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-rw-r--r--gnu/packages/bioinformatics.scm4
-rw-r--r--gnu/packages/emacs.scm72
-rw-r--r--gnu/packages/engineering.scm9
-rw-r--r--gnu/packages/games.scm82
-rw-r--r--gnu/packages/gtk.scm8
-rw-r--r--gnu/packages/libffcall.scm6
-rw-r--r--gnu/packages/linux.scm10
-rw-r--r--gnu/packages/maths.scm4
-rw-r--r--gnu/packages/patches/ruby-rubygems-276-for-ruby24.patch605
-rw-r--r--gnu/packages/pdf.scm13
-rw-r--r--gnu/packages/ruby.scm1
-rw-r--r--gnu/packages/scheme.scm2
-rw-r--r--gnu/packages/version-control.scm6
-rw-r--r--gnu/packages/xorg.scm4
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)))
generated by cgit v1.2.3 (git 2.45.0) at 2024-12-02 08:53:21 +0000