.expand_path destination
+ 
+     raise Gem::Package::PathError.new(destination, destination_dir) unless
+-      destination.start_with? destination_dir
++      destination.start_with? destination_dir + '/'
+ 
+     destination.untaint
+     destination
+   end
+ 
++  def mkdir_p_safe mkdir, mkdir_options, destination_dir, file_name
++    destination_dir = realpath File.expand_path(destination_dir)
++    parts = mkdir.split(File::SEPARATOR)
++    parts.reduce do |path, basename|
++      path = realpath path  unless path == ""
++      path = File.expand_path(path + File::SEPARATOR + basename)
++      lstat = File.lstat path rescue nil
++      if !lstat || !lstat.directory?
++        unless path.start_with? destination_dir and (FileUtils.mkdir path, mkdir_options rescue false)
++          raise Gem::Package::PathError.new(file_name, destination_dir)
++        end
++      end
++      path
++    end
++  end
++
+   ##
+   # Loads a Gem::Specification from the TarEntry +entry+
+ 
+@@ -603,6 +618,10 @@ def verify_files gem
+       raise Gem::Package::FormatError.new \
+               'package content (data.tar.gz) is missing', @gem
+     end
++
++    if duplicates = @files.group_by {|f| f }.select {|k,v| v.size > 1 }.map(&:first) and duplicates.any?
++      raise Gem::Security::Exception, "duplicate files in the package: (#{duplicates.map(&:inspect).join(', ')})"
++    end
+   end
+ 
+   ##
+@@ -616,6 +635,16 @@ def verify_gz entry # :nodoc:
+     raise Gem::Package::FormatError.new(e.message, entry.full_name)
+   end
+ 
++  if File.respond_to? :realpath
++    def realpath file
++      File.realpath file
++    end
++  else
++    def realpath file
++      file
++    end
++  end
++
+ end
+ 
+ require 'rubygems/package/digest_io'
+diff --git lib/rubygems/package/tar_header.rb lib/rubygems/package/tar_header.rb
+index c54bd14d57..d557357114 100644
+--- ruby-2.4.3/lib/rubygems/package/tar_header.rb
++++ ruby-2.4.3/lib/rubygems/package/tar_header.rb
+@@ -104,25 +104,30 @@ def self.from(stream)
+     fields = header.unpack UNPACK_FORMAT
+ 
+     new :name     => fields.shift,
+-        :mode     => fields.shift.oct,
+-        :uid      => fields.shift.oct,
+-        :gid      => fields.shift.oct,
+-        :size     => fields.shift.oct,
+-        :mtime    => fields.shift.oct,
+-        :checksum => fields.shift.oct,
++        :mode     => strict_oct(fields.shift),
++        :uid      => strict_oct(fields.shift),
++        :gid      => strict_oct(fields.shift),
++        :size     => strict_oct(fields.shift),
++        :mtime    => strict_oct(fields.shift),
++        :checksum => strict_oct(fields.shift),
+         :typeflag => fields.shift,
+         :linkname => fields.shift,
+         :magic    => fields.shift,
+-        :version  => fields.shift.oct,
++        :version  => strict_oct(fields.shift),
+         :uname    => fields.shift,
+         :gname    => fields.shift,
+-        :devmajor => fields.shift.oct,
+-        :devminor => fields.shift.oct,
++        :devmajor => strict_oct(fields.shift),
++        :devminor => strict_oct(fields.shift),
+         :prefix   => fields.shift,
+ 
+         :empty => empty
+   end
+ 
++  def self.strict_oct(str)
++    return str.oct if str =~ /\A[0-7]*\z/
++    raise ArgumentError, "#{str.inspect} is not an octal string"
++  end
++
+   ##
+   # Creates a new TarHeader using +vals+
+ 
+diff --git lib/rubygems/package/tar_writer.rb lib/rubygems/package/tar_writer.rb
+index f68b8d4c5e..390f7851a3 100644
+--- ruby-2.4.3/lib/rubygems/package/tar_writer.rb
++++ ruby-2.4.3/lib/rubygems/package/tar_writer.rb
+@@ -196,6 +196,8 @@ def add_file_signed name, mode, signer
+       digest_name == signer.digest_name
+     end
+ 
++    raise "no #{signer.digest_name} in #{digests.values.compact}" unless signature_digest
++
+     if signer.key then
+       signature = signer.sign signature_digest.digest
+ 
+diff --git lib/rubygems/server.rb lib/rubygems/server.rb
+index df4eb566d3..a7b5243ba0 100644
+--- ruby-2.4.3/lib/rubygems/server.rb
++++ ruby-2.4.3/lib/rubygems/server.rb
+@@ -631,6 +631,18 @@ def root(req, res)
+       executables = nil if executables.empty?
+       executables.last["is_last"] = true if executables
+ 
++      # Pre-process spec homepage for safety reasons
++      begin
++        homepage_uri = URI.parse(spec.homepage)
++        if [URI::HTTP, URI::HTTPS].member? homepage_uri.class
++          homepage_uri = spec.homepage
++        else
++          homepage_uri = "."
++        end
++      rescue URI::InvalidURIError
++        homepage_uri = "."
++      end
++
+       specs << {
+         "authors"             => spec.authors.sort.join(", "),
+         "date"                => spec.date.to_s,
+@@ -640,7 +652,7 @@ def root(req, res)
+         "only_one_executable" => (executables && executables.size == 1),
+         "full_name"           => spec.full_name,
+         "has_deps"            => !deps.empty?,
+-        "homepage"            => spec.homepage,
++        "homepage"            => homepage_uri,
+         "name"                => spec.name,
+         "rdoc_installed"      => Gem::RDoc.new(spec).rdoc_installed?,
+         "ri_installed"        => Gem::RDoc.new(spec).ri_installed?,
+diff --git lib/rubygems/specification.rb lib/rubygems/specification.rb
+index 40e3a70d47..0a154b9001 100644
+--- ruby-2.4.3/lib/rubygems/specification.rb
++++ ruby-2.4.3/lib/rubygems/specification.rb
+@@ -15,6 +15,7 @@
+ require 'rubygems/stub_specification'
+ require 'rubygems/util/list'
+ require 'stringio'
++require 'uri'
+ 
+ ##
+ # The Specification class contains the information for a Gem.  Typically
+@@ -2813,10 +2814,16 @@ def validate packaging = true
+       raise Gem::InvalidSpecificationException, "#{lazy} is not a summary"
+     end
+ 
+-    if homepage and not homepage.empty? and
+-       homepage !~ /\A[a-z][a-z\d+.-]*:/i then
+-      raise Gem::InvalidSpecificationException,
+-            "\"#{homepage}\" is not a URI"
++    # Make sure a homepage is valid HTTP/HTTPS URI
++    if homepage and not homepage.empty?
++      begin
++        homepage_uri = URI.parse(homepage)
++        unless [URI::HTTP, URI::HTTPS].member? homepage_uri.class
++          raise Gem::InvalidSpecificationException, "\"#{homepage}\" is not a valid HTTP URI"
++        end
++      rescue URI::InvalidURIError
++        raise Gem::InvalidSpecificationException, "\"#{homepage}\" is not a valid HTTP URI"
++      end
+     end
+ 
+     # Warnings
+diff --git test/rubygems/test_gem_commands_owner_command.rb test/rubygems/test_gem_commands_owner_command.rb
+index 44652c1093..53cac4ce87 100644
+--- ruby-2.4.3/test/rubygems/test_gem_commands_owner_command.rb
++++ ruby-2.4.3/test/rubygems/test_gem_commands_owner_command.rb
+@@ -43,6 +43,31 @@ def test_show_owners
+     assert_match %r{- 4}, @ui.output
+   end
+ 
++  def test_show_owners_dont_load_objects
++    skip "testing a psych-only API" unless defined?(::Psych::DisallowedClass)
++
++    response = <<EOF
++---
++- email: !ruby/object:Object {}
++  id: 1
++  handle: user1
++- email: user2@example.com
++- id: 3
++  handle: user3
++- id: 4
++EOF
++
++    @fetcher.data["#{Gem.host}/api/v1/gems/freewill/owners.yaml"] = [response, 200, 'OK']
++
++    assert_raises Psych::DisallowedClass do
++      use_ui @ui do
++        @cmd.show_owners("freewill")
++      end
++    end
++
++  end
++
++
+   def test_show_owners_setting_up_host_through_env_var
+     response = "- email: user1@example.com\n"
+     host = "http://rubygems.example"
+diff --git test/rubygems/test_gem_package.rb test/rubygems/test_gem_package.rb
+index 9d47f0dea4..5b93475314 100644
+--- ruby-2.4.3/test/rubygems/test_gem_package.rb
++++ ruby-2.4.3/test/rubygems/test_gem_package.rb
+@@ -455,6 +455,31 @@ def test_extract_tar_gz_symlink_relative_path
+                  File.read(extracted)
+   end
+ 
++  def test_extract_symlink_parent
++   skip 'symlink not supported' if Gem.win_platform?
++
++   package = Gem::Package.new @gem
++
++   tgz_io = util_tar_gz do |tar|
++     tar.mkdir       'lib',               0755
++     tar.add_symlink 'lib/link', '../..', 0644
++     tar.add_file    'lib/link/outside.txt', 0644 do |io| io.write 'hi' end
++   end
++
++   # Extract into a subdirectory of @destination; if this test fails it writes
++   # a file outside destination_subdir, but we want the file to remain inside
++   # @destination so it will be cleaned up.
++   destination_subdir = File.join @destination, 'subdir'
++   FileUtils.mkdir_p destination_subdir
++
++   e = assert_raises Gem::Package::PathError do
++     package.extract_tar_gz tgz_io, destination_subdir
++   end
++
++   assert_equal("installing into parent path lib/link/outside.txt of " +
++                 "#{destination_subdir} is not allowed", e.message)
++  end
++
+   def test_extract_tar_gz_directory
+     package = Gem::Package.new @gem
+ 
+@@ -566,6 +591,21 @@ def test_install_location_relative
+                  "#{@destination} is not allowed", e.message)
+   end
+ 
++  def test_install_location_suffix
++    package = Gem::Package.new @gem
++
++    filename = "../#{File.basename(@destination)}suffix.rb"
++
++    e = assert_raises Gem::Package::PathError do
++      package.install_location filename, @destination
++    end
++
++    parent = File.expand_path File.join @destination, filename
++
++    assert_equal("installing into parent path #{parent} of " +
++                 "#{@destination} is not allowed", e.message)
++  end
++
+   def test_load_spec
+     entry = StringIO.new Gem.gzip @spec.to_yaml
+     def entry.full_name() 'metadata.gz' end
+@@ -723,6 +763,32 @@ def test_verify_nonexistent
+     assert_match %r%nonexistent.gem$%,           e.message
+   end
+ 
++  def test_verify_duplicate_file
++    FileUtils.mkdir_p 'lib'
++    FileUtils.touch 'lib/code.rb'
++
++    build = Gem::Package.new @gem
++    build.spec = @spec
++    build.setup_signer
++    open @gem, 'wb' do |gem_io|
++      Gem::Package::TarWriter.new gem_io do |gem|
++        build.add_metadata gem
++        build.add_contents gem
++
++        gem.add_file_simple 'a.sig', 0444, 0
++        gem.add_file_simple 'a.sig', 0444, 0
++      end
++    end
++
++    package = Gem::Package.new @gem
++
++    e = assert_raises Gem::Security::Exception do
++      package.verify
++    end
++
++    assert_equal 'duplicate files in the package: ("a.sig")', e.message
++  end
++
+   def test_verify_security_policy
+     skip 'openssl is missing' unless defined?(OpenSSL::SSL)
+ 
+@@ -780,7 +846,13 @@ def test_verify_security_policy_checksum_missing
+ 
+         # write bogus data.tar.gz to foil signature
+         bogus_data = Gem.gzip 'hello'
+-        gem.add_file_simple 'data.tar.gz', 0444, bogus_data.length do |io|
++        fake_signer = Class.new do
++          def digest_name; 'SHA512'; end
++          def digest_algorithm; Digest(:SHA512); end
++          def key; 'key'; end
++          def sign(*); 'fake_sig'; end
++        end
++        gem.add_file_signed 'data2.tar.gz', 0444, fake_signer.new do |io|
+           io.write bogus_data
+         end
+ 
+diff --git test/rubygems/test_gem_package_tar_header.rb test/rubygems/test_gem_package_tar_header.rb
+index d33877057d..43f508df45 100644
+--- ruby-2.4.3/test/rubygems/test_gem_package_tar_header.rb
++++ ruby-2.4.3/test/rubygems/test_gem_package_tar_header.rb
+@@ -143,5 +143,26 @@ def test_update_checksum
+     assert_equal '012467', @tar_header.checksum
+   end
+ 
++  def test_from_bad_octal
++    test_cases = [
++      "00000006,44\000", # bogus character
++      "00000006789\000", # non-octal digit
++      "+0000001234\000", # positive sign
++      "-0000001000\000", # negative sign
++      "0x000123abc\000", # radix prefix
++    ]
++
++    test_cases.each do |val|
++      header_s = @tar_header.to_s
++      # overwrite the size field
++      header_s[124, 12] = val
++      io = TempIO.new header_s
++      assert_raises ArgumentError do
++        new_header = Gem::Package::TarHeader.from io
++      end
++      io.close! if io.respond_to? :close!
++    end
++  end
++
+ end
+ 
+diff --git test/rubygems/test_gem_server.rb test/rubygems/test_gem_server.rb
+index 4873fac5b6..96ed9194e9 100644
+--- ruby-2.4.3/test/rubygems/test_gem_server.rb
++++ ruby-2.4.3/test/rubygems/test_gem_server.rb
+@@ -336,6 +336,171 @@ def test_root_gemdirs
+     assert_match 'z 9', @res.body
+   end
+ 
++
++  def test_xss_homepage_fix_289313
++    data = StringIO.new "GET / HTTP/1.0\r\n\r\n"
++    dir = "#{@gemhome}2"
++
++    spec = util_spec 'xsshomepagegem', 1
++    spec.homepage = "javascript:confirm(document.domain)"
++
++    specs_dir = File.join dir, 'specifications'
++    FileUtils.mkdir_p specs_dir
++
++    open File.join(specs_dir, spec.spec_name), 'w' do |io|
++      io.write spec.to_ruby
++    end
++
++    server = Gem::Server.new dir, process_based_port, false
++
++    @req.parse data
++
++    server.root @req, @res
++
++    assert_equal 200, @res.status
++    assert_match 'xsshomepagegem 1', @res.body
++
++    # This verifies that the homepage for this spec is not displayed and is set to ".", because it's not a 
++    # valid HTTP/HTTPS URL and could be unsafe in an HTML context.  We would prefer to throw an exception here,
++    # but spec.homepage is currently free form and not currently required to be a URL, this behavior may be 
++    # validated in future versions of Gem::Specification.
++    #
++    # There are two variant we're checking here, one where rdoc is not present, and one where rdoc is present in the same regex:
++    #
++    # Variant #1 - rdoc not installed
++    #
++    #   <b>xsshomepagegem 1</b>
++    #
++    #
++    #  <span title="rdoc not installed">[rdoc]</span>
++    #
++    #
++    #
++    #  <a href="." title=".">[www]</a>
++    #
++    # Variant #2 - rdoc installed
++    #
++    #   <b>xsshomepagegem 1</b>
++    #
++    #
++    #  <a href="\/doc_root\/xsshomepagegem-1\/">\[rdoc\]<\/a>
++    #
++    #
++    #
++    #  <a href="." title=".">[www]</a>
++    regex_match = /xsshomepagegem 1<\/b>[\n\s]+(<span title="rdoc not installed">\[rdoc\]<\/span>|<a href="\/doc_root\/xsshomepagegem-1\/">\[rdoc\]<\/a>)[\n\s]+<a href="\." title="\.">\[www\]<\/a>/
++    assert_match regex_match, @res.body
++  end
++
++  def test_invalid_homepage
++    data = StringIO.new "GET / HTTP/1.0\r\n\r\n"
++    dir = "#{@gemhome}2"
++
++    spec = util_spec 'invalidhomepagegem', 1
++    spec.homepage = "notavalidhomepageurl"
++
++    specs_dir = File.join dir, 'specifications'
++    FileUtils.mkdir_p specs_dir
++
++    open File.join(specs_dir, spec.spec_name), 'w' do |io|
++      io.write spec.to_ruby
++    end
++
++    server = Gem::Server.new dir, process_based_port, false
++
++    @req.parse data
++
++    server.root @req, @res
++
++    assert_equal 200, @res.status
++    assert_match 'invalidhomepagegem 1', @res.body
++
++    # This verifies that the homepage for this spec is not displayed and is set to ".", because it's not a 
++    # valid HTTP/HTTPS URL and could be unsafe in an HTML context.  We would prefer to throw an exception here,
++    # but spec.homepage is currently free form and not currently required to be a URL, this behavior may be 
++    # validated in future versions of Gem::Specification.
++    #
++    # There are two variant we're checking here, one where rdoc is not present, and one where rdoc is present in the same regex:
++    #
++    # Variant #1 - rdoc not installed
++    #
++    #   <b>invalidhomepagegem 1</b>
++    #
++    #
++    #  <span title="rdoc not installed">[rdoc]</span>
++    #
++    #
++    #
++    #  <a href="." title=".">[www]</a>
++    #
++    # Variant #2 - rdoc installed
++    #
++    #   <b>invalidhomepagegem 1</b>
++    #
++    #
++    #  <a href="\/doc_root\/invalidhomepagegem-1\/">\[rdoc\]<\/a>
++    #
++    #
++    #
++    #  <a href="." title=".">[www]</a>
++    regex_match = /invalidhomepagegem 1<\/b>[\n\s]+(<span title="rdoc not installed">\[rdoc\]<\/span>|<a href="\/doc_root\/invalidhomepagegem-1\/">\[rdoc\]<\/a>)[\n\s]+<a href="\." title="\.">\[www\]<\/a>/
++    assert_match regex_match, @res.body
++  end
++
++  def test_valid_homepage_http
++    data = StringIO.new "GET / HTTP/1.0\r\n\r\n"
++    dir = "#{@gemhome}2"
++
++    spec = util_spec 'validhomepagegemhttp', 1
++    spec.homepage = "http://rubygems.org"
++
++    specs_dir = File.join dir, 'specifications'
++    FileUtils.mkdir_p specs_dir
++
++    open File.join(specs_dir, spec.spec_name), 'w' do |io|
++      io.write spec.to_ruby
++    end
++
++    server = Gem::Server.new dir, process_based_port, false
++
++    @req.parse data
++
++    server.root @req, @res
++
++    assert_equal 200, @res.status
++    assert_match 'validhomepagegemhttp 1', @res.body
++
++    regex_match = /validhomepagegemhttp 1<\/b>[\n\s]+(<span title="rdoc not installed">\[rdoc\]<\/span>|<a href="\/doc_root\/validhomepagegemhttp-1\/">\[rdoc\]<\/a>)[\n\s]+<a href="http:\/\/rubygems\.org" title="http:\/\/rubygems\.org">\[www\]<\/a>/
++    assert_match regex_match, @res.body
++  end
++
++  def test_valid_homepage_https
++    data = StringIO.new "GET / HTTP/1.0\r\n\r\n"
++    dir = "#{@gemhome}2"
++
++    spec = util_spec 'validhomepagegemhttps', 1
++    spec.homepage = "https://rubygems.org"
++
++    specs_dir = File.join dir, 'specifications'
++    FileUtils.mkdir_p specs_dir
++
++    open File.join(specs_dir, spec.spec_name), 'w' do |io|
++      io.write spec.to_ruby
++    end
++
++    server = Gem::Server.new dir, process_based_port, false
++
++    @req.parse data
++
++    server.root @req, @res
++
++    assert_equal 200, @res.status
++    assert_match 'validhomepagegemhttps 1', @res.body
++
++    regex_match = /validhomepagegemhttps 1<\/b>[\n\s]+(<span title="rdoc not installed">\[rdoc\]<\/span>|<a href="\/doc_root\/validhomepagegemhttps-1\/">\[rdoc\]<\/a>)[\n\s]+<a href="https:\/\/rubygems\.org" title="https:\/\/rubygems\.org">\[www\]<\/a>/
++    assert_match regex_match, @res.body
++  end
++
+   def test_specs
+     data = StringIO.new "GET /specs.#{Gem.marshal_version} HTTP/1.0\r\n\r\n"
+     @req.parse data
+diff --git test/rubygems/test_gem_specification.rb test/rubygems/test_gem_specification.rb
+index 0fcc11e78f..1c68826fb3 100644
+--- ruby-2.4.3/test/rubygems/test_gem_specification.rb
++++ ruby-2.4.3/test/rubygems/test_gem_specification.rb
+@@ -2890,7 +2890,22 @@ def test_validate_homepage
+         @a1.validate
+       end
+ 
+-      assert_equal '"over at my cool site" is not a URI', e.message
++      assert_equal '"over at my cool site" is not a valid HTTP URI', e.message
++
++      @a1.homepage = 'ftp://rubygems.org'
++
++      e = assert_raises Gem::InvalidSpecificationException do
++        @a1.validate
++      end
++
++      assert_equal '"ftp://rubygems.org" is not a valid HTTP URI', e.message
++
++      @a1.homepage = 'http://rubygems.org'
++      assert_equal true, @a1.validate
++
++      @a1.homepage = 'https://rubygems.org'
++      assert_equal true, @a1.validate
++
+     end
+   end
+ 
diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 82347f00c5..95f42c6751 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -323,7 +323,6 @@ reading and editing of existing PDF files.")
                (base32
                 "0r4viisycj39kaz4281cmkr7n9w5q96dmlf7nf45n8zq8qy2npw3"))))
     (native-inputs `(("pkg-config" ,pkg-config)))
-    (propagated-inputs `(("girara" ,girara)))
     (inputs `(("libarchive" ,libarchive)
               ("zathura" ,zathura)))
     (build-system gnu-build-system)
@@ -353,7 +352,6 @@ using libarchive.")
                (base32
                 "1x4knqja8pw2a5cb3y2209nr3iddj1z8nwasy48v5nprj61fdxqj"))))
     (native-inputs `(("pkg-config" ,pkg-config)))
-    (propagated-inputs `(("girara" ,girara)))
     (inputs `(("libspectre" ,libspectre)
               ("zathura" ,zathura)))
     (build-system gnu-build-system)
@@ -383,7 +381,6 @@ using libspectre.")
                (base32
                 "1sbfdsyp50qc85xc4458sn4w1rv1qbygdwmcr5kjlfpsmdq98vhd"))))
     (native-inputs `(("pkg-config" ,pkg-config)))
-    (propagated-inputs `(("girara" ,girara)))
     (inputs
      `(("djvulibre" ,djvulibre)
        ("zathura" ,zathura)))
@@ -414,7 +411,6 @@ using the DjVuLibre library.")
                (base32
                 "0xkajc3is7ncmb2fmymbzfgrran2bz12i7zsm1vvxhxds728h7ck"))))
     (native-inputs `(("pkg-config" ,pkg-config)))
-    (propagated-inputs `(("girara" ,girara)))
     (inputs
      `(("jbig2dec" ,jbig2dec)
        ("libjpeg" ,libjpeg)
@@ -448,7 +444,6 @@ by using the @code{mupdf} rendering library.")
                (base32
                 "1m55m7s7f8ng8a7lmcw9z4n5zv7xk4vp9n6fp9j84z6rk2imf7a2"))))
     (native-inputs `(("pkg-config" ,pkg-config)))
-    (propagated-inputs `(("girara" ,girara)))
     (inputs
      `(("poppler" ,poppler)
        ("zathura" ,zathura)))
@@ -486,7 +481,7 @@ by using the poppler rendering engine.")
 
                      ;; For tests.
                      ("check" ,check)
-                     ("xorg-server" ,xorg-server)))
+                     ("xorg-server" ,xorg-server-1.19.3)))
     (inputs `(("sqlite" ,sqlite)))
     ;; Listed in 'Requires.private' of 'zathura.pc'.
     (propagated-inputs `(("cairo" ,cairo)
@@ -501,6 +496,7 @@ by using the poppler rendering engine.")
        `(,(string-append "PREFIX=" (assoc-ref %outputs "out"))
          "CC=gcc" "COLOR=0")
        #:test-target "test"
+       #:disallowed-references (,xorg-server-1.19.3)
        #:phases (modify-phases %standard-phases
                   (delete 'configure)
                   (add-before 'check 'start-xserver
@@ -509,6 +505,11 @@ by using the poppler rendering engine.")
                       (let ((xorg-server (assoc-ref inputs "xorg-server"))
                             (display ":1"))
                         (setenv "DISPLAY" display)
+
+                        ;; On busy machines, tests may take longer than
+                        ;; the default of four seconds.
+                        (setenv "CK_DEFAULT_TIMEOUT" "20")
+
                         ;; Don't fail due to missing '/etc/machine-id'.
                         (setenv "DBUS_FATAL_WARNINGS" "0")
                         (zero? (system (string-append xorg-server "/bin/Xvfb "
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 409390ba4a..b15e1a2717 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -62,6 +62,7 @@
        (sha256
         (base32
          "0l9bv67dgsphk42lmiskhrnh47hbyj6rfg2rcjx22xivpx07srr3"))
+       (patches (search-patches "ruby-rubygems-276-for-ruby24.patch"))
        (modules '((guix build utils)))
        (snippet `(begin
                    ;; Remove bundled libffi
diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm
index ca885c690c..d5286b312e 100644
--- a/gnu/packages/scheme.scm
+++ b/gnu/packages/scheme.scm
@@ -207,7 +207,7 @@ features an integrated Emacs-like editor and a large runtime library.")
                                  version ".tar.gz"))
              (sha256
               (base32
-               "1xpzxjlq5g8j3jrb908kfaaa0pkynk4rd083hzvb08amhy68sx07"))
+               "1x7xdgsls277zlf6gcaxs2cj62xj6yvb0qxh0ddmxfamvxba0cf4"))
              ;; Remove bundled libraries.
              (modules '((guix build utils)))
              (snippet
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 29be20699d..75160c3376 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -138,14 +138,14 @@ as well as the classic centralized workflow.")
    (name "git")
    ;; XXX When updating Git, check if the special 'git:src' input to cgit needs
    ;; to be updated as well.
-   (version "2.16.1")
+   (version "2.16.2")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://kernel.org/software/scm/git/git-"
                                 version ".tar.xz"))
             (sha256
              (base32
-              "06gay8k29glg4giwphjalcc1fknxw4bmxkmbr3ic3gzxy8vl7bfg"))))
+              "05y7480f2p7fkncbhf08zz56jbykcp0ia5gl6y3djs0lsa5mfq2m"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("native-perl" ,perl)
@@ -158,7 +158,7 @@ as well as the classic centralized workflow.")
                 version ".tar.xz"))
           (sha256
            (base32
-            "1ympib7kd818v4wjgfrhxjrmv91n50lgxxg0i9gcqihgy3divrlp"))))))
+            "01fbmfsqcv7jmyh80yg3fv5jwv78zvxys9b0fd6bdcy89h9ybvj2"))))))
    (inputs
     `(("curl" ,curl)
       ("expat" ,expat)
diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 8bd8847ad9..30ca86d3a0 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -3401,7 +3401,7 @@ X server.")
 (define-public xf86-video-vesa
   (package
     (name "xf86-video-vesa")
-    (version "2.3.4")
+    (version "2.4.0")
     (source
       (origin
         (method url-fetch)
@@ -3411,7 +3411,7 @@ X server.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1haiw8r1z8ihk68d0jqph2wsld13w4qkl86biq46fvyxg7cg9pbv"))))
+            "1373vsxn6qh00na0s9c09kf09gj78rzi98zq93id8v5zsya3qi5z"))))
     (build-system gnu-build-system)
     (inputs `(("xorg-server" ,xorg-server)))
     (native-inputs `(("pkg-config" ,pkg-config)))