guix-install.sh: Use the "ci.guix.info.pub" file name for clarity.

* etc/guix-install.sh (sys_authorize_build_farms): Use the "ci.guix.info.pub" file name rather "berlin.guixsd.org.pub".
services: guix-daemon: Fix authorization of multiple keys.
2026-07-07 20:34:06 +02:00 · 2018-12-05 16:26:55 +01:00 · 2018-12-05 16:24:50 +01:00 · 2018-12-05 00:11:22 +01:00 · 2018-12-05 00:08:34 +01:00 · 2018-12-05 00:08:28 +01:00
761 changed files with 173479 additions and 73413 deletions
@@ -45,6 +45,7 @@
   (eval . (put 'manifest-pattern 'scheme-indent-function 0))
   (eval . (put 'substitute-keyword-arguments 'scheme-indent-function 1))
   (eval . (put 'with-store 'scheme-indent-function 1))
+   (eval . (put 'with-external-store 'scheme-indent-function 1))
   (eval . (put 'with-error-handling 'scheme-indent-function 0))
   (eval . (put 'with-mutex 'scheme-indent-function 1))
   (eval . (put 'with-atomic-file-output 'scheme-indent-function 1))
@@ -59,6 +60,7 @@
   (eval . (put 'emacs-substitute-variables 'scheme-indent-function 1))
   (eval . (put 'with-derivation-narinfo 'scheme-indent-function 1))
   (eval . (put 'with-derivation-substitute 'scheme-indent-function 2))
+   (eval . (put 'with-status-report 'scheme-indent-function 1))

   (eval . (put 'mlambda 'scheme-indent-function 1))
   (eval . (put 'mlambdaq 'scheme-indent-function 1))
@@ -90,7 +90,7 @@
 /nix/config.h.in
 /nix/nix-daemon/nix-daemon.cc
 /nix/nix-setuid-helper/nix-setuid-helper.cc
-/nix/scripts/guix-authenticate
+/nix/scripts/authenticate
 /nix/scripts/list-runtime-roots
 /nix/scripts/offload
 /nix/scripts/substitute
@@ -43,6 +43,7 @@ Mathieu Lirzin <mthl@gnu.org> <mathieu.lirzin@openmailbox.org>
 Mathieu Othacehe <m.othacehe@gmail.com>
 Nikita Karetnikov <nikita@karetnikov.org> <nikita.karetnikov@gmail.com>
 Nils Gillmann <ng0@n0.is> ng0 <ng0@n0.is>
+Nils Gillmann <ng0@n0.is> Nils Gillmann <gillmann@infotropique.org>
 Nils Gillmann <ng0@n0.is> ng0 <ng0@crash.cx>
 Nils Gillmann <ng0@n0.is> ng0 <ng0@crash.cx>
 Nils Gillmann <ng0@n0.is> <ng0@infotropique.org>
@@ -55,6 +56,8 @@ Nils Gillmann <ng0@n0.is> <ngillmann@runbox.com>
 Nils Gillmann <ng0@n0.is> <niasterisk@grrlz.net>
 Nils Gillmann <ng0@n0.is> <ng@niasterisk.space>
 Nils Gillmann <ng0@n0.is> <ng0@libertad.pw>
+Pierre Neidhardt <mail@ambrevar.xyz>
+Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
 Pjotr Prins <pjotr.guix@thebird.nl> <pjotr.public01@thebird.nl>
 Pjotr Prins <pjotr.guix@thebird.nl> <pjotr.public12@thebird.nl>
 Pjotr Prins <pjotr.guix@thebird.nl> <pjotr.public12@email>
@@ -27,7 +27,7 @@ mailing list.  When you get commit access, please make sure to follow the
 policy below (discussions of the policy can take place on guix-devel@gnu.org.)

 Non-trivial patches should always be posted to guix-patches@gnu.org (trivial
-patches include fixing typos, etc.)  This mailing list fills the
+patches include fixing typos, etc.).  This mailing list fills the
 patch-tracking database at [[https://bugs.gnu.org/guix-patches]]; see
 "Contributing" in the manual for details.

@@ -12,6 +12,7 @@
 # Copyright © 2018 Nils Gillmann <ng0@n0.is>
 # Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
 # Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+# Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 #
 # This file is part of GNU Guix.
 #
@@ -61,11 +62,10 @@ MODULES =					\
  guix/base16.scm				\
  guix/base32.scm				\
  guix/base64.scm				\
+  guix/ci.scm					\
  guix/cpio.scm					\
+  guix/docker.scm	   			\
  guix/records.scm				\
-  guix/gcrypt.scm				\
-  guix/hash.scm					\
-  guix/pk-crypto.scm				\
  guix/pki.scm					\
  guix/progress.scm				\
  guix/combinators.scm				\
@@ -77,6 +77,7 @@ MODULES =					\
  guix/discovery.scm				\
  guix/git-download.scm				\
  guix/hg-download.scm				\
+  guix/swh.scm					\
  guix/monads.scm				\
  guix/monad-repl.scm				\
  guix/gexp.scm					\
@@ -85,6 +86,9 @@ MODULES =					\
  guix/nar.scm					\
  guix/derivations.scm				\
  guix/grafts.scm				\
+  guix/inferior.scm				\
+  guix/describe.scm				\
+  guix/channels.scm				\
  guix/gnu-maintenance.scm			\
  guix/self.scm					\
  guix/upstream.scm				\
@@ -100,6 +104,7 @@ MODULES =					\
  guix/build-system/android-ndk.scm		\
  guix/build-system/ant.scm			\
  guix/build-system/cargo.scm			\
+  guix/build-system/clojure.scm			\
  guix/build-system/cmake.scm			\
  guix/build-system/dub.scm			\
  guix/build-system/emacs.scm			\
@@ -110,6 +115,7 @@ MODULES =					\
  guix/build-system/asdf.scm			\
  guix/build-system/glib-or-gtk.scm		\
  guix/build-system/gnu.scm			\
+  guix/build-system/guile.scm			\
  guix/build-system/haskell.scm			\
  guix/build-system/perl.scm			\
  guix/build-system/python.scm			\
@@ -130,6 +136,7 @@ MODULES =					\
  guix/svn-download.scm				\
  guix/i18n.scm					\
  guix/ui.scm					\
+  guix/status.scm				\
  guix/build/android-ndk-build-system.scm	\
  guix/build/ant-build-system.scm		\
  guix/build/download.scm			\
@@ -148,6 +155,7 @@ MODULES =					\
  guix/build/glib-or-gtk-build-system.scm	\
  guix/build/gnu-build-system.scm		\
  guix/build/gnu-dist.scm			\
+  guix/build/guile-build-system.scm		\
  guix/build/perl-build-system.scm		\
  guix/build/python-build-system.scm		\
  guix/build/ocaml-build-system.scm		\
@@ -168,6 +176,9 @@ MODULES =					\
  guix/build/svn.scm				\
  guix/build/syscalls.scm                       \
  guix/build/gremlin.scm			\
+  guix/build/debug-link.scm			\
+  guix/build/clojure-build-system.scm		\
+  guix/build/clojure-utils.scm			\
  guix/build/emacs-utils.scm			\
  guix/build/java-utils.scm			\
  guix/build/lisp-utils.scm			\
@@ -177,15 +188,24 @@ MODULES =					\
  guix/build/make-bootstrap.scm			\
  guix/search-paths.scm				\
  guix/packages.scm				\
-  guix/import/print.scm				\
-  guix/import/utils.scm				\
-  guix/import/gnu.scm				\
-  guix/import/snix.scm				\
  guix/import/cabal.scm				\
+  guix/import/cpan.scm				\
  guix/import/cran.scm				\
-  guix/import/hackage.scm			\
+  guix/import/crate.scm				\
  guix/import/elpa.scm   			\
+  guix/import/gem.scm				\
+  guix/import/github.scm   			\
+  guix/import/gnome.scm				\
+  guix/import/gnu.scm				\
+  guix/import/hackage.scm			\
+  guix/import/json.scm				\
+  guix/import/opam.scm				\
+  guix/import/print.scm				\
+  guix/import/pypi.scm				\
+  guix/import/snix.scm				\
+  guix/import/stackage.scm			\
  guix/import/texlive.scm   			\
+  guix/import/utils.scm				\
  guix/scripts.scm				\
  guix/scripts/download.scm			\
  guix/scripts/perform-download.scm		\
@@ -197,51 +217,39 @@ MODULES =					\
  guix/scripts/hash.scm				\
  guix/scripts/pack.scm				\
  guix/scripts/pull.scm				\
+  guix/scripts/processes.scm			\
  guix/scripts/substitute.scm			\
  guix/scripts/authenticate.scm			\
  guix/scripts/refresh.scm			\
+  guix/scripts/repl.scm				\
+  guix/scripts/describe.scm			\
  guix/scripts/system.scm			\
  guix/scripts/system/search.scm		\
  guix/scripts/lint.scm				\
  guix/scripts/challenge.scm			\
+  guix/scripts/import/crate.scm			\
  guix/scripts/import/cran.scm			\
-  guix/scripts/import/gnu.scm			\
-  guix/scripts/import/nix.scm			\
-  guix/scripts/import/hackage.scm		\
  guix/scripts/import/elpa.scm  		\
+  guix/scripts/import/gem.scm			\
+  guix/scripts/import/gnu.scm			\
+  guix/scripts/import/hackage.scm		\
+  guix/scripts/import/json.scm  		\
+  guix/scripts/import/nix.scm			\
+  guix/scripts/import/opam.scm			\
+  guix/scripts/import/pypi.scm			\
+  guix/scripts/import/stackage.scm		\
  guix/scripts/import/texlive.scm  		\
  guix/scripts/environment.scm			\
  guix/scripts/publish.scm			\
  guix/scripts/edit.scm				\
  guix/scripts/size.scm				\
  guix/scripts/graph.scm			\
+  guix/scripts/weather.scm			\
  guix/scripts/container.scm			\
  guix/scripts/container/exec.scm		\
  guix.scm					\
  $(GNU_SYSTEM_MODULES)

-if HAVE_GUILE_JSON
-
-MODULES +=					\
-  guix/ci.scm					\
-  guix/docker.scm	   			\
-  guix/import/cpan.scm				\
-  guix/import/crate.scm				\
-  guix/import/gem.scm				\
-  guix/import/github.scm   			\
-  guix/import/gnome.scm				\
-  guix/import/json.scm				\
-  guix/import/pypi.scm				\
-  guix/import/stackage.scm			\
-  guix/scripts/import/crate.scm			\
-  guix/scripts/import/gem.scm			\
-  guix/scripts/import/json.scm  		\
-  guix/scripts/import/pypi.scm			\
-  guix/scripts/import/stackage.scm		\
-  guix/scripts/weather.scm
-
-endif
-
 if HAVE_GUILE_SSH

 MODULES +=					\
@@ -271,10 +279,10 @@ dist_noinst_DATA = guix/tests.scm guix/tests/http.scm
 # Auxiliary files for packages.
 AUX_FILES =						\
  gnu/packages/aux-files/emacs/guix-emacs.el		\
-  gnu/packages/aux-files/linux-libre/4.17-arm.conf	\
-  gnu/packages/aux-files/linux-libre/4.17-arm64.conf	\
-  gnu/packages/aux-files/linux-libre/4.17-i686.conf	\
-  gnu/packages/aux-files/linux-libre/4.17-x86_64.conf	\
+  gnu/packages/aux-files/linux-libre/4.19-arm.conf	\
+  gnu/packages/aux-files/linux-libre/4.19-arm64.conf	\
+  gnu/packages/aux-files/linux-libre/4.19-i686.conf	\
+  gnu/packages/aux-files/linux-libre/4.19-x86_64.conf	\
  gnu/packages/aux-files/linux-libre/4.14-arm.conf	\
  gnu/packages/aux-files/linux-libre/4.14-i686.conf	\
  gnu/packages/aux-files/linux-libre/4.14-x86_64.conf	\
@@ -282,8 +290,6 @@ AUX_FILES =						\
  gnu/packages/aux-files/linux-libre/4.9-x86_64.conf	\
  gnu/packages/aux-files/linux-libre/4.4-i686.conf	\
  gnu/packages/aux-files/linux-libre/4.4-x86_64.conf	\
-  gnu/packages/aux-files/linux-libre/4.1-i686.conf	\
-  gnu/packages/aux-files/linux-libre/4.1-x86_64.conf	\
  gnu/packages/aux-files/run-in-namespace.c

 # Templates, examples.
@@ -323,9 +329,10 @@ SCM_TESTS =					\
  tests/base16.scm				\
  tests/base32.scm				\
  tests/base64.scm				\
+  tests/cpan.scm				\
  tests/cpio.scm				\
-  tests/hash.scm				\
-  tests/pk-crypto.scm				\
+  tests/crate.scm				\
+  tests/gem.scm					\
  tests/pki.scm					\
  tests/print.scm				\
  tests/sets.scm				\
@@ -337,7 +344,9 @@ SCM_TESTS =					\
  tests/glob.scm				\
  tests/grafts.scm				\
  tests/ui.scm					\
+  tests/status.scm				\
  tests/records.scm				\
+  tests/processes.scm				\
  tests/upstream.scm				\
  tests/combinators.scm				\
  tests/discovery.scm				\
@@ -357,7 +366,9 @@ SCM_TESTS =					\
  tests/profiles.scm				\
  tests/search-paths.scm			\
  tests/syscalls.scm				\
+  tests/inferior.scm				\
  tests/gremlin.scm				\
+  tests/debug-link.scm				\
  tests/bournish.scm				\
  tests/lint.scm				\
  tests/publish.scm				\
@@ -375,27 +386,22 @@ SCM_TESTS =					\
  tests/services.scm				\
  tests/scripts-build.scm			\
  tests/containers.scm				\
+  tests/opam.scm				\
  tests/pack.scm				\
+  tests/pypi.scm				\
  tests/import-utils.scm			\
  tests/store-database.scm			\
  tests/store-deduplication.scm

-if HAVE_GUILE_JSON
-
-SCM_TESTS += 					\
-  tests/pypi.scm				\
-  tests/cpan.scm				\
-  tests/gem.scm					\
-  tests/crate.scm
-
-endif
-
 SH_TESTS =					\
  tests/guix-build.sh				\
+  tests/guix-build-branch.sh			\
  tests/guix-download.sh			\
  tests/guix-gc.sh				\
  tests/guix-hash.sh				\
  tests/guix-pack.sh				\
+  tests/guix-pack-localstatedir.sh		\
+  tests/guix-pack-relocatable.sh		\
  tests/guix-package.sh				\
  tests/guix-package-net.sh			\
  tests/guix-system.sh				\
@@ -404,6 +410,7 @@ SH_TESTS =					\
  tests/guix-environment.sh			\
  tests/guix-environment-container.sh		\
  tests/guix-graph.sh				\
+  tests/guix-describe.sh			\
  tests/guix-lint.sh

 TESTS = $(SCM_TESTS) $(SH_TESTS)
@@ -451,8 +458,9 @@ check-system: $(GOBJECTS)

 # Public key used to sign substitutes from hydra.gnu.org & co.
 dist_pkgdata_DATA =				\
-  hydra.gnu.org.pub				\
-  berlin.guixsd.org.pub
+  etc/substitutes/hydra.gnu.org.pub		\
+  etc/substitutes/berlin.guixsd.org.pub		\
+  etc/substitutes/ci.guix.info.pub

 # Bash completion file.
 dist_bashcompletion_DATA = etc/completion/bash/guix	\
@@ -494,8 +502,6 @@ EXTRA_DIST +=						\
  build-aux/run-system-tests.scm			\
  d3.v3.js						\
  graph.js						\
-  srfi/srfi-64.scm					\
-  srfi/srfi-64.upstream.scm				\
  tests/test.drv					\
  tests/signing-key.pub					\
  tests/signing-key.sec					\
@@ -586,18 +592,17 @@ AM_DISTCHECK_CONFIGURE_FLAGS =			\
  --enable-daemon				\
  ac_cv_guix_test_root="$(GUIX_TEST_ROOT)"

-# The self-contained tarball.  Add 'glibc-utf8-locales' along with glibc just
-# so 'etc/profile' defines 'GUIX_LOCPATH' pointing to a valid set of locales.
+# The self-contained tarball.
 guix-binary.%.tar.xz:
 	$(AM_V_GEN)GUIX_PACKAGE_PATH=					\
 	tarball=`$(top_builddir)/pre-inst-env guix pack -K -C xz	\
-	  -s "$*" --localstatedir guix glibc-utf8-locales		\
-	  -e  '(@@ (gnu packages commencement) glibc-final)'` ;		\
+	  -s "$*" --localstatedir --profile-name=current-guix guix` ;	\
 	cp "$$tarball" "$@.tmp" ; mv "$@.tmp" "$@"


 dist-hook: $(distdir)/ChangeLog gen-AUTHORS gen-tarball-version
 dist-hook: assert-no-store-file-names
+dist-hook: doc-po-update

 distcheck-hook: assert-binaries-available assert-final-inputs-self-contained

@@ -758,7 +763,7 @@ assert-no-store-file-names: $(distdir)/ChangeLog
 	  exit 1 ;								\
 	fi

-# Make sure hydra.gnu.org has the important binaries.
+# Make sure important substitutes are available.
 assert-binaries-available: $(GOBJECTS)
 	$(AM_V_at)$(top_builddir)/pre-inst-env "$(GUILE)"			\
 	  "$(top_srcdir)/build-aux/check-available-binaries.scm"
@@ -3,6 +3,7 @@
 #+STARTUP: content hidestars

 Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>

  Copying and distribution of this file, with or without modification,
  are permitted in any medium without royalty provided the copyright
@@ -10,6 +11,110 @@ Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>

 Please send Guix bug reports to bug-guix@gnu.org.

+* Changes in 0.16.0 (since 0.15.0)
+
+** Package management
+
+*** Default substitute URL changed to https://ci.guix.info
+*** ‘guix pull -l’ lists new and upgraded packages
+*** ‘guix pull’ now supports channels via ~/.config/guix/channels.scm
+*** New ‘--profile’ or ‘-p’ option for ‘guix pull’
+*** ~/.config/guix/current is now a symlink to /var/guix/profiles
+*** New ‘guix describe’ command
+*** ‘guix package’ no longer shows build logs by default
+*** ‘guix’ commands now produce colored output by default
+*** User interface now reports grafts separately
+*** Manifests can now refer to arbitrary Guix commits using “inferiors”
+*** New ‘--with-branch’ and ‘--with-commit’ package transformation options
+*** ‘guix build -f’ now accepts any kind of “file-like object”
+*** Git checkouts may now be fetched from Software Heritage
+*** New ‘guix repl’ command for use by inferiors
+*** New ‘guix processes’ command
+*** ‘guix pack’ now honors ‘--localstatedir’ for all its backends
+*** New ‘opam’ importer for ‘guix import’
+*** ‘guix import pypi’ has a new ‘--recursive’ option
+*** ‘guix import hackage’ has a new ‘--recursive’ option
+*** ‘guix import stackage’ has a new ‘--recursive’ option
+The short option for ‘--lts-version’ is now ‘-l’ (used to be ‘-r’).
+*** ‘guix refresh’ now stores upstream keys in ~/.config/guix/upstream
+*** Guix now depends on Guile-Gcrypt
+*** Guix now requires Guile-JSON
+
+** Distribution
+
+*** Rust is now bootstrapped from mrustc
+*** The GNU Shepherd was upgraded to 0.5.0
+*** ‘guix system reconfigure’ now loads Shepherd service replacements
+*** ‘herd schedule mcron’ now displays mcron’s job schedule
+*** ‘herd statistics nscd’ now displays nscd statistics
+*** ‘herd invalidate nscd TABLE’ instructs nscd to invalidate TABLE
+*** New services
+
+ddclient, gitolite, iptables, pcscd, prometheus-node-exporter, varnish
+
+*** 985 new packages
+
+*** 1945 package updates
+
+Noteworthy updates:
+bash 4.4.23, binutils 2.31.1, cups 2.2.8, enlightenment 0.22.4, gcc 8.2.0,
+gdb 8.2, ghc 8.4.3, gimp 2.10.6, glibc 2.28, gnupg 2.2.11, go 1.11.1,
+guile 2.2.4, icecat 60.3.0-gnu1, icedtea 3.7.0, libreoffice 6.1.3.2,
+linux-libre 4.19.6, ocaml 4.07.1, octave 4.4.1, perl 5.28.0,
+python2 2.7.15, python 3.7.0, racket 7.0, rust 1.28.0, r 3.5.1,
+sbcl 1.4.13, shepherd 0.5.0, xorg-server 1.20.3
+
+** Programming interfaces
+
+*** New (guix channels) module, see “Channels” in the manual
+*** New (guix inferior) module, see “Inferiors” in the manual
+*** New (guix describe) module, used by ‘guix describe’
+*** New (guix status) module, for build progress reporting
+*** ‘packages->manifest’ now accepts inferior packages
+*** New build systems: ‘clojure’, ‘guile’
+*** New ‘git-checkout’ record constructor in (guix git)
+*** Shepherd services can now declare custom actions
+*** More of the (gnu system …) APIs are now non-monadic
+*** New ‘add-file-tree-to-store’ procedure in (guix store)
+*** New (guix swh) module to access Software Heritage
+*** New (guix build debug-link) module, for ELF ‘.gnu_debuglink’ sections
+
+** Noteworthy bug fixes
+
+*** Fix GCC crashes caused by a patch of ours (<https://bugs.gnu.org/31708>)
+*** ‘guix import hackage’ now supports ‘custom-setup’ field
+    (<https://bugs.gnu.org/23961>)
+*** ‘guix-daemon’ taken from ‘guix pull’ looks up ‘guix’ in the right place
+    (<https://bugs.gnu.org/32183>)
+*** Try several file names when looking up kernel modules
+    (<https://bugs.gnu.org/31714>)
+*** ‘file-system-*’ services are now always started after ‘udev’
+    (<https://bugs.gnu.org/32313>)
+*** Racket now ignores bytecode checksums for files in the store
+    (<https://bugs.gnu.org/30680>)
+*** Grafting now updates CRCs in ‘.gnu_debuglink’ ELF sections
+    (<https://bugs.gnu.org/19973>)
+*** UUID computation for VMs is now deterministic (<https://bugs.gnu.org/32652>)
+*** ‘git-predicate’ from (guix git) now uses Guile-Git, which fixes corner cases
+    (<https://bugs.gnu.org/27925>)
+*** (guix store database) registers each store item only once
+    (<https://bugs.gnu.org/32600>)
+*** The File > Open dialog in LibreOffice no longer triggers a crash
+    (<https://bugs.gnu.org/30642>)
+*** Account home directory is always honored (<https://bugs.gnu.org/33422>)
+
+** Native language support
+
+*** The manual is now partially translated into German, in addition to French
+
+To read the German manual, just type “info guix.de” or read it on-line at
+<https://gnu.org/s/guix/manual/de/html_node>.  Consider translating the manual
+to your native language by joining the Translation Project:
+<https://translationproject.org/domain/guix-manual.html>.
+
+*** Updated translations:
+*** New translations:
+
 * Changes in 0.15.0 (since 0.14.0)

 ** Package management
@@ -21,16 +21,17 @@ Guix is based on the [[https://nixos.org/nix/][Nix]] package manager.
 GNU Guix currently depends on the following packages:

  - [[https://gnu.org/software/guile/][GNU Guile 2.2.x or 2.0.x]], version 2.0.13 or later
-  - [[https://gnupg.org/][GNU libgcrypt]]
+  - [[https://notabug.org/cwebber/guile-gcrypt][Guile-Gcrypt]] 0.1.0 or later
  - [[https://www.gnu.org/software/make/][GNU Make]]
  - [[https://www.gnutls.org][GnuTLS]] compiled with guile support enabled
-  - [[https://notabug.org/civodul/guile-sqlite3][Guile-SQLite3]], version 0.1.0 or later
+  - [[https://notabug.org/guile-sqlite3/guile-sqlite3][Guile-SQLite3]], version 0.1.0 or later
  - [[https://gitlab.com/guile-git/guile-git][Guile-Git]]
  - [[http://www.zlib.net/][zlib]]
-  - optionally [[https://savannah.nongnu.org/projects/guile-json/][Guile-JSON]], for the 'guix import pypi' command
+  - [[https://savannah.nongnu.org/projects/guile-json/][Guile-JSON]]

 Unless `--disable-daemon' was passed, the following packages are needed:

+  - [[https://gnupg.org/][GNU libgcrypt]]
  - [[https://sqlite.org/][SQLite 3]]
  - [[https://gcc.gnu.org][GCC's g++]]
  - optionally [[http://www.bzip.org][libbz2]]
@@ -22,8 +22,11 @@
  #:use-module (guix ui)
  #:use-module (guix config)
  #:use-module (guix modules)
+  #:use-module (guix build-system gnu)
  #:use-module (srfi srfi-1)
  #:use-module (srfi srfi-19)
+  #:use-module (srfi srfi-34)
+  #:use-module (srfi srfi-35)
  #:use-module (rnrs io ports)
  #:use-module (ice-9 match)
  #:use-module (ice-9 popen)
@@ -72,7 +75,7 @@
                                      (variables rest ...))))))
    (variables %localstatedir %storedir %sysconfdir %system)))

-(define* (make-config.scm #:key libgcrypt zlib gzip xz bzip2
+(define* (make-config.scm #:key zlib gzip xz bzip2
                          (package-name "GNU Guix")
                          (package-version "0")
                          (bug-report-address "bug-guix@gnu.org")
@@ -92,7 +95,6 @@
                               %state-directory
                               %store-database-directory
                               %config-directory
-                               %libgcrypt
                               %libz
                               %gzip
                               %bzip2
@@ -137,9 +139,6 @@
                     (define %xz
                       #+(and xz (file-append xz "/bin/xz")))

-                     (define %libgcrypt
-                       #+(and libgcrypt
-                              (file-append libgcrypt "/lib/libgcrypt")))
                     (define %libz
                       #+(and zlib
                              (file-append zlib "/lib/libz")))))))
@@ -200,6 +199,54 @@ person's version identifier."
  ;; XXX: Replace with a Git commit id.
  (date->string (current-date 0) "~Y~m~d.~H"))

+(define guile-gcrypt
+  ;; The host Guix may or may not have 'guile-gcrypt', which was introduced in
+  ;; August 2018.  If it has it, it's at least version 0.1.0, which is good
+  ;; enough.  If it doesn't, specify our own package because the target Guix
+  ;; requires it.
+  (match (find-best-packages-by-name "guile-gcrypt" #f)
+    (()
+     (package
+       (name "guile-gcrypt")
+       (version "0.1.0")
+       (home-page "https://notabug.org/cwebber/guile-gcrypt")
+       (source (origin
+                 (method url-fetch)
+                 (uri (string-append home-page "/archive/v" version ".tar.gz"))
+                 (sha256
+                  (base32
+                   "1gir7ifknbmbvjlql5j6wzk7bkb5lnmq80q59ngz43hhpclrk5k3"))
+                 (file-name (string-append name "-" version ".tar.gz"))))
+       (build-system gnu-build-system)
+       (arguments
+        ;; The 'bootstrap' phase appeared in 'core-updates', which was merged
+        ;; into 'master' ca. June 2018.
+        '(#:phases (modify-phases %standard-phases
+                     (delete 'bootstrap)
+                     (add-before 'configure 'bootstrap
+                       (lambda _
+                         (unless (zero? (system* "autoreconf" "-vfi"))
+                           (error "autoreconf failed"))
+                         #t)))))
+       (native-inputs
+        `(("pkg-config" ,(specification->package "pkg-config"))
+          ("autoconf" ,(specification->package "autoconf"))
+          ("automake" ,(specification->package "automake"))
+          ("texinfo" ,(specification->package "texinfo"))))
+       (inputs
+        `(("guile" ,(specification->package "guile"))
+          ("libgcrypt" ,(specification->package "libgcrypt"))))
+       (synopsis "Cryptography library for Guile using Libgcrypt")
+       (description
+        "Guile-Gcrypt provides a Guile 2.x interface to a subset of the
+GNU Libgcrypt crytographic library.  It provides modules for cryptographic
+hash functions, message authentication codes (MAC), public-key cryptography,
+strong randomness, and more.  It is implemented using the foreign function
+interface (FFI) of Guile.")
+       (license #f)))                             ;license:gpl3+
+    ((package . _)
+     package)))
+
 (define* (build-program source version
                        #:optional (guile-version (effective-version))
                        #:key (pull-version 0))
@@ -212,10 +259,29 @@ person's version identifier."
      (('gnu _ ...)    #t)
      (_               #f)))

+  (define fake-gcrypt-hash
+    ;; Fake (gcrypt hash) module; see below.
+    (scheme-file "hash.scm"
+                 #~(define-module (gcrypt hash)
+                     #:export (sha1 sha256))))
+
+  (define fake-git
+    (scheme-file "git.scm" #~(define-module (git))))
+
  (with-imported-modules `(((guix config)
-                            => ,(make-config.scm
-                                 #:libgcrypt
-                                 (specification->package "libgcrypt")))
+                            => ,(make-config.scm))
+
+                           ;; To avoid relying on 'with-extensions', which was
+                           ;; introduced in 0.15.0, provide a fake (gcrypt
+                           ;; hash) just so that we can build modules, and
+                           ;; adjust %LOAD-PATH later on.
+                           ((gcrypt hash) => ,fake-gcrypt-hash)
+
+                           ;; (guix git-download) depends on (git) but only
+                           ;; for peripheral functionality.  Provide a dummy
+                           ;; (git) to placate it.
+                           ((git) => ,fake-git)
+
                           ,@(source-module-closure `((guix store)
                                                      (guix self)
                                                      (guix derivations)
@@ -237,13 +303,24 @@ person's version identifier."
                           (match %load-path
                             ((front _ ...)
                              (unless (string=? front source) ;already done?
-                                (set! %load-path (list source front)))))))
+                                (set! %load-path
+                                  (list source
+                                        (string-append #$guile-gcrypt
+                                                       "/share/guile/site/"
+                                                       (effective-version))
+                                        front)))))))

-                        ;; Only load our own modules or those of Guile.
+                        ;; Only load Guile-Gcrypt, our own modules, or those
+                        ;; of Guile.
                        (match %load-compiled-path
                          ((front _ ... sys1 sys2)
-                           (set! %load-compiled-path
-                             (list front sys1 sys2)))))
+                           (unless (string-prefix? #$guile-gcrypt front)
+                             (set! %load-compiled-path
+                               (list (string-append #$guile-gcrypt
+                                                    "/lib/guile/"
+                                                    (effective-version)
+                                                    "/site-ccache")
+                                     front sys1 sys2))))))

                      (use-modules (guix store)
                                   (guix self)
@@ -297,10 +374,15 @@ person's version identifier."
 ;; The procedure below is our return value.
 (define* (build source
                #:key verbose? (version (date-version-string)) system
-                (guile-version (match ((@ (guile) version))
-                                 ("2.2.2" "2.2.2")
-                                 (_       (effective-version))))
                (pull-version 0)
+
+                ;; For the standalone Guix, default to Guile 2.2.  For old
+                ;; versions of 'guix pull' (pre-0.15.0), we have to use the
+                ;; same Guile as the current one.
+                (guile-version (if (> pull-version 0)
+                                   "2.2"
+                                   (effective-version)))
+
                #:allow-other-keys
                #:rest rest)
  "Return a derivation that unpacks SOURCE into STORE and compiles Scheme
@@ -345,7 +427,15 @@ files."
           ;; Unsupported PULL-VERSION.
           (return #f))
          ((? string? str)
-           (error "invalid build result" (list build str))))))))
+           (raise (condition
+                   (&message
+                    (message (format #f "You found a bug: the program '~a'
+failed to compute the derivation for Guix (version: ~s; system: ~s;
+host version: ~s; pull-version: ~s).
+Please report it by email to <~a>.~%"
+                                     (derivation->output-path build)
+                                     version system %guix-version pull-version
+                                     %guix-bug-report-address)))))))))))

 ;; This file is loaded by 'guix pull'; return it the build procedure.
 build
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -17,7 +17,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

 ;;;
-;;; Check whether important binaries are available at hydra.gnu.org.
+;;; Check whether important binaries are available.
 ;;;

 (use-modules (guix store)
@@ -17,7 +17,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

 ;;;
-;;; Check whether important binaries are available at hydra.gnu.org.
+;;; Check whether important binaries are available.
 ;;;

 (use-modules (guix store)
@@ -20,13 +20,20 @@

 (use-modules (srfi srfi-26))

-;; Add ~/.config/guix/latest to the search path.
-(add-to-load-path
- (and=> (or (getenv "XDG_CONFIG_HOME")
-            (and=> (getenv "HOME")
-                   (cut string-append <> "/.config")))
-        (cute string-append <> "/guix/current/share/guile/site/"
-              (effective-version))))
+;; Add ~/.config/guix/current to the search path.
+(eval-when (expand load eval)
+  (and=> (or (getenv "XDG_CONFIG_HOME")
+             (and=> (getenv "HOME")
+                    (cut string-append <> "/.config/guix/current")))
+         (lambda (current)
+           (set! %load-path
+             (cons (string-append current "/share/guile/site/"
+                                  (effective-version))
+                   %load-path))
+           (set! %load-compiled-path
+             (cons (string-append current "/lib/guile/" (effective-version)
+                                  "/site-ccache")
+                   %load-compiled-path)))))

 (use-modules (guix) (guix ui)
             (guix git-download)
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -56,6 +57,7 @@
             (guix packages)
             (guix derivations)
             (guix monads)
+             (guix ui)
             ((guix licenses) #:select (gpl3+))
             ((guix utils) #:select (%current-system))
             ((guix scripts system) #:select (read-operating-system))
@@ -311,6 +313,29 @@ valid."
                          packages)))
                 #:select? (const #t)))           ;include hidden packages

+(define (arguments->manifests arguments)
+  "Return the list of manifests extracted from ARGUMENTS."
+  (map (match-lambda
+         ((input-name . relative-path)
+          (let* ((checkout (assq-ref arguments (string->symbol input-name)))
+                 (base (assq-ref checkout 'file-name)))
+            (in-vicinity base relative-path))))
+       (assq-ref arguments 'manifests)))
+
+(define (manifests->packages store manifests)
+  "Return the list of packages found in MANIFESTS."
+  (define (load-manifest manifest)
+    (save-module-excursion
+     (lambda ()
+       (set-current-module (make-user-module '((guix profiles) (gnu))))
+       (primitive-load manifest))))
+
+  (delete-duplicates!
+   (map manifest-entry-item
+        (append-map (compose manifest-entries
+                             load-manifest)
+                    manifests))))
+

 ;;;
 ;;; Hydra entry point.
@@ -323,6 +348,7 @@ valid."
      ("core" 'core)                              ; only build core packages
      ("hello" 'hello)                            ; only build hello
      (((? string?) (? string?) ...) 'list)       ; only build selected list of packages
+      ("manifests" 'manifests)                    ; only build packages in the list of manifests
      (_ 'all)))                                  ; build everything

  (define systems
@@ -419,6 +445,14 @@ valid."
                                                 package system))
                                  packages))
                         '()))
+                    ((manifests)
+                     ;; Build packages in the list of manifests.
+                     (let* ((manifests (arguments->manifests arguments))
+                            (packages (manifests->packages store manifests)))
+                       (map (lambda (package)
+                              (package-job store (job-name package)
+                                           package system))
+                            packages)))
                    (else
                     (error "unknown subset" subset))))
                systems)))
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -19,6 +19,7 @@
 (define-module (run-system-tests)
  #:use-module (gnu tests)
  #:use-module (guix store)
+  #:use-module (guix status)
  #:use-module (guix monads)
  #:use-module (guix derivations)
  #:use-module (guix ui)
@@ -63,25 +64,27 @@
          (length tests))

  (with-store store
-    (run-with-store store
-      (mlet* %store-monad ((drv (mapm %store-monad system-test-value tests))
-                           (out -> (map derivation->output-path drv)))
-        (mbegin %store-monad
-          (show-what-to-build* drv)
-          (set-build-options* #:keep-going? #t #:keep-failed? #t
-                              #:print-build-trace #t
-                              #:fallback? #t)
-          (built-derivations* drv)
-          (mlet %store-monad ((valid  (filterm (store-lift valid-path?)
-                                               out))
-                              (failed (filterm (store-lift
-                                                (negate valid-path?))
-                                               out)))
-            (format #t "TOTAL: ~a\n" (length drv))
-            (for-each (lambda (item)
-                        (format #t "PASS: ~a~%" item))
-                      valid)
-            (for-each (lambda (item)
-                        (format #t "FAIL: ~a~%" item))
-                      failed)
-            (exit (null? failed))))))))
+    (with-status-report print-build-event
+      (run-with-store store
+        (mlet* %store-monad ((drv (mapm %store-monad system-test-value tests))
+                             (out -> (map derivation->output-path drv)))
+          (mbegin %store-monad
+            (show-what-to-build* drv)
+            (set-build-options* #:keep-going? #t #:keep-failed? #t
+                                #:print-build-trace #t
+                                #:print-extended-build-trace? #t
+                                #:fallback? #t)
+            (built-derivations* drv)
+            (mlet %store-monad ((valid  (filterm (store-lift valid-path?)
+                                                 out))
+                                (failed (filterm (store-lift
+                                                  (negate valid-path?))
+                                                 out)))
+              (format #t "TOTAL: ~a\n" (length drv))
+              (for-each (lambda (item)
+                          (format #t "PASS: ~a~%" item))
+                        valid)
+              (for-each (lambda (item)
+                          (format #t "FAIL: ~a~%" item))
+                        failed)
+              (exit (null? failed)))))))))
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,6 +30,7 @@
             (ice-9 match)
             (ice-9 rdelim)
             (ice-9 regex)
+             (ice-9 vlist)
             (ice-9 pretty-print))

 (define %header-rx
@@ -98,47 +99,77 @@ paragraph."
                             (lambda (match port)
                               (let ((stars (match:substring match 1)))
                                 (format port
-                                         "~a ~a new packages~%~%~a~%~%"
-                                         stars (length added)
-                                         (enumeration->paragraph added)))))))))
+                                         "~a ~a new packages~%~%"
+                                         stars (length added)))))))))

 (define (write-packages-updates news-file old new)
  "Write to NEWS-FILE the list of packages upgraded between OLD and NEW."
-  (let ((upgraded (filter-map (match-lambda
-                                ((package . new-version)
-                                 (match (assoc package old)
-                                   ((_ . old-version)
-                                    (and (version>? new-version old-version)
-                                         (string-append package "@"
-                                                        new-version)))
-                                   (_ #f))))
-                              new)))
+  (define important
+    '("gcc" "glibc" "binutils" "gdb"                   ;toolchain
+      "shepherd" "linux-libre" "xorg-server" "cups"    ;OS
+      "gnome" "xfce" "enlightenment" "lxde" "mate"     ;desktop env.
+      "guile" "bash" "python" "python2" "perl"         ;languages
+      "ghc" "rust" "go" "julia" "r" "ocaml"
+      "icedtea" "openjdk" "clojure" "sbcl" "racket"
+      "emacs" "gimp" "inkscape" "libreoffice"          ;applications
+      "octave" "icecat" "gnupg"))
+
+  (let* ((table    (fold (lambda (package table)
+                           (match package
+                             ((name . version)
+                              (vhash-cons name version table))))
+                         vlist-null
+                         new))
+         (latest   (lambda (name)
+                     (let ((versions (vhash-fold* cons '() name table)))
+                       (match (sort versions version>?)
+                         ((latest . _) latest)))))
+         (upgraded (filter-map (match-lambda
+                                 ((package . new-version)
+                                  (match (assoc package old)
+                                    ((_ . old-version)
+                                     (and (string=? new-version
+                                                    (latest package))
+                                          (version>? new-version old-version)
+                                          (cons package new-version)))
+                                    (_ #f))))
+                               new))
+         (noteworthy (filter (match-lambda
+                               ((package . version)
+                                (member package important)))
+                             upgraded)))
    (with-atomic-file-replacement news-file
      (lambda (input output)
        (rewrite-org-section input output
                             (make-regexp "^(\\*+) (.*) package updates")
                             (lambda (match port)
-                               (let ((stars (match:substring match 1)))
+                               (let ((stars (match:substring match 1))
+                                     (lst   (map (match-lambda
+                                                   ((package . version)
+                                                    (string-append package " "
+                                                                   version)))
+                                                 noteworthy)))
                                 (format port
-                                         "~a ~a package updates~%~%~a~%~%"
+                                         "~a ~a package updates~%~%Noteworthy updates:~%~a~%~%"
                                         stars (length upgraded)
-                                         (enumeration->paragraph upgraded)))))))))
+                                         (enumeration->paragraph lst)))))))))


 (define (main . args)
  (match args
    ((news-file data-directory)
-     ;; Don't browse things listed in the user's $GUIX_PACKAGE_PATH.  Here we
-     ;; assume that the last item in (%package-module-path) is the distro
-     ;; directory.
+     ;; Don't browse things listed in the user's $GUIX_PACKAGE_PATH and
+     ;; in external channels.
     (parameterize ((%package-module-path
-                     (list (last (%package-module-path)))))
+                     %default-package-module-path))
       (define (package-file version)
         (string-append data-directory "/packages-"
                        version ".txt"))

       (let-values (((previous-version new-version)
                     (call-with-input-file news-file NEWS->versions)))
+         (format (current-error-port) "Updating NEWS for ~a to ~a...~%"
+                 previous-version new-version)
         (let* ((old (call-with-input-file (package-file previous-version)
                       read))
                (new (fold-packages (lambda (p r)
@@ -48,7 +48,7 @@ if test "x$guix_build_daemon" = "xyes"; then
  esac

  case "$LIBGCRYPT_LIBDIR" in
-    no)
+    no | "")
      LIBGCRYPT_LIBS="-lgcrypt"
      ;;
    *)
@@ -120,15 +120,7 @@ if test "x$guix_build_daemon" = "xyes"; then

  dnl Determine the appropriate default list of substitute URLs (GnuTLS
  dnl is required so we can default to 'https'.)
-  case "x$host_cpu" in
-    xaarch64)
-      # Currently only berlin.guixsd.org provides aarch64 binaries.
-      guix_substitute_urls="https://berlin.guixsd.org"
-      ;;
-    *)
-      guix_substitute_urls="https://mirror.hydra.gnu.org"
-      ;;
-  esac
+  guix_substitute_urls="https://ci.guix.info"

  AC_MSG_CHECKING([for default substitute URLs])
  AC_MSG_RESULT([$guix_substitute_urls])
@@ -163,8 +155,8 @@ if test "x$guix_build_daemon" = "xyes"; then
    [chmod +x nix/scripts/download])
  AC_CONFIG_FILES([nix/scripts/substitute],
    [chmod +x nix/scripts/substitute])
-  AC_CONFIG_FILES([nix/scripts/guix-authenticate],
-    [chmod +x nix/scripts/guix-authenticate])
+  AC_CONFIG_FILES([nix/scripts/authenticate],
+    [chmod +x nix/scripts/authenticate])
  AC_CONFIG_FILES([nix/scripts/offload],
    [chmod +x nix/scripts/offload])
 fi
@@ -87,7 +87,9 @@ dnl We require pkg.m4 (from pkg-config) and guile.m4 (from Guile.)
 dnl Make sure they are available.
 m4_pattern_forbid([PKG_CHECK_MODULES])
 m4_pattern_forbid([GUILE_MODULE_AVAILABLE])
-m4_pattern_forbid([^GUILE_P$])
+m4_pattern_forbid([^GUILE_P])
+m4_pattern_allow([^GUILE_PKG_ERRORS])
+m4_pattern_forbid([^GUIX_])

 dnl Search for 'guile' and 'guild'.  This macro defines
 dnl 'GUILE_EFFECTIVE_VERSION'.
@@ -120,9 +122,11 @@ if test "x$have_guile_git" != "xyes"; then
  AC_MSG_ERROR([Guile-Git is missing; please install it.])
 fi

-dnl Guile-JSON is used in various places.
+dnl Check for Guile-JSON.
 GUILE_MODULE_AVAILABLE([have_guile_json], [(json)])
-AM_CONDITIONAL([HAVE_GUILE_JSON], [test "x$have_guile_json" = "xyes"])
+if test "x$have_guile_json" != "xyes"; then
+  AC_MSG_ERROR([Guile-JSON is missing; please install it.])
+fi

 dnl Guile-Sqlite3 is used by the (guix store ...) modules.
 GUIX_CHECK_GUILE_SQLITE3
@@ -130,6 +134,11 @@ if test "x$guix_cv_have_recent_guile_sqlite3" != "xyes"; then
  AC_MSG_ERROR([A recent Guile-SQLite3 could not be found; please install it.])
 fi

+GUILE_MODULE_AVAILABLE([have_guile_gcrypt], [(gcrypt hash)])
+if test "x$have_guile_gcrypt" != "xyes"; then
+  AC_MSG_ERROR([Guile-Gcrypt could not be found; please install it.])
+fi
+
 dnl Make sure we have a full-fledged Guile.
 GUIX_ASSERT_GUILE_FEATURES([regex posix socket net-db threads])

@@ -213,16 +222,10 @@ AC_ARG_WITH([libgcrypt-libdir],
   esac])

 dnl If none of the --with-libgcrypt-* options was used, try to determine the
-dnl absolute file name of libgcrypt.so.
+dnl the library directory.
 case "x$LIBGCRYPT_PREFIX$LIBGCRYPT_LIBDIR" in
  xnono)
    GUIX_LIBGCRYPT_LIBDIR([LIBGCRYPT_LIBDIR])
-    if test "x$LIBGCRYPT_LIBDIR" != x; then
-      LIBGCRYPT="$LIBGCRYPT_LIBDIR/libgcrypt"
-    else
-      dnl 'config-daemon.ac' expects "no" in this case.
-      LIBGCRYPT_LIBDIR="no"
-    fi
    ;;
 esac

@@ -233,8 +236,6 @@ AC_SUBST([LIBGCRYPT])
 AC_SUBST([LIBGCRYPT_PREFIX])
 AC_SUBST([LIBGCRYPT_LIBDIR])

-GUIX_ASSERT_LIBGCRYPT_USABLE
-
 dnl Library name of zlib suitable for 'dynamic-link'.
 GUIX_LIBZ_LIBDIR([libz_libdir])
 if test "x$libz_libdir" = "x"; then
@@ -0,0 +1,534 @@
+@node Mitwirken
+@chapter Mitwirken
+
+Dieses Projekt basiert auf Kooperation, daher benötigen wir Ihre Hilfe, um
+es wachsen zu lassen! Bitte kontaktieren Sie uns auf
+@email{guix-devel@@gnu.org} und @code{#guix} im Freenode-IRC-Netzwerk. Wir
+freuen uns auf Ihre Ideen, Fehlerberichte, Patches und alles, was hilfreich
+für das Projekt sein könnte. Besonders willkommen ist Hilfe bei der
+Erstellung von Paketen (@pxref{Paketrichtlinien}).
+
+@cindex Verhaltensregeln, für Mitwirkende
+@cindex Verhaltenskodex für Mitwirkende
+Wir möchten eine angenehme, freundliche und von Belästigungen freie Umgebung
+bereitstellen, so dass jeder Beiträge nach seinen Fähigkeiten leisten
+kann. Zu diesem Zweck verwendet unser Projekt einen »Verhaltenskodex für
+Mitwirkende«, der von @url{http://contributor-covenant.org/} übernommen
+wurde. Eine übersetzte Fassung finden Sie auf
+@url{https://www.contributor-covenant.org/de/version/1/4/code-of-conduct}
+sowie eine mitgelieferte, englische Fassung in der Datei
+@file{CODE-OF-CONDUCT} im Quellbaum.
+
+Von Mitwirkenden wird nicht erwartet, dass sie in Patches oder in der
+Online-Kommunikation ihre echten Namen preisgeben. Sie können einen
+beliebigen Namen oder ein Pseudonym ihrer Wahl verwenden.
+
+@menu
+* Erstellung aus dem Git::   Das Neueste und Beste.
+* Guix vor der Installation ausführen::  Hacker-Tricks.
+* Perfekt eingerichtet::     Die richtigen Werkzeuge.
+* Code-Stil::                Wie Mitwirkende hygienisch arbeiten.
+* Einreichen von Patches::   Teilen Sie Ihre Arbeit.
+@end menu
+
+@node Erstellung aus dem Git
+@section Erstellung aus dem Git
+
+Wenn Sie an Guix selbst hacken wollen, ist es empfehlenswert, dass Sie die
+neueste Version aus dem Git-Softwarebestand verwenden:
+
+@example
+git clone https://git.savannah.gnu.org/git/guix.git
+@end example
+
+Wenn Sie Guix aus einem Checkout erstellen, sind außer den bereits in den
+Installationsanweisungen genannten Paketen weitere nötig
+(@pxref{Voraussetzungen}).
+
+@itemize
+@item @url{http://gnu.org/software/autoconf/, GNU Autoconf};
+@item @url{http://gnu.org/software/automake/, GNU Automake};
+@item @url{http://gnu.org/software/gettext/, GNU Gettext};
+@item @url{http://gnu.org/software/texinfo/, GNU Texinfo};
+@item @url{http://www.graphviz.org/, Graphviz};
+@item @url{http://www.gnu.org/software/help2man/, GNU Help2man (optional)}.
+@end itemize
+
+Der einfachste Weg, eine Entwicklungsumgebung für Guix einzurichten, ist
+natürlich, Guix zu benutzen! Der folgende Befehl startet eine neue Shell, in
+der alle Abhängigkeiten und Umgebungsvariablen bereits eingerichtet sind, um
+an Guix zu arbeiten:
+
+@example
+guix environment guix
+@end example
+
+In @xref{Aufruf von guix environment} finden Sie weitere Informationen zu
+diesem Befehl. Zusätzliche Abhängigkeiten können mit @option{--ad-hoc}
+hinzugefügt werden:
+
+@example
+guix environment guix --ad-hoc help2man git strace
+@end example
+
+Führen Sie @command{./bootstrap} aus, um die Infrastruktur des
+Erstellungssystems mit Autoconf und Automake zu erstellen. Möglicherweise
+erhalten Sie eine Fehlermeldung wie diese:
+
+@example
+configure.ac:46: error: possibly undefined macro: PKG_CHECK_MODULES
+@end example
+
+@noindent
+Das bedeutet wahrscheinlich, dass Autoconf @file{pkg.m4} nicht finden
+konnte, welches von pkg-config bereitgestellt wird. Stellen Sie sicher, dass
+@file{pkg.m4} verfügbar ist. Gleiches gilt für den von Guile
+bereitgestellten Makrosatz @file{guile.m4}. Wenn Sie beispielsweise Automake
+in @file{/usr/local} installiert haben, würde in @file{/usr/share} nicht
+nach @file{.m4}-Dateien geschaut. In einem solchen Fall müssen Sie folgenden
+Befehl aufrufen:
+
+@example
+export ACLOCAL_PATH=/usr/share/aclocal
+@end example
+
+In @xref{Macro Search Path,,, automake, The GNU Automake Manual} finden Sie
+weitere Informationen.
+
+Dann führen Sie wie gewohnt @command{./configure} aus. Achten Sie darauf,
+@code{--localstatedir=@var{Verzeichnis}} zu übergeben, wobei
+@var{Verzeichnis} der von Ihrer aktuellen Installation verwendete
+@code{localstatedir}-Wert ist (weitere Informationen auf @pxref{Der Store}).
+
+Zum Schluss müssen Sie @code{make check} aufrufen, um die Tests auszuführen
+(@pxref{Die Testsuite laufen lassen}). Falls etwas fehlschlägt, werfen Sie einen
+Blick auf die Installationsanweisungen (@pxref{Installation}) oder senden
+Sie eine E-Mail an die @email{guix-devel@@gnu.org, Mailingliste}.
+
+
+@node Guix vor der Installation ausführen
+@section Guix vor der Installation ausführen
+
+Um eine gesunde Arbeitsumgebung zu erhalten, ist es hilfreich, die im
+lokalen Quellbaum vorgenommenen Änderungen zunächst zu testen, ohne sie
+tatsächlich zu installieren. So können Sie zwischen Ihrem
+Endnutzer-»Straßenanzug« und Ihrem »Faschingskostüm« unterscheiden.
+
+To that end, all the command-line tools can be used even if you have not run
+@code{make install}.  To do that, you first need to have an environment with
+all the dependencies available (@pxref{Erstellung aus dem Git}), and then simply
+prefix each command with @command{./pre-inst-env} (the @file{pre-inst-env}
+script lives in the top build tree of Guix; it is generated by
+@command{./configure}), as in@footnote{The @option{-E} flag to
+@command{sudo} guarantees that @code{GUILE_LOAD_PATH} is correctly set such
+that @command{guix-daemon} and the tools it uses can find the Guile modules
+they need.}:
+
+@example
+$ sudo -E ./pre-inst-env guix-daemon --build-users-group=guixbuild
+$ ./pre-inst-env guix build hello
+@end example
+
+@noindent
+Entsprechend, um eine Guile-Sitzung zu öffnen, die die Guix-Module benutzt:
+
+@example
+$ ./pre-inst-env guile -c '(use-modules (guix utils)) (pk (%current-system))'
+
+;;; ("x86_64-linux")
+@end example
+
+@noindent
+@cindex REPL
+@cindex Lese-Auswerten-Schreiben-Schleife
+@dots{} und auf einer REPL (@pxref{Using Guile Interactively,,, guile, Guile
+Reference Manual}):
+
+@example
+$ ./pre-inst-env guile
+scheme@@(guile-user)> ,use(guix)
+scheme@@(guile-user)> ,use(gnu)
+scheme@@(guile-user)> (define snakes
+                       (fold-packages
+                         (lambda (package lst)
+                           (if (string-prefix? "python"
+                                               (package-name package))
+                               (cons package lst)
+                               lst))
+                         '()))
+scheme@@(guile-user)> (length snakes)
+$1 = 361
+@end example
+
+Das @command{pre-inst-env}-Skript richtet alle Umgebungsvariablen ein, die
+nötig sind, um dies zu ermöglichen, einschließlich @env{PATH} und
+@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/current}
+symlink (@pxref{Aufruf von guix pull}).  Run @command{git pull} instead if you
+want to upgrade your local source tree.
+
+
+@node Perfekt eingerichtet
+@section Perfekt eingerichtet
+
+Um perfekt für das Hacken an Guix eingerichtet zu sein, brauchen Sie an sich
+dasselbe wie um perfekt für das Hacken mit Guile (@pxref{Using Guile in
+Emacs,,, guile, Guile Reference Manual}).  Zunächst brauchen Sie mehr als
+ein Textverarbeitungsprogramm, Sie brauchen
+@url{http://www.gnu.org/software/emacs, Emacs}, ermächtigt vom wunderbaren
+@url{http://nongnu.org/geiser/, Geiser}.
+
+Geiser ermöglicht interaktive und inkrementelle Entwicklung aus Emacs
+heraus: Code kann in Puffern kompiliert und ausgewertet werden. Zugang zu
+Online-Dokumentation (Docstrings) steht ebenso zur Verfügung wie
+kontextabhängige Vervollständigung, @kbd{M-.} um zu einer Objektdefinition
+zu springen, eine REPL, um Ihren Code auszuprobieren, und mehr
+(@pxref{Einführung,,, geiser, Geiser User Manual}). Zur bequemen
+Guix-Entwicklung sollten Sie Guiles Ladepfad so ergänzen, dass die
+Quelldateien in Ihrem Checkout gefunden werden.
+
+@lisp
+;; @r{Angenommen das Guix-Checkout ist in ~/src/guix.}
+(with-eval-after-load 'geiser-guile
+  (add-to-list 'geiser-guile-load-path "~/src/guix"))
+@end lisp
+
+Um den Code tatsächlich zu bearbeiten, bietet Emacs schon einen netten
+Scheme-Modus. Aber Sie dürfen auch
+@url{http://www.emacswiki.org/emacs/ParEdit, Paredit} nicht verpassen. Es
+bietet Hilfsmittel, um direkt mit dem Syntaxbaum zu arbeiten, und kann so
+zum Beispiel einen S-Ausdruck hochheben oder ihn umhüllen, ihn verschlucken
+oder den nachfolgenden S-Ausdruck verwerfen, etc.
+
+@cindex Code-Schnipsel
+@cindex Vorlagen
+@cindex Tipparbeit sparen
+Wir bieten auch Vorlagen für häufige Git-Commit-Nachrichten und
+Paketdefinitionen im Verzeichnis @file{etc/snippets}. Diese Vorlagen können
+mit @url{http://joaotavora.github.io/yasnippet/, YASnippet} zusammen benutzt
+werden, um kurze Auslöse-Zeichenketten zu interaktiven Textschnipseln
+umzuschreiben. Vielleicht möchten Sie das Schnipselverzeichnis zu Ihrer
+@var{yas-snippet-dirs}-Variablen in Emacs hinzufügen.
+
+@lisp
+;; @r{Angenommen das Guix-Checkout ist in ~/src/guix.}
+(with-eval-after-load 'yasnippet
+  (add-to-list 'yas-snippet-dirs "~/src/guix/etc/snippets"))
+@end lisp
+
+The commit message snippets depend on @url{https://magit.vc/, Magit} to
+display staged files.  When editing a commit message type @code{add}
+followed by @kbd{TAB} to insert a commit message template for adding a
+package; type @code{update} followed by @kbd{TAB} to insert a template for
+updating a package; type @code{https} followed by @kbd{TAB} to insert a
+template for changing the home page URI of a package to HTTPS.
+
+Das Hauptschnipsel für @code{scheme-mode} wird ausgelöst, indem Sie
+@code{package...} gefolgt von @kbd{TAB} eintippen. Dieses Snippet fügt auch
+die Auslöse-Zeichenkette @code{origin...} ein, die danach weiter
+umgeschrieben werden kann. Das @code{origin}-Schnipsel kann wiederum andere
+Auslöse-Zeichenketten einfügen, die alle auf @code{...} enden, was selbst
+wieder weiter umgeschrieben werden kann.
+
+
+@node Code-Stil
+@section Code-Stil
+
+Im Allgemeinen folgt unser Code den GNU Coding Standards (@pxref{Top,,,
+standards, GNU Coding Standards}). Da diese aber nicht viel über Scheme zu
+sagen haben, folgen hier einige zusätzliche Regeln.
+
+@menu
+* Programmierparadigmen::    Wie Sie Ihre Elemente zusammenstellen.
+* Module::                   Wo Sie Ihren Code unterbringen.
+* Datentypen und Mustervergleich::  Implementierung von Datenstrukturen.
+* Formatierung von Code::    Schreibkonventionen.
+@end menu
+
+@node Programmierparadigmen
+@subsection Programmierparadigmen
+
+Scheme-Code wird in Guix auf rein funktionale Weise geschrieben. Eine
+Ausnahme ist Code, der mit Ein- und Ausgabe zu tun hat, und Prozeduren, die
+grundlegende Konzepte implementieren, wie zum Beispiel die Prozedur
+@code{memoize}.
+
+@node Module
+@subsection Module
+
+Guile-Module, die beim Erstellen nutzbar sein sollen, müssen im Namensraum
+@code{(guix build @dots{})} leben. Sie dürfen auf keine anderen Guix- oder
+GNU-Module Bezug nehmen. Jedoch ist es in Ordnung, wenn ein »wirtsseitiges«
+Modul ein erstellungsseitiges Modul benutzt.
+
+Module, die mit dem weiteren GNU-System zu tun haben, sollten im Namensraum
+@code{(gnu @dots{})} und nicht in @code{(guix @dots{})} stehen.
+
+@node Datentypen und Mustervergleich
+@subsection Datentypen und Mustervergleich
+
+Im klassischen Lisp gibt es die Tendenz, Listen zur Darstellung von allem zu
+benutzen, und diese dann »händisch« zu durchlaufen mit @code{car},
+@code{cdr}, @code{cadr} und so weiter. Dieser Stil ist aus verschiedenen
+Gründen problematisch, insbesondere wegen der Tatsache, dass er schwer zu
+lesen, schnell fehlerbehaftet und ein Hindernis beim Melden von Typfehlern
+ist.
+
+Guix-Code sollte angemessene Datentypen definieren (zum Beispiel mit
+@code{define-record-type*}) statt Listen zu missbrauchen. Außerdem sollte er
+das @code{(ice-9 match)}-Modul von Guile zum Mustervergleich benutzen,
+besonders mit Listen.
+
+@node Formatierung von Code
+@subsection Formatierung von Code
+
+@cindex Formatierung von Code
+@cindex Code-Stil
+Beim Schreiben von Scheme-Code halten wir uns an die üblichen
+Gepflogenheiten unter Scheme-Programmierern. Im Allgemeinen bedeutet das,
+dass wir uns an @url{http://mumble.net/~campbell/scheme/style.txt,
+Riastradh's Lisp Style Rules} halten. Es hat sich ergeben, dass dieses
+Dokument auch die Konventionen beschreibt, die im Code von Guile
+hauptsächlich verwendet werden. Es ist gut durchdacht und schön geschrieben,
+also lesen Sie es bitte.
+
+Ein paar in Guix eingeführte Sonderformen, wie zum Beispiel das
+@code{substitute*}-Makro, haben abweichende Regeln für die Einrückung. Diese
+sind in der Datei @file{.dir-locals.el} definiert, die Emacs automatisch
+benutzt. Beachten Sie auch, dass Emacs-Guix einen Modus namens
+@code{guix-devel-mode} bereitstellt, der Guix-Code richtig einrückt und
+hervorhebt (@pxref{Development,,, emacs-guix, The Emacs-Guix Reference
+Manual}).
+
+@cindex Einrückung, Code-
+@cindex Formatierung, Code-
+Falls Sie nicht Emacs verwenden, sollten Sie sicherstellen, dass Ihr Editor
+diese Regeln kennt. Um eine Paketdefinition automatisch einzurücken, können
+Sie auch Folgendes ausführen:
+
+@example
+./etc/indent-code.el gnu/packages/@var{Datei}.scm @var{Paket}
+@end example
+
+@noindent
+Dadurch wird die Definition von @var{Paket} in
+@file{gnu/packages/@var{Datei}.scm} automatisch eingerückt, indem Emacs im
+Batch-Modus läuft. Um die Einrückung in einer gesamten Datei vorzunehmen,
+lassen Sie das zweite Argument weg:
+
+@example
+./etc/indent-code.el gnu/services/@var{Datei}.scm
+@end example
+
+@cindex Vim, zum Editieren von Scheme-Code
+Wenn Sie Code mit Vim bearbeiten, empfehlen wir, dass Sie @code{:set
+autoindent} ausführen, damit Ihr Code automatisch eingerückt wird, während
+Sie ihn schreiben. Außerdem könnte Ihnen
+@uref{https://www.vim.org/scripts/script.php?script_id=3998,
+@code{paredit.vim}} dabei helfen, mit all diesen Klammern fertigzuwerden.
+
+Wir fordern von allen Prozeduren auf oberster Ebene, dass sie über einen
+Docstring verfügen. Diese Voraussetzung kann jedoch bei einfachen, privaten
+Prozeduren im Namensraum @code{(guix build @dots{})} aufgeweicht werden.
+
+Prozeduren sollten nicht mehr als vier positionsbestimmte Parameter
+haben. Benutzen Sie Schlüsselwort-Parameter für Prozeduren, die mehr als
+vier Parameter entgegennehmen.
+
+
+@node Einreichen von Patches
+@section Einreichen von Patches
+
+Die Entwicklung wird mit Hilfe des verteilten Versionskontrollsystems Git
+durchgeführt. Daher ist eine ständige Verbindung zum Repository nicht
+unbedingt erforderlich. Wir begrüßen Beiträge in Form von Patches, die
+mittels @code{git format-patch} erstellt und an die Mailingliste
+@email{guix-patches@@gnu.org} geschickt werden.
+
+Diese Mailing-Liste setzt auf einer Debbugs-Instanz auf, die zugänglich ist
+unter @uref{https://bugs.gnu.org/guix-patches}, wodurch wir den Überblick
+über Eingereichtes behalten können. Jede an diese Mailing-Liste gesendete
+Nachricht bekommt eine neue Folgenummer zugewiesen, so dass man eine
+Folge-Email zur Einreichung an @code{@var{NNN}@@debbugs.gnu.org} senden
+kann, wobei @var{NNN} für die Folgenummer steht (@pxref{Senden einer Patch-Reihe}).
+
+Bitte schreiben Sie Commit-Logs im ChangeLog-Format (@pxref{Change Logs,,,
+standards, GNU Coding Standards}); dazu finden Sie Beispiele unter den
+bisherigen Commits.
+
+Bevor Sie einen Patch einreichen, der eine Paketdefinition hinzufügt oder
+verändert, gehen Sie bitte diese Prüfliste durch:
+
+@enumerate
+@item
+Wenn die Autoren der verpackten Software eine kryptographische Signatur für
+den Tarball der Veröffentlichung anbieten, so machen Sie sich bitte die
+Mühe, die Echtheit des Archivs zu überprüfen.  Für eine abgetrennte
+GPG-Signaturdatei würden Sie das mit dem Befehl @code{gpg --verify} tun.
+
+@item
+Nehmen Sie sich die Zeit, eine passende Zusammenfassung und Beschreibung für
+das Paket zu verfassen. Unter @xref{Zusammenfassungen und Beschreibungen} finden Sie
+dazu einige Richtlinien.
+
+@item
+Verwenden Sie @code{guix lint @var{Paket}}, wobei @var{Paket} das neue oder
+geänderte Paket bezeichnet, und beheben Sie alle gemeldeten Fehler
+(@pxref{Aufruf von guix lint}).
+
+@item
+Stellen Sie sicher, dass das Paket auf Ihrer Plattform erstellt werden kann,
+indem Sie @code{guix build @var{Paket}} ausführen.
+
+@item
+@cindex gebündelt
+Achten Sie darauf, dass im Paket keine Software gebündelt mitgeliefert wird,
+die bereits in separaten Paketen zur Verfügung steht.
+
+Manchmal enthalten Pakete Kopien des Quellcodes ihrer Abhängigkeiten, um
+Nutzern die Installation zu erleichtern. Als eine Distribution wollen wir
+jedoch sicherstellen, dass solche Pakete die schon in der Distribution
+verfügbare Fassung benutzen, sofern es eine gibt. Dadurch wird sowohl der
+Ressourcenverbrauch optimiert (die Abhängigkeit wird so nur einmal erstellt
+und gespeichert) als auch der Distribution die Möglichkeit gegeben,
+ergänzende Änderungen durchzuführen, um beispielsweise
+Sicherheitsaktualisierungen für ein bestimmtes Paket an nur einem Ort
+einzuspielen, die aber das gesamte System betreffen — gebündelt
+mitgelieferte Kopien würden dies verhindern.
+
+@item
+Schauen Sie sich das von @command{guix size} ausgegebene Profil an
+(@pxref{Aufruf von guix size}). Dadurch können Sie Referenzen auf andere
+Pakete finden, die ungewollt vorhanden sind. Dies kann auch dabei helfen, zu
+entscheiden, ob das Paket aufgespalten werden sollte (@pxref{Pakete mit mehreren Ausgaben.}) und welche optionalen Abhängigkeiten verwendet werden
+sollten.
+
+@item
+Achten Sie bei wichtigen Änderungen darauf, dass abhängige Pakete (falls
+vorhanden) nicht von der Änderung beeinträchtigt werden; @code{guix refresh
+--list-dependent @var{Paket}} hilft Ihnen dabei (@pxref{Aufruf von guix refresh}).
+
+@c ===========================================================================
+@c
+@c This file was generated with po4a. Translate the source file.
+@c
+@c ===========================================================================
+@c See <https://lists.gnu.org/archive/html/guix-devel/2016-10/msg00933.html>.
+@cindex Branching-Strategie
+@cindex Neuerstellungs-Zeitplan
+Je nachdem, wieviele abhängige Pakete es gibt, und entsprechend wieviele
+Neuerstellungen dadurch nötig würden, finden Commits auf anderen Branches
+statt, nach ungefähr diesen Regeln:
+
+@table @asis
+@item 300 abhängige Pakete oder weniger
+@code{master}-Branch (störfreie Änderungen).
+
+@item zwischen 300 und 1200 abhängige Pakete
+@code{staging}-Branch (störfreie Änderungen). Dieser Branch wird circa alle
+3 Wochen in @code{master} gemerget. Themenbezogene Änderungen (z.B. eine
+Aktualisierung der GNOME-Plattform) können stattdessen auch auf einem
+eigenen Branch umgesetzt werden (wie @code{gnome-updates}).
+
+@item mehr als 1200 abhängige Pakete
+@code{core-updates}-Branch (kann auch größere und womöglich andere Software
+beeinträchtigende Änderungen umfassen). Dieser Branch wird planmäßig in
+@code{master} alle 2,5 Monate oder so gemerget.
+@end table
+
+All these branches are @uref{https://hydra.gnu.org/project/gnu, tracked by
+our build farm} and merged into @code{master} once everything has been
+successfully built.  This allows us to fix issues before they hit users, and
+to reduce the window during which pre-built binaries are not available.
+
+@c TODO: It would be good with badges on the website that tracks these
+@c branches.  Or maybe even a status page.
+Generally, branches other than @code{master} are considered @emph{frozen} if
+there has been a recent evaluation, or there is a corresponding @code{-next}
+branch.  Please ask on the mailing list or IRC if unsure where to place a
+patch.
+
+@item
+@cindex Determinismus, von Erstellungsprozessen
+@cindex Reproduzierbare Erstellungen, Überprüfung
+Überprüfen Sie, ob der Erstellungsprozess deterministisch ist. Dazu prüfen
+Sie typischerweise, ob eine unabhängige Erstellung des Pakets genau dasselbe
+Ergebnis wie Ihre Erstellung hat, Bit für Bit.
+
+Dies können Sie leicht tun, indem Sie dasselbe Paket mehrere Male
+hintereinander auf Ihrer Maschine erstellen (@pxref{Aufruf von guix build}):
+
+@example
+guix build --rounds=2 mein-paket
+@end example
+
+Dies reicht aus, um eine ganze Klasse häufiger Ursachen von
+Nichtdeterminismus zu finden, wie zum Beispiel Zeitstempel oder
+zufallsgenerierte Ausgaben im Ergebnis der Erstellung.
+
+Eine weitere Möglichkeit ist, @command{guix challenge} (@pxref{Aufruf von guix challenge}) zu benutzen. Sie können es ausführen, sobald ein Paket commitet
+und von @code{hydra.gnu.org} erstellt wurde, um zu sehen, ob dort dasselbe
+Ergebnis wie bei Ihnen geliefert wurde. Noch besser: Finden Sie eine andere
+Maschine, die das Paket erstellen kann, und führen Sie @command{guix
+publish} aus. Da sich die entfernte Erstellungsmaschine wahrscheinlich von
+Ihrer unterscheidet, können Sie auf diese Weise Probleme durch
+Nichtdeterminismus erkennen, die mit der Hardware zu tun haben — zum
+Beispiel die Nutzung anderer Befehlssatzerweiterungen — oder mit dem
+Betriebssystem-Kernel — zum Beispiel, indem @code{uname} oder
+@file{/proc}-Dateien verwendet werden.
+
+@item
+Beim Schreiben von Dokumentation achten Sie bitte auf eine
+geschlechtsneutrale Wortwahl, wenn Sie sich auf Personen beziehen, wie
+@uref{https://en.wikipedia.org/wiki/Singular_they, »they«@comma{}
+»their«@comma{} »them« im Singular}, und so weiter.
+
+@item
+Stelllen Sie sicher, dass Ihr Patch nur einen Satz zusammengehöriger
+Änderungen umfasst. Das Zusammenfassen nicht zusammengehöriger Änderungen
+erschwert und bremst das Durchsehen Ihres Patches.
+
+Beispiele für nicht zusammengehörige Änderungen sind das Hinzufügen mehrerer
+Pakete auf einmal, oder das Aktualisieren eines Pakets auf eine neue Version
+zusammen mit Fehlerbehebungen für das Paket.
+
+@item
+Bitte befolgen Sie unsere Richtlinien für die Code-Formatierung, womöglich
+wollen Sie dies automatisch tun lassen durch das Skript
+@command{etc/indent-code.el} (@pxref{Formatierung von Code}).
+
+@item
+When possible, use mirrors in the source URL (@pxref{Aufruf von guix download}).  Use reliable URLs, not generated ones.  For instance, GitHub
+archives are not necessarily identical from one generation to the next, so
+in this case it's often better to clone the repository.  Don't use the
+@command{name} field in the URL: it is not very useful and if the name
+changes, the URL will probably be wrong.
+
+@end enumerate
+
+Bitte benutzen Sie @samp{[PATCH] @dots{}} als Betreff, wenn Sie einen Patch
+an die Mailing-Liste schicken. Sie können dazu Ihr E-Mail-Programm oder den
+Befehl @command{git send-email} benutzen (@pxref{Senden einer Patch-Reihe}). Wir bevorzugen es, Patches als reine Textnachrichten zu erhalten,
+entweder eingebettet (inline) oder als MIME-Anhänge. Sie sind dazu
+angehalten, zu überprüfen, ob Ihr Mail-Programm solche Dinge wie
+Zeilenumbrüche oder die Einrückung verändert, wodurch die Patches womöglich
+nicht mehr funktionieren.
+
+Wenn dadurch ein Fehler behoben wurde, schließen Sie bitte den Thread, indem
+Sie eine E-Mail an @email{@var{NNN}-done@@debbugs.gnu.org} senden.
+
+@unnumberedsubsec Senden einer Patch-Reihe
+@anchor{Senden einer Patch-Reihe}
+@cindex Patch-Reihe
+@cindex @code{git send-email}
+@cindex @code{git-send-email}
+
+@c Debbugs bug: https://debbugs.gnu.org/db/15/15361.html
+Wenn Sie eine Patch-Reihe senden (z.B. mit @code{git send-email}), schicken
+Sie bitte als Erstes eine Nachricht an @email{guix-patches@@gnu.org} und
+dann nachfolgende Patches an @email{@var{NNN}@@debbugs.gnu.org}, um
+sicherzustellen, dass sie zusammen bearbeitet werden. Siehe
+@uref{https://debbugs.gnu.org/Advanced.html, die Debbugs-Dokumentation} für
+weitere Informationen.
@@ -111,13 +111,14 @@ distinguer votre rôle « d'utilisateur final » de celui parfois haut en
 couleur de « développeur ».

 Pour cela, tous les outils en ligne de commande sont utilisables même sans
-avoir lancé @code{make install}.  Vous devez pour cela préfixer chaque
-commande par @command{./pre-inst-env} (le script @file{pre-inst-env} se
-trouve dans le répertoire de plus haut niveau de l'arborescence des sources
-de Guix) comme cela@footnote{L'option @option{-E} de @command{sudo} garantie
-que @code{GUILE_LOAD_PATH} est bien paramétré pour @command{guix-daemon} et
-les outils qu'il utilise puissent trouver les modules Guile dont ils ont
-besoin.} :
+avoir lancé @code{make install}.  Pour cela, vous devez d'abord avoir un
+environnement avec toutes les dépendances disponibles (@pxref{Construire depuis Git}), puis préfixer chaque commande par @command{./pre-inst-env} (le script
+@file{pre-inst-env} se trouve dans le répertoire de plus haut niveau de
+l'arborescence des sources de Guix ; il est généré par
+@command{./configure}) comme cela@footnote{L'option @option{-E} de
+@command{sudo} garantie que @code{GUILE_LOAD_PATH} est bien paramétré pour
+@command{guix-daemon} et pour que les outils qu'il utilise puissent trouver
+les modules Guile dont ils ont besoin.} :

@example
 $ sudo -E ./pre-inst-env guix-daemon --build-users-group=guixbuild
@@ -217,7 +218,9 @@ Les extraits de messages de commit dépendent de @url{https://magit.vc/,
 Magit} pour afficher les fichiers sélectionnés.  Lors de la modification
 d'un message de commit, tapez @code{add} suivi de @kbd{TAB} pour insérer un
 modèle de message de commit pour ajouter un paquet ; tapez @code{update}
-suivi de @kbd{TAB} pour insérer un modèle pour la mise à jour d'un paquet.
+suivi de @kbd{TAB} pour insérer un modèle pour la mise à jour d'un paquet ;
+tapez @code{https} suivi de @kbd{TAB} pour insérer un modèle pour le
+changement à HTTPS de l'URI de la page d'accueil.

 L'extrait principal pour @code{scheme-mode} est lancé en tapant
@code{package…} suivi par @kbd{TAB}.  Cet extrait insère aussi la chaîne de
@@ -486,6 +489,13 @@ Suivez nos règles de formatage de code, éventuellement en lançant le script
@command{et/indent-code.el} pour le faire automatiquement (@pxref{Formatage
 du code}).

+@item
+Si possible, utilisez des miroirs dans l'URL des sources (@pxref{Invoquer guix download}).  Utilisez des URL stable, pas des URL générées.  Par
+exemple, les archives GitHub ne sont pas nécessairement identiques d'une
+génération à la suivante, donc il vaut mieux dans ce cas cloner le dépôt.
+N'utilisez pas le champ @command{name} dans l'URL : ce n'est pas très utile
+et si le nom change, l'URL sera probablement erronée.
+
@end enumerate

 Lorsque vous envoyez un correctif à la liste de diffusion, utilisez
@@ -112,7 +112,8 @@ run @code{make install}.  To do that, you first need to have an environment
 with all the dependencies available (@pxref{Building from Git}), and then
 simply prefix each command with
@command{./pre-inst-env} (the @file{pre-inst-env} script lives in the
-top build tree of Guix), as in@footnote{The @option{-E} flag to
+top build tree of Guix; it is generated by @command{./configure}),
+as in@footnote{The @option{-E} flag to
@command{sudo} guarantees that @code{GUILE_LOAD_PATH} is correctly set
 such that @command{guix-daemon} and the tools it uses can find the Guile
 modules they need.}:
@@ -212,7 +213,8 @@ The commit message snippets depend on @url{https://magit.vc/, Magit} to
 display staged files.  When editing a commit message type @code{add}
 followed by @kbd{TAB} to insert a commit message template for adding a
 package; type @code{update} followed by @kbd{TAB} to insert a template
-for updating a package.
+for updating a package; type @code{https} followed by @kbd{TAB} to
+insert a template for changing the home page URI of a package to HTTPS.

 The main snippet for @code{scheme-mode} is triggered by typing
@code{package...} followed by @kbd{TAB}.  This snippet also inserts the
@@ -441,7 +443,7 @@ as timestamps or randomly-generated output in the build result.

 Another option is to use @command{guix challenge} (@pxref{Invoking guix
 challenge}).  You may run it once the package has been committed and
-built by @code{hydra.gnu.org} to check whether it obtains the same
+built by @code{@value{SUBSTITUTE-SERVER}} to check whether it obtains the same
 result as you did.  Better yet: Find another machine that can build it
 and run @command{guix publish}.  Since the remote build machine is
 likely different from yours, this can catch non-determinism issues
@@ -467,6 +469,14 @@ Please follow our code formatting rules, possibly running the
@command{etc/indent-code.el} script to do that automatically for you
 (@pxref{Formatting Code}).

+@item
+When possible, use mirrors in the source URL (@pxref{Invoking guix download}).
+Use reliable URLs, not generated ones.  For instance, GitHub archives are not
+necessarily identical from one generation to the next, so in this case it's
+often better to clone the repository.  Don't use the @command{name} field in
+the URL: it is not very useful and if the name changes, the URL will probably
+be wrong.
+
@end enumerate

 When posting a patch to the mailing list, use @samp{[PATCH] @dots{}} as
@@ -22,7 +22,8 @@
 # along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

 info_TEXINFOS = %D%/guix.texi \
-  %D%/guix.fr.texi
+  %D%/guix.fr.texi \
+  %D%/guix.de.texi

 %C%_guix_TEXINFOS = \
  %D%/contributing.texi \
@@ -54,7 +55,9 @@ OS_CONFIG_EXAMPLES_TEXI =			\
  %D%/os-config-lightweight-desktop.texi

 TRANSLATED_INFO = \
+  %D%/guix.de.texi \
  %D%/guix.fr.texi \
+  %D%/contributing.de.texi \
  %D%/contributing.fr.texi

 # Bundle this file so that makeinfo finds it in out-of-source-tree builds.
@@ -1,5 +1,5 @@
 # GNU Guix --- Functional package management for GNU
-# Copyright © 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+# Copyright © 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 #
 # This file is part of GNU Guix.
 #
@@ -172,6 +172,8 @@ _guix_complete ()
                if _guix_is_dash_L
                then
                    _guix_complete_file
+		else
+		    _guix_complete_available_package "$word_at_point"
                fi
 	    elif _guix_is_command "download"
 	    then
@@ -7,4 +7,4 @@ start on runlevel [2345]

 stop on runlevel [016]

-exec @localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix-daemon --build-users-group=guixbuild
+exec @localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix-daemon --build-users-group=guixbuild
@@ -6,8 +6,8 @@
 Description=Build daemon for GNU Guix

 [Service]
-ExecStart=@localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix-daemon --build-users-group=guixbuild
-Environment=GUIX_LOCPATH=/root/.guix-profile/lib/locale
+ExecStart=@localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix-daemon --build-users-group=guixbuild
+Environment=GUIX_LOCPATH=@localstatedir@/guix/profiles/per-user/root/guix-profile/lib/locale
 RemainAfterExit=yes
 StandardOutput=syslog
 StandardError=syslog
@@ -160,6 +160,9 @@ chk_sys_arch()
        aarch64)
            local arch=aarch64
            ;;
+	armv7l)
+	    local arch=armhf
+	    ;;
        *)
            _err "${ERR}Unsupported CPU type: ${arch}"
            exit 1
@@ -266,12 +269,13 @@ sys_create_store()
    fi

    _msg "${INF}Linking the root user's profile"
-    ln -sf /var/guix/profiles/per-user/root/guix-profile \
-       "${ROOT_HOME}/.guix-profile"
+    mkdir -p "${ROOT_HOME}/.config/guix"
+    ln -sf /var/guix/profiles/per-user/root/current-guix \
+       "${ROOT_HOME}/.config/guix/current"

-    GUIX_PROFILE="${ROOT_HOME}/.guix-profile"
+    GUIX_PROFILE="${ROOT_HOME}/.config/guix/current"
    source "${GUIX_PROFILE}/etc/profile"
-    _msg "${PAS}activated root profile at /root/.guix-profile"
+    _msg "${PAS}activated root profile at ${ROOT_HOME}/.config/guix/current"
 }

 sys_create_build_user()
@@ -314,18 +318,18 @@ sys_enable_guix_daemon()

    info_path="/usr/local/share/info"
    local_bin="/usr/local/bin"
-    var_guix="/var/guix/profiles/per-user/root/guix-profile"
+    var_guix="/var/guix/profiles/per-user/root/current-guix"

    case "$INIT_SYS" in
        upstart)
            { initctl reload-configuration;
-              cp "${ROOT_HOME}/.guix-profile/lib/upstart/system/guix-daemon.conf" \
+              cp "${ROOT_HOME}/.config/guix/current/lib/upstart/system/guix-daemon.conf" \
                 /etc/init/ &&
                  start guix-daemon; } &&
                _msg "${PAS}enabled Guix daemon via upstart"
            ;;
        systemd)
-            { cp "${ROOT_HOME}/.guix-profile/lib/systemd/system/guix-daemon.service" \
+            { cp "${ROOT_HOME}/.config/guix/current/lib/systemd/system/guix-daemon.service" \
                 /etc/systemd/system/;
              chmod 664 /etc/systemd/system/guix-daemon.service;
              systemctl daemon-reload &&
@@ -335,7 +339,7 @@ sys_enable_guix_daemon()
            ;;
        NA|*)
            _msg "${ERR}unsupported init system; run the daemon manually:"
-            echo "  ${ROOT_HOME}/.guix-profile/bin/guix-daemon --build-users-group=guixbuild"
+            echo "  ${ROOT_HOME}/.config/guix/current/bin/guix-daemon --build-users-group=guixbuild"
            ;;
    esac

@@ -355,10 +359,10 @@ sys_authorize_build_farms()
    while true; do
        read -p "Permit downloading pre-built package binaries from the project's build farms? (yes/no) " yn
        case $yn in
-            [Yy]*) guix archive --authorize < "${ROOT_HOME}/.guix-profile/share/guix/hydra.gnu.org.pub" &&
+            [Yy]*) guix archive --authorize < "${ROOT_HOME}/.config/guix/current/share/guix/hydra.gnu.org.pub" &&
                         _msg "${PAS}Authorized public key for hydra.gnu.org";
-                   guix archive --authorize < "${ROOT_HOME}/.guix-profile/share/guix/berlin.guixsd.org.pub" &&
-                       _msg "${PAS}Authorized public key for berlin.guixsd.org";
+                   guix archive --authorize < "${ROOT_HOME}/.config/guix/current/share/guix/ci.guix.info.pub" &&
+                       _msg "${PAS}Authorized public key for ci.guix.info";
                   break;;
            [Nn]*) _msg "${INF}Skipped authorizing build farm public keys"
                   break;;
@@ -9,4 +9,4 @@ stop on runlevel [016]

 task

-exec @localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix publish --user=nobody --port=8181
+exec @localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix publish --user=nobody --port=8181
@@ -6,8 +6,8 @@
 Description=Publish the GNU Guix store

 [Service]
-ExecStart=@localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix publish --user=nobody --port=8181
-Environment=GUIX_LOCPATH=/root/.guix-profile/lib/locale
+ExecStart=@localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix publish --user=nobody --port=8181
+Environment=GUIX_LOCPATH=@localstatedir@/guix/profiles/per-user/root/guix-profile/lib/locale
 RemainAfterExit=yes
 StandardOutput=syslog
 StandardError=syslog
@@ -15,7 +15,9 @@
                 ((equal yas-text "hg-fetch")  "hg-reference...")
                 ((equal yas-text "cvs-fetch") "cvs-reference...")
                 (t "(string-append \\"https://\\" version \\".tar.gz\\")"))}$0)
- ${1:$(cond ((member yas-text '("git-fetch" "svn-fetch" "hg-fetch" "cvs-fetch"))
+ ${1:$(cond ((equal yas-text "git-fetch")
+             "(file-name (git-file-name name version))")
+            ((member yas-text '("svn-fetch" "hg-fetch" "cvs-fetch"))
             "(file-name (string-append name \\"-\\" version \\"-checkout\\"))")
            (t ""))}
 (sha256
@@ -7,7 +7,8 @@
    (name "$1")
    (version "$2")
    (source origin...$0)
-    (build-system ${3:$$(yas-choose-value "ant-build-system"
+    (build-system ${3:$$(yas-choose-value "android-ndk-build-system"
+                                          "ant-build-system"
                                          "asdf-build-system"
                                          "cargo-build-system"
                                          "cmake-build-system"
@@ -25,6 +26,7 @@
                                          "python-build-system"
                                          "r-build-system"
                                          "ruby-build-system"
+                                          "scons-build-system"
                                          "texlive-build-system"
                                          "trivial-build-system"
                                          "waf-build-system")})
@@ -0,0 +1,9 @@
+# -*- mode: snippet -*-
+# name: guix-commit-message-use-https-home-page
+# key: https
+# condition: git-commit-mode
+# --
+gnu: $1: Use HTTPS home page URI.
+
+* `(car (magit-staged-files))` ($1)[home-page]: Use HTTPS URI.
+`(mapconcat (lambda (file) (concat "* " file)) (cdr (magit-staged-files)) "\n")`
@@ -0,0 +1 @@
+berlin.guixsd.org.pub
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -33,7 +33,7 @@
    (origin
      (method git-fetch)
      (uri (git-reference
-             (url "git://git.savannah.gnu.org/guix/guix-artwork.git")
+             (url "https://git.savannah.gnu.org/git/guix/guix-artwork.git")
             (commit commit)))
      (file-name (string-append "guix-artwork-" (string-take commit 7)
                                "-checkout"))
@@ -19,12 +19,8 @@

 (define-module (gnu bootloader extlinux)
  #:use-module (gnu bootloader)
-  #:use-module (gnu system)
-  #:use-module (gnu build bootloader)
  #:use-module (gnu packages bootloaders)
  #:use-module (guix gexp)
-  #:use-module (guix monads)
-  #:use-module (guix records)
  #:use-module (guix utils)
  #:export (extlinux-bootloader
            extlinux-bootloader-gpt))
@@ -78,7 +74,7 @@ TIMEOUT ~a~%"
                      (format port "~%"))
                   #~())))))

-  (gexp->derivation "extlinux.conf" builder))
+  (computed-file "extlinux.conf" builder))



@@ -20,26 +20,18 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

 (define-module (gnu bootloader grub)
-  #:use-module (guix store)
-  #:use-module (guix packages)
-  #:use-module (guix derivations)
  #:use-module (guix records)
-  #:use-module (guix monads)
+  #:use-module ((guix utils) #:select (%current-system))
  #:use-module (guix gexp)
-  #:use-module (guix download)
  #:use-module (gnu artwork)
-  #:use-module (gnu system)
  #:use-module (gnu bootloader)
  #:use-module (gnu system uuid)
  #:use-module (gnu system file-systems)
  #:autoload   (gnu packages bootloaders) (grub)
-  #:autoload   (gnu packages compression) (gzip)
  #:autoload   (gnu packages gtk) (guile-cairo guile-rsvg)
-  #:autoload   (gnu packages guile) (guile-2.2)
  #:use-module (ice-9 match)
  #:use-module (ice-9 regex)
  #:use-module (srfi srfi-1)
-  #:use-module (rnrs bytevectors)
  #:export (grub-image
            grub-image?
            grub-image-aspect-ratio
@@ -121,14 +113,14 @@ otherwise."

 (define* (svg->png svg #:key width height)
  "Build a PNG of HEIGHT x WIDTH from SVG."
-  (gexp->derivation "grub-image.png"
-                    (with-imported-modules '((gnu build svg))
-                      (with-extensions (list guile-rsvg guile-cairo)
-                        #~(begin
-                            (use-modules (gnu build svg))
-                            (svg->png #+svg #$output
-                                      #:width #$width
-                                      #:height #$height))))))
+  (computed-file "grub-image.png"
+                 (with-imported-modules '((gnu build svg))
+                   (with-extensions (list guile-rsvg guile-cairo)
+                     #~(begin
+                         (use-modules (gnu build svg))
+                         (svg->png #+svg #$output
+                                   #:width #$width
+                                   #:height #$height))))))

 (define* (grub-background-image config #:key (width 1024) (height 768))
  "Return the GRUB background image defined in CONFIG with a ratio of
@@ -138,15 +130,13 @@ WIDTH/HEIGHT, or #f if none was found."
                        (= (grub-image-aspect-ratio image) ratio))
                      (grub-theme-images
                       (bootloader-theme config)))))
-    (if image
-        (svg->png (grub-image-file image)
-                  #:width width #:height height)
-        (with-monad %store-monad
-          (return #f)))))
+    (and image
+         (svg->png (grub-image-file image)
+                   #:width width #:height height))))

 (define* (eye-candy config store-device store-mount-point
                    #:key system port)
-  "Return in %STORE-MONAD a gexp that writes to PORT (a port-valued gexp) the
+  "Return a gexp that writes to PORT (a port-valued gexp) the
 'grub.cfg' part concerned with graphics mode, background images, colors, and
 all that.  STORE-DEVICE designates the device holding the store, and
 STORE-MOUNT-POINT is its mount point; these are used to determine where the
@@ -194,9 +184,11 @@ fi~%" #$font-file)
    (strip-mount-point store-mount-point
                       (file-append grub "/share/grub/unicode.pf2")))

-  (mlet* %store-monad ((image (grub-background-image config)))
-    (return (and image
-                 #~(format #$port "
+  (define image
+    (grub-background-image config))
+
+  (and image
+       #~(format #$port "
 function setup_gfxterm {~a}

 # Set 'root' to the partition that contains /gnu/store.
@@ -213,14 +205,14 @@ else
  set menu_color_normal=cyan/blue
  set menu_color_highlight=white/blue
 fi~%"
-                           #$setup-gfxterm-body
-                           #$(grub-root-search store-device font-file)
-                           #$(setup-gfxterm config font-file)
-                           #$(grub-setup-io config)
+                 #$setup-gfxterm-body
+                 #$(grub-root-search store-device font-file)
+                 #$(setup-gfxterm config font-file)
+                 #$(grub-setup-io config)

-                           #$(strip-mount-point store-mount-point image)
-                           #$(theme-colors grub-theme-color-normal)
-                           #$(theme-colors grub-theme-color-highlight))))))
+                 #$(strip-mount-point store-mount-point image)
+                 #$(theme-colors grub-theme-color-normal)
+                 #$(theme-colors grub-theme-color-highlight))))


 ;;;
@@ -331,36 +323,36 @@ entries corresponding to old generations of the system."
                  #$(grub-root-search device kernel)
                  #$kernel (string-join (list #$@arguments))
                  #$initrd))))
-  (mlet %store-monad ((sugar (eye-candy config
-                                        (menu-entry-device
-                                         (first all-entries))
-                                        (menu-entry-device-mount-point
-                                         (first all-entries))
-                                        #:system system
-                                        #:port #~port)))
-    (define builder
-      #~(call-with-output-file #$output
-          (lambda (port)
-            (format port
-                    "# This file was generated from your GuixSD configuration.  Any changes
+  (define sugar
+    (eye-candy config
+               (menu-entry-device (first all-entries))
+               (menu-entry-device-mount-point (first all-entries))
+               #:system system
+               #:port #~port))
+
+  (define builder
+    #~(call-with-output-file #$output
+        (lambda (port)
+          (format port
+                  "# This file was generated from your GuixSD configuration.  Any changes
 # will be lost upon reconfiguration.
 ")
-            #$sugar
-            (format port "
+          #$sugar
+          (format port "
 set default=~a
 set timeout=~a~%"
-                    #$(bootloader-configuration-default-entry config)
-                    #$(bootloader-configuration-timeout config))
-            #$@(map menu-entry->gexp all-entries)
+                  #$(bootloader-configuration-default-entry config)
+                  #$(bootloader-configuration-timeout config))
+          #$@(map menu-entry->gexp all-entries)

-            #$@(if (pair? old-entries)
-                   #~((format port "
+          #$@(if (pair? old-entries)
+                 #~((format port "
 submenu \"GNU system, old configurations...\" {~%")
-                      #$@(map menu-entry->gexp old-entries)
-                      (format port "}~%"))
-                   #~()))))
+                    #$@(map menu-entry->gexp old-entries)
+                    (format port "}~%"))
+                 #~()))))

-    (gexp->derivation "grub.cfg" builder)))
+  (computed-file "grub.cfg" builder))



@@ -20,23 +20,19 @@
 (define-module (gnu bootloader u-boot)
  #:use-module (gnu bootloader extlinux)
  #:use-module (gnu bootloader)
-  #:use-module (gnu system)
-  #:use-module (gnu build bootloader)
  #:use-module (gnu packages bootloaders)
  #:use-module (guix gexp)
-  #:use-module (guix monads)
-  #:use-module (guix records)
-  #:use-module (guix utils)
  #:export (u-boot-bootloader
            u-boot-a20-olinuxino-lime-bootloader
            u-boot-a20-olinuxino-lime2-bootloader
            u-boot-a20-olinuxino-micro-bootloader
-            u-boot-banana-pi-m2-ultra-bootloader
+            u-boot-bananapi-m2-ultra-bootloader
            u-boot-beaglebone-black-bootloader
            u-boot-mx6cuboxi-bootloader
            u-boot-nintendo-nes-classic-edition-bootloader
            u-boot-novena-bootloader
            u-boot-pine64-plus-bootloader
+            u-boot-pinebook-bootloader
            u-boot-puma-rk3399-bootloader
            u-boot-wandboard-bootloader))

@@ -148,10 +144,10 @@
   (inherit u-boot-allwinner-bootloader)
   (package u-boot-a20-olinuxino-micro)))

-(define u-boot-banana-pi-m2-ultra-bootloader
+(define u-boot-bananapi-m2-ultra-bootloader
  (bootloader
   (inherit u-boot-allwinner-bootloader)
-   (package u-boot-banana-pi-m2-ultra)))
+   (package u-boot-bananapi-m2-ultra)))

 (define u-boot-mx6cuboxi-bootloader
  (bootloader
@@ -173,6 +169,11 @@
   (inherit u-boot-allwinner64-bootloader)
   (package u-boot-pine64-plus)))

+(define u-boot-pinebook-bootloader
+  (bootloader
+   (inherit u-boot-allwinner64-bootloader)
+   (package u-boot-pinebook)))
+
 (define u-boot-puma-rk3399-bootloader
  (bootloader
   (inherit u-boot-bootloader)
@@ -148,11 +148,15 @@ properties.  Return #t on success."
                          `("-G" ,(string-join supplementary-groups ","))
                          '())
                    ,@(if comment `("-c" ,comment) '())
-                    ,@(if (and home create-home?)
-                          (if (file-exists? home)
-                              `("-d" ,home)     ; avoid warning from 'useradd'
-                              `("-d" ,home "--create-home"))
+                    ,@(if home `("-d" ,home) '())
+
+                    ;; Home directories of non-system accounts are created by
+                    ;; 'activate-user-home'.
+                    ,@(if (and home create-home? system?
+                               (not (file-exists? home)))
+                          '("--create-home")
                          '())
+
                    ,@(if shell `("-s" ,shell) '())
                    ,@(if password `("-p" ,password) '())
                    ,@(if system? '("--system") '())
@@ -229,10 +233,7 @@ numeric gid or #f."
                     #:supplementary-groups supplementary-groups
                     #:comment comment
                     #:home home
-
-                     ;; Home directories of non-system accounts are created by
-                     ;; 'activate-user-home'.
-                     #:create-home? (and create-home? system?)
+                     #:create-home? create-home?

                     #:shell shell
                     #:password password)
@@ -18,7 +18,6 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

 (define-module (gnu build install)
-  #:use-module (guix store database)
  #:use-module (guix build utils)
  #:use-module (guix build store-copy)
  #:use-module (srfi srfi-26)
@@ -27,6 +26,7 @@
            evaluate-populate-directive
            populate-root-file-system
            register-closure
+            install-database-and-gc-roots
            populate-single-profile-directory))

 ;;; Commentary:
@@ -141,41 +141,53 @@ includes /etc, /var, /run, /bin/sh, etc., and all the symlinks to SYSTEM."
                (try))
              (apply throw args)))))))

-(define* (register-closure prefix closure
-                           #:key
-                           (deduplicate? #t) (reset-timestamps? #t)
-                           (schema (sql-schema)))
-  "Register CLOSURE in PREFIX, where PREFIX is the directory name of the
-target store and CLOSURE is the name of a file containing a reference graph as
-produced by #:references-graphs..  As a side effect, if RESET-TIMESTAMPS? is
-true, reset timestamps on store files and, if DEDUPLICATE? is true,
-deduplicates files common to CLOSURE and the rest of PREFIX."
-  (let ((items (call-with-input-file closure read-reference-graph)))
-    (register-items items
-                    #:prefix prefix
-                    #:deduplicate? deduplicate?
-                    #:reset-timestamps? reset-timestamps?
-                    #:registration-time %epoch
-                    #:schema schema)))
+(define %root-profile
+  "/var/guix/profiles/per-user/root")
+
+(define* (install-database-and-gc-roots root database profile
+                                        #:key (profile-name "guix-profile"))
+  "Install DATABASE, the store database, under directory ROOT.  Create
+PROFILE-NAME and have it link to PROFILE, a store item."
+  (define (scope file)
+    (string-append root "/" file))
+
+  (define (mkdir-p* dir)
+    (mkdir-p (scope dir)))
+
+  (define (symlink* old new)
+    (symlink old (scope new)))
+
+  (install-file database (scope "/var/guix/db/"))
+  (chmod (scope "/var/guix/db/db.sqlite") #o644)
+  (mkdir-p* "/var/guix/profiles")
+  (mkdir-p* "/var/guix/gcroots")
+  (symlink* "/var/guix/profiles" "/var/guix/gcroots/profiles")
+
+  ;; Make root's profile, which makes it a GC root.
+  (mkdir-p* %root-profile)
+  (symlink* profile
+            (string-append %root-profile "/" profile-name "-1-link"))
+  (symlink* (string-append profile-name "-1-link")
+            (string-append %root-profile "/" profile-name)))

 (define* (populate-single-profile-directory directory
                                            #:key profile closure
-                                            deduplicate?
-                                            register? schema)
+                                            (profile-name "guix-profile")
+                                            database)
  "Populate DIRECTORY with a store containing PROFILE, whose closure is given
 in the file called CLOSURE (as generated by #:references-graphs.)  DIRECTORY
 is initialized to contain a single profile under /root pointing to PROFILE.
-When REGISTER? is true, initialize DIRECTORY/var/guix/db to reflect the
-contents of the store; DEDUPLICATE? determines whether to deduplicate files in
-the store.
+
+When DATABASE is true, copy it to DIRECTORY/var/guix/db and create
+DIRECTORY/var/guix/gcroots and friends.
+
+PROFILE-NAME is the name of the profile being created under
+/var/guix/profiles, typically either \"guix-profile\" or \"current-guix\".

 This is used to create the self-contained tarballs with 'guix pack'."
  (define (scope file)
    (string-append directory "/" file))

-  (define %root-profile
-    "/var/guix/profiles/per-user/root")
-
  (define (mkdir-p* dir)
    (mkdir-p (scope dir)))

@@ -185,25 +197,20 @@ This is used to create the self-contained tarballs with 'guix pack'."
  ;; Populate the store.
  (populate-store (list closure) directory)

-  (when register?
-    (register-closure (canonicalize-path directory) closure
-                      #:deduplicate? deduplicate?
-                      #:schema schema)
+  (when database
+    (install-database-and-gc-roots directory database profile
+                                   #:profile-name profile-name))

-    (mkdir-p* "/var/guix/profiles")
-    (mkdir-p* "/var/guix/gcroots")
-    (symlink* "/var/guix/profiles"
-              "/var/guix/gcroots/profiles"))
-
-  ;; Make root's profile, which makes it a GC root.
-  (mkdir-p* %root-profile)
-  (symlink* profile
-            (string-append %root-profile "/guix-profile-1-link"))
-  (symlink* (string-append %root-profile "/guix-profile-1-link")
-            (string-append %root-profile "/guix-profile"))
-
-  (mkdir-p* "/root")
-  (symlink* (string-append %root-profile "/guix-profile")
-            "/root/.guix-profile"))
+  (match profile-name
+    ("guix-profile"
+     (mkdir-p* "/root")
+     (symlink* (string-append %root-profile "/guix-profile")
+               "/root/.guix-profile"))
+    ("current-guix"
+     (mkdir-p* "/root/.config/guix")
+     (symlink* (string-append %root-profile "/current-guix")
+               "/root/.config/guix/current"))
+    (_
+     #t)))

 ;;; install.scm ends here
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -72,11 +72,23 @@ COMPRESS? is true, compress it using GZIP.  On success, return OUTPUT."
                               #:file->header cpio:file->cpio-header*)))

  (or (not compress?)
-      ;; Use '--no-name' so that gzip records neither a file name nor a time
-      ;; stamp in its output.
-      (and (zero? (system* gzip "--best" "--no-name" output))
-           (rename-file (string-append output ".gz")
-                        output))
+
+      ;; Gzip insists on adding a '.gz' suffix and does nothing if the input
+      ;; file already has that suffix.  Shuffle files around to placate it.
+      (let* ((gz-suffix? (string-suffix? ".gz" output))
+             (sans-gz    (if gz-suffix?
+                             (string-drop-right output 3)
+                             output)))
+        (when gz-suffix?
+          (rename-file output sans-gz))
+        ;; Use '--no-name' so that gzip records neither a file name nor a time
+        ;; stamp in its output.
+        (and (zero? (system* gzip "--best" "--no-name" sans-gz))
+             (begin
+               (unless gz-suffix?
+                 (rename-file (string-append output ".gz") output))
+               output)))
+
      output))

 (define (cache-compiled-file-name file)
@@ -139,6 +151,12 @@ REFERENCES-GRAPHS."

    (write-cpio-archive output "." #:gzip gzip))

+  ;; Make sure directories are writable so we can delete files.
+  (for-each make-file-writable
+            (find-files "contents"
+                        (lambda (file stat)
+                          (eq? 'directory (stat:type stat)))
+                        #:directories? #t))
  (delete-file-recursively "contents"))

 ;;; linux-initrd.scm ends here
@@ -21,6 +21,7 @@
  #:use-module (guix elf)
  #:use-module (guix glob)
  #:use-module (guix build syscalls)
+  #:use-module ((guix build utils) #:select (find-files))
  #:use-module (rnrs io ports)
  #:use-module (rnrs bytevectors)
  #:use-module (srfi srfi-1)
@@ -33,6 +34,8 @@
            module-aliases
            module-dependencies
            normalize-module-name
+            file-name->module-name
+            find-module-file
            recursive-module-dependencies
            modules-loaded
            module-loaded?
@@ -55,11 +58,10 @@

 (define (section-contents elf section)
  "Return the contents of SECTION in ELF as a bytevector."
-  (let* ((modinfo  (elf-section-by-name elf ".modinfo"))
-         (contents (make-bytevector (elf-section-size modinfo))))
-    (bytevector-copy! (elf-bytes elf) (elf-section-offset modinfo)
+  (let ((contents (make-bytevector (elf-section-size section))))
+    (bytevector-copy! (elf-bytes elf) (elf-section-offset section)
                      contents 0
-                      (elf-section-size modinfo))
+                      (elf-section-size section))
    contents))

 (define %not-nul
@@ -82,7 +84,8 @@ string list."
 key/value pairs.."
  (let* ((bv      (call-with-input-file file get-bytevector-all))
         (elf     (parse-elf bv))
-         (modinfo (section-contents elf ".modinfo")))
+         (section (elf-section-by-name elf ".modinfo"))
+         (modinfo (section-contents elf section)))
    (map key=value->pair
         (nul-separated-string->list (utf8->string modinfo)))))

@@ -130,6 +133,39 @@ underscores."
 and normalizing it."
  (normalize-module-name (basename file ".ko")))

+(define (find-module-file directory module)
+  "Lookup module NAME under DIRECTORY, and return its absolute file name.
+NAME can be a file name with or without '.ko', or it can be a module name.
+Raise an error if it could not be found.
+
+Module names can differ from file names in interesting ways; for instance,
+module names usually (always?) use underscores as the inter-word separator,
+whereas file names often, but not always, use hyphens.  Examples:
+\"usb-storage.ko\", \"serpent_generic.ko\"."
+  (define names
+    ;; List of possible file names.  XXX: It would of course be cleaner to
+    ;; have a database that maps module names to file names and vice versa,
+    ;; but everyone seems to be doing hacks like this one.  Oh well!
+    (map ensure-dot-ko
+         (delete-duplicates
+          (list module
+                (normalize-module-name module)
+                (string-map (lambda (chr) ;converse of 'normalize-module-name'
+                              (case chr
+                                ((#\_) #\-)
+                                (else chr)))
+                            module)))))
+
+  (match (find-files directory
+                     (lambda (file stat)
+                       (member (basename file) names)))
+    ((file)
+     file)
+    (()
+     (error "kernel module not found" module directory))
+    ((_ ...)
+     (error "several modules by that name" module directory))))
+
 (define* (recursive-module-dependencies files
                                        #:key (lookup-module dot-ko))
  "Return the topologically-sorted list of file names of the modules depended
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2018 Chris Marusich <cmmarusich@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,6 +28,7 @@
            marionette-eval
            wait-for-file
            wait-for-tcp-port
+            wait-for-unix-socket
            marionette-control
            marionette-screen-text
            wait-for-screen-text
@@ -214,6 +216,29 @@ MARIONETTE.  Raise an error on failure."
    ('failure
     (error "nobody's listening on port" port))))

+(define* (wait-for-unix-socket file-name marionette
+                                #:key (timeout 20))
+  "Wait for up to TIMEOUT seconds for FILE-NAME, a Unix domain socket, to
+accept connections in MARIONETTE.  Raise an error on failure."
+  (match (marionette-eval
+          `(begin
+             (let ((sock (socket PF_UNIX SOCK_STREAM 0)))
+               (let loop ((i 0))
+                 (catch 'system-error
+                   (lambda ()
+                     (connect sock AF_UNIX ,file-name)
+                     'success)
+                   (lambda args
+                     (if (< i ,timeout)
+                         (begin
+                           (sleep 1)
+                           (loop (+ 1 i)))
+                         'failure))))))
+          marionette)
+    ('success #t)
+    ('failure
+     (error "nobody's listening on unix domain socket" file-name))))
+
 (define (marionette-control command marionette)
  "Run COMMAND in the QEMU monitor of MARIONETTE.  COMMAND is a string such as
 \"sendkey ctrl-alt-f1\" or \"screendump foo.ppm\" (info \"(qemu-doc)
@@ -222,7 +247,8 @@ pcsys_monitor\")."
    (($ <marionette> _ _ monitor)
     (display command monitor)
     (newline monitor)
-     (wait-for-monitor-prompt monitor))))
+     ;; The "quit" command terminates QEMU immediately, with no output.
+     (unless (string=? command "quit") (wait-for-monitor-prompt monitor)))))

 (define* (marionette-screen-text marionette
                                 #:key
@@ -25,7 +25,7 @@
  #:use-module (guix build utils)
  #:use-module (guix build store-copy)
  #:use-module (guix build syscalls)
-  #:use-module ((guix store database) #:select (reset-timestamps))
+  #:use-module (guix store database)
  #:use-module (gnu build linux-boot)
  #:use-module (gnu build install)
  #:use-module (gnu system uuid)
@@ -191,6 +191,23 @@ the #:references-graphs parameter of 'derivation'."
          (mkdir output)
          (copy-recursively "xchg" output)))))

+(define* (register-closure prefix closure
+                           #:key
+                           (deduplicate? #t) (reset-timestamps? #t)
+                           (schema (sql-schema)))
+  "Register CLOSURE in PREFIX, where PREFIX is the directory name of the
+target store and CLOSURE is the name of a file containing a reference graph as
+produced by #:references-graphs..  As a side effect, if RESET-TIMESTAMPS? is
+true, reset timestamps on store files and, if DEDUPLICATE? is true,
+deduplicates files common to CLOSURE and the rest of PREFIX."
+  (let ((items (call-with-input-file closure read-reference-graph)))
+    (register-items items
+                    #:prefix prefix
+                    #:deduplicate? deduplicate?
+                    #:reset-timestamps? reset-timestamps?
+                    #:registration-time %epoch
+                    #:schema schema)))
+

 ;;;
 ;;; Partitions.
@@ -15,9 +15,11 @@
 # Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 # Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
 # Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
-# Copyright © 2017 Gábor Boskovits <boskovits@gmail.com>
+# Copyright © 2017, 2018 Gábor Boskovits <boskovits@gmail.com>
 # Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
 # Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+# Copyright © 2018 Stefan Stefanović <stefanx2ovic@gmail.com>
+# Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 #
 # This file is part of GNU Guix.
 #
@@ -59,6 +61,7 @@ GNU_SYSTEM_MODULES =				\
  %D%/packages/android.scm			\
  %D%/packages/animation.scm			\
  %D%/packages/anthy.scm			\
+  %D%/packages/antivirus.scm			\
  %D%/packages/apl.scm				\
  %D%/packages/apr.scm				\
  %D%/packages/aspell.scm			\
@@ -67,6 +70,7 @@ GNU_SYSTEM_MODULES =				\
  %D%/packages/attr.scm				\
  %D%/packages/audio.scm			\
  %D%/packages/augeas.scm			\
+  %D%/packages/authentication.scm		\
  %D%/packages/autogen.scm			\
  %D%/packages/autotools.scm			\
  %D%/packages/avahi.scm			\
@@ -75,6 +79,7 @@ GNU_SYSTEM_MODULES =				\
  %D%/packages/backup.scm			\
  %D%/packages/base.scm				\
  %D%/packages/bash.scm				\
+  %D%/packages/batik.scm			\
  %D%/packages/bdw-gc.scm			\
  %D%/packages/benchmark.scm			\
  %D%/packages/bioconductor.scm			\
@@ -96,6 +101,7 @@ GNU_SYSTEM_MODULES =				\
  %D%/packages/chez.scm				\
  %D%/packages/ci.scm				\
  %D%/packages/cinnamon.scm			\
+  %D%/packages/clojure.scm			\
  %D%/packages/cluster.scm			\
  %D%/packages/cmake.scm			\
  %D%/packages/cobol.scm			\
@@ -133,6 +139,7 @@ GNU_SYSTEM_MODULES =				\
  %D%/packages/display-managers.scm		\
  %D%/packages/django.scm			\
  %D%/packages/djvu.scm				\
+  %D%/packages/dlang.scm			\
  %D%/packages/dns.scm				\
  %D%/packages/docbook.scm			\
  %D%/packages/docker.scm			\
@@ -211,6 +218,7 @@ GNU_SYSTEM_MODULES =				\
  %D%/packages/guile-wm.scm			\
  %D%/packages/gv.scm				\
  %D%/packages/gxmessage.scm			\
+  %D%/packages/hardware.scm			\
  %D%/packages/haskell.scm			\
  %D%/packages/haskell-check.scm		\
  %D%/packages/haskell-crypto.scm		\
@@ -229,6 +237,7 @@ GNU_SYSTEM_MODULES =				\
  %D%/packages/imagemagick.scm			\
  %D%/packages/inklingreader.scm		\
  %D%/packages/inkscape.scm			\
+  %D%/packages/ipfs.scm			\
  %D%/packages/irc.scm  			\
  %D%/packages/iso-codes.scm			\
  %D%/packages/java.scm				\
@@ -242,7 +251,6 @@ GNU_SYSTEM_MODULES =				\
  %D%/packages/key-mon.scm			\
  %D%/packages/kodi.scm				\
  %D%/packages/language.scm			\
-  %D%/packages/ldc.scm				\
  %D%/packages/lego.scm				\
  %D%/packages/less.scm				\
  %D%/packages/lesstif.scm			\
@@ -340,6 +348,7 @@ GNU_SYSTEM_MODULES =				\
  %D%/packages/perl-check.scm			\
  %D%/packages/perl-web.scm			\
  %D%/packages/photo.scm			\
+  %D%/packages/phabricator.scm 			\
  %D%/packages/php.scm				\
  %D%/packages/pkg-config.scm			\
  %D%/packages/plotutils.scm			\
@@ -403,6 +412,7 @@ GNU_SYSTEM_MODULES =				\
  %D%/packages/sssd.scm				\
  %D%/packages/stalonetray.scm			\
  %D%/packages/statistics.scm			\
+  %D%/packages/stb.scm				\
  %D%/packages/storage.scm			\
  %D%/packages/suckless.scm			\
  %D%/packages/swig.scm				\
@@ -483,6 +493,7 @@ GNU_SYSTEM_MODULES =				\
  %D%/services/monitoring.scm			\
  %D%/services/networking.scm			\
  %D%/services/nfs.scm			\
+  %D%/services/security-token.scm		\
  %D%/services/shepherd.scm			\
  %D%/services/sound.scm			\
  %D%/services/herd.scm				\
@@ -524,18 +535,19 @@ GNU_SYSTEM_MODULES =				\
  %D%/build/vm.scm				\
 						\
  %D%/tests.scm					\
-  %D%/tests/admin.scm				\
  %D%/tests/audio.scm				\
  %D%/tests/base.scm				\
  %D%/tests/databases.scm			\
  %D%/tests/desktop.scm				\
  %D%/tests/dict.scm				\
+  %D%/tests/monitoring.scm                      \
  %D%/tests/nfs.scm				\
  %D%/tests/install.scm				\
  %D%/tests/mail.scm				\
  %D%/tests/messaging.scm			\
  %D%/tests/networking.scm			\
  %D%/tests/rsync.scm				\
+  %D%/tests/security-token.scm			\
  %D%/tests/ssh.scm				\
  %D%/tests/version-control.scm			\
  %D%/tests/virtualization.scm			\
@@ -562,8 +574,9 @@ dist_patch_DATA =						\
  %D%/packages/patches/aegis-perl-tempdir2.patch           	\
  %D%/packages/patches/aegis-test-fixup-1.patch            	\
  %D%/packages/patches/aegis-test-fixup-2.patch            	\
+  %D%/packages/patches/aegisub-icu59-include-unistr.patch	\
+  %D%/packages/patches/aegisub-boost68.patch                    \
  %D%/packages/patches/agg-am_c_prototype.patch			\
-  %D%/packages/patches/alsa-lib-add-environment-variable.patch \
  %D%/packages/patches/amule-crypto-6.patch			\
  %D%/packages/patches/ansible-wrap-program-hack.patch		\
  %D%/packages/patches/antiword-CVE-2014-8123.patch			\
@@ -578,39 +591,49 @@ dist_patch_DATA =						\
  %D%/packages/patches/audacity-build-with-system-portaudio.patch \
  %D%/packages/patches/automake-skip-amhello-tests.patch	\
  %D%/packages/patches/avahi-localstatedir.patch		\
+  %D%/packages/patches/avogadro-boost148.patch			\
+  %D%/packages/patches/avogadro-eigen3-update.patch		\
+  %D%/packages/patches/avogadro-python-eigen-lib.patch		\
  %D%/packages/patches/avidemux-install-to-lib.patch		\
  %D%/packages/patches/awesome-reproducible-png.patch		\
  %D%/packages/patches/azr3.patch				\
  %D%/packages/patches/bash-completion-directories.patch	\
+  %D%/packages/patches/bastet-change-source-of-unordered_set.patch	\
  %D%/packages/patches/bazaar-CVE-2017-14176.patch		\
+  %D%/packages/patches/beets-python-3.7-fix.patch		\
  %D%/packages/patches/beignet-correct-file-names.patch		\
-  %D%/packages/patches/bind-CVE-2018-5738.patch			\
-  %D%/packages/patches/binutils-aarch64-symbol-relocation.patch	\
  %D%/packages/patches/binutils-loongson-workaround.patch	\
  %D%/packages/patches/blast+-fix-makefile.patch		\
+  %D%/packages/patches/blender-newer-ffmpeg.patch		\
  %D%/packages/patches/boost-fix-icu-build.patch		\
-  %D%/packages/patches/btrfs-progs-e-value-block.patch		\
+  %D%/packages/patches/borg-respect-storage-quota.patch		\
  %D%/packages/patches/byobu-writable-status.patch		\
  %D%/packages/patches/cairo-CVE-2016-9082.patch			\
+  %D%/packages/patches/cairo-setjmp-wrapper.patch		\
  %D%/packages/patches/calibre-no-updates-dialog.patch		\
  %D%/packages/patches/calibre-use-packaged-feedparser.patch	\
+  %D%/packages/patches/casync-renameat2-declaration.patch	\
  %D%/packages/patches/catdoc-CVE-2017-11110.patch		\
  %D%/packages/patches/cdparanoia-fpic.patch			\
  %D%/packages/patches/cdrtools-3.01-mkisofs-isoinfo.patch 	\
+  %D%/packages/patches/ceph-detect-rocksdb.patch		\
  %D%/packages/patches/ceph-disable-cpu-optimizations.patch	\
-  %D%/packages/patches/ceph-rocksdb-compat.patch		\
  %D%/packages/patches/ceph-skip-collect-sys-info-test.patch	\
  %D%/packages/patches/ceph-skip-unittest_blockdev.patch	\
+  %D%/packages/patches/ceph-volume-respect-PATH.patch		\
  %D%/packages/patches/chmlib-inttypes.patch			\
+  %D%/packages/patches/clamav-config-llvm-libs.patch		\
+  %D%/packages/patches/clamav-system-tomsfastmath.patch		\
  %D%/packages/patches/clang-3.5-libc-search-path.patch		\
+  %D%/packages/patches/clang-3.5-libsanitizer-ustat-fix.patch	\
  %D%/packages/patches/clang-3.8-libc-search-path.patch		\
  %D%/packages/patches/clang-6.0-libc-search-path.patch		\
  %D%/packages/patches/clang-runtime-asan-build-fixes.patch	\
  %D%/packages/patches/clang-runtime-esan-build-fixes.patch	\
  %D%/packages/patches/classpath-aarch64-support.patch		\
+  %D%/packages/patches/clementine-fix-sqlite.patch		\
  %D%/packages/patches/clementine-remove-crypto++-dependency.patch	\
  %D%/packages/patches/clementine-use-openssl.patch		\
-  %D%/packages/patches/clisp-glibc-2.26.patch			\
  %D%/packages/patches/clisp-remove-failing-test.patch		\
  %D%/packages/patches/clucene-pkgconfig.patch			\
  %D%/packages/patches/clx-remove-demo.patch			\
@@ -624,7 +647,6 @@ dist_patch_DATA =						\
  %D%/packages/patches/cracklib-fix-buffer-overflow.patch	\
  %D%/packages/patches/crawl-upgrade-saves.patch		\
  %D%/packages/patches/crda-optional-gcrypt.patch		\
-  %D%/packages/patches/crossmap-allow-system-pysam.patch	\
  %D%/packages/patches/clucene-contribs-lib.patch               \
  %D%/packages/patches/cube-nocheck.patch			\
  %D%/packages/patches/cursynth-wave-rand.patch			\
@@ -633,7 +655,6 @@ dist_patch_DATA =						\
  %D%/packages/patches/datamash-arm-tests.patch			\
  %D%/packages/patches/dbus-helper-search-path.patch		\
  %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch	\
-  %D%/packages/patches/delly-use-system-libraries.patch		\
  %D%/packages/patches/dfu-programmer-fix-libusb.patch		\
  %D%/packages/patches/diffutils-gets-undeclared.patch		\
  %D%/packages/patches/diffutils-getopt.patch			\
@@ -641,11 +662,9 @@ dist_patch_DATA =						\
  %D%/packages/patches/doc++-include-directives.patch		\
  %D%/packages/patches/doc++-segfault-fix.patch			\
  %D%/packages/patches/dovecot-trees-support-dovecot-2.3.patch	\
-  %D%/packages/patches/doxygen-gcc-ice.patch			\
  %D%/packages/patches/doxygen-test.patch			\
+  %D%/packages/patches/dropbear-CVE-2018-15599.patch		\
  %D%/packages/patches/dvd+rw-tools-add-include.patch 		\
-  %D%/packages/patches/e2fsprogs-glibc-2.27.patch		\
-  %D%/packages/patches/eigen-arm-neon-fixes.patch		\
  %D%/packages/patches/elfutils-tests-ptrace.patch		\
  %D%/packages/patches/elogind-glibc-2.27.patch			\
  %D%/packages/patches/einstein-build.patch			\
@@ -653,14 +672,17 @@ dist_patch_DATA =						\
  %D%/packages/patches/emacs-fix-scheme-indent-function.patch	\
  %D%/packages/patches/emacs-json-reformat-fix-tests.patch	\
  %D%/packages/patches/emacs-highlight-stages-add-gexp.patch	\
+  %D%/packages/patches/emacs-pdf-tools-poppler.patch		\
  %D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch	\
  %D%/packages/patches/emacs-source-date-epoch.patch		\
+  %D%/packages/patches/emacs-realgud-fix-configure-ac.patch	\
  %D%/packages/patches/enlightenment-fix-setuid-path.patch	\
  %D%/packages/patches/erlang-man-path.patch			\
  %D%/packages/patches/eudev-rules-directory.patch		\
  %D%/packages/patches/evilwm-lost-focus-bug.patch		\
  %D%/packages/patches/exiv2-CVE-2017-14860.patch		\
  %D%/packages/patches/exiv2-CVE-2017-14859-14862-14864.patch	\
+  %D%/packages/patches/extundelete-e2fsprogs-1.44.patch		\
  %D%/packages/patches/fastcap-mulGlobal.patch			\
  %D%/packages/patches/fastcap-mulSetup.patch			\
  %D%/packages/patches/fasthenry-spAllocate.patch		\
@@ -672,20 +694,18 @@ dist_patch_DATA =						\
  %D%/packages/patches/fcgi-2.4.0-poll.patch			\
  %D%/packages/patches/fifo-map-fix-flags-for-gcc.patch		\
  %D%/packages/patches/fifo-map-remove-catch.hpp.patch		\
-  %D%/packages/patches/file-CVE-2017-1000249.patch		\
+  %D%/packages/patches/findutils-gnulib-libio.patch		\
  %D%/packages/patches/findutils-localstatedir.patch		\
+  %D%/packages/patches/findutils-makedev.patch			\
  %D%/packages/patches/findutils-test-xargs.patch		\
  %D%/packages/patches/flann-cmake-3.11.patch			\
  %D%/packages/patches/flint-ldconfig.patch			\
-  %D%/packages/patches/fltk-shared-lib-defines.patch		\
-  %D%/packages/patches/fltk-xfont-on-demand.patch		\
  %D%/packages/patches/foomatic-filters-CVE-2015-8327.patch	\
  %D%/packages/patches/foomatic-filters-CVE-2015-8560.patch	\
  %D%/packages/patches/freeimage-CVE-2015-0852.patch		\
  %D%/packages/patches/freeimage-CVE-2016-5684.patch		\
  %D%/packages/patches/freeimage-fix-build-with-gcc-5.patch	\
  %D%/packages/patches/freeimage-unbundle.patch		\
-  %D%/packages/patches/freetype-CVE-2018-6942.patch		\
  %D%/packages/patches/fuse-overlapping-headers.patch				\
  %D%/packages/patches/gawk-shell.patch				\
  %D%/packages/patches/gcc-arm-bug-71399.patch			\
@@ -693,8 +713,11 @@ dist_patch_DATA =						\
  %D%/packages/patches/gcc-asan-missing-include.patch		\
  %D%/packages/patches/gcc-cross-environment-variables.patch	\
  %D%/packages/patches/gcc-fix-texi2pod.patch			\
+  %D%/packages/patches/gcc-4.8-libsanitizer-fix.patch		\
  %D%/packages/patches/gcc-4.9-libsanitizer-fix.patch		\
+  %D%/packages/patches/gcc-4.9-libsanitizer-ustat.patch		\
  %D%/packages/patches/gcc-libsanitizer-fix.patch		\
+  %D%/packages/patches/gcc-libsanitizer-ustat.patch		\
  %D%/packages/patches/gcc-libvtv-runpath.patch			\
  %D%/packages/patches/gcc-strmov-store-file-names.patch	\
  %D%/packages/patches/gcc-4-compile-with-gcc-5.patch		 \
@@ -711,16 +734,19 @@ dist_patch_DATA =						\
  %D%/packages/patches/gcr-disable-failing-tests.patch		\
  %D%/packages/patches/gcr-fix-collection-tests-to-work-with-gpg-21.patch	\
  %D%/packages/patches/gd-CVE-2018-5711.patch			\
+  %D%/packages/patches/gd-CVE-2018-1000222.patch		\
  %D%/packages/patches/gd-fix-tests-on-i686.patch		\
  %D%/packages/patches/gd-freetype-test-failure.patch		\
-  %D%/packages/patches/gemma-intel-compat.patch			\
+  %D%/packages/patches/gdm-CVE-2018-14424.patch			\
  %D%/packages/patches/geoclue-config.patch			\
  %D%/packages/patches/ghc-8.0-fall-back-to-madv_dontneed.patch \
  %D%/packages/patches/ghc-dont-pass-linker-flags-via-response-files.patch	\
+  %D%/packages/patches/ghc-haddock-library-unbundle.patch		\
+  %D%/packages/patches/ghostscript-CVE-2018-16509.patch		\
+  %D%/packages/patches/ghostscript-bug-699708.patch		\
  %D%/packages/patches/ghostscript-no-header-id.patch		\
  %D%/packages/patches/ghostscript-no-header-uuid.patch		\
  %D%/packages/patches/ghostscript-no-header-creationdate.patch \
-  %D%/packages/patches/ghostscript-runpath.patch		\
  %D%/packages/patches/giflib-make-reallocarray-private.patch	\
  %D%/packages/patches/glib-networking-ssl-cert-file.patch	\
  %D%/packages/patches/glib-tests-timer.patch			\
@@ -743,6 +769,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/glibc-vectorized-strcspn-guards.patch	\
  %D%/packages/patches/glibc-versioned-locpath.patch		\
  %D%/packages/patches/glibc-2.27-git-fixes.patch		\
+  %D%/packages/patches/glibc-2.28-git-fixes.patch		\
  %D%/packages/patches/glusterfs-use-PATH-instead-of-hardcodes.patch		\
  %D%/packages/patches/glog-gcc-5-demangling.patch		\
  %D%/packages/patches/gmp-arm-asm-nothumb.patch		\
@@ -750,6 +777,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/gnome-todo-libical-compat.patch		\
  %D%/packages/patches/gnome-tweak-tool-search-paths.patch	\
  %D%/packages/patches/gnucash-price-quotes-perl.patch		\
+  %D%/packages/patches/gnucash-disable-failing-tests.patch	\
  %D%/packages/patches/gnutls-skip-trust-store-test.patch	\
  %D%/packages/patches/gnutls-skip-pkgconfig-test.patch		\
  %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \
@@ -761,6 +789,8 @@ dist_patch_DATA =						\
  %D%/packages/patches/grep-timing-sensitive-test.patch		\
  %D%/packages/patches/groff-source-date-epoch.patch		\
  %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch	\
+  %D%/packages/patches/grub-binutils-compat.patch		\
+  %D%/packages/patches/grub-check-error-efibootmgr.patch	\
  %D%/packages/patches/gsl-test-i686.patch			\
  %D%/packages/patches/gspell-dash-test.patch			\
  %D%/packages/patches/guile-1.8-cpp-4.5.patch			\
@@ -779,7 +809,8 @@ dist_patch_DATA =						\
  %D%/packages/patches/gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch \
  %D%/packages/patches/gtkglext-disable-disable-deprecated.patch \
  %D%/packages/patches/gzdoom-search-in-installed-share.patch	\
-  %D%/packages/patches/handbrake-pkg-config-path.patch		\
+  %D%/packages/patches/haskell-mode-unused-variables.patch	\
+  %D%/packages/patches/haskell-mode-make-check.patch		\
  %D%/packages/patches/hdf4-architectures.patch 		\
  %D%/packages/patches/hdf4-reproducibility.patch 		\
  %D%/packages/patches/hdf4-shared-fortran.patch 		\
@@ -791,23 +822,23 @@ dist_patch_DATA =						\
  %D%/packages/patches/hdf-eos5-remove-gctp.patch		\
  %D%/packages/patches/hdf-eos5-fix-szip.patch			\
  %D%/packages/patches/hdf-eos5-fortrantests.patch		\
-  %D%/packages/patches/hmmer-remove-cpu-specificity.patch	\
  %D%/packages/patches/higan-remove-march-native-flag.patch	\
  %D%/packages/patches/hubbub-sort-entities.patch		\
  %D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch        \
+  %D%/packages/patches/hplip-remove-imageprocessor.patch	\
  %D%/packages/patches/hydra-disable-darcs-test.patch		\
  %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
-  %D%/packages/patches/icecat-bug-1413868-pt1.patch		\
-  %D%/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch	\
-  %D%/packages/patches/icecat-use-system-graphite2.patch	\
-  %D%/packages/patches/icecat-use-system-harfbuzz.patch		\
+  %D%/packages/patches/icecat-use-system-graphite2+harfbuzz.patch	\
+  %D%/packages/patches/icecat-use-system-media-libs.patch	\
  %D%/packages/patches/icedtea-6-hotspot-gcc-segfault-workaround.patch  \
  %D%/packages/patches/icedtea-7-hotspot-gcc-segfault-workaround.patch  \
  %D%/packages/patches/id3lib-CVE-2007-4460.patch			\
  %D%/packages/patches/ilmbase-fix-tests.patch			\
  %D%/packages/patches/intltool-perl-compatibility.patch	\
+  %D%/packages/patches/irrlicht-use-system-libs.patch		\
  %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\
  %D%/packages/patches/jacal-fix-texinfo.patch			\
+  %D%/packages/patches/jamvm-arm.patch				\
  %D%/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch	\
  %D%/packages/patches/java-commons-collections-fix-java8.patch \
  %D%/packages/patches/java-jeromq-fix-tests.patch		\
@@ -816,10 +847,8 @@ dist_patch_DATA =						\
  %D%/packages/patches/java-xerces-bootclasspath.patch	\
  %D%/packages/patches/java-xerces-build_dont_unzip.patch	\
  %D%/packages/patches/java-xerces-xjavac_taskdef.patch	\
-  %D%/packages/patches/jemalloc-arm-address-bits.patch		\
  %D%/packages/patches/jbig2dec-ignore-testtest.patch		\
  %D%/packages/patches/json-glib-fix-tests-32bit.patch		\
-  %D%/packages/patches/jq-CVE-2015-8863.patch			\
  %D%/packages/patches/kdbusaddons-kinit-file-name.patch	\
  %D%/packages/patches/khmer-use-libraries.patch                \
  %D%/packages/patches/libziparchive-add-includes.patch		\
@@ -836,7 +865,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/kobodeluxe-graphics-window-signed-char.patch	\
  %D%/packages/patches/laby-make-install.patch			\
  %D%/packages/patches/ldc-bootstrap-disable-tests.patch	\
-  %D%/packages/patches/ldc-1.7.0-disable-phobos-tests.patch	\
+  %D%/packages/patches/ldc-disable-phobos-tests.patch		\
  %D%/packages/patches/ledger-fix-uninitialized.patch		\
  %D%/packages/patches/ledger-revert-boost-python-fix.patch	\
  %D%/packages/patches/liba52-enable-pic.patch			\
@@ -861,18 +890,18 @@ dist_patch_DATA =						\
  %D%/packages/patches/libevent-2.1-skip-failing-test.patch	\
  %D%/packages/patches/libexif-CVE-2016-6328.patch		\
  %D%/packages/patches/libexif-CVE-2017-7544.patch		\
+  %D%/packages/patches/libgcrypt-make-yat2m-reproducible.patch	\
  %D%/packages/patches/libgit2-mtime-0.patch			\
+  %D%/packages/patches/libgit2-oom-test.patch			\
  %D%/packages/patches/libgdata-fix-tests.patch			\
  %D%/packages/patches/libgdata-glib-duplicate-tests.patch	\
  %D%/packages/patches/libgnome-encoding.patch			\
  %D%/packages/patches/libgnomeui-utf8.patch			\
-  %D%/packages/patches/libgpg-error-aarch64-logging-fix.patch	\
-  %D%/packages/patches/libgxps-CVE-2017-11590.patch		\
  %D%/packages/patches/libffi-3.2.1-complex-alpha.patch		\
  %D%/packages/patches/libjxr-fix-function-signature.patch	\
  %D%/packages/patches/libjxr-fix-typos.patch			\
+  %D%/packages/patches/libopenshot-tests-with-system-libs.patch	\
  %D%/packages/patches/libotr-test-auth-fix.patch		\
-  %D%/packages/patches/liblxqt-include.patch			\
  %D%/packages/patches/libmad-armv7-thumb-pt1.patch		\
  %D%/packages/patches/libmad-armv7-thumb-pt2.patch		\
  %D%/packages/patches/libmad-frame-length.patch		\
@@ -880,6 +909,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/libmygpo-qt-fix-qt-5.11.patch		\
  %D%/packages/patches/libmygpo-qt-missing-qt5-modules.patch	\
  %D%/packages/patches/libreoffice-icu.patch			\
+  %D%/packages/patches/libreoffice-glm.patch			\
  %D%/packages/patches/libsndfile-armhf-type-checks.patch	\
  %D%/packages/patches/libsndfile-CVE-2017-8361-8363-8365.patch	\
  %D%/packages/patches/libsndfile-CVE-2017-8362.patch		\
@@ -899,6 +929,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/libutils-remove-damaging-includes.patch	\
  %D%/packages/patches/libvdpau-va-gl-unbundle.patch		\
  %D%/packages/patches/libvpx-CVE-2016-2818.patch		\
+  %D%/packages/patches/libvpx-use-after-free-in-postproc.patch	\
  %D%/packages/patches/libxslt-generated-ids.patch		\
  %D%/packages/patches/libxt-guix-search-paths.patch		\
  %D%/packages/patches/lierolibre-check-unaligned-access.patch	\
@@ -908,6 +939,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/lierolibre-try-building-other-arch.patch	\
  %D%/packages/patches/linux-pam-no-setfsuid.patch		\
  %D%/packages/patches/lirc-localstatedir.patch			\
+  %D%/packages/patches/lirc-reproducible-build.patch		\
  %D%/packages/patches/llvm-3.5-fix-clang-build-with-gcc5.patch	\
  %D%/packages/patches/llvm-for-extempore.patch			\
  %D%/packages/patches/lm-sensors-hwmon-attrs.patch		\
@@ -923,9 +955,9 @@ dist_patch_DATA =						\
  %D%/packages/patches/lvm2-static-link.patch			\
  %D%/packages/patches/lxsession-use-gapplication.patch         \
  %D%/packages/patches/lyx-2.2.3-fix-test.patch			\
-  %D%/packages/patches/mailutils-uninitialized-memory.patch	\
  %D%/packages/patches/make-glibc-compat.patch			\
  %D%/packages/patches/make-impure-dirs.patch			\
+  %D%/packages/patches/mariadb-client-test-32bit.patch		\
  %D%/packages/patches/mars-install.patch			\
  %D%/packages/patches/mars-sfml-2.3.patch			\
  %D%/packages/patches/maxima-defsystem-mkdir.patch		\
@@ -935,15 +967,17 @@ dist_patch_DATA =						\
  %D%/packages/patches/mcrypt-CVE-2012-4409.patch			\
  %D%/packages/patches/mcrypt-CVE-2012-4426.patch			\
  %D%/packages/patches/mcrypt-CVE-2012-4527.patch			\
+  %D%/packages/patches/meandmyshadow-define-paths-earlier.patch	\
  %D%/packages/patches/mesa-skip-disk-cache-test.patch		\
-  %D%/packages/patches/mesa-wayland-egl-symbols-check-mips.patch	\
  %D%/packages/patches/meson-for-build-rpath.patch		\
  %D%/packages/patches/metabat-fix-compilation.patch		\
  %D%/packages/patches/mhash-keygen-test-segfault.patch		\
  %D%/packages/patches/mingw-w64-5.0rc2-gcc-4.9.3.patch		\
  %D%/packages/patches/mpc123-initialize-ao.patch		\
  %D%/packages/patches/module-init-tools-moduledir.patch	\
+  %D%/packages/patches/monero-use-system-miniupnpc.patch			\
  %D%/packages/patches/mongodb-support-unknown-linux-distributions.patch	\
+  %D%/packages/patches/mono-mdoc-timestamping.patch		\
  %D%/packages/patches/mozjs17-aarch64-support.patch		\
  %D%/packages/patches/mozjs24-aarch64-support.patch		\
  %D%/packages/patches/mozjs38-pkg-config-version.patch		\
@@ -956,10 +990,11 @@ dist_patch_DATA =						\
  %D%/packages/patches/mupen64plus-ui-console-notice.patch	\
  %D%/packages/patches/mupen64plus-video-z64-glew-correct-path.patch    \
  %D%/packages/patches/mutt-store-references.patch		\
-  %D%/packages/patches/myrepos-CVE-2018-7032.patch		\
+  %D%/packages/patches/m4-gnulib-libio.patch			\
  %D%/packages/patches/net-tools-bitrot.patch			\
  %D%/packages/patches/netcdf-date-time.patch			\
  %D%/packages/patches/netcdf-tst_h_par.patch			\
+  %D%/packages/patches/netsurf-message-timestamp.patch		\
  %D%/packages/patches/netsurf-system-utf8proc.patch		\
  %D%/packages/patches/netsurf-y2038-tests.patch		\
  %D%/packages/patches/netsurf-longer-test-timeout.patch	\
@@ -970,7 +1005,9 @@ dist_patch_DATA =						\
  %D%/packages/patches/nvi-assume-preserve-path.patch		\
  %D%/packages/patches/nvi-dbpagesize-binpower.patch		\
  %D%/packages/patches/nvi-db4.patch				\
+  %D%/packages/patches/nyacc-binary-literals.patch		\
  %D%/packages/patches/nyx-show-header-stats-with-python3.patch	\
+  %D%/packages/patches/oath-toolkit-glibc-compat.patch		\
  %D%/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch	\
  %D%/packages/patches/ocaml-bitstring-fix-configure.patch \
  %D%/packages/patches/ocaml-CVE-2015-8869.patch		\
@@ -980,19 +1017,14 @@ dist_patch_DATA =						\
  %D%/packages/patches/ocaml-graph-honor-source-date-epoch.patch	\
  %D%/packages/patches/omake-fix-non-determinism.patch	\
  %D%/packages/patches/ola-readdir-r.patch			\
+  %D%/packages/patches/openbabel-fix-crash-on-nwchem-output.patch	\
  %D%/packages/patches/opencascade-oce-glibc-2.26.patch		\
-  %D%/packages/patches/openexr-missing-samples.patch		\
  %D%/packages/patches/openfoam-4.1-cleanup.patch			\
  %D%/packages/patches/openldap-CVE-2017-9287.patch		\
  %D%/packages/patches/openocd-nrf52.patch			\
-  %D%/packages/patches/openscenegraph-ffmpeg3.patch             \
  %D%/packages/patches/opensmtpd-fix-crash.patch		\
  %D%/packages/patches/openssl-runpath.patch			\
-  %D%/packages/patches/openssl-1.0.2-CVE-2018-0495.patch	\
-  %D%/packages/patches/openssl-1.0.2-CVE-2018-0732.patch	\
-  %D%/packages/patches/openssl-1.1.0-CVE-2018-0495.patch	\
-  %D%/packages/patches/openssl-1.1.0-CVE-2018-0732.patch	\
-  %D%/packages/patches/openssl-1.1.0-c-rehash-in.patch		\
+  %D%/packages/patches/openssl-1.1-c-rehash-in.patch		\
  %D%/packages/patches/openssl-c-rehash-in.patch		\
  %D%/packages/patches/orpheus-cast-errors-and-includes.patch	\
  %D%/packages/patches/osip-CVE-2017-7853.patch			\
@@ -1001,21 +1033,19 @@ dist_patch_DATA =						\
  %D%/packages/patches/p7zip-CVE-2016-9296.patch		\
  %D%/packages/patches/p7zip-CVE-2017-17969.patch		\
  %D%/packages/patches/p7zip-remove-unused-code.patch		\
+  %D%/packages/patches/parted-glibc-compat.patch		\
  %D%/packages/patches/patchelf-page-size.patch			\
  %D%/packages/patches/patchelf-rework-for-arm.patch		\
-  %D%/packages/patches/patchutils-xfail-gendiff-tests.patch	\
+  %D%/packages/patches/patchutils-test-perms.patch		\
  %D%/packages/patches/patch-hurd-path-max.patch		\
-  %D%/packages/patches/perf-gcc-ice.patch			\
-  %D%/packages/patches/perl-archive-tar-CVE-2018-12015.patch	\
-  %D%/packages/patches/perl-file-path-CVE-2017-6512.patch	\
  %D%/packages/patches/perl-autosplit-default-time.patch	\
-  %D%/packages/patches/perl-dbd-mysql-CVE-2017-10788.patch	\
  %D%/packages/patches/perl-deterministic-ordering.patch	\
  %D%/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch \
  %D%/packages/patches/perl-io-socket-ssl-openssl-1.0.2f-fix.patch \
  %D%/packages/patches/perl-net-amazon-s3-moose-warning.patch	\
  %D%/packages/patches/perl-net-dns-resolver-programmable-fix.patch	\
  %D%/packages/patches/perl-no-sys-dirs.patch			\
+  %D%/packages/patches/perl-text-markdown-discount-unbundle.patch	\
  %D%/packages/patches/perl-module-pluggable-search.patch	\
  %D%/packages/patches/perl-reproducible-build-date.patch	\
  %D%/packages/patches/perl-www-curl-remove-symbol.patch	\
@@ -1026,13 +1056,15 @@ dist_patch_DATA =						\
  %D%/packages/patches/pinball-missing-separators.patch		\
  %D%/packages/patches/pinball-src-deps.patch			\
  %D%/packages/patches/pinball-system-ltdl.patch		\
+  %D%/packages/patches/pinentry-efl.patch			\
  %D%/packages/patches/pingus-sdl-libs-config.patch		\
  %D%/packages/patches/pius.patch       			\
  %D%/packages/patches/pixman-CVE-2016-5296.patch		\
  %D%/packages/patches/plink-1.07-unclobber-i.patch		\
  %D%/packages/patches/plink-endian-detection.patch		\
  %D%/packages/patches/plotutils-libpng-jmpbuf.patch		\
-  %D%/packages/patches/polkit-drop-test.patch			\
+  %D%/packages/patches/podofo-cmake-3.12.patch			\
+  %D%/packages/patches/poppler-CVE-2018-19149.patch		\
  %D%/packages/patches/portaudio-audacity-compat.patch		\
  %D%/packages/patches/portmidi-modular-build.patch		\
  %D%/packages/patches/potrace-tests.patch			\
@@ -1044,12 +1076,14 @@ dist_patch_DATA =						\
  %D%/packages/patches/psm-ldflags.patch			\
  %D%/packages/patches/psm-repro.patch				\
  %D%/packages/patches/pulseaudio-fix-mult-test.patch		\
-  %D%/packages/patches/pulseaudio-glibc-2.27.patch		\
  %D%/packages/patches/pulseaudio-longer-test-timeout.patch	\
  %D%/packages/patches/pybugz-encode-error.patch		\
  %D%/packages/patches/pybugz-stty.patch			\
  %D%/packages/patches/pygpgme-disable-problematic-tests.patch  \
  %D%/packages/patches/pyqt-configure.patch			\
+  %D%/packages/patches/pyqt-public-sip.patch			\
+  %D%/packages/patches/python2-CVE-2018-14647.patch		\
+  %D%/packages/patches/python2-CVE-2018-1000802.patch		\
  %D%/packages/patches/python-2-deterministic-build-info.patch	\
  %D%/packages/patches/python-2.7-adjust-tests.patch		\
  %D%/packages/patches/python-2.7-search-paths.patch		\
@@ -1058,26 +1092,18 @@ dist_patch_DATA =						\
  %D%/packages/patches/python-3-deterministic-build-info.patch	\
  %D%/packages/patches/python-3-search-paths.patch		\
  %D%/packages/patches/python-3-fix-tests.patch			\
+  %D%/packages/patches/python-CVE-2018-14647.patch		\
  %D%/packages/patches/python-axolotl-AES-fix.patch		\
-  %D%/packages/patches/python-dendropy-fix-tests.patch		\
+  %D%/packages/patches/python-cairocffi-dlopen-path.patch	\
+  %D%/packages/patches/python-cffi-x87-stack-clean.patch	\
  %D%/packages/patches/python-fix-tests.patch			\
-  %D%/packages/patches/python-genshi-add-support-for-python-3.4-AST.patch	\
-  %D%/packages/patches/python-genshi-buildable-on-python-2.7.patch	\
-  %D%/packages/patches/python-genshi-disable-speedups-on-python-3.3.patch	\
-  %D%/packages/patches/python-genshi-fix-tests-on-python-3.5.patch	\
-  %D%/packages/patches/python-genshi-isstring-helper.patch	\
-  %D%/packages/patches/python-genshi-stripping-of-unsafe-script-tags.patch	\
  %D%/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch \
-  %D%/packages/patches/python-networkx2-reproducible-build.patch	\
-  %D%/packages/patches/python-pillow-fix-failing-tests.patch	\
  %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch	\
-  %D%/packages/patches/python-scikit-learn-fix-test-non-determinism.patch	\
  %D%/packages/patches/python-configobj-setuptools.patch	\
  %D%/packages/patches/python-faker-fix-build-32bit.patch	\
  %D%/packages/patches/python-mox3-python3.6-compat.patch	\
-  %D%/packages/patches/python-paste-remove-website-test.patch	\
+  %D%/packages/patches/python-testtools.patch			\
  %D%/packages/patches/python-paste-remove-timing-test.patch	\
-  %D%/packages/patches/python-pygit2-disable-network-tests.patch	\
  %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch	\
  %D%/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \
  %D%/packages/patches/python-pygpgme-fix-pinentry-tests.patch	\
@@ -1086,14 +1112,17 @@ dist_patch_DATA =						\
  %D%/packages/patches/python-unittest2-remove-argparse.patch	\
  %D%/packages/patches/python-waitress-fix-tests.patch		\
  %D%/packages/patches/qemu-glibc-2.27.patch 			\
-  %D%/packages/patches/qemu-CVE-2018-11806.patch 		\
  %D%/packages/patches/qt4-ldflags.patch			\
  %D%/packages/patches/qtbase-use-TZDIR.patch			\
-  %D%/packages/patches/qtoctave-qt-5.11-fix.patch		\
  %D%/packages/patches/qtscript-disable-tests.patch		\
+  %D%/packages/patches/qt-5-renameat2.patch			\
  %D%/packages/patches/quagga-reproducible-build.patch          \
-  %D%/packages/patches/quassel-qt-5.11.patch			\
  %D%/packages/patches/quickswitch-fix-dmenu-check.patch	\
+  %D%/packages/patches/quilt-test-fix-regex.patch		\
+  %D%/packages/patches/quilt-getopt-nondigit-param.patch	\
+  %D%/packages/patches/quilt-getopt-second-separator.patch	\
+  %D%/packages/patches/qtwebkit-pbutils-include.patch		\
+  %D%/packages/patches/randomjungle-disable-static-build.patch	\
  %D%/packages/patches/rapicorn-isnan.patch			\
  %D%/packages/patches/raptor2-heap-overflow.patch		\
  %D%/packages/patches/ratpoison-shell.patch			\
@@ -1106,20 +1135,25 @@ dist_patch_DATA =						\
  %D%/packages/patches/reptyr-fix-gcc-7.patch			\
  %D%/packages/patches/ripperx-missing-file.patch		\
  %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
-  %D%/packages/patches/rsem-makefile.patch			\
  %D%/packages/patches/rtags-separate-rct.patch			\
+  %D%/packages/patches/racket-store-checksum-override.patch	\
  %D%/packages/patches/ruby-rubygems-276-for-ruby24.patch	\
  %D%/packages/patches/ruby-concurrent-ignore-broken-test.patch	\
  %D%/packages/patches/ruby-concurrent-test-arm.patch		\
  %D%/packages/patches/ruby-rack-ignore-failing-test.patch      \
  %D%/packages/patches/ruby-tzinfo-data-ignore-broken-test.patch\
+  %D%/packages/patches/rust-1.19-mrustc.patch			\
+  %D%/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch \
+  %D%/packages/patches/rust-bootstrap-stage0-test.patch		\
+  %D%/packages/patches/rust-coresimd-doctest.patch		\
+  %D%/packages/patches/rust-reproducible-builds.patch		 \
  %D%/packages/patches/rxvt-unicode-escape-sequences.patch	\
  %D%/packages/patches/scheme48-tests.patch			\
  %D%/packages/patches/scotch-test-threading.patch		\
  %D%/packages/patches/scotch-build-parallelism.patch		\
  %D%/packages/patches/scotch-graph-diam-64.patch		\
  %D%/packages/patches/scotch-graph-induce-type-64.patch	\
-  %D%/packages/patches/sddm-fix-build-with-qt-5.11-1024.patch  \
+  %D%/packages/patches/scribus-poppler.patch			\
  %D%/packages/patches/sdl-libx11-1.6.patch			\
  %D%/packages/patches/seq24-rename-mutex.patch			\
  %D%/packages/patches/sharutils-CVE-2018-1000097.patch		\
@@ -1129,9 +1163,14 @@ dist_patch_DATA =						\
  %D%/packages/patches/slim-sigusr1.patch			\
  %D%/packages/patches/slim-reset.patch				\
  %D%/packages/patches/slim-login.patch				\
+  %D%/packages/patches/snappy-add-O2-flag-in-CmakeLists.txt.patch	\
  %D%/packages/patches/sooperlooper-build-with-wx-30.patch 	\
+  %D%/packages/patches/soundconverter-remove-gconf-dependency.patch	\
+  %D%/packages/patches/soundtouch-CVE-2018-14044-14045.patch 	\
+  %D%/packages/patches/soundtouch-CVE-2018-1000223.patch 	\
  %D%/packages/patches/steghide-fixes.patch			\
  %D%/packages/patches/superlu-dist-scotchmetis.patch		\
+  %D%/packages/patches/swig-guile-gc.patch			\
  %D%/packages/patches/swish-e-search.patch			\
  %D%/packages/patches/swish-e-format-security.patch		\
  %D%/packages/patches/synfigstudio-fix-ui-with-gtk3.patch 	\
@@ -1145,6 +1184,9 @@ dist_patch_DATA =						\
  %D%/packages/patches/tcsh-fix-out-of-bounds-read.patch	\
  %D%/packages/patches/teensy-loader-cli-help.patch		\
  %D%/packages/patches/teeworlds-use-latest-wavpack.patch	\
+  %D%/packages/patches/texinfo-perl-compat.patch		\
+  %D%/packages/patches/texinfo-5-perl-compat.patch		\
+  %D%/packages/patches/telegram-purple-adjust-test.patch	\
  %D%/packages/patches/texi2html-document-encoding.patch	\
  %D%/packages/patches/texi2html-i18n.patch			\
  %D%/packages/patches/thefuck-test-environ.patch		\
@@ -1153,12 +1195,18 @@ dist_patch_DATA =						\
  %D%/packages/patches/tipp10-fix-compiling.patch		\
  %D%/packages/patches/tipp10-remove-license-code.patch		\
  %D%/packages/patches/tk-find-library.patch			\
-  %D%/packages/patches/translate-shell-fix-curl-tests.patch	\
  %D%/packages/patches/ttf2eot-cstddef.patch			\
  %D%/packages/patches/ttfautohint-source-date-epoch.patch	\
-  %D%/packages/patches/tophat-build-with-later-seqan.patch	\
+  %D%/packages/patches/tomsfastmath-constness.patch		\
  %D%/packages/patches/totem-meson-easy-codec.patch		\
  %D%/packages/patches/tuxpaint-stamps-path.patch		\
+  %D%/packages/patches/twinkle-include-qregexpvalidator.patch	\
+  %D%/packages/patches/u-boot-pinebook-a64-update-dts.patch	\
+  %D%/packages/patches/u-boot-pinebook-mmc-calibration.patch	\
+  %D%/packages/patches/u-boot-pinebook-r_i2c-controller.patch	\
+  %D%/packages/patches/u-boot-pinebook-dts.patch		\
+  %D%/packages/patches/u-boot-pinebook-syscon-node.patch	\
+  %D%/packages/patches/u-boot-pinebook-video-bridge.patch	\
  %D%/packages/patches/unrtf-CVE-2016-10091.patch		\
  %D%/packages/patches/unzip-CVE-2014-8139.patch		\
  %D%/packages/patches/unzip-CVE-2014-8140.patch		\
@@ -1203,20 +1251,21 @@ dist_patch_DATA =						\
  %D%/packages/patches/wordnet-CVE-2008-3908-pt1.patch			\
  %D%/packages/patches/wordnet-CVE-2008-3908-pt2.patch			\
  %D%/packages/patches/wpa-supplicant-CVE-2017-13082.patch	\
+  %D%/packages/patches/wpa-supplicant-CVE-2018-14526.patch	\
  %D%/packages/patches/wpa-supplicant-fix-key-reuse.patch	\
  %D%/packages/patches/wpa-supplicant-fix-zeroed-keys.patch	\
  %D%/packages/patches/wpa-supplicant-fix-nonce-reuse.patch	\
  %D%/packages/patches/wpa-supplicant-krack-followups.patch	\
-  %D%/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch	\
-  %D%/packages/patches/x265-fix-ppc64le-build.patch		\
+  %D%/packages/patches/x265-arm-flags.patch			\
+  %D%/packages/patches/x265-detect512-all-arches.patch		\
  %D%/packages/patches/xboing-CVE-2004-0149.patch		\
-  %D%/packages/patches/xdotool-fix-makefile.patch               \
  %D%/packages/patches/xf86-video-ark-remove-mibstore.patch	\
-  %D%/packages/patches/xf86-video-ast-remove-mibstore.patch	\
  %D%/packages/patches/xf86-video-geode-glibc-2.20.patch	\
  %D%/packages/patches/xf86-video-i128-remove-mibstore.patch	\
  %D%/packages/patches/xf86-video-mach64-glibc-2.20.patch	\
+  %D%/packages/patches/xf86-video-savage-xorg-compat.patch 	\
  %D%/packages/patches/xf86-video-siliconmotion-fix-ftbfs.patch \
+  %D%/packages/patches/xf86-video-sis-xorg-compat.patch 	\
  %D%/packages/patches/xf86-video-tga-remove-mibstore.patch	\
  %D%/packages/patches/xfce4-panel-plugins.patch		\
  %D%/packages/patches/xfce4-session-fix-xflock4.patch		\
@@ -1224,9 +1273,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/xinetd-fix-fd-leak.patch			\
  %D%/packages/patches/xinetd-CVE-2013-4342.patch		\
  %D%/packages/patches/xmodmap-asprintf.patch 			\
-  %D%/packages/patches/zathura-plugindir-environment-variable.patch	\
-  %D%/packages/patches/zstd-fix-stdin-list-without-tty.patch	\
-  %D%/packages/patches/zstd-fix-stdin-list-test.patch
+  %D%/packages/patches/zathura-plugindir-environment-variable.patch

 MISC_DISTRO_FILES =				\
  %D%/packages/ld-wrapper.in
@@ -30,6 +30,7 @@
                #:select ((package-name->name+version
                           . hyphen-separated-name->name+version)))
  #:autoload   (guix profiles) (packages->manifest)
+  #:use-module (guix describe)
  #:use-module (ice-9 vlist)
  #:use-module (ice-9 match)
  #:use-module (srfi srfi-1)
@@ -46,6 +47,7 @@
            %auxiliary-files-path
            %bootstrap-binaries-path
            %package-module-path
+            %default-package-module-path

            fold-packages

@@ -130,22 +132,31 @@ for system '~a'")
         ("gnu/packages.scm"      gnu/)
         ("guix.scm"))))

+(define %default-package-module-path
+  ;; Default search path for package modules.
+  `((,%distro-root-directory . "gnu/packages")))
+
 (define %package-module-path
  ;; Search path for package modules.  Each item must be either a directory
  ;; name or a pair whose car is a directory and whose cdr is a sub-directory
  ;; to narrow the search.
  (let* ((not-colon   (char-set-complement (char-set #\:)))
         (environment (string-tokenize (or (getenv "GUIX_PACKAGE_PATH") "")
-                                       not-colon)))
-    ;; Automatically add items from $GUIX_PACKAGE_PATH to Guile's search path.
-    (for-each (lambda (directory)
-                (set! %load-path (cons directory %load-path))
-                (set! %load-compiled-path
-                      (cons directory %load-compiled-path)))
-              environment)
+                                       not-colon))
+         (channels    (package-path-entries)))
+    ;; Automatically add channels and items from $GUIX_PACKAGE_PATH to Guile's
+    ;; search path.  For historical reasons, $GUIX_PACKAGE_PATH goes to the
+    ;; front; channels go to the back so that they don't override Guix' own
+    ;; modules.
+    (set! %load-path
+      (append environment %load-path channels))
+    (set! %load-compiled-path
+      (append environment %load-compiled-path channels))

    (make-parameter
-     (append environment `((,%distro-root-directory . "gnu/packages"))))))
+     (append environment
+             %default-package-module-path
+             channels))))

 (define %patch-path
  ;; Define it after '%package-module-path' so that '%load-path' contains user
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Marek Benc <merkur32@gmail.com>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;;
@@ -62,7 +62,7 @@
    (build-system glib-or-gtk-build-system)
    (arguments                   ;; NOTE: rsvg is disabled, since Abiword
      `(#:configure-flags        ;; supports it directly, and its BS is broken.
-        (list
+        (list                    ;; wmf was removed from Guix for security.
          "--enable-clipart"     ;; TODO: The following plugins have unresolved
          "--enable-templates"   ;; dependencies: aiksaurus, grammar, wpg, gda,
          (string-append         ;; wordperfect, psion, mathview.
@@ -73,7 +73,7 @@
              "latex " "loadbindings " "mht " "mif " "mswrite " "opendocument "
              "openwriter " "openxml " "opml " "ots " "paint " "passepartout "
              "pdb " "pdf " "presentation " "s5 " "sdw " "t602 " "urldict "
-              "wikipedia " "wmf " "wml " "xslfo"))
+              "wikipedia " "wml " "xslfo"))
        ;; tests fail with: Gtk-CRITICAL **: gtk_settings_get_for_screen:
        ;;                  assertion 'GDK_IS_SCREEN (screen)' failed
        ;;                  GLib-GObject-CRITICAL **: g_object_get_qdata:
@@ -9,7 +9,7 @@
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Peter Feigl <peter.feigl@nexoid.at>
 ;;; Copyright © 2016 John J. Foerch <jjfoerch@earthlink.net>
 ;;; Copyright © 2016, 2017 Nils Gillmann <ng0@n0.is>
@@ -45,7 +45,9 @@
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system emacs)
  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system meson)
  #:use-module (guix build-system perl)
  #:use-module (guix build-system python)
  #:use-module (guix build-system trivial)
@@ -124,7 +126,9 @@
     `(("libgcrypt" ,libgcrypt)
       ("libgpg-error" ,libgpg-error)
       ("libmhash" ,libmhash)
+       ("pcre:static" ,pcre "static")
       ("pcre" ,pcre)
+       ("zlib:static" ,zlib "static")
       ("zlib" ,zlib)))
    (synopsis "File and directory integrity checker")
    (description
@@ -172,14 +176,14 @@ and provides a \"top-like\" mode (monitoring).")
 (define-public shepherd
  (package
    (name "shepherd")
-    (version "0.4.0")
+    (version "0.5.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://alpha.gnu.org/gnu/shepherd/shepherd-"
                                  version ".tar.gz"))
              (sha256
               (base32
-                "1lgmsbxn8i8xdasxzkdp2cml75n128pplw6icvmspl6s0n9xmw8n"))))
+                "1wmciqml9yplnx1s4ynn00giqyk06rbrcsgvpjj2df47sawk2jp8"))))
    (build-system gnu-build-system)
    (arguments
     '(#:configure-flags '("--localstatedir=/var")))
@@ -224,13 +228,15 @@ interface and is based on GNU Guile.")
       (modify-phases %standard-phases
         (add-after 'unpack 'chdir
           (lambda _
-             (chdir ,(string-append  name "-" version))))
+             (chdir ,(string-append name "-" version))
+             #t))
         (delete 'configure)
         (add-before 'build 'patch
           (lambda _
             (substitute* "src/error.h"
               (("extern int errno;")
-                "#include <errno.h>"))))
+                "#include <errno.h>"))
+             #t))
         (replace 'build
           (lambda _
             (invoke "package/compile")))
@@ -240,7 +246,8 @@ interface and is based on GNU Guile.")
                    (bin (string-append out "/bin")))
               (for-each (lambda (file)
                           (install-file file bin))
-                         (find-files "command"))))))))
+                         (find-files "command")))
+             #t)))))
    (synopsis "Tools for managing UNIX style services")
    (description
     "@code{daemontools} is a collection of tools for managing UNIX
@@ -610,9 +617,9 @@ connection alive.")
 (define-public isc-dhcp
  (let* ((bind-major-version "9")
         (bind-minor-version "11")
-         (bind-patch-version "3")
-         (bind-release-type "")         ; for patch release, use "-P"
-         (bind-release-version "")      ; for patch release, e.g. "6"
+         (bind-patch-version "4")
+         (bind-release-type "-P")         ; for patch release, use "-P"
+         (bind-release-version "2")      ; for patch release, e.g. "6"
         (bind-version (string-append bind-major-version
                                      "."
                                      bind-minor-version
@@ -625,7 +632,7 @@ connection alive.")
      (version "4.4.1")
      (source (origin
                (method url-fetch)
-                (uri (string-append "http://ftp.isc.org/isc/dhcp/"
+                (uri (string-append "https://ftp.isc.org/isc/dhcp/"
                                    version "/dhcp-" version ".tar.gz"))
                (sha256
                 (base32
@@ -724,12 +731,12 @@ connection alive.")
                ("bind-source-tarball"
                 ,(origin
                    (method url-fetch)
-                    (uri (string-append "http://ftp.isc.org/isc/bind9/"
+                    (uri (string-append "https://ftp.isc.org/isc/bind9/"
                                        bind-version
                                        "/bind-" bind-version ".tar.gz"))
                    (sha256
                     (base32
-                      "1xbnb2b11274z9frc9y7nvkyxr52qx09bwb97gf9qzzcn8adx78d"))))
+                      "04fq17zksd2b3w6w6padps5n7b6s2lasxpksbhl4378h56vgfnm8"))))

                ;; When cross-compiling, we need the cross Coreutils and sed.
                ;; Otherwise just use those from %FINAL-INPUTS.
@@ -738,7 +745,7 @@ connection alive.")
                        ("sed" ,sed))
                      '())))

-      (home-page "http://www.isc.org/products/DHCP/")
+      (home-page "https://www.isc.org/products/DHCP/")
      (synopsis "Dynamic Host Configuration Protocol (DHCP) tools")
      (description
       "ISC's Dynamic Host Configuration Protocol (DHCP) distribution provides a
@@ -750,27 +757,30 @@ tools: server, client, and relay agent.")
 (define-public libpcap
  (package
    (name "libpcap")
-    (version "1.8.1")
+    (version "1.9.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://www.tcpdump.org/release/libpcap-"
                                  version ".tar.gz"))
              (sha256
               (base32
-                "07jlhc66z76dipj4j5v3dig8x6h3k6cb36kmnmpsixf3zmlvqgb7"))))
+                "06bhydl4vr4z9c3vahl76f2j96z1fbrcl7wwismgs4sris08inrf"))))
    (build-system gnu-build-system)
-    (native-inputs `(("bison" ,bison) ("flex" ,flex)))
-    (arguments '(#:configure-flags '("--with-pcap=linux")
-                 #:tests? #f))                    ; no 'check' target
+    (native-inputs
+     `(("bison" ,bison)
+       ("flex" ,flex)))
+    (arguments
+     ;; There are some tests in testprogs/, but no automated test suite.
+     '(#:tests? #f))
    (home-page "https://www.tcpdump.org")
    (synopsis "Network packet capture library")
    (description
     "libpcap is an interface for user-level packet capture.  It provides a
 portable framework for low-level network monitoring.  Applications include
 network statistics collection, security monitoring, network debugging, etc.")
-
-    ;; fad-*.c and a couple other files are BSD-4, but the rest is BSD-3.
-    (license license:bsd-3)))
+    (license (list license:bsd-4        ; fad-*.c and several other source files
+                   license:bsd-3        ; pcap/, sockutils.* & others
+                   license:bsd-2))))    ; the rest

 (define-public tcpdump
  (package
@@ -865,7 +875,7 @@ over ssh connections.")
 (define-public rename
  (package
    (name "rename")
-    (version "0.35")
+    (version "1.00")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -873,8 +883,24 @@ over ssh connections.")
                    version ".tar.gz"))
              (sha256
               (base32
-                "052iqmn7ya3w1nadpiyavmr3rx566r0lbflx94y8b5wx9q5c16rq"))))
+                "03yhf8nmqsb0zyliv501fdvwlp589jqfn44yqkrflmpzrbik3zxl"))))
    (build-system perl-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'find-itself
+           ;; Fix run-time 'Can't locate File/Rename.pm in @INC' failure.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (with-directory-excursion bin
+                 (for-each
+                  (lambda (program)
+                    (wrap-program program
+                      `("PERL5LIB" ":" prefix
+                        (,(string-append out "/lib/perl5/site_perl")))))
+                  (find-files "." ".*")))
+               #t))))))
    (native-inputs
     `(("perl-module-build" ,perl-module-build)
       ("perl-test-pod" ,perl-test-pod)
@@ -943,7 +969,7 @@ at once based on a Perl regular expression.")
                      #t))
                  (add-after 'install 'install-info
                    (lambda _
-                      (zero? (system* "make" "install-info")))))))
+                      (invoke "make" "install-info"))))))
    (native-inputs `(("texinfo" ,texinfo)
                     ("util-linux" ,util-linux))) ; for 'cal'
    (home-page "https://www.gnu.org/software/rottlog/")
@@ -959,7 +985,7 @@ system administrator.")
 (define-public sudo
  (package
    (name "sudo")
-    (version "1.8.23")
+    (version "1.8.26")
    (source (origin
              (method url-fetch)
              (uri
@@ -969,7 +995,7 @@ system administrator.")
                                    version ".tar.gz")))
              (sha256
               (base32
-                "0yg62wq8rcrbr7qvh3wgfg2g4bwanbi50cr2lf2cfyy8dydx4qyq"))
+                "1qpyyfga8rs02p3186sns8qvh2bzwa48ka845nrcqh83dyd23nj0"))
              (modules '((guix build utils)))
              (snippet
               '(begin
@@ -979,7 +1005,7 @@ system administrator.")
    (arguments
     `(#:configure-flags
       (list "--with-logpath=/var/log/sudo.log"
-             "--with-rundir=/var/run/sudo"    ;must be cleaned up at boot time
+             "--with-rundir=/var/run/sudo" ; must be cleaned up at boot time
             "--with-vardir=/var/db/sudo"
             "--with-iologdir=/var/log/sudo-io"

@@ -1047,6 +1073,7 @@ commands and their arguments.")
                    version
                    ".tar.gz"))
              (patches (search-patches "wpa-supplicant-CVE-2017-13082.patch"
+                                       "wpa-supplicant-CVE-2018-14526.patch"
                                       "wpa-supplicant-fix-key-reuse.patch"
                                       "wpa-supplicant-fix-zeroed-keys.patch"
                                       "wpa-supplicant-fix-nonce-reuse.patch"
@@ -1073,7 +1100,8 @@ commands and their arguments.")
      CFLAGS += $(shell pkg-config libnl-3.0 --cflags)
      CONFIG_LIBNL32=y
      CONFIG_READLINE=y\n" port)
-               (close-port port))))
+               (close-port port))
+             #t))
         (add-after 'install 'install-man-pages
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out  (assoc-ref outputs "out"))
@@ -1173,9 +1201,6 @@ This package provides the 'wpa_supplicant' daemon and the 'wpa_cli' command.")
                    (lambda* (#:key inputs outputs #:allow-other-keys)
                      (let ((out (assoc-ref outputs "out"))
                            (qt '("qtbase" "qtsvg")))
-                        (substitute* "wpa_gui.desktop"
-                          (("Exec=wpa_gui")
-                           (string-append "Exec=" out "/bin/wpa_gui")))
                        (install-file "wpa_gui" (string-append out "/bin"))
                        (install-file "wpa_gui.desktop"
                                      (string-append out "/share/applications"))
@@ -1215,11 +1240,10 @@ This package provides the 'wpa_supplicant' daemon and the 'wpa_cli' command.")
               ;; It's an old configure script that doesn't understand
               ;; the extra options we pass.
               (setenv "CONFIG_SHELL" (which "bash"))
-               (zero?
-                (system* "./configure"
-                         (string-append "--prefix=" out)
-                         (string-append "--mandir=" out
-                                        "/share/man")))))))
+               (invoke "./configure"
+                       (string-append "--prefix=" out)
+                       (string-append "--mandir=" out
+                                      "/share/man"))))))
       #:tests? #f))
    (home-page "https://www.kernel.org") ; really, no home page
    (synopsis "Send a wake-on-LAN packet")
@@ -1231,7 +1255,7 @@ network, which causes enabled computers to power on.")
 (define-public dmidecode
  (package
    (name "dmidecode")
-    (version "3.1")
+    (version "3.2")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -1239,7 +1263,7 @@ network, which causes enabled computers to power on.")
                    version ".tar.xz"))
              (sha256
               (base32
-                "1h0sg0lxa15nzf8s7884p6q7p6md9idm0c79wyqmk32l4ndwwrnp"))))
+                "1pcfhcgs2ifdjwp7amnsr3lq95pgxpr150bjhdinvl505px0cw07"))))
    (build-system gnu-build-system)
    (arguments
     '(#:phases (modify-phases %standard-phases (delete 'configure))
@@ -1261,7 +1285,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
 (define-public acpica
  (package
    (name "acpica")
-    (version "20180629")
+    (version "20180810")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -1269,7 +1293,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
                    version ".tar.gz"))
              (sha256
               (base32
-                "0rsh7ya5brpbsj7y44k1z77cvgv3zahiy8hvwvl61d6fh3db7pdp"))))
+                "01drf32h0v1s8yd414rgc9bavb52yffrwpnbzfxd9sk1lwssr6v7"))))
    (build-system gnu-build-system)
    (native-inputs `(("flex" ,flex)
                     ("bison" ,bison)))
@@ -1321,25 +1345,30 @@ system is under heavy load.")
 (define-public detox
  (package
    (name "detox")
-    (version "1.2.0")
+    (version "1.3.0")
    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://sourceforge/detox/detox/" version
-                                  "/detox-" version ".tar.bz2"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/dharple/detox.git")
+                    (commit (string-append "v" version))))
              (sha256
               (base32
-                "1y6vvjqsg54kl49cry73jbfhr04s7wjs779vrr9zrq6kww7dkymb"))))
+                "1dd608c7g65s5lj02cddvani3q9kzirddgkjqa22ap9d4f8b9xgr"))))
    (build-system gnu-build-system)
-    ;; Both flex and popt are used in this case for their runtime libraries
-    ;; (libfl and libpopt).
-    (inputs
-     `(("flex" ,flex)
-       ("popt" ,popt)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("flex" ,flex)))
    (arguments
-     `(#:configure-flags `(,(string-append "--with-popt="
-                                           (assoc-ref %build-inputs "popt")))
-       #:tests? #f))                    ;no 'check' target
-    (home-page "http://detox.sourceforge.net")
+     `(#:tests? #f                    ;no 'check' target
+       #:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'delete-configure
+                    ;; The "configure" script is present, but otherwise the
+                    ;; project is not bootstrapped: missing install-sh and
+                    ;; Makefile.in, so delete it so the bootstrap phase will
+                    ;; take over.
+                    (lambda _ (delete-file "configure") #t)))))
+    (home-page "https://github.com/dharple/detox")
    (synopsis "Clean up file names")
    (description
     "Detox is a program that renames files to make them easier to work with
@@ -1571,34 +1600,31 @@ of supported upstream metrics systems simultaneously.")
 (define-public ansible
  (package
    (name "ansible")
-    (version "2.4.2.0")
+    (version "2.7.4")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "ansible" version))
       (sha256
        (base32
-         "0n3n9py4s3aykiii31xq8g4wmd6693jvby0424pjrg0bna01apri"))
+         "0p1n6yyc632522fl2r247p0jg4mncc7z4hqngzbh1zxq3dcb12s9"))
       (patches (search-patches "ansible-wrap-program-hack.patch"))))
    (build-system python-build-system)
    (native-inputs
-     `(("python2-bcrypt" ,python2-bcrypt)
-       ("python2-pycrypto" ,python2-pycrypto)
-       ("python2-pynacl" ,python2-pynacl)
-       ("python2-httplib2" ,python2-httplib2)
-       ("python2-passlib" ,python2-passlib)
-       ("python2-nose" ,python2-nose)
-       ("python2-mock" ,python2-mock)
-       ("python2-jinja2" ,python2-jinja2)
-       ("python2-pyyaml" ,python2-pyyaml)
-       ("python2-paramiko" ,python2-paramiko)))
+     `(("python-bcrypt" ,python-bcrypt)
+       ("python-pynacl" ,python-pynacl)
+       ("python-httplib2" ,python-httplib2)
+       ("python-passlib" ,python-passlib)
+       ("python-nose" ,python-nose)
+       ("python-mock" ,python-mock)
+       ("python-jinja2" ,python-jinja2)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-paramiko" ,python-paramiko)))
    (inputs
-     `(("python2-pycrypto" ,python2-pycrypto)
-       ("python2-jinja2" ,python2-jinja2)
-       ("python2-pyyaml" ,python2-pyyaml)
-       ("python2-paramiko" ,python2-paramiko)))
-    (arguments
-     `(#:python ,python-2)) ; incompatible with Python 3
+     `(("python-cryptography" ,python-cryptography)
+       ("python-jinja2" ,python-jinja2)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-paramiko" ,python-paramiko)))
    (home-page "https://www.ansible.com/")
    (synopsis "Radically simple IT automation")
    (description "Ansible is a radically simple IT automation system.  It
@@ -1607,6 +1633,34 @@ ad hoc task execution, and multinode orchestration---including trivializing
 things like zero-downtime rolling updates with load balancers.")
    (license license:gpl3+)))

+(define-public emacs-ansible-doc
+  (let ((commit "86083a7bb2ed0468ca64e52076b06441a2f8e9e0"))
+    (package
+      (name "emacs-ansible-doc")
+      (version (git-version "0.4" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/lunaryorn/ansible-doc.el")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0lap404ch74w99n3xip176jr42b38xhyzkfnkyqg0g3wk2cd3aq8"))))
+      (build-system emacs-build-system)
+      ;; Unmaintained by upstream.
+      (home-page "https://github.com/lunaryorn/ansible-doc.el")
+      (synopsis "Ansible documentation for Emacs")
+      (description
+       "This package provides an Ansible documentation for GNU Emacs.
+
+@code{ansible-doc} allows you to view the documentation of an Ansible
+module and @code{ansible-doc-mode} minor mode adds documentation
+lookup to YAML Mode.  You could enable the mode with @code{(add-hook
+'yaml-mode-hook #'ansible-doc-mode)}.")
+      (license license:gpl3+))))
+
 (define-public cpulimit
  (package
    (name "cpulimit")
@@ -1624,20 +1678,18 @@ things like zero-downtime rolling updates with load balancers.")
    (arguments
     `(#:phases (modify-phases %standard-phases
                  (delete 'configure)
-                  (replace
-                   'build
-                   (lambda _
-                     (zero? (system* "make" "CC=gcc" "-Csrc"))))
-                  (replace
-                   'check
-                   (lambda _
-                     (zero? (system* "make" "CC=gcc" "-Ctests"))))
-                  (replace
-                   'install
-                   (lambda* (#:key outputs #:allow-other-keys)
-                     (let* ((out (assoc-ref outputs "out"))
-                            (bin (string-append out "/bin")))
-                       (install-file "src/cpulimit" bin)))))))
+                  (replace 'build
+                    (lambda _
+                      (invoke "make" "CC=gcc" "-Csrc")))
+                  (replace 'check
+                    (lambda _
+                      (invoke "make" "CC=gcc" "-Ctests")))
+                  (replace 'install
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let* ((out (assoc-ref outputs "out"))
+                             (bin (string-append out "/bin")))
+                        (install-file "src/cpulimit" bin))
+                      #t)))))
    (home-page "https://github.com/opsengine/cpulimit")
    (synopsis "Limit CPU usage")
    (description
@@ -1772,27 +1824,18 @@ platform-specific methods.")
 (define-public audit
  (package
    (name "audit")
-    (version "2.4.5")
+    (home-page "https://people.redhat.com/sgrubb/audit/")
+    (version "2.8.4")
    (source (origin
              (method url-fetch)
-              (uri (string-append "https://people.redhat.com/sgrubb/audit/"
-                                  "audit-" version ".tar.gz"))
+              (uri (string-append home-page name "-" version ".tar.gz"))
              (sha256
               (base32
-                "1q1q51dvxscbi4kbakmd4bn0xrvwwaiwvaya79925cbrqwzxsg77"))))
+                "0f4ci6ffznnmgblwgv7ich9mjfk3p6y5l6m6h3chhmzw156nj454"))))
    (build-system gnu-build-system)
-    (home-page "https://people.redhat.com/sgrubb/audit/")
    (arguments
-     `(#:configure-flags (list "--with-python=no")
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-tests
-           (lambda _
-             ;; In the build environmnte /etc/passwd does not contain an entry
-             ;; for root/0, so we have to patch the expected value.
-             (substitute* "auparse/test/auparse_test.ref"
-               (("=0 \\(root\\)") "=0 (unknown(0))"))
-             #t)))))
+     `(#:configure-flags (list "--with-python=no"
+                               "--disable-static")))
    (inputs
     `(("openldap" ,openldap)
       ("gnutls" ,gnutls)
@@ -1855,10 +1898,9 @@ done with the @code{auditctl} utility.")
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (define (make out . args)
-               (unless (zero? (apply system* "make"
-                                     (string-append "prefix=" out)
-                                     args))
-                 (error "make failed")))
+               (apply invoke "make"
+                      (string-append "prefix=" out)
+                      args))
             (define (python-path dir)
               (string-append dir "/lib/python2.7/site-packages"))
             (let ((out (assoc-ref outputs "out"))
@@ -1872,13 +1914,14 @@ done with the @code{auditctl} utility.")
               (make ndiff "install-ndiff")
               (wrap-program (string-append ndiff "/bin/ndiff")
                 `("PYTHONPATH" prefix
-                   (,(python-path ndiff)))))))
+                   (,(python-path ndiff)))))
+             #t))
         ;; These are the tests that do not require network access.
         (replace 'check
-           (lambda _ (zero? (system* "make"
-                                     "check-nse"
-                                     "check-ndiff"
-                                     "check-dns")))))
+           (lambda _ (invoke "make"
+                             "check-nse"
+                             "check-ndiff"
+                             "check-dns"))))
       ;; Nmap can't cope with out-of-source building.
       #:out-of-source? #f))
    (home-page "https://nmap.org/")
@@ -1975,16 +2018,16 @@ a new command using the matched rule, and runs it.")
 (define-public di
  (package
    (name "di")
-    (version "4.46")
+    (version "4.47")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://gentoo.com/di/di-" version ".tar.gz"))
       (sha256
-        (base32 "0cskiqywiqkw44zdg4q78bjns6jjp1dz5lzdxrhpnpldc6075irw"))))
+        (base32 "0zlapxlzjizwzwa8xwrwibhcbkh0wx7n74gvjpp6wlwq7cgiq0xm"))))
    (build-system gnu-build-system)
    (arguments
-     `(#:tests? #f ; Obscure test failures.
+     `(#:tests? #f                      ; obscure test failures.
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
@@ -2184,15 +2227,15 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.")
             #t))
         (replace 'build
           (lambda* (#:key make-flags #:allow-other-keys)
-             (zero? (apply system* "make" "tools" "misc" make-flags))))
+             (apply invoke "make" "tools" "misc" make-flags)))
         (add-after 'build 'build-armhf
           (lambda* (#:key make-flags #:allow-other-keys)
             (setenv "LIBRARY_PATH" #f)
-             (zero? (apply system* "make" "target-tools" make-flags))))
+             (apply invoke "make" "target-tools" make-flags)))
         (replace 'install
           (lambda* (#:key make-flags #:allow-other-keys)
-             (zero? (apply system* "make" "install-all" "install-misc"
-                           make-flags)))))))
+             (apply invoke "make" "install-all" "install-misc"
+                    make-flags))))))
    (home-page "https://github.com/linux-sunxi/sunxi-tools")
    (synopsis "Hardware management tools for Allwinner computers")
    (description "This package contains tools for Allwinner devices:
@@ -2274,21 +2317,21 @@ With sedsed you can master any sed script.  No more secrets, no more hidden
 buffers.")
    (license license:expat)))

-(define-public intel-gpu-tools
+(define-public igt-gpu-tools
  (package
-    (name "intel-gpu-tools")
-    (version "1.22")
+    (name "igt-gpu-tools")
+    (version "1.23")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://cgit.freedesktop.org/xorg/app/"
                                  "intel-gpu-tools/snapshot/"
-                                  "intel-gpu-tools-" version ".tar.gz"))
+                                  name "-" version ".tar.gz"))
              (sha256
               (base32
-                "1jx5w5fr6jp67rcrlp5v79cn8kp9n0wgd5pbfgzamlah5cx6j3yd"))))
+                "0vzv2i4jfv2pkbqby5k3ap9pzidkmajwqmg3s7wnv8i1h33775iq"))))
    (build-system gnu-build-system)
    (arguments
-     `(#:tests? #f ; many of the tests try to load kernel modules
+     `(#:tests? #f              ; many of the tests try to load kernel modules
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'autogen
@@ -2297,16 +2340,17 @@ buffers.")
             (setenv "NOCONFIGURE" "1")
             (invoke "sh" "autogen.sh"))))))
    (inputs
-     `(("eudev" ,eudev)
-       ("util-macros" ,util-macros)
+     `(("cairo" ,cairo)
+       ("eudev" ,eudev)
+       ("glib" ,glib)
+       ("kmod" ,kmod)
       ("libdrm" ,libdrm)
       ("libpciaccess" ,libpciaccess)
-       ("kmod" ,kmod)
-       ("procps" ,procps)
-       ("cairo" ,cairo)
       ("libunwind" ,libunwind)
       ("libxrandr" ,libxrandr)
-       ("glib" ,glib)))
+       ("openssl" ,openssl)
+       ("procps" ,procps)
+       ("util-macros" ,util-macros)))
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
@@ -2314,17 +2358,20 @@ buffers.")
       ("pkg-config" ,pkg-config)))
    (home-page "https://cgit.freedesktop.org/xorg/app/intel-gpu-tools/")
    (synopsis "Tools for development and testing of the Intel DRM driver")
-    (description "Intel GPU Tools is a collection of tools for development and
+    (description "IGT GPU Tools is a collection of tools for development and
 testing of the Intel DRM driver.  There are many macro-level test suites that
 get used against the driver, including xtest, rendercheck, piglit, and
 oglconform, but failures from those can be difficult to track down to kernel
 changes, and many require complicated build procedures or specific testing
-environments to get useful results.  Therefore, Intel GPU Tools includes
+environments to get useful results.  Therefore, IGT GPU Tools includes
 low-level tools and tests specifically for development and testing of the
 Intel DRM Driver.")
    (supported-systems '("i686-linux" "x86_64-linux"))
    (license license:expat)))

+(define-public intel-gpu-tools
+  (deprecated-package "intel-gpu-tools" igt-gpu-tools))
+
 (define-public fabric
  (package
    (name "fabric")
@@ -2403,43 +2450,29 @@ you are running, what theme or icon set you are using, etc.")
 (define-public nnn
  (package
    (name "nnn")
-    (version "1.7")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/jarun/nnn/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
-              (sha256
-               (base32
-                "0z3lqbfx3y1caxvn7yq90b7whwyq2y32zf8kyd976ilbxpxnxqpv"))))
+    (version "1.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/jarun/nnn/releases/download/v"
+                           version "/" name "-v" version ".tar.gz"))
+       (sha256
+        (base32 "1d6z12y4rlg4dzhpm30irpq2ak8hjh5zykkp2n7vxnz5m4ki89zp"))))
    (build-system gnu-build-system)
-    (inputs `(("ncurses" ,ncurses)
-              ("readline" ,readline)))
+    (inputs
+     `(("ncurses" ,ncurses)
+       ("readline" ,readline)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
    (arguments
-     '(#:tests? #f ; no tests
+     '(#:tests? #f                      ; no tests
       #:phases
-       ;; We do not provide `ncurses.h' within an `ncursesw'
-       ;; sub-directory, so patch the source accordingly.  See
-       ;; <http://bugs.gnu.org/19018>.
-       ;; Thanks to gtypist maintainer.
       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-curses-lib
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (substitute* "Makefile"
-                 (("-lncursesw")
-                  "-lncurses"))
-               (substitute* "nnn.c"
-                 (("ncursesw\\/curses.h")
-                  "ncurses.h")))
-             #t))
-         (delete 'configure))
+         (delete 'configure))           ; no configure script
       #:make-flags
       (list
        (string-append "PREFIX="
                       (assoc-ref %outputs "out"))
-        (string-append "-Wl,-rpath="
-                       %output "/lib")
        "CC=gcc")))
    (home-page "https://github.com/jarun/nnn")
    (synopsis "Terminal file browser")
@@ -2456,26 +2489,20 @@ make it a perfect utility on modern distros.")
    (version "1.7.2")
    (source
     (origin
-      (method url-fetch)
-      (uri (string-append "https://github.com/01org/thermal_daemon/archive/v"
-                          version ".tar.gz"))
-      (file-name (string-append name "-" version ".tar.gz"))
-      (sha256 (base32
-               "15a6vb67y5wsmf0irrq7sxam18yqpz64130k83ryf24mp40h661b"))))
+      (method git-fetch)
+      (uri (git-reference
+             (url "https://github.com/01org/thermal_daemon")
+             (commit (string-append "v" version))))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32
+        "1cs2pq8xvfnsvrhg2bxawk4kn3z1qmfrnpnhs178pvfbglzh15hc"))))
    (build-system gnu-build-system)
    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'bootstrap
-           (lambda _
-             (invoke "sh" "autogen.sh")
-             #t)))
-       #:configure-flags
+     `(#:configure-flags
       (let ((out      (assoc-ref %outputs "out")))
         (list (string-append "--sysconfdir="
                              out "/etc")
-               (string-append "--with-udev-dir="
-                              out "/lib/udev")
               (string-append "--with-dbus-sys-dir="
                              out "/etc/dbus-1/system.d")
               "--localstatedir=/var"))))
@@ -2632,7 +2659,7 @@ Python loading in HPC environments.")
  (let ((real-name "inxi"))
    (package
      (name "inxi-minimal")
-      (version "3.0.13-1")
+      (version "3.0.20-1")
      (source
       (origin
         (method git-fetch)
@@ -2641,7 +2668,7 @@ Python loading in HPC environments.")
               (commit version)))
         (sha256
          (base32
-           "0732ligzmzwpwaxin4g8rbfj91ghyvf69lx2jyrahi4df0bfamh5"))))
+           "1k9148xnfznch1443niaa3w1kmsw4vp0xpwna6npgmi7zqg06ymy"))))
      (build-system trivial-build-system)
      (inputs
       `(("bash" ,bash)
@@ -2740,3 +2767,189 @@ support forum.  It runs with the @code{/exec} command in most IRC clients.")
       ;; perl-xml-dumper
       ;; ipmitool
       ,@(package-inputs inxi-minimal)))))
+
+(define-public pscircle
+  (package
+    (name "pscircle")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://gitlab.com/mildlyparallel/pscircle/-/archive/v"
+             version "/pscircle-v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1k757yf2bmgfrjd417l6kpcf83hlvi0z1791vz967mwcklrsb3fj"))))
+    (build-system meson-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("cairo" ,cairo)
+       ("libpng" ,libpng)
+       ("libx11" ,libx11)))
+    (home-page "https://gitlab.com/mildlyparallel/pscircle")
+    (synopsis "Visualize Linux processes in a form of radial tree")
+    (description
+     "@code{pscircle} visualizes Linux processes in the form of a radial tree.")
+    (license license:gpl2+)))
+
+(define-public python-pyudev
+  (package
+    (name "python-pyudev")
+    (version "0.21.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "pyudev" version))
+        (sha256
+          (base32
+            "0arz0dqp75sszsmgm6vhg92n1lsx91ihddx3m944f4ah0487ljq9"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f ; Tests require /sys
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-ctypes-udev
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((eudev (assoc-ref inputs "eudev")))
+               (substitute* "src/pyudev/core.py"
+                (("'udev'")
+                 (string-append "'" eudev "/lib/libudev.so'")))
+               (substitute* "src/pyudev/_ctypeslib/utils.py"
+                ;; Use absolute paths instead of keys.
+                (("= find_library") "= "))
+               #t))))))
+    (inputs
+     `(("eudev" ,eudev)))
+    (propagated-inputs
+     `(("python-six" ,python-six)))
+    (native-inputs
+     `(("python-docutils" ,python-docutils)
+       ("python-hypothesis" ,python-hypothesis)
+       ("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
+       ("python-sphinx" ,python-sphinx)))
+    (home-page "http://pyudev.readthedocs.org/")
+    (synopsis "Python udev binding")
+    (description "This package provides @code{udev} bindings for Python.")
+    (license license:lgpl2.1)))
+
+(define-public solaar
+  (package
+    (name "solaar")
+    (version "0.9.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pwr/Solaar.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "085mfa13dap3wqik1dqlad0d7kff4rv7j4ljh99c7l8nhczkqgwm"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-prefix-detection
+           (lambda _
+             (substitute* "setup.py"
+              (("'--prefix' in sys\\.argv")
+               "len([x.startswith('--prefix=') for x in sys.argv]) > 0"))
+             #t))
+         (replace 'build
+           (lambda _
+             (invoke "python" "setup.py" "build")))
+         (add-before 'check 'setenv-PATH
+           (lambda _
+             (setenv "PYTHONPATH" (string-append "lib:" (getenv "PYTHONPATH")))
+             #t)))))
+    (propagated-inputs
+     `(("python-pygobject" ,python-pygobject)
+       ("python-pyudev" ,python-pyudev)))
+    (home-page "https://smxi.org/docs/inxi.htm")
+    (synopsis "Linux devices manager for the Logitech Unifying Receiver")
+    (description "This package provides tools to manage clients of the
+Logitech Unifying Receiver.")
+    (license license:gpl2)))
+
+(define-public lynis
+  (package
+    (name "lynis")
+    (version "2.7.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/CISOfy/lynis")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0rzc0y8lk22bymf56249jzmllki2lh0rz5in4lkrc5fkmp29c2wv"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Remove proprietary plugins. As of now, all plugins supplied with
+           ;; lynis are proprietary. In the future, if free plugins are
+           ;; provided, whitelist them from deletion.
+           (for-each delete-file (find-files "plugins"))
+           #t))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(;; For tests
+       ("lynis-sdk"
+        ,(origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/CISOfy/lynis-sdk")
+                 (commit "3310aef4f2b3dd97d166c96ad0253c89c4ad390d")))
+           (file-name (git-file-name "lynis-sdk" version))
+           (sha256
+            (base32
+             "0sqsrm5wal742yrwps8bqb8a8lxd93n4b93n3kkm1b30nbs25g7y"))))))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (substitute* "lynis"
+               (("/usr/share/lynis")
+                (string-append (assoc-ref outputs "out") "/share/lynis")))
+             (substitute* "include/functions"
+               (("/usr/local/etc/lynis")
+                (string-append (assoc-ref outputs "out") "/etc/lynis")))
+             #t))
+         (delete 'build)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (install-file "lynis" (string-append out "/bin/"))
+               (install-file "default.prf" (string-append out "/etc/lynis"))
+               (for-each
+                (lambda (dir)
+                  (copy-recursively dir (string-append out "/share/lynis/" dir)))
+                (list "db" "include" "plugins"))
+               (install-file "lynis.8" (string-append out "/share/man/man8"))
+               #t)))
+         (replace 'check
+           (lambda* (#:key inputs #:allow-other-keys)
+             (copy-recursively (assoc-ref inputs "lynis-sdk") "../lynis-sdk")
+             (setenv "LANG" "en_US.UTF-8")
+             (let ((lynis-dir (getcwd)))
+               (with-directory-excursion "../lynis-sdk"
+                 (substitute* "config"
+                   (("\\.\\./lynis") lynis-dir))
+                 (substitute* "unit-tests/tests-language-translations.sh"
+                   (("\\.\\./lynis") lynis-dir))
+                 (invoke "sh" "lynis-devkit" "run" "unit-tests"))))))))
+    (home-page "https://cisofy.com/lynis/")
+    (synopsis "Security auditing tool")
+    (description "Lynis is a security auditing tool.  It performs an in-depth
+security scan and runs on the system itself.  The primary goal is to test
+security defenses and provide tips for further system hardening.  It will also
+scan for general system information, vulnerable software packages, and
+possible configuration issues.")
+    (license license:gpl3+)))
@@ -1,5 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Alex ter Weele <alex.ter.weele@gmail.com>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -20,6 +22,7 @@
  #:use-module (gnu packages haskell)
  #:use-module (gnu packages haskell-check)
  #:use-module (gnu packages haskell-web)
+  #:use-module (guix build-system emacs)
  #:use-module (guix build-system haskell)
  #:use-module (guix build-system trivial)
  #:use-module (guix download)
@@ -29,7 +32,7 @@
 (define-public agda
  (package
    (name "agda")
-    (version "2.5.3")
+    (version "2.5.4.1")
    (source
     (origin
       (method url-fetch)
@@ -38,7 +41,7 @@
             version ".tar.gz"))
       (sha256
        (base32
-         "0r80vw7vnvbgq47y50v050malv7zvv2p2kg6f47i04r0b2ix855a"))))
+         "0bxpibsk98n9xp42d92ma5vj2fam8rsnl61fbhr3askfjdvalnbp"))))
    (build-system haskell-build-system)
    (inputs
     `(("cpphs" ,cpphs)
@@ -50,14 +53,13 @@
       ("ghc-edisoncore" ,ghc-edisoncore)
       ("ghc-edit-distance" ,ghc-edit-distance)
       ("ghc-equivalence" ,ghc-equivalence)
+       ("ghc-filemanip" ,ghc-filemanip)
       ("ghc-geniplate-mirror" ,ghc-geniplate-mirror)
       ("ghc-gitrev" ,ghc-gitrev)
       ("ghc-happy" ,ghc-happy)
       ("ghc-hashable" ,ghc-hashable)
       ("ghc-hashtables" ,ghc-hashtables)
       ("ghc-ieee754" ,ghc-ieee754)
-       ("ghc-monadplus" ,ghc-monadplus)
-       ("ghc-mtl" ,ghc-mtl)
       ("ghc-murmur-hash" ,ghc-murmur-hash)
       ("ghc-uri-encode" ,ghc-uri-encode)
       ("ghc-parallel" ,ghc-parallel)
@@ -67,6 +69,60 @@
       ("ghc-text" ,ghc-text)
       ("ghc-unordered-containers" ,ghc-unordered-containers)
       ("ghc-zlib" ,ghc-zlib)))
+    (arguments
+     `(#:modules ((guix build haskell-build-system)
+                  (guix build utils)
+                  (srfi srfi-26)
+                  (ice-9 match))
+       #:phases
+       (modify-phases %standard-phases
+         ;; FIXME: This is a copy of the standard configure phase with a tiny
+         ;; difference: this package needs the -package-db flag to be passed
+         ;; to "runhaskell" in addition to the "configure" action, because
+         ;; Setup.hs depends on filemanip.  Without this option the Setup.hs
+         ;; file cannot be evaluated.  The haskell-build-system should be
+         ;; changed to pass "-package-db" to "runhaskell" in any case.
+         (replace 'configure
+           (lambda* (#:key outputs inputs tests? (configure-flags '())
+                     #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (name-version (strip-store-file-name out))
+                    (input-dirs (match inputs
+                                  (((_ . dir) ...)
+                                   dir)
+                                  (_ '())))
+                    (ghc-path (getenv "GHC_PACKAGE_PATH"))
+                    (params (append `(,(string-append "--prefix=" out))
+                                    `(,(string-append "--libdir=" out "/lib"))
+                                    `(,(string-append "--bindir=" out "/bin"))
+                                    `(,(string-append
+                                        "--docdir=" out
+                                        "/share/doc/" name-version))
+                                    '("--libsubdir=$compiler/$pkg-$version")
+                                    '("--package-db=../package.conf.d")
+                                    '("--global")
+                                    `(,@(map
+                                         (cut string-append "--extra-include-dirs=" <>)
+                                         (search-path-as-list '("include") input-dirs)))
+                                    `(,@(map
+                                         (cut string-append "--extra-lib-dirs=" <>)
+                                         (search-path-as-list '("lib") input-dirs)))
+                                    (if tests?
+                                        '("--enable-tests")
+                                        '())
+                                    configure-flags)))
+               (unsetenv "GHC_PACKAGE_PATH")
+               (apply invoke "runhaskell" "-package-db=../package.conf.d"
+                      "Setup.hs" "configure" params)
+               (setenv "GHC_PACKAGE_PATH" ghc-path)
+               #t)))
+         (add-after 'compile 'agda-compile
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (agda-compiler (string-append out "/bin/agda")))
+               (for-each (cut invoke agda-compiler <>)
+                         (find-files (string-append out "/share") "\\.agda$"))
+               #t))))))
    (home-page "http://wiki.portal.chalmers.se/agda/")
    (synopsis
     "Dependently typed functional programming language and proof assistant")
@@ -84,3 +140,19 @@ such as Coq, Epigram and NuPRL.")
    ;; Agda is distributed under the MIT license, and a couple of
    ;; source files are BSD-3.  See LICENSE for details.
    (license (list license:expat license:bsd-3))))
+
+(define-public emacs-agda2-mode
+  (package
+    (inherit agda)
+    (name "emacs-agda2-mode")
+    (build-system emacs-build-system)
+    (inputs '())
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'enter-elisp-dir
+           (lambda _ (chdir "src/data/emacs-mode") #t)))))
+    (home-page "https://agda.readthedocs.io/en/latest/tools/emacs-mode.html")
+    (synopsis "Emacs mode for Agda")
+    (description "This Emacs mode enables interactive development with
+Agda.  It also aids the input of Unicode characters.")))
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017, 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
@@ -139,7 +139,7 @@ solve the shortest vector problem.")
 (define-public pari-gp
  (package
   (name "pari-gp")
-   (version "2.9.4")
+   (version "2.11.0")
   (source (origin
            (method url-fetch)
            (uri (string-append
@@ -147,7 +147,7 @@ solve the shortest vector problem.")
                  version ".tar.gz"))
            (sha256
              (base32
-                "0ir6m3a8r46md5x6zk4xf159qra7aqparby9zk03k81hjrrxr72g"))))
+                "18f9yj8ffn3dxignbxj1x36771zbxy4js0r18mv6831ymb6cld9q"))))
   (build-system gnu-build-system)
   (native-inputs `(("texlive" ,texlive-tiny)))
   (inputs `(("gmp" ,gmp)
@@ -179,7 +179,7 @@ PARI is also available as a C library to allow for faster computations.")
 (define-public gp2c
  (package
   (name "gp2c")
-   (version "0.0.10")
+   (version "0.0.11pl1")
   (source (origin
            (method url-fetch)
            (uri (string-append
@@ -187,7 +187,7 @@ PARI is also available as a C library to allow for faster computations.")
                  version ".tar.gz"))
            (sha256
              (base32
-                "1xhpz5p81iw261ay1kip283ggr0ir8ydz8qx3v24z8jfms1r3y70"))))
+                "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s"))))
   (build-system gnu-build-system)
   (native-inputs `(("perl" ,perl)))
   (inputs `(("pari-gp" ,pari-gp)))
@@ -210,10 +210,40 @@ GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
   (license license:gpl2)
   (home-page "https://pari.math.u-bordeaux.fr/")))

+(define-public cmh
+  (package
+   (name "cmh")
+   (version "1.0")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://gforge.inria.fr/frs/download.php/33497/cmh-"
+                  version ".tar.gz"))
+            (sha256
+             (base32
+              "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
+   (build-system gnu-build-system)
+   (inputs
+     `(("gmp" ,gmp)
+       ("mpfr" ,mpfr)
+       ("mpc" ,mpc)
+       ("mpfrcx" ,mpfrcx)
+       ("fplll" ,fplll)
+       ("pari-gp"  ,pari-gp)))
+   (synopsis "Igusa class polynomial computations")
+   (description
+    "The CMH software computes Igusa (genus 2) class polynomials, which
+parameterize the CM points in the moduli space of 2-dimensional abelian
+varieties, i.e. Jacobians of hyperelliptic curves.
+It can also be used to compute theta constants at arbitrary
+precision.")
+   (license license:gpl3+)
+   (home-page "http://cmh.gforge.inria.fr/")))
+
 (define-public giac-xcas
  (package
    (name "giac-xcas")
-    (version "1.4.9-59")
+    (version "1.5.0-19")
    (source (origin
              (method url-fetch)
              ;; "~parisse/giac" is not used because the maintainer regularly
@@ -225,16 +255,48 @@ GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
                                  "source/giac_" version ".tar.gz"))
              (sha256
               (base32
-                "0dv5p5y6gkrsmz3xa7fw87rjyabwdwk09mqb09kb7gai9n9dgayk"))))
+                "0ds1zh712sr20qh0fih8jnm4nlv90andllp8n263qs7rlhblz551"))))
    (build-system gnu-build-system)
+    (outputs '("out" "doc"))            ;77MiB of documentation
    (arguments
-     `(#:phases
+     `(#:modules ((ice-9 ftw)
+                  (guix build utils)
+                  (guix build gnu-build-system))
+       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-bin-cp
+           ;; Some Makefiles contain hard-coded "/bin/cp".
           (lambda _
-             ;; Some Makefiles contain hard-coded "/bin/cp".
             (substitute* (find-files "doc" "^Makefile")
               (("/bin/cp") (which "cp")))
+             #t))
+         (add-after 'unpack 'disable-failing-test
+           ;; FIXME: Test failing.  Not sure why.
+           (lambda _
+             (substitute* "check/Makefile.in"
+               (("chk_fhan11") ""))
+             #t))
+         (add-after 'install 'install-doc
+           ;; Setting --docdir to "doc" output isn't sufficient as
+           ;; documentation and examples are scattered throughout the source.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (doc (assoc-ref outputs "doc"))
+                    (docdir (string-append doc
+                                           "/share/doc/"
+                                           (string-append ,name "-" ,version))))
+               ;; For some reason, the install process moves
+               ;; "share/giac/examples" instead of "share/giac/doc" to
+               ;; "$(docdir)".  Clean up the mess and start over.
+               (delete-file-recursively (string-append doc "/share"))
+               (mkdir-p docdir)
+               (with-directory-excursion out
+                 (for-each (lambda (f)
+                             (unless (member f '("." ".."))
+                               (copy-recursively (string-append "share/giac/" f)
+                                                 (string-append docdir "/" f))))
+                           (scandir "share/giac"))
+                 (delete-file-recursively "share/giac")))
             #t)))))
    (inputs
     `(("fltk" ,fltk)
@@ -314,48 +376,47 @@ fast arithmetic.")

 (define-public arb
  (package
-   (name "arb")
-   (version "2.12.0")
-   (source (origin
-            (method url-fetch)
-            (uri (string-append
-                  "https://github.com/fredrik-johansson/arb/archive/"
-                  version ".tar.gz"))
-            (file-name (string-append name "-" version ".tar.gz"))
-            (sha256
-              (base32
-                "0j37xkxbqpra4sf0a96x4sqbl5fkal8d7c94bi9wdsqqj6kgcsil"))))
-   (build-system gnu-build-system)
-   (propagated-inputs
-    `(("flint" ,flint))) ; flint.h is included by arf.h
-   (inputs
-    `(("gmp" ,gmp)
-      ("mpfr" ,mpfr)))
-   (arguments
-    `(#:phases
-      (modify-phases %standard-phases
-        (replace 'configure
-          (lambda* (#:key inputs outputs #:allow-other-keys)
-            (let ((out (assoc-ref outputs "out"))
-                  (flint (assoc-ref inputs "flint"))
-                  (gmp (assoc-ref inputs "gmp"))
-                  (mpfr (assoc-ref inputs "mpfr")))
-              ;; do not pass "--enable-fast-install", which makes the
-              ;; homebrew configure process fail
-              (zero? (system*
-                      "./configure"
-                      (string-append "--prefix=" out)
-                      (string-append "--with-flint=" flint)
-                      (string-append "--with-gmp=" gmp)
-                      (string-append "--with-mpfr=" mpfr)))))))))
-   (synopsis "Arbitrary precision floating-point ball arithmetic")
-   (description
-    "Arb is a C library for arbitrary-precision floating-point ball
+    (name "arb")
+    (version "2.14.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/fredrik-johansson/arb.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1ndxg7h4xvccjgp5l9z2f8b66dsff6fhf86bn5n7f75a1ksd7554"))))
+    (build-system gnu-build-system)
+    (propagated-inputs
+     `(("flint" ,flint)))               ; flint.h is included by arf.h
+    (inputs
+     `(("gmp" ,gmp)
+       ("mpfr" ,mpfr)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (flint (assoc-ref inputs "flint"))
+                   (gmp (assoc-ref inputs "gmp"))
+                   (mpfr (assoc-ref inputs "mpfr")))
+               ;; do not pass "--enable-fast-install", which makes the
+               ;; homebrew configure process fail
+               (invoke "./configure"
+                       (string-append "--prefix=" out)
+                       (string-append "--with-flint=" flint)
+                       (string-append "--with-gmp=" gmp)
+                       (string-append "--with-mpfr=" mpfr))))))))
+    (synopsis "Arbitrary precision floating-point ball arithmetic")
+    (description
+     "Arb is a C library for arbitrary-precision floating-point ball
 arithmetic.  It supports efficient high-precision computation with
 polynomials, power series, matrices and special functions over the
 real and complex numbers, with automatic, rigorous error control.")
-   (license license:gpl2+)
-   (home-page "http://fredrikj.net/arb/")))
+    (license license:lgpl2.1+)
+    (home-page "http://fredrikj.net/arb/")))

 (define-public ntl
  (package
@@ -400,15 +461,21 @@ matrices, and polynomials over the integers and over finite fields.")
 (define-public singular
  (package
   (name "singular")
-   (version "4.0.3")
-   (source (origin
-            (method url-fetch)
-            (uri (string-append "http://www.mathematik.uni-kl.de/ftp/pub/"
-                                "Math/Singular/SOURCES/"
-                                (string-join (string-split version #\.) "-")
-                                "/singular-" version ".tar.gz"))
-            (sha256 (base32
-                     "0viidy2fz62rln9p0s9qfs7fnm55c6fw1agydd1py26gxylp1ksc"))))
+   (version "4.1.1p3")
+   (source
+    (origin
+      (method url-fetch)
+      (uri
+       (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
+                      "Singular/SOURCES/"
+                      (string-join
+                       (string-split
+                        (string-trim-right version #\p
+                                           0 (1- (string-length version)))
+                        #\.) "-")
+                      "/singular-" version ".tar.gz"))
+             (sha256 (base32
+                      "1qqj9bm9pkzm0iyycpvm8x6s79wws3nq60lz25h8x1q61h3426sm"))))
   (build-system gnu-build-system)
   (native-inputs
    `(("doxygen" ,doxygen)
@@ -501,13 +568,14 @@ syntax is similar to that of C, so basic usage is familiar.  It also includes
    (name "kiss-fft-for-extempore")
    (version "1.3.0")
    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/extemporelang/kiss_fft/archive/"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/extemporelang/kiss_fft.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
              (sha256
               (base32
-                "0hkp9l6l4c92fb1l2sh6a6zv1hynpvb2s4d03vd8vxyvybc0l4pv"))))
+                "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
    (build-system cmake-build-system)
    (arguments `(#:tests? #f)) ; no tests included
    ;; Extempore refuses to build on architectures other than x86_64
@@ -523,14 +591,14 @@ a C program.")
 (define-public fftw
  (package
    (name "fftw")
-    (version "3.3.7")
+    (version "3.3.8")
    (source (origin
             (method url-fetch)
             (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
                                 version".tar.gz"))
             (sha256
              (base32
-               "0wsms8narnbhfsa8chdflv2j9hzspvflblnqdn7hw8x5xdzrnq1v"))))
+               "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags
@@ -698,16 +766,15 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
 (define-public eigen
  (package
    (name "eigen")
-    (version "3.3.4")
+    (version "3.3.5")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
                                  version ".tar.bz2"))
              (sha256
               (base32
-                "19m4406jvqnwh7kpcvx1lfx2vdc5zwia5q9ayv89bimg1gmln9fx"))
+                "1qh3yrwn78ms5yhwbpl5wvblk4gbz02cacdygxylr7i9xbrvylkk"))
              (file-name (string-append name "-" version ".tar.bz2"))
-	      (patches (search-patches "eigen-arm-neon-fixes.patch"))
              (modules '((guix build utils)))
              (snippet
               ;; There are 3 test failures in the "unsupported" directory,
@@ -717,16 +784,6 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
                  (substitute* "unsupported/CMakeLists.txt"
                    (("add_subdirectory\\(test.*")
                     "# Do not build the tests for unsupported features.\n"))
-		  (substitute* "CMakeLists.txt"
-                    ;; Work around
-                    ;; <http://eigen.tuxfamily.org/bz/show_bug.cgi?id=1114>.
-                    (("\"include/eigen3\"")
-                     "\"${CMAKE_INSTALL_PREFIX}/include/eigen3\""))
-		  (substitute* "test/bdcsvd.cpp"
-                    ;; See
-                    ;; https://bitbucket.org/eigen/eigen/commits/ea8c22ce6920e982d15245ee41d0531a46a28e5d
-                    ((".*svd_preallocate[^\n]*" &)
-                     (string-append "//" & " // Not supported by BDCSVD")))
                  #t))))
    (build-system cmake-build-system)
    (arguments
@@ -741,11 +798,11 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
 			(setenv "EIGEN_SEED" "1") ;for reproducibility
                        ;; First build the tests, in parallel.  See
                        ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
-                        (and (zero? (system* "make" "buildtests" dash-j))
+                        (invoke "make" "buildtests" dash-j)

-                             ;; Then run 'CTest' with -V so we get more
-                             ;; details upon failure.
-                             (zero? (system* "ctest" "-V" dash-j)))))))))
+                        ;; Then run 'CTest' with -V so we get more
+                        ;; details upon failure.
+                        (invoke "ctest" "-V" dash-j)))))))
    (home-page "https://eigen.tuxfamily.org")
    (synopsis "C++ template library for linear algebra")
    (description
@@ -762,16 +819,16 @@ features, and more.")
 (define-public xtensor
  (package
    (name "xtensor")
-    (version "0.15.9")
+    (version "0.17.1")
    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/QuantStack/xtensor/archive/"
-                    version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/QuantStack/xtensor.git")
+                    (commit version)))
              (sha256
               (base32
-                "0mlsw4p1w5mh7pscddfdamz27zq3wml5qla3vbzgvif34vsqc8ra"))
-              (file-name (string-append name "-" version ".tar.gz"))))
+                "0w40v5lp0hp8ihf8nnvak373sb5xx0768pxgiqh3nzn57wf8px4r"))
+              (file-name (git-file-name name version))))
    (build-system cmake-build-system)
    (native-inputs
     `(("googletest" ,googletest)
@@ -6,6 +6,7 @@
 ;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2017 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -34,13 +35,19 @@
  #:use-module (gnu packages)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
+  #:use-module (gnu packages docker)
  #:use-module (gnu packages gnupg)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-crypto)
+  #:use-module (gnu packages python-web)
  #:use-module (gnu packages selinux)
+  #:use-module (gnu packages serialization)
  #:use-module (gnu packages ssh)
-  #:use-module (gnu packages version-control)
  #:use-module (gnu packages tls)
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages virtualization)
+  #:use-module (gnu packages xdisorg)
  #:use-module (gnu packages linux))

 (define-public android-make-stub
@@ -101,7 +108,7 @@ use their packages mostly unmodified in our Android NDK build system.")
 ;; Big thanks to them for laying the groundwork.

 ;; The version tag is consistent between all repositories.
-(define (android-platform-version) "7.1.2_r6")
+(define (android-platform-version) "7.1.2_r36")

 (define (android-platform-system-core version)
  (origin
@@ -113,7 +120,7 @@ use their packages mostly unmodified in our Android NDK build system.")
                              version "-checkout"))
    (sha256
     (base32
-      "0xc2n7jxrf1iw9cc278pijdfjix2fkiig5ws27f6rwp40zg5mrgg"))
+      "1krnc2b9zfkzpdgs1dcbji59nszlx2qr723pg89m52622czc06hg"))
    (patches
     (search-patches "libbase-use-own-logging.patch"
                     "libbase-fix-includes.patch"
@@ -144,7 +151,7 @@ use their packages mostly unmodified in our Android NDK build system.")
                              version "-checkout"))
    (sha256
     (base32
-      "0n9wkz3ynqw39if1ss9n32m66iga14nndf29hpm7g1aqn4wvvgzk"))))
+      "15r4s20d7vw022f8vrc3jbghmqwdcqzprl7i2bfvdkz8z76wc1ps"))))

 (define (android-platform-external version subdirectory checksum)
  (origin
@@ -332,6 +339,13 @@ various Android core host applications.")
       (modify-phases %standard-phases
         (add-after 'unpack 'enter-source
           (lambda _ (chdir "adb") #t))
+         (add-after 'enter-source 'glibc-compat
+           (lambda _
+             ;; Include sysmacros.h for "major" and "minor" in Glibc 2.28.
+             (substitute* "usb_linux.cpp"
+               (("#include <sys/types.h>" all)
+                (string-append all "\n#include <sys/sysmacros.h>\n")))
+             #t))
         (add-after 'enter-source 'make-libs-available
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (substitute* "Android.mk"
@@ -807,3 +821,100 @@ script that you can put anywhere in your path.")
 Boot Images.  @code{abootimg} can work directly on block devices, or, the
 safest way, on a file image.")
    (license license:gpl2+)))
+
+(define-public python-androguard
+  (package
+    (name "python-androguard")
+    (version "3.2.1")
+    (source
+      (origin
+        ;; The pypi release doesn't have the tests, but the tests use
+        ;; packaged binaries, so we skip them.
+        (method url-fetch)
+        (uri (pypi-uri "androguard" version))
+        (sha256
+         (base32
+          "0ndsw00pkyda4i2s3wi5ap8gbk6a9d23xhhxpdbk02padv8sxkfv"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           ;; Adapted from .travis.yml
+           (lambda _
+             (invoke "nosetests" "--with-coverage" "--with-timer"
+                     "--timer-top-n" "50"))))))
+    (native-inputs
+     `(("python-codecov" ,python-codecov)
+       ("python-coverage" ,python-coverage)
+       ("python-mock" ,python-mock)
+       ("python-nose" ,python-nose)
+       ("python-nose-timer" ,python-nose-timer)))
+    (propagated-inputs
+     `(("python-asn1crypto" ,python-asn1crypto)
+       ("python-colorama" ,python-colorama)
+       ("python-future" ,python-future)
+       ("python-ipython" ,python-ipython)
+       ("python-lxml" ,python-lxml)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-networkx" ,python-networkx)
+       ("python-pygments" ,python-pygments)
+       ("python-pyperclip" ,python-pyperclip)))
+    (home-page "https://github.com/androguard/androguard")
+    (synopsis "Python tool to play with Android files")
+    (description
+     "Androguard is a full Python tool to manipulate Android files.  It is
+useful for reverse engineering, analysis of Android applications and more.")
+    (license license:asl2.0)))
+
+(define-public fdroidserver
+  (package
+    (name "fdroidserver")
+    (version "1.0.10")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "fdroidserver" version))
+        (sha256
+         (base32
+          "0n6kkby65qzqdx1jn72grfffvr1w1j1rby5pwm9z8rymmsh8s0pm"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-versioning
+           (lambda _
+             (substitute* "setup.py"
+               (("0.2.1") ,(package-version python-pyasn1-modules)))
+             #t)))))
+    (propagated-inputs
+     `(("python-androguard" ,python-androguard)
+       ("python-apache-libcloud" ,python-apache-libcloud)
+       ("python-clint" ,python-clint)
+       ("python-docker-py" ,python-docker-py)
+       ("python-gitpython" ,python-gitpython)
+       ("python-mwclient" ,python-mwclient)
+       ("python-paramiko" ,python-paramiko)
+       ("python-pillow" ,python-pillow)
+       ("python-pyasn1" ,python-pyasn1)
+       ("python-pyasn1-modules" ,python-pyasn1-modules)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-qrcode" ,python-qrcode)
+       ("python-ruamel.yaml" ,python-ruamel.yaml)
+       ("python-requests" ,python-requests)
+       ("python-vagrant" ,python-vagrant)))
+    (native-inputs
+     `(("python-babel" ,python-babel)
+       ("python-bcrypt" ,python-bcrypt)
+       ("python-docker-pycreds" ,python-docker-pycreds)
+       ("python-pynacl" ,python-pynacl)
+       ("python-websocket-client" ,python-websocket-client)))
+    (home-page "https://f-droid.org")
+    (synopsis "F-Droid server tools")
+    (description
+     "The F-Droid server tools provide various scripts and tools that are used
+to maintain F-Droid, the repository of free Android applications.  You can use
+these same tools to create your own additional or alternative repository for
+publishing, or to assist in creating, testing and submitting metadata to the
+main repository.")
+    (license license:agpl3+)))
@@ -0,0 +1,156 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
+;;;
+;;; 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 antivirus)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix utils)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages bison)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
+  #:use-module (gnu packages cyrus-sasl)
+  #:use-module (gnu packages flex)
+  #:use-module (gnu packages llvm)
+  #:use-module (gnu packages multiprecision)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages pcre)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages tls)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages xml))
+
+(define-public clamav
+  (package
+    (name "clamav")
+    (version "0.100.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://www.clamav.net/downloads/production/"
+                                  "clamav-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1mkd41sxbjkfjinpx5b9kb85q529gj2s3d0klysssqhysh64ybja"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (for-each delete-file-recursively
+                            '("win32"              ;unnecessary
+                              "libclamav/c++/llvm" ;use system llvm
+                              "libclamunrar"))))   ;non-free license
+              (patches
+               (search-patches "clamav-system-tomsfastmath.patch"
+                               "clamav-config-llvm-libs.patch"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("bison" ,bison)
+       ("check" ,check)                 ;for tests
+       ("flex" ,flex)
+       ("pkg-config" ,pkg-config)
+       ;; The tomsfastmath patch touches configure.ac and Makefile.am
+       ("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (inputs
+     `(("bzip2" ,bzip2)
+       ("libcurl" ,curl)
+       ("libjson" ,json-c)
+       ("libltdl" ,libltdl)
+       ("libmspack" ,libmspack)
+       ("llvm" ,llvm-3.6)               ;requires <3.7, for JIT/verifier
+       ("ncurses" ,ncurses)
+       ("openssl" ,libressl)
+       ("pcre" ,pcre "bin")             ;for pcre-config
+       ("sasl" ,cyrus-sasl)             ;for linking curl with libtool
+       ("tomsfastmath" ,tomsfastmath)
+       ("xml" ,libxml2)
+       ("zlib" ,zlib)))
+    (arguments
+     `(#:configure-flags
+       (let-syntax ((with (syntax-rules ()
+                            ((_ name)
+                             (string-append "--with-" name "="
+                                            (assoc-ref %build-inputs name))))))
+         (list "--disable-unrar"
+               "--enable-llvm"
+               "--with-system-llvm"
+               "--with-system-libmspack"
+               "--without-included-ltdl"
+               (with "xml")
+               (with "openssl")
+               (with "libjson")
+               (with "pcre")
+               (with "zlib")
+               (with "libcurl")
+               ;; For sanity, specifying --enable-* flags turns
+               ;; "support unavailable" warnings into errors.
+               "--enable-bzip2"
+               "--enable-check"
+               "--sysconfdir=/etc/clamav"
+               ;; Default database directory needs to be writeable
+               "--with-dbdir=/var/db/clamav"))
+       ;; install sample .conf files to %output/etc rather than /etc/clamav
+       #:make-flags (list (string-append "sysconfdir=" %output "/etc"))
+       #:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'reconf
+                    (lambda _ (zero? (system* "autoreconf" "-vfi"))))
+                  (add-before 'configure 'patch-llvm-config
+                    (lambda _
+                      (substitute* '("libclamav/c++/detect.cpp"
+                                     "libclamav/c++/ClamBCRTChecks.cpp"
+                                     "libclamav/c++/bytecode2llvm.cpp")
+                        (("llvm/Config/config.h") "llvm/Config/llvm-config.h"))
+                      ;; `llvm-config --libfiles` inappropriately lists lib*.a
+                      ;; libraries, rather than the lib*.so's that our llvm
+                      ;; contains.  They're used only for listing extra build
+                      ;; dependencies, so ignore them until that's fixed.
+                      (substitute* "libclamav/c++/Makefile.in"
+                        (("@LLVMCONFIG_LIBFILES@") ""))
+                      #t))
+                  (add-before 'check 'skip-clamd-tests
+                    ;; XXX: The check?_clamd tests fail inside the build
+                    ;; chroot, but pass outside.
+                    (lambda _
+                      (substitute* "unit_tests/Makefile"
+                        (("check2_clamd.sh.*check4_clamd.sh") ""))
+                      #t)))))
+    (home-page "https://www.clamav.net")
+    (synopsis "Antivirus engine")
+    (description
+     "Clam AntiVirus is an anti-virus toolkit, designed especially for e-mail
+scanning on mail gateways.  It provides a number of utilities including a
+flexible and scalable multi-threaded daemon, a command line scanner, and
+advanced tool for automatic database updates.  The core of the package is an
+anti-virus engine available in the form of a shared library.")
+    (license (list license:gpl2+        ;ClamAV itself
+                   license:lgpl2.1      ;libclamav/mspack.[ch]
+                   license:public-domain ;libclamav/7z/*, libclamav/rijndael.[ch], etc...
+                   (package-license bzip2) ;modified bzip2 source in libclamav/nsis
+                   license:bsd-2        ;several files in libclamav
+                   license:bsd-3        ;libclamav/{regex,qsort.c,swf.[ch]
+                   license:ncsa         ;libclamav/c++/PointerTracking.cpp
+                   license:zlib         ;libclamav/inf*.h
+                   license:x11          ;libclamav/lzw
+                   (license:non-copyleft "libclamav/strlcat.c") ;"OpenBSD" license
+                   license:asl2.0       ;libclamav/yara*
+                   license:expat))))    ;shared/getopt.[ch]
@@ -27,6 +27,7 @@
  #:use-module (guix download)
  #:use-module (guix build-system gnu)
  #:use-module (guix licenses)
+  #:use-module (guix utils)
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages compression)
@@ -49,6 +50,19 @@
    (arguments
     `(#:phases
       (modify-phases %standard-phases
+         (add-before 'build 'set-filter-path
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Change the default value of 'filter-path' so that filters such
+             ;; as 'tex-filter.so' can be found.  By default none of the
+             ;; filters would be found.
+             (let* ((out    (assoc-ref outputs "out"))
+                    (libdir (string-append out "/lib/aspell-"
+                                           ,(version-major+minor version))))
+               (substitute* "common/config.cpp"
+                 (("\"filter-path(.*)DICT_DIR" _ middle)
+                  (string-append "\"filter-path" middle
+                                 "\"" libdir "\"")))
+               #t)))
         (add-after 'install 'wrap-aspell
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin/aspell (string-append (assoc-ref outputs "out")
@@ -141,10 +155,10 @@ dictionaries, including personal ones.")

 (define-public aspell-dict-en
  (aspell-dictionary "en" "English"
-                     #:version "2017.08.24-0"
+                     #:version "2018.04.16-0"
                     #:sha256
                     (base32
-                      "0z2vvm1by485cm0sna21cmw6zb771c2l2lnn676zmrwm46q65d89")))
+                      "0bxxdzkk9g27plg22y9qzsx9cfjw3aa29w5bmzs561qc9gkp247i")))

 (define-public aspell-dict-eo
  (aspell-dictionary "eo" "Esperanto"
@@ -68,7 +68,7 @@ in FITS files.")
 (define-public wcslib
  (package
    (name "wcslib")
-    (version "5.18")
+    (version "5.20")
    (source
     (origin
       (method url-fetch)
@@ -76,7 +76,7 @@ in FITS files.")
             "ftp://ftp.atnf.csiro.au/pub/software/wcslib/" name "-" version
             ".tar.bz2"))
       (sha256
-        (base32 "16jh568k99c9p0y3qzcgps2rii933x9wlay7q1xm0lr59zqzp4xn"))))
+        (base32 "1c8g9kv4dxrnawnqi4spi2p10s2xs7x75pdfxhbqxgcc97dkgh0b"))))
    (inputs
     `(("cfitsio" ,cfitsio)))
    (build-system gnu-build-system)
@@ -89,8 +89,7 @@ in FITS files.")
               (("/bin/sh") "sh"))
             #t))
         (delete 'install-license-files)) ; installed by ‘make install’
-       ;; Both the build and tests fail randomly when run in parallel.
-       #:parallel-build? #f
+       ;; Parallel execution of the test suite is not supported.
       #:parallel-tests? #f))
    (home-page "https://www.atnf.csiro.au/people/mcalabre/WCS")
    (synopsis "Library which implements the FITS WCS standard")
@@ -103,7 +102,7 @@ header.")
 (define-public gnuastro
  (package
    (name "gnuastro")
-    (version "0.6")
+    (version "0.7")
    (source
     (origin
       (method url-fetch)
@@ -111,7 +110,7 @@ header.")
                           version ".tar.gz"))
       (sha256
        (base32
-         "16a212j9ghdirm11d25s5q5qw32bkjrxsh3rblfyyv29djch34w6"))))
+         "1h4hpj5dd1nz8hx0dkf43as0hl1grcaijg0k3zcd5djg7wgna46y"))))
    (inputs
     `(("cfitsio" ,cfitsio)
       ("gsl" ,gsl)
@@ -129,16 +128,15 @@ programs for the manipulation and analysis of astronomical data.")
 (define-public stellarium
  (package
    (name "stellarium")
-    (version "0.18.0")
+    (version "0.18.1")
    (source (origin
             (method url-fetch)
             (uri (string-append "https://github.com/Stellarium/" name
                                 "/releases/download/v" version
                                 "/" name "-" version ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
             (sha256
              (base32
-               "06lid4b9x6551swjxsbiqrd2pxh77fhzfxznhh1vwlvvqgxrimjs"))))
+               "0vjkwrjy22b4wdjkafm63pmb0fck14ffnylpq8xr91ywycw4blrq"))))
    (build-system cmake-build-system)
    (inputs
     `(("qtbase" ,qtbase)
@@ -166,7 +164,7 @@ programs for the manipulation and analysis of astronomical data.")
                      (setenv "QT_QPA_PLATFORM" "offscreen")
                      (setenv "HOME" "/tmp")
                      #t)))))
-    (home-page "http://stellarium.org/")
+    (home-page "https://stellarium.org/")
    (synopsis "3D sky viewer")
    (description "Stellarium is a planetarium.  It shows a realistic sky in
 3D, just like what you see with the naked eye, binoculars, or a telescope.  It
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -32,24 +32,14 @@
 (define-public augeas
  (package
    (name "augeas")
-    (version "1.10.1")
+    (version "1.11.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://download.augeas.net/augeas-"
                                  version ".tar.gz"))
              (sha256
               (base32
-                "0k9nssn7lk58cl5zv3c8kv2zx9cm2yks3sj7q4fd6qdjz9m2bnsj"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; The gnulib test-lock test is prone to writer starvation
-                  ;; with our glibc@2.25, which prefers readers, so disable it.
-                  ;; The gnulib commit b20e8afb0b2 should fix this once
-                  ;; incorporated here.
-                  (substitute* "gnulib/tests/Makefile.in"
-                    (("test-lock\\$\\(EXEEXT\\) ") ""))
-                  #t))))
+                "1c507qj6dfn2dnsl27w94zs9r45xrgm07y8bqba9ry2s0psfhg1r"))))
    (build-system gnu-build-system)
    ;; Marked as "required" in augeas.pc
    (propagated-inputs
@@ -0,0 +1,79 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;;
+;;; 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 authentication)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages))
+
+(define-public oath-toolkit
+  ;; If gcc@7 breaks this package before its next release, try patching it:
+  ;; <https://gitlab.com/oath-toolkit/oath-toolkit/issues/2#note_52958748>.
+  (package
+    (name "oath-toolkit")
+    (version "2.6.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://download.savannah.nongnu.org/releases/"
+                           name "/" name "-" version ".tar.gz"))
+       (patches (search-patches "oath-toolkit-glibc-compat.patch"))
+       (sha256
+        (base32 "182ah8vfbg0yhv6mh1b6ap944d0na6x7lpfkwkmzb6jl9gx4cd5h"))))
+    (build-system gnu-build-system)
+    (arguments
+     ;; TODO ‘--enable-pskc’ causes xmlsec-related test suite failures.
+     `(#:configure-flags
+       (list "--enable-pam")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'delete-static-libraries
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (lib (string-append out "/lib")))
+               (for-each delete-file (find-files lib "\\.a$"))
+               #t))))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("linux-pam" ,linux-pam)))       ; for --enable-pam
+    (home-page "https://www.nongnu.org/oath-toolkit/")
+    (synopsis "One-time password (OTP) components")
+    ;; TODO Add the following items after they've been enabled.
+    ;; @item @command{pskctool}, a command-line tool for manipulating secret key
+    ;; files in the Portable Symmetric Key Container (@dfn{PSKC}) format
+    ;; described in RFC6030.
+    ;; @item @code{libpskc}, a shared and static C library for PSKC handling.
+    (description
+     "The @dfn{OATH} (Open AuTHentication) Toolkit provides various components
+for building one-time password (@dfn{OTP}) authentication systems:
+
+@itemize
+@item @command{oathtool}, a command-line tool for generating & validating OTPs.
+@item @code{liboath}, a C library for OATH handling.
+@item @code{pam_oath}, a PAM module for pluggable login authentication.
+@end itemize
+
+Supported technologies include the event-based @dfn{HOTP} algorithm (RFC4226)
+and the time-based @dfn{TOTP} algorithm (RFC6238).")
+    (license (list license:lgpl2.1+     ; the libraries (liboath/ & libpskc/)
+                   license:gpl3+))))    ; the tools (everything else)
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -31,7 +32,7 @@
 (define-public autogen
  (package
    (name "autogen")
-    (version "5.18.12")
+    (version "5.18.14")
    (source
     (origin
      (method url-fetch)
@@ -39,12 +40,12 @@
                          "/autogen-" version ".tar.xz"))
      (sha256
       (base32
-        "1n5zq4872sakvz9c7ncsdcfp0z8rsybsxvbmhkpbd19ii0pacfxy"))))
+        "1r06gam7sicb9ssn02mhv6r0g5vr4k0l0c67shpqa5i172cspizz"))))
    (build-system gnu-build-system)
-    (native-inputs `(("perl" ,perl)     ;for doc generator mdoc
-                     ("pkg-config" ,pkg-config)))
-    (inputs `(("which" ,which)
-              ("guile" ,guile-2.0)))
+    (native-inputs `(("pkg-config" ,pkg-config)
+                     ("which" ,which)))
+    (inputs `(("guile" ,guile-2.0)
+              ("perl" ,perl)))          ; for doc generator mdoc
    (arguments
     '(#:phases
       (modify-phases %standard-phases
@@ -54,8 +55,7 @@
               (substitute*
                 (append (find-files "agen5/test" "\\.test$")
                         (find-files "autoopts/test" "\\.(test|in)$"))
-                 (("/bin/sh") sh)
-                 (("/usr/bin/tr") "tr"))
+                 (("/bin/sh") sh))
               #t))))))
    (home-page "https://www.gnu.org/software/autogen/")
    (synopsis "Automated program generator")
@@ -11,6 +11,7 @@
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,6 +31,7 @@
 (define-module (gnu packages backup)
  #:use-module (guix packages)
  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix git-download)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system gnu)
@@ -67,7 +69,7 @@
 (define-public duplicity
  (package
    (name "duplicity")
-    (version "0.7.17")
+    (version "0.7.18.1")
    (source
     (origin
      (method url-fetch)
@@ -77,10 +79,10 @@
                          version ".tar.gz"))
      (sha256
       (base32
-        "0jmh3h09680xyf33hzxxxl74bwz66zqhzvjlj7j89r9rz3qwa91p"))))
+        "17c0203y5qz9w8iyhs26l44qf6a1vp26b5ykz1ypdr2kv6g02df9"))))
    (build-system python-build-system)
    (native-inputs
-     `(("util-linux" ,util-linux)     ;setsid command, for the tests
+     `(("util-linux" ,util-linux)       ; setsid command, for the tests
       ("par2cmdline" ,par2cmdline)
       ("python-pexpect" ,python2-pexpect)
       ("python-fasteners" ,python2-fasteners)
@@ -91,28 +93,28 @@
    (inputs
     `(("librsync" ,librsync)
       ("lftp" ,lftp)
-       ("gnupg" ,gnupg)                 ;gpg executable needed
-       ("util-linux" ,util-linux)       ;for setsid
+       ("gnupg" ,gnupg)                 ; gpg executable needed
+       ("util-linux" ,util-linux)       ; for setsid
       ("tzdata" ,tzdata)))
    (arguments
-     `(#:python ,python-2               ;setup assumes Python 2
+     `(#:python ,python-2               ; setup assumes Python 2
       #:test-target "test"
       #:phases
       (modify-phases %standard-phases
-         (add-before 'build 'patch-source
+         (add-before 'build 'use-store-file-names
           (lambda* (#:key inputs #:allow-other-keys)
-             ;; embed gpg store name
             (substitute* "duplicity/gpginterface.py"
               (("self.call = 'gpg'")
                (string-append "self.call = '" (assoc-ref inputs "gnupg") "/bin/gpg'")))
+
             (substitute* '("testing/functional/__init__.py"
                            "testing/overrides/bin/lftp")
               (("/bin/sh") (which "sh")))
             #t))
         (add-before 'check 'check-setup
           (lambda* (#:key inputs #:allow-other-keys)
-             (setenv "HOME" (getcwd)) ;gpg needs to write to $HOME
-             (setenv "TZDIR"          ;some timestamp checks need TZDIR
+             (setenv "HOME" (getcwd))   ; gpg needs to write to $HOME
+             (setenv "TZDIR"            ; some timestamp checks need TZDIR
                     (string-append (assoc-ref inputs "tzdata")
                                    "/share/zoneinfo"))
             #t)))))
@@ -132,22 +134,18 @@ spying and/or modification by the server.")
    (name "par2cmdline")
    (version "0.8.0")
    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/Parchive/par2cmdline/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Parchive/par2cmdline.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1jpshmmcr81mxly0md2rr231qz9c8c680bbvcmhh100dg9i4a6s6"))))
+                "0f1jsd5sw2wynjzi7yjqjaf13yhyjfdid91p8yh0jn32y03kjyrz"))))
    (native-inputs
     `(("automake" ,automake)
       ("autoconf" ,autoconf)))
    (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
-           (lambda _ (invoke "autoreconf" "-vfi"))))))
    (synopsis "File verification and repair tools")
    (description "Par2cmdline uses Reed-Solomon error-correcting codes to
 generate and verify PAR2 recovery files.  These files can be distributed
@@ -445,9 +443,27 @@ rsnapshot uses hard links to deduplicate identical files.")
                "0fpdyxww41ba52d98blvnf543xvirq1v9xz1i3x1gm9lzlzpmc2g"))
              (patches (search-patches "diffutils-gets-undeclared.patch"))))
    (build-system gnu-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-before 'configure 'adjust-configure-script
+                    (lambda _
+                      ;; Mimic upstream commit
+                      ;; 25750ab5ef82fd3cfce5205d5f1ef07b47098091.
+                      (substitute* "configure"
+                        (("GUILE=(.*)--variable bindir`" _ middle)
+                         (string-append "GUILE=" middle
+                                        "--variable bindir`/guile")))
+                      #t))
+                  (add-before 'check 'skip-test
+                    (lambda _
+                      ;; XXX: This test fails (1) because current GnuTLS no
+                      ;; longer supports OpenPGP authentication, and (2) for
+                      ;; some obscure reason.  Better skip it.
+                      (setenv "XFAIL_TESTS" "utils/block-server")
+                      #t)))))
    (native-inputs
     `(("guile" ,guile-2.0)
-       ("gperf" ,gperf)
+       ("gperf" ,gperf-3.0)                  ;see <https://bugs.gnu.org/32382>
       ("pkg-config" ,pkg-config)))
    (inputs
     `(("guile" ,guile-2.0)
@@ -475,18 +491,33 @@ detection, and lossless compression.")
 (define-public borg
  (package
    (name "borg")
-    (version "1.1.6")
+    (version "1.1.7")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "borgbackup" version))
+       (patches (search-patches "borg-respect-storage-quota.patch"))
       (sha256
-        (base32 "0c09j46fi8i7klas0bh82a4whlwnajshk0izkgax6fjxr1sf9lm1"))
+        (base32
+         "1p3zia62vyg9vadkdjzzkzbj4dmgijr7ix5lmhfbxpwy5q9imdgp"))
       (modules '((guix build utils)))
       (snippet
        '(begin
+           ;; Delete files generated by Cython.  We used to have a regex
+           ;; that created the list of generated files but Borg has
+           ;; added new non-generated C files that cause the regex to
+           ;; generate the wrong list.
           (for-each delete-file
-                     (find-files "borg" "^(c|h|p).*\\.c$"))
+                     '("src/borg/algorithms/checksums.c"
+                       "src/borg/chunker.c"
+                       "src/borg/compress.c"
+                       "src/borg/crypto/low_level.c"
+                       "src/borg/hashindex.c"
+                       "src/borg/item.c"
+                       "src/borg/platform/darwin.c"
+                       "src/borg/platform/freebsd.c"
+                       "src/borg/platform/linux.c"
+                       "src/borg/platform/posix.c"))
           ;; Remove bundled shared libraries.
           (with-directory-excursion "src/borg/algorithms"
             (for-each delete-file-recursively
@@ -708,12 +739,15 @@ NTFS volumes using @code{ntfs-3g}, preserving NTFS-specific attributes.")
       ("python2-pep8" ,python2-pep8)
       ("python2-pylint" ,python2-pylint)))
    (home-page "https://obnam.org/")
-    (synopsis "Easy and secure backup program")
-    (description "Obnam is an easy, secure backup program.  Features
-include snapshot backups, data de-duplication and encrypted backups
-using GnuPG.  Backups can be stored on local hard disks, or online via
-the SSH SFTP protocol.  The backup server, if used, does not require
-any special software, on top of SSH.")
+    (synopsis "Retired backup program")
+    (description
+     "Warning: @uref{https://blog.liw.fi/posts/2017/08/13/retiring_obnam/,
+the Obnam project is retired}.  You should use another backup solution instead.
+
+Obnam was an easy, secure backup program.  Features included snapshot backups,
+data de-duplication and encrypted backups using GnuPG.  Backups can be stored on
+local hard disks, or online via the SSH SFTP protocol.  The backup server, if
+used, does not require any special software, on top of SSH.")
    (license license:gpl3+)))

 (define-public dirvish
@@ -826,7 +860,7 @@ is like a time machine for your data. ")
 (define-public restic
  (package
    (name "restic")
-    (version "0.9.1")
+    (version "0.9.3")
    ;; TODO Try packaging the bundled / vendored dependencies in the 'vendor/'
    ;; directory.
    (source (origin
@@ -837,7 +871,7 @@ is like a time machine for your data. ")
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
-                "15f0rsm2lxk4lmn4773q28g49p68pqyyx0ccp7r556asan73p79m"))))
+                "1l1ddnf61pfsrry97qwhhdzywin2mgnbrkhcc9pabsdfk602anmr"))))
    (build-system go-build-system)
    (arguments
     `(#:import-path "github.com/restic/restic"
@@ -851,8 +885,20 @@ is like a time machine for your data. ")
             (with-directory-excursion (string-append
                                        "src/github.com/restic/restic-"
                                        ,version)
+               ;; Disable 'restic self-update'.  It makes little sense in Guix.
+               (substitute* "build.go" (("selfupdate") ""))
+               (setenv "HOME" (getcwd)) ; for $HOME/.cache/go-build
               (invoke "go" "run" "build.go"))))

+         (replace 'check
+           (lambda _
+             (with-directory-excursion (string-append
+                                        "src/github.com/restic/restic-"
+                                        ,version)
+               ;; Disable FUSE tests.
+               (setenv "RESTIC_TEST_FUSE" "0")
+               (invoke "go" "run" "build.go" "--test"))))
+
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out"))
@@ -10,7 +10,7 @@
 ;;; Copyright © 2016, 2018 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2017 Rene Saavedra <rennes@openmailbox.org>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
-;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
@@ -102,6 +102,15 @@ command-line arguments, multiple languages, and so on.")
   (arguments
    `(#:phases
      (modify-phases %standard-phases
+        (add-before 'check 'disable-failing-tests
+          (lambda _
+            ;; These tests are expected to fail due to a glibc bug which has
+            ;; been fixed in 2.28, so they are unexpectedly passing.  They
+            ;; should be fixed for grep versions > 3.1.
+            (substitute* "tests/Makefile.in"
+              (("^[[:blank:]]+backref-alt[[:blank:]]+\\\\") "\\")
+              (("^[[:blank:]]+triple-backref[[:blank:]]+\\\\") "\\"))
+            #t))
        (add-after 'install 'fix-egrep-and-fgrep
          ;; Patch 'egrep' and 'fgrep' to execute 'grep' via its
          ;; absolute file name instead of searching for it in $PATH.
@@ -289,7 +298,9 @@ interactive means to merge two files.")
             (base32
              "178nn4dl7wbcw499czikirnkniwnx36argdnqgz4ik9i6zvwkm6y"))
            (patches (search-patches
+                      "findutils-gnulib-libio.patch"
                      "findutils-localstatedir.patch"
+                      "findutils-makedev.patch"
                      "findutils-test-xargs.patch"))
            (modules '((guix build utils)))
            (snippet
@@ -326,14 +337,14 @@ used to apply commands with arbitrarily long arguments.")
 (define-public coreutils
  (package
   (name "coreutils")
-   (version "8.29")
+   (version "8.30")
   (source (origin
            (method url-fetch)
            (uri (string-append "mirror://gnu/coreutils/coreutils-"
                                version ".tar.xz"))
            (sha256
             (base32
-              "0plm1zs9il6bb5mk881qvbghq4glc8ybbgakk2lfzb0w64fgml4j"))))
+              "0mxhw43d4wpqmvg0l4znk1vm10fy92biyh90lzdnqjcic2lb6cg8"))))
   (build-system gnu-build-system)
   (inputs `(("acl"  ,acl)                        ; TODO: add SELinux
             ("gmp"  ,gmp)                        ;bignums in 'expr', yay!
@@ -364,7 +375,17 @@ used to apply commands with arbitrarily long arguments.")
                     (substitute* (find-files "gnulib-tests" "\\.c$")
                       (("/bin/sh") (which "sh")))
                     (substitute* (find-files "tests" "\\.sh$")
-                       (("#!/bin/sh") (which "sh")))
+                       (("#!/bin/sh") (string-append "#!" (which "sh"))))
+                     #t))
+                 (add-before 'check 'disable-broken-test
+                   (lambda _
+                     ;; This test hits the 127 character shebang limit in the build
+                     ;; environment due to the way "env -S" splits arguments into
+                     ;; shebangs.  Note that "env-S-script.sh" works around this
+                     ;; specific issue, but "env-S.pl" is not adjusted for build
+                     ;; environments with long prefixes (/tmp/guix-build-...).
+                     (substitute* "Makefile"
+                       (("^.*tests/misc/env-S.pl.*$") ""))
                     #t)))

      ;; Work around a cross-compilation bug whereby libcoreutils.a would
@@ -435,14 +456,14 @@ change.  GNU make offers many powerful extensions over the standard utility.")
 (define-public binutils
  (package
   (name "binutils")
-   (version "2.30")
+   (version "2.31.1")
   (source (origin
            (method url-fetch)
            (uri (string-append "mirror://gnu/binutils/binutils-"
                                version ".tar.bz2"))
            (sha256
             (base32
-              "028cklfqaab24glva1ks2aqa1zxa6w6xmc8q34zs1sb7h22dxspg"))
+              "1l34hn1zkmhr1wcrgf0d4z7r3najxnw3cx2y2fk7v55zjlk3ik7z"))
            (patches (search-patches "binutils-loongson-workaround.patch"))))
   (build-system gnu-build-system)

@@ -480,17 +501,6 @@ included.")
   (license gpl3+)
   (home-page "https://www.gnu.org/software/binutils/")))

-(define-public binutils/fixed
-  ;; TODO: Incorporate this in binutils during the next rebuild cycle.
-  (hidden-package
-   (package
-     (inherit binutils)
-     (source (origin
-               (inherit (package-source binutils))
-               (patches (append (origin-patches (package-source binutils))
-                                (search-patches
-                                 "binutils-aarch64-symbol-relocation.patch"))))))))
-
 (define* (make-ld-wrapper name #:key
                          (target (const #f))
                          binutils
@@ -567,18 +577,20 @@ store.")

 (export make-ld-wrapper)

-(define-public glibc/linux
+(define-public glibc
+  ;; This is the GNU C Library, used on GNU/Linux and GNU/Hurd.  Prior to
+  ;; version 2.28, GNU/Hurd used a different glibc branch.
  (package
   (name "glibc")
   ;; Note: Always use a dot after the minor version since various places rely
   ;; on "version-major+minor" to determine where locales are found.
-   (version "2.27")
+   (version "2.28")
   (source (origin
            (method url-fetch)
            (uri (string-append "mirror://gnu/glibc/glibc-" version ".tar.xz"))
            (sha256
             (base32
-              "0wpwq7gsm7sd6ysidv0z575ckqdg13cr2njyfgrbgh4f65adwwji"))
+              "10iha5ynvdj5m62vgpgqbq4cwvc2yhyl2w9yyyjgfxmdmx8h145i"))
            (snippet
             ;; Disable 'ldconfig' and /etc/ld.so.cache.  The latter is
             ;; required on LFS distros to avoid loading the distro's libc.so
@@ -590,7 +602,7 @@ store.")
                #t))
            (modules '((guix build utils)))
            (patches (search-patches "glibc-ldd-x86_64.patch"
-                                     "glibc-2.27-git-fixes.patch"
+                                     "glibc-2.28-git-fixes.patch"
                                     "glibc-hidden-visibility-ldconfig.patch"
                                     "glibc-versioned-locpath.patch"
                                     "glibc-allow-kernel-2.6.32.patch"
@@ -598,8 +610,13 @@ store.")
   (build-system gnu-build-system)

   ;; Glibc's <limits.h> refers to <linux/limit.h>, for instance, so glibc
-   ;; users should automatically pull Linux headers as well.
-   (propagated-inputs `(("kernel-headers" ,linux-libre-headers)))
+   ;; users should automatically pull Linux headers as well.  On GNU/Hurd,
+   ;; libc provides <hurd.h>, which includes a bunch of Hurd and Mach headers,
+   ;; so both should be propagated.
+   (propagated-inputs
+    (if (hurd-target?)
+        `(("hurd-core-headers" ,hurd-core-headers))
+        `(("kernel-headers" ,linux-libre-headers))))

   (outputs '("out" "debug"
              "static"))                          ;9 MiB of .a files
@@ -654,7 +671,13 @@ store.")
            ;; Use our Bash instead of /bin/sh.
            (string-append "BASH_SHELL="
                           (assoc-ref %build-inputs "bash")
-                           "/bin/bash"))
+                           "/bin/bash")
+
+            ;; On GNU/Hurd we get discarded-qualifiers warnings for
+            ;; 'device_write_inband' among other things.  Ignore them.
+            ,@(if (hurd-target?)
+                  '("--disable-werror")
+                  '()))

      #:tests? #f                                 ; XXX
      #:phases (modify-phases %standard-phases
@@ -759,7 +782,18 @@ store.")
                                 (filter linker-script?
                                         (map (cut string-append slib "/" <>)
                                              files)))
-                       #t))))))
+                       #t)))
+
+                 ,@(if (hurd-target?)
+                       '((add-after 'install 'augment-libc.so
+                           (lambda* (#:key outputs #:allow-other-keys)
+                             (let* ((out (assoc-ref outputs "out")))
+                               (substitute* (string-append out "/lib/libc.so")
+                                 (("/[^ ]+/lib/libc.so.0.3")
+                                  (string-append out "/lib/libc.so.0.3"
+                                                 " libmachuser.so libhurduser.so"))))
+                             #t)))
+                       '()))))

   (inputs `(("static-bash" ,static-bash)))

@@ -768,7 +802,12 @@ store.")
   (native-inputs `(("texinfo" ,texinfo)
                    ("perl" ,perl)
                    ("bison" ,bison)
-                    ("gettext" ,gettext-minimal)))
+                    ("gettext" ,gettext-minimal)
+
+                    ,@(if (hurd-target?)
+                          `(("mig" ,mig)
+                            ("perl" ,perl))
+                          '())))

   (native-search-paths
    ;; Search path for packages that provide locale data.  This is useful
@@ -790,92 +829,26 @@ with the Linux kernel.")
   (license lgpl2.0+)
   (home-page "https://www.gnu.org/software/libc/")))

-(define-public glibc/hurd
-  ;; The Hurd's libc variant.
-  (package (inherit glibc/linux)
-    (name "glibc-hurd")
-    (version "2.23")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "http://alpha.gnu.org/gnu/hurd/glibc-"
-                                  version "-hurd+libpthread-20161218" ".tar.gz"))
-              (sha256
-               (base32
-                "0vpdv05j6j3ria5bw8gp468i64gij94cslxkxj9xkfgi6p615b8p"))))
-
-    ;; Libc provides <hurd.h>, which includes a bunch of Hurd and Mach headers,
-    ;; so both should be propagated.
-    (propagated-inputs `(("hurd-core-headers" ,hurd-core-headers)))
-    (native-inputs
-     `(,@(package-native-inputs glibc/linux)
-       ("mig" ,mig)
-       ("perl" ,perl)))
-
-    (arguments
-     (substitute-keyword-arguments (package-arguments glibc/linux)
-       ((#:phases original-phases)
-        ;; Add libmachuser.so and libhurduser.so to libc.so's search path.
-        ;; See <http://lists.gnu.org/archive/html/bug-hurd/2015-07/msg00051.html>.
-        `(modify-phases ,original-phases
-           (add-after 'install 'augment-libc.so
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let* ((out (assoc-ref outputs "out")))
-                 (substitute* (string-append out "/lib/libc.so")
-                   (("/[^ ]+/lib/libc.so.0.3")
-                    (string-append out "/lib/libc.so.0.3" " libmachuser.so" " libhurduser.so"))))
-               #t))
-           (add-after 'pre-configure 'pre-configure-set-pwd
-             (lambda _
-               ;; Use the right 'pwd'.
-               (substitute* "configure"
-                 (("/bin/pwd") "pwd"))
-               #t))
-           (replace 'build
-             (lambda _
-               ;; Force mach/hurd/libpthread subdirs to build first in order to avoid
-               ;; linking errors.
-               ;; See <https://lists.gnu.org/archive/html/bug-hurd/2016-11/msg00045.html>
-               (let ((flags (list "-j" (number->string (parallel-job-count)))))
-                 (define (make target)
-                   (apply invoke "make" target flags))
-                 (make "mach/subdir_lib")
-                 (make "hurd/subdir_lib")
-                 (make "libpthread/subdir_lib")
-                 (apply invoke "make" flags))))))
-        ((#:configure-flags original-configure-flags)
-        `(append (list "--host=i586-pc-gnu"
-
-                       ;; We need this to get a working openpty() function.
-                       "--enable-pt_chown"
-
-                       ;; <https://lists.gnu.org/archive/html/bug-hurd/2016-10/msg00033.html>
-                       "--disable-werror"
-
-                       ;; nscd fails to build for GNU/Hurd:
-                       ;; <https://lists.gnu.org/archive/html/bug-hurd/2014-07/msg00006.html>.
-                       ;; Disable it.
-                       "--disable-nscd")
-                 (filter (lambda (flag)
-                           (not (string-prefix? "--enable-kernel=" flag)))
-                         ,original-configure-flags)))))
-    (synopsis "The GNU C Library (GNU Hurd variant)")
-    (supported-systems %hurd-systems)))
-
-(define* (glibc-for-target #:optional
-                           (target (or (%current-target-system)
-                                       (%current-system))))
-  "Return the glibc for TARGET, GLIBC/LINUX for a Linux host or
-GLIBC/HURD for a Hurd host"
-  (match target
-    ((or "i586-pc-gnu" "i586-gnu") glibc/hurd)
-    (_ glibc/linux)))
-
-(define-syntax glibc
-  (identifier-syntax (glibc-for-target)))
-
 ;; Below are old libc versions, which we use mostly to build locale data in
 ;; the old format (which the new libc cannot cope with.)

+(define-public glibc-2.27
+  (package
+    (inherit glibc)
+    (version "2.27")
+    (source (origin
+              (inherit (package-source glibc))
+              (uri (string-append "mirror://gnu/glibc/glibc-" version ".tar.xz"))
+              (sha256
+               (base32
+                "0wpwq7gsm7sd6ysidv0z575ckqdg13cr2njyfgrbgh4f65adwwji"))
+              (patches (search-patches "glibc-ldd-x86_64.patch"
+                                       "glibc-2.27-git-fixes.patch"
+                                       "glibc-hidden-visibility-ldconfig.patch"
+                                       "glibc-versioned-locpath.patch"
+                                       "glibc-allow-kernel-2.6.32.patch"
+                                       "glibc-reinstate-prlimit64-fallback.patch"))))))
+
 (define-public glibc-2.26
  (package
    (inherit glibc)
@@ -1094,18 +1067,17 @@ command.")
    (license gpl3+))) ; some files are under GPLv2+

 (define-public glibc/hurd-headers
-  (package (inherit glibc/hurd)
+  (package (inherit glibc)
    (name "glibc-hurd-headers")
    (outputs '("out"))
    (propagated-inputs `(("gnumach-headers" ,gnumach-headers)
                         ("hurd-headers" ,hurd-headers)))
    (arguments
-     (substitute-keyword-arguments (package-arguments glibc/hurd)
+     (substitute-keyword-arguments (package-arguments glibc)
       ;; We just pass the flags really needed to build the headers.
       ((#:configure-flags _)
        `(list "--enable-add-ons"
-               "--host=i586-pc-gnu"
-               "--enable-obsolete-rpc"))
+               "--host=i586-pc-gnu"))
       ((#:phases _)
        '(modify-phases %standard-phases
           (replace 'install
@@ -1120,18 +1092,12 @@ command.")
                  (open-output-file
                   (string-append out "/include/gnu/stubs.h"))))
               #t))
-           (delete 'build)              ; nothing to build
-           (add-before 'configure 'patch-configure-script
-             (lambda _
-               ;; Use the right 'pwd'.
-               (substitute* "configure"
-                 (("/bin/pwd") "pwd"))
-               #t))))))))
+           (delete 'build)))))))                  ; nothing to build

 (define-public tzdata
  (package
    (name "tzdata")
-    (version "2018d")
+    (version "2018e")
    (source (origin
             (method url-fetch)
             (uri (string-append
@@ -1139,7 +1105,7 @@ command.")
                   version ".tar.gz"))
             (sha256
              (base32
-               "0m6020dnk9r40z7k36jp13fa06xip3hn0fdx3nly66jzxgffs1ji"))))
+               "0bk97fv2i5ns42prpmlaadsswdjwv0ifi7whj2s4q6l44rcqwa3b"))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f
@@ -1189,7 +1155,7 @@ command.")
                                version ".tar.gz"))
                          (sha256
                           (base32
-                            "1nd882yhsazmcfqmcqyfig3axycryl30gmizgqhqsx5dpa2lxr3x"))))))
+                            "1kpb02631s58i068mwq63xlamcv1ffj4p6y4wpb9kdl01vr0qd6a"))))))
    (home-page "https://www.iana.org/time-zones")
    (synopsis "Database of current and historical time zones")
    (description "The Time Zone Database (often called tz or zoneinfo)
@@ -1205,7 +1171,25 @@ and daylight-saving rules.")
 ;;; will typically be obsolete and should never be referred to by a built
 ;;; package.
 (define-public tzdata-for-tests
-  (hidden-package tzdata))
+  (hidden-package
+   (package
+     (inherit tzdata)
+     (version "2018d")
+     (source (origin
+               (method url-fetch)
+               (uri (string-append "https://www.iana.org/time-zones/repository"
+                                   "/releases/tzdata" version ".tar.gz"))
+               (sha256
+                (base32
+                 "0m6020dnk9r40z7k36jp13fa06xip3hn0fdx3nly66jzxgffs1ji"))))
+     (inputs `(("tzcode" ,(origin
+                            (method url-fetch)
+                            (uri (string-append
+                                  "http://www.iana.org/time-zones/repository/releases/tzcode"
+                                  version ".tar.gz"))
+                            (sha256
+                             (base32
+                              "1nd882yhsazmcfqmcqyfig3axycryl30gmizgqhqsx5dpa2lxr3x")))))))))

 (define-public libiconv
  (package
@@ -2,7 +2,7 @@
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2017 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -36,7 +36,7 @@
  #:use-module (guix store)
  #:use-module (guix build-system gnu)
  #:autoload   (guix gnupg) (gnupg-verify*)
-  #:autoload   (guix hash) (port-sha256)
+  #:autoload   (gcrypt hash) (port-sha256)
  #:autoload   (guix base32) (bytevector->nix-base32-string)
  #:use-module (srfi srfi-1)
  #:use-module (srfi srfi-26)
@@ -79,7 +79,11 @@
   (16 "1cgi1y6mifm8hsgv4avj5ih76535js3qba1sqwbfvp7si76927sh")
   (17 "0w6jpj2giakji1ir83rpkx1y7n7xqppah3j748m6dm38hywr0gvp")
   (18 "1k58h4wxbsg7r4rwhrvzx5hfbapba2nxjysbhh6qp6ki5ys99i2v")
-   (19 "07n1i5610lbs672x1s8g82qn3qfj06s0ip3z80sri0g8vxp0s5r7")))
+   (19 "07n1i5610lbs672x1s8g82qn3qfj06s0ip3z80sri0g8vxp0s5r7")
+   (20 "0b2jk5n1af1vh590qfc52hv65mafb4vl1xv26s8j5a3byb5y4h0q")
+   (21 "1hblcd2xmqqlp0idnavw66570n7m0yv5rbbr873c2gkn982mk3xx")
+   (22 "0yfbjzr79vzjs2hyi5m8iy2b38fq7vikdfa4zqdvjsp36q4iycs5")
+   (23 "1dlism6qdx60nvzj0v7ndr7lfahl4a8zmzckp13hqgdx7xpj7v2g")))

 (define (download-patches store count)
  "Download COUNT Bash patches into store.  Return a list of
@@ -0,0 +1,258 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Danny Milosavljevic <dannym@scratchpost.org>
+;;;
+;;; 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 batik)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix utils)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix packages)
+  #:use-module (guix build-system ant)
+  #:use-module (guix build utils)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages java)
+  #:use-module (gnu packages textutils)
+  #:use-module (gnu packages xml))
+
+(define-public java-w3c-smil-3.0
+  (package
+    (name "java-w3c-smil")
+    (version "3.0")
+    (source #f)
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "w3c-smil.jar"
+       #:source-dir "."
+       #:tests? #f ; No tests exist.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'unpack
+           (lambda* (#:key source #:allow-other-keys)
+             ;; https://www.w3.org/TR/SMIL3/smil-timing.html#q142
+             (mkdir-p "org/w3c/dom/smil")
+             (call-with-output-file "org/w3c/dom/smil/ElementTimeControl.java"
+               (lambda (port)
+                 (format port "
+package org.w3c.dom.smil;
+
+import org.w3c.dom.DOMException;
+
+public interface ElementTimeControl {
+    public boolean  beginElement();
+
+    public boolean  beginElementAt(float offset);
+
+    public boolean endElement();
+
+    public boolean endElementAt(float offset);
+}
+")))
+             (call-with-output-file "org/w3c/dom/smil/TimeEvent.java"
+               (lambda (port)
+                 (format port "
+package org.w3c.dom.smil;
+
+import org.w3c.dom.events.Event;
+import org.w3c.dom.views.AbstractView;
+
+public interface TimeEvent extends Event {
+    public AbstractView getView();
+
+    public int getDetail();
+
+    public void initTimeEvent(String typeArg,
+                              AbstractView viewArg,
+                              int detailArg);
+
+}
+")))
+             #t)))))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "https://www.w3.org/Style/CSS/SAC/")
+    (synopsis "W3C SAC interface for CSS parsers in Java")
+    (description "This package provides a SAC interface by the W3C.
+SAC is an interface for CSS parsers.")
+    (license license:w3c)))
+
+(define-public java-w3c-svg-1.0
+  (package
+    (name "java-w3c-svg")
+    (version "20010904")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "http://www.w3.org/TR/2001/REC-SVG-" version
+                            "/java-binding.zip"))
+        (sha256
+         (base32
+          "0gnxvx51bg6ijplf6l2q0i1m07101f7fickawshfygnsdjqfdnbp"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "w3c-svg.jar"
+       #:source-dir "."
+       #:tests? #f ; No tests exist.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'unpack
+           (lambda* (#:key source #:allow-other-keys)
+             (invoke "unzip" source)))
+         (add-after 'unpack 'patch-interface
+           (lambda _
+             ;; Make it compatible with batik.
+             ;; This is equivalent to usingxml commons externals'
+             ;; "externals" part from https://xerces.apache.org/mirrors.cgi
+             (substitute* "SVGFEConvolveMatrixElement.java"
+              (("public SVGAnimatedLength[ ]*getKernelUnitLength")
+               "public SVGAnimatedNumber getKernelUnitLength"))
+             (substitute* "SVGFEMorphologyElement.java"
+              (("public SVGAnimatedLength[ ]*getRadius")
+               "public SVGAnimatedNumber getRadius"))
+             (call-with-output-file "EventListenerInitializer.java"
+               (lambda (port)
+                 (format port "
+// License: http://www.apache.org/licenses/LICENSE-2.0
+package org.w3c.dom.svg;
+public interface EventListenerInitializer {
+    public void initializeEventListeners(SVGDocument doc);
+}
+
+")))
+             #t)))))
+    (propagated-inputs
+     `(("java-w3c-smil" ,java-w3c-smil-3.0)))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "https://www.w3.org/Style/CSS/SAC/")
+    (synopsis "W3C SVG 1.0 interface")
+    (description "This package provides a SVG 1.0 interface.")
+    (license license:w3c)))
+
+(define-public java-w3c-svg
+  (package
+    (inherit java-w3c-svg-1.0)
+    (version "20110816")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "http://www.w3.org/TR/2011/REC-SVG11-" version
+                            "/java-binding.zip"))
+        (sha256
+         (base32
+          "0jicqcrxav8ggs37amgvvwgc2f0qp1c5wns4rb2i3si83s2m09ns"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments java-w3c-svg-1.0)
+       ((#:phases phases)
+       `(modify-phases ,phases
+          (delete 'patch-interface)))))
+    (propagated-inputs
+     `())
+    (synopsis "W3C SVG interface")
+    (description "This package provides a SVG interface.")))
+
+(define-public java-w3c-sac
+  (package
+    (name "java-w3c-sac")
+    (version "1.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://www.w3.org/2002/06/sacjava-" version
+                            ".zip"))
+        (sha256
+         (base32
+          "1djp2nnzf8jchnwz1ij9i5jfx4cg1ryf3lbw133yzjy0wkhcla52"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "w3c-sac.jar"
+       #:source-dir "sac-1.3"
+       #:tests? #f ; No tests exist.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'unpack
+           (lambda* (#:key source #:allow-other-keys)
+             (invoke "unzip" source))))))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "https://www.w3.org/Style/CSS/SAC/")
+    (synopsis "W3C SAC interface for CSS parsers in Java")
+    (description "This package provides a SAC interface by the W3C.
+SAC is an interface for CSS parsers.")
+    (license license:w3c)))
+
+(define-public java-xmlgraphics-commons
+  (package
+    (name "java-xmlgraphics-commons")
+    (version "2.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append
+              "mirror://apache/xmlgraphics/commons/source/xmlgraphics-commons-"
+              version "-src.tar.gz"))
+        (sha256
+         (base32
+          "0a432a4ca3vgnbada5cy9mlmfzmq6hi4i176drfxrp17q2d43w23"))
+        (modules '((guix build utils)))
+        (snippet
+         `(begin
+            (delete-file-recursively "lib")
+            #t))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:build-target "jar-main"
+       #:test-target "junit"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-reproducible
+           (lambda _
+             (substitute* "build.xml"
+              (("<attribute name=\"Build-Id\" value=\"[^\"]*\"")
+               "<attribute name=\"Build-Id\" value=\"\""))
+             #t))
+         (add-before 'build 'prepare-build-directories
+           (lambda _
+             (mkdir "lib")
+             (mkdir "lib/build")
+             #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (out-share (string-append out "/share/java")))
+               (for-each (lambda (name)
+                           (install-file name out-share))
+                         (find-files "build"
+                                     "xmlgraphics-commons.*\\.jar$"))
+               #t))))))
+    (native-inputs
+     `(("java-apache-xml-commons-resolver" ,java-apache-xml-commons-resolver)
+       ("java-asm" ,java-asm)
+       ("java-cglib" ,java-cglib)
+       ("java-hamcrest" ,java-hamcrest-core)
+       ("java-junit" ,java-junit)
+       ("java-mockito" ,java-mockito-1)
+       ("java-objenesis" ,java-objenesis)))
+    (propagated-inputs
+     `(("java-commons-io" ,java-commons-io)
+       ("java-commons-logging-minimal" ,java-commons-logging-minimal)))
+    (home-page "https://xmlgraphics.apache.org/commons/")
+    (synopsis "XMLGraphics constants")
+    (description "This package provides XMLGraphics constants (originally
+from @code{batik}).")
+    (license license:asl2.0)))
@@ -30,14 +30,14 @@
 (define-public libgc
  (package
   (name "libgc")
-   (version "7.6.4")
+   (version "7.6.6")
   (source (origin
            (method url-fetch)
-            (uri (string-append "http://www.hboehm.info/gc/gc_source/gc-"
-                                version ".tar.gz"))
+            (uri (string-append "https://github.com/ivmai/bdwgc/releases"
+                                "/download/v" version "/gc-" version ".tar.gz"))
            (sha256
             (base32
-              "076dzsqqyxd3nlzs0z277vvhqjp8nv5dqi763s0m90zr6ljiyk5r"))))
+              "1p1r015a7jbpvkkbgzv1y8nxrbbp6dg0mq3ksi6ji0qdz3wfss79"))))
   (build-system gnu-build-system)
   (arguments
    `(#:configure-flags
@@ -91,7 +91,7 @@ C or C++ programs, though that is not its primary goal.")
 (define-public libatomic-ops
  (package
    (name "libatomic-ops")
-    (version "7.6.4")
+    (version "7.6.6")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -99,7 +99,7 @@ C or C++ programs, though that is not its primary goal.")
                    version "/libatomic_ops-" version ".tar.gz"))
              (sha256
               (base32
-                "0knxncsjhbknlyy6lx7ycxhpzfk3sykhvicgxyp0rmsxd1d3v0jv"))))
+                "0x7071z707msvyrv9dmgahd1sghbkw8fpbagvcag6xs8yp2spzlr"))))
    (build-system gnu-build-system)
    (outputs '("out" "debug"))
    (synopsis "Accessing hardware atomic memory update operations")
@@ -35,14 +35,14 @@
 (define-public fio
  (package
    (name "fio")
-    (version "3.7")
+    (version "3.11")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://brick.kernel.dk/snaps/"
-                                  "fio-" version ".tar.gz"))
+                                  "fio-" version ".tar.bz2"))
              (sha256
               (base32
-                "0rw9jf2ikm19lq4jizavdvvp3vfvlm3annq7jsxl2y5nf1pi2qr7"))))
+                "0s8m0wcz5j6sa1hblj80wk3syy5b4shg7y3gabvm9xa3wj0lzasa"))))
    (build-system gnu-build-system)
    (arguments
     '(#:test-target "test"
@@ -28,7 +28,9 @@
  #:use-module (gnu packages cran)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages graph)
-  #:use-module (gnu packages statistics))
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages web))

 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
  (package
@@ -167,17 +169,46 @@ Repeats Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by
 default."  )
    (license license:artistic2.0)))

+(define-public r-genelendatabase
+  (package
+    (name "r-genelendatabase")
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       ;; We cannot use bioconductor-uri here because this tarball is
+       ;; located under "data/experiment/" instead of "bioc/".
+       (uri (string-append "https://bioconductor.org/packages/"
+                           "release/data/experiment/src/contrib"
+                           "/geneLenDataBase_" version ".tar.gz"))
+       (sha256
+        (base32
+         "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5"))))
+    (properties
+     `((upstream-name . "geneLenDataBase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rtracklayer" ,r-rtracklayer)
+       ("r-genomicfeatures" ,r-genomicfeatures)))
+    (home-page "https://bioconductor.org/packages/geneLenDataBase/")
+    (synopsis "Lengths of mRNA transcripts for a number of genomes")
+    (description
+     "This package provides the lengths of mRNA transcripts for a number of
+genomes and gene ID formats, largely based on the UCSC table browser.")
+    (license license:lgpl2.0+)))
+
+
 (define-public r-hpar
  (package
    (name "r-hpar")
-    (version "1.22.2")
+    (version "1.24.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "hpar" version))
       (sha256
        (base32
-         "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
+         "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
    (build-system r-build-system)
    (home-page "https://bioconductor.org/packages/hpar/")
    (synopsis "Human Protein Atlas in R")
@@ -188,23 +219,24 @@ the Human Protein Atlas project.")
 (define-public r-regioner
  (package
    (name "r-regioner")
-    (version "1.12.0")
+    (version "1.14.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "regioneR" version))
       (sha256
        (base32
-         "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
+         "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
    (properties `((upstream-name . "regioneR")))
    (build-system r-build-system)
    (propagated-inputs
-     `(("r-memoise" ,r-memoise)
-       ("r-genomicranges" ,r-genomicranges)
+     `(("r-biostrings" ,r-biostrings)
       ("r-bsgenome" ,r-bsgenome)
-       ("r-rtracklayer" ,r-rtracklayer)
       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
       ("r-iranges" ,r-iranges)
+       ("r-memoise" ,r-memoise)
+       ("r-rtracklayer" ,r-rtracklayer)
       ("r-s4vectors" ,r-s4vectors)))
    (home-page "https://bioconductor.org/packages/regioneR/")
    (synopsis "Association analysis of genomic regions")
@@ -216,14 +248,14 @@ region sets and other genomic features.")
 (define-public r-diffbind
  (package
    (name "r-diffbind")
-    (version "2.8.0")
+    (version "2.10.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "DiffBind" version))
       (sha256
        (base32
-         "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
+         "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
    (properties `((upstream-name . "DiffBind")))
    (build-system r-build-system)
    (inputs
@@ -261,14 +293,14 @@ occupancy (overlap) analysis and plotting functions.")
 (define-public r-ripseeker
  (package
    (name "r-ripseeker")
-    (version "1.20.0")
+    (version "1.22.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "RIPSeeker" version))
       (sha256
        (base32
-         "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
+         "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
    (properties `((upstream-name . "RIPSeeker")))
    (build-system r-build-system)
    (propagated-inputs
@@ -294,14 +326,14 @@ processing to visualization and annotation.")
 (define-public r-multtest
  (package
    (name "r-multtest")
-    (version "2.36.0")
+    (version "2.38.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "multtest" version))
       (sha256
        (base32
-         "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
+         "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-survival" ,r-survival)
@@ -329,21 +361,69 @@ cutoffs.  The procedures are directly applicable to identifying differentially
 expressed genes in DNA microarray experiments.")
    (license license:lgpl3)))

+(define-public r-graph
+  (package
+    (name "r-graph")
+    (version "1.60.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "graph" version))
+              (sha256
+               (base32
+                "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)))
+    (home-page "https://bioconductor.org/packages/graph")
+    (synopsis "Handle graph data structures in R")
+    (description
+     "This package implements some simple graph handling capabilities for R.")
+    (license license:artistic2.0)))
+
+(define-public r-codedepends
+  (package
+    (name "r-codedepends")
+    (version "0.6.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "CodeDepends" version))
+       (sha256
+        (base32
+         "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
+    (properties `((upstream-name . "CodeDepends")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-codetools" ,r-codetools)
+       ("r-graph" ,r-graph)
+       ("r-xml" ,r-xml)))
+    (home-page "http://cran.r-project.org/web/packages/CodeDepends")
+    (synopsis "Analysis of R code for reproducible research and code comprehension")
+    (description
+     "This package provides tools for analyzing R expressions or blocks of
+code and determining the dependencies between them.  It focuses on R scripts,
+but can be used on the bodies of functions.  There are many facilities
+including the ability to summarize or get a high-level view of code,
+determining dependencies between variables, code improvement suggestions.")
+    ;; Any version of the GPL
+    (license (list license:gpl2+ license:gpl3+))))
+
 (define-public r-chippeakanno
  (package
    (name "r-chippeakanno")
-    (version "3.14.0")
+    (version "3.16.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "ChIPpeakAnno" version))
       (sha256
        (base32
-         "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0"))))
+         "09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3"))))
    (properties `((upstream-name . "ChIPpeakAnno")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
       ("r-biostrings" ,r-biostrings)
       ("r-delayedarray" ,r-delayedarray)
       ("r-go-db" ,r-go-db)
@@ -359,7 +439,6 @@ expressed genes in DNA microarray experiments.")
       ("r-multtest" ,r-multtest)
       ("r-rbgl" ,r-rbgl)
       ("r-graph" ,r-graph)
-       ("r-biocinstaller" ,r-biocinstaller)
       ("r-regioner" ,r-regioner)
       ("r-dbi" ,r-dbi)
       ("r-ensembldb" ,r-ensembldb)
@@ -387,12 +466,12 @@ enrichedGO (addGeneIDs).")
 (define-public r-marray
  (package
    (name "r-marray")
-    (version "1.58.0")
+    (version "1.60.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "marray" version))
              (sha256
-               (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
+               (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-limma" ,r-limma)))
@@ -406,12 +485,12 @@ normalization and quality checking.")
 (define-public r-cghbase
  (package
   (name "r-cghbase")
-   (version "1.40.0")
+   (version "1.42.0")
   (source (origin
            (method url-fetch)
            (uri (bioconductor-uri "CGHbase" version))
            (sha256
-             (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
+             (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
   (properties `((upstream-name . "CGHbase")))
   (build-system r-build-system)
   (propagated-inputs
@@ -426,12 +505,12 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
  (package
   (name "r-cghcall")
-   (version "2.42.0")
+   (version "2.44.0")
   (source (origin
            (method url-fetch)
            (uri (bioconductor-uri "CGHcall" version))
            (sha256
-             (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
+             (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
   (properties `((upstream-name . "CGHcall")))
   (build-system r-build-system)
   (propagated-inputs
@@ -449,12 +528,12 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
  (package
    (name "r-qdnaseq")
-    (version "1.16.0")
+    (version "1.18.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "QDNAseq" version))
              (sha256
-               (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
+               (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
    (properties `((upstream-name . "QDNAseq")))
    (build-system r-build-system)
    (propagated-inputs
@@ -481,14 +560,14 @@ respectively.")
 (define-public r-bayseq
  (package
    (name "r-bayseq")
-    (version "2.14.0")
+    (version "2.16.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "baySeq" version))
       (sha256
        (base32
-         "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
+         "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
    (properties `((upstream-name . "baySeq")))
    (build-system r-build-system)
    (propagated-inputs
@@ -507,14 +586,14 @@ more complex hypotheses) via empirical Bayesian methods.")
 (define-public r-chipcomp
  (package
    (name "r-chipcomp")
-    (version "1.10.0")
+    (version "1.12.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "ChIPComp" version))
       (sha256
        (base32
-         "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
+         "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
    (properties `((upstream-name . "ChIPComp")))
    (build-system r-build-system)
    (propagated-inputs
@@ -541,14 +620,14 @@ datasets.")
 (define-public r-riboprofiling
  (package
    (name "r-riboprofiling")
-    (version "1.10.0")
+    (version "1.12.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "RiboProfiling" version))
       (sha256
        (base32
-         "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0"))))
+         "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
    (properties `((upstream-name . "RiboProfiling")))
    (build-system r-build-system)
    (propagated-inputs
@@ -580,14 +659,14 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
  (package
    (name "r-riboseqr")
-    (version "1.14.0")
+    (version "1.16.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "riboSeqR" version))
       (sha256
        (base32
-         "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn"))))
+         "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
    (properties `((upstream-name . "riboSeqR")))
    (build-system r-build-system)
    (propagated-inputs
@@ -608,14 +687,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
 (define-public r-interactionset
  (package
    (name "r-interactionset")
-    (version "1.8.0")
+    (version "1.10.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "InteractionSet" version))
       (sha256
        (base32
-         "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n"))))
+         "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
    (properties
     `((upstream-name . "InteractionSet")))
    (build-system r-build-system)
@@ -640,14 +719,14 @@ experiments.")
 (define-public r-genomicinteractions
  (package
    (name "r-genomicinteractions")
-    (version "1.14.0")
+    (version "1.16.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "GenomicInteractions" version))
       (sha256
        (base32
-         "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
+         "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
    (properties
     `((upstream-name . "GenomicInteractions")))
    (build-system r-build-system)
@@ -675,3 +754,317 @@ experiments.")
 such as ChIA-PET/Hi-C, annotating genomic features with interaction
 information and producing various plots and statistics.")
    (license license:gpl3)))
+
+(define-public r-ctc
+  (package
+    (name "r-ctc")
+    (version "1.56.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ctc" version))
+       (sha256
+        (base32
+         "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-amap" ,r-amap)))
+    (home-page "https://bioconductor.org/packages/ctc/")
+    (synopsis "Cluster and tree conversion")
+    (description
+     "This package provides tools for exporting and importing classification
+trees and clusters to other programs.")
+    (license license:gpl2)))
+
+(define-public r-goseq
+  (package
+    (name "r-goseq")
+    (version "1.34.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "goseq" version))
+       (sha256
+        (base32
+         "1401x0jn5f8hqc12r3gd1wammp1nxir3is1k5ldd03ln97x00i7a"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biasedurn" ,r-biasedurn)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-genelendatabase" ,r-genelendatabase)
+       ("r-go-db" ,r-go-db)
+       ("r-mgcv" ,r-mgcv)))
+    (home-page "https://bioconductor.org/packages/goseq/")
+    (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
+    (description
+     "This package provides tools to detect Gene Ontology and/or other user
+defined categories which are over/under represented in RNA-seq data.")
+    (license license:lgpl2.0+)))
+
+(define-public r-glimma
+  (package
+    (name "r-glimma")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Glimma" version))
+       (sha256
+        (base32
+         "0cbsi6g8k1whkh21jxfn22sj7wry2g3rshiracf5nyvrl2fnl947"))))
+    (properties `((upstream-name . "Glimma")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-edger" ,r-edger)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://github.com/Shians/Glimma")
+    (synopsis "Interactive HTML graphics")
+    (description
+     "This package generates interactive visualisations for analysis of
+RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
+HTML page.  The interactions are built on top of the popular static
+representations of analysis results in order to provide additional
+information.")
+    (license license:lgpl3)))
+
+(define-public r-rots
+  (package
+    (name "r-rots")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ROTS" version))
+       (sha256
+        (base32
+         "137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5"))))
+    (properties `((upstream-name . "ROTS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://bioconductor.org/packages/ROTS/")
+    (synopsis "Reproducibility-Optimized Test Statistic")
+    (description
+     "This package provides tools for calculating the
+@dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
+in omics data.")
+    (license license:gpl2+)))
+
+(define-public r-inspect
+  (package
+    (name "r-inspect")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "INSPEcT" version))
+       (sha256
+        (base32
+         "0b671x5v2wyq5np2flq2m1fnjz32f303yjlw64a1inwc9k2w2pz2"))))
+    (properties `((upstream-name . "INSPEcT")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-desolve" ,r-desolve)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-preprocesscore" ,r-preprocesscore)
+       ("r-proc" ,r-proc)
+       ("r-rootsolve" ,r-rootsolve)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/INSPEcT")
+    (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
+    (description
+     "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
+Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
+order to evaluate synthesis, processing and degradation rates and assess via
+modeling the rates that determines changes in mature mRNA levels.")
+    (license license:gpl2)))
+
+(define-public r-dnabarcodes
+  (package
+    (name "r-dnabarcodes")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DNABarcodes" version))
+       (sha256
+        (base32
+         "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
+    (properties `((upstream-name . "DNABarcodes")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://bioconductor.org/packages/DNABarcodes")
+    (synopsis "Create and analyze DNA barcodes")
+    (description
+     "This package offers tools to create DNA barcode sets capable of
+correcting insertion, deletion, and substitution errors.  Existing barcodes
+can be analyzed regarding their minimal, maximal and average distances between
+barcodes.  Finally, reads that start with a (possibly mutated) barcode can be
+demultiplexed, i.e. assigned to their original reference barcode.")
+    (license license:gpl2)))
+
+(define-public r-ruvseq
+  (package
+    (name "r-ruvseq")
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RUVSeq" version))
+       (sha256
+        (base32
+         "0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m"))))
+    (properties `((upstream-name . "RUVSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-edaseq" ,r-edaseq)
+       ("r-edger" ,r-edger)
+       ("r-mass" ,r-mass)))
+    (home-page "https://github.com/drisso/RUVSeq")
+    (synopsis "Remove unwanted variation from RNA-Seq data")
+    (description
+     "This package implements methods to @dfn{remove unwanted variation} (RUV)
+of Risso et al. (2014) for the normalization of RNA-Seq read counts between
+samples.")
+    (license license:artistic2.0)))
+
+(define-public r-biocneighbors
+  (package
+    (name "r-biocneighbors")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BiocNeighbors" version))
+       (sha256
+        (base32
+         "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
+    (properties `((upstream-name . "BiocNeighbors")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppannoy" ,r-rcppannoy)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/BiocNeighbors")
+    (synopsis "Nearest Neighbor Detection for Bioconductor packages")
+    (description
+     "This package implements exact and approximate methods for nearest
+neighbor detection, in a framework that allows them to be easily switched
+within Bioconductor packages or workflows.  The exact algorithm is implemented
+using pre-clustering with the k-means algorithm.  Functions are also provided
+to search for all neighbors within a given distance.  Parallelization is
+achieved for all methods using the BiocParallel framework.")
+    (license license:gpl3)))
+
+(define-public r-destiny
+  (package
+    (name "r-destiny")
+    (version "2.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "destiny" version))
+       (sha256
+        (base32
+         "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-fnn" ,r-fnn)
+       ("r-ggthemes" ,r-ggthemes)
+       ("r-hmisc" ,r-hmisc)
+       ("r-igraph" ,r-igraph)
+       ("r-matrix" ,r-matrix)
+       ("r-proxy" ,r-proxy)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)
+       ("r-scales" ,r-scales)
+       ("r-scatterplot3d" ,r-scatterplot3d)
+       ("r-smoother" ,r-smoother)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-vim" ,r-vim)))
+    (home-page "https://bioconductor.org/packages/destiny/")
+    (synopsis "Create and plot diffusion maps")
+    (description "This package provides tools to create and plot diffusion
+maps.")
+    ;; Any version of the GPL
+    (license license:gpl3+)))
+
+(define-public r-savr
+  (package
+    (name "r-savr")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "savR" version))
+       (sha256
+        (base32
+         "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
+    (properties `((upstream-name . "savR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-reshape2" ,r-reshape2)
+       ("r-scales" ,r-scales)
+       ("r-xml" ,r-xml)))
+    (home-page "https://github.com/bcalder/savR")
+    (synopsis "Parse and analyze Illumina SAV files")
+    (description
+     "This package provides tools to parse Illumina Sequence Analysis
+Viewer (SAV) files, access data, and generate QC plots.")
+    (license license:agpl3+)))
+
+(define-public r-chipexoqual
+  (package
+    (name "r-chipexoqual")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ChIPexoQual" version))
+       (sha256
+        (base32
+         "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
+    (properties `((upstream-name . "ChIPexoQual")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-biovizbase" ,r-biovizbase)
+       ("r-broom" ,r-broom)
+       ("r-data-table" ,r-data-table)
+       ("r-dplyr" ,r-dplyr)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-hexbin" ,r-hexbin)
+       ("r-iranges" ,r-iranges)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scales" ,r-scales)
+       ("r-viridis" ,r-viridis)))
+    (home-page "https://github.com/keleslab/ChIPexoQual")
+    (synopsis "Quality control pipeline for ChIP-exo/nexus data")
+    (description
+     "This package provides a quality control pipeline for ChIP-exo/nexus
+sequencing data.")
+    (license license:gpl2+)))
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,7 +30,7 @@
 (define-public bison
  (package
    (name "bison")
-    (version "3.0.4")
+    (version "3.0.5")
    (source
     (origin
      (method url-fetch)
@@ -37,10 +38,10 @@
                          version ".tar.xz"))
      (sha256
       (base32
-        "1qbgf6q1n2z17k8g33444m0q68kf3fbiq65q7jlrzpvvj73jh957"))))
+        "0f7kjygrckkx8vas2nm673592jif0a9mw5g8207f6hj6h4pfyp07"))))
    (build-system gnu-build-system)
    (native-inputs `(("perl" ,perl)
-                     ;; m4 is not present in PATH when cross-building
+                     ;; m4 is not present in PATH when cross-building.
                     ("m4" ,m4)))
    (inputs `(("flex" ,flex)))
    (propagated-inputs `(("m4" ,m4)))
@@ -52,15 +53,3 @@ deterministic or generalized LR parser from an annotated, context-free
 grammar.  It is versatile enough to have many applications, from parsers for
 simple tools through complex programming languages.")
    (license gpl3+)))
-
-(define-public bison-2.7
-  (package (inherit bison)
-    (version "2.7")
-    (source
-     (origin
-      (method url-fetch)
-      (uri (string-append "mirror://gnu/bison/bison-"
-                          version ".tar.xz"))
-      (sha256
-       (base32
-        "1zd77ilmpv5mi3kr55jrj6ncqlcnyhpianhrwzak2q28cv2cbn23"))))))
@@ -1,13 +1,14 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2018 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
+;;; Copyright © 2018 Nam Nguyen <namn@berkeley.edu>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -42,6 +43,7 @@
  #:use-module (gnu packages cyrus-sasl)
  #:use-module (gnu packages databases)
  #:use-module (gnu packages file)
+  #:use-module (gnu packages freedesktop)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages gnome)
  #:use-module (gnu packages gnupg)
@@ -54,6 +56,7 @@
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-crypto)
  #:use-module (gnu packages qt)
  #:use-module (gnu packages ssh)
  #:use-module (gnu packages tls)
@@ -179,51 +182,49 @@ XML-RPC over SCGI.")
    (license l:gpl2+)))

 (define-public tremc
-  (let ((commit "e06d08d8d76aa0559593ffc1188f4a90100cdbdb")
-        (revision "2"))
-    (package
-      (name "tremc")
-      (version (git-version "0.9.0" revision commit))
-      (source
-        (origin
-          (method git-fetch)
-          (uri (git-reference
-                 (url "https://github.com/louipc/tremc.git")
-                 (commit commit)))
-          (file-name (git-file-name name version))
-          (sha256
-           (base32
-            "17rf74sajcn5fl718rgl2qk5mw5yz9hrh58hbcg4p55wrazzrm1i"))))
-      (build-system gnu-build-system)
-      (arguments
-       `(#:tests? #f ; no test suite
-         #:make-flags
-         (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
-         #:phases
-         (modify-phases %standard-phases
-           ;; The software is just a Python script that must be copied into
-           ;; place.
-           (delete 'configure)
-           (delete 'build))))
-      (synopsis "Console client for the Transmission BitTorrent daemon")
-      (description "Tremc is a console client, with a curses interface, for the
+  (package
+    (name "tremc")
+    (version "0.9.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/tremc/tremc.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1yhwvlcyv1s830p5a7q5x3mkb3mbvr5cn5nh7y62l5b6iyyynlvm"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; no test suite
+       #:make-flags
+       (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         ;; The software is just a Python script that must be copied into place.
+         (delete 'configure)
+         (delete 'build))))
+    (inputs
+     `(("python" ,python)))
+    (synopsis "Console client for the Transmission BitTorrent daemon")
+    (description "Tremc is a console client, with a curses interface, for the
 Transmission BitTorrent daemon.")
-      (home-page "https://github.com/louipc/tremc")
-      (license l:gpl3+))))
+    (home-page "https://github.com/tremc/tremc")
+    (license l:gpl3+)))

 (define-public transmission-remote-cli
  (package
    (name "transmission-remote-cli")
    (version "1.7.1")
    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/fagga/"
-                                  "transmission-remote-cli/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/fagga/transmission-remote-cli.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1y0hkpcjf6jw9xig8yf484hbhy63nip0pkchx401yxj81m25l4z9"))))
+                "09w9f8vrm61lapin8fmq4rgahr95y3c6wss10g0fgd0kl16f895v"))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2 ; only supports Python 2
@@ -340,13 +341,14 @@ downloads, download scheduling, download rate limiting.")
    (name "mktorrent")
    (version "1.1")
    (source (origin
-              (method url-fetch)
-              (file-name (string-append name "-" version ".tar.gz"))
-              (uri (string-append "https://github.com/Rudde/mktorrent/archive/v"
-                                  version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Rudde/mktorrent.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1j9qc4fxa9isnaygqk6jazsiklqywl2wcs95b8dx01963407bx6h"))))
+                "17pdc5mandl739f8q26n5is8ga56s83aqcrwhlnnplbxwx2inidr"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases (modify-phases %standard-phases
@@ -373,17 +375,17 @@ and will take advantage of multiple processor cores where possible.")
 (define-public libtorrent-rasterbar
  (package
    (name "libtorrent-rasterbar")
-    (version "1.1.7")
+    (version "1.1.11")
    (source (origin
              (method url-fetch)
              (uri
               (string-append
-                "https://github.com/arvidn/libtorrent/releases/download/libtorrent-"
+                "https://github.com/arvidn/libtorrent/releases/download/libtorrent_"
                (string-join (string-split version #\.) "_")
                "/libtorrent-rasterbar-" version ".tar.gz"))
              (sha256
               (base32
-                "1agkcyjs7xscx4sgkg2ri4nm4v736xsg3br2v8jcrph86dlbycw1"))))
+                "0isqidr11fnhybr0wvk0qxd97jaikmh8fx9h89b84yd2gyxdw8vw"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags
@@ -395,7 +397,18 @@ and will take advantage of multiple processor cores where possible.")
             "CXXFLAGS=-std=c++11")     ; Use std::chrono instead of boost
       #:make-flags (list
                     (string-append "LDFLAGS=-Wl,-rpath="
-                                    (assoc-ref %outputs "out") "/lib"))))
+                                    (assoc-ref %outputs "out") "/lib"))
+       #:phases (modify-phases %standard-phases
+           (add-after 'unpack 'compile-python-c++11
+             (lambda _
+               ;; Make sure the Python bindings are compiled in C++ mode to
+               ;; avoid undefined references as mentioned in
+               ;; <https://github.com/qbittorrent/qBittorrent/issues/638>.
+               ;; XXX: This can be removed for 1.2+.
+               (substitute* "bindings/python/setup.py"
+                 (("\\+ target_specific\\(\\)\\,")
+                  "+ target_specific() + ['-std=c++11'],"))
+               #t)))))
    (inputs `(("boost" ,boost)
              ("openssl" ,openssl)))
    (native-inputs `(("python" ,python-2)
@@ -411,7 +424,7 @@ desktops.")
 (define-public qbittorrent
  (package
    (name "qbittorrent")
-    (version "4.0.4")
+    (version "4.1.3")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -420,7 +433,7 @@ desktops.")
              (file-name (string-append name "-release-" version ".tar.gz"))
              (sha256
               (base32
-                "145r4lv7rqdhrm5znn3ndxsfdf579n46zvj7c53c422am8ir5xhp"))))
+                "00zrpnwanq9f7maky2z4wnzw08xy902s77scm2gcvxxxankr4j92"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags
@@ -436,7 +449,7 @@ desktops.")
     `(("boost" ,boost)
       ("libtorrent-rasterbar" ,libtorrent-rasterbar)
       ("openssl" ,openssl)
-       ("python" ,python)
+       ("python" ,python-wrapper)
       ("qtbase" ,qtbase)
       ("qtsvg" ,qtsvg)
       ("zlib" ,zlib)))
@@ -450,3 +463,40 @@ It aims to be a good alternative to all other BitTorrent clients out there.
 qBittorrent is fast, stable and provides unicode support as well as many
 features.")
    (license l:gpl2+)))
+
+(define-public deluge
+  (package
+    (name "deluge")
+    (version "1.3.15")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://download.deluge-torrent.org/source/deluge-"
+             version ".tar.xz"))
+       (sha256
+        (base32
+         "0b7rri4x0wrcj7rjghrnw1kfrsd5i7i6aq85dsg5dg1w1qa0ar59"))))
+    (build-system python-build-system)
+    (inputs
+     `(("libtorrent" ,libtorrent-rasterbar)
+       ("python2-chardet" ,python2-chardet)
+       ("python2-pygtk" ,python2-pygtk)
+       ("python2-pyopenssl" ,python2-pyopenssl)
+       ("python2-pyxdg" ,python2-pyxdg)
+       ("python2-service-identity" ,python2-service-identity)
+       ("python2-twisted" ,python2-twisted)))
+    (native-inputs
+     `(("intltool" ,intltool)))
+    (arguments
+     `(#:python ,python-2))
+    (home-page "https://www.deluge-torrent.org/")
+    (synopsis  "Fully-featured cross-platform BitTorrent client")
+    (description
+     "Deluge contains the common features to BitTorrent clients such as
+Protocol Encryption, DHT, Local Peer Discovery (LSD), Peer Exchange
+(PEX), UPnP, NAT-PMP, Proxy support, Web seeds, global and per-torrent
+speed limits.  Deluge heavily utilises the libtorrent library.  It is
+designed to run as both a normal standalone desktop application and as a
+client-server.")
+    (license l:gpl3+)))
@@ -9,6 +9,7 @@
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,6 +28,7 @@

 (define-module (gnu packages boost)
  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix utils)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix git-download)
@@ -43,7 +45,7 @@
 (define-public boost
  (package
    (name "boost")
-    (version "1.66.0")
+    (version "1.68.0")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -52,7 +54,7 @@
                    ".tar.bz2"))
              (sha256
               (base32
-                "1aaw48cmimsskzgiclwn0iifp62a5iw9cbqrhfari876af1828ap"))
+                "1dyqsr9yb01y0nnjdq9b8q5s2kvhxbayk34832k5cpzn7jy30qbz"))
              (patches (search-patches "boost-fix-icu-build.patch"))))
    (build-system gnu-build-system)
    (inputs `(("icu4c" ,icu4c)
@@ -78,7 +80,6 @@
                   (out (assoc-ref outputs "out")))
               (substitute* '("libs/config/configure"
                              "libs/spirit/classic/phoenix/test/runtest.sh"
-                              "tools/build/doc/bjam.qbk"
                              "tools/build/src/engine/execunix.c"
                              "tools/build/src/engine/Jambase"
                              "tools/build/src/engine/jambase.c")
@@ -100,7 +101,18 @@
                    make-flags)))
         (replace 'install
           (lambda* (#:key make-flags #:allow-other-keys)
-             (apply invoke "./b2" "install" make-flags))))))
+             (apply invoke "./b2" "install" make-flags)))
+         (add-after 'install 'provide-libboost_python
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               ;; Boost can build support for both Python 2 and Python 3 since
+               ;; version 1.67.0, and suffixes each library with the Python
+               ;; version.  Many consumers only check for libboost_python
+               ;; however, so we provide it here as suggested in
+               ;; <https://github.com/boostorg/python/issues/203>.
+               (with-directory-excursion (string-append out "/lib")
+                 (symlink "libboost_python27.so" "libboost_python.so"))
+               #t))))))

    (home-page "https://www.boost.org")
    (synopsis "Peer-reviewed portable C++ source libraries")
@@ -110,6 +122,31 @@ across a broad spectrum of applications.")
    (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt"
                                "Some components have other similar licences."))))

+(define-public boost-for-mysql
+  ;; Older version for MySQL 5.7.23.
+  (package
+    (inherit boost)
+    (version "1.59.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://sourceforge/boost/boost/" version "/boost_"
+                    (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version)
+                    ".tar.bz2"))
+              (sha256
+               (base32
+                "1jj1aai5rdmd72g90a3pd8sw9vi32zad46xv5av8fhnr48ir6ykj"))))
+    (arguments (substitute-keyword-arguments (package-arguments boost)
+      ((#:phases phases)
+       `(modify-phases ,phases
+          ;; This was removed after boost-1.67.
+          (add-before 'configure 'more-bin-sh-patching
+            (lambda _
+              (substitute* "tools/build/doc/bjam.qbk"
+                (("/bin/sh") (which "sh")))))
+          (delete 'provide-libboost_python)))))
+    (properties '((hidden? . #t)))))
+
 (define-public boost-sync
  (let ((commit "c72891d9b90e2ceb466ec859f640cd012b2d8709")
        (version "1.55")
@@ -145,14 +182,14 @@ Boost.Thread.")
 (define-public mdds
  (package
    (name "mdds")
-    (version "1.3.1")
+    (version "1.4.3")
    (source (origin
             (method url-fetch)
             (uri (string-append
                   "http://kohei.us/files/mdds/src/mdds-" version ".tar.bz2"))
             (sha256
              (base32
-               "18g511z1lgfxrga2ld9yr95phmyfbd3ymbv4q5g5lyjn4ljcvf6w"))))
+               "10cw6irdm6d15nxnys2v5akp8yz52qijpcjvw0frwq7nz5d3vki5"))))
    (build-system gnu-build-system)
    (propagated-inputs
      `(("boost" ,boost))) ; inclusion of header files
@@ -34,6 +34,7 @@
  #:use-module (gnu packages bison)
  #:use-module (gnu packages cdrom)
  #:use-module (gnu packages check)
+  #:use-module (gnu packages compression)
  #:use-module (gnu packages cross-base)
  #:use-module (gnu packages disk)
  #:use-module (gnu packages firmware)
@@ -52,6 +53,7 @@
  #:use-module (gnu packages tls)
  #:use-module (gnu packages sdl)
  #:use-module (gnu packages swig)
+  #:use-module (gnu packages valgrind)
  #:use-module (gnu packages virtualization)
  #:use-module (gnu packages web)
  #:use-module (guix build-system gnu)
@@ -84,7 +86,9 @@
             (uri (string-append "mirror://gnu/grub/grub-" version ".tar.xz"))
             (sha256
              (base32
-               "03vvdfhdmf16121v7xs8is2krwnv15wpkhkf16a4yf8nsfc3f2w1"))))
+               "03vvdfhdmf16121v7xs8is2krwnv15wpkhkf16a4yf8nsfc3f2w1"))
+             (patches (search-patches "grub-check-error-efibootmgr.patch"
+                                      "grub-binutils-compat.patch"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases (modify-phases %standard-phases
@@ -302,15 +306,15 @@ menu to select one of the installed operating systems.")
           (delete 'configure)
           (add-before 'build 'set-permissions
             (lambda _
-               (zero? (system* "chmod" "a+w" "utils/isohybrid.in"))))
+               (invoke "chmod" "a+w" "utils/isohybrid.in")))
           (replace 'check
             (lambda _
               (setenv "CC" "gcc")
               (substitute* "tests/unittest/include/unittest/unittest.h"
                 ;; Don't look up headers under /usr.
                 (("/usr/include/") ""))
-               (zero? (system* "make" "unittest")))))))
-      (home-page "http://www.syslinux.org")
+               (invoke "make" "unittest"))))))
+      (home-page "https://www.syslinux.org")
      (synopsis "Lightweight Linux bootloader")
      (description "Syslinux is a lightweight Linux bootloader.")
      (license (list license:gpl2+
@@ -322,7 +326,7 @@ menu to select one of the installed operating systems.")
 (define-public dtc
  (package
    (name "dtc")
-    (version "1.4.6")
+    (version "1.4.7")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -330,12 +334,13 @@ menu to select one of the installed operating systems.")
                    "dtc-" version ".tar.xz"))
              (sha256
               (base32
-                "0zkvih0fpwvk31aqyyfy9kn13nbi76c21ihax15p6h1wrjzh48rq"))))
+                "1rydi5jvhlhsr110h6n0pavv3daqa0cb4m5vcps50qzq1zqfhhv6"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("bison" ,bison)
       ("flex" ,flex)
-       ("swig" ,swig)))
+       ("swig" ,swig)
+       ("valgrind" ,valgrind)))
    (inputs
     `(("python-2" ,python-2)))
    (arguments
@@ -357,7 +362,7 @@ tree binary files.  These are board description files used by Linux and BSD.")
 (define u-boot
  (package
    (name "u-boot")
-    (version "2018.05")
+    (version "2018.11")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -365,10 +370,13 @@ tree binary files.  These are board description files used by Linux and BSD.")
                    "u-boot-" version ".tar.bz2"))
              (sha256
               (base32
-                "0j60p4iskzb4hamxgykc6gd7xchxfka1zwh8hv08r9rrc4m3r8ad"))))
+                "0znkwljfwwn4y7j20pzz4ilqw8znphrfxns0x1lwdzh3xbr96z3k"))))
    (native-inputs
     `(("bc" ,bc)
+       ("bison" ,bison)
       ("dtc" ,dtc)
+       ("flex" ,flex)
+       ("lz4" ,lz4)
       ("openssl" ,openssl)
       ("python-2" ,python-2)
       ("python2-coverage" ,python2-coverage)
@@ -376,7 +384,7 @@ tree binary files.  These are board description files used by Linux and BSD.")
       ("sdl" ,sdl)
       ("swig" ,swig)))
    (build-system  gnu-build-system)
-    (home-page "http://www.denx.de/wiki/U-Boot/")
+    (home-page "https://www.denx.de/wiki/U-Boot/")
    (synopsis "ARM bootloader")
    (description "U-Boot is a bootloader used mostly for ARM boards. It
 also initializes the boards (RAM etc).")
@@ -398,6 +406,12 @@ also initializes the boards (RAM etc).")
              (("/bin/false") (which "false")))
             (substitute* "tools/dtoc/fdt_util.py"
              (("'cc'") "'gcc'"))
+             (substitute* "tools/patman/test_util.py"
+              ;; python-coverage is simply called coverage in guix.
+              (("python-coverage") "coverage")
+              ;; XXX Allow for only 99% test coverage.
+              ;; TODO: Find out why that is needed.
+              (("if coverage != '100%':") "if not int(coverage.rstrip('%')) >= 99:"))
             (substitute* "test/run"
              ;; Make it easier to find test failures.
              (("#!/bin/bash") "#!/bin/bash -x")
@@ -412,8 +426,6 @@ also initializes the boards (RAM etc).")
              (("def test_ctrl_c")
               "@pytest.mark.skip(reason='Guix has problems with SIGINT')
 def test_ctrl_c"))
-             (substitute* "tools/binman/binman.py"
-              (("100%") "99%")) ; TODO: Find out why that is needed.
             #t))
         (replace 'configure
           (lambda* (#:key make-flags #:allow-other-keys)
@@ -423,8 +435,7 @@ def test_ctrl_c"))
             (apply invoke "make" "tools_defconfig" make-flags)))
         (replace 'build
           (lambda* (#:key inputs make-flags #:allow-other-keys)
-             (apply invoke "make" "tools-only" make-flags)
-             (apply invoke "make" "envtools" make-flags)))
+             (apply invoke "make" "tools-all" make-flags)))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
@@ -441,7 +452,8 @@ def test_ctrl_c"))
                           "tools/mkimage"
                           "tools/proftool"
                           "tools/fdtgrep"
-                           "tools/env/fw_printenv"))
+                           "tools/env/fw_printenv"
+                           "tools/sunxi-spl-image-builder"))
               #t)))
           (delete 'check)
           (add-after 'install 'check
@@ -474,7 +486,10 @@ board-independent tools.")))
             `(("gcc-7" ,gcc-7)))
         ,@(package-native-inputs u-boot)))
      (arguments
-       `(#:modules ((ice-9 ftw) (guix build utils) (guix build gnu-build-system))
+       `(#:modules ((ice-9 ftw)
+                    (srfi srfi-1)
+                    (guix build utils)
+                    (guix build gnu-build-system))
         #:test-target "test"
         #:make-flags
         (list "HOSTCC=gcc"
@@ -506,7 +521,18 @@ board-independent tools.")))
               (let* ((out (assoc-ref outputs "out"))
                      (libexec (string-append out "/libexec"))
                      (uboot-files (append
-                                    (find-files "." ".*\\.(bin|efi|img|spl|itb|dtb|rksd)$")
+                                    (remove
+                                     ;; Those would not be reproducible
+                                     ;; because of the randomness used
+                                     ;; to produce them.
+                                     ;; It's expected that the user will
+                                     ;; use u-boot-tools to generate them
+                                     ;; instead.
+                                     (lambda (name)
+                                       (string-suffix?
+                                        "sunxi-spl-with-ecc.bin"
+                                        name))
+                                     (find-files "." ".*\\.(bin|efi|img|spl|itb|dtb|rksd)$"))
                                    (find-files "." "^(MLO|SPL)$"))))
                 (mkdir-p libexec)
                 (install-file ".config" libexec)
@@ -517,7 +543,8 @@ board-independent tools.")))
                    (let ((target-file (string-append libexec "/" file)))
                      (mkdir-p (dirname target-file))
                      (copy-file file target-file)))
-                  uboot-files))))))))))
+                  uboot-files)
+                 #t)))))))))

 (define-public u-boot-vexpress
  (make-u-boot-package "vexpress_ca9x4" "arm-linux-gnueabihf"))
@@ -528,8 +555,8 @@ board-independent tools.")))
 (define-public u-boot-beagle-bone-black
  (make-u-boot-package "am335x_boneblack" "arm-linux-gnueabihf"))

-(define-public u-boot-pine64-plus
-  (let ((base (make-u-boot-package "pine64_plus" "aarch64-linux-gnu")))
+(define-public (make-u-boot-sunxi64-package board triplet)
+  (let ((base (make-u-boot-package board triplet)))
    (package
      (inherit base)
      (arguments
@@ -547,10 +574,29 @@ board-independent tools.")))
                    )
                  #t))))))
      (native-inputs
-       `(("firmware" ,arm-trusted-firmware-pine64-plus)
+       `(("firmware" ,arm-trusted-firmware-sun50i-a64)
         ,@(package-native-inputs base))))))

-(define-public u-boot-banana-pi-m2-ultra
+(define-public u-boot-pine64-plus
+  (make-u-boot-sunxi64-package "pine64_plus" "aarch64-linux-gnu"))
+
+(define-public u-boot-pinebook
+  (let ((base (make-u-boot-sunxi64-package "pinebook" "aarch64-linux-gnu")))
+    (package
+      (inherit base)
+      (source (origin
+              (inherit (package-source u-boot))
+              (patches (search-patches
+                        ;; Add patches to enable Pinebook support from sunxi
+                        ;; maintainer tree: git://git.denx.de/u-boot-sunxi.git
+                        "u-boot-pinebook-a64-update-dts.patch"
+                        "u-boot-pinebook-syscon-node.patch"
+                        "u-boot-pinebook-mmc-calibration.patch"
+                        "u-boot-pinebook-video-bridge.patch"
+                        "u-boot-pinebook-r_i2c-controller.patch"
+                        "u-boot-pinebook-dts.patch")))))))
+
+(define-public u-boot-bananapi-m2-ultra
  (make-u-boot-package "Bananapi_M2_Ultra" "arm-linux-gnueabihf"))

 (define-public u-boot-a20-olinuxino-lime
@@ -577,6 +623,9 @@ board-independent tools.")))
 (define-public u-boot-cubieboard
  (make-u-boot-package "Cubieboard" "arm-linux-gnueabihf"))

+(define-public u-boot-cubietruck
+  (make-u-boot-package "Cubietruck" "arm-linux-gnueabihf"))
+
 (define-public u-boot-puma-rk3399
  (let ((base (make-u-boot-package "puma-rk3399" "aarch64-linux-gnu")))
    (package
@@ -1,9 +1,11 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Corentin Bocquillon <corentin@nybble.fr>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,9 +27,11 @@
  #:use-module (guix utils)
  #:use-module (guix packages)
  #:use-module (guix download)
+  #:use-module (guix git-download)
  #:use-module (guix build-system cmake)
  #:use-module (gnu packages)
  #:use-module (gnu packages compression)
+  #:use-module (gnu packages lua)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-crypto)
  #:use-module (gnu packages python-web)
@@ -38,33 +42,30 @@
 (define-public bam
  (package
    (name "bam")
-    (version "0.4.0")
+    (version "0.5.1")
    (source (origin
-              (method url-fetch)
-              (uri (string-append "http://github.com/downloads/matricks/"
-                                  "bam/bam-" version ".tar.bz2"))
+              ;; do not use auto-generated tarballs
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/matricks/bam.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
              (sha256
               (base32
-                "0z90wvyd4nfl7mybdrv9dsd4caaikc6fxw801b72gqi1m9q0c0sn"))))
+                "13br735ig7lygvzyfd15fc2rdygrqm503j6xj5xkrl1r7w2wipq6"))))
    (build-system gnu-build-system)
    (arguments
-     `(#:phases
+     `(#:make-flags `("CC=gcc"
+                      ,(string-append "INSTALL_PREFIX="
+                                      (assoc-ref %outputs "out")))
+       #:test-target "test"
+       #:phases
       (modify-phases %standard-phases
-         (delete 'configure)
-         (replace 'build
-           (lambda _
-             (zero? (system* "bash" "make_unix.sh"))))
-         (replace 'check
-           (lambda _
-             (zero? (system* "python" "scripts/test.py"))))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-               (mkdir-p bin)
-               (install-file "bam" bin)
-               #t))))))
+         (delete 'configure))))
    (native-inputs
     `(("python" ,python-2)))
+    (inputs
+     `(("lua" ,lua)))
    (home-page "https://matricks.github.io/bam/")
    (synopsis "Fast and flexible build system")
    (description "Bam is a fast and flexible build system.  Bam uses Lua to
@@ -76,16 +77,16 @@ makes a few sacrifices to acquire fast full and incremental build times.")
 (define-public bear
  (package
    (name "bear")
-    (version "2.3.11")
+    (version "2.3.12")
    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/rizsotto/Bear/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/rizsotto/Bear")
+                    (commit version)))
+              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1m0w0wqnz983l7fpp5p9pdsqr7n3ybrzp8ywjcvn0rihsrzj65j6"))))
+                "1zzz2yiiny9pm4h6ayb82xzxc2j5djcpf8va2wagcw92m7w6miqw"))))
    (build-system cmake-build-system)
    (inputs
     `(("python" ,python-wrapper)))
@@ -97,10 +98,67 @@ it is easy to re-run the compilation with alternate programs.  Bear is used to
 generate such a compilation database.")
    (license license:gpl3+)))

+(define-public gn
+  (let ((commit "f73698ebb33e26a0bf120e2b55d12528fd1dbe7d")
+        (revision "1481"))          ;as returned by `git describe`, used below
+    (package
+      (name "gn")
+      (version (git-version "0.0" revision commit))
+      (home-page "https://gn.googlesource.com/gn")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference (url home-page) (commit commit)))
+                (sha256
+                 (base32
+                  "078ydwak4424bkqh3hd7q955zxp2c3qlw44lsb29i8jqap140f9d"))
+                (file-name (git-file-name name version))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                    ;FIXME: How to run?
+         #:phases (modify-phases %standard-phases
+                    (add-before 'configure 'set-build-environment
+                      (lambda _
+                        (setenv "CC" "gcc") (setenv "CXX" "g++")
+                        (setenv "AR" "ar")
+                        #t))
+                    (replace 'configure
+                      (lambda _
+                        (invoke "python" "build/gen.py" "--no-sysroot"
+                                "--no-last-commit-position")))
+                    (add-after 'configure 'create-last-commit-position
+                      (lambda _
+                        ;; Create "last_commit_position.h" to avoid a dependency
+                        ;; on 'git' (and the checkout..).
+                        (call-with-output-file "out/last_commit_position.h"
+                          (lambda (port)
+                            (format port
+                                    "#define LAST_COMMIT_POSITION \"~a (~a)\"\n"
+                                    ,revision ,(string-take commit 8))
+                            #t))))
+                    (replace 'build
+                      (lambda _
+                        (invoke "ninja" "-C" "out" "gn"
+                                "-j" (number->string (parallel-job-count)))))
+                    (replace 'install
+                      (lambda* (#:key outputs #:allow-other-keys)
+                        (let ((out (assoc-ref outputs "out")))
+                          (install-file "out/gn" (string-append out "/bin"))
+                          #t))))))
+      (native-inputs
+       `(("ninja" ,ninja)
+         ("python" ,python-2)))
+      (synopsis "Generate Ninja build files")
+      (description
+       "GN is a tool that collects information about a project from @file{.gn}
+files and generates build instructions for the Ninja build system.")
+      ;; GN is distributed as BSD-3, but bundles some files from ICU using the
+      ;; X11 license.
+      (license (list license:bsd-3 license:x11)))))
+
 (define-public meson
  (package
    (name "meson")
-    (version "0.45.1")
+    (version "0.47.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/mesonbuild/meson/"
@@ -108,7 +166,7 @@ generate such a compilation database.")
                                  version ".tar.gz"))
              (sha256
               (base32
-                "1yqa4337nb8w92bvr91rsxmn0xkf7pmdybq9ljvnqmdvn7dv02sd"))))
+                "1swmycf6p9p0ag6yiywyyri42ffkxxj38r2ic7in24km47cszn4j"))))
    (build-system python-build-system)
    (arguments
     `(;; FIXME: Tests require many additional inputs, a fix for the RUNPATH
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 John Darrington <jmd@gnu.org>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -31,7 +31,7 @@
 (define-public busybox
  (package
    (name "busybox")
-    (version "1.26.2")
+    (version "1.29.3")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -39,11 +39,18 @@
                    version ".tar.bz2"))
              (sha256
               (base32
-                "05mg6rh5smkzfwqfcazkpwy6h6555llsazikqnvwkaf17y8l8gns"))))
+                "1dzg45vgy2w1xcd3p6h8d76ykhabbvk1h0lf8yb24ikrwlv8cr4p"))))
    (build-system gnu-build-system)
    (arguments
     '(#:phases
       (modify-phases %standard-phases
+         (add-before 'configure 'disable-taskset
+           ;; This feature fails its tests in the build environment,
+           ;; was default 'n' until after 1.26.2.
+           (lambda _
+             (substitute* "util-linux/taskset.c"
+               (("default y") "default n"))
+             #t))
         (replace 'configure
           (lambda _ (invoke "make" "defconfig")))
         (replace 'check
@@ -1,7 +1,8 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -22,6 +23,7 @@
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
+  #:use-module (guix git-download)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system trivial)
  #:use-module (gnu packages bootstrap)
@@ -30,6 +32,12 @@
  #:use-module (gnu packages perl)
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages guile)
+  #:use-module (gnu packages multiprecision)
+  #:use-module (gnu packages pcre)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages gettext)
+  #:use-module (gnu packages pkg-config)
  #:use-module (srfi srfi-1))

 (define-public tcc
@@ -152,8 +160,7 @@ standard.")
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
-           (lambda _
-             (zero? (system* "make" "-C" "cc/cpp" "test")))))))
+           (lambda _ (invoke "make" "-C" "cc/cpp" "test") #t)))))
    (native-inputs
     `(("bison" ,bison)
       ("flex" ,flex)))
@@ -166,3 +173,83 @@ compiler while still keeping it small, simple, fast and understandable.")
    ;; PCC incorporates code under various BSD licenses; for new code bsd-2 is
    ;; preferred.  See http://pcc.ludd.ltu.se/licenses/ for more details.
    (license (list license:bsd-2 license:bsd-3))))
+
+(define-public libbytesize
+  (package
+    (name "libbytesize")
+    (version "1.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/storaged-project/libbytesize/releases/"
+                    "download/" version "/libbytesize-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0bbqzln1nhjxl71aydq9k4jg3hvki9lqsb4w10s1i27jgibxqkdv"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; This Makefile hard-codes MSGMERGE et al. instead of
+                  ;; honoring what 'configure' detected.  Fix that.
+                  (substitute* "po/Makefile.in"
+                    (("^MSGMERGE = msgmerge")
+                     "MSGMERGE = @MSGMERGE@\n"))
+                  #t))))
+    (build-system gnu-build-system)
+    (arguments
+     ;; When running "make", the POT files are built with the build time as
+     ;; their "POT-Creation-Date".  Later on, "make" notices that .pot
+     ;; files were updated and goes on to run "msgmerge"; as a result, the
+     ;; non-deterministic POT-Creation-Date finds its way into .po files,
+     ;; and then in .gmo files.  To avoid that, simply make sure 'msgmerge'
+     ;; never runs.  See <https://bugs.debian.org/792687>.
+     '(#:configure-flags '("ac_cv_path_MSGMERGE=true")
+
+       #:phases (modify-phases %standard-phases
+                  (add-after 'configure 'create-merged-po-files
+                    (lambda _
+                      ;; Create "merged PO" (.mpo) files so that 'msgmerge'
+                      ;; doesn't need to run.
+                      (for-each (lambda (po-file)
+                                  (let ((merged-po
+                                         (string-append (dirname po-file) "/"
+                                                        (basename po-file
+                                                                  ".po")
+                                                        ".mpo")))
+                                    (copy-file po-file merged-po)))
+                                (find-files "po" "\\.po$"))
+                      #t)))
+
+       ;; One test fails because busctl (systemd only?) and python2-pocketlint
+       ;; are missing.  Should we fix it, we would need the "python-2" ,
+       ;; "python2-polib" and "python2-six" native-inputs.
+       #:tests? #f))
+    (native-inputs
+     `(("gettext" ,gettext-minimal)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python)))
+    (inputs
+     `(("mpfr" ,mpfr)
+       ("pcre" ,pcre)))
+    (home-page "https://github.com/storaged-project/libbytesize")
+    (synopsis "Tiny C library for working with arbitrary big sizes in bytes")
+    (description
+     "The goal of this project is to provide a tiny library that would
+facilitate the common operations with sizes in bytes.  Many projects need to
+work with sizes in bytes (be it sizes of storage space, memory...) and all of
+them need to deal with the same issues like:
+
+@itemize
+@item How to get a human-readable string for the given size?
+@item How to store the given size so that no significant information is lost?
+@item If we store the size in bytes, what if the given size gets over the
+MAXUINT64 value?
+@item How to interpret sizes entered by users according to their locale and
+typing conventions?
+@item How to deal with the decimal/binary units (MB versus MiB) ambiguity?
+@end itemize
+
+@code{libbytesize} offers a generally usable solution that could be used by
+every project that needs to deal with sizes in bytes.  It is written in the C
+language with thin bindings for other languages.")
+    (license license:lgpl2.1+)))
@@ -34,7 +34,7 @@
    (source
     (origin
      (method url-fetch)
-      (uri (string-append "http://calcurse.org/files/calcurse-"
+      (uri (string-append "https://calcurse.org/files/calcurse-"
                          version ".tar.gz"))
      (sha256
       (base32
@@ -57,7 +57,7 @@
                      (setenv "TZDIR"   ;for test/ical-007.sh
                              (string-append (assoc-ref inputs "tzdata")
                                             "/share/zoneinfo")))))))
-    (home-page "http://www.calcurse.org")
+    (home-page "https://www.calcurse.org")
    (synopsis "Text-based calendar and scheduling")
    (description
     "Calcurse is a text-based calendar and scheduling application.  It helps
@@ -48,7 +48,7 @@
 (define-public libical
  (package
    (name "libical")
-    (version "3.0.3")
+    (version "3.0.4")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -56,7 +56,7 @@
                    version "/libical-" version ".tar.gz"))
              (sha256
               (base32
-                "0hcjyf35b8rrvy8xziqxc4imi28mmkixb09gknisvp6jsa5fp4av"))))
+                "0ifisnh42cw5z53hp9p52l3ggc7k877zlqk0n06gdhrk0bhidckj"))))
    (build-system cmake-build-system)
    (arguments
     '(#:tests? #f ; test suite appears broken
@@ -96,13 +96,13 @@ data units.")
 (define-public khal
  (package
    (name "khal")
-    (version "0.9.9")
+    (version "0.9.10")
    (source (origin
             (method url-fetch)
             (uri (pypi-uri "khal" version))
             (sha256
              (base32
-               "0dq9aqb9pqjfqrnfg43mhpb7m0szmychxy1ydb3lwzf3500c9rsh"))))
+               "03h0j0d3xyqh98x5v2gv63wv3g91hip3vsaxvybsn5iz331d23h4"))))
    (build-system python-build-system)
    (arguments
     `(#:phases (modify-phases %standard-phases
@@ -30,7 +30,7 @@
 (define-public ccache
  (package
    (name "ccache")
-    (version "3.4.2")
+    (version "3.5")
    (source
     (origin
      (method url-fetch)
@@ -38,9 +38,9 @@
                          version ".tar.xz"))
      (sha256
       (base32
-        "1qpy6k9f06kpr6bxy26ncdxcszqv1skcncvczcvksgfncx1v3a0q"))))
+        "04n0xram2416pv98qrd7pi5lfsk0bjqyz7zgvvia41j5mrr4pm5x"))))
    (build-system gnu-build-system)
-    (native-inputs `(("perl" ,perl)     ; for test.sh
+    (native-inputs `(("perl" ,perl)     ; for test/run
                     ("which" ,(@ (gnu packages base) which))))
    (inputs `(("zlib" ,zlib)))
    (arguments
@@ -49,13 +49,6 @@
                   (lambda _
                     (substitute* '("unittest/test_hashutil.c" "test/suites/base.bash")
                       (("#!/bin/sh") (string-append "#!" (which "sh"))))
-                     #t))
-                 (add-before 'check 'munge-failing-test
-                   (lambda _
-                     ;; XXX The new ‘Multiple -fdebug-prefix-map’ test added in
-                     ;; 3.3.5 fails (why?).  Force it to report success instead.
-                     (substitute* "test/suites/debug_prefix_map.bash"
-                       (("grep \"name\"") "true"))
                     #t)))))
    (home-page "https://ccache.samba.org/")
    (synopsis "Compiler cache")
@@ -10,6 +10,8 @@
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
+;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,6 +30,7 @@

 (define-module (gnu packages cdrom)
  #:use-module (guix download)
+  #:use-module (guix git-download)
  #:use-module (guix packages)
  #:use-module ((guix licenses) #:select (lgpl2.1+ gpl2 gpl2+ gpl3+ cddl1.0))
  #:use-module (guix build-system cmake)
@@ -151,14 +154,14 @@ libcdio.")
 (define-public xorriso
  (package
    (name "xorriso")
-    (version "1.4.8")
+    (version "1.5.0")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/xorriso/xorriso-"
                                 version ".tar.gz"))
             (sha256
              (base32
-               "10c44yr3dpmwxa7rf23mwfsy1bahny3jpcg9ig0xjv090jg0d0pc"))))
+               "0aq6lvlwlkxz56l5sbvgycr6j5c82ch2bv6zrnc2345ibfpafgx9"))))
    (build-system gnu-build-system)
    (inputs
     `(("acl" ,acl)
@@ -290,17 +293,26 @@ images.")
     `(#:tests? #f ; No tests.
       #:phases
       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-glibc-compatability
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; We use sed --in-place because substitute* cannot handle the
+             ;; character encoding used by growisofs.c.
+             (invoke "sed" "-i" "-e"
+                     (string-append
+                       "s,<sys/stat.h>,"
+                       "<sys/stat.h>\\\n#include <sys/sysmacros.h>,")
+                     "growisofs.c")))
         (replace 'configure
           (lambda _ (setenv "prefix" (assoc-ref %outputs "out")) #t))
         (add-before 'build 'embed-mkisofs
-           (lambda*  (#:key inputs #:allow-other-keys)
+           (lambda* (#:key inputs #:allow-other-keys)
             ;; We use sed --in-place because substitute* cannot handle the
             ;; character encoding used by growisofs.c.
-             (zero? (system* "sed" "-i" "-e"
-                             (string-append
-                              "s,\"mkisofs\","
-                              "\"" (which "mkisofs") "\",")
-                             "growisofs.c")))))))
+             (invoke "sed" "-i" "-e"
+                     (string-append
+                       "s,\"mkisofs\","
+                       "\"" (which "mkisofs") "\",")
+                     "growisofs.c"))))))
    (home-page "http://fy.chalmers.se/~appro/linux/DVD+RW/")
    (synopsis "DVD and Blu-ray Disc burning tools")
    (description "dvd+rw-tools, mostly known for its command
@@ -418,17 +430,19 @@ graphical interface.")
 (define-public libcue
  (package
    (name "libcue")
-    (version "2.2.0")
+    (version "2.2.1")
    (source (origin
-             (method url-fetch)
-             (uri (string-append
-                   "https://github.com/lipnitsk/libcue/archive/v"
-                   version ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/lipnitsk/libcue.git")
+                   (commit (string-append "v" version))))
+             (file-name (git-file-name name version))
             (sha256
              (base32
-               "0y9808vbly1w6i3diaad9csjmmw6iaw572wjjr68ssqamsw193rj"))))
+               "1iqw4n01rv2jyk9lksagyxj8ml0kcfwk67n79zy1r6zv1xfp5ywm"))))
    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")))
    (native-inputs
     `(("bison" ,bison)
       ("flex" ,flex)))
@@ -474,7 +488,7 @@ from an audio CD.")
 (define-public abcde
  (package
    (name "abcde")
-    (version "2.9.1")
+    (version "2.9.2")
    (home-page "https://abcde.einval.com/")
    (source (origin
              (method url-fetch)
@@ -482,11 +496,15 @@ from an audio CD.")
                                  version ".tar.gz"))
              (sha256
               (base32
-                "1msm5snyckynbspz54p9krarn7v9izsi7qyyi2z5y4cinw36xv3h"))
+                "13c5yvp87ckqgha160ym5rdr1a4divgvyqbjh0yb6ffclip6qd9l"))
              (modules '((guix build utils)))
              (snippet
-               '(begin
+               `(begin
                  (substitute* "Makefile"
+                    ;; Fix abcde 2.9.2 still thinking it's 2.9.1.
+                    ;; XXX This will be fixed in the next release.
+                    (("(abcde_version = abcde-)(2.9.1)" _ good bad)
+                     (string-append good ,version))
                    (("/usr/bin/install")
                     "install")
                    (("^etcdir = .*$")
@@ -720,14 +738,14 @@ laid out on the image.")
 (define-public libburn
  (package
    (name "libburn")
-    (version "1.4.8")
+    (version "1.5.0")
    (source (origin
             (method url-fetch)
             (uri (string-append "http://files.libburnia-project.org/releases/"
                                 "libburn-" version ".tar.gz"))
             (sha256
              (base32
-               "19lxnzn8bz70glrrrn2hs43gf5g7gfbcka9rcbckhv1pb7is509y"))))
+               "1gg2kgnqvaa2fwghai62prxz6slpak1f6bvgjh8m4dn16v114asq"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("pkg-config" ,pkg-config)))
@@ -742,14 +760,14 @@ DVD-RW, DVD-R, DVD-R/DL, BD-R, and BD-RE.")
 (define-public libisofs
  (package
    (name "libisofs")
-    (version "1.4.8")
+    (version "1.5.0")
    (source (origin
             (method url-fetch)
             (uri (string-append "http://files.libburnia-project.org/releases/"
                                 "libisofs-" version ".tar.gz"))
             (sha256
              (base32
-               "0scvqb72qq24wcg814p1iw1dknldl21hr1hxsc1wy9vc6vgyk7fw"))))
+               "001l3akf3wb6msl9man776w560iqyvsbwwzs7d7y7msx13irspys"))))
    (build-system gnu-build-system)
    (inputs
     `(("zlib" ,zlib)
@@ -767,3 +785,43 @@ to produce new complete file system images or add-on images to be appended
 to the read file system image.
 Supported extensions to ISO 9660 are Rock Ridge, Joliet, AAIP, zisofs.")
    (license gpl2+)))
+
+(define-public cdrkit-libre
+  (package
+    (name "cdrkit-libre")
+    (version "1.1.11")
+    (source (origin
+              (method url-fetch)
+              ;; cdrkit.org is dead.
+              ;;
+              ;; ‘cdrkit-libre’ removes a couple of problematic files,
+              ;; see <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=32165#14>.
+              (uri (string-append
+                    "https://repo.parabola.nu/other/cdrkit-libre/cdrkit-libre-"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "0g2zyzb56czh429qy87lvaddzjnlcq8c616ddxsmsshz3clhyzrh"))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("bzip2" ,bzip2)
+       ("libcap" ,libcap)
+       ("perl" ,perl)
+       ("zlib" ,zlib)))
+    (arguments
+     `(#:tests? #f ;no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'old-cdrecord
+           (lambda* (#:key outputs #:allow-other-keys)
+             (with-directory-excursion (string-append (assoc-ref outputs "out")
+                                                      "/bin")
+               (symlink "genisoimage" "mkisofs")
+               (symlink "wodim" "cdrecord"))
+             #t)))))
+    (home-page "https://repo.parabola.nu/other/cdrkit-libre/")
+    (synopsis "Command-line CD/DVD recorder")
+    (description "Cdrkit is a suite of programs for recording CDs and DVDs,
+blanking CD-RW media, creating ISO-9660 file system images, extracting audio
+CD data, and more.  It's mostly compatible with @code{cdrtools}.")
+    (license gpl2+)))
@@ -76,7 +76,7 @@
 (define-public nss-certs
  (package
    (name "nss-certs")
-    (version "3.36.1")
+    (version "3.39")
    (source (origin
              (method url-fetch)
              (uri (let ((version-with-underscores
@@ -87,7 +87,7 @@
                      "nss-" version ".tar.gz")))
              (sha256
               (base32
-                "1zrb49mp7cy3snnday1zv8d76h1mgppbcwxnlkqsgxlga8fl89b0"))))
+                "0jw6qlfl2g47hhx056nvnj6h92bk3sn46hy3ig61a911dzblvrkb"))))
    (build-system gnu-build-system)
    (outputs '("out"))
    (native-inputs
@@ -7,7 +7,7 @@
 ;;; Copyright © 2015, 2017 Cyril Roelandt <tipecaml@gmail.com>
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016, 2017 Danny Milosavljevic <dannym+a@scratchpost.org>
@@ -26,7 +26,7 @@
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -51,6 +51,7 @@
  #:use-module (gnu packages compression)
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages golang)
+  #:use-module (gnu packages perl)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages time)
@@ -250,7 +251,7 @@ a multi-paradigm automated test framework for C++ and Objective-C.")
             ;; the build environment. Hence assuming-failure test fails.
             (delete-file "yarn.tests/assuming-failure.script")
             (delete-file "yarn.tests/assuming-failure.stdout")
-             (zero? (system* "python" "setup.py" "check")))))))
+             (invoke "python" "setup.py" "check"))))))
    (native-inputs
     `(("python2-coverage-test-runner" ,python2-coverage-test-runner)))
    (propagated-inputs
@@ -269,7 +270,7 @@ problem, and shows the differences.")
 (define-public cmocka
  (package
    (name "cmocka")
-    (version "1.1.1")
+    (version "1.1.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://cmocka.org/files/"
@@ -277,10 +278,10 @@ problem, and shows the differences.")
                                  version ".tar.xz"))
              (sha256
               (base32
-                "1283zi9qf5613g8iadm1fxmjh4rzxqd5np2j3lcpgairf25g8bph"))))
+                "1p9b6ccv939wjsgapn7wx24xw278awsw9h81lm0g4zw257hx276i"))))
    (build-system cmake-build-system)
    (arguments
-     `(#:tests? #f)) ; No test target
+     `(#:tests? #f))                    ; no test target
    (home-page "https://cmocka.org/")
    (synopsis "Unit testing framework for C")
    (description "Cmocka is a unit testing framework for C with support for
@@ -293,13 +294,13 @@ format.")
 (define-public cppcheck
  (package
    (name "cppcheck")
-    (version "1.84")
+    (version "1.85")
    (source (origin
      (method url-fetch)
      (uri (string-append "https://github.com/danmar/cppcheck/archive/"
                          version ".tar.gz"))
      (sha256
-       (base32 "1ibz07dgs1dpfb8bmjh3qsma37wl5p6s6b4qlv5ccpshj4yjk9ma"))
+       (base32 "18qlddf1i9bk5nnvy1v2nfxjd46y8wvp3rqz2hrfxjxsyvrfq5yw"))
      (file-name (string-append name "-" version ".tar.gz"))))
    (build-system cmake-build-system)
    (home-page "http://cppcheck.sourceforge.net")
@@ -619,14 +620,14 @@ standard library.")
 (define-public python-pytest
  (package
    (name "python-pytest")
-    (version "3.5.0")
+    (version "3.8.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "pytest" version))
       (sha256
        (base32
-         "1q832zd07zak2lyxbycxjydh0jp7y3hvawjqzlvra6aghz8r3r7s"))))
+         "17grcfvd6ggvvqmprwv5y8g319nayam70hr43ssjwj40ws27z858"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
@@ -642,9 +643,11 @@ standard library.")
                (string-append "@pytest.mark.skip"
                               "(reason=\"Assumes that /usr exists.\")\n    "
                               line)))
-             #t)))))
+             #t))
+         (replace 'check (lambda _ (invoke "pytest" "-vv"))))))
    (propagated-inputs
-     `(("python-attrs" ,python-attrs-bootstrap)
+     `(("python-atomicwrites" ,python-atomicwrites)
+       ("python-attrs" ,python-attrs-bootstrap)
       ("python-more-itertools" ,python-more-itertools)
       ("python-pluggy" ,python-pluggy)
       ("python-py" ,python-py)
@@ -655,6 +658,7 @@ standard library.")
       ("python-hypothesis" ,python-hypothesis)
       ("python-nose" ,python-nose)
       ("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest-bootstrap)
       ("python-setuptools-scm" ,python-setuptools-scm)))
    (home-page "http://pytest.org")
    (synopsis "Python testing library")
@@ -672,6 +676,7 @@ and many external plugins.")
      (inherit pytest)
      (propagated-inputs
       `(("python2-funcsigs" ,python2-funcsigs)
+         ("python2-pathlib2" ,python2-pathlib2)
         ,@(package-propagated-inputs pytest))))))

 (define-public python-pytest-bootstrap
@@ -688,19 +693,20 @@ and many external plugins.")
    (package (inherit pytest)
             (propagated-inputs
              `(("python2-funcsigs" ,python2-funcsigs-bootstrap)
+                ("python2-pathlib2" ,python2-pathlib2-bootstrap)
                ,@(package-propagated-inputs pytest))))))

 (define-public python-pytest-cov
  (package
    (name "python-pytest-cov")
-    (version "2.4.0")
+    (version "2.5.1")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-cov" version))
        (sha256
         (base32
-          "03c2qc42r4bczyw93gd7n0qi1h1jfhw7fnbhi33c3vp1hs81gm2k"))))
+          "0bbfpwdh9k3636bxc88vz9fa7vf4akchgn513ql1vd0xy4n7bah3"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
@@ -710,8 +716,8 @@ and many external plugins.")
            ;; options taken from tox.ini
            ;; TODO: make "--restructuredtext" tests pass. They currently fail
            ;; with "Duplicate implicit target name"
-            (zero? (system* "python" "./setup.py" "check"
-                            "--strict" "--metadata")))))))
+            (invoke "python" "./setup.py" "check"
+                    "--strict" "--metadata"))))))
    (propagated-inputs
     `(("python-coverage" ,python-coverage)
       ("python-pytest" ,python-pytest)))
@@ -729,26 +735,15 @@ supports coverage of subprocesses.")
 (define-public python-pytest-runner
  (package
    (name "python-pytest-runner")
-    (version "2.11.1")
+    (version "4.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "pytest-runner" version))
       (sha256
        (base32
-         "1cw978kqqcq916b9gfns1qjqvg33c5ail5jhw9054dsynkm32flq"))))
+         "1gkpyphawxz38ni1gdq1fmwyqcg02m7ypzqvv46z06crwdxi2gyj"))))
    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; The fancy way of setting the version with setuptools_scm does not
-         ;; seem to work here.
-         (add-after 'unpack 'set-version
-          (lambda _
-            (substitute* "docs/conf.py"
-              (("version = setuptools_scm\\.get_version\\(root='\\.\\.')")
-               (string-append "version = \"" ,version "\"")))
-            #t)))))
    (native-inputs
     `(("python-pytest" ,python-pytest-bootstrap)
       ("python-setuptools-scm" ,python-setuptools-scm)))
@@ -765,14 +760,14 @@ supports coverage of subprocesses.")
 (define-public python-pytest-mock
  (package
    (name "python-pytest-mock")
-    (version "1.6.3")
+    (version "1.10.0")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-mock" version))
        (sha256
         (base32
-          "075v7b2wm5f839r1a30n21wfk5rfqp3d05q7zb9jlb2wmxki23cj"))))
+          "1h6lgpmsvs9s8j2s80v06f9f3iaw1n1rc51mbrxk1f12sw4q56nq"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-setuptools-scm" ,python-setuptools-scm)))
@@ -885,7 +880,8 @@ subprocess and see the output as well as any file modifications.")
       (uri (pypi-uri "testtools" version))
       (sha256
        (base32
-         "0n8519lk8aaa91vymz842831181wf7fss98hyllhygi3z1nfq9sq"))))
+         "0n8519lk8aaa91vymz842831181wf7fss98hyllhygi3z1nfq9sq"))
+       (patches (search-patches "python-testtools.patch"))))
    (build-system python-build-system)
    (arguments '(#:tests? #f))
    (propagated-inputs
@@ -1105,8 +1101,8 @@ python-fixtures package instead.")
       (modify-phases %standard-phases
         (replace 'check
           (lambda _
-             (zero? (system* "python" "-m" "testtools.run"
-                             "fixtures.test_suite")))))))
+             (invoke "python" "-m" "testtools.run"
+                     "fixtures.test_suite"))))))
    (propagated-inputs
     ;; Fixtures uses pbr at runtime to check versions, etc.
     `(("python-pbr" ,python-pbr)
@@ -1223,6 +1219,30 @@ testing frameworks.")
 (define-public python2-cov-core
 (package-with-python2 python-cov-core))

+(define-public python-codecov
+  (package
+    (name "python-codecov")
+    (version "2.0.15")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "codecov" version))
+        (sha256
+         (base32
+          "1217c0vqf7ii65635gvl27a5pfhv0r7zhrpdp9cx640hg73bgn4f"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-unittest2" ,python-unittest2)))
+    (propagated-inputs
+     `(("python-coverage" ,python-coverage)
+       ("python-requests" ,python-requests)))
+    (home-page "http://github.com/codecov/codecov-python")
+    (synopsis "Upload code coverage reports to @code{codecov.io}")
+    (description
+     "Codecov collects code coverage reports from code written in Python, Java,
+C/C++, R, and more, and uploads it to the @code{codecov.io} service.")
+    (license license:asl2.0)))
+
 (define-public python-testpath
  (package
    (name "python-testpath")
@@ -1322,20 +1342,20 @@ the last py.test invocation.")
 (define-public python-pytest-localserver
  (package
    (name "python-pytest-localserver")
-    (version "0.4.1")
+    (version "0.5.0")
    (source (origin
-             (method url-fetch)
-             (uri (pypi-uri "pytest-localserver" version))
-             (sha256
-              (base32
-               "08f06rvj31wqf0vgmd1waya87r7vy6x8ck48lxl3dxy83q5gcam7"))))
+              (method url-fetch)
+              (uri (pypi-uri "pytest-localserver" version))
+              (sha256
+               (base32
+                "1hpgpxrpfq5c731ndnsay2lc0y9nh2wy9fn1f83s3z8xkn82fm1s"))))
    (build-system python-build-system)
    (arguments
-      `(#:phases (modify-phases %standard-phases
+     '(#:phases
+       (modify-phases %standard-phases
         (replace 'check
           (lambda _
-             (zero? (system* "py.test" "--genscript=runtests.py"))
-             (zero? (system* "py.test")))))))
+             (invoke "py.test" "-v"))))))
    (native-inputs
     `(("python-pytest" ,python-pytest)
       ("python-requests" ,python-requests)
@@ -1397,16 +1417,17 @@ normally the case.")
 (define-public python-hypothesis
  (package
    (name "python-hypothesis")
-    (version "3.52.0")
+    (version "3.70.3")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "hypothesis" version))
              (sha256
               (base32
-                "0g54cypfi5qj6cgxfr7l1nb41r1cqhhngx4qxn4ga9h720rcsbr8"))))
+                "1rshs1japfmwgar98yrkq4hg4z2q76hlnq7w2n3lfbjnscn1jd9b"))))
    (build-system python-build-system)
    (native-inputs
-     `(("python-flake8" ,python-flake8)
+     `(;; FIXME: Change to python-flake8 in the next rebuild cycle.
+       ("python-flake8" ,python-flake8-3.5)
       ("python-pytest" ,python-pytest-bootstrap)))
    (propagated-inputs
     `(("python-attrs" ,python-attrs-bootstrap)
@@ -1503,7 +1524,7 @@ failures.")
             ;; It's easier to run tests after install.
             ;; Make installed package available for running the tests
             (add-installed-pythonpath inputs outputs)
-             (zero? (system* "py.test" "-vv")))))))
+             (invoke "py.test" "-vv"))))))
    (native-inputs
     `(("python-coverage" ,python-coverage)
       ("python-pytest" ,python-pytest)
@@ -1540,7 +1561,7 @@ failures.")
       (modify-phases %standard-phases
         (replace 'check
           (lambda _
-             (zero? (system* "./testrun")))))))
+             (invoke "./testrun"))))))
    (propagated-inputs
     `(("python2-coverage" ,python2-coverage)))
    (home-page "https://liw.fi/coverage-test-runner/")
@@ -1586,9 +1607,9 @@ statements in the module it tests.")
                              (string-append (getenv "PYTHONPATH") ":" work))
                      (copy-recursively "." work)
                      (with-directory-excursion "/tmp"
-                        (zero? (system* "python" "-m" "unittest" "discover"
-                                        "-s" (string-append work "/pylint/test")
-                                        "-p" "*test_*.py")))))))))
+                        (invoke "python" "-m" "unittest" "discover"
+                                "-s" (string-append work "/pylint/test")
+                                "-p" "*test_*.py"))))))))
    (home-page "https://github.com/PyCQA/pylint")
    (synopsis "Python source code analyzer which looks for coding standard
 errors")
@@ -1821,7 +1842,8 @@ tests written in a natural language style, backed up by Python code.")
           (lambda _
             (substitute* "setup.py"
               (("'wheel'") "")                ; We don't use it.
-               (("'ordereddict==1.1'") ""))))))) ; Python >= 2.7 has it built-in.
+               (("'ordereddict==1.1'") ""))    ; Python >= 2.7 has it built-in.
+             #t)))))
    (propagated-inputs
     `(("behave" ,behave)
       ("python-requests" ,python-requests)))
@@ -1902,14 +1924,14 @@ create data based on random numbers and yet remain repeatable.")
 (define-public python-nose-timer
  (package
    (name "python-nose-timer")
-    (version "0.7.2")
+    (version "0.7.3")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "nose-timer" version))
        (sha256
          (base32
-            "0ywg223p528014z5s0vzck74r4xyw3kvcp2casfnc85dkvir1zj7"))))
+            "0hfz5aqnhf493i9kyb6prm4zm8vx7wmfsyg3nvsnh24lzh2kwx44"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-nose" ,python-nose)
@@ -2067,3 +2089,42 @@ aspects of UnitTest++.  UnitTest++ is mostly standard C++ and makes minimal use
 of advanced library and language features, which means it should be easily
 portable to just about any platform.")
    (license license:expat)))
+
+(define-public libfaketime
+  (package
+    (name "libfaketime")
+    (version "0.9.7")
+    (home-page "https://github.com/wolfcw/libfaketime")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url home-page)
+                    (commit (string-append "v" version))))
+              (sha256
+               (base32
+                "1cin1pqwpsswcv7amiwijirvcg3x1zf2l00s1x84nxc5602fzr5c"))
+              (file-name (git-file-name name version))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (replace 'configure
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let ((out (assoc-ref outputs "out")))
+                        (setenv "CC" "gcc")
+                        (setenv "PREFIX" out)
+                        #t)))
+                  (add-before 'check 'pre-check
+                    (lambda _
+                      (substitute* "test/functests/test_exclude_mono.sh"
+                        (("/bin/bash") (which "bash")))
+                      #t)))
+       #:test-target "test"))
+    (native-inputs
+     `(("perl" ,perl)))                           ;for tests
+    (synopsis "Fake the system time for single applications")
+    (description
+     "The libfaketime library allows users to modify the system time that an
+application \"sees\".  It is meant to be loaded using the dynamic linker's
+@code{LD_PRELOAD} environment variable.  The @command{faketime} command
+provides a simple way to achieve this.")
+    (license license:gpl2)))
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
+;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -20,11 +21,98 @@
  #:use-module (guix packages)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix download)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages algebra)
+  #:use-module (gnu packages boost)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages documentation)
+  #:use-module (gnu packages gl)
  #:use-module (gnu packages gv)
  #:use-module (gnu packages maths)
+  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
+  #:use-module (gnu packages qt)
+  #:use-module (gnu packages xml)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python))

+(define-public avogadro
+  (package
+    (name "avogadro")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/cryos/avogadro/archive/"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "02v4h6hi1m7ilv0apdf74a8l1cm6dxnxyqp0rdaidrp3i9pf6lv4"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (patches
+               (search-patches "avogadro-eigen3-update.patch"
+                               "avogadro-python-eigen-lib.patch"
+                               "avogadro-boost148.patch"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:tests? #f
+       #:configure-flags
+       (list "-DENABLE_GLSL=ON"
+             (string-append "-DPYTHON_LIBRARIES="
+                            (assoc-ref %build-inputs "python")
+                            "/lib")
+             (string-append "-DPYTHON_INCLUDE_DIRS="
+                            (assoc-ref %build-inputs "python")
+                            "/include/python2.7"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-python-lib-path
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; This is necessary to install the Python module in the correct
+             ;; directory.
+             (substitute* "libavogadro/src/python/CMakeLists.txt"
+               (("^EXECUTE_PROCESS.*$") "")
+               (("^.*from sys import stdout.*$") "")
+               (("^.*OUTPUT_VARIABLE.*")
+                (string-append "set(PYTHON_LIB_PATH \""
+                               (assoc-ref outputs "out")
+                               "/lib/python2.7/site-packages\")")))
+             #t))
+         (add-after 'install 'wrap-program
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Make sure 'avogadro' runs with the correct PYTHONPATH.
+             (let* ((out (assoc-ref outputs "out")))
+               (setenv "PYTHONPATH"
+                       (string-append
+                        (assoc-ref outputs "out")
+                        "/lib/python2.7/site-packages:"
+                        (getenv "PYTHONPATH")))
+               (wrap-program (string-append out "/bin/avogadro")
+                 `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))
+             #t)))))
+    (native-inputs
+     `(("doxygen" ,doxygen)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("boost" ,boost)
+       ("eigen" ,eigen)
+       ("glew" ,glew)
+       ("openbabel" ,openbabel)
+       ("python" ,python-2)
+       ("python-numpy" ,python2-numpy)
+       ("python-pyqt" ,python2-pyqt-4)
+       ("python-sip" ,python2-sip)
+       ("qt" ,qt-4)
+       ("zlib" ,zlib)))
+    (home-page "https://avogadro.cc")
+    (synopsis "Advanced molecule editor")
+    (description
+     "Avogadro is an advanced molecule editor and visualizer designed for use
+in computational chemistry, molecular modeling, bioinformatics, materials
+science, and related areas.  It offers flexible high quality rendering and a
+powerful plugin architecture.")
+    (license license:gpl2+)))
+
 (define-public domainfinder
  (package
    (name "domainfinder")
@@ -54,6 +142,84 @@ single structure.  The software is currently not actively maintained and works
 only with Python 2 and NumPy < 1.9.")
    (license license:cecill-c)))

+(define-public inchi
+  (package
+    (name "inchi")
+    (version "1.05")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://www.inchi-trust.org/download/"
+                                  (string-join (string-split version #\.) "")
+                                  "/INCHI-1-SRC.zip"))
+              (sha256
+               (base32
+                "081pcjx1z5jm23fs1pl2r3bccia0ww8wfkzcjpb7byhn7b513hsa"))
+              (file-name (string-append name "-" version ".zip"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f ; no check target
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; no configure script
+         (add-before 'build 'chdir-to-build-directory
+           (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
+         (add-after 'build 'build-library
+           (lambda _
+             (chdir "../../../INCHI_API/libinchi/gcc")
+             (invoke "make")))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (doc (string-append out "/share/doc/inchi"))
+                    (include-dir (string-append out "/include/inchi"))
+                    (lib (string-append out "/lib/inchi"))
+                    (inchi-doc (assoc-ref inputs "inchi-doc"))
+                    (unzip (string-append (assoc-ref inputs "unzip")
+                                          "/bin/unzip")))
+               (chdir "../../..")
+               ;; Install binary.
+               (with-directory-excursion "INCHI_EXE/bin/Linux"
+                 (rename-file "inchi-1" "inchi")
+                 (install-file "inchi" bin))
+               ;; Install libraries.
+               (with-directory-excursion "INCHI_API/bin/Linux"
+                 (for-each (lambda (file)
+                             (install-file file lib))
+                           (find-files "." "libinchi\\.so\\.1\\.*")))
+               ;; Install header files.
+               (with-directory-excursion "INCHI_BASE/src"
+                 (for-each (lambda (file)
+                             (install-file file include-dir))
+                           (find-files "." "\\.h$")))
+               ;; Install documentation.
+               (mkdir-p doc)
+               (invoke unzip "-j" "-d" doc inchi-doc)
+               #t))))))
+    (native-inputs
+     `(("unzip" ,unzip)
+       ("inchi-doc"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append "http://www.inchi-trust.org/download/"
+                                  (string-join (string-split version #\.) "")
+                                  "/INCHI-1-DOC.zip"))
+           (sha256
+            (base32
+             "1id1qb2y4lwsiw91qr2yqpn6kxbwjwhjk0hb2rwk4fxhdqib6da6"))
+           (file-name (string-append name "-" version ".zip"))))))
+    (home-page "https://www.inchi-trust.org")
+    (synopsis "Utility for manipulating machine-readable chemical structures")
+    (description
+     "The @dfn{InChI} (IUPAC International Chemical Identifier) algorithm turns
+chemical structures into machine-readable strings of information.  InChIs are
+unique to the compound they describe and can encode absolute stereochemistry
+making chemicals and chemistry machine-readable and discoverable.  A simple
+analogy is that InChI is the bar-code for chemistry and chemical structures.")
+    (license (license:non-copyleft
+              "file://LICENCE"
+              "See LICENCE in the distribution."))))
+
 (define with-numpy-1.8
  (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))

@@ -117,3 +283,42 @@ neutron scattering spectra, but also computes other quantities.  The software
 is currently not actively maintained and works only with Python 2 and
 NumPy < 1.9.")
    (license license:cecill)))
+
+(define-public openbabel
+  (package
+    (name "openbabel")
+    (version "2.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/" name "/" name "/"
+                                  version "/" name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))
+              (patches
+               (search-patches "openbabel-fix-crash-on-nwchem-output.patch"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list "-DOPENBABEL_USE_SYSTEM_INCHI=ON"
+             (string-append "-DINCHI_LIBRARY="
+                            (assoc-ref %build-inputs "inchi")
+                            "/lib/inchi/libinchi.so.1")
+             (string-append "-DINCHI_INCLUDE_DIR="
+                            (assoc-ref %build-inputs "inchi") "/include/inchi"))
+       #:test-target "test"))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("eigen" ,eigen)
+       ("inchi" ,inchi)
+       ("libxml2" ,libxml2)
+       ("zlib" ,zlib)))
+    (home-page "http://openbabel.org/wiki/Main_Page")
+    (synopsis "Chemistry data manipulation toolbox")
+    (description
+     "Open Babel is a chemical toolbox designed to speak the many languages of
+chemical data.  It's a collaborative project allowing anyone to search, convert,
+analyze, or store data from molecular modeling, chemistry, solid-state
+materials, biochemistry, or related areas.")
+    (license license:gpl2)))
@@ -85,6 +85,7 @@
       ("xorg-rgb" ,xorg-rgb)
       ("nanopass" ,nanopass)
       ("zlib" ,zlib)
+       ("zlib:static" ,zlib "static")
       ("stex" ,stex)))
    (native-inputs
     `(("texlive" ,texlive)
@@ -128,6 +129,7 @@
                   (nanopass (assoc-ref inputs "nanopass"))
                   (stex (assoc-ref inputs "stex"))
                   (zlib (assoc-ref inputs "zlib"))
+                   (zlib-static (assoc-ref inputs "zlib:static"))
                   (unpack (assoc-ref %standard-phases 'unpack))
                   (patch-source-shebangs
                    (assoc-ref %standard-phases 'patch-source-shebangs)))
@@ -148,7 +150,7 @@
                 (("\\$\\{Kernel\\}: \\$\\{kernelobj\\} \\.\\./zlib/libz\\.a")
                  "${Kernel}: ${kernelobj}")
                 (("ld ([-a-zA-Z0-9_${} ]+) \\.\\./zlib/libz\\.a" all args)
-                  (string-append "ld " args " " zlib "/lib/libz.a"))
+                  (string-append "ld " args " " zlib-static "/lib/libz.a"))
                 (("\\(cd \\.\\./zlib; ([-a-zA-Z0-9=./ ]+))")
                  (which "true")))
               (substitute* (find-files "mats" "Mf-.*")
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016, 2017 Mathieu Lirzin <mthl@gnu.org>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -31,6 +32,7 @@
  #:use-module (gnu packages compression)
  #:use-module (gnu packages databases)
  #:use-module (gnu packages guile)
+  #:use-module (gnu packages gnupg)
  #:use-module (gnu packages mail)
  #:use-module (gnu packages package-management)
  #:use-module (gnu packages perl)
@@ -184,8 +186,8 @@ their dependencies.")
      (license l:gpl3+))))

 (define-public cuirass
-  (let ((commit "238f856e48ee333ed3e19fa32ce5e1742c650c67")
-        (revision "16"))
+  (let ((commit "0b40dca734468e8b12b3ff58e3e779679f17d38e")
+        (revision "21"))
    (package
      (name "cuirass")
      (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -197,7 +199,7 @@ their dependencies.")
                (file-name (string-append name "-" version))
                (sha256
                 (base32
-                  "15iwdgy561gnsr224rs5z8qn7nrsh1wdlsxr8gwxyk0v4zp6yvbf"))))
+                  "1kdxs8dzdyldfs4wsz5hb64hprkbrnq5ljdll631f3bj8pbvvvc1"))))
      (build-system gnu-build-system)
      (arguments
       '(#:modules ((guix build utils)
@@ -222,39 +224,42 @@ their dependencies.")
             (lambda* (#:key inputs outputs #:allow-other-keys)
               ;; Wrap the 'cuirass' command to refer to the right modules.
               (let* ((out    (assoc-ref outputs "out"))
+                      (gcrypt (assoc-ref inputs "guile-gcrypt"))
                      (json   (assoc-ref inputs "guile-json"))
                      (sqlite (assoc-ref inputs "guile-sqlite3"))
                      (git    (assoc-ref inputs "guile-git"))
                      (bytes  (assoc-ref inputs "guile-bytestructures"))
                      (fibers (assoc-ref inputs "guile-fibers"))
                      (guix   (assoc-ref inputs "guix"))
+                      (deps   (list gcrypt json sqlite git bytes fibers guix))
                      (guile  (assoc-ref %build-inputs "guile"))
                      (effective (read-line
                                  (open-pipe* OPEN_READ
                                              (string-append guile "/bin/guile")
                                              "-c" "(display (effective-version))")))
-                      (mods   (string-append json "/share/guile/site/"
-                                             effective ":"
-                                             git "/share/guile/site/"
-                                             effective ":"
-                                             bytes "/share/guile/site/"
-                                             effective ":"
-                                             sqlite "/share/guile/site/"
-                                             effective ":"
-                                             fibers "/share/guile/site/"
-                                             effective ":"
-                                             guix "/share/guile/site/"
-                                             effective)))
+                      (mods   (string-drop-right  ;drop trailing colon
+                               (string-join deps
+                                            (string-append "/share/guile/site/"
+                                                           effective ":")
+                                            'suffix)
+                               1))
+                      (objs   (string-drop-right
+                               (string-join deps
+                                            (string-append "/lib/guile/" effective
+                                                           "/site-ccache:")
+                                            'suffix)
+                               1)))
                 ;; Make sure 'cuirass' can find the 'evaluate' command, as
                 ;; well as the relevant Guile modules.
                 (wrap-program (string-append out "/bin/cuirass")
                   `("PATH" ":" prefix (,(string-append out "/bin")))
                   `("GUILE_LOAD_PATH" ":" prefix (,mods))
-                   `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,mods)))
+                   `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,objs)))
                 #t))))))
      (inputs
       `(("guile" ,guile-2.2)
         ("guile-fibers" ,guile-fibers)
+         ("guile-gcrypt" ,guile-gcrypt)
         ("guile-json" ,guile-json)
         ("guile-sqlite3" ,guile-sqlite3)
         ("guile-git" ,guile-git)
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -50,13 +51,10 @@
    (arguments
     `(#:phases
       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
+         (add-before 'bootstrap 'skip-premature-configure
           (lambda _
-             (mkdir-p "m4")
-             (zero?
-              (and (system* "glib-gettextize" "--force" "--copy")
-                   (system* "intltoolize" "--force" "--copy" "--automake")
-                   (system* "autoreconf" "--verbose" "--force" "--install"))))))))
+             (setenv "NOCONFIGURE" "set")
+             #t)))))
    ;; TODO: package 'libgsystem'.
    (inputs
     `(("accountsservice" ,accountsservice)
@@ -0,0 +1,293 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
+;;;
+;;; 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 clojure)
+  #:use-module (gnu packages)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system ant)
+  #:use-module (guix build-system clojure)
+  #:use-module (ice-9 match))
+
+(define-public clojure
+  (let* ((lib (lambda (prefix version hash)
+                (origin (method url-fetch)
+                        (uri (string-append "https://github.com/clojure/"
+                                            prefix version ".tar.gz"))
+                        (sha256 (base32 hash)))))
+         ;; The libraries below are needed to run the tests.
+         (libraries
+          `(("core-specs-alpha-src"
+             ,(lib "core.specs.alpha/archive/core.specs.alpha-"
+                   "0.1.24"
+                   "0v2a0svf1ar2y42ajxwsjr7zmm5j7pp2zwrd2jh3k7xzd1p9x1fv"))
+            ("data-generators-src"
+             ,(lib "data.generators/archive/data.generators-"
+                   "0.1.2"
+                   "0kki093jp4ckwxzfnw8ylflrfqs8b1i1wi9iapmwcsy328dmgzp1"))
+            ("spec-alpha-src"
+             ,(lib "spec.alpha/archive/spec.alpha-"
+                   "0.1.143"
+                   "00alf0347licdn773w2jarpllyrbl52qz4d8mw61anjksacxylzz"))
+            ("test-check-src"
+             ,(lib "test.check/archive/test.check-"
+                   "0.9.0"
+                   "0p0mnyhr442bzkz0s4k5ra3i6l5lc7kp6ajaqkkyh4c2k5yck1md"))
+            ("test-generative-src"
+             ,(lib "test.generative/archive/test.generative-"
+                   "0.5.2"
+                   "1pjafy1i7yblc7ixmcpfq1lfbyf3jaljvkgrajn70sws9xs7a9f8"))
+            ("tools-namespace-src"
+             ,(lib "tools.namespace/archive/tools.namespace-"
+                   "0.2.11"
+                   "10baak8v0hnwz2hr33bavshm7y49mmn9zsyyms1dwjz45p5ymhy0"))))
+         (library-names (match libraries
+                          (((library-name _) ...)
+                           library-name))))
+
+    (package
+      (name "clojure")
+      (version "1.9.0")
+      (source
+       (origin
+         (method url-fetch)
+         (uri
+          (string-append "https://github.com/clojure/clojure/archive/clojure-"
+                         version ".tar.gz"))
+         (sha256
+          (base32 "0xjbzcw45z32vsn9pifp7ndysjzqswp5ig0jkjpivigh2ckkdzha"))))
+      (build-system ant-build-system)
+      (arguments
+       `(#:imported-modules ((guix build clojure-utils)
+                             (guix build guile-build-system)
+                             ,@%ant-build-system-modules)
+         #:modules ((guix build ant-build-system)
+                    (guix build clojure-utils)
+                    (guix build java-utils)
+                    (guix build utils)
+                    (srfi srfi-26))
+         #:test-target "test"
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'unpack-library-sources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (define (extract-library name)
+                 (mkdir-p name)
+                 (with-directory-excursion name
+                   (invoke "tar"
+                           "--extract"
+                           "--verbose"
+                           "--file" (assoc-ref inputs name)
+                           "--strip-components=1"))
+                 (copy-recursively (string-append name "/src/main/clojure/")
+                                   "src/clj/"))
+               (for-each extract-library ',library-names)
+               #t))
+           (add-after 'unpack-library-sources 'fix-manifest-classpath
+             (lambda _
+               (substitute* "build.xml"
+                 (("<attribute name=\"Class-Path\" value=\".\"/>") ""))
+               #t))
+           (add-after 'build 'build-javadoc ant-build-javadoc)
+           (replace 'install (install-jars "./"))
+           (add-after 'install-license-files 'install-doc
+             (cut install-doc #:doc-dirs '("doc/clojure/") <...>))
+           (add-after 'install-doc 'install-javadoc
+             (install-javadoc "target/javadoc/")))))
+      (native-inputs libraries)
+      (home-page "https://clojure.org/")
+      (synopsis "Lisp dialect running on the JVM")
+      (description "Clojure is a dynamic, general-purpose programming language,
+combining the approachability and interactive development of a scripting
+language with an efficient and robust infrastructure for multithreaded
+programming.  Clojure is a compiled language, yet remains completely dynamic
+– every feature supported by Clojure is supported at runtime.  Clojure
+provides easy access to the Java frameworks, with optional type hints and type
+inference, to ensure that calls to Java can avoid reflection.
+
+Clojure is a dialect of Lisp, and shares with Lisp the code-as-data philosophy
+and a powerful macro system.  Clojure is predominantly a functional programming
+language, and features a rich set of immutable, persistent data structures.
+When mutable state is needed, Clojure offers a software transactional memory
+system and reactive Agent system that ensure clean, correct, multithreaded
+designs.")
+      ;; Clojure is licensed under EPL1.0
+      ;; ASM bytecode manipulation library is licensed under BSD-3
+      ;; Guava Murmur3 hash implementation is licensed under APL2.0
+      ;; src/clj/repl.clj is licensed under CPL1.0
+
+      ;; See readme.html or readme.txt for details.
+      (license (list license:epl1.0
+                     license:bsd-3
+                     license:asl2.0
+                     license:cpl1.0)))))
+
+(define-public clojure-algo-generic
+  (package
+    (name "clojure-algo-generic")
+    (version "0.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "https://github.com/clojure/algo.generic/archive"
+                       "/algo.generic-" version ".tar.gz"))
+       (sha256
+        (base32 "12w9681i545gp1af4576z1qbixwps1j13c16fmcc7zsb0bd1zr7w"))))
+    (build-system clojure-build-system)
+    (arguments
+     '(#:source-dirs '("src/main/clojure/")
+       #:test-dirs '("src/test/clojure/")
+       #:doc-dirs '()))
+    (synopsis "Generic versions of common functions")
+    (description
+     "Generic versions of commonly used functions, implemented as multimethods
+that can be implemented for any data type.")
+    (home-page "https://github.com/clojure/algo.generic")
+    (license license:epl1.0)))
+
+(define-public clojure-algo-monads
+  (package
+    (name "clojure-algo-monads")
+    (version "0.1.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "https://github.com/clojure/algo.monads/archive"
+                       "/algo.monads-" version ".tar.gz"))
+       (sha256
+        (base32 "14gbvfgmrda990h45yn7zag83vp1kdkz4f4yzmyvkr0sjihlgdmq"))))
+    (build-system clojure-build-system)
+    (arguments
+     '(#:source-dirs '("src/main/clojure/")
+       #:test-dirs '("src/test/clojure/")
+       #:doc-dirs '()))
+    (native-inputs
+     `(("clojure-tools-macro" ,clojure-tools-macro)))
+    (synopsis
+     "Monad Macros and Definitions")
+    (description
+     "This library contains the most commonly used monads as well as macros for
+defining and using monads and useful monadic functions.")
+    (home-page "https://github.com/clojure/algo.monads")
+    (license license:epl1.0)))
+
+(define-public clojure-core-match
+  (let ((commit "1837ffbd4a150e8f3953b2d9ed5cf4a4ad3720a7")
+        (revision "1")) ; this is the 1st commit buildable with clojure 1.9
+    (package
+      (name "clojure-core-match")
+      (version (git-version "0.3.0-alpha5" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/clojure/core.match.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "04bdlp5dgkrqzrz0lw3mfwmygj2218qnm1cz3dkb9wy4m0238s4d"))))
+      (build-system clojure-build-system)
+      (arguments
+       '(#:source-dirs '("src/main/clojure")
+         #:test-dirs '("src/test/clojure")
+         #:doc-dirs '()))
+      (synopsis "Optimized pattern matching for Clojure")
+      (description
+       "An optimized pattern matching library for Clojure.
+It supports Clojure 1.5.1 and later as well as ClojureScript.")
+      (home-page "https://github.com/clojure/core.match")
+      (license license:epl1.0))))
+
+(define-public clojure-instaparse
+  (let ((commit "dcfffad5b065e750f0f5835f017cdd8188b8ca2e")
+        (version "1.4.9")) ; upstream forget to tag this release
+    (package
+      (name "clojure-instaparse")
+      (version version)
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/Engelberg/instaparse.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "002mrgin4z3dqy88r1lak7smd0m7x8d22vmliw0m6w6mh5pa17lk"))))
+      (build-system clojure-build-system)
+      (arguments
+       '(#:doc-dirs '("docs/")))
+      (synopsis "No grammar left behind")
+      (description
+       "Instaparse aims to be the simplest way to build parsers in Clojure.
+
+@itemize
+@item Turns @emph{standard EBNF or ABNF notation} for context-free grammars
+into an executable parser that takes a string as an input and produces a parse
+tree for that string.
+
+@item @dfn{No Grammar Left Behind}: Works for @emph{any} context-free grammar,
+including @emph{left-recursive}, @emph{right-recursive}, and @emph{ambiguous}
+grammars.
+
+@item Extends the power of context-free grammars with PEG-like syntax for
+lookahead and negative lookahead.
+
+@item Supports both of Clojure's most popular tree formats (hiccup and enlive)
+as output targets
+
+@item Detailed reporting of parse errors.
+
+@item Optionally produces lazy sequence of all parses (especially useful for
+diagnosing and debugging ambiguous grammars).
+
+@item ``Total parsing'' mode where leftover string is embedded in the parse
+tree.
+
+@item Optional combinator library for building grammars programmatically.
+
+@item Performant.
+@end itemize")
+      (home-page "https://github.com/Engelberg/instaparse")
+      (license license:epl1.0))))
+
+(define-public clojure-tools-macro
+  (package
+    (name "clojure-tools-macro")
+    (version "0.1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "https://github.com/clojure/tools.macro/archive"
+                       "/tools.macro-" version ".tar.gz"))
+       (sha256
+        (base32 "0fs64a0g63xx6g7sj6vrsqknhl90s0isf6k053nw8vv5prfzc7v6"))))
+    (build-system clojure-build-system)
+    (arguments
+     '(#:source-dirs '("src/main/clojure/")
+       #:test-dirs '("src/test/clojure/")
+       #:doc-dirs '()))
+    (synopsis "Utilities for macro writers")
+    (description "Tools for writing macros.")
+    (home-page "https://github.com/clojure/tools.macro")
+    (license license:epl1.0)))
@@ -31,7 +31,7 @@
 (define-public keepalived
  (package
    (name "keepalived")
-    (version "2.0.4")
+    (version "2.0.5")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -39,7 +39,7 @@
                    version ".tar.gz"))
              (sha256
               (base32
-                "0qf46bfxv4w7qx7d73qq26pp72cvbyfjvna3hxn208vynvapalh0"))))
+                "021a7c1lq4aqx7dbwhlm5km6w039hapfzp5hf6wb5bfq79s25g38"))))
    (build-system gnu-build-system)
    (arguments
     '(#:phases
@@ -7,6 +7,7 @@
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -43,7 +44,7 @@
 (define-public cmake
  (package
    (name "cmake")
-    (version "3.11.0")
+    (version "3.12.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://www.cmake.org/files/v"
@@ -51,7 +52,7 @@
                                  "/cmake-" version ".tar.gz"))
              (sha256
               (base32
-                "0sv5k9q6braa8hhw0y3w19avqn0xn5czv5jf5fz5blnlf7ivw4y3"))
+                "19410mxgcyvk5q42phaclb1hz6rl08z4yj8iriq706p5k5bli5qg"))
              (modules '((guix build utils)))
              (snippet
               '(begin
@@ -86,6 +87,13 @@
           " --exclude-regex ^\\(" (string-join skipped-tests "\\|") "\\)$")))
       #:phases
       (modify-phases %standard-phases
+         (add-after 'unpack 'split-package
+           ;; Remove files that have been packaged in other package recipes.
+           (lambda _
+             (delete-file "Auxiliary/cmake-mode.el")
+             (substitute* "Auxiliary/CMakeLists.txt"
+               ((".*cmake-mode.el.*") ""))
+             #t))
         (add-before 'configure 'patch-bin-sh
           (lambda _
             ;; Replace "/bin/sh" by the right path in... a lot of
@@ -7,7 +7,7 @@
 ;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
@@ -211,7 +211,7 @@ COCOMO model or user-provided parameters.")
 (define-public cloc
  (package
    (name "cloc")
-    (version "1.76")
+    (version "1.80")
    (source
     (origin
       (method url-fetch)
@@ -220,7 +220,7 @@ COCOMO model or user-provided parameters.")
             "/cloc-" version ".tar.gz"))
       (sha256
        (base32
-         "05srlvzwisr7y7ymvzb5yfdsrspja27ysqdmkwhiiivy84mq2gnl"))))
+         "0rqxnaskg5b736asyzfda1113zvpkajyqjf49vl9wgzf1r9m6bq8"))))
    (build-system gnu-build-system)
    (inputs
     `(("coreutils" ,coreutils)
@@ -231,8 +231,8 @@ COCOMO model or user-provided parameters.")
       ("perl-regexp-common" ,perl-regexp-common)))
    (arguments
     `(#:phases (modify-phases %standard-phases
-                  (delete 'configure)
-                  (delete 'build)
+                  (delete 'configure)   ; nothing to configure
+                  (delete 'build)       ; nothing to build
                  (replace 'install
                    (lambda* (#:key inputs outputs #:allow-other-keys)
                      (let* ((out (assoc-ref outputs "out")))
@@ -266,15 +266,15 @@ cloc can handle a greater variety of programming languages.")
 (define-public the-silver-searcher
  (package
    (name "the-silver-searcher")
-    (version "2.1.0")
+    (version "2.2.0")
    (source (origin
              (method url-fetch)
              (uri (string-append
-                    "http://geoff.greer.fm/ag/releases/the_silver_searcher-"
+                    "https://geoff.greer.fm/ag/releases/the_silver_searcher-"
                    version ".tar.gz"))
              (sha256
               (base32
-                "1m0mih1x4jpswc8ganhqh0gmwbmd2hzmz7402mxfh19s3kcjnrfl"))))
+                "0w1icjqd8hd45rn1y6nbfznk1a6ip54whwbfbhxp7ws2hn3ilqnr"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("pkg-config" ,pkg-config)))
@@ -282,7 +282,7 @@ cloc can handle a greater variety of programming languages.")
     `(("pcre" ,pcre)
       ("xz" ,xz)
       ("zlib" ,zlib)))
-    (home-page "http://geoff.greer.fm/ag/")
+    (home-page "https://geoff.greer.fm/ag/")
    (synopsis "Fast code searching tool")
    (description
     "The Silver Searcher (@command{ag}) is a tool for quickly searching large
@@ -403,13 +403,13 @@ functionality such as HTML output.")
  (package
    (name "rtags")
    (version "2.18")
-    (home-page "https://github.com/Andersbakken/rtags")
    (source
     (origin
-       (method url-fetch)
-       (uri
-        (string-append home-page "/archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Andersbakken/rtags.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
       (patches (search-patches "rtags-separate-rct.patch"))
       (modules '((guix build utils)))
       (snippet
@@ -424,7 +424,7 @@ functionality such as HTML output.")
             #t)))
       (sha256
        (base32
-         "0scjbp1z201q8njvrxqz7lk2m9b6k2rxd5q1shrng6532r7ndif2"))))
+         "0raqjbkl1ykga4ahgl9xw49cgh3cyqcf42z36z7d6fz1fw192kg0"))))
    (build-system cmake-build-system)
    (arguments
     '(#:build-type "RelWithDebInfo"
@@ -442,6 +442,7 @@ functionality such as HTML output.")
       ("lua" ,lua)
       ("rct" ,rct)
       ("selene" ,selene)))
+    (home-page "https://github.com/Andersbakken/rtags")
    (synopsis "Indexer for the C language family with Emacs integration")
    (description
     "RTags is a client/server application that indexes C/C++ code and keeps a
@@ -539,18 +540,20 @@ independent targets.")
 (define-public uncrustify
  (package
    (name "uncrustify")
-    (version "0.67")
+    (version "0.68.1")
    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/uncrustify/uncrustify/archive/"
-                    "uncrustify-" version ".zip"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/uncrustify/uncrustify/")
+                    (commit (string-append name "-" version))))
+              (file-name (git-file-name name version))
              (sha256
               (base32
-                "0n13kq0nsm35fxhdp0f275n4x0w88hdv3bdjy0hgvv42x0dx5zyp"))))
+                "0gf6vjcfy8pl7idvwsd500ffj9hri62q0n79kpb6cnfprrqpbgf4"))))
    (build-system cmake-build-system)
    (native-inputs
-     `(("unzip" ,unzip)))
+     `(("unzip" ,unzip)
+       ("python" ,python-wrapper)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
@@ -651,6 +654,19 @@ extensions over the standard utility.")
   (license license:gpl3+)
   (home-page "https://www.gnu.org/software/indent/")))

+(define-public indent-2.2.12
+  (package
+    (inherit indent)
+    (version "2.2.12")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnu/indent/indent-" version
+                                  ".tar.gz"))
+              (sha256
+               (base32
+                "12xvcd16cwilzglv9h7sgh4h1qqjd1h8s48ji2dla58m4706hzg7"))))
+    (native-inputs `(("texinfo" ,texinfo)))))
+
 (define-public amalgamate
  (let* ((commit "c91f07eea1133aa184f652b8f1398eaf03586208")
         (revision "0")
@@ -186,12 +186,25 @@
                    ,cf)))))
     (inputs %boot0-inputs))))

+;; Use a "fixed" package source for this early libstdc++ variant so we can
+;; update GCC 4.9 without triggering a full rebuild.
+(define gcc-for-libstdc++
+  (package
+    (inherit gcc-4.9)
+    (source (origin
+              (inherit (package-source gcc-4.9))
+              (patches (search-patches "gcc-4.9-libsanitizer-fix.patch"
+                                       "gcc-arm-bug-71399.patch"
+                                       "gcc-asan-missing-include.patch"
+                                       "gcc-libvtv-runpath.patch"
+                                       "gcc-fix-texi2pod.patch"))))))
+
 (define libstdc++-boot0
  ;; GCC's libcc1 is always built as a shared library (the top-level
  ;; 'Makefile.def' forcefully adds --enable-shared) and thus needs to refer
  ;; to libstdc++.so.  We cannot build libstdc++-5.3 because it relies on
  ;; C++14 features missing in some of our bootstrap compilers.
-  (let ((lib (package-with-bootstrap-guile (make-libstdc++ gcc-4.9))))
+  (let ((lib (package-with-bootstrap-guile (make-libstdc++ gcc-for-libstdc++))))
    (package
      (inherit lib)
      (name "libstdc++-boot0")
@@ -7,7 +7,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2016 Danny Milosavljevic <dannym@scratchpost.org>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -22,7 +22,7 @@
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -85,6 +85,7 @@
       (base32
        "18dighcs333gsvajvvgqp8l4cx7h1x7yx9gd5xacnk80spyykrf3"))))
    (build-system gnu-build-system)
+    (outputs '("out" "static"))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
@@ -99,7 +100,15 @@
                     `((setenv "CHOST" ,(%current-target-system)))
                     '())
               (invoke "./configure"
-                       (string-append "--prefix=" out))))))))
+                       (string-append "--prefix=" out)))))
+         (add-after 'install 'move-static-library
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (static (assoc-ref outputs "static")))
+               (with-directory-excursion (string-append out "/lib")
+                 (install-file "libz.a" (string-append static "/lib"))
+                 (delete-file "libz.a")
+                 #t)))))))
    (home-page "https://zlib.net/")
    (synopsis "Compression library")
    (description
@@ -124,10 +133,7 @@ in compression.")
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'enter-source
-           (lambda _ (chdir "contrib/minizip") #t))
-         (add-after 'enter-source 'autoreconf
-           (lambda _
-             (invoke "autoreconf" "-vif"))))))
+           (lambda _ (chdir "contrib/minizip") #t)))))
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
@@ -179,12 +185,7 @@ utility.  Instead of being written in Java, FastJar is written in C.")
              "02cihzl77ia0dcz7z2cga2412vyhhs5pa2355q4wpwbyga2lrwjh"))
            (patches (search-patches "libtar-CVE-2013-4420.patch"))))
   (build-system gnu-build-system)
-   (arguments
-    `(#:tests? #f ;no "check" target
-      #:phases
-      (modify-phases %standard-phases
-        (add-after 'unpack 'autoconf
-          (lambda _ (invoke "sh" "autoreconf" "-vfi"))))))
+   (arguments `(#:tests? #f)) ; no "check" target
   (native-inputs
    `(("autoconf" ,autoconf)
      ("automake" ,automake)
@@ -216,6 +217,21 @@ adding and extracting files to/from a tar archive.")
    '(#:tests? #f
      #:phases
      (modify-phases %standard-phases
+        (add-after 'unpack 'patch-for-glibc-2.28
+          (lambda _
+            ;; Adjust the bundled gnulib to work with glibc 2.28.  See e.g.
+            ;; "m4-gnulib-libio.patch".  This is a phase rather than patch
+            ;; or snippet to work around <https://bugs.gnu.org/32347>.
+            (substitute* (find-files "lib" "\\.c$")
+              (("#if defined _IO_ftrylockfile")
+               "#if defined _IO_EOF_SEEN"))
+            (substitute* "lib/stdio-impl.h"
+              (("^/\\* BSD stdio derived implementations")
+               (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n"
+                              "# define _IO_IN_BACKUP 0x100\n"
+                              "#endif\n\n"
+                              "/* BSD stdio derived implementations")))
+            #t))
        (add-after 'unpack 'use-absolute-name-of-gzip
          (lambda* (#:key outputs #:allow-other-keys)
            (substitute* "gunzip.in"
@@ -237,8 +253,10 @@ file; as a result, it is often used in conjunction with \"tar\", resulting in
    (version "1.0.6")
    (source (origin
              (method url-fetch)
-              (uri (string-append "http://www.bzip.org/" version "/bzip2-"
-                                  version ".tar.gz"))
+              ;; XXX The bzip.org domain was allowed to expire.
+              (uri (string-append "https://web.archive.org/web/20180624184806/"
+                                  "http://www.bzip.org/"
+                                  version "/bzip2-" version ".tar.gz"))
              (sha256
               (base32
                "1kfrc7f0ja9fdn6j1y6yir6li818npy6217hvr3wzmnmzhs8z152"))))
@@ -246,6 +264,7 @@ file; as a result, it is often used in conjunction with \"tar\", resulting in
    (arguments
     `(#:modules ((guix build gnu-build-system)
                  (guix build utils)
+                  (ice-9 ftw)
                  (srfi srfi-1))
       #:phases
       (modify-phases %standard-phases
@@ -274,25 +293,32 @@ file; as a result, it is often used in conjunction with \"tar\", resulting in
             ;; it create all the (un)versioned symlinks, so we handle it here.
             (let* ((out    (assoc-ref outputs "out"))
                    (libdir (string-append out "/lib"))
-                    ;; Find the actual library (e.g. "libbz2.so.1.0.6").
-                    (lib (string-drop
-                          (car (find-files
-                                "."
-                                (lambda (file stat)
-                                  (and (string-prefix? "./libbz2.so" file)
-                                       (eq? 'regular (stat:type stat))))))
-                          2))
-                    (soversion (string-drop lib (string-length "libbz2.so."))))
+                    (soname "libbz2.so")
+                    ;; Locate the built library (e.g. "libbz2.so.1.0.6").
+                    (lib (car (scandir "."
+                                       (lambda (file)
+                                         (and (string-prefix? soname file)
+                                              (eq? 'regular
+                                                   (stat:type (lstat file))))))))
+                    (soversion (string-drop lib (+ 1 (string-length soname)))))
               (install-file lib libdir)
               (with-directory-excursion libdir
                 ;; Create symlinks libbz2.so.1 -> libbz2.so.1.0, etc.
-                 (let loop ((base "libbz2.so")
+                 (let loop ((base soname)
                            (numbers (string-split soversion #\.)))
                   (unless (null? numbers)
                     (let ((so-file (string-append base "." (car numbers))))
                       (symlink so-file base)
                       (loop so-file (cdr numbers))))))
               #t)))
+         (add-after 'install-shared-lib 'move-static-lib
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (static (assoc-ref outputs "static")))
+               (with-directory-excursion (string-append out "/lib")
+                 (install-file "libbz2.a" (string-append static "/lib"))
+                 (delete-file "libbz2.a")
+                 #t))))
         (add-after 'install-shared-lib 'patch-scripts
           (lambda* (#:key outputs inputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out")))
@@ -307,6 +333,7 @@ file; as a result, it is often used in conjunction with \"tar\", resulting in
       ,@(if (%current-target-system)
             '(#:tests? #f)
             '())))
+    (outputs '("out" "static"))
    (synopsis "High-quality data compression program")
    (description
     "bzip2 is a freely available, patent free (see below), high-quality data
@@ -316,7 +343,7 @@ being around twice as fast at compression and six times faster at
 decompression.")
    (license (license:non-copyleft "file://LICENSE"
                                   "See LICENSE in the distribution."))
-    (home-page "http://www.bzip.org/")))
+    (home-page "https://web.archive.org/web/20180801004107/http://www.bzip.org/")))

 (define-public lbzip2
  (package
@@ -328,7 +355,20 @@ decompression.")
                                  version ".tar.gz"))
              (sha256
               (base32
-                "1sahaqc5bw4i0iyri05syfza4ncf5cml89an033fspn97klmxis6"))))
+                "1sahaqc5bw4i0iyri05syfza4ncf5cml89an033fspn97klmxis6"))
+             (modules '((guix build utils)))
+             (snippet
+              '(begin
+                 (substitute* (find-files "lib" "\\.c$")
+                   (("#if defined _IO_ftrylockfile")
+                    "#if defined _IO_EOF_SEEN"))
+                 (substitute* "lib/stdio-impl.h"
+                   (("^/\\* BSD stdio derived implementations")
+                    (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n"
+                                   "# define _IO_IN_BACKUP 0x100\n"
+                                   "#endif\n\n"
+                                   "/* BSD stdio derived implementations")))
+                 #t))))
    (build-system gnu-build-system)
    (synopsis "Parallel bzip2 compression utility")
    (description
@@ -374,7 +414,7 @@ compressed with pbzip2 can be decompressed with bzip2).")
 (define-public xz
  (package
   (name "xz")
-   (version "5.2.3")
+   (version "5.2.4")
   (source (origin
            (method url-fetch)
            (uri (list (string-append "http://tukaani.org/xz/xz-" version
@@ -383,7 +423,7 @@ compressed with pbzip2 can be decompressed with bzip2).")
                                      version ".tar.gz")))
            (sha256
             (base32
-              "1jr8pxnz55ifc8cvp3ivgl79ph9iik5aypsc9cma228aglsqp4ki"))))
+              "0ibi2zsfaz6l756spjwc5rayf4ckgc9hwmy8qinppcyk4svz64mm"))))
   (build-system gnu-build-system)
   (synopsis "General-purpose data compression")
   (description
@@ -428,14 +468,14 @@ format are designed to be portable across platforms.")
 (define-public python-lzo
  (package
    (name "python-lzo")
-    (version "1.11")
+    (version "1.12")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "python-lzo" version))
       (sha256
        (base32
-         "11p3ifg14p086byhhin6azx5svlkg8dzw2b5abixik97xd6fm81q"))))
+         "0iakqgd51n1cd7r3lpdylm2rgbmd16y74cra9kcapwg84mlf9a4p"))))
    (build-system python-build-system)
    (arguments
     `(#:test-target "check"
@@ -549,7 +589,20 @@ decompressors when faced with corrupted input.")
      (patches (search-patches "sharutils-CVE-2018-1000097.patch"))
      (sha256
       (base32
-        "16isapn8f39lnffc3dp4dan05b7x6mnc76v6q5nn8ysxvvvwy19b"))))
+        "16isapn8f39lnffc3dp4dan05b7x6mnc76v6q5nn8ysxvvvwy19b"))
+      (modules '((guix build utils)))
+      (snippet
+       '(begin
+          (substitute* (find-files "lib" "\\.c$")
+            (("#if defined _IO_ftrylockfile")
+             "#if defined _IO_EOF_SEEN"))
+          (substitute* "lib/stdio-impl.h"
+            (("^/\\* BSD stdio derived implementations")
+             (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n"
+                            "# define _IO_IN_BACKUP 0x100\n"
+                            "#endif\n\n"
+                            "/* BSD stdio derived implementations")))
+          #t))))
    (build-system gnu-build-system)
    (inputs
     `(("which" ,which)))
@@ -642,16 +695,17 @@ sfArk file format to the uncompressed sf2 format.")
 (define-public libmspack
  (package
    (name "libmspack")
-    (version "0.6")
+    (home-page "https://cabextract.org.uk/libmspack/")
+    (version "0.9.1")
    (source
     (origin
      (method url-fetch)
-      (uri (string-append "http://www.cabextract.org.uk/libmspack/libmspack-"
-                          version "alpha.tar.gz"))
+      (uri (string-append home-page name "-" version "alpha.tar.gz"))
      (sha256
-       (base32 "08gr2pcinas6bdqz3k0286g5cnksmcx813skmdwyca6bmj1fxnqy"))))
+       (base32 "0h1f5w8rjnq7dcqpqm1mpx5m8q80691kid6f7npqlqwqqzckd8v2"))))
    (build-system gnu-build-system)
-    (home-page "http://www.cabextract.org.uk/libmspack/")
+    (arguments
+     `(#:configure-flags '("--disable-static")))
    (synopsis "Compression tools for some formats used by Microsoft")
    (description
     "The purpose of libmspack is to provide both compression and
@@ -672,7 +726,7 @@ decompression of some loosely related file formats used by Microsoft.")
         "081mpkjy688lg48997fqh3d7ja12vazmz02fw84495civg4vb4l6"))))
    (build-system perl-build-system)
    ;; TODO: Use our bzip2 package.
-    (home-page "http://search.cpan.org/dist/Compress-Raw-Bzip2")
+    (home-page "https://metacpan.org/release/Compress-Raw-Bzip2")
    (synopsis "Low-level interface to bzip2 compression library")
    (description "This module provides a Perl interface to the bzip2
 compression library.")
@@ -706,8 +760,9 @@ INCLUDE = ~a/include
 LIB = ~:*~a/lib
 OLD_ZLIB = False
 GZIP_OS_CODE = AUTO_DETECT"
-                                 (assoc-ref inputs "zlib")))))))))
-    (home-page "http://search.cpan.org/dist/Compress-Raw-Zlib")
+                                 (assoc-ref inputs "zlib"))))
+                     #t)))))
+    (home-page "https://metacpan.org/release/Compress-Raw-Zlib")
    (synopsis "Low-level interface to zlib compression library")
    (description "This module provides a Perl interface to the zlib
 compression library.")
@@ -729,7 +784,7 @@ compression library.")
    (propagated-inputs
     `(("perl-compress-raw-zlib" ,perl-compress-raw-zlib)     ; >=2.081
       ("perl-compress-raw-bzip2" ,perl-compress-raw-bzip2))) ; >=2.081
-    (home-page "http://search.cpan.org/dist/IO-Compress")
+    (home-page "https://metacpan.org/release/IO-Compress")
    (synopsis "IO Interface to compressed files/buffers")
    (description "IO-Compress provides a Perl interface to allow reading and
 writing of compressed data created with the zlib and bzip2 libraries.")
@@ -796,14 +851,14 @@ the LZ4 frame format.")
 (define-public python-lzstring
  (package
    (name "python-lzstring")
-    (version "1.0.3")
+    (version "1.0.4")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "lzstring" version))
       (sha256
        (base32
-         "1d3ck454y41mii0gcjabpmp2skb7n0f9zk232gycqdv8z2jxakfm"))))
+         "18ly9pppy2yspxzw7k1b23wk77k7m44rz2g0271bqgqrk3jn3yhs"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-future" ,python-future)))
@@ -839,8 +894,16 @@ the LZ4 frame format.")
       #:phases
       (modify-phases %standard-phases
         (replace 'configure
-                  (lambda _
-                    (chdir "squashfs-tools"))))))
+           (lambda _
+             (chdir "squashfs-tools")
+             #t))
+         (add-after 'unpack 'fix-glibc-compatability
+           (lambda _
+             (substitute* '("squashfs-tools/mksquashfs.c"
+                            "squashfs-tools/unsquashfs.c")
+               (("<sys/sysinfo.h>")
+                "<sys/sysinfo.h>\n#include <sys/sysmacros.h>"))
+             #t)))))
    (inputs
     `(("lz4" ,lz4)
       ("lzo" ,lzo)
@@ -981,24 +1044,82 @@ provides encoder and a decoder libraries: libbrotlienc and libbrotlidec,
 respectively, based on the reference implementation from Google.")
      (license license:expat))))

+(define-public bsdiff
+  (package
+    (name "bsdiff")
+    (version "4.3")
+    (home-page "https://www.daemonology.net/bsdiff/")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append home-page name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0j2zm3z271x5aw63mwhr3vymzn45p2vvrlrpm9cz2nywna41b0hq"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags (list "INSTALL=install" "CC=gcc"
+                          (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:phases (modify-phases %standard-phases
+                  (delete 'configure)
+                  (add-before 'build 'fix-Makefile
+                    (lambda _
+                      (substitute* "Makefile"
+                        ;; Adjust syntax to make it compatible with GNU Make.
+                        (("^\\.") "")
+                        ;; Help install(1) create the target directory.
+                        (("\\$\\{PREFIX\\}") "-D -t ${PREFIX}"))
+                      #t)))
+       #:tests? #f)) ;no tests
+    (inputs
+     `(("bzip2" ,bzip2)))
+    (synopsis "Patch binary files")
+    (description
+     "@command{bsdiff} and @command{bspatch} are tools for building and
+applying patches to binary files.  By using suffix sorting (specifically
+Larsson and Sadakane's @code{qsufsort}) and taking advantage of how
+executable files change, bsdiff routinely produces binary patches 50-80%
+smaller than those produced by @code{Xdelta}.")
+    (license license:bsd-2)))
+
 (define-public cabextract
 (package
   (name "cabextract")
-   (version "1.6")
+   (home-page "https://cabextract.org.uk/")
+   (version "1.9")
   (source (origin
              (method url-fetch)
-              (uri (string-append
-                    "http://cabextract.org.uk/cabextract-" version ".tar.gz"))
+              (uri (string-append home-page name "-" version ".tar.gz"))
              (sha256
               (base32
-                "1ysmmz25fjghq7mxb2anyyvr1ljxqxzi4piwjhk0sdamcnsn3rnf"))))
+                "1hf4zhjxfdgq9x172r5zfdnafma9q0zf7372syn8hcn7hcypkg0v"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Delete bundled libmspack.
+                  (delete-file-recursively "mspack")
+                  #t))))
    (build-system gnu-build-system)
-    (arguments '(#:configure-flags '("--with-external-libmspack")))
+    (arguments
+     '(#:configure-flags '("--with-external-libmspack")
+       #:phases
+       (modify-phases %standard-phases
+         ;; cabextract needs some of libmspack's header files.
+         ;; These are located in the "mspack" directory of libmspack.
+         (add-before 'build 'unpack-libmspack
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((dir-name "libmspack-src"))
+               (mkdir dir-name)
+               (invoke "tar" "-xvf" (assoc-ref inputs "libmspack-source")
+                       "-C" dir-name "--strip-components" "1")
+               (rename-file (string-append dir-name "/mspack")
+                            "mspack")
+               (delete-file-recursively dir-name)
+               #t))))))
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (inputs
-     `(("libmspack" ,libmspack)))
-    (home-page "http://www.cabextract.org.uk/")
+     `(("libmspack" ,libmspack)
+       ("libmspack-source" ,(package-source libmspack))))
    (synopsis "Tool to unpack Cabinet archives")
    (description "Extracts files out of Microsoft Cabinet (.cab) archives")
    ;; Some source files specify gpl2+, lgpl2+, however COPYING is gpl3.
@@ -1010,13 +1131,14 @@ respectively, based on the reference implementation from Google.")
    (version "3.1.0")
    (source
     (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/jmacd/xdelta/archive/v"
-                           version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/jmacd/xdelta.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
       (sha256
        (base32
-         "17g2pbbqy6h20qgdjq7ykib7kg5ajh8fwbsfgyjqg8pwg19wy5bm"))
-       (file-name (string-append name "-" version ".tar.gz"))
+         "09mmsalc7dwlvgrda56s2k927rpl3a5dzfa88aslkqcjnr790wjy"))
       (snippet
        ;; This file isn't freely distributable and has no effect on building.
        '(begin
@@ -1030,9 +1152,7 @@ respectively, based on the reference implementation from Google.")
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'enter-build-directory
-           (lambda _ (chdir "xdelta3") #t))
-         (add-after 'enter-build-directory 'autoconf
-           (lambda _ (invoke "autoreconf" "-vfi"))))))
+           (lambda _ (chdir "xdelta3") #t)))))
    (home-page "http://xdelta.org")
    (synopsis "Delta encoder for binary files")
    (description "xdelta encodes only the differences between two binary files
@@ -1082,16 +1202,30 @@ well as bzip2.")
 (define-public bitshuffle
  (package
    (name "bitshuffle")
-    (version "0.3.4")
+    (version "0.3.5")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "bitshuffle" version))
              (sha256
               (base32
-                "0ydawb01ghsvmw0lraczhrgvkjj97bpg98f1qqs1cnfp953mdd5v"))))
+                "1823x61kyax4dc2hjmc1xraskxi1193y8lvxd03vqv029jrj8cjy"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Remove generated Cython files.
+                  (delete-file "bitshuffle/h5.c")
+                  (delete-file "bitshuffle/ext.c")
+                  #t))))
    (build-system python-build-system)
    (arguments
-     `(#:tests? #f))           ; fail: https://github.com/h5py/h5py/issues/769
+     `(#:tests? #f             ; fail: https://github.com/h5py/h5py/issues/769
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'dont-build-native
+           (lambda _
+             (substitute* "setup.py"
+               (("'-march=native', ") ""))
+             #t)))))
    (inputs
     `(("numpy" ,python-numpy)
       ("h5py" ,python-h5py)
@@ -1109,14 +1243,15 @@ algorithm within the Numpy framework.")
  (package
    (name "snappy")
    (version "1.1.7")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/google/snappy/archive/"
-                                  version ".tar.gz"))
-              (file-name (string-append "snappy-" version ".tar.gz"))
-              (sha256
-               (base32
-                "1m7rcdqzkys5lspj8jcsaah8w33zh28s771bw0ga2lgzfgl05yix"))))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/google/snappy/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append "snappy-" version ".tar.gz"))
+       (sha256
+        (base32 "1m7rcdqzkys5lspj8jcsaah8w33zh28s771bw0ga2lgzfgl05yix"))
+       (patches (search-patches "snappy-add-O2-flag-in-CmakeLists.txt.patch"))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")))
@@ -1170,7 +1305,7 @@ install: libbitshuffle.so
 (define-public java-snappy
  (package
    (name "java-snappy")
-    (version "1.1.7")
+    (version "1.1.7.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/xerial/snappy-java/archive/"
@@ -1178,7 +1313,7 @@ install: libbitshuffle.so
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
-                "0q4kxz2n97czf6g5gzq0d8yz22cgiaj7wp51rzsswh3bi99bpgg5"))))
+                "1p557vdv006ysgxbpp83krmq0066k46108vyiyka69w8i4i8rbbm"))))
    (build-system ant-build-system)
    (arguments
     `(#:jar-name "snappy.jar"
@@ -1226,7 +1361,8 @@ install: libbitshuffle.so
         (add-after 'build-jni 'copy-jni
           (lambda _
             (copy-recursively "src/main/resources/org/xerial/snappy/native"
-                               "build/classes/org/xerial/snappy/native")))
+                               "build/classes/org/xerial/snappy/native")
+             #t))
         (add-before 'check 'fix-failing
           (lambda _
             (with-directory-excursion "src/test/java/org/xerial/snappy"
@@ -1252,8 +1388,8 @@ install: libbitshuffle.so
       ("perl" ,perl)))
    (home-page "https://github.com/xerial/snappy-java")
    (synopsis "Compression/decompression algorithm in Java")
-    (description "Snappy-java is a Java port of the snappy, a fast C++
-compresser/decompresser.")
+    (description "Snappy-java is a Java port of snappy, a fast C++
+compressor/decompressor.")
    (license license:asl2.0)))

 (define-public java-snappy-1
@@ -1344,7 +1480,8 @@ compresser/decompresser.")
                       class))
             (invoke "ant" "compile-tests")
             (test "org.iq80.snappy.SnappyFramedStreamTest")
-             (test "org.iq80.snappy.SnappyStreamTest")))
+             (test "org.iq80.snappy.SnappyStreamTest")
+             #t))
         (add-before 'build 'remove-hadoop-dependency
           (lambda _
             ;; We don't have hadoop
@@ -1649,19 +1786,14 @@ or junctions, and always follows hard links.")
 (define-public zstd
  (package
    (name "zstd")
-    (version "1.3.5")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/facebook/zstd/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
-              (sha256
-               (base32
-                "1sifbq18p0hc978g0pq8fymrlpzz1fcxqkbxfqk44z6v9jg5bqfn"))
-              ;; Fix a regression that causes the tests to fail.  Both patches
-              ;; have been merged upstream and will be part of the next release.
-              (patches (search-patches "zstd-fix-stdin-list-without-tty.patch"
-                                       "zstd-fix-stdin-list-test.patch"))))
+    (version "1.3.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/facebook/zstd/releases/download/"
+                           "v" version "/zstd-" version ".tar.gz"))
+       (sha256
+        (base32 "0gapsdzqfsfqqddzv22592iwa0008xjyi15f06pfv9hcvwvg4xrj"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
@@ -1704,7 +1836,7 @@ speed.")
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'enter-subdirectory
-           (lambda _ (chdir "contrib/pzstd")))
+           (lambda _ (chdir "contrib/pzstd") #t))
         (delete 'configure)            ; no configure script
         (add-before 'check 'compile-tests
           (lambda* (#:key make-flags #:allow-other-keys)
@@ -1883,25 +2015,25 @@ recreates the stored directory structure by default.")
    (synopsis  "Provides an interface to Zip archive files")
    (description "The @code{Archive::Zip} module allows a Perl program to
 create, manipulate, read, and write Zip archive files.")
-    (home-page "http://search.cpan.org/dist/Archive-Zip/")
+    (home-page "https://metacpan.org/release/Archive-Zip")
    (license license:perl-license)))

 (define-public libzip
  (package
    (name "libzip")
-    (version "1.3.2")
+    (version "1.5.1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://libzip.org/download/" name "-" version ".tar.xz"))
              (sha256
               (base32
-                "11g1hvm2bxa2v5plakfzcwyk5hb5fz4kgrkp38l0xhnv21888xv2"))))
+                "0wnkkvkq90wyawj9221i77sf3nix1vj3ygzdy59k8yvcjnv3bsh4"))))
    (native-inputs
     `(("perl" ,perl)))
    (inputs
     `(("zlib" ,zlib)))
-    (build-system gnu-build-system)
+    (build-system cmake-build-system)
    (home-page "https://libzip.org")
    (synopsis "C library for reading, creating, and modifying zip archives")
    (description "Libzip is a C library for reading, creating, and modifying
@@ -1959,7 +2091,7 @@ of archives.")
        (base32
         "1x15j1q6w6z8hqyqgap0lz4qbq2174wfhksy1fdd653ccbaw5jr5"))))
    (build-system perl-build-system)
-    (home-page "http://search.cpan.org/dist/Archive-Extract/")
+    (home-page "https://metacpan.org/release/Archive-Extract")
    (synopsis "Generic archive extracting mechanism")
    (description "It allows you to extract any archive file of the type .tar,
 .tar.gz, .gz, .Z, tar.bz2, .tbz, .bz2, .zip, .xz,, .txz, .tar.xz or .lzma
@@ -1986,14 +2118,16 @@ type by using either Perl modules, or command-line tools on your system.")
           (lambda _
             ;; Our build system enters the first directory in the archive, but
             ;; the package is not contained in a subdirectory
-             (chdir "..")))
+             (chdir "..")
+             #t))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             ;; Do we want to install *Demo.jar?
             (install-file "build/jar/xz.jar"
                           (string-append
                             (assoc-ref outputs "out")
-                             "/share/java/xz.jar")))))))
+                             "/share/java/xz.jar"))
+             #t)))))
    (native-inputs
     `(("unzip" ,unzip)))
    (home-page "https://tukaani.org")
@@ -236,22 +236,23 @@ as ordering relation.")
    (build-system cmake-build-system)
    (synopsis "JSON parser and printer library for C++")
    (description "JSON for Modern C++ is a C++ JSON library that provides
-intutive syntax and trivial integration.")
+intuitive syntax and trivial integration.")
    (license license:expat)))

 (define-public xtl
  (package
    (name "xtl")
-    (version "0.4.8")
+    (version "0.4.14")
    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/QuantStack/xtl/archive/"
-                    version ".tar.gz"))
+              (method git-fetch)
+              (uri
+               (git-reference
+                (url "https://github.com/QuantStack/xtl.git")
+                (commit version)))
              (sha256
               (base32
-                "05bcz9y590b77bxcip0k31rgsapmkwqi1smvsvc84zz7m87d4jvy"))
-              (file-name (string-append name "-" version ".tar.gz"))))
+                "0wwnd9adc1wav2299id17k5fbp0ib5gxkbihlk6jlh3v4i5nz11x"))
+              (file-name (git-file-name name version))))
    (native-inputs
     `(("googletest" ,googletest)
       ("json-modern-cxx" ,json-modern-cxx)))
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
@@ -356,7 +356,7 @@ target that libc."
             ,@(package-arguments glibc/hurd-headers))
         ((#:phases phases)
          `(modify-phases ,phases
-             (add-before 'pre-configure 'set-cross-headers-path
+             (add-after 'unpack 'set-cross-headers-path
               (lambda* (#:key inputs #:allow-other-keys)
                 (let* ((mach (assoc-ref inputs "gnumach-headers"))
                        (hurd (assoc-ref inputs "hurd-headers"))
@@ -426,17 +426,9 @@ target that libc."
                     (xheaders (cross-kernel-headers target)))
  "Return a libc cross-built for TARGET, a GNU triplet.  Use XGCC and
 XBINUTILS and the cross tool chain."
-  (define (cross-libc-for-target target)
-    "Return libc depending on TARGET."
-    (match target
-      ((or "i586-pc-gnu" "i586-gnu") glibc/hurd)
-      (_ glibc/linux)))
-
-  ;; Use (cross-libc-for-target ...) to determine the correct libc to use.
-
  (if (cross-newlib? target)
      (native-libc target)
-      (let ((libc (cross-libc-for-target target)))
+      (let ((libc glibc))
        (package (inherit libc)
          (name (string-append "glibc-cross-" target))
          (arguments
@@ -457,7 +449,9 @@ XBINUTILS and the cross tool chain."
                 ,@(package-arguments libc))
             ((#:configure-flags flags)
              `(cons ,(string-append "--host=" target)
-                   ,flags))
+                     ,(if (hurd-triplet? target)
+                          `(cons "--disable-werror" ,flags)
+                          flags)))
             ((#:phases phases)
              `(modify-phases ,phases
                 (add-before 'configure 'set-cross-kernel-headers-path
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 David Thompson <davet@gnu.org>
-;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -10,6 +10,7 @@
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2018 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -40,6 +41,7 @@
  #:use-module (gnu packages gettext)
  #:use-module (gnu packages gnupg)
  #:use-module (gnu packages image)
+  #:use-module (gnu packages kerberos)
  #:use-module (gnu packages libbsd)
  #:use-module (gnu packages libffi)
  #:use-module (gnu packages linux)
@@ -92,7 +94,7 @@ communication, encryption, decryption, signatures, etc.")
 (define-public libmd
  (package
    (name "libmd")
-    (version "1.0.0")
+    (version "1.0.1")
    (source (origin
            (method url-fetch)
            (uri
@@ -103,7 +105,7 @@ communication, encryption, decryption, signatures, etc.")
                             version ".tar.xz")))
            (sha256
             (base32
-              "1iv45npzv0gncjgcpx5m081861zdqxw667ysghqb8721yrlyl6pj"))))
+              "0waclg2d5qin3r26gy5jvy4584ik60njc8pqbzwk0lzq3j9ynkp1"))))
    (build-system gnu-build-system)
    (synopsis "Message Digest functions from BSD systems")
    (description
@@ -125,7 +127,7 @@ communication, encryption, decryption, signatures, etc.")
 (define-public signify
  (package
    (name "signify")
-    (version "23")
+    (version "24")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/aperezdc/signify/"
@@ -133,7 +135,7 @@ communication, encryption, decryption, signatures, etc.")
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
-                "0c70mzawgahsvmsv4xdrass4pgyynd67ipd9lij0fgi8wkq0ns8w"))))
+                "0594vyvkq176xxzaz9xbq8qs0xdnr8s9gkd1prblwpdvnzmw0xvc"))))
    (build-system gnu-build-system)
    ;; TODO Build with libwaive (described in README.md), to implement something
    ;; like OpenBSD's pledge().
@@ -162,34 +164,31 @@ OpenBSD tool of the same name.")
                                          "See base64.c in the distribution for
                                           the license from IBM.")))))

-
 (define-public opendht
  (package
    (name "opendht")
    (version "0.6.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append
-         "https://github.com/savoirfairelinux/" name
-         "/archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           (delete-file-recursively "src/argon2")
-           (substitute* "src/Makefile.am"
-             (("./argon2/libargon2.la") "")
-             (("SUBDIRS = argon2") ""))
-           (substitute* "src/crypto.cpp"
-             (("argon2/argon2.h") "argon2.h"))
-           (substitute* "configure.ac"
-             (("src/argon2/Makefile") ""))
-           #t))
-       (sha256
-        (base32
-         "09yvkmbqbym3b5md4n96qc1s9sf2n8ji404hagih45rmsj49599x"))))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/savoirfairelinux/opendht.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (delete-file-recursively "src/argon2")
+                  (substitute* "src/Makefile.am"
+                    (("./argon2/libargon2.la") "")
+                    (("SUBDIRS = argon2") ""))
+                  (substitute* "src/crypto.cpp"
+                    (("argon2/argon2.h") "argon2.h"))
+                  (substitute* "configure.ac"
+                    (("src/argon2/Makefile") ""))
+                  #t))
+              (sha256
+               (base32
+                "1akk613f18rc8kqs0cxdm34iq7wwc9kffhgp5rng09arwlw8gw3w"))))
    (build-system gnu-build-system)
    (inputs
     `(("gnutls" ,gnutls)
@@ -204,11 +203,7 @@ OpenBSD tool of the same name.")
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (arguments
-     `(#:configure-flags '("--disable-tools" "--disable-python")
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'autoconf
-                    (lambda _
-                      (zero? (system* "autoreconf" "-vfi")))))))
+     `(#:configure-flags '("--disable-tools" "--disable-python")))
    (home-page "https://github.com/savoirfairelinux/opendht/")
    (synopsis "Distributed Hash Table (DHT) library")
    (description "OpenDHT is a Distributed Hash Table (DHT) library.  It may
@@ -277,7 +272,7 @@ the wrong hands.")
 (define-public keyutils
  (package
    (name "keyutils")
-    (version "1.5.10")
+    (version "1.5.11")
    (source
     (origin
       (method url-fetch)
@@ -286,9 +281,9 @@ the wrong hands.")
                       version ".tar.bz2"))
       (sha256
        (base32
-         "1dmgjcf7mnwc6h72xkvpaqpzxw8vmlnsmzz0s27pg0giwzm3sp0i"))
+         "1ddig6j5xjyk6g9l2wlqc7k1cgvryxdqbsv3c9rk1p3f42448n0i"))
       (modules '((guix build utils)))
-       ;; Create relative symbolic links instead of absolute ones to /lib/*
+       ;; Create relative symbolic links instead of absolute ones to /lib/*.
       (snippet '(begin
                   (substitute* "Makefile" (("\\$\\(LNS\\) \\$\\(LIBDIR\\)/")
                                            "$(LNS) "))
@@ -306,6 +301,8 @@ the wrong hands.")
                          "MANDIR=/share/man"
                          "SHAREDIR=/share/keyutils")
       #:test-target "test"))
+    (inputs
+     `(("mit-krb5" ,mit-krb5)))
    (home-page "https://people.redhat.com/dhowells/keyutils/")
    (synopsis "Linux key management utilities")
    (description
@@ -523,7 +520,7 @@ attacks than alternative functions such as @code{PBKDF2} or @code{bcrypt}.")
    (native-inputs
     `(("perl-module-build" ,perl-module-build)
       ("perl-test-nowarnings" ,perl-test-nowarnings)))
-    (home-page "http://search.cpan.org/dist/Math-Random-ISAAC-XS")
+    (home-page "https://metacpan.org/release/Math-Random-ISAAC-XS")
    (synopsis "C implementation of the ISAAC PRNG algorithm")
    (description "ISAAC (Indirection, Shift, Accumulate, Add, and Count) is a
 fast pseudo-random number generator.  It is suitable for applications where a
@@ -551,7 +548,7 @@ This package implements the same interface as @code{Math::Random::ISAAC}.")
     `(("perl-test-nowarnings" ,perl-test-nowarnings)))
    (propagated-inputs
     `(("perl-math-random-isaac-xs" ,perl-math-random-isaac-xs)))
-    (home-page "http://search.cpan.org/dist/Math-Random-ISAAC")
+    (home-page "https://metacpan.org/release/Math-Random-ISAAC")
    (synopsis "Perl interface to the ISAAC PRNG algorithm")
    (description "ISAAC (Indirection, Shift, Accumulate, Add, and Count) is a
 fast pseudo-random number generator.  It is suitable for applications where a
@@ -587,7 +584,7 @@ generator.")
       ("perl-namespace-clean" ,perl-namespace-clean)
       ("perl-sub-exporter" ,perl-sub-exporter)
       ("perl-type-tiny" ,perl-type-tiny)))
-    (home-page "http://search.cpan.org/dist/Crypt-Random-Source")
+    (home-page "https://metacpan.org/release/Crypt-Random-Source")
    (synopsis "Get weak or strong random data from pluggable sources")
    (description "This module provides implementations for a number of
 byte-oriented sources of random data.")
@@ -616,7 +613,7 @@ byte-oriented sources of random data.")
       ("perl-math-random-isaac" ,perl-math-random-isaac)
       ("perl-math-random-isaac-xs" ,perl-math-random-isaac-xs)
       ("perl-moo" ,perl-moo)))
-    (home-page "http://search.cpan.org/dist/Math-Random-Secure")
+    (home-page "https://metacpan.org/release/Math-Random-Secure")
    (synopsis "Cryptographically secure replacement for rand()")
    (description "This module is intended to provide a
 cryptographically-secure replacement for Perl's built-in @code{rand} function.
@@ -668,39 +665,32 @@ data on your platform, so the seed itself will be as random as possible.
    (license (list license:boost1.0 license:public-domain))))

 (define-public libb2
-  (let ((revision "1")                  ; upstream doesn't ‘do’ releases
-        (commit "60ea749837362c226e8501718f505ab138e5c19d"))
-    (package
-      (name "libb2")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/BLAKE2/libb2")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "07a2m8basxrsj9dsp5lj24y8jraj85lfy56756a7za1nfkgy04z7"))))
-      (build-system gnu-build-system)
-      (native-inputs
-       `(("autoconf" ,autoconf)
-         ("automake" ,automake)
-         ("libtool" ,libtool)))
-      (arguments
-       `(#:configure-flags
-         (list
-           ,@(if (any (cute string-prefix? <> (or (%current-system)
-                                                  (%current-target-system)))
-                      '("x86_64" "i686"))
-               ;; fat only checks for Intel optimisations
-               '("--enable-fat")
-               '())
-           "--disable-native")))                 ;don't optimise at build time
-      (home-page "https://blake2.net/")
-      (synopsis "Library implementing the BLAKE2 family of hash functions")
-      (description
-       "libb2 is a portable implementation of the BLAKE2 family of cryptographic
+  (package
+    (name "libb2")
+    (version "0.98")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/BLAKE2/libb2/releases/download/v"
+                    version "/libb2-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0vq39cvwy05754l565xl11rqr2jvjb6ykjzca886vi9vm71y0sg8"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list
+        ,@(if (any (cute string-prefix? <> (or (%current-system)
+                                               (%current-target-system)))
+                   '("x86_64" "i686"))
+              ;; fat only checks for Intel optimisations
+              '("--enable-fat")
+              '())
+        "--disable-native")))           ;don't optimise at build time
+    (home-page "https://blake2.net/")
+    (synopsis "Library implementing the BLAKE2 family of hash functions")
+    (description
+     "libb2 is a portable implementation of the BLAKE2 family of cryptographic
 hash functions.  It includes optimised implementations for IA-32 and AMD64
 processors, and an interface layer that automatically selects the best
 implementation for the processor it is run on.
@@ -709,7 +699,7 @@ implementation for the processor it is run on.
 that are faster than MD5, SHA-1, SHA-2, and SHA-3, yet are at least as secure
 as the latest standard, SHA-3.  It is an improved version of the SHA-3 finalist
 BLAKE.")
-      (license license:public-domain))))
+    (license license:public-domain)))

 (define-public rhash
  (package
@@ -755,14 +745,14 @@ SHA256, SHA512, SHA3, AICH, ED2K, Tiger, DC++ TTH, BitTorrent BTIH, GOST R
 (define-public botan
  (package
    (name "botan")
-    (version "2.6.0")
+    (version "2.7.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://botan.randombit.net/releases/"
                                  "Botan-" version ".tgz"))
              (sha256
               (base32
-                "1iawmymmnp5j2mcjj70slivn6bgg8gbpppldc1rjqw5sbdan3wn1"))))
+                "142aqabwc266jxn8wrp0f1ffrmcvdxwvyh8frb38hx9iaqazjbg4"))))
    (build-system gnu-build-system)
    (arguments
     '(#:phases
@@ -797,3 +787,97 @@ specifically designed to be easy to call from other languages.  A Python binding
 using ctypes is included, and several other language bindings are available.")
    (home-page "https://botan.randombit.net")
    (license license:bsd-2)))
+
+(define-public ccrypt
+  (package
+    (name "ccrypt")
+    (version "1.11")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/ccrypt/"
+                                  version "/ccrypt-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0kx4a5mhmp73ljknl2lcccmw9z3f5y8lqw0ghaymzvln1984g75i"))))
+    (build-system gnu-build-system)
+    (home-page "http://ccrypt.sourceforge.net")
+    (synopsis "Command-line utility for encrypting and decrypting files and streams")
+    (description "@command{ccrypt} is a utility for encrypting and decrypting
+files and streams.  It was designed as a replacement for the standard unix
+@command{crypt} utility, which is notorious for using a very weak encryption
+algorithm.  @command{ccrypt} is based on the Rijndael block cipher, a version of
+which is also used in the Advanced Encryption Standard (AES, see
+@url{http://www.nist.gov/aes}).  This cipher is believed to provide very strong
+security.")
+    (license license:gpl2)))
+
+(define-public asignify
+  (let ((commit "f58e7977a599f040797975d649ed318e25cbd2d5")
+        (revision "0"))
+    (package
+      (name "asignify")
+      (version (git-version "1.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/vstakhov/asignify.git")
+                       (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1zl68qq6js6fdahxzyhvhrpyrwlv8c2zhdplycnfxyr1ckkhq8dw"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:configure-flags
+         (list "--enable-openssl"
+               (string-append "--with-openssl="
+                              (assoc-ref %build-inputs "openssl")))))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("libtool" ,libtool)))
+      (inputs
+       `(("openssl" ,openssl-next)))
+      (home-page "https://github.com/vstakhov/asignify")
+      (synopsis "Cryptographic authentication and encryption tool and library")
+      (description "Asignify offers public cryptographic signatures and
+encryption with a library or a command-line tool.  The tool is heavily inspired
+by signify as used in OpenBSD.  The main goal of this project is to define a
+high level API for signing files, validating signatures and encrypting using
+public-key cryptography.  Asignify is designed to be portable and self-contained
+with zero external dependencies.  Asignify can verify OpenBSD signatures, but it
+cannot sign messages in OpenBSD format yet.")
+      (license license:bsd-2))))
+
+(define-public enchive
+  (package
+    (name "enchive")
+    (version "3.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/skeeto/" name "/archive/"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "17hrxpp4cpn10bk48sfvfjc8hghky34agsnypam1v9f36kbalqfk"))
+              (file-name (string-append name "-" version ".tar.gz"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f                      ; no check target         '
+       #:make-flags (list "CC=gcc" "PREFIX=$(out)")
+       #:phases (modify-phases %standard-phases
+                  (delete 'configure)
+                  (add-after 'install 'post-install
+                    (lambda _
+                      (let* ((out (assoc-ref %outputs "out"))
+                             (lisp (string-append out "/share/emacs/site-lisp")))
+                        (install-file "enchive-mode.el" lisp)
+                        #t))))))
+    (synopsis "Encrypted personal archives")
+    (description
+     "Enchive is a tool to encrypt files to yourself for long-term
+archival.  It's a focused, simple alternative to more complex solutions such as
+GnuPG or encrypted filesystems.  Enchive has no external dependencies and is
+trivial to build for local use.  Portability is emphasized over performance.")
+    (home-page "https://github.com/skeeto/enchive")
+    (license license:unlicense)))
--- a/Show More
+++ b/Show More