Merge branch 'master' into core-updates

Makefile.am

@@ -56,6 +56,7 @@ MODULES =					\
   guix/graph.scm				\
   guix/cve.scm					\
   guix/build-system.scm				\
+  guix/build-system/ant.scm			\
   guix/build-system/cmake.scm			\
   guix/build-system/emacs.scm			\
   guix/build-system/glib-or-gtk.scm		\
@@ -75,6 +76,7 @@ MODULES =					\
   guix/cvs-download.scm				\
   guix/svn-download.scm				\
   guix/ui.scm					\
+  guix/build/ant-build-system.scm		\
   guix/build/download.scm			\
   guix/build/cmake-build-system.scm		\
   guix/build/emacs-build-system.scm		\
@@ -109,7 +111,6 @@ MODULES =					\
   guix/import/cran.scm				\
   guix/import/hackage.scm			\
   guix/import/elpa.scm   			\
-  guix/import/github.scm   			\
   guix/scripts.scm				\
   guix/scripts/download.scm			\
   guix/scripts/build.scm			\
@@ -143,6 +144,7 @@ MODULES =					\
 if HAVE_GUILE_JSON
 
 MODULES +=					\
+  guix/import/github.scm   			\
   guix/import/json.scm				\
   guix/import/pypi.scm				\
   guix/scripts/import/pypi.scm			\
@@ -171,8 +173,10 @@ dist_noinst_DATA = guix/tests.scm
 
 # Linux-Libre configurations.
 KCONFIGS =					\
-  gnu/packages/linux-libre-i686.conf		\
+  gnu/packages/linux-libre-4.5-i686.conf	\
-  gnu/packages/linux-libre-x86_64.conf		\
+  gnu/packages/linux-libre-4.5-x86_64.conf	\
+  gnu/packages/linux-libre-4.4-i686.conf	\
+  gnu/packages/linux-libre-4.4-x86_64.conf	\
   gnu/packages/linux-libre-4.1-i686.conf	\
   gnu/packages/linux-libre-4.1-x86_64.conf
 
@@ -225,6 +229,7 @@ SCM_TESTS =					\
   tests/grafts.scm				\
   tests/ui.scm					\
   tests/records.scm				\
+  tests/upstream.scm				\
   tests/utils.scm				\
   tests/build-utils.scm				\
   tests/packages.scm				\
@@ -416,7 +421,11 @@ include daemon.am
 endif BUILD_DAEMON
 
 ACLOCAL_AMFLAGS = -I m4
+
+# Pass an explicit '--localstatedir' so that configure does not error out if
+# it finds an existing installation with a different localstatedir.
 AM_DISTCHECK_CONFIGURE_FLAGS =			\
+  --localstatedir="$$dc_install_base/var"	\
   --with-libgcrypt-prefix="$(LIBGCRYPT_PREFIX)"	\
   --with-libgcrypt-libdir="$(LIBGCRYPT_LIBDIR)"	\
   --with-nix-prefix="$(NIX_PREFIX)"		\

NEWS

@@ -14,18 +14,30 @@ Please send Guix bug reports to bug-guix@gnu.org.
 
 ** Package management
 
+*** New syntax for separating package names and version numbers
+
+Use ‘@’ instead of ‘-’ as a separator, as in ‘gnupg@2.0’.  This new separator
+is a reserved character which is not allowed both in package names and version
+numbers.
+
+The old syntax to specify a package’s version—e.g., as “gnupg-2.0”—is obsolete
+and support for it will be removed in the future.
+
 *** Emacs interface for licenses
 *** Emacs interface for system generations
 *** Emacs interface for hydra.gnu.org
 *** Changes in Emacs interface variables and faces
+
 In the following names, BUFFER-TYPE means "info" or "list";
 ENTRY-TYPE means "package", "output" or "generation".
 
 **** Removed
+
 - guix-info-fill-column
 - guix-info-insert-ENTRY-TYPE-function
 
 **** Renamed
+
 - guix-info-ignore-empty-vals -> guix-info-ignore-empty-values
 - guix-output-name-width -> guix-generation-output-name-width
 - guix-buffer-name-function -> guix-ui-buffer-name-function
@@ -34,6 +46,7 @@ ENTRY-TYPE means "package", "output" or "generation".
 - guix-BUFFER-TYPE-file-path (face) -> guix-BUFFER-TYPE-file-name
 
 **** Replaced
+
 - guix-list-column-format, guix-list-column-value-methods ->
   guix-ENTRY-TYPE-list-format
 - guix-info-displayed-params, guix-info-insert-methods,
@@ -44,6 +57,10 @@ ENTRY-TYPE means "package", "output" or "generation".
   guix-ENTRY-TYPE-list-describe-warning-count
 - guix-package-info-fill-heading -> guix-info-fill
 
+** Noteworthy bug fixes
+
+*** Numbers in package names are correctly handled (http://bugs.gnu.org/19219)
+
 * Changes in 0.9.0 (since 0.8.3)
 
 ** Package management

build-aux/check-available-binaries.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,6 +21,7 @@
 ;;;
 
 (use-modules (guix store)
+             (guix grafts)
              (guix packages)
              (guix derivations)
              (gnu packages emacs)

build-aux/check-final-inputs-self-contained.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,6 +21,7 @@
 ;;;
 
 (use-modules (guix store)
+             (guix grafts)
              (guix packages)
              (guix derivations)
              (guix ui)

build-aux/hydra/gnu-system.scm

@@ -38,6 +38,7 @@
 
 (use-modules (guix config)
              (guix store)
+             (guix grafts)
              (guix packages)
              (guix derivations)
              (guix monads)
@@ -248,27 +249,35 @@ valid."
                        %packages-to-cross-build))
                 (remove (either from-32-to-64? same?) %cross-targets)))
 
-  ;; Return one job for each package, except bootstrap packages.
+  ;; Turn off grafts.  Grafting is meant to happen on the user's machines.
-  (append-map (lambda (system)
+  (parameterize ((%graft? #f))
-                (case subset
+    ;; Return one job for each package, except bootstrap packages.
-                  ((all)
+    (append-map (lambda (system)
-                   ;; Build everything.
+                  (case subset
-                   (fold-packages (lambda (package result)
+                    ((all)
-                                    (let ((job (package->job store package
+                     ;; Build everything, including replacements.
-                                                             system)))
+                     (let ((all (fold-packages
-                                      (if job
+                                 (lambda (package result)
-                                          (cons job result)
+                                   (if (package-replacement package)
-                                          result)))
+                                       (cons* package
-                                  (append (qemu-jobs store system)
+                                              (package-replacement package)
-                                          (tarball-jobs store system)
+                                              result)
-                                          (cross-jobs system))))
+                                       (cons package result)))
-                  ((core)
+                                 '()))
-                   ;; Build core packages only.
+                           (job (lambda (package)
-                   (append (map (lambda (package)
+                                  (package->job store package
-                                  (package-job store (job-name package)
+                                                system))))
-                                               package system))
+                       (append (filter-map job all)
-                                %core-packages)
+                               (qemu-jobs store system)
-                           (cross-jobs system)))
+                               (tarball-jobs store system)
-                  (else
+                               (cross-jobs system))))
-                   (error "unknown subset" subset))))
+                    ((core)
-              %hydra-supported-systems))
+                     ;; Build core packages only.
+                     (append (map (lambda (package)
+                                    (package-job store (job-name package)
+                                                 package system))
+                                  %core-packages)
+                             (cross-jobs system)))
+                    (else
+                     (error "unknown subset" subset))))
+                %hydra-supported-systems)))

config-daemon.ac

@@ -110,6 +110,20 @@ if test "x$guix_build_daemon" = "xyes"; then
   dnl Check for <linux/fs.h> (for immutable file support).
   AC_CHECK_HEADERS([linux/fs.h])
 
+  dnl Determine the appropriate default list of substitute URLs.
+  GUILE_MODULE_AVAILABLE([have_gnutls], [(gnutls)])
+  if test "x$have_gnutls" = "xyes"; then
+    guix_substitute_urls="https://mirror.hydra.gnu.org https://hydra.gnu.org"
+  else
+    AC_MSG_WARN([GnuTLS is missing, substitutes will be downloaded in the clear])
+    guix_substitute_urls="http://mirror.hydra.gnu.org http://hydra.gnu.org"
+  fi
+  AC_MSG_CHECKING([for default substitute URLs])
+  AC_MSG_RESULT([$guix_substitute_urls])
+
+  AC_DEFINE_UNQUOTED([GUIX_SUBSTITUTE_URLS], ["$guix_substitute_urls"],
+    [Default list of substitute URLs used by 'guix-daemon'.])
+
   dnl Check whether the 'offload' build hook can be built (uses
   dnl 'restore-file-set', which requires unbuffered custom binary input
   dnl ports from Guile >= 2.0.10.)
@@ -126,6 +140,8 @@ if test "x$guix_build_daemon" = "xyes"; then
   GUIX_TEST_ROOT="$ac_cv_guix_test_root"
   AC_SUBST([GUIX_TEST_ROOT])
 
+  GUIX_CHECK_LOCALSTATEDIR
+
   AC_CONFIG_FILES([nix/scripts/list-runtime-roots],
     [chmod +x nix/scripts/list-runtime-roots])
   AC_CONFIG_FILES([nix/scripts/substitute],

doc.am

@@ -98,45 +98,48 @@ dvi-local: ps-local
 ##  Man pages. ##
 ## ----------- ##
 
+# The man pages are generated using GNU Help2man.  In makefiles rules they
+# depend not on the binary, but on the source files.  This usage allows a
+# manual page to be generated by the maintainer and included in the
+# distribution without requiring the end-user to have 'help2man' installed.
+# They are built in $(srcdir) like info manuals.
+
 sub_commands_mans =				\
-  doc/guix-archive.1				\
+  $(srcdir)/doc/guix-archive.1			\
-  doc/guix-build.1				\
+  $(srcdir)/doc/guix-build.1			\
-  doc/guix-challenge.1				\
+  $(srcdir)/doc/guix-challenge.1		\
-  doc/guix-download.1				\
+  $(srcdir)/doc/guix-download.1			\
-  doc/guix-edit.1				\
+  $(srcdir)/doc/guix-edit.1			\
-  doc/guix-environment.1			\
+  $(srcdir)/doc/guix-environment.1		\
-  doc/guix-gc.1					\
+  $(srcdir)/doc/guix-gc.1			\
-  doc/guix-hash.1				\
+  $(srcdir)/doc/guix-hash.1			\
-  doc/guix-import.1				\
+  $(srcdir)/doc/guix-import.1			\
-  doc/guix-lint.1				\
+  $(srcdir)/doc/guix-lint.1			\
-  doc/guix-package.1				\
+  $(srcdir)/doc/guix-package.1			\
-  doc/guix-publish.1				\
+  $(srcdir)/doc/guix-publish.1			\
-  doc/guix-pull.1				\
+  $(srcdir)/doc/guix-pull.1			\
-  doc/guix-refresh.1				\
+  $(srcdir)/doc/guix-refresh.1			\
-  doc/guix-size.1				\
+  $(srcdir)/doc/guix-size.1			\
-  doc/guix-system.1
+  $(srcdir)/doc/guix-system.1
 
 dist_man1_MANS =				\
-  doc/guix.1					\
+  $(srcdir)/doc/guix.1				\
   $(sub_commands_mans)
 
-# Man pages are generated using GNU help2man.
 gen_man =						\
   LANGUAGE= $(top_builddir)/pre-inst-env $(HELP2MAN)	\
   $(HELP2MANFLAGS)
 
 HELP2MANFLAGS = --source=GNU --info-page=$(PACKAGE_TARNAME)
 
-# Note: Do not depend on 'scripts/guix' since that would trigger a rebuild
+$(srcdir)/doc/guix.1: scripts/guix.in $(sub_commands_mans)
-# even for people building from a tarball.
-doc/guix.1: $(sub_commands_mans)
 	-$(AM_V_HELP2MAN)$(gen_man) --output="$@" `basename "$@" .1`
 
-# Note: The dependency on $(GOBJECTS) is meant to force these docs to be made
+# The 'case' ensures the man pages are only generated if the corresponding
-# only after all Guile modules have been compiled.  The 'case' ensures the man
+# source script (the first prerequisite) has been changed.  The $(GOBJECTS)
-# pages are only generated if the corresponding script source has been
+# prerequisite is solely meant to force these docs to be made only after all
-# changed.
+# Guile modules have been compiled.
-doc/guix-%.1: guix/scripts/%.scm $(GOBJECTS)
+$(srcdir)/doc/guix-%.1: guix/scripts/%.scm $(GOBJECTS)
 	-@case '$?' in \
 	  *$<*) $(AM_V_P) && set -x || echo "  HELP2MAN $@"; \
 	        $(gen_man) --output="$@" "guix $*";; \
@@ -145,11 +148,9 @@ doc/guix-%.1: guix/scripts/%.scm $(GOBJECTS)
 
 if BUILD_DAEMON
 
-dist_man1_MANS += doc/guix-daemon.1
+dist_man1_MANS += $(srcdir)/doc/guix-daemon.1
 
-# Note: Do not depend on 'guix-daemon' since that would trigger a rebuild even
+$(srcdir)/doc/guix-daemon.1: nix/nix-daemon/guix-daemon.cc
-# for people building from a tarball.
-doc/guix-daemon.1: nix/nix-daemon/guix-daemon.cc
 	-$(AM_V_HELP2MAN)$(gen_man) --output="$@" `basename "$@" .1`
 
 endif

doc/contributing.texi

@@ -140,7 +140,13 @@ necessary to support this, including @env{PATH} and @env{GUILE_LOAD_PATH}.
 Note that @command{./pre-inst-env guix pull} does @emph{not} upgrade the
 local source tree; it simply updates the @file{~/.config/guix/latest}
 symlink (@pxref{Invoking guix pull}).  Run @command{git pull} instead if
-you want to upgrade your local source tree.
+you want to upgrade your local source tree.@footnote{If you would like
+to set up @command{guix} to use your Git checkout, you can point the
+@file{~/.config/guix/latest} symlink to your Git checkout directory.
+If you are the sole user of your system, you may also consider pointing
+the @file{/root/.config/guix/latest} symlink to point to
+@file{~/.config/guix/latest}; this way it will always use the same
+@command{guix} as your user does.}
 
 
 @node The Perfect Setup

emacs.am

@@ -64,7 +64,7 @@ $(AUTOLOADS): $(ELFILES)
 	$(AM_V_EMACS)$(EMACS) --batch --eval				\
 	  "(let ((backup-inhibited t)					\
 	         (generated-autoload-file				\
-	          (expand-file-name \"$(AUTOLOADS)\" \"$(srcdir)\")))	\
+	          (expand-file-name \"$(AUTOLOADS)\" \"$(builddir)\")))	\
 	     (update-directory-autoloads				\
 	      (expand-file-name \"emacs\" \"$(srcdir)\")))"
 

emacs/guix-base.el

@@ -44,7 +44,7 @@
 
 (defun guix-package-name-specification (name version &optional output)
   "Return Guix package specification by its NAME, VERSION and OUTPUT."
-  (concat name "-" version
+  (concat name "@" version
           (when output (concat ":" output))))
 
 

emacs/guix-hydra.el

@@ -36,6 +36,10 @@
   (concat ".*\\." (regexp-opt guix-help-system-types) "\\'")
   "Regexp matching a full name of Hydra job (including system).")
 
+(defun guix-hydra-job-name-specification (name version)
+  "Return Hydra's job name specification by NAME and VERSION."
+  (concat name "-" version))
+
 (defun guix-hydra-message (entries search-type &rest _)
   "Display a message after showing Hydra ENTRIES."
   ;; XXX Add more messages maybe.

emacs/guix-main.scm

@@ -86,13 +86,13 @@
 (define (full-name->name+version spec)
   "Given package specification SPEC with or without output,
 return two values: name and version.  For example, for SPEC
-\"foo-0.9.1b:lib\", return \"foo\" and \"0.9.1b\"."
+\"foo@0.9.1b:lib\", return \"foo\" and \"0.9.1b\"."
   (let-values (((name version output)
                 (package-specification->name+version+output spec)))
     (values name version)))
 
 (define (name+version->full-name name version)
-  (string-append name "-" version))
+  (string-append name "@" version))
 
 (define* (make-package-specification name #:optional version output)
   (let ((full-name (if version
@@ -263,7 +263,8 @@ Example:
   "Return a list of full names of the packages from package INPUTS."
   (filter-map (match-lambda
                ((_ (? package? package))
-                (package-full-name package))
+                (make-package-specification (package-name package)
+                                            (package-version package)))
                ((_ (? package? package) output)
                 (make-package-specification (package-name package)
                                             (package-version package)
@@ -953,10 +954,11 @@ GENERATIONS is a list of generation numbers."
 
 (define (package-location-string id-or-name)
   "Return a location string of a package with ID-OR-NAME."
-  (and-let* ((package  (or (package-by-id id-or-name)
+  (and=> (or (package-by-id id-or-name)
-                           (first (packages-by-name id-or-name))))
+             (match (packages-by-name id-or-name)
-             (location (package-location package)))
+               (()              #f)
-    (location->string location)))
+               ((package _ ...) package)))
+         (compose location->string package-location)))
 
 (define (package-source-derivation->store-path derivation)
   "Return a store path of the package source DERIVATION."

emacs/guix-ui-package.el

@@ -34,6 +34,7 @@
 (require 'guix-guile)
 (require 'guix-entry)
 (require 'guix-utils)
+(require 'guix-hydra)
 (require 'guix-hydra-build)
 (require 'guix-read)
 (require 'guix-license)
@@ -388,7 +389,7 @@ formatted with this string, an action button is inserted.")
                           :system (button-label btn))))
                (apply #'guix-hydra-build-get-display
                       'latest args)))
-   'job-name (guix-package-name-specification
+   'job-name (guix-hydra-job-name-specification
               (guix-entry-value entry 'name)
               (guix-entry-value entry 'version))))
 
@@ -776,7 +777,7 @@ for all ARGS."
   (interactive
    (let ((entry (guix-list-current-entry)))
      (guix-hydra-build-latest-prompt-args
-      :job (guix-package-name-specification
+      :job (guix-hydra-job-name-specification
             (guix-entry-value entry 'name)
             (guix-entry-value entry 'version)))))
   (apply #'guix-hydra-latest-builds number args))
@@ -945,7 +946,7 @@ See `guix-find-location' for the meaning of DIRECTORY."
 (defun guix-packages-by-name (name &optional profile)
   "Display Guix packages with NAME.
 NAME is a string with name specification.  It may optionally contain
-a version number.  Examples: \"guile\", \"guile-2.0.11\".
+a version number.  Examples: \"guile\", \"guile@2.0.11\".
 
 If PROFILE is nil, use `guix-current-profile'.
 Interactively with prefix, prompt for PROFILE."

gnu-system.am

@@ -166,12 +166,13 @@ GNU_SYSTEM_MODULES =				\
   gnu/packages/indent.scm			\
   gnu/packages/inklingreader.scm		\
   gnu/packages/inkscape.scm			\
-  gnu/packages/irssi.scm			\
+  gnu/packages/irc.scm  			\
   gnu/packages/iso-codes.scm			\
   gnu/packages/java.scm				\
   gnu/packages/jemalloc.scm			\
   gnu/packages/jrnl.scm				\
   gnu/packages/julia.scm			\
+  gnu/packages/kde.scm              \
   gnu/packages/kde-frameworks.scm		\
   gnu/packages/key-mon.scm			\
   gnu/packages/kodi.scm				\
@@ -336,7 +337,6 @@ GNU_SYSTEM_MODULES =				\
   gnu/packages/wdiff.scm			\
   gnu/packages/web.scm				\
   gnu/packages/webkit.scm			\
-  gnu/packages/weechat.scm			\
   gnu/packages/wget.scm				\
   gnu/packages/wicd.scm				\
   gnu/packages/wine.scm				\
@@ -426,7 +426,6 @@ dist_patch_DATA =						\
   gnu/packages/patches/bigloo-gc-shebangs.patch			\
   gnu/packages/patches/binutils-ld-new-dtags.patch		\
   gnu/packages/patches/binutils-loongson-workaround.patch	\
-  gnu/packages/patches/bitlbee-configure-doc-fix.patch		\
   gnu/packages/patches/byobu-writable-status.patch		\
   gnu/packages/patches/calibre-drop-unrar.patch			\
   gnu/packages/patches/calibre-no-updates-dialog.patch		\
@@ -455,6 +454,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/duplicity-piped-password.patch		\
   gnu/packages/patches/duplicity-test_selection-tmp.patch	\
   gnu/packages/patches/elfutils-tests-ptrace.patch		\
+  gnu/packages/patches/einstein-build.patch			\
   gnu/packages/patches/emacs-constants-lisp-like.patch		\
   gnu/packages/patches/emacs-exec-path.patch			\
   gnu/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch	\
@@ -484,7 +484,6 @@ dist_patch_DATA =						\
   gnu/packages/patches/geoclue-config.patch			\
   gnu/packages/patches/ghostscript-CVE-2015-3228.patch		\
   gnu/packages/patches/ghostscript-runpath.patch		\
-  gnu/packages/patches/gitolite-openssh-6.8-compat.patch	\
   gnu/packages/patches/glib-networking-ssl-cert-file.patch	\
   gnu/packages/patches/glib-tests-desktop.patch			\
   gnu/packages/patches/glib-tests-homedir.patch			\
@@ -526,10 +525,29 @@ dist_patch_DATA =						\
   gnu/packages/patches/hydra-disable-darcs-test.patch		\
   gnu/packages/patches/icecat-avoid-bundled-includes.patch	\
   gnu/packages/patches/icecat-update-graphite2.patch		\
+  gnu/packages/patches/icecat-update-graphite2-pt2.patch	\
   gnu/packages/patches/icecat-re-enable-DHE-cipher-suites.patch	\
+  gnu/packages/patches/icecat-CVE-2015-4477.patch		\
+  gnu/packages/patches/icecat-CVE-2015-7207.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1952-pt01.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1952-pt02.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1952-pt03.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1952-pt04.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1952-pt05.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1952-pt06.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1954.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1960.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1961.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1962.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1964.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1965.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1966.patch		\
+  gnu/packages/patches/icecat-CVE-2016-1974.patch		\
+  gnu/packages/patches/icecat-bug-1248851.patch			\
   gnu/packages/patches/icu4c-CVE-2014-6585.patch		\
   gnu/packages/patches/icu4c-CVE-2015-1270.patch		\
   gnu/packages/patches/icu4c-CVE-2015-4760.patch		\
+  gnu/packages/patches/ilmbase-fix-tests.patch			\
   gnu/packages/patches/imagemagick-test-segv.patch		\
   gnu/packages/patches/irrlicht-mesa-10.patch			\
   gnu/packages/patches/jasper-CVE-2007-2721.patch		\
@@ -541,7 +559,10 @@ dist_patch_DATA =						\
   gnu/packages/patches/jasper-CVE-2014-8157.patch		\
   gnu/packages/patches/jasper-CVE-2014-8158.patch		\
   gnu/packages/patches/jasper-CVE-2014-9029.patch		\
+  gnu/packages/patches/jasper-CVE-2016-1577.patch		\
   gnu/packages/patches/jasper-CVE-2016-1867.patch		\
+  gnu/packages/patches/jasper-CVE-2016-2089.patch		\
+  gnu/packages/patches/jasper-CVE-2016-2116.patch		\
   gnu/packages/patches/jbig2dec-ignore-testtest.patch		\
   gnu/packages/patches/kmod-module-directory.patch		\
   gnu/packages/patches/ldc-disable-tests.patch			\
@@ -561,6 +582,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/libevent-dns-tests.patch			\
   gnu/packages/patches/libmtp-devices.patch			\
   gnu/packages/patches/liboop-mips64-deplibs-fix.patch		\
+  gnu/packages/patches/libotr-test-auth-fix.patch		\
   gnu/packages/patches/liblxqt-include.patch			\
   gnu/packages/patches/libmad-armv7-thumb-pt1.patch		\
   gnu/packages/patches/libmad-armv7-thumb-pt2.patch		\
@@ -614,7 +636,6 @@ dist_patch_DATA =						\
   gnu/packages/patches/module-init-tools-moduledir.patch	\
   gnu/packages/patches/mumps-build-parallelism.patch		\
   gnu/packages/patches/mupen64plus-ui-console-notice.patch	\
-  gnu/packages/patches/mupdf-buildsystem-fix.patch		\
   gnu/packages/patches/mutt-store-references.patch		\
   gnu/packages/patches/net-tools-bitrot.patch			\
   gnu/packages/patches/ngircd-handle-zombies.patch		\
@@ -632,6 +653,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/openjpeg-use-after-free-fix.patch	\
   gnu/packages/patches/openssl-runpath.patch			\
   gnu/packages/patches/openssl-c-rehash.patch			\
+  gnu/packages/patches/openssl-c-rehash-in.patch		\
   gnu/packages/patches/orpheus-cast-errors-and-includes.patch	\
   gnu/packages/patches/ots-no-include-missing-file.patch	\
   gnu/packages/patches/patchelf-page-size.patch			\
@@ -639,6 +661,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/patchutils-xfail-gendiff-tests.patch	\
   gnu/packages/patches/patch-hurd-path-max.patch		\
   gnu/packages/patches/perl-CVE-2015-8607.patch			\
+  gnu/packages/patches/perl-CVE-2016-2381.patch			\
   gnu/packages/patches/perl-autosplit-default-time.patch	\
   gnu/packages/patches/perl-deterministic-ordering.patch	\
   gnu/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch \
@@ -661,6 +684,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/plotutils-libpng-jmpbuf.patch		\
   gnu/packages/patches/polkit-drop-test.patch			\
   gnu/packages/patches/portaudio-audacity-compat.patch		\
+  gnu/packages/patches/procmail-ambiguous-getline-debian.patch  \
   gnu/packages/patches/pt-scotch-build-parallelism.patch	\
   gnu/packages/patches/pulseaudio-fix-mult-test.patch		\
   gnu/packages/patches/pulseaudio-longer-test-timeout.patch	\
@@ -677,6 +701,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/python-disable-ssl-test.patch		\
   gnu/packages/patches/python-fix-tests.patch			\
   gnu/packages/patches/python-ipython-inputhook-ctype.patch	\
+  gnu/packages/patches/python-rarfile-fix-tests.patch		\
   gnu/packages/patches/python2-rdflib-drop-sparqlwrapper.patch	\
   gnu/packages/patches/python-configobj-setuptools.patch	\
   gnu/packages/patches/python-paste-remove-website-test.patch	\
@@ -702,7 +727,6 @@ dist_patch_DATA =						\
   gnu/packages/patches/sed-hurd-path-max.patch			\
   gnu/packages/patches/scheme48-tests.patch			\
   gnu/packages/patches/scotch-test-threading.patch		\
-  gnu/packages/patches/scribus-qobject.patch			\
   gnu/packages/patches/sdl-libx11-1.6.patch			\
   gnu/packages/patches/serf-comment-style-fix.patch		\
   gnu/packages/patches/serf-deflate-buckets-test-fix.patch	\
@@ -746,6 +770,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/util-linux-tests.patch			\
   gnu/packages/patches/upower-builddir.patch			\
   gnu/packages/patches/valgrind-enable-arm.patch		\
+  gnu/packages/patches/vorbis-tools-CVE-2015-6749.patch		\
   gnu/packages/patches/vpnc-script.patch			\
   gnu/packages/patches/vtk-mesa-10.patch			\
   gnu/packages/patches/w3m-libgc.patch				\

gnu/build/activation.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -91,7 +91,8 @@
     (mkdir-p home)
     (for-each (lambda (file)
                 (let ((target (string-append home "/" file)))
-                  (copy-file (string-append directory "/" file) target)
+                  (copy-recursively (string-append directory "/" file)
+                                    target)
                   (make-file-writable target)))
               files)))
 

gnu/build/install.scm

@@ -159,7 +159,7 @@ as created and modified at the Epoch."
                 ;; read-only store.
                 (unless (eq? (stat:type s) 'symlink)
                   (utime file 0 0 0 0))))
-            (find-files directory "")))
+            (find-files directory #:directories? #t)))
 
 (define* (register-closure store closure
                            #:key (deduplicate? #t))

gnu/packages.scm

@@ -1,8 +1,9 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Alex Kost <alezost@gmail.com>
+;;; Copyright © 2016 Mathieu Lirzin <mthl@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,6 +24,9 @@
   #:use-module (guix packages)
   #:use-module (guix ui)
   #:use-module (guix utils)
+  #:use-module ((guix build utils)
+                #:select ((package-name->name+version
+                           . hyphen-separated-name->name+version)))
   #:use-module (ice-9 ftw)
   #:use-module (ice-9 vlist)
   #:use-module (ice-9 match)
@@ -276,56 +280,63 @@ return its return value."
                     (lambda (k signum)
                       (handler signum))))
 
-(define (specification->package spec)
+
-  "Return a package matching SPEC.  SPEC may be a package name, or a package
+;;;
-name followed by a hyphen and a version number.  If the version number is not
+;;; Package specification.
-present, return the preferred newest version."
+;;;
-  (let-values (((name version)
+
-                (package-name->name+version spec)))
+(define* (%find-package spec name version #:key fallback?)
-    (match (find-best-packages-by-name name version)
+  (match (find-best-packages-by-name name version)
-      ((p)                                      ; one match
+    ((pkg . pkg*)
-       p)
+     (unless (null? pkg*)
-      ((p x ...)                                ; several matches
        (warning (_ "ambiguous package specification `~a'~%") spec)
        (warning (_ "choosing ~a from ~a~%")
-                (package-full-name p)
+                (package-full-name pkg)
-                (location->string (package-location p)))
+                (location->string (package-location pkg))))
-       p)
+     (when fallback?
-      (_                                        ; no matches
+       (warning (_ "deprecated NAME-VERSION syntax; \
-       (if version
+use NAME@VERSION instead~%")))
-           (leave (_ "~A: package not found for version ~a~%")
+     pkg)
-                  name version)
+    (_
-           (leave (_ "~A: unknown package~%") name))))))
+     (if version
+         (leave (_ "~A: package not found for version ~a~%") name version)
+         (if (not fallback?)
+             ;; XXX: Fallback to the older specification style with an hyphen
+             ;; between NAME and VERSION, for backward compatibility.
+             (call-with-values
+                 (lambda ()
+                   (hyphen-separated-name->name+version name))
+               (cut %find-package spec <> <> #:fallback? #t))
+
+             ;; The fallback case didn't find anything either, so bail out.
+             (leave (_ "~A: unknown package~%") name))))))
+
+(define (specification->package spec)
+  "Return a package matching SPEC.  SPEC may be a package name, or a package
+name followed by an at-sign and a version number.  If the version number is not
+present, return the preferred newest version."
+  (let-values (((name version) (package-name->name+version spec)))
+    (%find-package spec name version)))
 
 (define* (specification->package+output spec #:optional (output "out"))
   "Return the package and output specified by SPEC, or #f and #f; SPEC may
 optionally contain a version number and an output name, as in these examples:
 
   guile
-  guile-2.0.9
+  guile@2.0.9
   guile:debug
-  guile-2.0.9:debug
+  guile@2.0.9:debug
 
 If SPEC does not specify a version number, return the preferred newest
 version; if SPEC does not specify an output, return OUTPUT."
-  (define (ensure-output p sub-drv)
-    (if (member sub-drv (package-outputs p))
-        sub-drv
-        (leave (_ "package `~a' lacks output `~a'~%")
-               (package-full-name p)
-               sub-drv)))
-
   (let-values (((name version sub-drv)
                 (package-specification->name+version+output spec output)))
-    (match (find-best-packages-by-name name version)
+    (match (%find-package spec name version)
-      ((p)
+      (#f
-       (values p (ensure-output p sub-drv)))
+       (values #f #f))
-      ((p p* ...)
+      (package
-       (warning (_ "ambiguous package specification `~a'~%")
+       (if (member sub-drv (package-outputs package))
-                spec)
+           (values package sub-drv)
-       (warning (_ "choosing ~a from ~a~%")
+           (leave (_ "package `~a' lacks output `~a'~%")
-                (package-full-name p)
+                  (package-full-name package)
-                (location->string (package-location p)))
+                  sub-drv))))))
-       (values p (ensure-output p sub-drv)))
-      (()
-       (leave (_ "~a: package not found~%") spec)))))

gnu/packages/admin.scm

@@ -9,6 +9,7 @@
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -424,7 +425,7 @@ connection alive.")
          (bind-minor-version "9")
          (bind-patch-version "8")
          (bind-release-type "-P")
-         (bind-release-version "3")
+         (bind-release-version "4")
          (bind-version (string-append bind-major-version
                                       "."
                                       bind-minor-version
@@ -540,7 +541,7 @@ connection alive.")
                                         "/bind-" bind-version ".tar.gz"))
                     (sha256
                      (base32
-                      "01qa17479jghy90lb2j8b1bpg3ay6k6aaajpigyirwzsvyc9yj3a"))))
+                      "1wl9kl0630dc1qjrf7fnp8cscagfm5qgmisi0zhr1p6iwi9bil2y"))))
 
                 ;; When cross-compiling, we need the cross Coreutils and sed.
                 ;; Otherwise just use those from %FINAL-INPUTS.

gnu/packages/algebra.scm

@@ -67,7 +67,7 @@ multiplication routines such as Toom–Cook and the FFT.")
 (define-public cm
   (package
    (name "cm")
-   (version "0.2.1")
+   (version "0.3")
    (source (origin
             (method url-fetch)
             (uri (string-append
@@ -75,7 +75,7 @@ multiplication routines such as Toom–Cook and the FFT.")
                   version ".tar.gz"))
             (sha256
              (base32
-              "1r5dx5qy0ka2sq26n9jll9iy4sjqg0jp5r3jnbjhpgxvmj8jbhq8"))))
+              "1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc"))))
    (build-system gnu-build-system)
    (propagated-inputs
      `(("mpfrcx" ,mpfrcx)
@@ -89,7 +89,7 @@ imaginary quadratic number fields and of elliptic curves with complex
 multiplication via floating point approximations.  It consists of libraries
 that can be called from within a C program and of executable command
 line applications.")
-   (license license:gpl2+)
+   (license license:gpl3+)
    (home-page "http://cm.multiprecision.org/")))
 
 (define-public fplll

gnu/packages/aspell.scm

@@ -139,3 +139,11 @@ dictionaries, including personal ones.")
                      #:sha256
                      (base32
                       "1gdf7bc1a0kmxsmphdqq8pl01h667mjsj6hihy6kqy14k5qdq69v")))
+
+(define-public aspell-dict-nl
+  (aspell-dictionary "nl" "Dutch"
+                     #:version "0.50-2"
+                     #:prefix "aspell-"
+                     #:sha256
+                     (base32
+                      "0ffb87yjsh211hllpc4b9khqqrblial4pzi1h9r3v465z1yhn3j4")))

gnu/packages/audio.scm

@@ -80,6 +80,17 @@
                (base32
                 "1azbrhpfk4nnybr7kgmc7w6al6xnzppg853vas8gmkh185kk11l0"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags '("--enable-qt5")
+       #:phases
+       (modify-phases %standard-phases
+         ;; Insert an extra space between linker flags.
+         (add-before 'configure 'add-missing-space
+           (lambda _
+             (substitute* "configure"
+               (("LIBS\\+=\\$LIBSsave") "LIBS+=\" $LIBSsave\"")
+               (("CFLAGS\\+=\\$CFLAGSsave") "CFLAGS+=\" $CFLAGSsave\""))
+             #t)))))
     (inputs
      `(("alsa-lib" ,alsa-lib)
        ;; We cannot use zita-alsa-pcmi (the successor of clalsadrv) due to
@@ -89,7 +100,7 @@
        ("jack" ,jack-1)
        ("ladspa" ,ladspa)
        ("liblo" ,liblo)
-       ("qt" ,qt-4)))
+       ("qt" ,qt)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (home-page "http://alsamodular.sourceforge.net/")
@@ -395,6 +406,319 @@ language and software synthesizer.")
 ALSA PCM devices.")
     (license license:gpl2+)))
 
+(define-public amb-plugins
+  (package
+    (name "amb-plugins")
+    (version "0.8.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://kokkinizita.linuxaudio.org"
+                    "/linuxaudio/downloads/AMB-plugins-"
+                    version ".tar.bz2"))
+              (sha256
+               (base32
+                "0x4blm4visjqj0ndqr0cg776v3b7lvplpc8cgi9n51llhavn0jpl"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         ;; no configure script
+         (delete 'configure)
+         (add-before 'install 'prepare-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/lib/ladspa"))
+             #t))
+         (add-after 'unpack 'override-target-directory-and-tool-paths
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("/usr/lib/ladspa")
+                (string-append (assoc-ref outputs "out") "/lib/ladspa"))
+               (("/usr/bin/install") (which "install"))
+               (("/bin/rm") "#"))
+             #t)))))
+    (home-page "http://kokkinizita.linuxaudio.org")
+    (synopsis "LADSPA ambisonics plugins")
+    (description
+     "The AMB plugins are a set of LADSPA ambisonics plugins, mainly to be
+used within Ardour.  Features include: mono and stereo to B-format panning,
+horizontal rotator, square, hexagon and cube decoders.")
+    (license license:gpl2+)))
+
+(define-public mcp-plugins
+  (package
+    (name "mcp-plugins")
+    (version "0.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://kokkinizita.linuxaudio.org"
+                    "/linuxaudio/downloads/MCP-plugins-"
+                    version ".tar.bz2"))
+              (sha256
+               (base32
+                "06a9r1l85jmg7l1cvc3788mk8ra0xagjfy1rmhw3b80y4n0vlnvc"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         ;; no configure script
+         (delete 'configure)
+         (add-before 'install 'prepare-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/lib/ladspa"))
+             #t))
+         (add-after 'unpack 'override-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("/usr") (assoc-ref outputs "out")))
+             #t)))))
+    (home-page "http://kokkinizita.linuxaudio.org")
+    (synopsis "Chorus, phaser, and vintage high-pass and low-pass filters")
+    (description
+     "This package provides various LADSPA plugins.  @code{cs_chorus} and
+@code{cs_phaser} provide chorus and phaser effects, respectively;
+@code{mvclpf24} provides four implementations of the low-pass filter used in
+vintage Moog synthesizers; @code{mvchpf24} is based on the voltage-controlled
+high-pass filter by Robert Moog.  The filters attempt to accurately emulate
+the non-linear circuit elements of their original analog counterparts.")
+    (license license:gpl2+)))
+
+(define-public rev-plugins
+  (package
+    (name "rev-plugins")
+    (version "0.7.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://kokkinizita.linuxaudio.org"
+                    "/linuxaudio/downloads/REV-plugins-"
+                    version ".tar.bz2"))
+              (sha256
+               (base32
+                "1ikpinxm00pkfi259bnkzhsy3miagrjgdihaaf5x4v7zac29j3g7"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         ;; no configure script
+         (delete 'configure)
+         (add-before 'install 'prepare-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/lib/ladspa"))
+             #t))
+         (add-after 'unpack 'override-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("/usr") (assoc-ref outputs "out")))
+             #t)))))
+    (home-page "http://kokkinizita.linuxaudio.org")
+    (synopsis "LADSPA reverb plugin")
+    (description
+     "This package provides a stereo reverb LADSPA plugin based on the
+well-known greverb.")
+    (license license:gpl2+)))
+
+(define-public fil-plugins
+  (package
+    (name "fil-plugins")
+    (version "0.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://kokkinizita.linuxaudio.org"
+                    "/linuxaudio/downloads/FIL-plugins-"
+                    version ".tar.bz2"))
+              (sha256
+               (base32
+                "1scfv9j7jrp50r565haa4rvxn1vk2ss86xssl5qgcr8r45qz42qw"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         ;; no configure script
+         (delete 'configure)
+         (add-before 'install 'prepare-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/lib/ladspa"))
+             #t))
+         (add-after 'unpack 'override-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("/usr") (assoc-ref outputs "out")))
+             #t)))))
+    (home-page "http://kokkinizita.linuxaudio.org")
+    (synopsis "LADSPA four-band parametric equalizer plugin")
+    (description
+     "This package provides a LADSPA plugin for a four-band parametric
+equalizer.  Each section has an active/bypass switch, frequency, bandwidth and
+gain controls.  There is also a global bypass switch and gain control.
+
+The 2nd order resonant filters are implemented using a Mitra-Regalia style
+lattice filter, which is stable even while parameters are being changed.
+
+All switches and controls are internally smoothed, so they can be used 'live'
+without any clicks or zipper noises.  This makes this plugin suitable for use
+in systems that allow automation of plugin control ports, such as Ardour, or
+for stage use.")
+    (license license:gpl2+)))
+
+(define-public ste-plugins
+  (package
+    (name "ste-plugins")
+    (version "0.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://kokkinizita.linuxaudio.org"
+                    "/linuxaudio/downloads/STE-plugins-"
+                    version ".tar.bz2"))
+              (sha256
+               (base32
+                "0s3c9w5xihs87cnd1lh9xgj3maabjdyh6bl766qp5lhkg3ax8zy6"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         ;; no configure script
+         (delete 'configure)
+         (add-before 'install 'prepare-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/lib/ladspa"))
+             #t))
+         (add-after 'unpack 'override-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("/usr") (assoc-ref outputs "out")))
+             #t)))))
+    (home-page "http://kokkinizita.linuxaudio.org")
+    (synopsis "LADSPA stereo width plugin")
+    (description
+     "This package provides a LADSPA plugin to manipulate the stereo width of
+audio signals.")
+    (license license:gpl2+)))
+
+(define-public vco-plugins
+  (package
+    (name "vco-plugins")
+    (version "0.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://kokkinizita.linuxaudio.org"
+                    "/linuxaudio/downloads/VCO-plugins-"
+                    version ".tar.bz2"))
+              (sha256
+               (base32
+                "1xzqdg3b07r7zww05y9bb737l9dxvfkv28m3fyak1aazaci3rsgl"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         ;; no configure script
+         (delete 'configure)
+         (add-before 'install 'prepare-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/lib/ladspa"))
+             #t))
+         (add-after 'unpack 'override-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("/usr") (assoc-ref outputs "out"))
+               (("/bin/cp") (which "cp")))
+             #t)))))
+    (home-page "http://kokkinizita.linuxaudio.org")
+    (synopsis "LADSPA plugin for synthesizer oscillators")
+    (description
+     "The @code{blvco} LADSPA plugin provides three anti-aliased oscillators:
+
+@enumerate
+@item Pulse-VCO, a dirac pulse oscillator with flat amplitude spectrum
+@item Saw-VCO, a sawtooth oscillator with 1/F amplitude spectrum
+@item Rec-VCO, a square / rectange oscillator
+@end enumerate\n
+
+All oscillators are low-pass filtered to provide waveforms similar to the
+output of analog synthesizers such as the Moog Voyager.")
+    (license license:gpl2+)))
+
+(define-public wah-plugins
+  (package
+    (name "wah-plugins")
+    (version "0.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://kokkinizita.linuxaudio.org"
+                    "/linuxaudio/downloads/WAH-plugins-"
+                    version ".tar.bz2"))
+              (sha256
+               (base32
+                "1wkbjarxdhjixkh7d5abralj11dj2xxg644fz3ycd7qyfgfvjfgd"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         ;; no configure script
+         (delete 'configure)
+         (add-before 'install 'prepare-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/lib/ladspa"))
+             #t))
+         (add-after 'unpack 'override-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("/usr") (assoc-ref outputs "out")))
+             #t)))))
+    (home-page "http://kokkinizita.linuxaudio.org")
+    (synopsis "LADSPA Autowah effect plugin")
+    (description
+     "This package provides a LADSPA plugin for a Wah effect with envelope
+follower.")
+    (license license:gpl2+)))
+
+(define-public g2reverb
+  (package
+    (name "g2reverb")
+    (version "0.7.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://kokkinizita.linuxaudio.org"
+                    "/linuxaudio/downloads/g2reverb-"
+                    version ".tar.bz2"))
+              (sha256
+               (base32
+                "18wb8vj1kky5glr76s34awbi8qzplsmf3wjbd7a12hfv4j0bkwrj"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         ;; no configure script
+         (delete 'configure)
+         (add-before 'install 'prepare-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/lib/ladspa"))
+             #t))
+         (add-after 'unpack 'override-target-directory
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("/usr") (assoc-ref outputs "out")))
+             #t)))))
+    (home-page "http://kokkinizita.linuxaudio.org")
+    (synopsis "LADSPA stereo reverb plugin")
+    (description
+     "This package provides a LADSPA plugin for a stereo reverb effect.")
+    (license license:gpl2+)))
+
 (define-public fluidsynth
   (package
     (name "fluidsynth")
@@ -803,7 +1127,6 @@ synchronous execution of all clients, and low latency operation.")
        ("suil" ,suil)
        ("gtk" ,gtk+-2)
        ("gtkmm" ,gtkmm-2)
-       ("qt" ,qt-4)
        ("jack" ,jack-1)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -2063,3 +2386,38 @@ module to handle that particular file type.")
     (home-page "http://etree.org/shnutils/shntool/")
     ;; 'install-sh' bears the x11 license
     (license (list license:gpl2+ license:x11))))
+
+(define-public dcadec
+  (package
+    (name "dcadec")
+    (version "0.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/foo86/dcadec/archive/v"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0i0dpypgqkhhi4v1fmsp2way6w9kbcix3c7q79pmg39yvrzj17gd"))))
+    (build-system gnu-build-system)
+    (arguments
+     ;; Test files are missing: https://github.com/foo86/dcadec/issues/53
+     '(#:tests? #f
+       #:make-flags
+       (list "CC=gcc"
+             ;; Build shared library.
+             "CONFIG_SHARED=1"
+             (string-append "PREFIX=" (assoc-ref %outputs "out"))
+             ;; Set proper runpath.
+             (string-append "LDFLAGS=-Wl,-rpath="
+                            (assoc-ref %outputs "out")
+                            "/lib"))
+       #:phases
+       (modify-phases %standard-phases
+         ;; No configure script, just a hand-written Makefile.
+         (delete 'configure))))
+    (synopsis "DTS Coherent Acoustics decoder")
+    (description "Dcadec is a DTS Coherent Acoustics surround sound decoder
+with support for HD extensions.")
+    (home-page "https://github.com/foo86/dcadec")
+    (license license:lgpl2.1+)))

gnu/packages/bioinformatics.scm

@@ -1,9 +1,9 @@
-
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
-;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl>
+;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,6 +26,7 @@
   #:use-module (guix utils)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix build-system ant)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system perl)
@@ -37,11 +38,13 @@
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpio)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages doxygen)
+  #:use-module (gnu packages datastructures)
   #:use-module (gnu packages file)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
@@ -247,6 +250,47 @@ intervals from multiple files in widely-used genomic file formats such as BAM,
 BED, GFF/GTF, VCF.")
     (license license:gpl2)))
 
+(define-public bioawk
+  (package
+    (name "bioawk")
+    (version "1.0")
+    (source (origin
+      (method url-fetch)
+      (uri (string-append "https://github.com/lh3/bioawk/archive/v"
+                          version ".tar.gz"))
+      (file-name (string-append name "-" version ".tar.gz"))
+      (sha256
+       (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (native-inputs
+     `(("bison" ,bison)))
+    (arguments
+     `(#:tests? #f ; There are no tests to run.
+       ;; Bison must generate files, before other targets can build.
+       #:parallel-build? #f
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; There is no configure phase.
+         (replace 'install
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let* ((out (assoc-ref outputs "out"))
+                   (bin  (string-append out "/bin"))
+                   (man (string-append out "/share/man/man1")))
+              (mkdir-p man)
+              (copy-file "awk.1" (string-append man "/bioawk.1"))
+              (install-file "bioawk" bin)))))))
+    (home-page "https://github.com/lh3/bioawk")
+    (synopsis "AWK with bioinformatics extensions")
+    (description "Bioawk is an extension to Brian Kernighan's awk, adding the
+support of several common biological data formats, including optionally gzip'ed
+BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.  It
+also adds a few built-in functions and a command line option to use TAB as the
+input/output delimiter.  When the new functionality is not used, bioawk is
+intended to behave exactly the same as the original BWK awk.")
+    (license license:x11)))
+
 (define-public python2-pybedtools
   (package
     (name "python2-pybedtools")
@@ -535,10 +579,11 @@ confidence to have in an alignment.")
               (snippet
                `(begin
                   ;; Remove bundled boost, pigz, zlib, and .git directory
-                  ;; FIXME: also remove bundled sources for google-sparsehash,
+                  ;; FIXME: also remove bundled sources for murmurhash3 and
-                  ;; murmurhash3, kmc once packaged.
+                  ;; kmc once packaged.
                   (delete-file-recursively "boost")
                   (delete-file-recursively "pigz")
+                  (delete-file-recursively "google-sparsehash")
                   (delete-file-recursively "zlib")
                   (delete-file-recursively ".git")
                   #t))))
@@ -588,6 +633,7 @@ confidence to have in an alignment.")
     (inputs
      `(("openmpi" ,openmpi)
        ("boost" ,boost)
+       ("sparsehash" ,sparsehash)
        ("pigz" ,pigz)
        ("zlib" ,zlib)))
     (supported-systems '("x86_64-linux"))
@@ -774,6 +820,35 @@ and more accurate.  BWA-MEM also has better performance than BWA-backtrack for
 70-100bp Illumina reads.")
     (license license:gpl3+)))
 
+(define-public bwa-pssm
+  (package (inherit bwa)
+    (name "bwa-pssm")
+    (version "0.5.11")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/"
+                                  "archive/" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("gdsl" ,gdsl)
+       ("zlib" ,zlib)
+       ("perl" ,perl)))
+    (home-page "http://bwa-pssm.binf.ku.dk/")
+    (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
+    (description
+     "BWA-PSSM is a probabilistic short genomic sequence read aligner based on
+the use of @dfn{position specific scoring matrices} (PSSM).  Like many of the
+existing aligners it is fast and sensitive.  Unlike most other aligners,
+however, it is also adaptible in the sense that one can direct the alignment
+based on known biases within the data set.  It is coded as a modification of
+the original BWA alignment program and shares the genome index structure as
+well as many of the command line options.")
+    (license license:gpl3+)))
+
 (define-public python2-bx-python
   (package
     (name "python2-bx-python")
@@ -809,6 +884,91 @@ and more accurate.  BWA-MEM also has better performance than BWA-backtrack for
 multiple sequence alignments.")
     (license license:expat)))
 
+(define-public python-pysam
+  (package
+    (name "python-pysam")
+    (version "0.8.4")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pysam" version))
+              (sha256
+               (base32
+                "1slx5mb94mzm5qzk52q270sab0sar95j67w1g1k452nz3s9j7krh"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f ; tests are excluded in the manifest
+       #:phases
+       (alist-cons-before
+        'build 'set-flags
+        (lambda _
+          (setenv "LDFLAGS" "-lncurses")
+          (setenv "CFLAGS" "-D_CURSES_LIB=1"))
+        %standard-phases)))
+    (inputs
+     `(("ncurses"           ,ncurses)
+       ("zlib"              ,zlib)))
+    (native-inputs
+     `(("python-cython"     ,python-cython)
+       ("python-setuptools" ,python-setuptools)))
+    (home-page "https://github.com/pysam-developers/pysam")
+    (synopsis "Python bindings to the SAMtools C API")
+    (description
+     "Pysam is a Python module for reading and manipulating files in the
+SAM/BAM format.  Pysam is a lightweight wrapper of the SAMtools C API.  It
+also includes an interface for tabix.")
+    (license license:expat)))
+
+(define-public python2-pysam
+  (package-with-python2 python-pysam))
+
+(define-public cd-hit
+  (package
+    (name "cd-hit")
+    (version "4.6.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/weizhongli/cdhit"
+                                  "/releases/download/V" version
+                                  "/cd-hit-v" version "-2016-0304.tar.gz"))
+              (sha256
+               (base32
+                "15db0hq38yyifwqx9b6l34z14jcq576dmjavhj8a426c18lvnhp3"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are no tests
+       #:make-flags
+       ;; Executables are copied directly to the PREFIX.
+       (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
+       #:phases
+       (modify-phases %standard-phases
+         ;; No "configure" script
+         (delete 'configure)
+         ;; Remove sources of non-determinism
+         (add-after 'unpack 'be-timeless
+           (lambda _
+             (substitute* "cdhit-utility.c++"
+               ((" \\(built on \" __DATE__ \"\\)") ""))
+             (substitute* "cdhit-common.c++"
+               (("__DATE__") "\"0\"")
+               (("\", %s, \" __TIME__ \"\\\\n\", date") ""))
+             #t))
+         ;; The "install" target does not create the target directory
+         (add-before 'install 'create-target-dir
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
+             #t)))))
+    (inputs
+     `(("perl" ,perl)))
+    (home-page "http://weizhongli-lab.org/cd-hit/")
+    (synopsis "Cluster and compare protein or nucleotide sequences")
+    (description
+     "CD-HIT is a program for clustering and comparing protein or nucleotide
+sequences.  CD-HIT is designed to be fast and handle extremely large
+databases.")
+    ;; The manual says: "It can be copied under the GNU General Public License
+    ;; version 2 (GPLv2)."
+    (license license:gpl2)))
+
 (define-public clipper
   (package
     (name "clipper")
@@ -848,6 +1008,46 @@ multiple sequence alignments.")
      "CLIPper is a tool to define peaks in CLIP-seq datasets.")
     (license license:gpl2)))
 
+(define-public codingquarry
+  (package
+    (name "codingquarry")
+    (version "2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://sourceforge/codingquarry/CodingQuarry_v"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (doc (string-append out "/share/doc/codingquarry")))
+               (install-file "INSTRUCTIONS.pdf" doc)
+               (copy-recursively "QuarryFiles"
+                                 (string-append out "/QuarryFiles"))
+               (install-file "CodingQuarry" bin)
+               (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
+    (inputs `(("openmpi" ,openmpi)))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "QUARRY_PATH")
+            (files '("QuarryFiles")))))
+    (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
+    (synopsis "Fungal gene predictor")
+    (description "CodingQuarry is a highly accurate, self-training GHMM fungal
+gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
+    (home-page "https://sourceforge.net/projects/codingquarry/")
+    (license license:gpl3+)))
+
 (define-public couger
   (package
     (name "couger")
@@ -1129,28 +1329,70 @@ other types of unwanted sequence from high-throughput sequencing reads.")
 files.")
     (license license:expat)))
 
+(define-public python-pybigwig
+  (package
+    (name "python-pybigwig")
+    (version "0.2.5")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pyBigWig" version))
+              (sha256
+               (base32
+                "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Delete bundled libBigWig sources
+                  (delete-file-recursively "libBigWig")))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'link-with-libBigWig
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "setup.py"
+               (("libs=\\[") "libs=[\"BigWig\", "))
+             #t)))))
+    (inputs
+     `(("libbigwig" ,libbigwig)
+       ("zlib" ,zlib)
+       ("curl" ,curl)))
+    (home-page "https://github.com/dpryan79/pyBigWig")
+    (synopsis "Access bigWig files in Python using libBigWig")
+    (description
+     "This package provides Python bindings to the libBigWig library for
+accessing bigWig files.")
+    (license license:expat)))
+
+(define-public python2-pybigwig
+  (let ((pybigwig (package-with-python2 python-pybigwig)))
+    (package (inherit pybigwig)
+      (native-inputs
+       `(("python-setuptools" ,python2-setuptools))))))
+
 (define-public deeptools
   (package
     (name "deeptools")
-    (version "1.5.11")
+    (version "2.1.1")
     (source (origin
               (method url-fetch)
-              (uri (string-append
+              (uri (string-append "https://github.com/fidelram/deepTools/"
-                    "https://github.com/fidelram/deepTools/archive/"
+                                  "archive/" version ".tar.gz"))
-                    version ".tar.gz"))
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1kaagygcbvjs9sxd9cqmskd02wcfp9imvb735r087w7hwqpvz6fs"))))
+                "1nmfin0zjdby3vay3r4flvz94dr6qjhj41ax4yz3vx13j6wz8izd"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2))
-    (propagated-inputs
+    (inputs
      `(("python-scipy" ,python2-scipy)
        ("python-numpy" ,python2-numpy)
+       ("python-numpydoc" ,python2-numpydoc)
        ("python-matplotlib" ,python2-matplotlib)
        ("python-bx-python" ,python2-bx-python)
-       ("python-pysam" ,python2-pysam)))
+       ("python-pysam" ,python2-pysam)
+       ("python-pybigwig" ,python2-pybigwig)))
     (native-inputs
      `(("python-mock" ,python2-mock) ;for tests
        ("python-pytz" ,python2-pytz) ;for tests
@@ -1851,24 +2093,17 @@ from high-throughput sequencing assays.")
               (snippet '(substitute* "build.xml"
                           (("failifexecutionfails=\"true\"")
                            "failifexecutionfails=\"false\"")))))
-    (build-system gnu-build-system)
+    (build-system ant-build-system)
     (arguments
-     `(#:modules ((srfi srfi-1)
+     `(#:tests? #f ; test require Internet access
-                  (guix build gnu-build-system)
+       #:make-flags
-                  (guix build utils))
+       (list (string-append "-Ddist=" (assoc-ref %outputs "out")
-       #:phases (alist-replace
+                            "/share/java/htsjdk/"))
-                 'build
+       #:build-target "all"
-                 (lambda _
+       #:phases
-                   (setenv "JAVA_HOME" (assoc-ref %build-inputs "jdk"))
+       (modify-phases %standard-phases
-                   (zero? (system* "ant" "all"
+         ;; The build phase also installs the jars
-                                   (string-append "-Ddist="
+         (delete 'install))))
-                                                  (assoc-ref %outputs "out")
-                                                  "/share/java/htsjdk/"))))
-                 (fold alist-delete %standard-phases
-                       '(configure install check)))))
-    (native-inputs
-     `(("ant" ,ant)
-       ("jdk" ,icedtea "jdk")))
     (home-page "http://samtools.github.io/htsjdk/")
     (synopsis "Java API for high-throughput sequencing data (HTS) formats")
     (description
@@ -2405,6 +2640,44 @@ the phenotype as it models the data.")
 generated using the PacBio Iso-Seq protocol.")
       (license license:bsd-3))))
 
+(define-public pyicoteo
+  (package
+    (name "pyicoteo")
+    (version "2.0.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
+                           "pyicoteo/get/v" version ".tar.bz2"))
+       (file-name (string-append name "-" version ".tar.bz2"))
+       (sha256
+        (base32
+         "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2 ; does not work with Python 3
+       #:tests? #f))      ; there are no tests
+    (inputs
+     `(("python2-matplotlib" ,python2-matplotlib)))
+    (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
+    (synopsis "Analyze high-throughput genetic sequencing data")
+    (description
+     "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
+sequencing data.  It works with genomic coordinates.  There are currently six
+different command-line tools:
+
+@enumerate
+@item pyicoregion: for generating exploratory regions automatically;
+@item pyicoenrich: for differential enrichment between two conditions;
+@item pyicoclip: for calling CLIP-Seq peaks without a control;
+@item pyicos: for genomic coordinates manipulation;
+@item pyicoller: for peak calling on punctuated ChIP-Seq;
+@item pyicount: to count how many reads from N experiment files overlap in a
+  region file;
+@item pyicotrocol: to combine operations from pyicoteo.
+@end enumerate\n")
+    (license license:gpl3+)))
+
 (define-public prodigal
   (package
     (name "prodigal")
@@ -3664,16 +3937,38 @@ barplots or heatmaps.")
 packages.")
     (license license:artistic2.0)))
 
+(define-public r-dnacopy
+  (package
+    (name "r-dnacopy")
+    (version "1.44.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "DNAcopy" version))
+              (sha256
+               (base32
+                "1c1px4rbr36xx929hp59k7ca9k5ab66qmn8k63fk13278ncm6h66"))))
+    (properties
+     `((upstream-name . "DNAcopy")))
+    (build-system r-build-system)
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://bioconductor.org/packages/DNAcopy")
+    (synopsis "Implementation of a circular binary segmentation algorithm")
+    (description "This package implements the circular binary segmentation (CBS)
+algorithm to segment DNA copy number data and identify genomic regions with
+abnormal copy number.")
+    (license license:gpl2+)))
+
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.8.5")
+    (version "0.8.11")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "10f4jxwlwsiy7zhb3kgp6anid0d7wkvrrljl80r3nhx38yr24l5k"))))
+                "12iibcs63m9iy7f45wgjcqsna2dnqwckphk682389grshz0g4x66"))))
     (properties
      `((upstream-name . "S4Vectors")
        (r-repository . bioconductor)))
@@ -3695,13 +3990,13 @@ S4Vectors package itself.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.4.6")
+    (version "2.4.8")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "00x0266sys1fc5ipa639y84p6m6mgspk2xb099vcwmd3w4hypj9d"))))
+                "0hi5k1j5jm4xrg1l506g279qw1xkvp1gg1zgsjzpbng4vx4k4iyl"))))
     (properties
      `((upstream-name . "IRanges")
        (r-repository . bioconductor)))
@@ -4141,7 +4436,9 @@ extracting the desired features in a convenient format.")
     (version "3.2.2")
     (source (origin
               (method url-fetch)
-              (uri (bioconductor-uri "GO.db" version))
+              (uri (string-append "http://www.bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib/GO.db_"
+                                  version ".tar.gz"))
               (sha256
                (base32
                 "00gariag9ampz82dh0xllrc26r85d7vdcwc0vca5zdy147rwxr7f"))))
@@ -4453,3 +4750,44 @@ Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
 identify genotyping errors, and to perform single-QTL and two-QTL,
 two-dimensional genome scans.")
   (license license:gpl3)))
+
+(define-public pepr
+  (package
+    (name "pepr")
+    (version "1.0.9")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://pypi.python.org/packages/source/P"
+                                  "/PePr/PePr-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2 ; python2 only
+       #:tests? #f ; no tests included
+       #:phases
+       (modify-phases %standard-phases
+         ;; When setuptools is used a ".egg" archive is generated and
+         ;; installed.  This makes it hard to actually run PePr.  This issue
+         ;; has been reported upstream:
+         ;; https://github.com/shawnzhangyx/PePr/issues/9
+         (add-after 'unpack 'disable-egg-generation
+           (lambda _
+             (substitute* "setup.py"
+               (("from setuptools import setup")
+                "from distutils.core import setup"))
+             #t)))))
+    (propagated-inputs
+     `(("python2-numpy" ,python2-numpy)
+       ("python2-scipy" ,python2-scipy)
+       ("python2-pysam" ,python2-pysam)))
+    (home-page "https://code.google.com/p/pepr-chip-seq/")
+    (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
+    (description
+     "PePr is a ChIP-Seq peak calling or differential binding analysis tool
+that is primarily designed for data with biological replicates.  It uses a
+negative binomial distribution to model the read counts among the samples in
+the same group, and look for consistent differences between ChIP and control
+group or two ChIP groups run under different conditions.")
+    (license license:gpl3+)))

gnu/packages/bittorrent.scm

@@ -202,7 +202,7 @@ interface, for the Transmission BitTorrent daemon.")
 (define-public aria2
   (package
     (name "aria2")
-    (version "1.20.0")
+    (version "1.21.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/tatsuhiro-t/aria2/"
@@ -210,7 +210,7 @@ interface, for the Transmission BitTorrent daemon.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1l4gzz3yr0cl6a9xdy7843c5sb7afyq0i80wi2hasfpfdx5k95mz"))))
+                "1035rzx9y7qv4p7cv04f461343dxha7ikprch059x2fci8n5yp12"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--enable-libaria2")

gnu/packages/cdrom.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2013, 2014 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
-;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -44,14 +44,14 @@
 (define-public libcddb
   (package
     (name "libcddb")
-    (version "1.3.0")
+    (version "1.3.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/libcddb/libcddb-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "1y8bfy12dwm41m1jahayn3v47dm34fmz7m9cjxyh7xcw6fp3lzaf"))))
+               "0fr21a7vprdyy1bq6s99m0x420c9jm5fipsd63pqv8qyfkhhxkim"))))
     (build-system gnu-build-system)
     (arguments '(#:tests? #f))      ; tests rely on access to external servers
     (home-page "http://libcddb.sourceforge.net/")
@@ -189,14 +189,14 @@ reconstruction capability.")
 (define-public dvdisaster
   (package
     (name "dvdisaster")
-    (version "0.72.6")
+    (version "0.79.5")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://dvdisaster.net/downloads/dvdisaster-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "0sqrprc5rh3shnfli25m2wy0i5f83db54iv04s5s7bxf77m7sy79"))))
+               "0f8gjnia2fxcbmhl8b3qkr5b7idl8m855dw7xw2fnmbqwvcm6k4w"))))
     (build-system gnu-build-system)
     (inputs
      `(("gtk+" ,gtk+-2)))
@@ -208,14 +208,7 @@ reconstruction capability.")
      `(;; Parallel builds appear to be unsafe, see
        ;; <http://hydra.gnu.org/build/49331/nixlog/1/raw>.
        #:parallel-build? #f
-       #:tests? #f ; no check target
+       #:tests? #f)) ; no check target
-       #:phases
-         (alist-cons-before
-          'patch-source-shebangs 'sanitise
-          (lambda _
-            ;; delete dangling symlink
-            (delete-file ".#GNUmakefile"))
-          %standard-phases)))
     (home-page "http://dvdisaster.net/en/index.html")
     (synopsis "Error correcting codes for optical media images")
     (description "Optical media (CD,DVD,BD) keep their data only for a
@@ -240,9 +233,8 @@ capacity is user-selectable.")
     (version "1.4.0")
     (source (origin
              (method url-fetch)
-             (uri (string-append "https://github.com/lipnitsk/libcue/releases"
+             (uri (string-append "https://github.com/lipnitsk/libcue/archive/v"
-                                 "/download/v" version
+                                 version ".tar.bz2"))
-                                 "/libcue-" version ".tar.bz2"))
              (sha256
               (base32
                "17kjd7rjz1bvfn44n3n2bjb7a1ywd0yc0g4sqp5ihf9b5bn7cwlb"))))
@@ -287,15 +279,15 @@ from an audio CD.")
 (define-public abcde
   (package
     (name "abcde")
-    (version "2.7")
+    (version "2.7.1")
-    (home-page "http://abcde.einval.com/")
+    (home-page "https://abcde.einval.com/")
     (source (origin
               (method url-fetch)
               (uri (string-append home-page "/download/abcde-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0ikpffzvacadh6vj9qlary8126j1zrd2knp9gvivmp7y1656jj01"))
+                "0l7j0nk8p30s97285i418rv9ym9bgns7bn6l8gldw3mjhnby609l"))
               (modules '((guix build utils)))
               (snippet
                '(substitute* "Makefile"
@@ -305,37 +297,36 @@ from an audio CD.")
                    (string-append "etcdir = $(prefix)/etc\n"))))))
     (build-system gnu-build-system)
     (arguments
-     '(#:phases (alist-replace
+     '(#:phases
-                 'configure
+       (modify-phases %standard-phases
-                 (lambda* (#:key outputs inputs #:allow-other-keys)
+         (replace 'configure
-                   (substitute* "Makefile"
+           (lambda* (#:key outputs inputs #:allow-other-keys)
-                     (("^prefix = .*$")
+             (substitute* "Makefile"
-                      (string-append "prefix = "
+               (("^prefix = .*$")
-                                     (assoc-ref outputs "out")
+                (string-append "prefix = "
-                                     "\n"))))
+                               (assoc-ref outputs "out")
-                 (alist-cons-after
+                               "\n")))))
-                  'install 'wrap
+         (add-after 'install 'wrap
-                  (lambda* (#:key inputs outputs #:allow-other-keys)
+           (lambda* (#:key inputs outputs #:allow-other-keys)
-                    (let ((wget   (assoc-ref inputs "wget"))
+             (let ((wget   (assoc-ref inputs "wget"))
-                          (vorbis (assoc-ref inputs "vorbis-tools"))
+                   (vorbis (assoc-ref inputs "vorbis-tools"))
-                          (parano (assoc-ref inputs "cdparanoia"))
+                   (parano (assoc-ref inputs "cdparanoia"))
-                          (which  (assoc-ref inputs "which"))
+                   (which  (assoc-ref inputs "which"))
-                          (discid (assoc-ref inputs "cd-discid"))
+                   (discid (assoc-ref inputs "cd-discid"))
-                          (out    (assoc-ref outputs "out")))
+                   (out    (assoc-ref outputs "out")))
-                      (define (wrap file)
+               (define (wrap file)
-                        (wrap-program file
+                 (wrap-program file
-                                      `("PATH" ":" prefix
+                               `("PATH" ":" prefix
-                                        (,(string-append out "/bin:"
+                                 (,(string-append out "/bin:"
-                                                         wget "/bin:"
+                                                  wget "/bin:"
-                                                         which "/bin:"
+                                                  which "/bin:"
-                                                         vorbis "/bin:"
+                                                  vorbis "/bin:"
-                                                         discid "/bin:"
+                                                  discid "/bin:"
-                                                         parano "/bin")))))
+                                                  parano "/bin")))))
 
-                      (for-each wrap
+               (for-each wrap
-                                (find-files (string-append out "/bin")
+                         (find-files (string-append out "/bin")
-                                            ".*"))))
+                                     ".*"))))))
-                  %standard-phases))
        #:tests? #f))
 
     (inputs `(("wget" ,wget)

gnu/packages/check.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -89,15 +90,14 @@ with a flexible variety of user interfaces.")
 (define-public cppunit
   (package
     (name "cppunit")
-    (version "1.12.1")
+    (version "1.13.2")
     (source (origin
              (method url-fetch)
-              (uri (string-append "mirror://sourceforge/cppunit/" name "/"
+              (uri (string-append "http://dev-www.libreoffice.org/src/"
-                                  name "-"
+                                  name "-" version ".tar.gz"))
-                                  version ".tar.gz"))
              (sha256
               (base32
-               "0jm49v5rmc5qw34vqs56gy8xja1dhci73bmh23cig4kcir6a0a5c"))))
+               "17s2kzmkw3kfjhpp72rfppyd7syr7bdq5s69syj2nvrlwd3d4irz"))))
     ;; Explicitly link with libdl. This is expected to be done by packages
     ;; relying on cppunit for their tests. However, not all of them do.
     ;; If we added the linker flag to such packages, we would pollute all
@@ -105,7 +105,7 @@ with a flexible variety of user interfaces.")
     (arguments
      `(#:make-flags '("LDFLAGS=-ldl")))
     (build-system gnu-build-system)
-    (home-page "http://sourceforge.net/projects/cppunit/")
+    (home-page "https://wiki.freedesktop.org/www/Software/cppunit/")
     (synopsis "Unit testing framework for C++")
     (description "CppUnit is the C++ port of the famous JUnit framework for
 unit testing.  Test output is in XML for automatic testing and GUI based for
@@ -115,17 +115,17 @@ supervised tests.")
 (define-public catch-framework
   (package
     (name "catch")
-    (version "1.1.3")                  ;Sub-minor is the build number
+    (version "1.3.5")                  ;Sub-minor is the build number
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/philsquared/Catch")
                     ;; Semi-arbitrary.
-                    (commit "c51e86819d")))
+                    (commit "ae5ee2cf63d6d67bd1369b512d2a7b60b571c907")))
               (file-name (string-append name "-" version))
               (sha256
                (base32
-                "0kgi7wxxysgjbpisqfj4dj0k19cyyai92f001zi8gzkybd4fkgv5"))))
+                "1yfb3lxv929szqy1nw9xw3d45wzkppziqshkjxvrb1fdmf46x564"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))
@@ -172,3 +172,24 @@ different compilers.  Cmocka supports several different message output formats
 like Test Anything Protocol, Subunit, xUnit XML or the original cmockery output
 format.")
     (license asl2.0)))
+
+(define-public cppcheck
+  (package
+    (name "cppcheck")
+    (version "1.72")
+    (source (origin
+      (method url-fetch)
+      (uri (string-append "https://github.com/danmar/cppcheck/archive/"
+                          version ".tar.gz"))
+      (sha256
+       (base32 "0zxaixhqi4vmj7xj56gzadggcbjhbjjm6abyr86qlan23sg98667"))
+      (file-name (string-append name "-" version ".tar.gz"))))
+    (build-system cmake-build-system)
+    (home-page "http://cppcheck.sourceforge.net")
+    (synopsis "Static C/C++ code analyzer")
+    (description "Cppcheck is a static code analyzer for C and C++.  Unlike
+C/C++ compilers and many other analysis tools it does not detect syntax errors
+in the code.  Cppcheck primarily detects the types of bugs that the compilers
+normally do not detect.  The goal is to detect only real errors in the code
+(i.e. have zero false positives).")
+    (license gpl3+)))

gnu/packages/code.scm

@@ -68,14 +68,14 @@ a major mode for Emacs for examining the flowcharts that it produces.")
 (define-public complexity
   (package
     (name "complexity")
-    (version "1.3")
+    (version "1.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/complexity/complexity-"
-                                  version ".tar.gz"))
+                                  version ".tar.xz"))
               (sha256
                (base32
-                "19bc64sxpqd5rqylqaa7dijz2x7qp2b0dg3ah3fb3qbcvd8b4wgy"))))
+                "0lr0l9kj2w3jilz9h9y4np9pf9i9ccpy6331lanki2fnz4z8ldvd"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("texinfo" ,texinfo)
@@ -190,7 +190,7 @@ COCOMO model or user-provided parameters.")
 (define-public the-silver-searcher
   (package
     (name "the-silver-searcher")
-    (version "0.29.1")
+    (version "0.31.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -198,7 +198,7 @@ COCOMO model or user-provided parameters.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0ah7vcqprl9hhafi68bvzaiywy7dfm28zf7kpw3xrlqzfn0vg7kp"))
+                "1a3xncsq3x8pci194k484s5mdqij2sirpz6dj6711n2p8mzq5g31"))
               (file-name (string-append name "-" version ".tar.gz"))))
     (build-system gnu-build-system)
     (native-inputs
@@ -284,14 +284,14 @@ stack traces.")
 (define-public lcov
   (package
     (name "lcov")
-    (version "1.10")
+    (version "1.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/ltp/lcov-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "13xq2ln4jjasslqzzhr5g11q1c19gwpng1jphzbzmylmrjz62ila"))))
+                "19wfifdpxxivhq9adbphanjfga9bg9spms9v7c3589wndjff8x5l"))))
     (build-system gnu-build-system)
     (arguments
      '(#:make-flags (let ((out (assoc-ref %outputs "out")))

gnu/packages/commencement.scm

@@ -268,6 +268,7 @@
   (let ((perl (package
                 (inherit perl)
                 (name "perl-boot0")
+                (replacement #f)
                 (arguments
                  (substitute-keyword-arguments (package-arguments perl)
                    ((#:phases phases)
@@ -870,10 +871,10 @@ and binaries, plus debugging symbols in the 'debug' output), and Binutils.")
               ("libc-debug" ,glibc-final "debug")))))
 
 (define-public gcc-toolchain-4.8
-  (gcc-toolchain gcc-final))
+  (gcc-toolchain gcc-4.8))
 
 (define-public gcc-toolchain-4.9
-  (gcc-toolchain gcc-4.9))
+  (gcc-toolchain gcc-final))
 
 (define-public gcc-toolchain-5
   (gcc-toolchain gcc-5))

gnu/packages/curl.scm

@@ -54,16 +54,7 @@
    (inputs `(("gnutls" ,gnutls)
              ("gss" ,gss)
              ("libidn" ,libidn)
-
+             ("libssh2" ,libssh2)
-             ;; XXX libssh2-1.4 is a temporary package for use only by curl,
-             ;; to allow most users of libssh2 to get the security update for
-             ;; CVE-2016-7087 while postponing the large number of rebuilds
-             ;; entailed by updating curl.  Soon, curl should be updated to
-             ;; use the latest libssh2 and libssh2-1.4 should be removed.
-
-             ;; XXX libssh2-1.4 is vulnerable to CVE-2016-0787.
-             ("libssh2" ,libssh2-1.4)
-
              ("openldap" ,openldap)
              ("zlib" ,zlib)))
    (native-inputs

gnu/packages/databases.scm

@@ -28,6 +28,7 @@
 (define-module (gnu packages databases)
   #:use-module (gnu packages)
   #:use-module (gnu packages bash)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages language)
   #:use-module (gnu packages linux)
@@ -132,16 +133,19 @@ SQL, Key/Value, XML/XQuery or Java Object storage for their data model.")
 (define-public mysql
   (package
     (name "mysql")
-    (version "5.6.25")
+    (version "5.7.11")
     (source (origin
              (method url-fetch)
-             (uri (string-append
+             (uri (list (string-append
-                   "http://dev.mysql.com/get/Downloads/MySQL-"
+                          "http://dev.mysql.com/get/Downloads/MySQL-"
-                   (version-major+minor version) "/"
+                          (version-major+minor version) "/"
-                   name "-" version ".tar.gz"))
+                          name "-" version ".tar.gz")
+                        (string-append
+                          "http://downloads.mysql.com/archives/get/file/"
+                          name "-" version ".tar.gz")))
              (sha256
               (base32
-               "1gbz5i1z3nswpq3q8f477vrx7g15j8n41pyb94k0jfnkhc5rq1qm"))))
+               "03hzd2ikabxhh5ch2yvml2nks2wpv3qbkqmx3520in6khypwgy2l"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags
@@ -167,16 +171,11 @@ SQL, Key/Value, XML/XQuery or Java Object storage for their data model.")
          "-DINSTALL_SQLBENCHDIR=")
        #:phases (modify-phases %standard-phases
                   (add-after
-                   'install 'strip-extra-references
+                   'unpack 'patch-boost-version
-                   (lambda* (#:key outputs #:allow-other-keys)
+                   (lambda _
-                     ;; Strip references to GCC and other build-time
+                     ;; Mysql wants boost-1.59.0 specifically
-                     ;; dependencies.
+                     (substitute* "cmake/boost.cmake"
-                     (let ((out (assoc-ref outputs "out")))
+                                  (("59") "60"))))
-                       (for-each remove-store-references
-                                 (list (string-append out "/bin/mysqlbug")
-                                       (string-append
-                                        out "/share/mysql/docs/INFO_BIN")))
-                       #t)))
                   (add-after
                    'install 'remove-extra-binaries
                    (lambda* (#:key outputs #:allow-other-keys)
@@ -191,10 +190,11 @@ SQL, Key/Value, XML/XQuery or Java Object storage for their data model.")
      `(("bison" ,bison)
        ("perl" ,perl)))
     (inputs
-     `(("libaio" ,libaio)
+     `(("boost" ,boost)
+       ("libaio" ,libaio)
+       ("ncurses" ,ncurses)
        ("openssl" ,openssl)
-       ("zlib" ,zlib)
+       ("zlib" ,zlib)))
-       ("ncurses" ,ncurses)))
     (home-page "http://www.mysql.com/")
     (synopsis "Fast, easy to use, and popular database")
     (description
@@ -206,7 +206,7 @@ Language.")
 (define-public mariadb
   (package
     (name "mariadb")
-    (version "10.0.23")
+    (version "10.1.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://downloads.mariadb.org/f/"
@@ -214,7 +214,7 @@ Language.")
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0x52gfxk7zr84al83x62s4gh7mbngahy1svafdkbwd18i5lysvhm"))))
+                "1rzlc2ns84x540asbkgdp9562haxhlszfpdqh64i9pz4q1m4cpvr"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags

gnu/packages/datastructures.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,6 +23,29 @@
   #:use-module (guix download)
   #:use-module (guix build-system gnu))
 
+(define-public gdsl
+  (package
+    (name "gdsl")
+    (version "1.8")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://download.gna.org/gdsl/"
+                                  "gdsl-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1v64jvlnj8jfpphphgjgb36p0kv50kwfyqncf0y12f16v8ydyiaw"))))
+    (build-system gnu-build-system)
+    (home-page "http://home.gna.org/gdsl/")
+    (synopsis "Generic data structures library")
+    (description "The Generic Data Structures Library (GDSL) is a collection
+of routines for generic data structures manipulation.  It is a re-entrant
+library fully written from scratch in pure ANSI C.  It is designed to offer
+for C programmers common data structures with powerful algorithms, and hidden
+implementation.  Available structures are lists, queues, stacks, hash tables,
+binary trees, binary search trees, red-black trees, 2D arrays, permutations
+and heaps.")
+    (license license:gpl2+)))
+
 (define-public sparsehash
   (package
     (name "sparsehash")

gnu/packages/dav.scm

@@ -52,21 +52,16 @@ clients.")
 (define-public vdirsyncer
   (package
     (name "vdirsyncer")
-    (version "0.9.0")
+    (version "0.9.2")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "vdirsyncer" version))
              (sha256
               (base32
-               "0s9awjr9v60rr80xcpwmdhkf4v1yqnydahjmxwvxmh64565is465"))))
+               "1g1107cz4sk41d2z6k6pn9n2fzd26m72j8aj33zn483vfvmyrc4q"))))
     (build-system python-build-system)
     (arguments
       `(#:phases (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (setenv "DAV_SERVER" "radicale")
-             (setenv "REMOTESTORAGE_SERVER" "skip")
-             (zero? (system* "py.test"))))
          ;; vdirsyncer requires itself to be installed in order to build
          ;; the manpage.
          (add-after 'install 'manpage
@@ -80,17 +75,24 @@ clients.")
                "docs/_build/man/vdirsyncer.1"
                (string-append
                  (assoc-ref outputs "out")
-                 "/share/man/man1")))))))
+                 "/share/man/man1"))))
+         ;; vdirsyncer requires itself to be installed in order to run the test
+         ;; suite.
+         (delete 'check)
+         (add-after 'install 'check-later
+           (lambda _
+             (setenv "DETERMINISTIC_TESTS" "true")
+             (setenv "DAV_SERVER" "radicale")
+             (setenv "REMOTESTORAGE_SERVER" "skip")
+             (zero? (system* "make" "test")))))))
     (native-inputs
-     `(("python-oauthlib" ,python-oauthlib)
+     `(("python-setuptools-scm" ,python-setuptools-scm)
-       ("python-setuptools-scm" ,python-setuptools-scm)
        ("python-sphinx" ,python-sphinx)
        ;; Required for testing
        ("python-hypothesis" ,python-hypothesis)
        ("python-pytest" ,python-pytest)
        ("python-pytest-localserver" ,python-pytest-localserver)
        ("python-pytest-subtesthack" ,python-pytest-subtesthack)
-       ("python-pytest-xprocess" ,python-pytest-xprocess)
        ("python-wsgi-intercept" ,python-wsgi-intercept)
        ("radicale" ,radicale)))
     (propagated-inputs
@@ -98,7 +100,7 @@ clients.")
        ("python-click" ,python-click)
        ("python-click-log" ,python-click-log)
        ("python-click-threading" ,python-click-threading)
-       ("python-lxml" ,python-lxml) ; which one?
+       ("python-lxml" ,python-lxml)
        ("python-requests-toolbelt" ,python-requests-toolbelt)))
     (synopsis "Synchronize calendars and contacts")
     (description "Vdirsyncer synchronizes your calendars and addressbooks

gnu/packages/disk.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@gnu.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Tobias Geerinckx-Rice <tobias.geerinckx.rice@gmail.com>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -99,7 +100,7 @@ tables, and it understands a variety of different formats.")
 (define-public ddrescue
   (package
     (name "ddrescue")
-    (version "1.20")
+    (version "1.21")
     (source
      (origin
       (method url-fetch)
@@ -107,7 +108,7 @@ tables, and it understands a variety of different formats.")
                           version ".tar.lz"))
       (sha256
        (base32
-        "1gb0ak2c47nass7qdf9pnfrshcb38c318z1fx5v5v1k7l6qr7yc3"))))
+        "1b71hb42lh33y9843nd1mxlwkk9qh9ajvnz6ivzd1jq9lav4x7ph"))))
     (build-system gnu-build-system)
     (home-page "http://www.gnu.org/software/ddrescue/ddrescue.html")
     (synopsis "Data recovery utility")
@@ -171,3 +172,35 @@ transport), SCSI and ATAPI tape drives, and SCSI enclosures.  This utility can
 also send commands associated with starting and stopping the media, loading
 and unloading removable media and some other housekeeping functions.")
     (license bsd-3)))
+
+(define-public idle3-tools
+  (package
+    (name "idle3-tools")
+    (version "0.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/idle3-tools/idle3-tools-"
+                           version ".tgz"))
+       (sha256
+        (base32
+         "00ia7xq9yldxyl9gz0mr4xa568nav14p0fnv82f2rbbkg060cy4p"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no test suite
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))
+       #:make-flags (list "CC=gcc"
+                          (string-append "manprefix=")
+                          (string-append "DESTDIR="
+                                         (assoc-ref %outputs "out")))))
+    (home-page "http://idle3-tools.sourceforge.net")
+    (synopsis "Change or disable Western Digital hard drives' Idle3 timer")
+    (description
+     "Idle3-tools provides a utility to get, set, or disable the Idle3 timer
+present in many Western Digital hard drives.  This timer is part of the
+\"IntelliPark\" feature that stops the disk when not in use.  Unfortunately,
+the default timer setting is not well suited to Linux or other *nix systems,
+and can dramatically shorten the lifespan of the drive if left unchecked.")
+    (license gpl3+)))

gnu/packages/dns.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -65,14 +66,14 @@ and BOOTP/TFTP for network booting of diskless machines.")
 (define-public bind-utils
   (package
     (name "bind-utils")
-    (version "9.10.3-P3")
+    (version "9.10.3-P4")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://ftp.isc.org/isc/bind9/" version
                                   "/bind-" version ".tar.gz"))
               (sha256
                (base32
-                "10yblk8qbb85qxakzdjy5qmqvqj4rlcqsqvlkriglampzg8i0239"))))
+                "0giys46ifypysf799w9v58kbaz1v3fbdzw3s212znifzzfsl9h1a"))))
     (build-system gnu-build-system)
     (inputs
      ;; it would be nice to add GeoIP and gssapi once there is package

gnu/packages/emacs.scm

@@ -308,7 +308,7 @@ when typing parentheses directly or commenting out code line by line.")
 (define-public git-modes
   (package
     (name "git-modes")
-    (version "1.2.0")
+    (version "1.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -317,7 +317,7 @@ when typing parentheses directly or commenting out code line by line.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "09dv7ikbj2bi4y3lmvjfzqpdmx2f9bd4w7jkp10bkap62d05iqhk"))))
+                "088wyddh8y0yw77i0hx449n9zg4wzyc90h63wlmxba1ijg4dzm0p"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((guix build gnu-build-system)
@@ -1018,44 +1018,47 @@ single buffer.")
     (arguments
      `(#:tests? #f ; there are no tests
        #:modules ((guix build gnu-build-system)
+                  ((guix build emacs-build-system) #:prefix emacs:)
                   (guix build utils)
                   (guix build emacs-utils))
        #:imported-modules (,@%gnu-build-system-modules
+                           (guix build emacs-build-system)
                            (guix build emacs-utils))
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'enter-dir (lambda _ (chdir "server") #t))
+         ;; Build server side using 'gnu-build-system'.
-         (add-before
+         (add-after 'unpack 'enter-server-dir
-          'configure 'autogen
+           (lambda _ (chdir "server") #t))
-          (lambda _
+         (add-before 'configure 'autogen
-            (zero? (system* "bash" "autogen.sh"))))
+           (lambda _
-         (add-before
+             (zero? (system* "bash" "autogen.sh"))))
-          'build 'patch-variables
+
-          (lambda* (#:key outputs #:allow-other-keys)
+         ;; Build emacs side using 'emacs-build-system'.
-            (with-directory-excursion "../lisp"
+         (add-after 'compress-documentation 'enter-lisp-dir
-              ;; Set path to epdfinfo program.
+           (lambda _ (chdir "../lisp") #t))
-              (emacs-substitute-variables "pdf-info.el"
+         (add-after 'enter-lisp-dir 'emacs-patch-variables
-                ("pdf-info-epdfinfo-program"
+           (lambda* (#:key outputs #:allow-other-keys)
-                 (string-append (assoc-ref outputs "out")
+             ;; Set path to epdfinfo program.
-                                "/bin/epdfinfo")))
+             (emacs-substitute-variables "pdf-info.el"
-              ;; Set 'pdf-tools-handle-upgrades' to nil to avoid "auto
+               ("pdf-info-epdfinfo-program"
-              ;; upgrading" that pdf-tools tries to perform.
+                (string-append (assoc-ref outputs "out")
-              (emacs-substitute-variables "pdf-tools.el"
+                               "/bin/epdfinfo")))
-                ("pdf-tools-handle-upgrades" '())))))
+             ;; Set 'pdf-tools-handle-upgrades' to nil to avoid "auto
-         (add-after
+             ;; upgrading" that pdf-tools tries to perform.
-          'install 'install-lisp
+             (emacs-substitute-variables "pdf-tools.el"
-          (lambda* (#:key outputs #:allow-other-keys)
+               ("pdf-tools-handle-upgrades" '()))))
-            (let ((target (string-append (assoc-ref outputs "out")
+         (add-after 'emacs-patch-variables 'emacs-install
-                                         "/share/emacs/site-lisp/")))
+           (assoc-ref emacs:%standard-phases 'install))
-              (for-each (lambda (file)
+         (add-after 'emacs-install 'emacs-build
-                          (install-file file target))
+           (assoc-ref emacs:%standard-phases 'build))
-                        (find-files "../lisp" "^(pdf|tab).*\\.elc?"))
+         (add-after 'emacs-install 'emacs-make-autoloads
-              (emacs-byte-compile-directory target)
+           (assoc-ref emacs:%standard-phases 'make-autoloads)))))
-              (emacs-generate-autoloads "pdf-tools" target)))))))
     (native-inputs `(("autoconf" ,autoconf)
                      ("automake" ,automake)
                      ("pkg-config" ,pkg-config)
                      ("emacs" ,emacs-no-x)))
+    (propagated-inputs
+     `(("let-alist" ,let-alist)))
     (inputs `(("poppler" ,poppler)
               ("cairo" ,cairo)
               ("glib" ,glib)

gnu/packages/enlightenment.scm

@@ -273,7 +273,7 @@ Libraries with some extra bells and whistles.")
 (define-public enlightenment
   (package
     (name "enlightenment")
-    (version "0.20.5")
+    (version "0.20.6")
     (source (origin
               (method url-fetch)
               (uri
@@ -281,7 +281,7 @@ Libraries with some extra bells and whistles.")
                               name "/" name "-" version ".tar.xz"))
               (sha256
                (base32
-                 "1l02m2d7d5r0vnfgn44glhvqhc8ygbjxjkf6cdd2vxpxsa29ax12"))))
+                 "11ahll68nlci214ka05whp5l32hy9lznmcdfqx3hxsmq2p7bl7zj"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--enable-mount-eeze")))

gnu/packages/fonts.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014 Joshua Grant <tadni@riseup.net>
 ;;; Copyright © 2014 Alex Kost <alezost@gmail.com>
@@ -7,6 +7,7 @@
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Nils Gillmann <niasterisk@grrlz.net>
+;;; Copyright © 2016 Jookia <166291@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24,6 +25,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages fonts)
+  #:use-module (guix utils)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -67,14 +69,15 @@ in print.  With attention to detail for high resolution rendering.")
 (define-public font-ubuntu
   (package
     (name "font-ubuntu")
-    (version "0.80")
+    (version "0.83")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://font.ubuntu.com/download/ubuntu-font-family-"
+              (uri (string-append
-                                  version ".zip"))
+                    "http://font.ubuntu.com/download/ubuntu-font-family-"
+                    version ".zip"))
               (sha256
                (base32
-                "0k4f548riq23gmw4zhn30qqkcpaj4g2ab5rbc3lflfxwkc4p0w8h"))))
+                "0hjvq2x758dx0sfwqhzflns0ns035qm7h6ygskbx1svzg517sva5"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))
@@ -235,6 +238,25 @@ package provides the TrueType (TTF) files.")
      (license:x11-style
       "http://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"))))
 
+(define-public font-cantarell
+  (package
+    (name "font-abattis-cantarell")
+    (version "0.0.24")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnome/sources/cantarell-fonts/"
+                                  (version-major+minor version)
+                                  "/cantarell-fonts-" version ".tar.xz"))
+              (sha256
+               (base32
+                "0r4jnc2x9yncf40lixjb1pqgpq8rzbi2fz33pshlqzjgx2d69bcw"))))
+    (build-system gnu-build-system)
+    (home-page "https://wiki.gnome.org/Projects/CantarellFonts")
+    (synopsis "Cantarell sans-serif typeface")
+    (description "The Cantarell font family is a contemporary Humanist
+sans-serif designed for on-screen reading.  It is used by GNOME@tie{}3.")
+    (license license:silofl1.1)))
+
 (define-public font-gnu-freefont-ttf
   (package
     (name "font-gnu-freefont-ttf")
@@ -628,3 +650,113 @@ Unicode's Basic Multilingual Plane.  The package also includes
 utilities to ease adding new glyphs to the font.")
     (home-page "http://unifoundry.com/unifont.html")
     (license license:gpl2+)))
+
+(define-public font-google-noto
+  (package
+    (name "font-google-noto")
+    (version "20150929")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://noto-website-2.storage.googleapis.com/"
+                                  "pkgs/Noto-hinted.zip"))
+              (sha256
+               (base32
+                "13jhpqzhsqhyby8n0ksqg155a3jyaif3nzj9anzbq8s2gn1xjyd9"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder (begin
+                   (use-modules (guix build utils)
+                                (srfi srfi-26))
+
+                   (let ((PATH     (string-append (assoc-ref %build-inputs
+                                                             "unzip")
+                                                  "/bin"))
+                         (font-dir (string-append %output
+                                                  "/share/fonts/truetype")))
+                     (setenv "PATH" PATH)
+                     (system* "unzip" (assoc-ref %build-inputs "source"))
+
+                     (mkdir-p font-dir)
+                     (for-each (lambda (ttf)
+                                 (copy-file ttf
+                                            (string-append font-dir "/" ttf)))
+                               (find-files "." "\\.ttf$"))
+                     (for-each (lambda (otf)
+                                 (copy-file otf
+                                            (string-append font-dir "/" otf)))
+                               (find-files "." "\\.otf$"))))))
+    (native-inputs `(("unzip" ,unzip)))
+    (home-page "https://www.google.com/get/noto/")
+    (synopsis "Fonts aimed to cover all languages")
+    (description "Googe Noto Fonts is a family of fonts aimed to support all
+languages with a consistent look and aesthetic.  It's goal is to have no Unicode
+symbols unable to be displayed properly.")
+    (license license:silofl1.1)))
+
+(define-public font-un
+  (package
+    (name "font-un")
+    (version "1.0.2-080608")
+    ;; The upstream server at kldp.net is serving us broken MIME.
+    ;; See <http://bugs.gnu.org/22908>.
+    (source (origin
+              (method url-fetch)
+              (uri (list
+                    (string-append
+                     "http://krosos.sdf.org/static/unix/"
+                     "un-fonts-core-" version ".tar.gz")
+                    ;; XXX: The upstream server at kldp.net
+                    (string-append
+                     "https://kldp.net/projects/unfonts/download/4695?filename="
+                     "un-fonts-core-" version ".tar.gz")))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "13liaz2pmww3aqabm55la5npd08m1skh334ky7qfidxaz5s742iv"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+
+         (let ((tar      (string-append (assoc-ref %build-inputs "tar")
+                                        "/bin/tar"))
+               (PATH     (string-append (assoc-ref %build-inputs "gzip")
+                                        "/bin"))
+               (font-dir (string-append %output "/share/fonts/truetype"))
+               (doc-dir  (string-append %output "/share/doc/" ,name)))
+           (setenv "PATH" PATH)
+           (system* tar "xvf" (assoc-ref %build-inputs "source"))
+           (mkdir-p font-dir)
+           (mkdir-p doc-dir)
+           (chdir (string-append "un-fonts"))
+           (for-each (lambda (ttf)
+                       (copy-file ttf
+                                  (string-append font-dir "/"
+                                                 (basename ttf))))
+                     (find-files "." "\\.ttf$"))
+           (for-each (lambda (doc)
+                       (copy-file doc
+                                  (string-append doc-dir "/"
+                                                 (basename doc))))
+                     '("COPYING" "README"))))))
+    (native-inputs
+     `(("tar" ,tar)
+       ("gzip" ,gzip)))
+    (home-page "https://kldp.net/projects/unfonts/")
+    (synopsis "Collection of Korean fonts")
+    (description
+     "Un-fonts is a family of mainly Korean fonts.
+It contains the following fonts and styles:
+
+@enumerate
+@item UnBatang, UnBatangBold: serif;
+@item UnDotum, UnDotumBold: sans-serif;
+@item UnGraphic, UnGraphicBold: sans-serif style;
+@item UnDinaru, UnDinaruBold, UnDinaruLight;
+@item UnPilgi, UnPilgiBold: script;
+@item UnGungseo: cursive, brush-stroke.
+@end enumerate\n")
+    (license license:gpl2+)))

gnu/packages/fontutils.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -93,8 +94,12 @@ anti-aliased glyph bitmap generation with 256 gray levels.")
             (string-append "--with-default-fonts="
                            (assoc-ref %build-inputs "gs-fonts")
                            "/share/fonts")
+
             ;; register fonts from user profile
+            ;; TODO: Add /run/current-system/profile/share/fonts and remove
+            ;; the skeleton that works around it from 'default-skeletons'.
             "--with-add-fonts=~/.guix-profile/share/fonts"
+
             ;; python is not actually needed
             "PYTHON=false")
       #:phases
@@ -203,6 +208,7 @@ applications should be.")
 
 (define-public graphite2
   (package
+   (replacement graphite2-1.3.6)
    (name "graphite2")
    (version "1.3.5")
    (source
@@ -229,6 +235,21 @@ and returns a sequence of positioned glyphids from the font.")
    (license license:lgpl2.1+)
    (home-page "https://github.com/silnrsi/graphite")))
 
+(define graphite2-1.3.6
+  (package
+    (inherit graphite2)
+    (replacement #f)
+    (source
+     (let ((name "graphite2") (version "1.3.6"))
+       (origin
+         (method url-fetch)
+         (uri (string-append "https://github.com/silnrsi/graphite/archive/"
+                             version ".tar.gz"))
+         (file-name (string-append name "-" version ".tar.gz"))
+         (sha256
+          (base32
+           "1frd9mjaqzvh9gs74ngc43igi53vzjzlwr5chbrs6ii1hc4aa23s")))))))
+
 (define-public potrace
   (package
     (name "potrace")
@@ -305,7 +326,7 @@ smooth contours with constant curvature at the spline joins.")
 (define-public libuninameslist
   (package
     (name "libuninameslist")
-    (version "0.4.20140731")
+    (version "0.5.20150701")
     (source
      (origin
        (method url-fetch)
@@ -314,7 +335,7 @@ smooth contours with constant curvature at the spline joins.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "016zxffpc8iwpxxmnjkdirn6dsbcvdb2wjdrp123sf79f4nsynyj"))))
+         "1j6147l100rppw7axlrkdx0p35fax6bz2zh1xgpg7a3b4pmqaj3v"))))
     (build-system gnu-build-system)
     (native-inputs `(("autoconf" ,autoconf)
                      ("automake" ,automake)
@@ -336,37 +357,51 @@ definitions.")
 (define-public fontforge
   (package
    (name "fontforge")
-   (version "20120731-b")               ;aka 1.0
+   (version "20150824")
    (source (origin
             (method url-fetch)
-            (uri (string-append "mirror://sourceforge/fontforge/fontforge_full-"
+            (uri (string-append
-                                version ".tar.bz2"))
+                  "https://github.com/fontforge/fontforge/releases/download/"
+                  version "/fontforge-" version ".tar.gz"))
             (sha256 (base32
-                     "1dhg0i2pf76j40cb9g1wzpag21fgarpjaad0hdbk27i1zz588q8v"))))
+                     "0gfcm8yn1d30giqhdwbchnfnspcqypqdzrxlhqhwy1i18wgl0v2v"))
+            (modules '((guix build utils)))
+            (snippet
+             ;; Make builds bit-reproducible by using fixed date strings.
+             '(substitute* "configure"
+                (("^FONTFORGE_MODTIME=.*$")
+                 "FONTFORGE_MODTIME=\"1458399002\"\n")
+                (("^FONTFORGE_MODTIME_STR=.*$")
+                 "FONTFORGE_MODTIME_STR=\"15:50 CET 19-Mar-2016\"\n")
+                (("^FONTFORGE_VERSIONDATE=.*$")
+                 "FONTFORGE_VERSIONDATE=\"20160319\"\n")))))
    (build-system gnu-build-system)
-   ;; TODO: Add python for scripting support.
+   (native-inputs
-   (inputs `(("gettext"         ,gnu-gettext)
+    `(("pkg-config" ,pkg-config)))
-             ("libtiff"         ,libtiff)
+   (inputs `(("cairo"           ,cairo)
-             ("libjpeg"         ,libjpeg)
+             ("fontconfig"      ,fontconfig) ;dlopen'd
-             ("libpng"          ,libpng)
+             ("freetype"        ,freetype)
+             ("gettext"         ,gnu-gettext)
              ("giflib"          ,giflib) ;needs giflib 4.*
-             ("libxml2"         ,libxml2)
+             ("glib"            ,glib) ;needed for pango detection
-             ("libX11"          ,libx11)
-             ("libXi"           ,libxi)
              ("libICE"          ,libice)
              ("libSM"           ,libsm)
-             ("freetype"        ,freetype)
+             ("libX11"          ,libx11)
-             ("potrace"         ,potrace)
+             ("libXi"           ,libxi)
+             ("libjpeg"         ,libjpeg)
+             ("libltdl"         ,libltdl)
+             ("libpng"          ,libpng)
              ("libspiro"        ,libspiro)
-             ("zlib"            ,zlib)
+             ("libtiff"         ,libtiff)
-             ("cairo"           ,cairo)
-             ("fontconfig"      ,fontconfig) ;dlopen'd
              ("libuninameslist" ,libuninameslist)
+             ("libxft"          ,libxft)
+             ("libxml2"         ,libxml2)
              ("pango"           ,pango)
-             ("glib"            ,glib))) ;needed for pango detection
+             ("potrace"         ,potrace)
+             ("python"          ,python)
+             ("zlib"            ,zlib)))
    (arguments
-    '(#:configure-flags `("--enable-double")
+    '(#:tests? #f
-      #:tests? #f
       #:phases
       (alist-cons-before
        'configure 'patch-configure
@@ -406,5 +441,5 @@ definitions.")
     "FontForge allows you to create and modify postscript, truetype and
 opentype fonts.  You can save fonts in many different outline formats, and
 generate bitmaps.")
-   (license license:bsd-3)
+   (license license:gpl3+)
    (home-page "http://fontforge.org/")))

gnu/packages/freedesktop.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015 Andy Wingo <wingo@pobox.com>
-;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 David Hashe <david.hashe@dhashe.com>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
@@ -82,14 +82,14 @@ freedesktop.org project.")
 (define-public libinput
   (package
     (name "libinput")
-    (version "1.1.902")
+    (version "1.2.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://freedesktop.org/software/libinput/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "19wa5yizc3nfq3gibyqb3ygdvcs7v7bz1m5ifv0f4va3igxc3nk3"))))
+                "0b3f67xsy1s84cvzw22mjfkbcv6pj4p4yns4h3m0fmb7zqbvjm0p"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -142,14 +142,14 @@ the freedesktop.org XDG Base Directory specification.")
 (define-public elogind
   (package
     (name "elogind")
-    (version "219.12")
+    (version "219.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://wingolog.org/pub/" name "/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "13qc4f0dl7ynnfp1y565z2k0jjizly5w3dqhiqkdk7v6jr4pksb7"))
+                "1jckc4wx199n1q4r4fv43ibjs6nlq91s39w9r78ilk1z383m1hcx"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -165,11 +165,17 @@ the freedesktop.org XDG Base Directory specification.")
                             (assoc-ref %build-inputs "libcap"))
              (string-append "--with-udevrulesdir="
                             (assoc-ref %outputs "out")
-                            "/lib/udev/rules.d")
+                            "/lib/udev/rules.d"))
-             ;; XXX: fail with:
+       #:make-flags '("PKTTYAGENT=/run/current-system/profile/bin/pkttyagent")
-             ;;  src/shared/clean-ipc.c:315: undefined reference to `mq_unlink'
+       #:phases (modify-phases %standard-phases
-             "LDFLAGS=-lrt")
+                  (add-before 'build 'fix-service-file
-       #:make-flags '("PKTTYAGENT=/run/current-system/profile/bin/pkttyagent")))
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      ;; Fix the file name of the 'elogind' binary in the D-Bus
+                      ;; '.service' file.
+                      (substitute* "src/login/org.freedesktop.login1.service"
+                        (("^Exec=.*")
+                         (string-append "Exec=" (assoc-ref %outputs "out")
+                                        "/libexec/elogind/elogind\n"))))))))
     (native-inputs
      `(("intltool" ,intltool)
        ("gettext" ,gnu-gettext)
@@ -188,7 +194,7 @@ the freedesktop.org XDG Base Directory specification.")
                                              ;when pressing the power button
        ("dbus" ,dbus)
        ("eudev" ,eudev)))
-    (home-page "https://github.com/andywingo/elogind")
+    (home-page "https://github.com/wingo/elogind")
     (synopsis "User, seat, and session management service")
     (description "Elogind is the systemd project's \"logind\" service,
 extracted out as a separate project.  Elogind integrates with PAM to provide
@@ -247,15 +253,16 @@ Python.")
 (define-public wayland
   (package
     (name "wayland")
-    (version "1.9.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://wayland.freedesktop.org/releases/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1yhy62vkbq8j8c9zaa6yzvn75cd99kfa8n2zfdwl80x019r711ww"))))
+                "1p307ly1yyqjnzn9dbv78yffql2qszn84qk74lwanl3gma8fgxjb"))))
     (build-system gnu-build-system)
+    (arguments `(#:parallel-tests? #f))
     (native-inputs
      `(("doxygen" ,doxygen)
        ("graphviz" ,graphviz)
@@ -268,7 +275,7 @@ Python.")
        ("expat" ,expat)
        ("libffi" ,libffi)
        ("libxml2" ,libxml2))) ; for XML_CATALOG_FILES
-    (home-page "http://wayland.freedesktop.org/")
+    (home-page "https://wayland.freedesktop.org/")
     (synopsis "Display server protocol")
     (description
      "Wayland is a protocol for a compositor to talk to its clients as well as
@@ -358,6 +365,7 @@ Analysis and Reporting Technology) functionality.")
                "doc"))                            ;5 MiB of gtk-doc HTML
     (arguments
      `(#:tests? #f ; requiring system message dbus
+       #:disallowed-references ("doc")            ;enforce separation of "doc"
        #:configure-flags
        (list "--disable-man"
              "--localstatedir=/var"
@@ -404,7 +412,7 @@ message bus.")
     (version "0.6.40")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://www.freedesktop.org/software/"
+              (uri (string-append "https://www.freedesktop.org/software/"
                                   name "/" name "-" version ".tar.xz"))
               (sha256
                (base32
@@ -444,7 +452,7 @@ interfaces, based on the useradd, usermod and userdel commands.")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://www.freedesktop.org/software/" name "/"
+                    "https://www.freedesktop.org/software/" name "/"
                     name "-" version ".tar.xz"))
               (sha256
                (base32
@@ -471,15 +479,15 @@ which speak the Mobile Interface Broadband Model (MBIM) protocol.")
 (define-public libqmi
   (package
     (name "libqmi")
-    (version "1.12.6")
+    (version "1.12.8")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://www.freedesktop.org/software/" name "/"
+                    "https://www.freedesktop.org/software/" name "/"
                     name "-" version ".tar.xz"))
               (sha256
                (base32
-                "101ppan2q1h4pyp2zbn9b8sdwy2c7fk9rp91yykxz3afrvzbymq8"))))
+                "19w2zkm5xl6i3vm1xhjjclks4awas17gfbb2k5y66gwnkiykjfnj"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("glib:bin" ,glib "bin") ; for glib-mkenums
@@ -488,7 +496,7 @@ which speak the Mobile Interface Broadband Model (MBIM) protocol.")
     (propagated-inputs
      `(("glib" ,glib))) ; required by qmi-glib.pc
     (synopsis "Library to communicate with QMI-powered modems")
-    (home-page "http://www.freedesktop.org/wiki/Software/libqmi/")
+    (home-page "https://www.freedesktop.org/wiki/Software/libqmi/")
     (description
      "Libqmi is a GLib-based library for talking to WWAN modems and devices
 which speak the Qualcomm MSM Interface (QMI) protocol.")

gnu/packages/game-development.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2015, 2016 David Thompson <davet@gnu.org>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -127,7 +128,7 @@ provide connectivity for client applications written in any language.")
 (define-public tiled
   (package
     (name "tiled")
-    (version "0.13.1")
+    (version "0.15.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/bjorn/tiled/archive/v"
@@ -135,19 +136,18 @@ provide connectivity for client applications written in any language.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "057a5cna3vhznpl9hyql2sxz995aprv43r8wva89x4vdphxv04lm"))))
+                "10bbjdv5r36229r1dqg32bxcj9yvpkx9jgs9v4s1qb71v856b15h"))))
     (build-system gnu-build-system)
     (inputs `(("qt" ,qt)
               ("zlib" ,zlib)))
     (arguments
      '(#:phases
-       (alist-replace
+       (modify-phases %standard-phases
-        'configure
+         (replace 'configure
-        (lambda* (#:key outputs #:allow-other-keys)
+           (lambda* (#:key outputs #:allow-other-keys)
-          (let ((out (assoc-ref outputs "out")))
+             (let ((out (assoc-ref outputs "out")))
-            (system* "qmake"
+               (system* "qmake"
-                     (string-append "PREFIX=" out))))
+                        (string-append "PREFIX=" out))))))))
-        %standard-phases)))
     (home-page "http://www.mapeditor.org/")
     (synopsis "Tile map editor")
     (description

gnu/packages/games.scm

@@ -7,7 +7,7 @@
 ;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2015, 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 David Hashe <david.hashe@dhashe.com>
 ;;; Copyright © 2015 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
@@ -15,6 +15,8 @@
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2016 Rodger Fox <thylakoid@openmailbox.org>
+;;; Copyright © 2016 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
+;;; Copyright © 2016 Nils Gillmann <niasterisk@grrlz.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -69,6 +71,7 @@
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages bash)
@@ -1182,7 +1185,7 @@ is programmed in Haskell.")
 (define-public manaplus
   (package
     (name "manaplus")
-    (version "1.6.1.16")
+    (version "1.6.3.12")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1190,7 +1193,7 @@ is programmed in Haskell.")
                     version "/manaplus-" version ".tar.xz"))
               (sha256
                (base32
-                "1vrsjvdbdzbnqmr8sp110b2d93kp5yfnifsn6zjm60kdvvbphdir"))))
+                "02bnd4nk1qzrfqckqkwb6sbjzsmacv968ih74cdgcykslpsr684d"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags
@@ -1917,3 +1920,109 @@ Catan.  It can be played on a local network, on the internet, and with AI
 players.")
     (home-page "http://pio.sourceforge.net/")
     (license license:gpl2+)))
+
+(define-public desmume
+  (package
+    (name "desmume")
+    (version "0.9.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://sourceforge/desmume/desmume/"
+             version "/desmume-" version ".tar.gz"))
+       (sha256
+        (base32
+         "15l8wdw3q61fniy3h93d84dnm6s4pyadvh95a0j6d580rjk4pcrs"))))
+    (build-system gnu-build-system)
+    (arguments
+     ;; Enable support for WiFi and microphone.
+     `(#:configure-flags '("--enable-wifi"
+                           "--enable-openal")))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("intltool" ,intltool)))
+    (inputs
+     `(("zlib" ,zlib)
+       ("sdl" ,sdl)
+       ("glib" ,glib)
+       ("gtk+" ,gtk+-2)
+       ("glu" ,glu)))
+    (home-page "http://desmume.org/")
+    (synopsis "Nintendo DS emulator")
+    (description
+     "DeSmuME is an emulator for the Nintendo DS handheld gaming console.")
+    (license license:gpl2)))
+
+(define-public einstein
+  (package
+    (name "einstein")
+    (version "2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://http.debian.net/debian/pool/main/e/"
+                                  "einstein/einstein_2.0.dfsg.2.orig.tar.gz"))
+              (sha256
+               (base32
+                "1hxrlv6n8py48j487i6wbb4n4vd55w0na69r7ccmmr9vmrsw5mlk"))
+              (patches (list (search-patch "einstein-build.patch")))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("freetype" ,freetype)
+       ("sdl" ,(sdl-union (list sdl sdl-mixer sdl-ttf)))
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("font-dejavu" ,font-dejavu)))
+    (arguments
+     `(#:tests? #f ; no check target
+       #:phases
+        (modify-phases %standard-phases
+          (replace 'configure
+          (lambda* (#:key outputs inputs #:allow-other-keys)
+            (let ((out (assoc-ref outputs "out"))
+                  (dejavu (string-append (assoc-ref inputs "font-dejavu")
+                                         "/share/fonts/truetype/DejaVuSans.ttf")))
+              (substitute* "Makefile"
+                (("PREFIX=/usr/local") (string-append "PREFIX=" out)))
+              ;; The patch above registers a free font for use by the binary,
+              ;; but the font is copied during the compile phase into a
+              ;; resources file, so we need to make the ttf file available.
+              (symlink dejavu "res/DejaVuSans.ttf")
+              #t))))))
+    (synopsis "Logic puzzle game")
+    (description "The goal of this logic game is to open all cards in a 6x6
+grid, using a number of hints as to their relative position.  The game idea
+is attributed to Albert Einstein.")
+    ;; The original home page has disappeared.
+    (home-page (string-append "http://web.archive.org/web/20120521062745/"
+                              "http://games.flowix.com/en/index.html"))
+    ;; License according to
+    ;; http://web.archive.org/web/20150222180355/http://www.babichev.info/en/projects/index.html
+    ;; The source code is a DFSG-sanitized tarball and does not contain any
+    ;; license information.
+    (license license:gpl3+)))
+
+(define-public powwow
+  (package
+    (name "powwow")
+    (version "1.2.17")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://www.hoopajoo.net/static/projects/powwow-"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1xmsg2y7qcvj67i9ilnih0mvfxcpni7fzrz343x9rdfnkkzf3pp8"))))
+    (inputs
+     `(("ncurses" ,ncurses)))
+    (build-system gnu-build-system)
+    (home-page "http://www.hoopajoo.net/projects/powwow.html")
+    (synopsis "MUD and telnet client")
+    (description
+     "POWWOW is a client software which can be used for telnet as well as for
+@dfn{Multi-User Dungeon} (MUD).  Additionally it can serve as a nice client for
+the chat server psyced with the specific config located at
+http://lavachat.symlynx.com/unix/")
+    (license license:gpl2+)))

gnu/packages/gcc.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
 ;;;
@@ -354,6 +354,8 @@ Go.  It also includes runtime support libraries for these languages.")
                 "1ny4smkp5bzs3cp8ss7pl6lk8yss0d9m4av1mvdp72r1x695akxq"))
               (patches (list (search-patch "gcc-5.0-libvtv-runpath.patch")))))))
 
+;; Note: When changing the default gcc version, update
+;;       the gcc-toolchain-* definitions accordingly.
 (define-public gcc gcc-4.9)
 
 (define-public (make-libstdc++ gcc)
@@ -440,7 +442,15 @@ as the 'native-search-paths' field."
         `(cons (string-append "--enable-languages="
                               ,(string-join languages ","))
                (remove (cut string-match "--enable-languages.*" <>)
-                       ,flags)))))))
+                       ,flags)))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'install 'remove-broken-or-conflicting-files
+             (lambda* (#:key outputs #:allow-other-keys)
+               (for-each delete-file
+                         (find-files (string-append (assoc-ref outputs "out") "/bin")
+                                     ".*(c\\+\\+|cpp|g\\+\\+|gcov|gcc.*)"))
+               #t))))))))
 
 (define %generic-search-paths
   ;; This is the language-neutral search path for GCC.  Entries in $CPATH are

gnu/packages/gettext.scm

@@ -144,7 +144,7 @@ catalogs.  Nearly all GNU packages use Gettext.")
        ("perl-module-build" ,perl-module-build)
        ("docbook-xsl" ,docbook-xsl)
        ("docbook-xml" ,docbook-xml) ;for tests
-       ("texlive-bin" ,texlive-bin) ;for tests
+       ("texlive" ,texlive-minimal) ;for tests
        ("libxml2" ,libxml2)
        ("xsltproc" ,libxslt)))
     (home-page "http://po4a.alioth.debian.org/")

gnu/packages/glib.scm

@@ -524,9 +524,11 @@ useful for C++.")
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("python" ,python)
-       ("glib"   ,glib)
        ("python-pycairo" ,python-pycairo)
-       ("gobject-introspection" ,gobject-introspection)
+       ("gobject-introspection" ,gobject-introspection)))
+    (propagated-inputs
+     ;; pygobject-3.0.pc refers to all these.
+     `(("glib" ,glib)
        ("libffi" ,libffi)))
     (arguments
      ;; TODO: failing tests: test_native_calls_async
@@ -538,6 +540,8 @@ useful for C++.")
      ;; test_callback_user_data_middle_single
      ;; test_callback_user_data_middle_tuple
      '(#:tests? #f))
+    ;; For finding typelib files, since gobject-introscpetion isn't propagated.
+    (native-search-paths (package-native-search-paths gobject-introspection))
     (home-page "https://live.gnome.org/PyGObject")
     (synopsis "Python bindings for GObject")
     (description
@@ -550,10 +554,8 @@ useful for C++.")
     (name "python2-pygobject")
     (inputs
      `(("python" ,python-2)
-       ("glib" ,glib)
        ("python-pycairo" ,python2-pycairo)
-       ("gobject-introspection" ,gobject-introspection)
+       ("gobject-introspection" ,gobject-introspection)))))
-       ("libffi" ,libffi)))))
 
 (define telepathy-glib
   (package

gnu/packages/gnome.scm

@@ -34,6 +34,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system glib-or-gtk)
@@ -107,6 +108,7 @@
   #:use-module (gnu packages cdrom)
   #:use-module (gnu packages samba)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages fonts)
   #:use-module (srfi srfi-1))
 
 (define-public brasero
@@ -1463,7 +1465,7 @@ Hints specification (EWMH).")
     (license license:lgpl2.0+)))
 
 ;; stable version for gtk2, required by xfwm4.
-(define-public libwnck-1
+(define-public libwnck-2
   (package (inherit libwnck)
     (name "libwnck")
     (version "2.30.7")
@@ -3381,7 +3383,7 @@ USB transfers with your high-level application or system daemon.")
 (define-public simple-scan
   (package
     (name "simple-scan")
-    (version "3.17.4")
+    (version "3.19.91")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://launchpad.net/simple-scan/"
@@ -3390,7 +3392,7 @@ USB transfers with your high-level application or system daemon.")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "1pslbv45g01g039zj2b01k08f763kkhzqw8wwz7yh27m7bjllnx6"))))
+                "1c5glf5vxgld41w4jxfqcv17q76qnh43fawpv33hncgh8d283xkf"))))
     (build-system glib-or-gtk-build-system)
     (inputs
      `(("gtk" ,gtk+)
@@ -3408,6 +3410,21 @@ USB transfers with your high-level application or system daemon.")
        ("pkg-config" ,pkg-config)
        ("vala" ,vala)
        ("xmllint" ,libxml2)))
+    (arguments
+     '(#:configure-flags '("--disable-packagekit")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'clean
+                    (lambda _
+                      ;; Remove a left-over reference to PackageKit.
+
+                      ;; https://bugs.launchpad.net/simple-scan/+bug/1462769
+
+                      ;; There are some generated C files erroneously
+                      ;; included in the source distribution, and this
+                      ;; one breaks the build by referring to a
+                      ;; non-existent header (packagekit.h)
+                      (delete-file "src/ui.c"))))))
     (home-page "https://launchpad.net/simple-scan")
     (synopsis "Document and image scanner")
     (description "Simple Scan is an easy-to-use application, designed to let
@@ -3778,6 +3795,46 @@ such as gzip tarballs.")
               (sha256
                (base32
                 "0icajbzqf5llvp5s8nafwkhwz6a6jmwn4hhs81bk0bpzawyq4zdk"))))
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'pre-configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Use elogind instead of systemd.
+             (substitute* "configure"
+               (("libsystemd-login >= 183 libsystemd-daemon libsystemd-journal")
+                "libelogind")
+               (("systemd") "elogind"))
+             (substitute* "gnome-session/gsm-systemd.c"
+               (("#include <systemd/sd-login.h>")
+                "#include <elogind/sd-login.h>"))
+             ;; Remove uses of the systemd journal.
+             (substitute* "gnome-session/main.c"
+               (("#ifdef HAVE_SYSTEMD") "#if 0"))
+             (substitute* "gnome-session/gsm-manager.c"
+               (("#ifdef HAVE_SYSTEMD") "#if 0"))
+             #t))
+         (add-after 'install 'wrap-gnome-session
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Make sure 'gnome-session' finds the 'gsettings' program.
+             (let ((glib (assoc-ref inputs "glib:bin"))
+                   (out  (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/gnome-session")
+                 `("PATH" ":" prefix (,(string-append glib "/bin"))))
+               #t)))
+         (add-after 'install 'disable-hardware-acceleration-check
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Do not abort if hardware acceleration is missing.  This allows
+             ;; GNOME to run in QEMU and on low-end devices.
+             (let ((out (assoc-ref outputs "out")))
+               (substitute* (string-append out
+                                           "/share/xsessions/gnome.desktop")
+                 (("gnome-session")
+                  "gnome-session --disable-acceleration-check"))
+               #t))))
+
+       #:configure-flags
+       '("--enable-elogind")))
     (build-system glib-or-gtk-build-system)
     (native-inputs
      `(("glib:bin" ,glib "bin") ; for glib-compile-schemas, etc.
@@ -3785,7 +3842,8 @@ such as gzip tarballs.")
        ("intltool" ,intltool)
        ("xsltproc" ,libxslt)))
     (inputs
-     `(("gnome-desktop" ,gnome-desktop)
+     `(("elogind" ,elogind)
+       ("gnome-desktop" ,gnome-desktop)
        ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
        ("gtk+" ,gtk+)
        ("json-glib" ,json-glib)
@@ -4147,22 +4205,10 @@ Evolution (hence the name), but is now used by other packages as well.")
 users.")
     (license license:lgpl2.1)))
 
-(define %network-manager-glib-duplicate-test-patch
-  (origin
-    (method url-fetch)
-    (uri (string-append
-          "http://cgit.freedesktop.org/NetworkManager/NetworkManager/"
-          "patch/libnm-core/tests/test-general.c"
-          "?id=874f455d6d47c5a34ed9861a6710f4b78202e0d6"))
-    (file-name "network-manager-glib-duplicate-test.patch")
-    (sha256
-     (base32
-      "1v0vpxzf0p0b1y5lmq8w7rjndp216gr60nbf2dpdz5rgxx3p3ml6"))))
-
 (define-public network-manager
   (package
     (name "network-manager")
-    (version "1.0.6")
+    (version "1.0.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/NetworkManager/"
@@ -4170,8 +4216,7 @@ users.")
                                   "NetworkManager-" version ".tar.xz"))
               (sha256
                (base32
-                "1galh9j95yw33iv1jj8zz0h88ahx8gm5mqmam7zq9f730cj01siq"))
+                "1g4z2wg036n0njqp8fycrisj46l3yda6pl00l4rg9nfz862cxkqv"))))
-              (patches (list %network-manager-glib-duplicate-test-patch))))
     (build-system gnu-build-system)
     (outputs '("out"
                "doc")) ; 8 MiB of gtk-doc HTML
@@ -4194,6 +4239,19 @@ users.")
                (string-append "--with-dhclient=" dhclient)))
        #:phases
        (modify-phases %standard-phases
+         (add-before 'configure 'pre-configure
+           (lambda _
+             ;; These tests try to test aspects of network-manager's
+             ;; functionality within restricted containers, but they don't
+             ;; cope with being already in the Guix build jail as that jail
+             ;; lacks some features that they would like to proxy over (like
+             ;; a /sys mount).
+             (substitute* '("src/platform/Makefile.in")
+               (("SUBDIRS = tests") ""))
+             (substitute* '("src/tests/Makefile.in")
+               (("\ttest-route-manager-linux") "\t")
+               (("\ttest-route-manager-fake") "\t"))
+             #t))
          (add-before 'check 'pre-check
            (lambda _
              ;; For the missing /etc/machine-id.
@@ -4242,7 +4300,7 @@ services.")
 (define-public network-manager-applet
   (package
     (name "network-manager-applet")
-    (version "1.0.6")
+    (version "1.0.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -4250,7 +4308,7 @@ services.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1yj0m6fb9v12d0di0rfmk3hx1vmygjkiff2c476rf792sbh56kax"))))
+                "1szh5jyijxm6z55irkp5s44pwah0nikss40mx7pvpk38m8zaqidh"))))
     (build-system glib-or-gtk-build-system)
     (arguments '(#:configure-flags '("--disable-migration")))
     (native-inputs
@@ -4634,13 +4692,17 @@ as SASL, TLS and VeNCrypt.  Additionally it supports encoding extensions.")
        ("gobject-introspection" ,gobject-introspection)
        ("intltool" ,intltool)
        ("pkg-config" ,pkg-config)))
-    (propagated-inputs
-     `(("gtk+" ,gtk+))) ; required by libnautilus-extension.pc
     (inputs
      ;; TODO: add gvfs support.
      `(("dconf" ,dconf)
        ("exempi" ,exempi)
        ("gnome-desktop" ,gnome-desktop)
+       ;; XXX: gtk+ is required by libnautilus-extension.pc
+       ;;
+       ;; Don't propagate it to reduces "profile pollution" of the 'gnome' meta
+       ;; package.  See:
+       ;; <http://lists.gnu.org/archive/html/guix-devel/2016-03/msg00283.html>.
+       ("gtk+" ,gtk+)
        ("libexif" ,libexif)
        ("libxml2" ,libxml2)))
     (synopsis "File manager for GNOME")
@@ -4783,6 +4845,7 @@ software that do not provide their own configuration interface.")
      ;; TODO: Add more packages according to:
      ;;       <https://packages.debian.org/jessie/gnome-core>.
      `(("adwaita-icon-theme"        ,adwaita-icon-theme)
+       ("font-cantarell"            ,font-cantarell)
        ("at-spi2-core"              ,at-spi2-core)
        ("dbus"                      ,dbus)
        ("dconf"                     ,dconf)
@@ -4805,9 +4868,63 @@ software that do not provide their own configuration interface.")
        ("totem"                     ,totem)
        ("yelp"                      ,yelp)
        ("zenity"                    ,zenity)))
-    (synopsis "Desktop environment (meta-package)")
+    (synopsis "The GNU desktop environment")
     (home-page "https://www.gnome.org/")
     (description
-     "GNOME is an intutive and attractive desktop environment.  It aims to be
+     "GNOME is the graphical desktop for GNU.  It includes a wide variety of
-an easy and elegant way to use your computer.")
+applications for browsing the web, editing text and images, creating
+documents and diagrams, playing media, scanning, and much more.")
     (license license:gpl2+)))
+
+(define-public byzanz
+  ;; The last stable release of Byzanz was in 2011, but there have been many
+  ;; useful commits made to the Byzanz repository since then that it would be
+  ;; silly to use such an old release.
+  (let ((commit "f7af3a5bd252db84af8365bd059c117a7aa5c4af"))
+    (package
+      (name "byzanz")
+      (version (string-append "0.2-1." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "git://git.gnome.org/byzanz")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1l60myzxf9cav27v5v3nsijlslz9r7ip6d5kiirfpkf9k0w26hz3"))))
+      (build-system glib-or-gtk-build-system)
+      (arguments
+       '(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'bootstrap
+             (lambda _
+               ;; The build system cleverly detects that we're not building from
+               ;; a release tarball and turns on -Werror for GCC.
+               ;; Unsurprisingly, there is a warning during compilation that
+               ;; causes the build to fail unnecessarily, so we remove the flag.
+               (substitute* '("configure.ac")
+                 (("-Werror") ""))
+               ;; The autogen.sh script in gnome-common will run ./configure
+               ;; by default, which is problematic because source shebangs
+               ;; have not yet been patched.
+               (setenv "NOCONFIGURE" "t")
+               (zero? (system* "sh" "autogen.sh")))))))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("gnome-common" ,gnome-common)
+         ("intltool" ,intltool)
+         ("libtool" ,libtool)
+         ("pkg-config" ,pkg-config)
+         ("which" ,which)))
+      (inputs
+       `(("glib" ,glib)
+         ("gstreamer" ,gstreamer)
+         ("gst-plugins-base" ,gst-plugins-base)
+         ("gtk+" ,gtk+)))
+      (synopsis "Desktop recording program")
+      (description "Byzanz is a simple desktop recording program with a
+command-line interface.  It can record part or all of an X display for a
+specified duration and save it as a GIF encoded animated image file.")
+      (home-page "https://git.gnome.org/browse/byzanz")
+      (license license:gpl2+))))

gnu/packages/gnuzilla.scm

@@ -177,7 +177,7 @@ in the Mozilla clients.")
 (define-public nss
   (package
     (name "nss")
-    (version "3.21")
+    (version "3.21.1")
     (source (origin
               (method url-fetch)
               (uri (let ((version-with-underscores
@@ -188,7 +188,7 @@ in the Mozilla clients.")
                       "nss-" version ".tar.gz")))
               (sha256
                (base32
-                "0fbjx3xsdm4gjc1gyzy2z315cvyw7yilsm7p9w75rpbwgl15nyiz"))
+                "0knr99yc8sba2ga6x1gwhg9gr1dmgcl344g3bmxm8c364i2vpxns"))
               ;; Create nss.pc and nss-config.
               (patches (list (search-patch "nss-pkgconfig.patch")))))
     (build-system gnu-build-system)
@@ -290,7 +290,25 @@ standards.")
       (patches (map search-patch
                     '("icecat-avoid-bundled-includes.patch"
                       "icecat-re-enable-DHE-cipher-suites.patch"
-                      "icecat-update-graphite2.patch")))
+                      "icecat-update-graphite2.patch"
+                      "icecat-update-graphite2-pt2.patch"
+                      "icecat-CVE-2015-4477.patch"
+                      "icecat-CVE-2015-7207.patch"
+                      "icecat-CVE-2016-1952-pt01.patch"
+                      "icecat-CVE-2016-1952-pt02.patch"
+                      "icecat-CVE-2016-1952-pt03.patch"
+                      "icecat-CVE-2016-1952-pt04.patch"
+                      "icecat-CVE-2016-1952-pt05.patch"
+                      "icecat-CVE-2016-1952-pt06.patch"
+                      "icecat-CVE-2016-1954.patch"
+                      "icecat-CVE-2016-1960.patch"
+                      "icecat-CVE-2016-1961.patch"
+                      "icecat-CVE-2016-1962.patch"
+                      "icecat-CVE-2016-1964.patch"
+                      "icecat-CVE-2016-1965.patch"
+                      "icecat-CVE-2016-1966.patch"
+                      "icecat-CVE-2016-1974.patch"
+                      "icecat-bug-1248851.patch")))
       (modules '((guix build utils)))
       (snippet
        '(begin

gnu/packages/graphics.scm

@@ -1,6 +1,8 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Tomáš Čech <sleep_walker@gnu.org>
+;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,6 +27,8 @@
   #:use-module (guix build-system cmake)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
+  #:use-module (gnu packages algebra)
+  #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages boost)
@@ -32,14 +36,96 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages pulseaudio)  ;libsndfile, libsamplerate
   #:use-module (gnu packages compression)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages gl)
+  #:use-module (gnu packages image)
+  #:use-module (gnu packages jemalloc)
+  #:use-module (gnu packages photo)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages sdl)
+  #:use-module (gnu packages video)
   #:use-module (gnu packages xorg))
 
+(define-public blender
+  (package
+    (name "blender")
+    (version "2.76b")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://download.blender.org/source/"
+                                  "blender-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0pb0mlj4vj0iir528ifqq67nsh3ca1942933d9cwlbpcja2jm1dx"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(;; Test files are very large and not included in the release tarball.
+       #:tests? #f
+       #:configure-flags
+       (list "-DWITH_CODEC_FFMPEG=ON"
+             "-DWITH_CODEC_SNDFILE=ON"
+             "-DWITH_CYCLES=ON"
+             "-DWITH_DOC_MANPAGE=ON"
+             "-DWITH_FFTW3=ON"
+             "-DWITH_GAMEENGINE=ON"
+             "-DWITH_IMAGE_OPENJPEG=ON"
+             "-DWITH_INPUT_NDOF=ON"
+             "-DWITH_INSTALL_PORTABLE=OFF"
+             "-DWITH_JACK=ON"
+             "-DWITH_MOD_OCEANSIM=ON"
+             "-DWITH_PLAYER=ON"
+             "-DWITH_PYTHON_INSTALL=OFF"
+             "-DWITH_SYSTEM_OPENJPEG=ON")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-broken-import
+           (lambda _
+             (substitute* "release/scripts/addons/io_scene_fbx/json2fbx.py"
+               (("import encode_bin") "from . import encode_bin"))
+             #t))
+         (add-after 'set-paths 'add-ilmbase-include-path
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; OpenEXR propagates ilmbase, but its include files do not appear
+             ;; in the CPATH, so we need to add "$ilmbase/include/OpenEXR/" to
+             ;; the CPATH to satisfy the dependency on "half.h".
+             (setenv "CPATH"
+                     (string-append (assoc-ref inputs "ilmbase")
+                                    "/include/OpenEXR"
+                                    ":" (or (getenv "CPATH") "")))
+             #t)))))
+    (inputs
+     `(("boost" ,boost)
+       ("jemalloc" ,jemalloc)
+       ("libx11" ,libx11)
+       ("openimageio" ,openimageio)
+       ("openexr" ,openexr)
+       ("ilmbase" ,ilmbase)
+       ("openjpeg" ,openjpeg-1)
+       ("libjpeg" ,libjpeg)
+       ("libpng" ,libpng)
+       ("libtiff" ,libtiff)
+       ("ffmpeg" ,ffmpeg)
+       ("fftw" ,fftw)
+       ("jack" ,jack-1)
+       ("libsndfile" ,libsndfile)
+       ("freetype" ,freetype)
+       ("glew" ,glew)
+       ("openal" ,openal)
+       ("python" ,python-wrapper)
+       ("zlib" ,zlib)))
+    (home-page "http://blender.org/")
+    (synopsis "3D graphics creation suite")
+    (description
+     "Blender is a 3D graphics creation suite.  It supports the entirety of
+the 3D pipeline—modeling, rigging, animation, simulation, rendering,
+compositing and motion tracking, even video editing and game creation.  The
+application can be customized via its API for Python scripting.")
+    (license license:gpl2+)))
+
 (define-public cgal
   (package
     (name "cgal")
@@ -89,7 +175,8 @@ many more.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1izddjwbh1grs8080vmaix72z469qy29wrvkphgmqmcm0sv1by7c"))))
+                "1izddjwbh1grs8080vmaix72z469qy29wrvkphgmqmcm0sv1by7c"))
+              (patches (map search-patch '("ilmbase-fix-tests.patch")))))
     (build-system gnu-build-system)
     (home-page "http://www.openexr.com/")
     (synopsis "Utility C++ libraries for threads, maths, and exceptions")
@@ -119,6 +206,20 @@ exception-handling library.")
                    "\"/tmp/\"")))
               (patches (list (search-patch "openexr-missing-samples.patch")))))
     (build-system gnu-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-broken-test
+           ;; This test fails on i686. Upstream developers suggest that
+           ;; this test is broken on i686 and can be safely disabled:
+           ;; https://github.com/openexr/openexr/issues/67#issuecomment-21169748
+           (lambda _
+             (substitute* "IlmImfTest/main.cpp"
+               (("#include \"testOptimizedInterleavePatterns.h\"")
+                 "//#include \"testOptimizedInterleavePatterns.h\"")
+               (("TEST \\(testOptimizedInterleavePatterns")
+                 "//TEST (testOptimizedInterleavePatterns"))
+             #t)))))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (propagated-inputs

gnu/packages/gstreamer.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 John Darrington <jmd@gnu.org>
-;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
+;;; Copyright © 2015, 2016 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -20,10 +20,11 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages gstreamer)
-  #:use-module ((guix licenses) #:select (lgpl2.0+ bsd-2 bsd-3 gpl2+))
+  #:use-module ((guix licenses) #:select (lgpl2.0+ lgpl2.1+ bsd-2 bsd-3 gpl2+))
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages audio)
   #:use-module (gnu packages bison)
@@ -61,14 +62,14 @@
 (define-public orc
   (package
     (name "orc")
-    (version "0.4.24")
+    (version "0.4.25")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gstreamer.freedesktop.org/data/src/"
                                   "orc/orc-" version ".tar.xz"))
               (sha256
                (base32
-                "16ykgdrgxr6pfpy931p979cs68klvwmk3ii1k0a00wr4nn9x931k"))))
+                "1lak3hyvvb0w9avzmf0a8vayb7vqhj4m709q1czlhvgjb15dbcf1"))))
     (build-system gnu-build-system)
     (arguments `(#:phases
                  (alist-cons-before
@@ -400,3 +401,54 @@ distribution problems in some jurisdictions, e.g. due to patent threats.")
      "This GStreamer plugin supports a large number of audio and video
 compression formats through the use of the libav library.")
     (license gpl2+)))
+
+(define-public python-gst
+  (package
+    (name "python-gst")
+    (version "1.6.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://gstreamer.freedesktop.org/src/gst-python/"
+                    "gst-python-" version ".tar.xz"))
+              (sha256
+               (base32
+                "09ci5zvr7lms7mvgbjgsjwaxcl4nq45n1g9pdwnqmx3rf0qkwxjf"))))
+    (build-system gnu-build-system)
+    (arguments
+     ;; XXX: Factorize python-sitedir with python-build-system.
+     `(#:imported-modules (,@%gnu-build-system-modules
+                           (guix build python-build-system))
+       #:configure-flags
+       (let* ((python (assoc-ref %build-inputs "python"))
+              (python-version ((@@ (guix build python-build-system)
+                                   get-python-version)
+                               python))
+              (python-sitedir (string-append
+                               "lib/python" python-version "/site-packages")))
+         (list (string-append
+                "--with-pygi-overrides-dir=" %output "/" python-sitedir
+                "/gi/overrides")))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("python" ,python)))
+    (propagated-inputs
+     `(("gst-plugins-base" ,gst-plugins-base)
+       ("python-pygobject" ,python-pygobject)))
+    (home-page "http://gstreamer.freedesktop.org/")
+    (synopsis "GStreamer GObject Introspection overrides for Python")
+    (description
+     "This package contains GObject Introspection overrides for Python that can
+be used by Python applications using GStreamer.")
+    (license lgpl2.1+)
+    (properties `((python2-variant . ,(delay python2-gst))))))
+
+(define-public python2-gst
+  (package (inherit python-gst)
+    (name "python2-gst")
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("python" ,python-2)))
+    (propagated-inputs
+     `(("gst-plugins-base" ,gst-plugins-base)
+       ("python-pygobject" ,python2-pygobject)))))

gnu/packages/gtk.scm

@@ -433,6 +433,35 @@ in the GNOME project.")
    (license license:lgpl2.0+)
    (home-page "https://developer.gnome.org/gdk-pixbuf/")))
 
+;; To build gdk-pixbuf with SVG support, we need librsvg, and librsvg depends
+;; on gdk-pixbuf, so this new varibale.  Also, librsvg adds 90MiB to the
+;; closure size.
+(define-public gdk-pixbuf+svg
+  (package (inherit gdk-pixbuf)
+    (name "gdk-pixbuf+svg")
+    (inputs
+     `(("librsvg" ,librsvg)
+       ,@(package-inputs gdk-pixbuf)))
+    (arguments
+     '(#:configure-flags '("--with-x11")
+       #:tests? #f ; tested by the gdk-pixbuf package already
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'register-svg-loader
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out     (assoc-ref outputs "out"))
+                    (librsvg (assoc-ref inputs "librsvg"))
+                    (loaders
+                     (append
+                      (find-files out "^libpixbufloader-.*\\.so$")
+                      (find-files librsvg "^libpixbufloader-.*\\.so$")))
+                    (gdk-pixbuf-query-loaders
+                     (string-append out "/bin/gdk-pixbuf-query-loaders")))
+               (zero? (apply system* `(,gdk-pixbuf-query-loaders
+                                       "--update-cache" ,@loaders)))))))))
+    (synopsis
+     "GNOME image loading and manipulation library, with SVG support")))
+
 (define-public at-spi2-core
   (package
    (name "at-spi2-core")

gnu/packages/guile.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016 Alex Sassmannshausen <alex@pompo.co>
+;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -255,7 +256,16 @@ without requiring the source code to be rewritten.")
        ("flex" ,flex)
        ("texinfo" ,texinfo)
        ("gettext" ,gnu-gettext)
-       ,@(package-native-inputs guile-next)))))
+       ,@(package-native-inputs guile-next)))
+    ;; Same as in guile-2.0
+    (native-search-paths
+     (list (search-path-specification
+            (variable "GUILE_LOAD_PATH")
+            (files '("share/guile/site/2.0")))
+           (search-path-specification
+            (variable "GUILE_LOAD_COMPILED_PATH")
+            (files '("lib/guile/2.0/ccache"
+                     "share/guile/site/2.0")))))))
 
 
 ;;;

gnu/packages/image.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2015 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2013, 2015, 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014, 2015 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2014 Ricardo Wurmus <rekado@elephly.net>
@@ -7,6 +7,7 @@
 ;;; Copyright © 2015 Amirouche Boubekki <amirouche@hypermove.net>
 ;;; Copyright © 2014 John Darrington <jmd@gnu.org>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -547,14 +548,15 @@ graphics image formats like PNG, BMP, JPEG, TIFF and others.")
 (define-public vigra
   (package
    (name "vigra")
-   (version "1.10.0")
+   (version "1.11.0")
    (source
-     (origin
+    (origin
-       (method url-fetch)
+      (method url-fetch)
-       (uri (string-append "https://hci.iwr.uni-heidelberg.de/vigra/vigra-"
+      (uri (string-append "https://github.com/ukoethe/vigra/releases/download/"
-                           version "-src.tar.gz"))
+                          "Version-1-11-0/vigra-"
-       (sha256 (base32
+                          version "-src.tar.gz"))
-                 "16d0jvz3k49niljg9qvvlyxxl15yk0300xkymvyznlmvn1hs7m22"))))
+      (sha256 (base32
+                "1jzm79kqiiilvys3b8mlzy9cvmiirrcwsrlg19qd9rza8zipsqb8"))))
    (build-system cmake-build-system)
    (inputs
     `(("boost" ,boost)
@@ -576,6 +578,7 @@ graphics image formats like PNG, BMP, JPEG, TIFF and others.")
       ("python2-sphinx" ,python2-sphinx)))
    (arguments
     `(#:test-target "check"
+      #:parallel-build? #f ; parallel builds trigger an ICE
       #:configure-flags
         (list "-Wno-dev" ; suppress developer mode with lots of warnings
               (string-append "-DVIGRANUMPY_INSTALL_DIR="
@@ -731,7 +734,10 @@ convert, manipulate, filter and display a wide variety of image formats.")
                   (search-patch "jasper-CVE-2014-8157.patch")
                   (search-patch "jasper-CVE-2014-8158.patch")
                   (search-patch "jasper-CVE-2014-9029.patch")
-                  (search-patch "jasper-CVE-2016-1867.patch")))))
+                  (search-patch "jasper-CVE-2016-1577.patch")
+                  (search-patch "jasper-CVE-2016-1867.patch")
+                  (search-patch "jasper-CVE-2016-2089.patch")
+                  (search-patch "jasper-CVE-2016-2116.patch")))))
     (build-system gnu-build-system)
     (native-inputs
      `(("unzip" ,unzip)))

gnu/packages/irc.scm

@@ -1,6 +1,8 @@
 ;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
 ;;; Copyright © 2014 Kevin Lemonnier <lemonnierk@ulrar.net>
 ;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -17,32 +19,117 @@
 ;;; You should have received a copy of the GNU General Public License
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
-;; TODO: Add ruby
+(define-module (gnu packages irc)
-
+  #:use-module ((guix licenses) #:prefix license:)
-(define-module (gnu packages weechat)
+  #:use-module (guix download)
+  #:use-module (guix packages)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
-  #:use-module (gnu packages ncurses)
-  #:use-module (gnu packages base)
-  #:use-module (gnu packages gettext)
-  #:use-module (gnu packages gnupg)
-  #:use-module (gnu packages file)
-  #:use-module (gnu packages compression)
-  #:use-module (gnu packages lua)
-  #:use-module (gnu packages python)
-  #:use-module (gnu packages perl)
-  #:use-module (gnu packages tcl)
   #:use-module (gnu packages aspell)
-  #:use-module (gnu packages curl)
-  #:use-module (gnu packages guile)
-  #:use-module (gnu packages cyrus-sasl)
   #:use-module (gnu packages autogen)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
+  #:use-module (gnu packages cyrus-sasl)
+  #:use-module (gnu packages file)
+  #:use-module (gnu packages gettext)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages guile)
+  #:use-module (gnu packages lua)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages kde)
+  #:use-module (gnu packages kde-frameworks)
+  #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages tls)
+  #:use-module (gnu packages python)
-  #:use-module (guix packages)
+  #:use-module (gnu packages qt)
-  #:use-module (guix download)
+  #:use-module (gnu packages tcl)
-  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages tls))
-  #:use-module ((guix licenses) #:select (gpl3)))
+
+(define-public quassel
+  (package
+    (name "quassel")
+    (version "0.12.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "http://quassel-irc.org/pub/quassel-"
+                            version ".tar.bz2"))
+        (sha256
+         (base32
+          "0d6lwf6qblj1ia5j9mjy112zrmpbbg9mmxgscbgxiqychldyjgjd"))))
+    (build-system cmake-build-system)
+    (arguments
+      ;; The three binaries are not mutually exlusive, and are all built
+      ;; by default.
+     `(#:configure-flags '(;;"-DWANT_QTCLIENT=OFF" ; 5.0 MiB
+                           ;;"-DWANT_CORE=OFF" ; 2.3 MiB
+                           ;;"-DWANT_MONO=OFF" ; 6.3 MiB
+                           "-DUSE_QT5=ON" ; default is qt4
+                           "-DWITH_KDE=OFF" ; no to integration
+                           "-DWITH_OXYGEN=ON" ; on=embed icons
+                           "-DWITH_WEBKIT=ON") ; wants qtwebkit, in qt5
+       #:tests? #f)) ; no test target
+    (native-inputs `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("oxygen-icons" ,oxygen-icons)
+       ("qca" ,qca)
+       ("qt", qt)
+       ("snorenotify" ,snorenotify)
+       ("zlib" ,zlib)))
+    (home-page "http://quassel-irc.org/")
+    (synopsis "Distributed IRC client")
+    (description "Quassel is a distributed IRC client, meaning that one or more
+clients can attach to and detach from the central core.  It resembles the
+popular combination of screen and a text-based IRC client such as WeeChat or
+irssi, but graphical.")
+    (license (list license:gpl2 license:gpl3)))) ;; dual licensed
+
+(define-public irssi
+  (package
+    (name "irssi")
+    (version "0.8.18")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/irssi/irssi/"
+                                 "releases/download/" version "/irssi-"
+                                 version ".tar.xz"))
+             (sha256
+              (base32
+               "0h3q0p5rnm6h0hcv06m8vrs97kyr1l7snjdy3qbjsz3m97vpg8f0"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (ncurses (assoc-ref inputs "ncurses")))
+               (setenv "CONFIG_SHELL" (which "bash"))
+               (zero?
+                (system* "./configure"
+                         (string-append "--prefix=" out)
+                         (string-append "--with-ncurses=" ncurses)
+                         (string-append "--with-proxy")
+                         (string-append "--with-socks")
+                         (string-append "--with-bot")))))))))
+    (inputs
+     `(("glib" ,glib)
+       ("ncurses" ,ncurses)
+       ("openssl" ,openssl)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("perl" ,perl)))
+    (home-page "http://www.irssi.org/")
+    (synopsis "Terminal-based IRC client")
+    (description
+     "Irssi is a terminal based IRC client for UNIX systems.  It also supports
+SILC and ICB protocols via plugins.")
+    (license license:gpl2+)))
 
 (define-public weechat
   (package
@@ -103,4 +190,4 @@ for Web, Qt, Android and Emacs.  In WeeChat everything can be done
 with a keyboard, though it also supports mouse.  It is customizable
 and extensible with plugins and scripts.")
     (home-page "http://www.weechat.org/")
-    (license gpl3)))
+    (license license:gpl3)))

gnu/packages/irssi.scm

@@ -1,70 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
-;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
-
-(define-module (gnu packages irssi)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix build-system gnu)
-  #:use-module (gnu packages)
-  #:use-module (gnu packages glib)
-  #:use-module (gnu packages ncurses)
-  #:use-module (gnu packages perl)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages tls))
-
-(define-public irssi
-  (package
-    (name "irssi")
-    (version "0.8.17")
-    (source (origin
-             (method url-fetch)
-             (uri (string-append "https://github.com/irssi-import/irssi/"
-                                 "releases/download/0.8.17/irssi-"
-                                 version ".tar.bz2"))
-             (sha256
-              (base32
-               "01v82q2pfiimx6lh271kdvgp8hl4pahc3srg04fqzxgdsb5015iw"))))
-    (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (alist-replace
-        'configure
-        (lambda* (#:key inputs outputs #:allow-other-keys)
-          (let ((out (assoc-ref outputs "out"))
-                (ncurses (assoc-ref inputs "ncurses")))
-            (setenv "CONFIG_SHELL" (which "bash"))
-            (zero?
-             (system* "./configure"
-                      (string-append "--prefix=" out)
-                      (string-append "--with-ncurses=" ncurses)))))
-        %standard-phases)))
-    (inputs
-     `(("glib" ,glib)
-       ("ncurses" ,ncurses)
-       ("openssl" ,openssl)))
-    (native-inputs
-     `(("pkg-config" ,pkg-config)
-       ("perl" ,perl)))
-    (home-page "http://www.irssi.org/")
-    (synopsis "Terminal-based IRC client")
-    (description
-     "Irssi is a terminal based IRC client for UNIX systems.  It also supports
-SILC and ICB protocols via plugins.")
-    (license license:gpl2+)))

gnu/packages/java.scm

@@ -139,9 +139,8 @@ is implemented.")
     (version "1.9.6")
     (source (origin
               (method url-fetch)
-              (uri (string-append
+              (uri (string-append "mirror://apache/ant/source/apache-ant-"
-                    "https://www.apache.org/dist/ant/source/apache-ant-"
+                                  version "-src.tar.gz"))
-                    version "-src.tar.gz"))
               (sha256
                (base32
                 "1396wflczyxjxl603dhxjvd559f289lha9y2f04f71c7hapjl3am"))))

gnu/packages/jrnl.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Eric Bavier <address@hidden>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,7 +28,7 @@
 (define-public jrnl
   (package
     (name "jrnl")
-    (version "1.8.4")
+    (version "1.9.7")
     (source
      (origin
       (method url-fetch)
@@ -36,11 +37,10 @@
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
        (base32
-        "019ky09sj5i7frmca0imv4jm46mn3f4lzah2wmiwxh22cisj7ksn"))))
+        "0mfq7hhw5np2dj9jlxpyyk2cg9i0xgz2brb894d928hczszy97bq"))))
     (build-system python-build-system)
     (native-inputs
-     `(("python-setuptools" ,python-setuptools)
+     `(("behave" ,behave)))
-       ("behave" ,behave)))
     (inputs
      `(("python" ,python)
        ("python-keyring" ,python-keyring)

gnu/packages/kde-frameworks.scm

@@ -91,3 +91,27 @@ lower level classes for interaction with the X Windowing System.")
     ;; Some source files mention lgpl2.0+, but the included license is
     ;; the lgpl2.1. Some source files are under non-copyleft licenses.
     (license license:lgpl2.1+)))
+
+(define-public oxygen-icons
+  (package
+    (name "oxygen-icons")
+    (version kde-frameworks-version)
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "http://download.kde.org/stable/frameworks/"
+                            (version-major+minor version) "/"
+                            name "5-"version ".tar.xz"))
+        (sha256
+         (base32
+          "09vfwcyidj3bl0qr4sq78bkc69zp9x8dwp8bsay5y05q8591dkg0"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("qt" ,qt)))
+    (home-page "https://community.kde.org/Frameworks")
+    (synopsis "Oxygen provides the standard icon theme for the KDE desktop.")
+    (description "Oxygen icon theme for the KDE desktop")
+    (license license:lgpl3+)))

gnu/packages/kde.scm

@@ -0,0 +1,79 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages kde)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (gnu packages kde-frameworks)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages tls)
+  #:use-module (gnu packages qt))
+
+(define-public qca
+  (package
+    (name "qca")
+    (version "2.1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "http://download.kde.org/stable/qca/" version
+                            "/src/qca-" version ".tar.xz"))
+        (sha256
+         (base32
+          "10z9icq28fww4qbzwra8d9z55ywbv74qk68nhiqfrydm21wkxplm"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("openssl" ,openssl)
+       ("qt" ,qt)))
+    (home-page "http://delta.affinix.com/qca/")
+    (synopsis "Libraries for the Qt Cryptographic Architecture")
+    (description "The Qt Cryptographic Architecture (QCA) provides a
+straightforward and cross-platform API for a range of cryptographic features,
+including SSL/TLS, X.509 certificates, SASL, OpenPGP, S/MIME CMS, and smart
+cards.")
+    (license license:lgpl2.1)))
+
+(define-public snorenotify
+  (package
+    (name "snorenotify")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "http://download.kde.org/stable/snorenotify/"
+                            version "/src/snorenotify-" version ".tar.xz"))
+        (sha256
+         (base32
+          "0jz6ivk90h7iwgyxar7xzzj8yvzn6s1my6cqs9bdnwqswfk1nhbd"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f)) ; both tests fail, require display
+    (inputs
+     `(("extra-cmake-modules" ,extra-cmake-modules)
+       ("qt" ,qt)))
+    (home-page "https://techbase.kde.org/Projects/Snorenotify")
+    (synopsis "Qt notification framework")
+    (description "Snorenotify is a multi platform Qt notification framework.
+Using a plugin system it is possible to create notifications with many
+different notification systems.")
+    (license license:lgpl3)))

gnu/packages/kodi.scm

@@ -21,6 +21,7 @@
   #:use-module (guix utils)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages audio)
@@ -68,18 +69,67 @@
   #:use-module (gnu packages yasm)
   #:use-module (gnu packages zip))
 
+(define-public crossguid
+  (let ((commit "8f399e8bd4252be9952f3dfa8199924cc8487ca4"))
+    (package
+      (name "crossguid")
+      (version (string-append "0.0-1." (string-take commit 7)))
+      ;; There's no official release.  Just a Git repository.
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/graeme-hill/crossguid.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1i29y207qqddvaxbn39pk2fbh3gx8zvdprfp35wasj9rw2wjk3s9"))))
+      (build-system gnu-build-system)
+      (arguments
+       '(#:phases
+         (modify-phases %standard-phases
+           (delete 'configure) ; no configure script
+           ;; There's no build system here, so we have to do it ourselves.
+           (replace 'build
+             (lambda _
+               (and (zero? (system* "g++" "-c" "guid.cpp" "-o" "guid.o"
+                                    "-std=c++11" "-DGUID_LIBUUID"))
+                    (zero? (system* "ar" "rvs" "libcrossguid.a" "guid.o")))))
+           (replace 'check
+             (lambda _
+               (and (zero? (system* "g++" "-c" "test.cpp" "-o" "test.o"
+                                    "-std=c++11"))
+                    (zero? (system* "g++" "-c" "testmain.cpp" "-o" "testmain.o"
+                                    "-std=c++11"))
+                    (zero? (system* "g++" "test.o" "guid.o" "testmain.o"
+                                    "-o" "test" "-luuid"))
+                    (zero? (system* (string-append (getcwd) "/test"))))))
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out")))
+                 (install-file "guid.h" (string-append out "/include"))
+                 (install-file "libcrossguid.a"
+                               (string-append out "/lib"))
+                 #t))))))
+      (inputs
+       `(("util-linux" ,util-linux)))
+      (synopsis "Lightweight universal identifier library")
+      (description "CrossGuid is a minimal GUID/UUID
+generator library for C++.")
+      (home-page "https://github.com/graeme-hill/crossguid")
+      (license license:expat))))
+
 (define-public kodi
   (package
     (name "kodi")
-    (version "15.2")
+    (version "16.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://mirrors.kodi.tv/releases/source/"
-                                  version "-Isengard.tar.gz"))
+                                  version "-Jarvis.tar.gz"))
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "043i0f1crx9glwxil4xm45z5kxpkrx316gi4ir4d3rbd5safp2nx"))
+                "0iirspvv7czf785l2lqf232dvdaj87srbn9ni97ngvnd6w9yl884"))
               (snippet
                ;; Delete bundled ffmpeg.
                ;; TODO: Delete every other bundled library.
@@ -161,7 +211,9 @@
        ("bluez" ,bluez)
        ("boost" ,boost)
        ("bzip2" ,bzip2)
+       ("crossguid" ,crossguid)
        ("curl" ,curl)
+       ("dcadec" ,dcadec)
        ("dbus" ,dbus)
        ("enca" ,enca)
        ("eudev" ,eudev)
@@ -213,6 +265,7 @@
        ("taglib" ,taglib)
        ("tinyxml" ,tinyxml)
        ("unzip" ,unzip)
+       ("util-linux" ,util-linux)
        ("zip" ,zip)
        ("zlib" ,zlib)))
     (synopsis "Media center for home theater computers")

gnu/packages/libevent.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;;
@@ -32,16 +32,15 @@
 (define-public libevent
   (package
     (name "libevent")
-    (version "2.0.21")
+    (version "2.0.22")
     (source (origin
              (method url-fetch)
              (uri (string-append
-                   "https://github.com/downloads/libevent/libevent/libevent-"
+                   "https://github.com/libevent/libevent/releases/download/release-"
-                   version
+                   version "-stable/libevent-" version "-stable.tar.gz"))
-                   "-stable.tar.gz"))
              (sha256
               (base32
-               "1xblymln9vihdmf1aqkp8chwvnhpdch3786bh30bj75slnl31992"))
+               "18qz9qfwrkakmazdlwxvjmw8p76g70n3faikwvdwznns1agw9hki"))
              (patches (list (search-patch "libevent-dns-tests.patch")))))
     (build-system gnu-build-system)
     (inputs

gnu/packages/libreoffice.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 John Darrington <jmd@gnu.org>
+;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,7 +22,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix download)
   #:use-module ((guix licenses)
-                #:select (gpl2+ lgpl2.1+ mpl1.1 mpl2.0
+                #:select (gpl2+ lgpl2.1+ lgpl3+ mpl1.1 mpl2.0
                           non-copyleft x11-style))
   #:use-module (guix packages)
   #:use-module (guix utils)
@@ -373,6 +374,33 @@ CorelDRAW documents of all versions.")
 Apple Keynote documents.  It currently supports Keynote versions 2 to 5.")
     (license mpl2.0)))
 
+(define-public liblangtag
+  (package
+    (name "liblangtag")
+    (version "0.5.8")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://bitbucket.org/tagoh/liblangtag/downloads/"
+                            name "-" version ".tar.bz2"))
+        (sha256
+         (base32
+          "1akf0d7yp29pv3j2pw2riii4n5kyjr9szc0y77khnx9zzr5zdqh8"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("libxml2" ,libxml2)))
+    (home-page "http://tagoh.bitbucket.org/liblangtag/")
+    (synopsis "Library to access tags for identifying languages")
+    (description "Liblangtag implements an interface to work with tags
+for identifying languages as described in RFC 5646.  It supports the
+extensions described in RFC6067 and RFC6497, and Extension T for
+language/locale identifiers as described in the Unicode CLDR
+standard 21.0.2.")
+    (license (list lgpl3+ mpl2.0)))) ; dual license
+
 (define-public libexttextcat
   (package
     (name "libexttextcat")
@@ -681,7 +709,7 @@ and to return information on pronunciations, meanings and synonyms.")
 (define-public libreoffice
   (package
     (name "libreoffice")
-    (version "5.0.3.2")
+    (version "5.0.5.2")
     (source
      (origin
       (method url-fetch)
@@ -690,7 +718,7 @@ and to return information on pronunciations, meanings and synonyms.")
           "http://download.documentfoundation.org/libreoffice/src/"
           (version-prefix version 3) "/libreoffice-" version ".tar.xz"))
       (sha256 (base32
-               "1gflcsnw7bx02jbb2x5darf56x0qgia03ylaycadk68ikibckybp"))))
+               "120vcxpxzs0za76fyfry281ysv6d1ianb37d1yq8py8chkdjkrqy"))))
     (build-system gnu-build-system)
     (native-inputs
      `(;; autoreconf is run by the LibreOffice build system, since after
@@ -762,8 +790,7 @@ and to return information on pronunciations, meanings and synonyms.")
        ("xmlsec-src" ,xmlsec-src-libreoffice)
        ("zip" ,zip)))
     (arguments
-     `(#:parallel-build? #f ; Otherwise the build fails.
+     `(#:tests? #f ; Building the tests already fails.
-       #:tests? #f ; Building the tests already fails.
        #:make-flags '("build-nocheck") ; Do not build unit tests, which fails.
        #:phases
          (modify-phases %standard-phases

gnu/packages/linux.scm

@@ -220,7 +220,7 @@ for SYSTEM and optionally VARIANT, or #f if there is no such configuration."
     (search-path %load-path file)))
 
 (define-public linux-libre
-  (let* ((version "4.4.3")
+  (let* ((version "4.5")
          (build-phase
           '(lambda* (#:key system inputs #:allow-other-keys #:rest args)
              ;; Apply the neat patch.
@@ -294,7 +294,7 @@ for SYSTEM and optionally VARIANT, or #f if there is no such configuration."
              (uri (linux-libre-urls version))
              (sha256
               (base32
-               "06wl6gvhds6j6aaryzpz4jngdf3v70spvp1xb7k2c03kvm9v5f4v"))))
+               "0km863vwy557flpygkr869yshpjs1v11ni78p8k9p9nm31ai6yn3"))))
     (build-system gnu-build-system)
     (supported-systems '("x86_64-linux" "i686-linux"))
     (native-inputs `(("perl" ,perl)
@@ -303,8 +303,10 @@ for SYSTEM and optionally VARIANT, or #f if there is no such configuration."
                      ("module-init-tools" ,module-init-tools)
                      ("patch/freedo+gnu" ,%boot-logo-patch)
 
-                     ,@(let ((conf (kernel-config (or (%current-target-system)
+                     ,@(let ((conf (kernel-config
-                                                      (%current-system)))))
+                                    (or (%current-target-system)
+                                        (%current-system))
+                                    #:variant (version-major+minor version))))
                          (if conf
                              `(("kconfig" ,conf))
                              '()))))
@@ -326,16 +328,33 @@ It has been modified to remove all non-free binary blobs.")
     (license license:gpl2)
     (home-page "http://www.gnu.org/software/linux-libre/"))))
 
-(define-public linux-libre-4.1
+(define-public linux-libre-4.4
   (package
     (inherit linux-libre)
-    (version "4.1.18")
+    (version "4.4.6")
     (source (origin
               (method url-fetch)
               (uri (linux-libre-urls version))
               (sha256
                (base32
-                "1bddh2rg645lavhjkk9z75vflba5y0g73z2fjwgbfrj5jb44x9i7"))))
+                "0sf623knc4j23p96r0w1ng725kj45ra50bwix01z5nvl5aqpnsrp"))))
+    (native-inputs
+     (let ((conf (kernel-config (or (%current-target-system)
+                                    (%current-system))
+                                #:variant "4.4")))
+       `(,@(alist-delete "kconfig" (package-native-inputs linux-libre))
+         ("kconfig" ,conf))))))
+
+(define-public linux-libre-4.1
+  (package
+    (inherit linux-libre)
+    (version "4.1.19")
+    (source (origin
+              (method url-fetch)
+              (uri (linux-libre-urls version))
+              (sha256
+               (base32
+                "0xkj94xmnmxr768qp6n68r1g68ix1sds95nv6zfg4x8fc7fzn8km"))))
     (native-inputs
      (let ((conf (kernel-config (or (%current-target-system)
                                     (%current-system))
@@ -2472,7 +2491,7 @@ and copy/paste text in the console and in xterm.")
 (define-public btrfs-progs
   (package
     (name "btrfs-progs")
-    (version "4.4")
+    (version "4.4.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://kernel.org/linux/kernel/"
@@ -2480,7 +2499,7 @@ and copy/paste text in the console and in xterm.")
                                   "btrfs-progs-v" version ".tar.xz"))
               (sha256
                (base32
-                "0jssv1ys4nw2jf7mkp58c19yspaa8ybf48fxsrhhp0683mzpr73p"))))
+                "1z5882zx9jx02vyg067siws0irsl8pg37myx17hr4imn9ypf6r4r"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"
@@ -2505,3 +2524,35 @@ easy administration.")
     ;; GPL2+: crc32.c, radix-tree.c, raid6.c, rbtree.c.
     ;; GPL2: Everything else.
     (license (list license:gpl2 license:gpl2+))))
+
+(define-public freefall
+  (package
+    (name "freefall")
+    (version (package-version linux-libre))
+    (source (package-source linux-libre))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'enter-subdirectory
+                    (lambda _
+                      (chdir "tools/laptop/freefall")))
+                  (delete 'configure)
+                  (add-before 'build 'increase-timeout
+                    (lambda _
+                      ;; The default of 2 seconds is too low: it assumes an
+                      ;; open lid and AC power without actually checking.
+                      (substitute* "freefall.c"
+                        (("alarm\\(2\\)") "alarm(5)")))))
+       #:make-flags (list (string-append "PREFIX="
+                                         (assoc-ref %outputs "out")))
+       #:tests? #f)) ;no tests
+    (home-page (package-home-page linux-libre))
+    (synopsis "Free-fall protection for spinning laptop hard drives")
+    (description
+     "Prevents shock damage to the internal spinning hard drive(s) of some
+HP and Dell laptops.  When sudden movement is detected, all input/output
+operations on the drive are suspended and its heads are parked on the ramp,
+where they are less likely to cause damage to the spinning disc.  Requires a
+drive that supports the ATA/ATAPI-7 IDLE IMMEDIATE command with unload
+feature, and a laptop with an accelerometer.  It has no effect on SSDs.")
+    (license license:gpl2)))

gnu/packages/mail.scm

@@ -11,6 +11,8 @@
 ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016 Al McElrath <hello@yrns.org>
+;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -69,8 +71,8 @@
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
   #:use-module ((guix licenses)
-                #:select (gpl2 gpl2+ gpl3+ lgpl2.1 lgpl2.1+ lgpl3+ non-copyleft
+                #:select (gpl2 gpl2+ gpl3 gpl3+ lgpl2.1 lgpl2.1+ lgpl3+
-                          (expat . license:expat)))
+                           non-copyleft (expat . license:expat)))
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -287,7 +289,7 @@ and corrections.  It is based on a Bayesian filter.")
 (define-public offlineimap
   (package
     (name "offlineimap")
-    (version "6.6.1")
+    (version "6.7.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/OfflineIMAP/offlineimap/"
@@ -295,7 +297,7 @@ and corrections.  It is based on a Bayesian filter.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1c2b03856a78ripkpl9jjzj6yzyfb3rlrdnjx300s647l1xx8gxg"))))
+                "0462mal2fxvavxhwjk1a6vsnspx07yniifa687dwg46aplqznin4"))))
     (build-system python-build-system)
     (native-inputs `(("python" ,python-2)))
     (arguments
@@ -629,7 +631,19 @@ which can add many functionalities to the base client.")
     (arguments
      `(#:configure-flags (list "--with-libgsasl"
                                "--with-libidn"
-                               "--with-tls=gnutls")))
+                               "--with-tls=gnutls")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-msmtpq
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (doc (string-append out "/share/doc/msmtp"))
+                    (msmtpq (string-append "scripts/msmtpq")))
+               (install-file (string-append msmtpq "/msmtpq") bin)
+               (install-file (string-append msmtpq "/msmtp-queue") bin)
+               (install-file (string-append msmtpq "/README.msmtpq") doc)
+               #t))))))
     (synopsis
      "Simple and easy to use SMTP client with decent sendmail compatibility")
     (description
@@ -641,7 +655,7 @@ delivery.")
 (define-public exim
   (package
     (name "exim")
-    (version "4.86")
+    (version "4.86.2")
     (source
      (origin
        (method url-fetch)
@@ -651,7 +665,7 @@ delivery.")
                                  version ".tar.bz2")))
        (sha256
         (base32
-         "0mn4bxih9slrmll5262ayhf41ji43pjf1rv0y6xpy6x55v7g5k7i"))))
+         "1cvfcc1hi60lydv8h3a2rxlfc0v2nflwpvzjj7h7cdsqs2pxwmkp"))))
     (build-system gnu-build-system)
     (inputs
      `(("bdb" ,bdb)
@@ -1085,4 +1099,97 @@ deliver it in various ways.")
      ;; with that information.
      (non-copyleft "https://github.com/nicm/fdm/blob/master/command.c"))))
 
-;;; mail.scm ends here
+
+(define-public procmail
+  (package
+    (name "procmail")
+    (version "3.22")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "ftp://ftp.fu-berlin.de/pub/unix/mail/procmail/procmail-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "05z1c803n5cppkcq99vkyd5myff904lf9sdgynfqngfk9nrpaz08"))
+       ;; The following patch fixes an ambiguous definition of
+       ;; getline() in formail.c.  The patch is provided by Debian as
+       ;; patch 24.
+       (patches
+        (list
+         (search-patch "procmail-ambiguous-getline-debian.patch")))))
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (replace 'configure
+                    (lambda _
+                      (substitute* "Makefile"
+                        (("/bin/sh")
+                         (which "sh"))
+                        (("/usr")
+                         (assoc-ref %outputs "out"))
+                        (("/bin/rm")
+                         (which "rm")))
+                      #t)))
+       #:tests? #f)) ;; There are no tests indicating a successful
+    ;; build.  Some tests of basic locking mechanisms provided by the
+    ;; filesystem are performed during 'make install'.  However, these
+    ;; are performed before the actual build process.
+    (build-system gnu-build-system)
+    (inputs `(("glibc" ,glibc)
+              ("exim" ,exim)))
+    (home-page "http://www.procmail.org/")
+    (synopsis "Versatile mail delivery agent (MDA)")
+    (description "Procmail is a mail delivery agent (MDA) featuring support
+for a variety of mailbox formats such as mbox, mh and maildir.  Incoming mail
+can be sorted into separate files/directories and arbitrary commands can be
+executed on mail arrival.  Procmail is considered stable, but is no longer
+maintained.")
+    (license gpl2+))) ;; procmail allows to choose the
+                      ;; nonfree Artistic License 1.0
+                      ;; as alternative to the GPL2+.
+                      ;; This option is not listed here.
+
+(define-public khard
+  (package
+    (name "khard")
+    (version "0.8.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri name version))
+              (sha256
+               (base32
+                "098gs94qmnspdfn6ar8lycx7dbsz9bcff90aps0cmn47mw7llch0"))))
+    (build-system python-build-system)
+    (arguments
+      `(#:python ,python-2 ; only python-2 is supported.
+        #:phases
+        (modify-phases %standard-phases
+          (add-before 'build 'disable-egg-compression
+            ;; Do not compress the egg.
+            (lambda _
+              (let ((port (open-file "setup.cfg" "a")))
+                (display "\n[easy_install]\nzip_ok = 0\n"
+                         port)
+                (close-port port)
+                #t)))
+          (add-after 'install 'install-doc
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (doc (string-append out "/share/doc/khard")))
+                (copy-recursively "misc/khard" doc)))))))
+    (native-inputs
+     `(("python2-setuptools" ,python2-setuptools)))
+    (propagated-inputs
+     `(("python2-vobject" ,python2-vobject)
+       ("python2-pyyaml" ,python2-pyyaml)
+       ("python2-atomicwrites" ,python2-atomicwrites)
+       ("python2-configobj" ,python2-configobj)))
+    (synopsis "Console address book using CardDAV")
+    (description "Khard is an address book for the console.  It creates, reads,
+modifies and removes CardDAV address book entries at your local machine.  For
+synchronizing with a remote address book, @command{vdirsyncer} is recommended.
+Khard can also be used from within the email client @command{mutt}.")
+    (home-page "https://github.com/scheibler/khard")
+    (license gpl3+)))

gnu/packages/maths.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2014 John Darrington <jmd@gnu.org>
-;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
@@ -177,7 +177,7 @@ numbers.")
 (define-public glpk
   (package
     (name "glpk")
-    (version "4.58")
+    (version "4.59")
     (source
      (origin
       (method url-fetch)
@@ -185,7 +185,7 @@ numbers.")
                           version ".tar.gz"))
       (sha256
        (base32
-        "1jmrya04hgwnrxrqqs40i6m9cqka3q601cx3nh9ijyvlg90zlq24"))))
+        "1bpbp5z0378kaj5bqmc5m2j5h9c7553p0s2j6a28badqghpbx673"))))
     (build-system gnu-build-system)
     (inputs
      `(("gmp" ,gmp)))
@@ -354,9 +354,7 @@ singular value problems.")
               ("pango" ,pango)
               ("gd" ,gd)))
     (native-inputs `(("pkg-config" ,pkg-config)
-                     ;; Need 'tex', 'latex', 'pdflatex', 'kpsexand', and
+                     ("texlive" ,texlive-minimal)))
-                     ;; 'texhash' binaries.
-                     ("texlive" ,texlive-bin)))
     (home-page "http://www.gnuplot.info")
     (synopsis "Command-line driven graphing utility")
     (description "Gnuplot is a portable command-line driven graphing
@@ -567,16 +565,15 @@ ASCII text files using Gmsh's own scripting language.")
           'install 'clean-install
           ;; Try to keep installed files from leaking build directory names.
           (lambda* (#:key inputs outputs #:allow-other-keys)
-            (let ((out     (assoc-ref outputs "out"))
+            (let ((out     (assoc-ref outputs "out")))
-                  (fortran (assoc-ref inputs  "gfortran")))
               (substitute* (map (lambda (file)
                                   (string-append out "/lib/petsc/conf/" file))
                                 '("petscvariables" "PETScConfig.cmake"))
                 (((getcwd)) out))
               ;; Make compiler references point to the store
               (substitute* (string-append out "/lib/petsc/conf/petscvariables")
-                (("= g(cc|\\+\\+|fortran)" _ suffix)
+                (("= (gcc|g\\+\\+|gfortran)" _ compiler)
-                 (string-append "= " fortran "/bin/g" suffix)))
+                 (string-append "= " (which compiler))))
               ;; PETSc installs some build logs, which aren't necessary.
               (for-each (lambda (file)
                           (let ((f (string-append out "/lib/petsc/conf/" file)))
@@ -643,6 +640,7 @@ scientific applications modeled by partial differential equations.")
        (method url-fetch)
        (uri (string-append "http://slepc.upv.es/download/download.php?"
                            "filename=slepc-" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
          "1pv5iqz2kc8sj49zsabyz4arnfpana8mjrhq31vzgk16xldk3d1a"))))

gnu/packages/messaging.scm

@@ -63,17 +63,21 @@
 (define-public libotr
   (package
     (name "libotr")
-    (version "4.1.0")
+    (version "4.1.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://otr.cypherpunks.ca/libotr-"
                                   version ".tar.gz"))
               (sha256
-               (base32 "0c6rkh58s6wqzcrpccwdik5qs91qj6dgd60a340d72gc80cqknsg"))))
+               (base32
+                "1x8rliydhbibmzwdbyr7pd7n87m2jmxnqkpvaalnf4154hj1hfwb"))
+              (patches
+               (list (search-patch "libotr-test-auth-fix.patch")))))
     (build-system gnu-build-system)
     (propagated-inputs
      `(("libgcrypt" ,libgcrypt)))  ; libotr headers include gcrypt.h
     (inputs `(("libgpg-error" ,libgpg-error)))
+    (native-inputs `(("perl" ,perl))) ; for the test suite
     (synopsis "Off-the-Record (OTR) Messaging Library and Toolkit")
     (description
      "OTR allows you to have private conversations over instant messaging by
@@ -88,27 +92,16 @@ keys, no previous conversation is compromised.")
     (home-page "https://otr.cypherpunks.ca/")
     (license (list lgpl2.1 gpl2))))
 
-(define-public libotr-3
-  (package (inherit libotr)
-    (version "3.2.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://otr.cypherpunks.ca/libotr-"
-                                  version ".tar.gz"))
-              (sha256
-               (base32 "1x6dd4rh499hdraiqfhz81igrj0a5rs0gjhc8l4sljwqhjjyla6l"))))))
-
 (define-public bitlbee
   (package
     (name "bitlbee")
-    (version "3.4")
+    (version "3.4.1")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://get.bitlbee.org/src/bitlbee-"
+              (uri (string-append "https://get.bitlbee.org/src/bitlbee-"
                                   version ".tar.gz"))
               (sha256
-               (base32 "0plx4dryf8i6hz7vghg84z5f6w6rkw1l8ckl4c4wh5zxpd3ddfnf"))
+               (base32 "1qf0ypa9ba5jvsnpg9slmaran16hcc5fnfzbb1sdch1hjhchn2jh"))))
-              (patches (list (search-patch "bitlbee-configure-doc-fix.patch")))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)
                      ("check" ,check)))
@@ -327,14 +320,14 @@ chat protocols.")
 (define-public pidgin-otr
   (package
     (name "pidgin-otr")
-    (version "4.0.1")
+    (version "4.0.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://otr.cypherpunks.ca/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "02pkkf86fh5jvzsdn9y78impsgzj1n0p81kc2girvk3vq941yy0v"))))
+                "1i5s9rrgbyss9rszq6c6y53hwqyw1k86s40cpsfx5ccl9bprxdgl"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)

gnu/packages/mpd.scm

@@ -28,6 +28,7 @@
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (gnu packages avahi)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages icu4c)
@@ -40,6 +41,7 @@
   #:use-module (gnu packages mp3)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages databases)
@@ -240,3 +242,34 @@ information about tracks being played to a scrobbler, such as Libre.FM.")
     ;; instead.
     (home-page "http://mpd.wikia.com/wiki/Client:Mpdscribble")
     (license license:gpl2+)))
+
+(define-public python-mpd2
+  (package
+    (name "python-mpd2")
+    (version "0.5.5")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "python-mpd2" version))
+              (sha256
+               (base32
+                "0laypd7h1j14b4vrmiayqlzdsh2j5hc3zv4l0fqvbrbw9y6763ii"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _ (zero? (system* "python" "mpd_test.py")))))))
+    (native-inputs `(("python-mock" ,python-mock)))
+    (home-page "https://github.com/Mic92/python-mpd2")
+    (synopsis "Python MPD client library")
+    (description "Python-mpd2 is a Python library which provides a client
+interface for the Music Player Daemon.")
+    (license license:lgpl3+)
+    (properties `((python2-variant . ,(delay python2-mpd2))))))
+
+(define-public python2-mpd2
+  (let ((mpd2 (package-with-python2
+               (strip-python2-variant python-mpd2))))
+    (package (inherit mpd2)
+      (native-inputs `(("python2-setuptools" ,python2-setuptools)
+                       ,@(package-native-inputs mpd2))))))

gnu/packages/music.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2016 Al McElrath <hello@yrns.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -49,6 +50,7 @@
   #:use-module (gnu packages fltk)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages gettext)
@@ -64,6 +66,7 @@
   #:use-module (gnu packages linux) ; for alsa-utils
   #:use-module (gnu packages man)
   #:use-module (gnu packages mp3)
+  #:use-module (gnu packages mpd)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages netpbm)
   #:use-module (gnu packages pdf)
@@ -817,7 +820,7 @@ projects.")
 (define-public frescobaldi
   (package
     (name "frescobaldi")
-    (version "2.18.1")
+    (version "2.18.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -825,7 +828,7 @@ projects.")
                     version "/frescobaldi-" version ".tar.gz"))
               (sha256
                (base32
-                "1hflc6gck6dn17czc2ldai5j0ynfg3df8lqcggdry06qxsdbnns7"))))
+                "1yns7nq2a2hz5rv4xjp21bgcdi1xj6fq48lqjrld7ypqqi5nfjp5"))))
     (build-system python-build-system)
     (inputs
      `(("lilypond" ,lilypond)
@@ -1134,3 +1137,167 @@ personalized online radio pandora.com.  It has configurable keys for playing
 and managing stations, can be controlled remotely via fifo, and can run
 event-based scripts for scrobbling, notifications, etc.")
     (license license:expat)))
+
+(define-public python-mutagen
+  (package
+    (name "python-mutagen")
+    (version "1.31")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "mutagen" version))
+              (sha256
+               (base32
+                "16fnnhspniac2i7qswxafawsh2x2a803hmc6bn9k1zl5fxq1380a"))))
+    (build-system python-build-system)
+    (home-page "https://bitbucket.org/lazka/mutagen")
+    (synopsis "Read and write audio tags")
+    (description "Mutagen is a Python module to handle audio metadata.  It
+supports ASF, FLAC, M4A, Monkey’s Audio, MP3, Musepack, Ogg FLAC, Ogg Speex, Ogg
+Theora, Ogg Vorbis, True Audio, WavPack and OptimFROG audio files.  All versions
+of ID3v2 are supported, and all standard ID3v2.4 frames are parsed.  It can read
+Xing headers to accurately calculate the bitrate and length of MP3s.  ID3 and
+APEv2 tags can be edited regardless of audio format.  It can also manipulate Ogg
+streams on an individual packet/page level.")
+    (license license:gpl2))) ; "later version" never mentioned
+
+(define-public python2-mutagen
+  (package-with-python2 python-mutagen))
+
+(define-public python-musicbrainzngs
+  (package
+    (name "python-musicbrainzngs")
+    (version "0.5")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "musicbrainzngs" version))
+              (sha256
+               (base32
+                "12f48llmdf5rkiqxcb70k2k1dmhm8byq0ifazvlrca8dfnmqh4r8"))))
+    (build-system python-build-system)
+    (home-page "https://python-musicbrainzngs.readthedocs.org/")
+    (synopsis "Python bindings for MusicBrainz NGS webservice")
+    (description "Musicbrainzngs implements Python bindings of the MusicBrainz
+web service.  This library can be used to retrieve music metadata from the
+MusicBrainz database.")
+    ;; 'musicbrainzngs/compat.py' is ISC licensed.
+    (license (list license:bsd-2 license:isc))))
+
+(define-public python2-musicbrainzngs
+  (package-with-python2 python-musicbrainzngs))
+
+(define-public python-pyechonest
+  (package
+    (name "python-pyechonest")
+    (version "9.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pyechonest" version))
+              (sha256
+               (base32
+                "1584nira3rkiman9dm81kdshihmkj21s8navndz2l8spnjwb790x"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/echonest/pyechonest")
+    (synopsis "Python interface to The Echo Nest APIs")
+    (description "Pyechonest is an open source Python library for the Echo Nest
+API.  With Pyechonest you have Python access to the entire set of API methods
+including:
+
+@enumerate
+@item artist - search for artists by name, description, or attribute, and get
+back detailed information about any artist including audio, similar artists,
+blogs, familiarity, hotttnesss, news, reviews, urls and video.
+@item song - search songs by artist, title, description, or attribute (tempo,
+duration, etc) and get detailed information back about each song, such as
+hotttnesss, audio_summary, or tracks.
+@item track - upload a track to the Echo Nest and receive summary information
+about the track including key, duration, mode, tempo, time signature along with
+detailed track info including timbre, pitch, rhythm and loudness information.
+@end enumerate\n")
+    (license license:bsd-3)
+    (properties `((python2-variant . ,(delay python2-pyechonest))))))
+
+(define-public python2-pyechonest
+  (package (inherit (package-with-python2
+                     (strip-python2-variant python-pyechonest)))
+    (native-inputs `(("python2-setuptools" ,python2-setuptools)))))
+
+(define-public python-pylast
+  (package
+    (name "python-pylast")
+    (version "1.5.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pylast" version))
+              (sha256
+               (base32
+                "10znd9xr1vs2ix519jkz3ccm90zciaddcdr2w2wrrh2jyy3bc59a"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-coverage" ,python-coverage)
+       ("python-mock" ,python-mock)
+       ("python-pep8" ,python-pep8)
+       ("python-pytest" ,python-pytest)
+       ("python-pyflakes" ,python-pyflakes)
+       ("python-pyyaml" ,python-pyyaml)))
+    (propagated-inputs
+     `(("python-six" ,python-six)))
+    (home-page "https://github.com/pylast/pylast")
+    (synopsis "Python interface to Last.fm and Libre.fm")
+    (description "A Python interface to Last.fm and other API-compatible
+websites such as Libre.fm.")
+    (license license:asl2.0)
+    (properties `((python2-variant . ,(delay python2-pylast))))))
+
+(define-public python2-pylast
+  (let ((pylast (package-with-python2
+                 (strip-python2-variant python-pylast))))
+    (package (inherit pylast)
+      (native-inputs
+       `(("python2-setuptools" ,python2-setuptools)
+         ,@(package-native-inputs pylast))))))
+
+(define-public beets
+  (package
+    (name "beets")
+    (version "1.3.17")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri name version))
+              (sha256
+               (base32
+                "0yg7sp18sdpszkinhb0bi6yinbn316jy1baxrwiw0m4byrj3rr6c"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2 ; only Python 2 is supported
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-HOME
+           (lambda _ (setenv "HOME" (string-append (getcwd) "/tmp")))))))
+    (native-inputs
+     `(("python2-beautifulsoup4" ,python2-beautifulsoup4)
+       ("python2-flask" ,python2-flask)
+       ("python2-setuptools" ,python2-setuptools)
+       ("python2-mock" ,python2-mock)
+       ("python2-mpd2" ,python2-mpd2)
+       ("python2-pathlib" ,python2-pathlib)
+       ("python2-pyxdg" ,python2-pyxdg)
+       ("python2-pyechonest" ,python2-pyechonest)
+       ("python2-pylast" ,python2-pylast)
+       ("python2-rarfile" ,python2-rarfile)
+       ("python2-responses" ,python2-responses)))
+    ;; TODO: Install optional plugins and dependencies.
+    (propagated-inputs
+     `(("python2-enum34" ,python2-enum34)
+       ("python2-jellyfish" ,python2-jellyfish)
+       ("python2-munkres" ,python2-munkres)
+       ("python2-musicbrainzngs" ,python2-musicbrainzngs)
+       ("python2-mutagen" ,python2-mutagen)
+       ("python2-pyyaml" ,python2-pyyaml)
+       ("python2-unidecode" ,python2-unidecode)))
+    (home-page "http://beets.io")
+    (synopsis "Music organizer")
+    (description "The purpose of beets is to get your music collection right
+once and for all.  It catalogs your collection, automatically improving its
+metadata as it goes using the MusicBrainz database.  Then it provides a variety
+of tools for manipulating and accessing your music.")
+    (license license:expat)))

gnu/packages/nano.scm

@@ -28,7 +28,7 @@
 (define-public nano
   (package
     (name "nano")
-    (version "2.5.2")
+    (version "2.5.3")
     (source
      (origin
       (method url-fetch)
@@ -36,7 +36,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "0hgbmqzjy1pashb1g3qby75pqb7r5g9bmn1iajlx50082b2nmgc9"))))
+        "1vhjrcydcfxqq1719vcsvqqnbjbq2523m00dhzag5vwzkc961c5j"))))
     (build-system gnu-build-system)
     (inputs
      `(("gettext" ,gnu-gettext)

gnu/packages/networking.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Stefan Reichör <stefan@xsteve.at>
+;;; Copyright © 2016 Raimon Grau <raimonster@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -187,3 +188,25 @@ needed/wanted real-time traffic statistics of multiple network
 interfaces, with a simple and efficient view on the command line.  It is
 intended as a substitute for the PPPStatus and EthStatus projects.")
     (license license:gpl2+)))
+
+(define-public nload
+  (package
+    (name "nload")
+    (version "0.7.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/nload/nload-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1rb9skch2kgqzigf19x8bzk211jdfjfdkrcvaqyj89jy2pkm3h61"))))
+    (build-system gnu-build-system)
+    (inputs `(("ncurses" ,ncurses)))
+    (home-page "http://www.roland-riegel.de/nload/")
+    (synopsis "Realtime console network usage monitor")
+    (description
+     "Nload is a console application which monitors network traffic and
+bandwidth usage in real time.  It visualizes the in- and outgoing traffic using
+two graphs and provides additional info like total amount of transfered data
+and min/max network usage.")
+    (license license:gpl2+)))

gnu/packages/package-management.scm

@@ -195,7 +195,7 @@ the Nix package manager.")
   ;;
   ;; Note: use a short commit id; when using the long one, the limit on socket
   ;; file names is exceeded while running the tests.
-  (let ((commit "c3f29bc928d5900971f65965feaae59e1272a3f7"))
+  (let ((commit "71e2065a38cf2641b7eb8c557b0f043f5a42a649"))
     (package (inherit guix-0.9.0)
       (version (string-append "0.9.0." (string-take commit 7)))
       (source (origin
@@ -205,7 +205,7 @@ the Nix package manager.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "1mbikn6awgx3h08bzk3nz8xrqvxdjsbvzrbn26d6m8nrz96ya53a"))
+                  "0wrrywfdc27yxjns55qdz5si49c8zcb9q5557g2kx48dbm7p0dzw"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (arguments
        (substitute-keyword-arguments (package-arguments guix-0.9.0)

gnu/packages/parallel.scm

@@ -42,7 +42,7 @@
 (define-public parallel
   (package
     (name "parallel")
-    (version "20160122")
+    (version "20160222")
     (source
      (origin
       (method url-fetch)
@@ -50,7 +50,7 @@
                           version ".tar.bz2"))
       (sha256
        (base32
-        "1xs8y8jh7wyjs27079xz0ja7xfi4dywz8d6hbkl44mafdnnfjfiy"))))
+        "1sjmvinwr9j2a0jdk9y9nf2x4hhzcbl529slkwpz0vva0cwybywd"))))
     (build-system gnu-build-system)
     (inputs `(("perl" ,perl)))
     (home-page "http://www.gnu.org/software/parallel/")

gnu/packages/password-utils.scm

@@ -3,6 +3,8 @@
 ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Aljosha Papsch <misc@rpapsch.de>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
+;;; Copyright © 2016 Jessica Tallon <tsyesika@tsyesika.se>
+;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,16 +27,20 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix download)
   #:use-module (guix packages)
+  #:use-module (gnu packages admin)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages man)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages qt)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xorg)
   #:use-module (guix build-system python))
@@ -241,3 +247,51 @@ JSON files.  It has a command line interface as well as a very simple
 graphical interface, which can even \"type\" your passwords into
 any X11 window.")
     (license license:gpl3+)))
+
+(define-public password-store
+  (package
+    (name "password-store")
+    (version "1.6.5")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append "https://git.zx2c4.com/password-store/snapshot/"
+                              name "-" version ".tar.xz"))
+              (sha256
+               (base32
+                "05bk3lrp5jwg0v338lvylp7glpliydzz4jf5pjr6k3kagrv3jyik"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-after
+          ;; The script requires 'getopt' at run-time, and this allows
+          ;; the user to not install the providing package 'util-linux'
+          ;; in their profile.
+          'unpack 'patch-path
+          (lambda* (#:key inputs outputs #:allow-other-keys)
+            (let ((getopt (string-append (assoc-ref inputs "getopt")
+                                         "/bin/getopt")))
+              (substitute* "src/password-store.sh"
+                (("GETOPT=\"getopt\"")
+                 (string-append "GETOPT=\"" getopt "\"")))
+              #t))))
+       #:make-flags (list "CC=gcc" (string-append "PREFIX=" %output))
+       #:test-target "test"))
+    (native-inputs `(("getopt" ,util-linux))) ; getopt for the tests
+    (inputs `(("gnupg" ,gnupg)
+              ("pwgen" ,pwgen)
+              ("xclip" ,xclip)
+              ("git" ,git)
+              ("tree" ,tree)
+              ("which" ,which)))
+    (home-page "http://www.passwordstore.org/")
+    (synopsis "Encrypted password manager")
+    (description "Password-store is a password manager which uses GnuPG to
+store and retrieve passwords.  The tool stores each password in its own
+GnuPG-encrypted file, allowing the program to be simple yet secure.
+Synchronization is possible using the integrated git support, which commits
+changes to your password database to a git repository that can be managed
+through the pass command.")
+    (license license:gpl2+)))

gnu/packages/patches/bitlbee-configure-doc-fix.patch

@@ -1,15 +0,0 @@
-Fix the check for the prebuilt helpfile when xsltproc is not available.
-
---- bitlbee-3.4/configure.orig	2015-03-25 18:09:10.000000000 -0400
-+++ bitlbee-3.4/configure	2015-05-20 14:51:33.627975970 -0400
-@@ -650,8 +650,8 @@
- 
- if [ "$doc" = "1" ]; then
- 	if [ ! -e doc/user-guide/help.txt ] && \
--	     ! type xmlto > /dev/null 2> /dev/null || \
--	     ! type xsltproc > /dev/null 2> /dev/null
-+	     (! type xmlto > /dev/null 2> /dev/null || \
-+	      ! type xsltproc > /dev/null 2> /dev/null)
- 	then
- 		echo
- 		echo 'WARNING: Building from an unreleased source tree without prebuilt helpfile.'

gnu/packages/patches/einstein-build.patch

@@ -0,0 +1,401 @@
+These patches are required to build with a modern GCC; most of them
+are taken from the Debian package. Upstream has disappeared.
+
+diff -r -u einstein-2.0.orig/convert.h einstein-2.0/convert.h
+--- einstein-2.0.orig/convert.h	2005-08-14 04:40:58.000000000 +0200
++++ einstein-2.0/convert.h	2016-03-05 18:25:08.488917021 +0100
+@@ -5,6 +5,7 @@
+ #include <iostream>
+ #include <sstream>
+ #include <string>
++#include <typeinfo>
+ 
+ #include "exceptions.h"
+ #include "unicode.h"
+diff -r -u einstein-2.0.orig/descr.cpp einstein-2.0/descr.cpp
+--- einstein-2.0.orig/descr.cpp	2005-08-17 15:42:29.000000000 +0200
++++ einstein-2.0/descr.cpp	2016-03-05 18:29:27.960352230 +0100
+@@ -139,9 +139,9 @@
+ {
+     currentPage = 0;
+     //area.add(parentArea, false);
+-    titleFont = new Font(L"nova.ttf", 26);
+-    buttonFont = new Font(L"laudcn2.ttf", 14);
+-    textFont = new Font(L"laudcn2.ttf", 16);
++    titleFont = new Font(L"DejaVuSans.ttf", 26);
++    buttonFont = new Font(L"DejaVuSans.ttf", 14);
++    textFont = new Font(L"DejaVuSans.ttf", 16);
+     textHeight = (int)(textFont->getHeight(L"A") * 1.0);
+     text = new TextParser(msg(L"rulesText"), *textFont, START_X, START_Y, 
+                 CLIENT_WIDTH, CLIENT_HEIGHT);
+diff -r -u einstein-2.0.orig/font.h einstein-2.0/font.h
+--- einstein-2.0.orig/font.h	2005-08-16 00:33:17.000000000 +0200
++++ einstein-2.0/font.h	2016-03-05 18:22:05.563794039 +0100
+@@ -3,7 +3,7 @@
+ 
+ 
+ #include <string>
+-#include <SDL_ttf.h>
++#include <SDL/SDL_ttf.h>
+ 
+ 
+ class Font
+diff -r -u einstein-2.0.orig/formatter.cpp einstein-2.0/formatter.cpp
+--- einstein-2.0.orig/formatter.cpp	2005-08-14 04:40:58.000000000 +0200
++++ einstein-2.0/formatter.cpp	2016-03-05 18:18:41.146882565 +0100
+@@ -58,7 +58,7 @@
+             if ((c.type == INT_ARG) || (c.type == STRING_ARG) ||
+                     (c.type == FLOAT_ARG) || (c.type == DOUBLE_ARG))
+             {
+-                int no = (int)c.data;
++                long no = (long)c.data;
+                 args[no - 1] = c.type;
+             }
+         }
+@@ -123,7 +123,7 @@
+ std::wstring Formatter::format(std::vector<ArgValue*> &argValues) const
+ {
+     std::wstring s;
+-    int no;
++    long no;
+ 
+     for (int i = 0; i < commandsCnt; i++) {
+         Command *cmd = &commands[i];
+@@ -135,8 +135,8 @@
+                 
+             case STRING_ARG:
+             case INT_ARG:
+-                no = (int)cmd->data - 1;
+-                if (no < (int)argValues.size())
++                no = (long)cmd->data - 1;
++                if (no < (long)argValues.size())
+                     s += argValues[no]->format(cmd);
+                 break;
+ 
+diff -r -u einstein-2.0.orig/game.cpp einstein-2.0/game.cpp
+--- einstein-2.0.orig/game.cpp	2005-08-23 00:44:54.000000000 +0200
++++ einstein-2.0/game.cpp	2016-03-05 18:29:27.960352230 +0100
+@@ -33,7 +33,7 @@
+     screen.draw(8, 10, tile);
+     SDL_FreeSurface(tile);
+     
+-    Font titleFont(L"nova.ttf", 28);
++    Font titleFont(L"DejaVuSans.ttf", 28);
+     titleFont.draw(screen.getSurface(), 20, 20, 255,255,0, true, 
+             msg(L"einsteinPuzzle"));
+     
+@@ -89,7 +89,7 @@
+ {
+     lastRun = elapsed = lastUpdate = 0;
+     stop();
+-    font = new Font(L"luximb.ttf", 16);
++    font = new Font(L"DejaVuSans.ttf", 16);
+ }
+ 
+ Watch::Watch(std::istream &stream)
+@@ -97,7 +97,7 @@
+     elapsed = readInt(stream);
+     lastUpdate = 0;
+     stop();
+-    font = new Font(L"luximb.ttf", 16);
++    font = new Font(L"DejaVuSans.ttf", 16);
+ }
+ 
+ Watch::~Watch()
+@@ -178,7 +178,7 @@
+             watch->stop();
+             Area area;
+             area.add(background, false);
+-            Font font(L"laudcn2.ttf", 16);
++            Font font(L"DejaVuSans.ttf", 16);
+             area.add(new Window(280, 275, 240, 50, L"greenpattern.bmp", 6));
+             area.add(new Label(&font, 280, 275, 240, 50, Label::ALIGN_CENTER,
+                 Label::ALIGN_MIDDLE, 255,255,0, msg(L"paused")));
+@@ -209,7 +209,7 @@
+         virtual void doAction() {
+             sound->play(L"applause.wav");
+             watch->stop();
+-            Font font(L"laudcn2.ttf", 20);
++            Font font(L"DejaVuSans.ttf", 20);
+             showMessageWindow(gameArea, L"marble1.bmp", 
+                     500, 70, &font, 255,0,0, msg(L"won"));
+             gameArea->draw();
+@@ -257,8 +257,8 @@
+             sound->play(L"glasbk2.wav");
+             bool restart = false;
+             bool newGame = false;
+-            Font font(L"laudcn2.ttf", 24);
+-            Font btnFont(L"laudcn2.ttf", 14);
++            Font font(L"DejaVuSans.ttf", 24);
++            Font btnFont(L"DejaVuSans.ttf", 14);
+             Area area;
+             area.add(gameArea);
+             area.add(new Window(220, 240, 360, 140, L"redpattern.bmp", 6));
+@@ -329,7 +329,7 @@
+         CheatCommand(Area *a) { gameArea = a; };
+         
+         virtual void doAction() {
+-            Font font(L"nova.ttf", 30);
++            Font font(L"DejaVuSans.ttf", 30);
+             showMessageWindow(gameArea, L"darkpattern.bmp", 
+                     500, 100, &font, 255,255,255, 
+                     msg(L"iddqd"));
+@@ -475,7 +475,7 @@
+     drawWallpaper(L"rain.bmp");
+     Window window(230, 260, 340, 80, L"greenpattern.bmp", 6);
+     window.draw();
+-    Font font(L"laudcn2.ttf", 16);
++    Font font(L"DejaVuSans.ttf", 16);
+     Label label(&font, 280, 275, 240, 50, Label::ALIGN_CENTER,
+                 Label::ALIGN_MIDDLE, 255,255,0, msg(L"loading"));
+     label.draw();
+@@ -533,7 +533,7 @@
+ void Game::run()
+ {
+     Area area;
+-    Font btnFont(L"laudcn2.ttf", 14);
++    Font btnFont(L"DejaVuSans.ttf", 14);
+     
+     area.setTimer(300, watch);
+ 
+diff -r -u einstein-2.0.orig/main.cpp einstein-2.0/main.cpp
+--- einstein-2.0.orig/main.cpp	2005-09-26 12:32:54.000000000 +0200
++++ einstein-2.0/main.cpp	2016-03-05 18:29:27.960352230 +0100
+@@ -2,7 +2,7 @@
+ #include <iostream>
+ #include <SDL.h>
+ #include <SDL_main.h>
+-#include <SDL_ttf.h>
++#include <SDL/SDL_ttf.h>
+ #include "main.h"
+ #include "utils.h"
+ #include "storage.h"
+@@ -78,7 +78,7 @@
+ /*static void checkBetaExpire()
+ {
+     if (1124832535L + 60L*60L*24L*40L < time(NULL)) {
+-        Font font(L"laudcn2.ttf", 16);
++        Font font(L"DejaVuSans.ttf", 16);
+         Area area;
+         showMessageWindow(&area, L"darkpattern.bmp", 
+                 700, 100, &font, 255,255,255, 
+diff -r -u einstein-2.0.orig/Makefile einstein-2.0/Makefile
+--- einstein-2.0.orig/Makefile	2005-09-25 23:20:30.000000000 +0200
++++ einstein-2.0/Makefile	2016-03-05 18:14:22.365450608 +0100
+@@ -49,10 +49,14 @@
+ 
+ 
+ $(TARGET): $(OBJECTS)
++	cd mkres && make
++	cd res && ../mkres/mkres --source resources.descr --output ../einstein.res
+ 	$(CXX) $(LNFLAGS) $(OBJECTS) -o $(TARGET)
+ 
+ clean:
+ 	rm -f $(OBJECTS) core* *core $(TARGET) *~
++	cd res && rm -f einstein.res
++	cd mkres && make clean
+ 
+ depend:
+ 	@makedepend $(SOURCES) 2> /dev/null
+diff -r -u einstein-2.0.orig/menu.cpp einstein-2.0/menu.cpp
+--- einstein-2.0.orig/menu.cpp	2005-09-25 22:51:00.000000000 +0200
++++ einstein-2.0/menu.cpp	2016-03-05 18:29:27.960352230 +0100
+@@ -23,11 +23,11 @@
+     SDL_Surface *title = loadImage(L"nova.bmp");
+     screen.draw(0, 0, title);
+     SDL_FreeSurface(title);
+-    Font font(L"nova.ttf", 28);
++    Font font(L"DejaVuSans.ttf", 28);
+     std::wstring s(msg(L"einsteinFlowix"));
+     int width = font.getWidth(s);
+     font.draw((screen.getWidth() - width) / 2, 30, 255,255,255, true, s);
+-    Font urlFont(L"luximb.ttf", 16);
++    Font urlFont(L"DejaVuSans.ttf", 16);
+     s = L"http://games.flowix.com";
+     width = urlFont.getWidth(s);
+     urlFont.draw((screen.getWidth() - width) / 2, 60, 255,255,0, true, s);
+@@ -133,9 +133,9 @@
+ 
+         virtual void doAction() {
+             Area area;
+-            Font titleFont(L"nova.ttf", 26);
+-            Font font(L"laudcn2.ttf", 14);
+-            Font urlFont(L"luximb.ttf", 16);
++            Font titleFont(L"DejaVuSans.ttf", 26);
++            Font font(L"DejaVuSans.ttf", 14);
++            Font urlFont(L"DejaVuSans.ttf", 16);
+ 
+ #define LABEL(pos, c, f, text) area.add(new Label(&f, 220, pos, 360, 20, \
+             Label::ALIGN_CENTER, Label::ALIGN_MIDDLE, 255,255,c, text));
+@@ -171,7 +171,7 @@
+ void menu()
+ {
+     Area area;
+-    Font font(L"laudcn2.ttf", 20);
++    Font font(L"DejaVuSans.ttf", 20);
+ 
+     area.add(new MenuBackground());
+     area.draw();
+diff -r -u einstein-2.0.orig/mkres/compressor.cpp einstein-2.0/mkres/compressor.cpp
+--- einstein-2.0.orig/mkres/compressor.cpp	2005-08-14 04:40:58.000000000 +0200
++++ einstein-2.0/mkres/compressor.cpp	2016-03-05 18:26:13.194264129 +0100
+@@ -2,6 +2,7 @@
+ #include <zlib.h>
+ #include "convert.h"
+ #include "exceptions.h"
++#include "string.h"
+ 
+ 
+ ResourceCompressor::ResourceCompressor() 
+diff -r -u einstein-2.0.orig/mkres/convert.h einstein-2.0/mkres/convert.h
+--- einstein-2.0.orig/mkres/convert.h	2005-08-14 04:40:58.000000000 +0200
++++ einstein-2.0/mkres/convert.h	2016-03-05 18:25:21.479990669 +0100
+@@ -5,6 +5,7 @@
+ #include <iostream>
+ #include <sstream>
+ #include <string>
++#include <typeinfo>
+ 
+ #include "exceptions.h"
+ #include "unicode.h"
+diff -r -u einstein-2.0.orig/mkres/main.cpp einstein-2.0/mkres/main.cpp
+--- einstein-2.0.orig/mkres/main.cpp	2005-08-14 04:40:58.000000000 +0200
++++ einstein-2.0/mkres/main.cpp	2016-03-05 18:25:55.062765900 +0100
+@@ -1,5 +1,6 @@
+ #include "compressor.h"
+ #include "exceptions.h"
++#include "string.h"
+ #include "unicode.h"
+ #include "table.h"
+ 
+diff -r -u einstein-2.0.orig/mkres/unicode.cpp einstein-2.0/mkres/unicode.cpp
+--- einstein-2.0.orig/mkres/unicode.cpp	2005-08-14 04:40:58.000000000 +0200
++++ einstein-2.0/mkres/unicode.cpp	2016-03-05 18:26:28.065492890 +0100
+@@ -5,6 +5,7 @@
+ #endif
+ #include "unicode.h"
+ #include "exceptions.h"
++#include "string.h"
+ 
+ 
+ /// Returns length of wide character in utf-8
+diff -r -u einstein-2.0.orig/opensave.cpp einstein-2.0/opensave.cpp
+--- einstein-2.0.orig/opensave.cpp	2005-08-14 23:33:36.000000000 +0200
++++ einstein-2.0/opensave.cpp	2016-03-05 18:29:27.960352230 +0100
+@@ -160,7 +160,7 @@
+ static void showListWindow(SavesList &list, Command **commands,
+         const std::wstring &title, Area &area, Font *font)
+ {
+-    Font titleFont(L"nova.ttf", 26);
++    Font titleFont(L"DejaVuSans.ttf", 26);
+ 
+     area.add(new Window(250, 90, 300, 420, L"blue.bmp"));
+     area.add(new Label(&titleFont, 250, 95, 300, 40, Label::ALIGN_CENTER,
+@@ -189,7 +189,7 @@
+     
+     Area area;
+     area.add(parentArea, false);
+-    Font font(L"laudcn2.ttf", 14);
++    Font font(L"DejaVuSans.ttf", 14);
+     bool saved = false;
+     
+     SavesList list;
+@@ -258,7 +258,7 @@
+     
+     Area area;
+     area.add(parentArea, false);
+-    Font font(L"laudcn2.ttf", 14);
++    Font font(L"DejaVuSans.ttf", 14);
+     
+     Game *newGame = NULL;
+     
+diff -r -u einstein-2.0.orig/options.cpp einstein-2.0/options.cpp
+--- einstein-2.0.orig/options.cpp	2005-09-26 12:33:18.000000000 +0200
++++ einstein-2.0/options.cpp	2016-03-05 18:29:27.960352230 +0100
+@@ -53,8 +53,8 @@
+ 
+ void showOptionsWindow(Area *parentArea)
+ {
+-    Font titleFont(L"nova.ttf", 26);
+-    Font font(L"laudcn2.ttf", 14);
++    Font titleFont(L"DejaVuSans.ttf", 26);
++    Font font(L"DejaVuSans.ttf", 14);
+ 
+     bool fullscreen = (getStorage()->get(L"fullscreen", 1) != 0);
+     bool niceCursor = (getStorage()->get(L"niceCursor", 1) != 0);
+diff -r -u einstein-2.0.orig/res/resources.descr einstein-2.0/res/resources.descr
+--- einstein-2.0.orig/res/resources.descr	2005-09-25 22:51:14.000000000 +0200
++++ einstein-2.0/res/resources.descr	2016-03-05 18:30:08.563704873 +0100
+@@ -89,13 +89,11 @@
+     { name = "title.bmp" }
+     { name = "marble1.bmp" }
+     { name = "blue.bmp" }
+-    { name = "luximb.ttf" }
+     { name = "redpattern.bmp" }
+     { name = "greenpattern.bmp" }
+     { name = "darkpattern.bmp" }
+     { name = "nova.bmp" }
+-    { name = "nova.ttf" }
+-    { name = "laudcn2.ttf" }
++    { name = "DejaVuSans.ttf" }
+     { name = "btn.bmp" }
+     { name = "rules.txt", format = "messages" group = "messages" }
+     { name = "rules_ru.txt", format = "messages" group = "messages" }
+Only in einstein-2.0/res: resources.descr.orig
+diff -r -u einstein-2.0.orig/sound.h einstein-2.0/sound.h
+--- einstein-2.0.orig/sound.h	2005-09-24 08:24:20.000000000 +0200
++++ einstein-2.0/sound.h	2016-03-05 18:22:19.314931225 +0100
+@@ -4,7 +4,7 @@
+ 
+ #include <string>
+ #include <map>
+-#include <SDL_mixer.h>
++#include <SDL/SDL_mixer.h>
+ 
+ 
+ class Sound
+diff -r -u einstein-2.0.orig/topscores.cpp einstein-2.0/topscores.cpp
+--- einstein-2.0.orig/topscores.cpp	2005-08-14 23:08:43.000000000 +0200
++++ einstein-2.0/topscores.cpp	2016-03-05 18:29:27.970353055 +0100
+@@ -103,9 +103,9 @@
+ ScoresWindow::ScoresWindow(int x, int y, TopScores *scores, int highlight): 
+                 Window(x, y, 320, 350, L"blue.bmp")
+ {
+-    Font titleFont(L"nova.ttf", 26);
+-    Font entryFont(L"laudcn2.ttf", 14);
+-    Font timeFont(L"luximb.ttf", 14);
++    Font titleFont(L"DejaVuSans.ttf", 26);
++    Font entryFont(L"DejaVuSans.ttf", 14);
++    Font timeFont(L"DejaVuSans.ttf", 14);
+     
+     std::wstring txt = msg(L"topScores");
+     int w = titleFont.getWidth(txt);
+@@ -139,7 +139,7 @@
+ {
+     Area area;
+ 
+-    Font font(L"laudcn2.ttf", 16);
++    Font font(L"DejaVuSans.ttf", 16);
+     area.add(parentArea);
+     area.add(new ScoresWindow(240, 125, scores, highlight));
+     ExitCommand exitCmd(area);
+@@ -154,7 +154,7 @@
+ {
+     Area area;
+     
+-    Font font(L"laudcn2.ttf", 16);
++    Font font(L"DejaVuSans.ttf", 16);
+     area.add(parentArea);
+     area.add(new Window(170, 280, 460, 100, L"blue.bmp"));
+     Storage *storage = getStorage();
+diff -r -u einstein-2.0.orig/unicode.cpp einstein-2.0/unicode.cpp
+--- einstein-2.0.orig/unicode.cpp	2005-08-14 04:40:58.000000000 +0200
++++ einstein-2.0/unicode.cpp	2016-03-05 18:26:55.747780024 +0100
+@@ -5,6 +5,7 @@
+ #endif
+ #include "unicode.h"
+ #include "exceptions.h"
++#include "string.h"
+ 
+ 
+ /// Returns length of wide character in utf-8

gnu/packages/patches/gitolite-openssh-6.8-compat.patch

@@ -1,25 +0,0 @@
-From ed807a40c6683960e357bc995b3acf721ec088b4 Mon Sep 17 00:00:00 2001
-From: Sitaram Chamarty <sitaram@atc.tcs.com>
-Date: Thu, 19 Mar 2015 05:17:59 +0530
-Subject: [PATCH] openssh 6.8 compat
-
----
- src/triggers/post-compile/ssh-authkeys | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/triggers/post-compile/ssh-authkeys b/src/triggers/post-compile/ssh-authkeys
-index 84dda73..d5f5d8b 100755
---- a/src/triggers/post-compile/ssh-authkeys
-+++ b/src/triggers/post-compile/ssh-authkeys
-@@ -115,7 +115,7 @@ sub fp_file {
-     my $f  = shift;
-     my $fp = `ssh-keygen -l -f '$f'`;
-     chomp($fp);
--    _die "fingerprinting failed for '$f'" unless $fp =~ /([0-9a-f][0-9a-f](:[0-9a-f][0-9a-f])+)/;
-+    _die "fingerprinting failed for '$f'" unless $fp =~ /([0-9a-f][0-9a-f](:[0-9a-f][0-9a-f])+)/ or $fp =~ m(SHA256:([A-ZA-z0-9+/]+));
-     $fp = $1;
-     return $fp;
- }
---
-2.2.1
-

gnu/packages/patches/icecat-CVE-2015-4477.patch

@@ -0,0 +1,37 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/beae8783b8c2
+
+# HG changeset patch
+# User Paul Adenot <paul@paul.cx>
+# Date 1456422965 0
+# Node ID beae8783b8c2c672da12a95c70ae663cbd0d5016
+# Parent  3a606f8182c82480f8f350b622ab55a170ec1eb6
+Bug 1179484. r=roc
+
+MozReview-Commit-ID: HNaYLyMe3sM
+
+diff --git a/dom/media/webaudio/MediaStreamAudioDestinationNode.cpp b/dom/media/webaudio/MediaStreamAudioDestinationNode.cpp
+--- a/dom/media/webaudio/MediaStreamAudioDestinationNode.cpp
++++ b/dom/media/webaudio/MediaStreamAudioDestinationNode.cpp
+@@ -69,16 +69,20 @@ MediaStreamAudioDestinationNode::MediaSt
+               ChannelInterpretation::Speakers)
+   , mDOMStream(DOMAudioNodeMediaStream::CreateTrackUnionStream(GetOwner(),
+                                                                this))
+ {
+   TrackUnionStream* tus = static_cast<TrackUnionStream*>(mDOMStream->GetStream());
+   MOZ_ASSERT(tus == mDOMStream->GetStream()->AsProcessedStream());
+   tus->SetTrackIDFilter(FilterAudioNodeStreamTrack);
+ 
++  if (aContext->Graph() != tus->Graph()) {
++    return;
++  }
++
+   MediaStreamDestinationEngine* engine = new MediaStreamDestinationEngine(this, tus);
+   mStream = aContext->Graph()->CreateAudioNodeStream(engine, MediaStreamGraph::INTERNAL_STREAM);
+   mPort = tus->AllocateInputPort(mStream, 0);
+ 
+   nsIDocument* doc = aContext->GetParentObject()->GetExtantDoc();
+   if (doc) {
+     mDOMStream->CombineWithPrincipal(doc->NodePrincipal());
+   }
+

gnu/packages/patches/icecat-CVE-2016-1952-pt01.patch

@@ -0,0 +1,356 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/c1d67bd4c993
+
+# HG changeset patch
+# User Timothy Nikkel <tnikkel@gmail.com>
+# Date 1454023801 21600
+# Node ID c1d67bd4c993b9e344c68954e6f0392c82b81e38
+# Parent  530559abe159d3c23f078d673d30ff03d9c244e2
+Bug 1224979 - Check if we compute usable filters for the downscaler, and if not put the downscaler in error state so it's not used. r=edwin, a=al
+
+diff --git a/image/Downscaler.cpp b/image/Downscaler.cpp
+new file mode 100644
+--- /dev/null
++++ b/image/Downscaler.cpp
+@@ -0,0 +1,340 @@
++/* -*- Mode: C++; tab-width: 2; indent-tabs-mode: nil; c-basic-offset: 2 -*-
++ *
++ * This Source Code Form is subject to the terms of the Mozilla Public
++ * License, v. 2.0. If a copy of the MPL was not distributed with this
++ * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
++
++#include "Downscaler.h"
++
++#include <algorithm>
++#include <ctime>
++#include "gfxPrefs.h"
++#include "image_operations.h"
++#include "mozilla/SSE.h"
++#include "convolver.h"
++#include "skia/include/core/SkTypes.h"
++
++using std::max;
++using std::swap;
++
++namespace mozilla {
++namespace image {
++
++Downscaler::Downscaler(const nsIntSize& aTargetSize)
++  : mTargetSize(aTargetSize)
++  , mOutputBuffer(nullptr)
++  , mXFilter(MakeUnique<skia::ConvolutionFilter1D>())
++  , mYFilter(MakeUnique<skia::ConvolutionFilter1D>())
++  , mWindowCapacity(0)
++  , mHasAlpha(true)
++  , mFlipVertically(false)
++{
++  MOZ_ASSERT(gfxPrefs::ImageDownscaleDuringDecodeEnabled(),
++             "Downscaling even though downscale-during-decode is disabled?");
++  MOZ_ASSERT(mTargetSize.width > 0 && mTargetSize.height > 0,
++             "Invalid target size");
++}
++
++Downscaler::~Downscaler()
++{
++  ReleaseWindow();
++}
++
++void
++Downscaler::ReleaseWindow()
++{
++  if (!mWindow) {
++    return;
++  }
++
++  for (int32_t i = 0; i < mWindowCapacity; ++i) {
++    delete[] mWindow[i];
++  }
++
++  mWindow = nullptr;
++  mWindowCapacity = 0;
++}
++
++nsresult
++Downscaler::BeginFrame(const nsIntSize& aOriginalSize,
++                       const Maybe<nsIntRect>& aFrameRect,
++                       uint8_t* aOutputBuffer,
++                       bool aHasAlpha,
++                       bool aFlipVertically /* = false */)
++{
++  MOZ_ASSERT(aOutputBuffer);
++  MOZ_ASSERT(mTargetSize != aOriginalSize,
++             "Created a downscaler, but not downscaling?");
++  MOZ_ASSERT(mTargetSize.width <= aOriginalSize.width,
++             "Created a downscaler, but width is larger");
++  MOZ_ASSERT(mTargetSize.height <= aOriginalSize.height,
++             "Created a downscaler, but height is larger");
++  MOZ_ASSERT(aOriginalSize.width > 0 && aOriginalSize.height > 0,
++             "Invalid original size");
++
++  mFrameRect = aFrameRect.valueOr(nsIntRect(nsIntPoint(), aOriginalSize));
++  MOZ_ASSERT(mFrameRect.x >= 0 && mFrameRect.y >= 0 &&
++             mFrameRect.width >= 0 && mFrameRect.height >= 0,
++             "Frame rect must have non-negative components");
++  MOZ_ASSERT(nsIntRect(0, 0, aOriginalSize.width, aOriginalSize.height)
++               .Contains(mFrameRect),
++             "Frame rect must fit inside image");
++  MOZ_ASSERT_IF(!nsIntRect(0, 0, aOriginalSize.width, aOriginalSize.height)
++                  .IsEqualEdges(mFrameRect),
++                aHasAlpha);
++
++  mOriginalSize = aOriginalSize;
++  mScale = gfxSize(double(mOriginalSize.width) / mTargetSize.width,
++                   double(mOriginalSize.height) / mTargetSize.height);
++  mOutputBuffer = aOutputBuffer;
++  mHasAlpha = aHasAlpha;
++  mFlipVertically = aFlipVertically;
++
++  ReleaseWindow();
++
++  auto resizeMethod = skia::ImageOperations::RESIZE_LANCZOS3;
++
++  skia::resize::ComputeFilters(resizeMethod,
++                               mOriginalSize.width, mTargetSize.width,
++                               0, mTargetSize.width,
++                               mXFilter.get());
++
++  if (mXFilter->max_filter() <= 0 || mXFilter->num_values() != mTargetSize.width) {
++    NS_WARNING("Failed to compute filters for image downscaling");
++    return NS_ERROR_OUT_OF_MEMORY;
++  }
++
++  skia::resize::ComputeFilters(resizeMethod,
++                               mOriginalSize.height, mTargetSize.height,
++                               0, mTargetSize.height,
++                               mYFilter.get());
++
++  if (mYFilter->max_filter() <= 0 || mYFilter->num_values() != mTargetSize.height) {
++    NS_WARNING("Failed to compute filters for image downscaling");
++    return NS_ERROR_OUT_OF_MEMORY;
++  }
++
++  // Allocate the buffer, which contains scanlines of the original image.
++  // pad by 15 to handle overreads by the simd code
++  size_t bufferLen = mOriginalSize.width * sizeof(uint32_t) + 15;
++  mRowBuffer.reset(new (fallible) uint8_t[bufferLen]);
++  if (MOZ_UNLIKELY(!mRowBuffer)) {
++    return NS_ERROR_OUT_OF_MEMORY;
++  }
++
++  // Zero buffer to keep valgrind happy.
++  memset(mRowBuffer.get(), 0, bufferLen);
++
++  // Allocate the window, which contains horizontally downscaled scanlines. (We
++  // can store scanlines which are already downscale because our downscaling
++  // filter is separable.)
++  mWindowCapacity = mYFilter->max_filter();
++  mWindow.reset(new (fallible) uint8_t*[mWindowCapacity]);
++  if (MOZ_UNLIKELY(!mWindow)) {
++    return NS_ERROR_OUT_OF_MEMORY;
++  }
++
++  bool anyAllocationFailed = false;
++  // pad by 15 to handle overreads by the simd code
++  const int rowSize = mTargetSize.width * sizeof(uint32_t) + 15;
++  for (int32_t i = 0; i < mWindowCapacity; ++i) {
++    mWindow[i] = new (fallible) uint8_t[rowSize];
++    anyAllocationFailed = anyAllocationFailed || mWindow[i] == nullptr;
++  }
++
++  if (MOZ_UNLIKELY(anyAllocationFailed)) {
++    // We intentionally iterate through the entire array even if an allocation
++    // fails, to ensure that all the pointers in it are either valid or nullptr.
++    // That in turn ensures that ReleaseWindow() can clean up correctly.
++    return NS_ERROR_OUT_OF_MEMORY;
++  }
++
++  ResetForNextProgressivePass();
++
++  return NS_OK;
++}
++
++void
++Downscaler::SkipToRow(int32_t aRow)
++{
++  if (mCurrentInLine < aRow) {
++    ClearRow();
++    do {
++      CommitRow();
++    } while (mCurrentInLine < aRow);
++  }
++}
++
++void
++Downscaler::ResetForNextProgressivePass()
++{
++  mPrevInvalidatedLine = 0;
++  mCurrentOutLine = 0;
++  mCurrentInLine = 0;
++  mLinesInBuffer = 0;
++
++  if (mFrameRect.IsEmpty()) {
++    // Our frame rect is zero size; commit rows until the end of the image.
++    SkipToRow(mOriginalSize.height - 1);
++  } else {
++    // If we have a vertical offset, commit rows to shift us past it.
++    SkipToRow(mFrameRect.y);
++  }
++}
++
++static void
++GetFilterOffsetAndLength(UniquePtr<skia::ConvolutionFilter1D>& aFilter,
++                         int32_t aOutputImagePosition,
++                         int32_t* aFilterOffsetOut,
++                         int32_t* aFilterLengthOut)
++{
++  MOZ_ASSERT(aOutputImagePosition < aFilter->num_values());
++  aFilter->FilterForValue(aOutputImagePosition,
++                          aFilterOffsetOut,
++                          aFilterLengthOut);
++}
++
++void
++Downscaler::ClearRow(uint32_t aStartingAtCol)
++{
++  MOZ_ASSERT(int64_t(mOriginalSize.width) > int64_t(aStartingAtCol));
++  uint32_t bytesToClear = (mOriginalSize.width - aStartingAtCol)
++                        * sizeof(uint32_t);
++  memset(mRowBuffer.get() + (aStartingAtCol * sizeof(uint32_t)),
++         0, bytesToClear);
++}
++
++void
++Downscaler::CommitRow()
++{
++  MOZ_ASSERT(mOutputBuffer, "Should have a current frame");
++  MOZ_ASSERT(mCurrentInLine < mOriginalSize.height, "Past end of input");
++
++  if (mCurrentOutLine < mTargetSize.height) {
++    int32_t filterOffset = 0;
++    int32_t filterLength = 0;
++    GetFilterOffsetAndLength(mYFilter, mCurrentOutLine,
++                             &filterOffset, &filterLength);
++
++    int32_t inLineToRead = filterOffset + mLinesInBuffer;
++    MOZ_ASSERT(mCurrentInLine <= inLineToRead, "Reading past end of input");
++    if (mCurrentInLine == inLineToRead) {
++      skia::ConvolveHorizontally(mRowBuffer.get(), *mXFilter,
++                                 mWindow[mLinesInBuffer++], mHasAlpha,
++                                 supports_sse2());
++    }
++
++    MOZ_ASSERT(mCurrentOutLine < mTargetSize.height,
++               "Writing past end of output");
++
++    while (mLinesInBuffer == filterLength) {
++      DownscaleInputLine();
++
++      if (mCurrentOutLine == mTargetSize.height) {
++        break;  // We're done.
++      }
++
++      GetFilterOffsetAndLength(mYFilter, mCurrentOutLine,
++                               &filterOffset, &filterLength);
++    }
++  }
++
++  mCurrentInLine += 1;
++
++  // If we're at the end of the part of the original image that has data, commit
++  // rows to shift us to the end.
++  if (mCurrentInLine == (mFrameRect.y + mFrameRect.height)) {
++    SkipToRow(mOriginalSize.height - 1);
++  }
++}
++
++bool
++Downscaler::HasInvalidation() const
++{
++  return mCurrentOutLine > mPrevInvalidatedLine;
++}
++
++DownscalerInvalidRect
++Downscaler::TakeInvalidRect()
++{
++  if (MOZ_UNLIKELY(!HasInvalidation())) {
++    return DownscalerInvalidRect();
++  }
++
++  DownscalerInvalidRect invalidRect;
++
++  // Compute the target size invalid rect.
++  if (mFlipVertically) {
++    // We need to flip it. This will implicitly flip the original size invalid
++    // rect, since we compute it by scaling this rect.
++    invalidRect.mTargetSizeRect =
++      IntRect(0, mTargetSize.height - mCurrentOutLine,
++              mTargetSize.width, mCurrentOutLine - mPrevInvalidatedLine);
++  } else {
++    invalidRect.mTargetSizeRect =
++      IntRect(0, mPrevInvalidatedLine,
++              mTargetSize.width, mCurrentOutLine - mPrevInvalidatedLine);
++  }
++
++  mPrevInvalidatedLine = mCurrentOutLine;
++
++  // Compute the original size invalid rect.
++  invalidRect.mOriginalSizeRect = invalidRect.mTargetSizeRect;
++  invalidRect.mOriginalSizeRect.ScaleRoundOut(mScale.width, mScale.height);
++
++  return invalidRect;
++}
++
++void
++Downscaler::DownscaleInputLine()
++{
++  typedef skia::ConvolutionFilter1D::Fixed FilterValue;
++
++  MOZ_ASSERT(mOutputBuffer);
++  MOZ_ASSERT(mCurrentOutLine < mTargetSize.height,
++             "Writing past end of output");
++
++  int32_t filterOffset = 0;
++  int32_t filterLength = 0;
++  MOZ_ASSERT(mCurrentOutLine < mYFilter->num_values());
++  auto filterValues =
++    mYFilter->FilterForValue(mCurrentOutLine, &filterOffset, &filterLength);
++
++  int32_t currentOutLine = mFlipVertically
++                         ? mTargetSize.height - (mCurrentOutLine + 1)
++                         : mCurrentOutLine;
++  MOZ_ASSERT(currentOutLine >= 0);
++
++  uint8_t* outputLine =
++    &mOutputBuffer[currentOutLine * mTargetSize.width * sizeof(uint32_t)];
++  skia::ConvolveVertically(static_cast<const FilterValue*>(filterValues),
++                           filterLength, mWindow.get(), mXFilter->num_values(),
++                           outputLine, mHasAlpha, supports_sse2());
++
++  mCurrentOutLine += 1;
++
++  if (mCurrentOutLine == mTargetSize.height) {
++    // We're done.
++    return;
++  }
++
++  int32_t newFilterOffset = 0;
++  int32_t newFilterLength = 0;
++  GetFilterOffsetAndLength(mYFilter, mCurrentOutLine,
++                           &newFilterOffset, &newFilterLength);
++
++  int diff = newFilterOffset - filterOffset;
++  MOZ_ASSERT(diff >= 0, "Moving backwards in the filter?");
++
++  // Shift the buffer. We're just moving pointers here, so this is cheap.
++  mLinesInBuffer -= diff;
++  mLinesInBuffer = max(mLinesInBuffer, 0);
++  for (int32_t i = 0; i < mLinesInBuffer; ++i) {
++    swap(mWindow[i], mWindow[filterLength - mLinesInBuffer + i]);
++  }
++}
++
++
++
++} // namespace image
++} // namespace mozilla
+

gnu/packages/patches/icecat-CVE-2016-1952-pt02.patch

@@ -0,0 +1,58 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/9719b71d72dd
+
+# HG changeset patch
+# User Byron Campen [:bwc] <docfaraday@gmail.com>
+# Date 1454100887 21600
+# Node ID 9719b71d72dd2a3c5ee12ace156af2a63d9595ac
+# Parent  b68673d974a10f65390f80b36d4307eb31e44669
+Bug 1234578 - Assert if PCM is destroyed improperly. r=rjesup, a=sylvestre
+
+diff --git a/media/webrtc/signaling/src/peerconnection/PeerConnectionMedia.cpp b/media/webrtc/signaling/src/peerconnection/PeerConnectionMedia.cpp
+--- a/media/webrtc/signaling/src/peerconnection/PeerConnectionMedia.cpp
++++ b/media/webrtc/signaling/src/peerconnection/PeerConnectionMedia.cpp
+@@ -712,16 +712,18 @@ PeerConnectionMedia::SelfDestruct_m()
+ {
+   CSFLogDebug(logTag, "%s: ", __FUNCTION__);
+ 
+   ASSERT_ON_THREAD(mMainThread);
+ 
+   mLocalSourceStreams.Clear();
+   mRemoteSourceStreams.Clear();
+ 
++  mMainThread = nullptr;
++
+   // Final self-destruct.
+   this->Release();
+ }
+ 
+ void
+ PeerConnectionMedia::ShutdownMediaTransport_s()
+ {
+   ASSERT_ON_THREAD(mSTSThread);
+diff --git a/media/webrtc/signaling/src/peerconnection/PeerConnectionMedia.h b/media/webrtc/signaling/src/peerconnection/PeerConnectionMedia.h
+--- a/media/webrtc/signaling/src/peerconnection/PeerConnectionMedia.h
++++ b/media/webrtc/signaling/src/peerconnection/PeerConnectionMedia.h
+@@ -210,17 +210,20 @@ class RemoteSourceStreamInfo : public So
+   std::vector<std::string> mTrackIdMap;
+ 
+   // True iff SetPullEnabled(true) has been called on the DOMMediaStream. This
+   // happens when offer/answer concludes.
+   bool mReceiving;
+ };
+ 
+ class PeerConnectionMedia : public sigslot::has_slots<> {
+-  ~PeerConnectionMedia() {}
++  ~PeerConnectionMedia()
++  {
++    MOZ_RELEASE_ASSERT(!mMainThread);
++  }
+ 
+  public:
+   explicit PeerConnectionMedia(PeerConnectionImpl *parent);
+ 
+   PeerConnectionImpl* GetPC() { return mParent; }
+   nsresult Init(const std::vector<NrIceStunServer>& stun_servers,
+                 const std::vector<NrIceTurnServer>& turn_servers);
+   // WARNING: This destroys the object!
+

gnu/packages/patches/icecat-CVE-2016-1952-pt03.patch

@@ -0,0 +1,60 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/2839062f84fb
+
+# HG changeset patch
+# User Jan de Mooij <jdemooij@mozilla.com>
+# Date 1455119320 -3600
+# Node ID 2839062f84fb6cba2781ea8d59150f13d4813ddc
+# Parent  185b233ea03f3811404e3979b65ec86b29d13555
+Bug 1242279 - r=bhackett1024 a=sylvestre
+
+diff --git a/js/src/vm/TypeInference.cpp b/js/src/vm/TypeInference.cpp
+--- a/js/src/vm/TypeInference.cpp
++++ b/js/src/vm/TypeInference.cpp
+@@ -3961,16 +3961,22 @@ JSScript::maybeSweepTypes(AutoClearTypeI
+ 
+     unsigned num = TypeScript::NumTypeSets(this);
+     StackTypeSet* typeArray = types_->typeArray();
+ 
+     // Remove constraints and references to dead objects from stack type sets.
+     for (unsigned i = 0; i < num; i++)
+         typeArray[i].sweep(zone(), *oom);
+ 
++    if (oom->hadOOM()) {
++        // It's possible we OOM'd while copying freeze constraints, so they
++        // need to be regenerated.
++        hasFreezeConstraints_ = false;
++    }
++
+     // Update the recompile indexes in any IonScripts still on the script.
+     if (hasIonScript())
+         ionScript()->recompileInfoRef().shouldSweep(types);
+ }
+ 
+ void
+ TypeScript::destroy()
+ {
+diff --git a/js/src/vm/TypeInference.h b/js/src/vm/TypeInference.h
+--- a/js/src/vm/TypeInference.h
++++ b/js/src/vm/TypeInference.h
+@@ -566,16 +566,19 @@ class AutoClearTypeInferenceStateOnOOM
+       : zone(zone), oom(false)
+     {}
+ 
+     ~AutoClearTypeInferenceStateOnOOM();
+ 
+     void setOOM() {
+         oom = true;
+     }
++    bool hadOOM() const {
++        return oom;
++    }
+ };
+ 
+ /* Superclass common to stack and heap type sets. */
+ class ConstraintTypeSet : public TypeSet
+ {
+   public:
+     /* Chain of constraints which propagate changes out from this type set. */
+     TypeConstraint* constraintList;
+

gnu/packages/patches/icecat-CVE-2016-1952-pt04.patch

@@ -0,0 +1,53 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/9dd60e798819
+
+# HG changeset patch
+# User Olli Pettay <bugs@pettay.fi>
+# Date 1455204078 -3600
+# Node ID 9dd60e798819fe2ebf1e5bd36aa9006ecd2f82c9
+# Parent  c1d67bd4c993b9e344c68954e6f0392c82b81e38
+Bug 1244250 - r=mats, a=al
+
+diff --git a/layout/style/nsAnimationManager.cpp b/layout/style/nsAnimationManager.cpp
+--- a/layout/style/nsAnimationManager.cpp
++++ b/layout/style/nsAnimationManager.cpp
+@@ -715,16 +715,17 @@ nsAnimationManager::FlushAnimations(Flus
+   }
+ 
+   DispatchEvents(); // may destroy us
+ }
+ 
+ void
+ nsAnimationManager::DoDispatchEvents()
+ {
++  nsRefPtr<nsAnimationManager> kungFuDeathGrip(this);
+   EventArray events;
+   mPendingEvents.SwapElements(events);
+   for (uint32_t i = 0, i_end = events.Length(); i < i_end; ++i) {
+     AnimationEventInfo &info = events[i];
+     EventDispatcher::Dispatch(info.mElement, mPresContext, &info.mEvent);
+ 
+     if (!mPresContext) {
+       break;
+diff --git a/layout/style/nsTransitionManager.cpp b/layout/style/nsTransitionManager.cpp
+--- a/layout/style/nsTransitionManager.cpp
++++ b/layout/style/nsTransitionManager.cpp
+@@ -753,16 +753,17 @@ nsTransitionManager::FlushTransitions(Fl
+       }
+     }
+   }
+ 
+   if (didThrottle) {
+     mPresContext->Document()->SetNeedStyleFlush();
+   }
+ 
++  nsRefPtr<nsTransitionManager> kungFuDeathGrip(this);
+   for (uint32_t i = 0, i_end = events.Length(); i < i_end; ++i) {
+     TransitionEventInfo &info = events[i];
+     EventDispatcher::Dispatch(info.mElement, mPresContext, &info.mEvent);
+ 
+     if (!mPresContext) {
+       break;
+     }
+   }
+

gnu/packages/patches/icecat-CVE-2016-1952-pt05.patch

@@ -0,0 +1,32 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/1dd0ca8e70bd
+
+# HG changeset patch
+# User Nicolas B. Pierron <nicolas.b.pierron@mozilla.com>
+# Date 1456161361 0
+# Node ID 1dd0ca8e70bd77b6fd93f36cc4e9c2cebfe8ba0a
+# Parent  95ff874886905ef46a7bbc760981d15ad0831096
+Bug 1221872 - ValueNumbering: Set the dominator index of fixup blocks when they are created. r=sunfish, a=ritu
+
+diff --git a/js/src/jit/ValueNumbering.cpp b/js/src/jit/ValueNumbering.cpp
+--- a/js/src/jit/ValueNumbering.cpp
++++ b/js/src/jit/ValueNumbering.cpp
+@@ -433,16 +433,17 @@ ValueNumberer::fixupOSROnlyLoop(MBasicBl
+     MBasicBlock* fake = MBasicBlock::NewAsmJS(graph_, block->info(),
+                                               nullptr, MBasicBlock::NORMAL);
+     if (fake == nullptr)
+         return false;
+ 
+     graph_.insertBlockBefore(block, fake);
+     fake->setImmediateDominator(fake);
+     fake->addNumDominated(1);
++    fake->setDomIndex(fake->id());
+ 
+     // Create zero-input phis to use as inputs for any phis in |block|.
+     // Again, this is a little odd, but it's the least-odd thing we can do
+     // without significant complexity.
+     for (MPhiIterator iter(block->phisBegin()), end(block->phisEnd()); iter != end; ++iter) {
+         MPhi* phi = *iter;
+         MPhi* fakePhi = MPhi::New(graph_.alloc(), phi->type());
+         fake->addPhi(fakePhi);
+

gnu/packages/patches/icecat-CVE-2016-1952-pt06.patch

@@ -0,0 +1,103 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/6f4d51302387
+
+# HG changeset patch
+# User Andrew McCreight <continuation@gmail.com>
+# Date 1456273423 28800
+# Node ID 6f4d5130238790fa5810c76ffeb9eccc65efa8c9
+# Parent  70f6c59d9d73a5edefd216b48ca74a931da12cf1
+Bug 1249685 - Use more nsCOMPtrs for stack variables in DOM code. r=smaug, a=ritu
+
+diff --git a/dom/base/nsRange.cpp b/dom/base/nsRange.cpp
+--- a/dom/base/nsRange.cpp
++++ b/dom/base/nsRange.cpp
+@@ -1985,17 +1985,17 @@ nsRange::CutContents(DocumentFragment** 
+       rv = closestAncestor ? PrependChild(closestAncestor, nodeToResult)
+                            : PrependChild(commonCloneAncestor, nodeToResult);
+       NS_ENSURE_SUCCESS(rv, rv);
+       NS_ENSURE_STATE(!guard.Mutated(parent ? 2 : 1) ||
+                       ValidateCurrentNode(this, iter));
+     } else if (nodeToResult) {
+       nsMutationGuard guard;
+       nsCOMPtr<nsINode> node = nodeToResult;
+-      nsINode* parent = node->GetParentNode();
++      nsCOMPtr<nsINode> parent = node->GetParentNode();
+       if (parent) {
+         mozilla::ErrorResult error;
+         parent->RemoveChild(*node, error);
+         NS_ENSURE_FALSE(error.Failed(), error.ErrorCode());
+       }
+       NS_ENSURE_STATE(!guard.Mutated(1) ||
+                       ValidateCurrentNode(this, iter));
+     }
+diff --git a/dom/base/nsTreeSanitizer.cpp b/dom/base/nsTreeSanitizer.cpp
+--- a/dom/base/nsTreeSanitizer.cpp
++++ b/dom/base/nsTreeSanitizer.cpp
+@@ -1423,18 +1423,18 @@ nsTreeSanitizer::SanitizeChildren(nsINod
+                              mAllowStyles,
+                              false);
+         }
+         node = node->GetNextNonChildNode(aRoot);
+         continue;
+       }
+       if (MustFlatten(ns, localName)) {
+         RemoveAllAttributes(node);
+-        nsIContent* next = node->GetNextNode(aRoot);
+-        nsIContent* parent = node->GetParent();
++        nsCOMPtr<nsIContent> next = node->GetNextNode(aRoot);
++        nsCOMPtr<nsIContent> parent = node->GetParent();
+         nsCOMPtr<nsIContent> child; // Must keep the child alive during move
+         ErrorResult rv;
+         while ((child = node->GetFirstChild())) {
+           parent->InsertBefore(*child, node, rv);
+           if (rv.Failed()) {
+             break;
+           }
+         }
+diff --git a/dom/html/HTMLSelectElement.cpp b/dom/html/HTMLSelectElement.cpp
+--- a/dom/html/HTMLSelectElement.cpp
++++ b/dom/html/HTMLSelectElement.cpp
+@@ -624,17 +624,17 @@ HTMLSelectElement::Add(nsGenericHTMLElem
+ {
+   if (!aBefore) {
+     Element::AppendChild(aElement, aError);
+     return;
+   }
+ 
+   // Just in case we're not the parent, get the parent of the reference
+   // element
+-  nsINode* parent = aBefore->Element::GetParentNode();
++  nsCOMPtr<nsINode> parent = aBefore->Element::GetParentNode();
+   if (!parent || !nsContentUtils::ContentIsDescendantOf(parent, this)) {
+     // NOT_FOUND_ERR: Raised if before is not a descendant of the SELECT
+     // element.
+     aError.Throw(NS_ERROR_DOM_NOT_FOUND_ERR);
+     return;
+   }
+ 
+   // If the before parameter is not null, we are equivalent to the
+diff --git a/dom/html/HTMLTableElement.cpp b/dom/html/HTMLTableElement.cpp
+--- a/dom/html/HTMLTableElement.cpp
++++ b/dom/html/HTMLTableElement.cpp
+@@ -516,18 +516,18 @@ HTMLTableElement::InsertRow(int32_t aInd
+   if (rowCount > 0) {
+     if (refIndex == rowCount || aIndex == -1) {
+       // we set refIndex to the last row so we can get the last row's
+       // parent we then do an AppendChild below if (rowCount<aIndex)
+ 
+       refIndex = rowCount - 1;
+     }
+ 
+-    Element* refRow = rows->Item(refIndex);
+-    nsINode* parent = refRow->GetParentNode();
++    RefPtr<Element> refRow = rows->Item(refIndex);
++    nsCOMPtr<nsINode> parent = refRow->GetParentNode();
+ 
+     // create the row
+     nsRefPtr<mozilla::dom::NodeInfo> nodeInfo;
+     nsContentUtils::NameChanged(mNodeInfo, nsGkAtoms::tr,
+                                 getter_AddRefs(nodeInfo));
+ 
+     newRow = NS_NewHTMLTableRowElement(nodeInfo.forget());
+ 
+

gnu/packages/patches/icecat-CVE-2016-1954.patch

@@ -0,0 +1,32 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/a5c4c18849b4
+
+# HG changeset patch
+# User Christoph Kerschbaumer <mozilla@christophkerschbaumer.com>
+# Date 1456157874 28800
+# Node ID a5c4c18849b486ef8693e20421b69239a2cbe574
+# Parent  e93aeb25e2a44df8d22f5a065b4410620e2c8730
+Bug 1243178: CSP - Skip sending reports for non http schemes (r=dveditz) a=ritu
+
+diff --git a/dom/security/nsCSPContext.cpp b/dom/security/nsCSPContext.cpp
+--- a/dom/security/nsCSPContext.cpp
++++ b/dom/security/nsCSPContext.cpp
+@@ -798,16 +798,17 @@ nsCSPContext::SendReports(nsISupports* a
+       (NS_SUCCEEDED(reportURI->SchemeIs("https", &isHttpScheme)) && isHttpScheme);
+ 
+     if (!isHttpScheme) {
+       const char16_t* params[] = { reportURIs[r].get() };
+       CSP_LogLocalizedStr(NS_LITERAL_STRING("reportURInotHttpsOrHttp2").get(),
+                           params, ArrayLength(params),
+                           aSourceFile, aScriptSample, aLineNum, 0,
+                           nsIScriptError::errorFlag, "CSP", mInnerWindowID);
++      continue;
+     }
+ 
+     // make sure this is an anonymous request (no cookies) so in case the
+     // policy URI is injected, it can't be abused for CSRF.
+     nsLoadFlags flags;
+     rv = reportChannel->GetLoadFlags(&flags);
+     NS_ENSURE_SUCCESS(rv, rv);
+     flags |= nsIRequest::LOAD_ANONYMOUS;
+

gnu/packages/patches/icecat-CVE-2016-1960.patch

@@ -0,0 +1,55 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/185b233ea03f
+
+# HG changeset patch
+# User Henri Sivonen <hsivonen@hsivonen.fi>
+# Date 1455100746 -7200
+# Node ID 185b233ea03f3811404e3979b65ec86b29d13555
+# Parent  271e3a5a53d96871141e89271f611033b512e3e4
+Bug 1246014. r=wchen. a=sylvestre
+
+diff --git a/parser/html/javasrc/TreeBuilder.java b/parser/html/javasrc/TreeBuilder.java
+--- a/parser/html/javasrc/TreeBuilder.java
++++ b/parser/html/javasrc/TreeBuilder.java
+@@ -4437,17 +4437,17 @@ public abstract class TreeBuilder<T> imp
+         return TreeBuilder.NOT_FOUND_ON_STACK;
+     }
+ 
+     private void clearStackBackTo(int eltPos) throws SAXException {
+         int eltGroup = stack[eltPos].getGroup();
+         while (currentPtr > eltPos) { // > not >= intentional
+             if (stack[currentPtr].ns == "http://www.w3.org/1999/xhtml"
+                     && stack[currentPtr].getGroup() == TEMPLATE
+-                    && (eltGroup == TABLE || eltGroup == TBODY_OR_THEAD_OR_TFOOT|| eltGroup == TR || eltGroup == HTML)) {
++                    && (eltGroup == TABLE || eltGroup == TBODY_OR_THEAD_OR_TFOOT|| eltGroup == TR || eltPos == 0)) {
+                 return;
+             }
+             pop();
+         }
+     }
+ 
+     private void resetTheInsertionMode() {
+         StackNode<T> node;
+diff --git a/parser/html/nsHtml5TreeBuilder.cpp b/parser/html/nsHtml5TreeBuilder.cpp
+--- a/parser/html/nsHtml5TreeBuilder.cpp
++++ b/parser/html/nsHtml5TreeBuilder.cpp
+@@ -3301,17 +3301,17 @@ nsHtml5TreeBuilder::findLastInTableScope
+   return NS_HTML5TREE_BUILDER_NOT_FOUND_ON_STACK;
+ }
+ 
+ void 
+ nsHtml5TreeBuilder::clearStackBackTo(int32_t eltPos)
+ {
+   int32_t eltGroup = stack[eltPos]->getGroup();
+   while (currentPtr > eltPos) {
+-    if (stack[currentPtr]->ns == kNameSpaceID_XHTML && stack[currentPtr]->getGroup() == NS_HTML5TREE_BUILDER_TEMPLATE && (eltGroup == NS_HTML5TREE_BUILDER_TABLE || eltGroup == NS_HTML5TREE_BUILDER_TBODY_OR_THEAD_OR_TFOOT || eltGroup == NS_HTML5TREE_BUILDER_TR || eltGroup == NS_HTML5TREE_BUILDER_HTML)) {
++    if (stack[currentPtr]->ns == kNameSpaceID_XHTML && stack[currentPtr]->getGroup() == NS_HTML5TREE_BUILDER_TEMPLATE && (eltGroup == NS_HTML5TREE_BUILDER_TABLE || eltGroup == NS_HTML5TREE_BUILDER_TBODY_OR_THEAD_OR_TFOOT || eltGroup == NS_HTML5TREE_BUILDER_TR || !eltPos)) {
+       return;
+     }
+     pop();
+   }
+ }
+ 
+ void 
+ nsHtml5TreeBuilder::resetTheInsertionMode()
+

gnu/packages/patches/icecat-CVE-2016-1961.patch

@@ -0,0 +1,33 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/e93aeb25e2a4
+
+# HG changeset patch
+# User Andrew McCreight <continuation@gmail.com>
+# Date 1455891967 28800
+# Node ID e93aeb25e2a44df8d22f5a065b4410620e2c8730
+# Parent  221de852fda32714a9e484774ceafafb450ea73c
+Bug 1249377 - Hold a strong reference to |root| in nsHTMLDocument::SetBody. r=bz, a=sylvestre
+
+diff --git a/dom/html/nsHTMLDocument.cpp b/dom/html/nsHTMLDocument.cpp
+--- a/dom/html/nsHTMLDocument.cpp
++++ b/dom/html/nsHTMLDocument.cpp
+@@ -1044,17 +1044,17 @@ nsHTMLDocument::SetBody(nsIDOMHTMLElemen
+   ErrorResult rv;
+   SetBody(static_cast<nsGenericHTMLElement*>(newBody.get()), rv);
+   return rv.ErrorCode();
+ }
+ 
+ void
+ nsHTMLDocument::SetBody(nsGenericHTMLElement* newBody, ErrorResult& rv)
+ {
+-  Element* root = GetRootElement();
++  nsCOMPtr<Element> root = GetRootElement();
+ 
+   // The body element must be either a body tag or a frameset tag. And we must
+   // have a html root tag, otherwise GetBody will not return the newly set
+   // body.
+   if (!newBody || !(newBody->Tag() == nsGkAtoms::body ||
+                     newBody->Tag() == nsGkAtoms::frameset) ||
+       !root || !root->IsHTML() ||
+       root->Tag() != nsGkAtoms::html) {
+

gnu/packages/patches/icecat-CVE-2016-1962.patch

@@ -0,0 +1,107 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/221de852fda3
+
+# HG changeset patch
+# User Randell Jesup <rjesup@jesup.org>
+# Date 1455862087 18000
+# Node ID 221de852fda32714a9e484774ceafafb450ea73c
+# Parent  b03db72e32f6e3acdc9f8705371cb222d7e6c456
+Bug 1240760: Update DataChannel::Close() r=mcmanus, a=ritu
+
+MozReview-Commit-ID: 7nN9h3M3O8w
+
+diff --git a/netwerk/sctp/datachannel/DataChannel.cpp b/netwerk/sctp/datachannel/DataChannel.cpp
+--- a/netwerk/sctp/datachannel/DataChannel.cpp
++++ b/netwerk/sctp/datachannel/DataChannel.cpp
+@@ -1771,17 +1771,17 @@ DataChannelConnection::HandleStreamReset
+           }
+           NS_DispatchToMainThread(new DataChannelOnMessageAvailable(
+                                     DataChannelOnMessageAvailable::ON_CHANNEL_CLOSED, this,
+                                     channel));
+           mStreams[channel->mStream] = nullptr;
+ 
+           LOG(("Disconnected DataChannel %p from connection %p",
+                (void *) channel.get(), (void *) channel->mConnection.get()));
+-          channel->Destroy();
++          channel->DestroyLocked();
+           // At this point when we leave here, the object is a zombie held alive only by the DOM object
+         } else {
+           LOG(("Can't find incoming channel %d",i));
+         }
+       }
+     }
+   }
+ 
+@@ -2498,17 +2498,17 @@ DataChannelConnection::CloseInt(DataChan
+       mStreams[channel->mStream] = nullptr;
+     } else {
+       SendOutgoingStreamReset();
+     }
+   }
+   aChannel->mState = CLOSING;
+   if (mState == CLOSED) {
+     // we're not going to hang around waiting
+-    channel->Destroy();
++    channel->DestroyLocked();
+   }
+   // At this point when we leave here, the object is a zombie held alive only by the DOM object
+ }
+ 
+ void DataChannelConnection::CloseAll()
+ {
+   LOG(("Closing all channels (connection %p)", (void*) this));
+   // Don't need to lock here
+@@ -2552,23 +2552,25 @@ DataChannel::~DataChannel()
+   // wrong, nothing bad happens.  A worst it's a leak.
+   NS_ASSERTION(mState == CLOSED || mState == CLOSING, "unexpected state in ~DataChannel");
+ }
+ 
+ void
+ DataChannel::Close()
+ {
+   ENSURE_DATACONNECTION;
++  RefPtr<DataChannelConnection> connection(mConnection);
+   mConnection->Close(this);
+ }
+ 
+ // Used when disconnecting from the DataChannelConnection
+ void
+-DataChannel::Destroy()
++DataChannel::DestroyLocked()
+ {
++  mConnection->mLock.AssertCurrentThreadOwns();
+   ENSURE_DATACONNECTION;
+ 
+   LOG(("Destroying Data channel %u", mStream));
+   MOZ_ASSERT_IF(mStream != INVALID_STREAM,
+                 !mConnection->FindChannelByStream(mStream));
+   mStream = INVALID_STREAM;
+   mState = CLOSED;
+   mConnection = nullptr;
+diff --git a/netwerk/sctp/datachannel/DataChannel.h b/netwerk/sctp/datachannel/DataChannel.h
+--- a/netwerk/sctp/datachannel/DataChannel.h
++++ b/netwerk/sctp/datachannel/DataChannel.h
+@@ -331,19 +331,20 @@ public:
+     {
+       NS_ASSERTION(mConnection,"NULL connection");
+     }
+ 
+ private:
+   ~DataChannel();
+ 
+ public:
+-  void Destroy(); // when we disconnect from the connection after stream RESET
++  NS_INLINE_DECL_THREADSAFE_REFCOUNTING(DataChannel)
+ 
+-  NS_INLINE_DECL_THREADSAFE_REFCOUNTING(DataChannel)
++  // when we disconnect from the connection after stream RESET
++  void DestroyLocked();
+ 
+   // Close this DataChannel.  Can be called multiple times.  MUST be called
+   // before destroying the DataChannel (state must be CLOSED or CLOSING).
+   void Close();
+ 
+   // Set the listener (especially for channels created from the other side)
+   void SetListener(DataChannelListener *aListener, nsISupports *aContext);
+ 
+

gnu/packages/patches/icecat-CVE-2016-1964.patch

@@ -0,0 +1,54 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/a653013e7b50
+
+# HG changeset patch
+# User Peter Van der Beken <peterv@propagandism.org>
+# Date 1454340035 -3600
+# Node ID a653013e7b503912a32621e8da64a37171316588
+# Parent  0d0d7e8292f7ecf5f1149d528c0524f04447c4ad
+Bug 1243335 - report bad QName. r=sicking, a=sylvestre
+
+diff --git a/dom/xslt/xslt/txInstructions.cpp b/dom/xslt/xslt/txInstructions.cpp
+--- a/dom/xslt/xslt/txInstructions.cpp
++++ b/dom/xslt/xslt/txInstructions.cpp
+@@ -93,16 +93,19 @@ txAttribute::txAttribute(nsAutoPtr<Expr>
+                          txNamespaceMap* aMappings)
+     : mName(Move(aName)), mNamespace(Move(aNamespace)), mMappings(aMappings)
+ {
+ }
+ 
+ nsresult
+ txAttribute::execute(txExecutionState& aEs)
+ {
++    nsAutoPtr<txTextHandler> handler(
++        static_cast<txTextHandler*>(aEs.popResultHandler()));
++
+     nsAutoString name;
+     nsresult rv = mName->evaluateToString(aEs.getEvalContext(), name);
+     NS_ENSURE_SUCCESS(rv, rv);
+ 
+     const char16_t* colon;
+     if (!XMLUtils::isValidQName(name, &colon) ||
+         TX_StringEqualsAtom(name, nsGkAtoms::xmlns)) {
+         return NS_OK;
+@@ -125,19 +128,16 @@ txAttribute::execute(txExecutionState& a
+         if (!nspace.IsEmpty()) {
+             nsId = txNamespaceManager::getNamespaceID(nspace);
+         }
+     }
+     else if (colon) {
+         nsId = mMappings->lookupNamespace(prefix);
+     }
+ 
+-    nsAutoPtr<txTextHandler> handler(
+-        static_cast<txTextHandler*>(aEs.popResultHandler()));
+-
+     // add attribute if everything was ok
+     return nsId != kNameSpaceID_Unknown ?
+            aEs.mResultHandler->attribute(prefix, Substring(name, lnameStart),
+                                          nsId, handler->mValue) :
+            NS_OK;
+ }
+ 
+ txCallTemplate::txCallTemplate(const txExpandedName& aName)
+

gnu/packages/patches/icecat-CVE-2016-1965.patch

@@ -0,0 +1,44 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/b4467681abd6
+
+# HG changeset patch
+# User Gijs Kruitbosch <gijskruitbosch@gmail.com>
+# Date 1455276061 0
+# Node ID b4467681abd676cd5575cbdf922927f8f54d2ad9
+# Parent  8c1d40e45a72c6432e879137a0afa519dc6c9841
+Bug 1245264 - r=bz, r=ritu
+
+MozReview-Commit-ID: I0sVdritpD3
+
+diff --git a/dom/base/nsLocation.cpp b/dom/base/nsLocation.cpp
+--- a/dom/base/nsLocation.cpp
++++ b/dom/base/nsLocation.cpp
+@@ -735,16 +735,27 @@ nsLocation::SetProtocol(const nsAString&
+     return rv;
+   }
+ 
+   rv = uri->SetScheme(NS_ConvertUTF16toUTF8(aProtocol));
+   if (NS_WARN_IF(NS_FAILED(rv))) {
+     return rv;
+   }
+ 
++  nsAutoCString newSpec;
++  rv = uri->GetSpec(newSpec);
++  if (NS_FAILED(rv)) {
++    return rv;
++  }
++  // We may want a new URI class for the new URI, so recreate it:
++  rv = NS_NewURI(getter_AddRefs(uri), newSpec);
++  if (NS_FAILED(rv)) {
++    return rv;
++  }
++
+   return SetURI(uri);
+ }
+ 
+ void
+ nsLocation::GetUsername(nsAString& aUsername, ErrorResult& aError)
+ {
+   if (!CallerSubsumes()) {
+     aError.Throw(NS_ERROR_DOM_SECURITY_ERR);
+

gnu/packages/patches/icecat-CVE-2016-1966.patch

@@ -0,0 +1,36 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/291c2f31c48c
+
+# HG changeset patch
+# User Nicholas Nethercote <nnethercote@mozilla.com>
+# Date 1454650565 -39600
+# Node ID 291c2f31c48c7e96b1884b55273355970fa0fc30
+# Parent  11e6614756551cfd7291e73eefb90c52873a8480
+Bug 1246054 - Fix an erroneous nsNPObjWrapper assertion. r=froydnj. a=ritu
+
+diff --git a/dom/plugins/base/nsJSNPRuntime.cpp b/dom/plugins/base/nsJSNPRuntime.cpp
+--- a/dom/plugins/base/nsJSNPRuntime.cpp
++++ b/dom/plugins/base/nsJSNPRuntime.cpp
+@@ -1915,18 +1915,19 @@ nsNPObjWrapper::GetNewOrUsed(NPP npp, JS
+   // No existing JSObject, create one.
+ 
+   JS::Rooted<JSObject*> obj(cx, ::JS_NewObject(cx, js::Jsvalify(&sNPObjectJSWrapperClass)));
+ 
+   if (generation != sNPObjWrappers.Generation()) {
+       // Reload entry if the JS_NewObject call caused a GC and reallocated
+       // the table (see bug 445229). This is guaranteed to succeed.
+ 
+-      NS_ASSERTION(PL_DHashTableSearch(&sNPObjWrappers, npobj),
+-                   "Hashtable didn't find what we just added?");
++      entry = static_cast<NPObjWrapperHashEntry*>
++        (PL_DHashTableSearch(&sNPObjWrappers, npobj));
++      NS_ASSERTION(entry, "Hashtable didn't find what we just added?");
+   }
+ 
+   if (!obj) {
+     // OOM? Remove the stale entry from the hash.
+ 
+     PL_DHashTableRawRemove(&sNPObjWrappers, entry);
+ 
+     return nullptr;
+

gnu/packages/patches/icecat-CVE-2016-1974.patch

@@ -0,0 +1,530 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/271e3a5a53d9
+
+# HG changeset patch
+# User Henri Sivonen <hsivonen@hsivonen.fi>
+# Date 1455014759 -7200
+# Node ID 271e3a5a53d96871141e89271f611033b512e3e4
+# Parent  9719b71d72dd2a3c5ee12ace156af2a63d9595ac
+Bug 1228103. r=smaug. a=sylvestre
+
+diff --git a/parser/htmlparser/nsExpatDriver.cpp b/parser/htmlparser/nsExpatDriver.cpp
+--- a/parser/htmlparser/nsExpatDriver.cpp
++++ b/parser/htmlparser/nsExpatDriver.cpp
+@@ -1127,22 +1127,28 @@ nsExpatDriver::ConsumeToken(nsScanner& a
+       XML_Size lastLineLength = XML_GetCurrentColumnNumber(mExpatParser);
+ 
+       if (lastLineLength <= consumed) {
+         // The length of the last line was less than what expat consumed, so
+         // there was at least one line break in the consumed data. Store the
+         // last line until the point where we stopped parsing.
+         nsScannerIterator startLastLine = currentExpatPosition;
+         startLastLine.advance(-((ptrdiff_t)lastLineLength));
+-        CopyUnicodeTo(startLastLine, currentExpatPosition, mLastLine);
++        if (!CopyUnicodeTo(startLastLine, currentExpatPosition, mLastLine)) {
++          return (mInternalState = NS_ERROR_OUT_OF_MEMORY);
++        }
+       }
+       else {
+         // There was no line break in the consumed data, append the consumed
+         // data.
+-        AppendUnicodeTo(oldExpatPosition, currentExpatPosition, mLastLine);
++        if (!AppendUnicodeTo(oldExpatPosition,
++                             currentExpatPosition,
++                             mLastLine)) {
++          return (mInternalState = NS_ERROR_OUT_OF_MEMORY);
++        }
+       }
+     }
+ 
+     mExpatBuffered += length - consumed;
+ 
+     if (BlockedOrInterrupted()) {
+       PR_LOG(GetExpatDriverLog(), PR_LOG_DEBUG,
+              ("Blocked or interrupted parser (probably for loading linked "
+diff --git a/parser/htmlparser/nsParser.cpp b/parser/htmlparser/nsParser.cpp
+--- a/parser/htmlparser/nsParser.cpp
++++ b/parser/htmlparser/nsParser.cpp
+@@ -1508,17 +1508,19 @@ nsParser::ResumeParse(bool allowIteratio
+                 DidBuildModel(mStreamStatus);
+                 return NS_OK;
+               }
+             } else {
+               CParserContext* theContext = PopContext();
+               if (theContext) {
+                 theIterationIsOk = allowIteration && theContextIsStringBased;
+                 if (theContext->mCopyUnused) {
+-                  theContext->mScanner->CopyUnusedData(mUnusedInput);
++                  if (!theContext->mScanner->CopyUnusedData(mUnusedInput)) {
++                    mInternalState = NS_ERROR_OUT_OF_MEMORY;
++                  }
+                 }
+ 
+                 delete theContext;
+               }
+ 
+               result = mInternalState;
+               aIsFinalChunk = mParserContext &&
+                               mParserContext->mStreamListenerState == eOnStop;
+diff --git a/parser/htmlparser/nsScanner.cpp b/parser/htmlparser/nsScanner.cpp
+--- a/parser/htmlparser/nsScanner.cpp
++++ b/parser/htmlparser/nsScanner.cpp
+@@ -379,17 +379,19 @@ nsresult nsScanner::Peek(nsAString& aStr
+   if (mCountRemaining < uint32_t(aNumChars + aOffset)) {
+     end = mEndPosition;
+   }
+   else {
+     end = start;
+     end.advance(aNumChars);
+   }
+ 
+-  CopyUnicodeTo(start, end, aStr);
++  if (!CopyUnicodeTo(start, end, aStr)) {
++    return NS_ERROR_OUT_OF_MEMORY;
++  }
+ 
+   return NS_OK;
+ }
+ 
+ 
+ /**
+  *  Skip whitespace on scanner input stream
+  *  
+@@ -542,17 +544,19 @@ nsresult nsScanner::ReadTagIdentifier(ns
+ 
+     if (!found) {
+       ++current;
+     }
+   }
+ 
+   // Don't bother appending nothing.
+   if (current != mCurrentPosition) {
+-    AppendUnicodeTo(mCurrentPosition, current, aString);
++    if (!AppendUnicodeTo(mCurrentPosition, current, aString)) {
++      return NS_ERROR_OUT_OF_MEMORY;
++    }
+   }
+ 
+   SetPosition(current);  
+   if (current == end) {
+     result = kEOF;
+   }
+ 
+   //DoErrTest(aString);
+@@ -597,26 +601,30 @@ nsresult nsScanner::ReadEntityIdentifier
+         default:
+           found = ('a'<=theChar && theChar<='z') ||
+                   ('A'<=theChar && theChar<='Z') ||
+                   ('0'<=theChar && theChar<='9');
+           break;
+       }
+ 
+       if(!found) {
+-        AppendUnicodeTo(mCurrentPosition, current, aString);
++        if (!AppendUnicodeTo(mCurrentPosition, current, aString)) {
++          return NS_ERROR_OUT_OF_MEMORY;
++        }
+         break;
+       }
+     }
+     ++current;
+   }
+   
+   SetPosition(current);
+   if (current == end) {
+-    AppendUnicodeTo(origin, current, aString);
++    if (!AppendUnicodeTo(origin, current, aString)) {
++      return NS_ERROR_OUT_OF_MEMORY;
++    }
+     return kEOF;
+   }
+ 
+   //DoErrTest(aString);
+ 
+   return result;
+ }
+ 
+@@ -646,26 +654,30 @@ nsresult nsScanner::ReadNumber(nsString&
+   while(current != end) {
+     theChar=*current;
+     if(theChar) {
+       done = (theChar < '0' || theChar > '9') && 
+              ((aBase == 16)? (theChar < 'A' || theChar > 'F') &&
+                              (theChar < 'a' || theChar > 'f')
+                              :true);
+       if(done) {
+-        AppendUnicodeTo(origin, current, aString);
++        if (!AppendUnicodeTo(origin, current, aString)) {
++          return NS_ERROR_OUT_OF_MEMORY;
++        }
+         break;
+       }
+     }
+     ++current;
+   }
+ 
+   SetPosition(current);
+   if (current == end) {
+-    AppendUnicodeTo(origin, current, aString);
++    if (!AppendUnicodeTo(origin, current, aString)) {
++      return NS_ERROR_OUT_OF_MEMORY;
++    }
+     return kEOF;
+   }
+ 
+   //DoErrTest(aString);
+ 
+   return result;
+ }
+ 
+@@ -712,37 +724,43 @@ nsresult nsScanner::ReadWhitespace(nsSca
+           char16_t thePrevChar = theChar;
+           theChar = (++current != end) ? *current : '\0';
+           if ((thePrevChar == '\r' && theChar == '\n') ||
+               (thePrevChar == '\n' && theChar == '\r')) {
+             theChar = (++current != end) ? *current : '\0'; // CRLF == LFCR => LF
+             haveCR = true;
+           } else if (thePrevChar == '\r') {
+             // Lone CR becomes CRLF; callers should know to remove extra CRs
+-            AppendUnicodeTo(origin, current, aString);
++            if (!AppendUnicodeTo(origin, current, aString)) {
++              return NS_ERROR_OUT_OF_MEMORY;
++            }
+             aString.writable().Append(char16_t('\n'));
+             origin = current;
+             haveCR = true;
+           }
+         }
+         break;
+       case ' ' :
+       case '\t':
+         theChar = (++current != end) ? *current : '\0';
+         break;
+       default:
+         done = true;
+-        AppendUnicodeTo(origin, current, aString);
++        if (!AppendUnicodeTo(origin, current, aString)) {
++          return NS_ERROR_OUT_OF_MEMORY;
++        }
+         break;
+     }
+   }
+ 
+   SetPosition(current);
+   if (current == end) {
+-    AppendUnicodeTo(origin, current, aString);
++    if (!AppendUnicodeTo(origin, current, aString)) {
++      return NS_ERROR_OUT_OF_MEMORY;
++    }
+     result = kEOF;
+   }
+ 
+   aHaveCR = haveCR;
+   return result;
+ }
+ 
+ //XXXbz callers of this have to manage their lone '\r' themselves if they want
+@@ -846,34 +864,38 @@ nsresult nsScanner::ReadUntil(nsAString&
+     if(!(theChar & aEndCondition.mFilter)) {
+       // They were. Do a thorough check.
+ 
+       setcurrent = setstart;
+       while (*setcurrent) {
+         if (*setcurrent == theChar) {
+           if(addTerminal)
+             ++current;
+-          AppendUnicodeTo(origin, current, aString);
++          if (!AppendUnicodeTo(origin, current, aString)) {
++            return NS_ERROR_OUT_OF_MEMORY;
++          }
+           SetPosition(current);
+ 
+           //DoErrTest(aString);
+ 
+           return NS_OK;
+         }
+         ++setcurrent;
+       }
+     }
+     
+     ++current;
+   }
+ 
+   // If we are here, we didn't find any terminator in the string and
+   // current = mEndPosition
+   SetPosition(current);
+-  AppendUnicodeTo(origin, current, aString);
++  if (!AppendUnicodeTo(origin, current, aString)) {
++    return NS_ERROR_OUT_OF_MEMORY;
++  }
+   return kEOF;
+ }
+ 
+ nsresult nsScanner::ReadUntil(nsScannerSharedSubstring& aString,
+                               const nsReadEndCondition& aEndCondition,
+                               bool addTerminal)
+ {  
+   if (!mSlidingBuffer) {
+@@ -906,34 +928,38 @@ nsresult nsScanner::ReadUntil(nsScannerS
+     if(!(theChar & aEndCondition.mFilter)) {
+       // They were. Do a thorough check.
+ 
+       setcurrent = setstart;
+       while (*setcurrent) {
+         if (*setcurrent == theChar) {
+           if(addTerminal)
+             ++current;
+-          AppendUnicodeTo(origin, current, aString);
++          if (!AppendUnicodeTo(origin, current, aString)) {
++            return NS_ERROR_OUT_OF_MEMORY;
++          }
+           SetPosition(current);
+ 
+           //DoErrTest(aString);
+ 
+           return NS_OK;
+         }
+         ++setcurrent;
+       }
+     }
+     
+     ++current;
+   }
+ 
+   // If we are here, we didn't find any terminator in the string and
+   // current = mEndPosition
+   SetPosition(current);
+-  AppendUnicodeTo(origin, current, aString);
++  if (!AppendUnicodeTo(origin, current, aString)) {
++    return NS_ERROR_OUT_OF_MEMORY;
++  }
+   return kEOF;
+ }
+ 
+ nsresult nsScanner::ReadUntil(nsScannerIterator& aStart, 
+                               nsScannerIterator& aEnd,
+                               const nsReadEndCondition &aEndCondition,
+                               bool addTerminal)
+ {
+@@ -1025,26 +1051,30 @@ nsresult nsScanner::ReadUntil(nsAString&
+     if (theChar == '\0') {
+       ReplaceCharacter(current, sInvalid);
+       theChar = sInvalid;
+     }
+ 
+     if (aTerminalChar == theChar) {
+       if(addTerminal)
+         ++current;
+-      AppendUnicodeTo(origin, current, aString);
++      if (!AppendUnicodeTo(origin, current, aString)) {
++        return NS_ERROR_OUT_OF_MEMORY;
++      }
+       SetPosition(current);
+       return NS_OK;
+     }
+     ++current;
+   }
+ 
+   // If we are here, we didn't find any terminator in the string and
+   // current = mEndPosition
+-  AppendUnicodeTo(origin, current, aString);
++  if (!AppendUnicodeTo(origin, current, aString)) {
++    return NS_ERROR_OUT_OF_MEMORY;
++  }
+   SetPosition(current);
+   return kEOF;
+ 
+ }
+ 
+ void nsScanner::BindSubstring(nsScannerSubstring& aSubstring, const nsScannerIterator& aStart, const nsScannerIterator& aEnd)
+ {
+   aSubstring.Rebind(*mSlidingBuffer, aStart, aEnd);
+@@ -1142,29 +1172,29 @@ bool nsScanner::AppendToBuffer(nsScanner
+ }
+ 
+ /**
+  *  call this to copy bytes out of the scanner that have not yet been consumed
+  *  by the tokenization process.
+  *  
+  *  @update  gess 5/12/98
+  *  @param   aCopyBuffer is where the scanner buffer will be copied to
+- *  @return  nada
++ *  @return  true if OK or false on OOM
+  */
+-void nsScanner::CopyUnusedData(nsString& aCopyBuffer) {
++bool nsScanner::CopyUnusedData(nsString& aCopyBuffer) {
+   if (!mSlidingBuffer) {
+     aCopyBuffer.Truncate();
+-    return;
++    return true;
+   }
+ 
+   nsScannerIterator start, end;
+   start = mCurrentPosition;
+   end = mEndPosition;
+ 
+-  CopyUnicodeTo(start, end, aCopyBuffer);
++  return CopyUnicodeTo(start, end, aCopyBuffer);
+ }
+ 
+ /**
+  *  Retrieve the name of the file that the scanner is reading from.
+  *  In some cases, it's just a given name, because the scanner isn't
+  *  really reading from a file.
+  *  
+  *  @update  gess 5/12/98
+diff --git a/parser/htmlparser/nsScanner.h b/parser/htmlparser/nsScanner.h
+--- a/parser/htmlparser/nsScanner.h
++++ b/parser/htmlparser/nsScanner.h
+@@ -204,19 +204,19 @@ class nsScanner {
+                       nsIRequest *aRequest);
+ 
+       /**
+        *  Call this to copy bytes out of the scanner that have not yet been consumed
+        *  by the tokenization process.
+        *  
+        *  @update  gess 5/12/98
+        *  @param   aCopyBuffer is where the scanner buffer will be copied to
+-       *  @return  nada
++       *  @return  true if OK or false on OOM
+        */
+-      void CopyUnusedData(nsString& aCopyBuffer);
++      bool CopyUnusedData(nsString& aCopyBuffer);
+ 
+       /**
+        *  Retrieve the name of the file that the scanner is reading from.
+        *  In some cases, it's just a given name, because the scanner isn't
+        *  really reading from a file.
+        *  
+        *  @update  gess 5/12/98
+        *  @return  
+diff --git a/parser/htmlparser/nsScannerString.cpp b/parser/htmlparser/nsScannerString.cpp
+--- a/parser/htmlparser/nsScannerString.cpp
++++ b/parser/htmlparser/nsScannerString.cpp
+@@ -461,61 +461,63 @@ copy_multifragment_string( nsScannerIter
+         sink_traits::write(result, source_traits::read(first), distance);
+         NS_ASSERTION(distance > 0, "|copy_multifragment_string| will never terminate");
+         source_traits::advance(first, distance);
+       }
+ 
+     return result;
+   }
+ 
+-void
++bool
+ CopyUnicodeTo( const nsScannerIterator& aSrcStart,
+                const nsScannerIterator& aSrcEnd,
+                nsAString& aDest )
+   {
+     nsAString::iterator writer;
+     if (!aDest.SetLength(Distance(aSrcStart, aSrcEnd), mozilla::fallible)) {
+       aDest.Truncate();
+-      return; // out of memory
++      return false; // out of memory
+     }
+     aDest.BeginWriting(writer);
+     nsScannerIterator fromBegin(aSrcStart);
+     
+     copy_multifragment_string(fromBegin, aSrcEnd, writer);
++    return true;
+   }
+ 
+-void
++bool
+ AppendUnicodeTo( const nsScannerIterator& aSrcStart,
+                  const nsScannerIterator& aSrcEnd,
+                  nsScannerSharedSubstring& aDest )
+   {
+     // Check whether we can just create a dependent string.
+     if (aDest.str().IsEmpty()) {
+       // We can just make |aDest| point to the buffer.
+       // This will take care of copying if the buffer spans fragments.
+       aDest.Rebind(aSrcStart, aSrcEnd);
+-    } else {
+-      // The dest string is not empty, so it can't be a dependent substring.
+-      AppendUnicodeTo(aSrcStart, aSrcEnd, aDest.writable());
++      return true;
+     }
++    // The dest string is not empty, so it can't be a dependent substring.
++    return AppendUnicodeTo(aSrcStart, aSrcEnd, aDest.writable());
+   }
+ 
+-void
++bool
+ AppendUnicodeTo( const nsScannerIterator& aSrcStart,
+                  const nsScannerIterator& aSrcEnd,
+                  nsAString& aDest )
+   {
+     nsAString::iterator writer;
+     uint32_t oldLength = aDest.Length();
+     if (!aDest.SetLength(oldLength + Distance(aSrcStart, aSrcEnd), mozilla::fallible))
+-      return; // out of memory
++      return false; // out of memory
+     aDest.BeginWriting(writer).advance(oldLength);
+     nsScannerIterator fromBegin(aSrcStart);
+     
+     copy_multifragment_string(fromBegin, aSrcEnd, writer);
++    return true;
+   }
+ 
+ bool
+ FindCharInReadable( char16_t aChar,
+                     nsScannerIterator& aSearchStart,
+                     const nsScannerIterator& aSearchEnd )
+   {
+     while ( aSearchStart != aSearchEnd )
+diff --git a/parser/htmlparser/nsScannerString.h b/parser/htmlparser/nsScannerString.h
+--- a/parser/htmlparser/nsScannerString.h
++++ b/parser/htmlparser/nsScannerString.h
+@@ -539,43 +539,43 @@ nsScannerBufferList::Position::operator=
+ inline
+ size_t
+ Distance( const nsScannerIterator& aStart, const nsScannerIterator& aEnd )
+   {
+     typedef nsScannerBufferList::Position Position;
+     return Position::Distance(Position(aStart), Position(aEnd));
+   }
+ 
+-void
++bool
+ CopyUnicodeTo( const nsScannerIterator& aSrcStart,
+                const nsScannerIterator& aSrcEnd,
+                nsAString& aDest );
+ 
+ inline
+-void
++bool
+ CopyUnicodeTo( const nsScannerSubstring& aSrc, nsAString& aDest )
+   {
+     nsScannerIterator begin, end;
+-    CopyUnicodeTo(aSrc.BeginReading(begin), aSrc.EndReading(end), aDest);
++    return CopyUnicodeTo(aSrc.BeginReading(begin), aSrc.EndReading(end), aDest);
+   }
+ 
+-void
++bool
+ AppendUnicodeTo( const nsScannerIterator& aSrcStart,
+                  const nsScannerIterator& aSrcEnd,
+                  nsAString& aDest );
+ 
+ inline
+-void
++bool
+ AppendUnicodeTo( const nsScannerSubstring& aSrc, nsAString& aDest )
+   {
+     nsScannerIterator begin, end;
+-    AppendUnicodeTo(aSrc.BeginReading(begin), aSrc.EndReading(end), aDest);
++    return AppendUnicodeTo(aSrc.BeginReading(begin), aSrc.EndReading(end), aDest);
+   }
+ 
+-void
++bool
+ AppendUnicodeTo( const nsScannerIterator& aSrcStart,
+                  const nsScannerIterator& aSrcEnd,
+                  nsScannerSharedSubstring& aDest );
+ 
+ bool
+ FindCharInReadable( char16_t aChar,
+                     nsScannerIterator& aStart,
+                     const nsScannerIterator& aEnd );
+

gnu/packages/patches/icecat-bug-1248851.patch

@@ -0,0 +1,37 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/8c1d40e45a72
+
+# HG changeset patch
+# User Xidorn Quan <quanxunzhen@gmail.com>
+# Date 1456199544 -28800
+# Node ID 8c1d40e45a72c6432e879137a0afa519dc6c9841
+# Parent  1dd0ca8e70bd77b6fd93f36cc4e9c2cebfe8ba0a
+Bug 1248851 - r=sicking, a=ritu
+
+diff --git a/dom/indexedDB/ActorsParent.cpp b/dom/indexedDB/ActorsParent.cpp
+--- a/dom/indexedDB/ActorsParent.cpp
++++ b/dom/indexedDB/ActorsParent.cpp
+@@ -14823,22 +14823,19 @@ ObjectStoreAddOrPutRequestOp::DoDatabase
+     }
+ 
+     snappy::RawCompress(uncompressed, uncompressedLength, compressed,
+                         &compressedLength);
+ 
+     uint8_t* dataBuffer = reinterpret_cast<uint8_t*>(compressed);
+     size_t dataBufferLength = compressedLength;
+ 
+-    // If this call succeeds, | compressed | is now owned by the statement, and
+-    // we are no longer responsible for it.
+     rv = stmt->BindAdoptedBlobByName(NS_LITERAL_CSTRING("data"), dataBuffer,
+                                      dataBufferLength);
+     if (NS_WARN_IF(NS_FAILED(rv))) {
+-      moz_free(compressed);
+       return rv;
+     }
+   }
+ 
+   nsCOMPtr<nsIFile> fileDirectory;
+   nsCOMPtr<nsIFile> journalDirectory;
+ 
+   if (mFileManager) {
+

gnu/packages/patches/icecat-update-graphite2-pt2.patch

@@ -0,0 +1,861 @@
+Copied from upstream:
+https://hg.mozilla.org/releases/mozilla-esr38/raw-rev/ec9cff7bb543
+
+# HG changeset patch
+# User Jonathan Kew <jkew@mozilla.com>
+# Date 1456760339 0
+# Node ID ec9cff7bb5439b2b4c1249ff9376d07a80172c27
+# Parent  6f4d5130238790fa5810c76ffeb9eccc65efa8c9
+Bug 1248876 - Update graphite2 to upstream release 1.3.6. r=jrmuizel a=sledru
+
+diff --git a/gfx/graphite2/README.mozilla b/gfx/graphite2/README.mozilla
+--- a/gfx/graphite2/README.mozilla
++++ b/gfx/graphite2/README.mozilla
+@@ -1,7 +1,3 @@
+-This directory contains the Graphite2 library release 1.3.5 from
+-https://github.com/silnrsi/graphite/releases/download/1.3.5/graphite2-minimal-1.3.5.tgz
++This directory contains the Graphite2 library release 1.3.6 from
++https://github.com/silnrsi/graphite/releases/download/1.3.6/graphite-minimal-1.3.6.tgz
+ See gfx/graphite2/moz-gr-update.sh for update procedure.
+-
+-Also includes two post-1.3.5 fixes:
+-a8b3ac2aed0eb132cd80efe7de88f8153e73c829
+-e569e28d83491fedb31b9220493f3c07f6ec6d80
+diff --git a/gfx/graphite2/include/graphite2/Font.h b/gfx/graphite2/include/graphite2/Font.h
+--- a/gfx/graphite2/include/graphite2/Font.h
++++ b/gfx/graphite2/include/graphite2/Font.h
+@@ -25,17 +25,17 @@
+     either version 2 of the License or (at your option) any later version.
+ */
+ #pragma once
+ 
+ #include "graphite2/Types.h"
+ 
+ #define GR2_VERSION_MAJOR   1
+ #define GR2_VERSION_MINOR   3
+-#define GR2_VERSION_BUGFIX  5
++#define GR2_VERSION_BUGFIX  6
+ 
+ #ifdef __cplusplus
+ extern "C"
+ {
+ #endif
+ 
+ typedef struct gr_face          gr_face;
+ typedef struct gr_font          gr_font;
+diff --git a/gfx/graphite2/moz-gr-update.sh b/gfx/graphite2/moz-gr-update.sh
+--- a/gfx/graphite2/moz-gr-update.sh
++++ b/gfx/graphite2/moz-gr-update.sh
+@@ -14,17 +14,17 @@
+ RELEASE=$1
+ 
+ if [ "x$RELEASE" == "x" ]
+ then
+     echo "Must provide the version number to be used."
+     exit 1
+ fi
+ 
+-TARBALL="https://github.com/silnrsi/graphite/releases/download/$RELEASE/graphite2-minimal-$RELEASE.tgz"
++TARBALL="https://github.com/silnrsi/graphite/releases/download/$RELEASE/graphite-minimal-$RELEASE.tgz"
+ 
+ foo=`basename $0`
+ TMPFILE=`mktemp -t ${foo}` || exit 1
+ 
+ curl -L "$TARBALL" -o "$TMPFILE"
+ tar -x -z -C gfx/graphite2/ --strip-components 1 -f "$TMPFILE" || exit 1
+ rm "$TMPFILE"
+ 
+diff --git a/gfx/graphite2/src/CmapCache.cpp b/gfx/graphite2/src/CmapCache.cpp
+--- a/gfx/graphite2/src/CmapCache.cpp
++++ b/gfx/graphite2/src/CmapCache.cpp
+@@ -33,43 +33,43 @@ of the License or (at your option) any l
+ 
+ 
+ using namespace graphite2;
+ 
+ const void * bmp_subtable(const Face::Table & cmap)
+ {
+     const void * stbl;
+     if (!cmap.size()) return 0;
+-    if (TtfUtil::CheckCmapSubtable4(stbl = TtfUtil::FindCmapSubtable(cmap, 3, 1, cmap.size()), cmap.size())
+-     || TtfUtil::CheckCmapSubtable4(stbl = TtfUtil::FindCmapSubtable(cmap, 0, 3, cmap.size()), cmap.size())
+-     || TtfUtil::CheckCmapSubtable4(stbl = TtfUtil::FindCmapSubtable(cmap, 0, 2, cmap.size()), cmap.size())
+-     || TtfUtil::CheckCmapSubtable4(stbl = TtfUtil::FindCmapSubtable(cmap, 0, 1, cmap.size()), cmap.size())
+-     || TtfUtil::CheckCmapSubtable4(stbl = TtfUtil::FindCmapSubtable(cmap, 0, 0, cmap.size()), cmap.size()))
++    if (TtfUtil::CheckCmapSubtable4(stbl = TtfUtil::FindCmapSubtable(cmap, 3, 1, cmap.size()), cmap + cmap.size())
++     || TtfUtil::CheckCmapSubtable4(stbl = TtfUtil::FindCmapSubtable(cmap, 0, 3, cmap.size()), cmap + cmap.size())
++     || TtfUtil::CheckCmapSubtable4(stbl = TtfUtil::FindCmapSubtable(cmap, 0, 2, cmap.size()), cmap + cmap.size())
++     || TtfUtil::CheckCmapSubtable4(stbl = TtfUtil::FindCmapSubtable(cmap, 0, 1, cmap.size()), cmap + cmap.size())
++     || TtfUtil::CheckCmapSubtable4(stbl = TtfUtil::FindCmapSubtable(cmap, 0, 0, cmap.size()), cmap + cmap.size()))
+         return stbl;
+     return 0;
+ }
+ 
+ const void * smp_subtable(const Face::Table & cmap)
+ {
+     const void * stbl;
+     if (!cmap.size()) return 0;
+-    if (TtfUtil::CheckCmapSubtable12(stbl = TtfUtil::FindCmapSubtable(cmap, 3, 10, cmap.size()), cmap.size())
+-     || TtfUtil::CheckCmapSubtable12(stbl = TtfUtil::FindCmapSubtable(cmap, 0, 4, cmap.size()), cmap.size()))
++    if (TtfUtil::CheckCmapSubtable12(stbl = TtfUtil::FindCmapSubtable(cmap, 3, 10, cmap.size()), cmap + cmap.size())
++     || TtfUtil::CheckCmapSubtable12(stbl = TtfUtil::FindCmapSubtable(cmap, 0, 4, cmap.size()), cmap + cmap.size()))
+         return stbl;
+     return 0;
+ }
+ 
+ template <unsigned int (*NextCodePoint)(const void *, unsigned int, int *),
+           uint16 (*LookupCodePoint)(const void *, unsigned int, int)>
+ bool cache_subtable(uint16 * blocks[], const void * cst, const unsigned int limit)
+ {
+     int rangeKey = 0;
+     uint32          codePoint = NextCodePoint(cst, 0, &rangeKey),
+                     prevCodePoint = 0;
+-    while (codePoint != limit)
++    while (codePoint < limit)
+     {
+         unsigned int block = codePoint >> 8;
+         if (!blocks[block])
+         {
+             blocks[block] = grzeroalloc<uint16>(0x100);
+             if (!blocks[block])
+                 return false;
+         }
+diff --git a/gfx/graphite2/src/Code.cpp b/gfx/graphite2/src/Code.cpp
+--- a/gfx/graphite2/src/Code.cpp
++++ b/gfx/graphite2/src/Code.cpp
+@@ -79,18 +79,19 @@ struct context
+ 
+ 
+ class Machine::Code::decoder
+ {
+ public:
+     struct limits;
+     struct analysis
+     {
++        static const int NUMCONTEXTS = 256;
+         uint8     slotref;
+-        context   contexts[256];
++        context   contexts[NUMCONTEXTS];
+         byte      max_ref;
+         
+         analysis() : slotref(0), max_ref(0) {};
+         void set_ref(int index, bool incinsert=false) throw();
+         void set_noref(int index) throw();
+         void set_changed(int index) throw();
+ 
+     };
+@@ -363,29 +364,33 @@ opcode Machine::Code::decoder::fetch_opc
+             break;
+         case ATTR_SET :
+         case ATTR_ADD :
+         case ATTR_SUB :
+         case ATTR_SET_SLOT :
+             if (--_stack_depth < 0)
+                 failure(underfull_stack);
+             valid_upto(gr_slatMax, bc[0]);
++            if (attrCode(bc[0]) == gr_slatUserDefn)     // use IATTR for user attributes
++                failure(out_of_range_data);
+             test_context();
+             break;
+         case IATTR_SET_SLOT :
+             if (--_stack_depth < 0)
+                 failure(underfull_stack);
+             if (valid_upto(gr_slatMax, bc[0]))
+                 valid_upto(_max.attrid[bc[0]], bc[1]);
+             test_context();
+             break;
+         case PUSH_SLOT_ATTR :
+             ++_stack_depth;
+             valid_upto(gr_slatMax, bc[0]);
+             valid_upto(_rule_length, _pre_context + int8(bc[1]));
++            if (attrCode(bc[0]) == gr_slatUserDefn)     // use IATTR for user attributes
++                failure(out_of_range_data);
+             break;
+         case PUSH_GLYPH_ATTR_OBS :
+             ++_stack_depth;
+             valid_upto(_max.glyf_attrs, bc[0]);
+             valid_upto(_rule_length, _pre_context + int8(bc[1]));
+             break;
+         case PUSH_GLYPH_METRIC :
+             ++_stack_depth;
+@@ -656,24 +661,24 @@ bool Machine::Code::decoder::validate_op
+         return false;
+     }
+     return true;
+ }
+ 
+ 
+ bool Machine::Code::decoder::valid_upto(const uint16 limit, const uint16 x) const throw()
+ {
+-    const bool t = x < limit;
++    const bool t = (limit != 0) && (x < limit);
+     if (!t) failure(out_of_range_data);
+     return t;
+ }
+ 
+ bool Machine::Code::decoder::test_context() const throw()
+ {
+-    if (_pre_context >= _rule_length)
++    if (_pre_context >= _rule_length || _analysis.slotref >= analysis::NUMCONTEXTS - 1)
+     {
+         failure(out_of_range_data);
+         return false;
+     }
+     return true;
+ }
+ 
+ inline 
+@@ -681,34 +686,34 @@ void Machine::Code::failure(const status
+     release_buffers();
+     _status = s;
+ }
+ 
+ 
+ inline
+ void Machine::Code::decoder::analysis::set_ref(int index, bool incinsert) throw() {
+     if (incinsert && contexts[slotref].flags.inserted) --index;
+-    if (index + slotref < 0) return;
++    if (index + slotref < 0 || index + slotref >= NUMCONTEXTS) return;
+     contexts[index + slotref].flags.referenced = true;
+     if ((index > 0 || !contexts[index + slotref].flags.inserted) && index + slotref > max_ref) max_ref = index + slotref;
+ }
+ 
+ 
+ inline
+ void Machine::Code::decoder::analysis::set_noref(int index) throw() {
+     if (contexts[slotref].flags.inserted) --index;
+-    if (index + slotref < 0) return;
++    if (index + slotref < 0 || index + slotref >= NUMCONTEXTS) return;
+     if ((index > 0 || !contexts[index + slotref].flags.inserted) && index + slotref > max_ref) max_ref = index + slotref;
+ }
+ 
+ 
+ inline
+ void Machine::Code::decoder::analysis::set_changed(int index) throw() {
+     if (contexts[slotref].flags.inserted) --index;
+-    if (index + slotref < 0) return;
++    if (index + slotref < 0 || index + slotref >= NUMCONTEXTS) return;
+     contexts[index + slotref].flags.changed = true;
+     if ((index > 0 || !contexts[index + slotref].flags.inserted) && index + slotref > max_ref) max_ref = index + slotref;
+ }
+ 
+ 
+ void Machine::Code::release_buffers() throw()
+ {
+     if (_own)
+diff --git a/gfx/graphite2/src/GlyphCache.cpp b/gfx/graphite2/src/GlyphCache.cpp
+--- a/gfx/graphite2/src/GlyphCache.cpp
++++ b/gfx/graphite2/src/GlyphCache.cpp
+@@ -260,17 +260,17 @@ GlyphCache::Loader::Loader(const Face & 
+         _head = Face::Table();
+         return;
+     }
+ 
+     if (!dumb_font)
+     {
+         if ((m_pGlat = Face::Table(face, Tag::Glat, 0x00030000)) == NULL
+             || (m_pGloc = Face::Table(face, Tag::Gloc)) == NULL
+-            || m_pGloc.size() < 6)
++            || m_pGloc.size() < 8)
+         {
+             _head = Face::Table();
+             return;
+         }
+         const byte    * p = m_pGloc;
+         int       version = be::read<uint32>(p);
+         const uint16    flags = be::read<uint16>(p);
+         _num_attrs = be::read<uint16>(p);
+diff --git a/gfx/graphite2/src/Pass.cpp b/gfx/graphite2/src/Pass.cpp
+--- a/gfx/graphite2/src/Pass.cpp
++++ b/gfx/graphite2/src/Pass.cpp
+@@ -233,17 +233,17 @@ bool Pass::readRules(const byte * rule_m
+     m_codes = new Code [m_numRules*2];
+     const size_t prog_pool_sz = vm::Machine::Code::estimateCodeDataOut(ac_end - ac_data + rc_end - rc_data);
+     m_progs = gralloc<byte>(prog_pool_sz);
+     byte * prog_pool_free = m_progs,
+          * prog_pool_end  = m_progs + prog_pool_sz;
+     if (e.test(!(m_rules && m_codes && m_progs), E_OUTOFMEM)) return face.error(e);
+ 
+     Rule * r = m_rules + m_numRules - 1;
+-    for (size_t n = m_numRules; n; --n, --r, ac_end = ac_begin, rc_end = rc_begin)
++    for (size_t n = m_numRules; r >= m_rules; --n, --r, ac_end = ac_begin, rc_end = rc_begin)
+     {
+         face.error_context((face.error_context() & 0xFFFF00) + EC_ARULE + ((n - 1) << 24));
+         r->preContext = *--precontext;
+         r->sort       = be::peek<uint16>(--sort_key);
+ #ifndef NDEBUG
+         r->rule_idx   = n - 1;
+ #endif
+         if (r->sort > 63 || r->preContext >= r->sort || r->preContext > m_maxPreCtxt || r->preContext < m_minPreCtxt)
+@@ -405,16 +405,17 @@ bool Pass::runGraphite(vm::Machine & m, 
+         json::closer rules_array_closer(fsm.dbgout);
+ #endif
+ 
+         m.slotMap().highwater(currHigh);
+         int lc = m_iMaxLoop;
+         do
+         {
+             findNDoRule(s, m, fsm);
++            if (m.status() != Machine::finished) return false;
+             if (s && (s == m.slotMap().highwater() || m.slotMap().highpassed() || --lc == 0)) {
+                 if (!lc)
+                     s = m.slotMap().highwater();
+                 lc = m_iMaxLoop;
+                 if (s)
+                     m.slotMap().highwater(s->next());
+             }
+         } while (s);
+@@ -495,17 +496,22 @@ void Pass::findNDoRule(Slot * & slot, Ma
+ {
+     assert(slot);
+ 
+     if (runFSM(fsm, slot))
+     {
+         // Search for the first rule which passes the constraint
+         const RuleEntry *        r = fsm.rules.begin(),
+                         * const re = fsm.rules.end();
+-        while (r != re && !testConstraint(*r->rule, m)) ++r;
++        while (r != re && !testConstraint(*r->rule, m))
++        {
++            ++r;
++            if (m.status() != Machine::finished)
++                return;
++        }
+ 
+ #if !defined GRAPHITE2_NTRACING
+         if (fsm.dbgout)
+         {
+             if (fsm.rules.size() != 0)
+             {
+                 *fsm.dbgout << json::item << json::object;
+                 dumpRuleEventConsidered(fsm, *r);
+@@ -530,16 +536,17 @@ void Pass::findNDoRule(Slot * & slot, Ma
+             }
+         }
+         else
+ #endif
+         {
+             if (r != re)
+             {
+                 const int adv = doAction(r->rule->action, slot, m);
++                if (m.status() != Machine::finished) return;
+                 if (r->rule->action->deletes()) fsm.slots.collectGarbage(slot);
+                 adjustSlot(adv, slot, fsm.slots);
+                 return;
+             }
+         }
+     }
+ 
+     slot = slot->next();
+diff --git a/gfx/graphite2/src/Segment.cpp b/gfx/graphite2/src/Segment.cpp
+--- a/gfx/graphite2/src/Segment.cpp
++++ b/gfx/graphite2/src/Segment.cpp
+@@ -205,18 +205,23 @@ Slot *Segment::newSlot()
+ void Segment::freeSlot(Slot *aSlot)
+ {
+     if (m_last == aSlot) m_last = aSlot->prev();
+     if (m_first == aSlot) m_first = aSlot->next();
+     if (aSlot->attachedTo())
+         aSlot->attachedTo()->removeChild(aSlot);
+     while (aSlot->firstChild())
+     {
+-        aSlot->firstChild()->attachTo(NULL);
+-        aSlot->removeChild(aSlot->firstChild());
++        if (aSlot->firstChild()->attachedTo() == aSlot)
++        {
++            aSlot->firstChild()->attachTo(NULL);
++            aSlot->removeChild(aSlot->firstChild());
++        }
++        else
++            aSlot->firstChild(NULL);
+     }
+     // reset the slot incase it is reused
+     ::new (aSlot) Slot(aSlot->userAttrs());
+     memset(aSlot->userAttrs(), 0, m_silf->numUser() * sizeof(int16));
+     // Update generation counter for debug
+ #if !defined GRAPHITE2_NTRACING
+     if (m_face->logger())
+         ++aSlot->userAttrs()[m_silf->numUser()];
+diff --git a/gfx/graphite2/src/Slot.cpp b/gfx/graphite2/src/Slot.cpp
+--- a/gfx/graphite2/src/Slot.cpp
++++ b/gfx/graphite2/src/Slot.cpp
+@@ -192,16 +192,18 @@ int32 Slot::clusterMetric(const Segment 
+ #define SLOTGETCOLATTR(x) { SlotCollision *c = seg->collisionInfo(this); return c ? int(c-> x) : 0; }
+ 
+ int Slot::getAttr(const Segment *seg, attrCode ind, uint8 subindex) const
+ {
+     if (ind == gr_slatUserDefnV1)
+     {
+         ind = gr_slatUserDefn;
+         subindex = 0;
++        if (seg->numAttrs() == 0)
++            return 0;
+     }
+     else if (ind >= gr_slatJStretch && ind < gr_slatJStretch + 20 && ind != gr_slatJWidth)
+     {
+         int indx = ind - gr_slatJStretch;
+         return getJustify(seg, indx / 5, indx % 5);
+     }
+ 
+     switch (ind)
+@@ -269,16 +271,18 @@ int Slot::getAttr(const Segment *seg, at
+         break; }
+ 
+ void Slot::setAttr(Segment *seg, attrCode ind, uint8 subindex, int16 value, const SlotMap & map)
+ {
+     if (ind == gr_slatUserDefnV1)
+     {
+         ind = gr_slatUserDefn;
+         subindex = 0;
++        if (seg->numAttrs() == 0)
++            return;
+     }
+     else if (ind >= gr_slatJStretch && ind < gr_slatJStretch + 20 && ind != gr_slatJWidth)
+     {
+         int indx = ind - gr_slatJStretch;
+         return setJustify(seg, indx / 5, indx % 5, value);
+     }
+ 
+     switch (ind)
+@@ -416,32 +420,32 @@ bool Slot::sibling(Slot *ap)
+ }
+ 
+ bool Slot::removeChild(Slot *ap)
+ {
+     if (this == ap || !m_child) return false;
+     else if (ap == m_child)
+     {
+         Slot *nSibling = m_child->nextSibling();
+-        m_child->sibling(NULL);
++        m_child->removeSibling(nSibling);
+         m_child = nSibling;
+         return true;
+     }
+     else
+         return m_child->removeSibling(ap);
+     return true;
+ }
+ 
+ bool Slot::removeSibling(Slot *ap)
+ {
+     if (this == ap || !m_sibling) return false;
+     else if (ap == m_sibling)
+     {
+         m_sibling = m_sibling->nextSibling();
+-        ap->sibling(NULL);
++        if (m_sibling) ap->removeSibling(m_sibling);
+         return true;
+     }
+     else
+         return m_sibling->removeSibling(ap);
+     return true;
+ }
+ 
+ void Slot::setGlyph(Segment *seg, uint16 glyphid, const GlyphFace * theGlyph)
+diff --git a/gfx/graphite2/src/TtfUtil.cpp b/gfx/graphite2/src/TtfUtil.cpp
+--- a/gfx/graphite2/src/TtfUtil.cpp
++++ b/gfx/graphite2/src/TtfUtil.cpp
+@@ -884,18 +884,19 @@ const void * FindCmapSubtable(const void
+     }
+ 
+     return 0;
+ }
+ 
+ /*----------------------------------------------------------------------------------------------
+     Check the Microsoft Unicode subtable for expected values
+ ----------------------------------------------------------------------------------------------*/
+-bool CheckCmapSubtable4(const void * pCmapSubtable4, size_t table_len /*, unsigned int maxgid*/)
++bool CheckCmapSubtable4(const void * pCmapSubtable4, const void * pCmapEnd /*, unsigned int maxgid*/)
+ {
++    size_t table_len = (const byte *)pCmapEnd - (const byte *)pCmapSubtable4;
+     if (!pCmapSubtable4) return false;
+     const Sfnt::CmapSubTable * pTable = reinterpret_cast<const Sfnt::CmapSubTable *>(pCmapSubtable4);
+     // Bob H say some freeware TT fonts have version 1 (eg, CALIGULA.TTF) 
+     // so don't check subtable version. 21 Mar 2002 spec changes version to language.
+     if (be::swap(pTable->format) != 4) return false;
+     const Sfnt::CmapSubTableFormat4 * pTable4 = reinterpret_cast<const Sfnt::CmapSubTableFormat4 *>(pCmapSubtable4);
+     uint16 length = be::swap(pTable4->length);
+     if (length > table_len)
+@@ -1044,17 +1045,17 @@ unsigned int CmapSubtable4NextCodepoint(
+             *pRangeKey = nRange - 1;
+         return 0xFFFF;
+     }
+ 
+     int iRange = (pRangeKey) ? *pRangeKey : 0;
+     // Just in case we have a bad key:
+     while (iRange > 0 && be::peek<uint16>(pStartCode + iRange) > nUnicodePrev)
+         iRange--;
+-    while (be::peek<uint16>(pTable->end_code + iRange) < nUnicodePrev)
++    while (iRange < nRange - 1 && be::peek<uint16>(pTable->end_code + iRange) < nUnicodePrev)
+         iRange++;
+ 
+     // Now iRange is the range containing nUnicodePrev.
+     unsigned int nStartCode = be::peek<uint16>(pStartCode + iRange);
+     unsigned int nEndCode = be::peek<uint16>(pTable->end_code + iRange);
+ 
+     if (nStartCode > nUnicodePrev)
+         // Oops, nUnicodePrev is not in the cmap! Adjust so we get a reasonable
+@@ -1069,36 +1070,37 @@ unsigned int CmapSubtable4NextCodepoint(
+         return nUnicodePrev + 1;
+     }
+ 
+     // Otherwise the next codepoint is the first one in the next range.
+     // There is guaranteed to be a next range because there must be one that
+     // ends with 0xFFFF.
+     if (pRangeKey)
+         *pRangeKey = iRange + 1;
+-    return be::peek<uint16>(pStartCode + iRange + 1);
++    return (iRange + 1 >= nRange) ? 0xFFFF : be::peek<uint16>(pStartCode + iRange + 1);
+ }
+ 
+ /*----------------------------------------------------------------------------------------------
+     Check the Microsoft UCS-4 subtable for expected values.
+ ----------------------------------------------------------------------------------------------*/
+-bool CheckCmapSubtable12(const void *pCmapSubtable12, size_t table_len /*, unsigned int maxgid*/)
++bool CheckCmapSubtable12(const void *pCmapSubtable12, const void *pCmapEnd /*, unsigned int maxgid*/)
+ {
++    size_t table_len = (const byte *)pCmapEnd - (const byte *)pCmapSubtable12;
+     if (!pCmapSubtable12)  return false;
+     const Sfnt::CmapSubTable * pTable = reinterpret_cast<const Sfnt::CmapSubTable *>(pCmapSubtable12);
+     if (be::swap(pTable->format) != 12)
+         return false;
+     const Sfnt::CmapSubTableFormat12 * pTable12 = reinterpret_cast<const Sfnt::CmapSubTableFormat12 *>(pCmapSubtable12);
+     uint32 length = be::swap(pTable12->length);
+     if (length > table_len)
+         return false;
+     if (length < sizeof(Sfnt::CmapSubTableFormat12))
+         return false;
+     uint32 num_groups = be::swap(pTable12->num_groups);
+-    if (length != (sizeof(Sfnt::CmapSubTableFormat12) + (num_groups - 1) * sizeof(uint32) * 3))
++    if (num_groups > 0x10000000 || length != (sizeof(Sfnt::CmapSubTableFormat12) + (num_groups - 1) * sizeof(uint32) * 3))
+         return false;
+ #if 0
+     for (unsigned int i = 0; i < num_groups; ++i)
+     {
+         if (be::swap(pTable12->group[i].end_char_code)  - be::swap(pTable12->group[i].start_char_code) + be::swap(pTable12->group[i].start_glyph_id) > maxgid)
+             return false;
+         if (i > 0 && be::swap(pTable12->group[i].start_char_code) <= be::swap(pTable12->group[i-1].end_char_code))
+             return false;
+@@ -1161,17 +1163,17 @@ unsigned int CmapSubtable12NextCodepoint
+             *pRangeKey = nRange;
+         return 0x10FFFF;
+     }
+ 
+     int iRange = (pRangeKey) ? *pRangeKey : 0;
+     // Just in case we have a bad key:
+     while (iRange > 0 && be::swap(pTable->group[iRange].start_char_code) > nUnicodePrev)
+         iRange--;
+-    while (be::swap(pTable->group[iRange].end_char_code) < nUnicodePrev)
++    while (iRange < nRange - 1 && be::swap(pTable->group[iRange].end_char_code) < nUnicodePrev)
+         iRange++;
+ 
+     // Now iRange is the range containing nUnicodePrev.
+ 
+     unsigned int nStartCode = be::swap(pTable->group[iRange].start_char_code);
+     unsigned int nEndCode = be::swap(pTable->group[iRange].end_char_code);
+ 
+     if (nStartCode > nUnicodePrev)
+diff --git a/gfx/graphite2/src/call_machine.cpp b/gfx/graphite2/src/call_machine.cpp
+--- a/gfx/graphite2/src/call_machine.cpp
++++ b/gfx/graphite2/src/call_machine.cpp
+@@ -67,32 +67,34 @@ using namespace vm;
+ struct regbank  {
+     slotref         is;
+     slotref *       map;
+     SlotMap       & smap;
+     slotref * const map_base;
+     const instr * & ip;
+     uint8           direction;
+     int8            flags;
++    Machine::status_t & status;
+ };
+ 
+ typedef bool        (* ip_t)(registers);
+ 
+ // Pull in the opcode definitions
+ // We pull these into a private namespace so these otherwise common names dont
+ // pollute the toplevel namespace.
+ namespace {
+ #define smap    reg.smap
+ #define seg     smap.segment
+ #define is      reg.is
+ #define ip      reg.ip
+ #define map     reg.map
+ #define mapb    reg.map_base
+ #define flags   reg.flags
+ #define dir     reg.direction
++#define status  reg.status
+ 
+ #include "inc/opcodes.h"
+ 
+ #undef smap
+ #undef seg
+ #undef is
+ #undef ip
+ #undef map
+@@ -108,17 +110,17 @@ Machine::stack_t  Machine::run(const ins
+ {
+     assert(program != 0);
+ 
+     // Declare virtual machine registers
+     const instr   * ip = program-1;
+     const byte    * dp = data;
+     stack_t       * sp = _stack + Machine::STACK_GUARD,
+             * const sb = sp;
+-    regbank         reg = {*map, map, _map, _map.begin()+_map.context(), ip, _map.dir(), 0};
++    regbank         reg = {*map, map, _map, _map.begin()+_map.context(), ip, _map.dir(), 0, _status};
+ 
+     // Run the program        
+     while ((reinterpret_cast<ip_t>(*++ip))(dp, sp, sb, reg)) {}
+     const stack_t ret = sp == _stack+STACK_GUARD+1 ? *sp-- : 0;
+ 
+     check_final_stack(sp);
+     map = reg.map;
+     *map = reg.is;
+diff --git a/gfx/graphite2/src/direct_machine.cpp b/gfx/graphite2/src/direct_machine.cpp
+--- a/gfx/graphite2/src/direct_machine.cpp
++++ b/gfx/graphite2/src/direct_machine.cpp
+@@ -57,36 +57,37 @@ using namespace vm;
+ namespace {
+ 
+ const void * direct_run(const bool          get_table_mode,
+                         const instr       * program,
+                         const byte        * data,
+                         Machine::stack_t  * stack,
+                         slotref         * & __map,
+                         uint8                _dir,
++                        Machine::status_t & status,
+                         SlotMap           * __smap=0)
+ {
+     // We need to define and return to opcode table from within this function 
+     // other inorder to take the addresses of the instruction bodies.
+     #include "inc/opcode_table.h"
+     if (get_table_mode)
+         return opcode_table;
+ 
+     // Declare virtual machine registers
+-    const instr       * ip = program;
+-    const byte        * dp = data;
+-    Machine::stack_t  * sp = stack + Machine::STACK_GUARD,
+-                * const sb = sp;
+-    SlotMap         & smap = *__smap;
+-    Segment          & seg = smap.segment;
+-    slotref             is = *__map,
+-                     * map = __map,
+-              * const mapb = smap.begin()+smap.context();
+-    uint8            dir = _dir;
+-    int8             flags = 0;
++    const instr           * ip = program;
++    const byte            * dp = data;
++    Machine::stack_t      * sp = stack + Machine::STACK_GUARD,
++                    * const sb = sp;
++    SlotMap             & smap = *__smap;
++    Segment              & seg = smap.segment;
++    slotref                 is = *__map,
++                         * map = __map,
++                  * const mapb = smap.begin()+smap.context();
++    uint8                  dir = _dir;
++    int8                 flags = 0;
+     
+     // start the program
+     goto **ip;
+ 
+     // Pull in the opcode definitions
+     #include "inc/opcodes.h"
+     
+     end:
+@@ -95,25 +96,26 @@ const void * direct_run(const bool      
+     return sp;
+ }
+ 
+ }
+ 
+ const opcode_t * Machine::getOpcodeTable() throw()
+ {
+     slotref * dummy;
+-    return static_cast<const opcode_t *>(direct_run(true, 0, 0, 0, dummy, 0));
++    Machine::status_t dumstat = Machine::finished;
++    return static_cast<const opcode_t *>(direct_run(true, 0, 0, 0, dummy, 0, dumstat));
+ }
+ 
+ 
+ Machine::stack_t  Machine::run(const instr   * program,
+                                const byte    * data,
+                                slotref     * & is)
+ {
+     assert(program != 0);
+     
+     const stack_t *sp = static_cast<const stack_t *>(
+-                direct_run(false, program, data, _stack, is, _map.dir(), &_map));
++                direct_run(false, program, data, _stack, is, _map.dir(), _status, &_map));
+     const stack_t ret = sp == _stack+STACK_GUARD+1 ? *sp-- : 0;
+     check_final_stack(sp);
+     return ret;
+ }
+ 
+diff --git a/gfx/graphite2/src/inc/Code.h b/gfx/graphite2/src/inc/Code.h
+--- a/gfx/graphite2/src/inc/Code.h
++++ b/gfx/graphite2/src/inc/Code.h
+@@ -109,17 +109,17 @@ public:
+     int32 run(Machine &m, slotref * & map) const;
+     
+     CLASS_NEW_DELETE;
+ };
+ 
+ inline
+ size_t  Machine::Code::estimateCodeDataOut(size_t n_bc)
+ {
+-    return n_bc * (sizeof(instr)+sizeof(byte));
++    return (n_bc + 1) * (sizeof(instr)+sizeof(byte));
+ }
+ 
+ 
+ inline Machine::Code::Code() throw()
+ : _code(0), _data(0), _data_size(0), _instr_count(0), _max_ref(0),
+   _status(loaded), _constraint(false), _modify(false), _delete(false),
+   _own(false)
+ {
+diff --git a/gfx/graphite2/src/inc/Machine.h b/gfx/graphite2/src/inc/Machine.h
+--- a/gfx/graphite2/src/inc/Machine.h
++++ b/gfx/graphite2/src/inc/Machine.h
+@@ -135,17 +135,18 @@ public:
+ 
+     class Code;
+ 
+     enum status_t {
+         finished = 0,
+         stack_underflow,
+         stack_not_empty,
+         stack_overflow,
+-        slot_offset_out_bounds
++        slot_offset_out_bounds,
++        died_early
+     };
+ 
+     Machine(SlotMap &) throw();
+     static const opcode_t *   getOpcodeTable() throw();
+ 
+     CLASS_NEW_DELETE;
+ 
+     SlotMap   & slotMap() const throw();
+diff --git a/gfx/graphite2/src/inc/TtfUtil.h b/gfx/graphite2/src/inc/TtfUtil.h
+--- a/gfx/graphite2/src/inc/TtfUtil.h
++++ b/gfx/graphite2/src/inc/TtfUtil.h
+@@ -132,21 +132,21 @@ public:
+     int GetLangsForNames(const void * pName, int nPlatformId, int nEncodingId,
+         int *nameIdList, int cNameIds, short *langIdList);
+     void SwapWString(void * pWStr, size_t nSize = 0); // throw (std::invalid_argument);
+ #endif
+ 
+     ////////////////////////////////// cmap lookup tools 
+     const void * FindCmapSubtable(const void * pCmap, int nPlatformId = 3, 
+         int nEncodingId = 1, size_t length = 0);
+-    bool CheckCmapSubtable4(const void * pCmap31, size_t table_len /*, unsigned int maxgid*/);
++    bool CheckCmapSubtable4(const void * pCmap31, const void * pCmapEnd /*, unsigned int maxgid*/);
+     gid16 CmapSubtable4Lookup(const void * pCmapSubtabel4, unsigned int nUnicodeId, int rangeKey = 0);
+     unsigned int CmapSubtable4NextCodepoint(const void *pCmap31, unsigned int nUnicodeId,
+         int * pRangeKey = 0);
+-    bool CheckCmapSubtable12(const void *pCmap310, size_t table_len /*, unsigned int maxgid*/);
++    bool CheckCmapSubtable12(const void *pCmap310, const void * pCmapEnd /*, unsigned int maxgid*/);
+     gid16 CmapSubtable12Lookup(const void * pCmap310, unsigned int uUnicodeId, int rangeKey = 0);
+     unsigned int CmapSubtable12NextCodepoint(const void *pCmap310, unsigned int nUnicodeId,
+         int * pRangeKey = 0);
+ 
+     ///////////////////////////////// horizontal metric data for a glyph
+     bool HorMetrics(gid16 nGlyphId, const void * pHmtx, size_t lHmtxSize, 
+         const void * pHhea, int & nLsb, unsigned int & nAdvWid);
+ 
+diff --git a/gfx/graphite2/src/inc/opcodes.h b/gfx/graphite2/src/inc/opcodes.h
+--- a/gfx/graphite2/src/inc/opcodes.h
++++ b/gfx/graphite2/src/inc/opcodes.h
+@@ -71,17 +71,17 @@ of the License or (at your option) any l
+ #define use_params(n)       dp += n
+ 
+ #define declare_params(n)   const byte * param = dp; \
+                             use_params(n);
+ 
+ #define push(n)             { *++sp = n; }
+ #define pop()               (*sp--)
+ #define slotat(x)           (map[(x)])
+-#define DIE                 { is=seg.last(); EXIT(1); }
++#define DIE                 { is=seg.last(); status = Machine::died_early; EXIT(1); }
+ #define POSITIONED          1
+ 
+ STARTOP(nop)
+     do {} while (0);
+ ENDOP
+ 
+ STARTOP(push_byte)
+     declare_params(1);
+@@ -387,30 +387,30 @@ STARTOP(attr_set)
+ ENDOP
+ 
+ STARTOP(attr_add)
+     declare_params(1);
+     const attrCode      slat = attrCode(uint8(*param));
+     const          int  val  = int(pop());
+     if ((slat == gr_slatPosX || slat == gr_slatPosY) && (flags & POSITIONED) == 0)
+     {
+-        seg.positionSlots(0, *smap.begin(), *(smap.end()-1), dir);
++        seg.positionSlots(0, *smap.begin(), *(smap.end()-1), seg.currdir());
+         flags |= POSITIONED;
+     }
+     int res = is->getAttr(&seg, slat, 0);
+     is->setAttr(&seg, slat, 0, val + res, smap);
+ ENDOP
+ 
+ STARTOP(attr_sub)
+     declare_params(1);
+     const attrCode      slat = attrCode(uint8(*param));
+     const          int  val  = int(pop());
+     if ((slat == gr_slatPosX || slat == gr_slatPosY) && (flags & POSITIONED) == 0)
+     {
+-        seg.positionSlots(0, *smap.begin(), *(smap.end()-1), dir);
++        seg.positionSlots(0, *smap.begin(), *(smap.end()-1), seg.currdir());
+         flags |= POSITIONED;
+     }
+     int res = is->getAttr(&seg, slat, 0);
+     is->setAttr(&seg, slat, 0, res - val, smap);
+ ENDOP
+ 
+ STARTOP(attr_set_slot)
+     declare_params(1);
+@@ -429,17 +429,17 @@ STARTOP(iattr_set_slot)
+ ENDOP
+ 
+ STARTOP(push_slot_attr)
+     declare_params(2);
+     const attrCode      slat     = attrCode(uint8(param[0]));
+     const int           slot_ref = int8(param[1]);
+     if ((slat == gr_slatPosX || slat == gr_slatPosY) && (flags & POSITIONED) == 0)
+     {
+-        seg.positionSlots(0, *smap.begin(), *(smap.end()-1), dir);
++        seg.positionSlots(0, *smap.begin(), *(smap.end()-1), seg.currdir());
+         flags |= POSITIONED;
+     }
+     slotref slot = slotat(slot_ref);
+     if (slot)
+     {
+         int res = slot->getAttr(&seg, slat, 0);
+         push(res);
+     }
+@@ -505,17 +505,17 @@ ENDOP
+ 
+ STARTOP(push_islot_attr)
+     declare_params(3);
+     const attrCode  slat     = attrCode(uint8(param[0]));
+     const int           slot_ref = int8(param[1]),
+                         idx      = uint8(param[2]);
+     if ((slat == gr_slatPosX || slat == gr_slatPosY) && (flags & POSITIONED) == 0)
+     {
+-        seg.positionSlots(0, *smap.begin(), *(smap.end()-1), dir);
++        seg.positionSlots(0, *smap.begin(), *(smap.end()-1), seg.currdir());
+         flags |= POSITIONED;
+     }
+     slotref slot = slotat(slot_ref);
+     if (slot)
+     {
+         int res = slot->getAttr(&seg, slat, idx);
+         push(res);
+     }
+

gnu/packages/patches/ilmbase-fix-tests.patch

@@ -0,0 +1,149 @@
+Fix FTBFS on i686-linux due to rounding issue (see references).
+
+Fixes Guix bug #22049 (see below).
+
+Copied from Debian.
+
+Source:
+https://sources.debian.net/src/ilmbase/2.2.0-11/debian/patches/testBoxAlgo.patch/
+https://sources.debian.net/src/ilmbase/2.2.0-11/debian/patches/testBox.patch/
+
+References:
+https://lists.nongnu.org/archive/html/openexr-devel/2015-12/msg00001.html
+https://debbugs.gnu.org/cgi/bugreport.cgi?bug=22049
+https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=815712
+https://anonscm.debian.org/cgit/pkg-phototools/ilmbase.git/commit/?id=ab28bb45cdad8adc32e345b777ab8e692b1d9a9c
+
+---
+
+Subject: testBoxAlgo: allow fuzzy match of b12 == b2
+From: Steven Chamberlain <steven@pyro.eu.org>
+Date: Wed, 24 Feb 2016 01:04:11 +0000
+
+Also fix a pre-existing typo.
+
+Index: ilmbase/ImathTest/testBoxAlgo.cpp
+===================================================================
+--- ilmbase.orig/ImathTest/testBoxAlgo.cpp
++++ ilmbase/ImathTest/testBoxAlgo.cpp
+@@ -886,10 +886,11 @@ boxMatrixTransform ()
+ 
+     assert (approximatelyEqual (b2.min, b4.min, e));
+     assert (approximatelyEqual (b2.max, b4.max, e));
+-    assert (approximatelyEqual (b3.max, b4.max, e));
++    assert (approximatelyEqual (b3.min, b4.min, e));
+     assert (approximatelyEqual (b3.max, b4.max, e));
+ 
+-    assert (b21 == b2);
++    assert (approximatelyEqual (b2.min, b21.min, e));
++    assert (approximatelyEqual (b2.max, b21.max, e));
+     assert (b31 == b3);
+ 
+     M[0][3] = 1;
+
+---
+
+Subject: testBox: allow fuzzy comparison of floats, doubles
+From: Steven Chamberlain <steven@pyro.eu.org>
+Date: Wed, 24 Feb 2016 01:10:11 +0000
+
+Allow for inexact values, as long as the error is smaller than the
+epsilon of the data type.
+
+On 32-bit x86, allow even greater discrepency at double
+precision, due to possible double-rounding.  See
+https://lists.nongnu.org/archive/html/openexr-devel/2015-12/msg00001.html
+
+Index: ilmbase/ImathTest/testBox.cpp
+===================================================================
+--- ilmbase.orig/ImathTest/testBox.cpp
++++ ilmbase/ImathTest/testBox.cpp
+@@ -47,6 +47,58 @@ using namespace IMATH_INTERNAL_NAMESPACE
+ 
+ namespace {
+ 
++template <class T>
++bool
++approximatelyEqual (const T &p1, const T &p2)
++{
++	/* int and short should be exact */
++	return (p1 == p2);
++}
++
++bool
++approximatelyEqual (const Vec2<float> &p1, const Vec2<float> &p2)
++{
++    float e = limits<float>::epsilon();
++    float m = 0;
++
++    for (int i = 0; i < 2; ++i)
++    {
++	m = max (m, abs (p1[i]));
++	m = max (m, abs (p2[i]));
++    }
++
++    for (int i = 0; i < 2; ++i)
++	if (!equalWithAbsError (p1[i], p2[i], m * e))
++	    return false;
++
++    return true;
++}
++
++bool
++approximatelyEqual (const Vec2<double> &p1, const Vec2<double> &p2)
++{
++#if defined(__i386__) || defined(_M_IX86)
++    /* double-rounding on 32-bit x86 may cause larger error:
++       use epsilon of float rather than double */
++    double e = limits<float>::epsilon();
++#else
++    double e = limits<double>::epsilon();
++#endif
++    double m = 0;
++
++    for (int i = 0; i < 2; ++i)
++    {
++	m = max (m, abs (p1[i]));
++	m = max (m, abs (p2[i]));
++    }
++
++    for (int i = 0; i < 2; ++i)
++	if (!equalWithAbsError (p1[i], p2[i], m * e))
++	    return false;
++
++    return true;
++}
++
+ //
+ // Test case generation utility - create a vector of IMATH_INTERNAL_NAMESPACE::Vec{2,3,4}
+ // with all permutations of integers 1..T::dimensions().
+@@ -250,7 +302,8 @@ testExtendByPoint(const char *type)
+                               
+         IMATH_INTERNAL_NAMESPACE::Box<T> b;
+         b.extendBy(p);
+-        assert(b.min == p && b.max == p);
++        assert (approximatelyEqual (b.min, p));
++        assert (approximatelyEqual (b.max, p));
+     }
+ 
+     //
+@@ -283,7 +336,8 @@ testExtendByPoint(const char *type)
+ 
+             b.extendBy(p);
+ 
+-            assert(b.min == min && b.max == max);
++            assert (approximatelyEqual (b.min, min));
++            assert (approximatelyEqual (b.max, max));
+         }
+     }
+ }
+@@ -358,7 +412,8 @@ testExtendByBox(const char *type)
+             }
+             b.extendBy(IMATH_INTERNAL_NAMESPACE::Box<T>(p0, p1));
+ 
+-            assert(b.min == min && b.max == max);
++            assert (approximatelyEqual (b.min, min));
++            assert (approximatelyEqual (b.max, max));
+         }
+     }
+ }

gnu/packages/patches/jasper-CVE-2016-1577.patch

@@ -0,0 +1,19 @@
+Description: CVE-2016-1577: Prevent double-free in jas_iccattrval_destroy()
+Origin: vendor, http://www.openwall.com/lists/oss-security/2016/03/03/12
+Bug-Ubuntu: https://launchpad.net/bugs/1547865
+Bug-Debian: https://bugs.debian.org/816625
+Forwarded: not-needed
+Author: Tyler Hicks <tyhicks@canonical.com>
+Reviewed-by: Salvatore Bonaccorso <carnil@debian.org>
+Last-Update: 2016-03-05
+
+--- a/src/libjasper/base/jas_icc.c
++++ b/src/libjasper/base/jas_icc.c
+@@ -300,6 +300,7 @@ jas_iccprof_t *jas_iccprof_load(jas_stre
+ 				if (jas_iccprof_setattr(prof, tagtabent->tag, attrval))
+ 					goto error;
+ 				jas_iccattrval_destroy(attrval);
++				attrval = 0;
+ 			} else {
+ #if 0
+ 				jas_eprintf("warning: skipping unknown tag type\n");

gnu/packages/patches/jasper-CVE-2016-2089.patch

@@ -0,0 +1,90 @@
+Description: CVE-2016-2089: matrix rows_ NULL pointer dereference in jas_matrix_clip()
+Origin: vendor
+Bug-RedHat: https://bugzilla.redhat.com/show_bug.cgi?id=1302636
+Bug-Debian: https://bugs.debian.org/812978
+Forwarded: not-needed
+Author: Tomas Hoger <thoger@redhat.com>
+Reviewed-by: Salvatore Bonaccorso <carnil@debian.org>
+Last-Update: 2016-03-05
+
+--- a/src/libjasper/base/jas_image.c
++++ b/src/libjasper/base/jas_image.c
+@@ -426,6 +426,10 @@ int jas_image_readcmpt(jas_image_t *imag
+ 		return -1;
+ 	}
+ 
++	if (!data->rows_) {
++		return -1;
++	}
++
+ 	if (jas_matrix_numrows(data) != height || jas_matrix_numcols(data) != width) {
+ 		if (jas_matrix_resize(data, height, width)) {
+ 			return -1;
+@@ -479,6 +483,10 @@ int jas_image_writecmpt(jas_image_t *ima
+ 		return -1;
+ 	}
+ 
++	if (!data->rows_) {
++		return -1;
++	}
++
+ 	if (jas_matrix_numrows(data) != height || jas_matrix_numcols(data) != width) {
+ 		return -1;
+ 	}
+--- a/src/libjasper/base/jas_seq.c
++++ b/src/libjasper/base/jas_seq.c
+@@ -262,6 +262,10 @@ void jas_matrix_divpow2(jas_matrix_t *ma
+ 	int rowstep;
+ 	jas_seqent_t *data;
+ 
++	if (!matrix->rows_) {
++		return;
++	}
++
+ 	rowstep = jas_matrix_rowstep(matrix);
+ 	for (i = matrix->numrows_, rowstart = matrix->rows_[0]; i > 0; --i,
+ 	  rowstart += rowstep) {
+@@ -282,6 +286,10 @@ void jas_matrix_clip(jas_matrix_t *matri
+ 	jas_seqent_t *data;
+ 	int rowstep;
+ 
++	if (!matrix->rows_) {
++		return;
++	}
++
+ 	rowstep = jas_matrix_rowstep(matrix);
+ 	for (i = matrix->numrows_, rowstart = matrix->rows_[0]; i > 0; --i,
+ 	  rowstart += rowstep) {
+@@ -306,6 +314,10 @@ void jas_matrix_asr(jas_matrix_t *matrix
+ 	int rowstep;
+ 	jas_seqent_t *data;
+ 
++	if (!matrix->rows_) {
++		return;
++	}
++
+ 	assert(n >= 0);
+ 	rowstep = jas_matrix_rowstep(matrix);
+ 	for (i = matrix->numrows_, rowstart = matrix->rows_[0]; i > 0; --i,
+@@ -325,6 +337,10 @@ void jas_matrix_asl(jas_matrix_t *matrix
+ 	int rowstep;
+ 	jas_seqent_t *data;
+ 
++	if (!matrix->rows_) {
++		return;
++	}
++
+ 	rowstep = jas_matrix_rowstep(matrix);
+ 	for (i = matrix->numrows_, rowstart = matrix->rows_[0]; i > 0; --i,
+ 	  rowstart += rowstep) {
+@@ -367,6 +383,10 @@ void jas_matrix_setall(jas_matrix_t *mat
+ 	int rowstep;
+ 	jas_seqent_t *data;
+ 
++	if (!matrix->rows_) {
++		return;
++	}
++
+ 	rowstep = jas_matrix_rowstep(matrix);
+ 	for (i = matrix->numrows_, rowstart = matrix->rows_[0]; i > 0; --i,
+ 	  rowstart += rowstep) {

gnu/packages/patches/jasper-CVE-2016-2116.patch

@@ -0,0 +1,19 @@
+Description: CVE-2016-2116: Prevent jas_stream_t memory leak in jas_iccprof_createfrombuf()
+Origin: vendor, http://www.openwall.com/lists/oss-security/2016/03/03/12
+Bug-Debian: https://bugs.debian.org/816626
+Forwarded: not-needed
+Author: Tyler Hicks <tyhicks@canoonical.com>
+Reviewed-by: Salvatore Bonaccorso <carnil@debian.org>
+Last-Update: 2016-03-05
+
+--- a/src/libjasper/base/jas_icc.c
++++ b/src/libjasper/base/jas_icc.c
+@@ -1693,6 +1693,8 @@ jas_iccprof_t *jas_iccprof_createfrombuf
+ 	jas_stream_close(in);
+ 	return prof;
+ error:
++	if (in)
++		jas_stream_close(in);
+ 	return 0;
+ }
+