From a91d75ecbde59b5400e4812868c3a55e12a220d9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 26 Oct 2016 18:01:34 +0200
Subject: [PATCH 01/27] tests: Skip 'pivot-root' test on Linux > 4.7.5.

* tests/syscalls.scm ("pivot-root"): Skip when 'uname' returns a
'utsname:release' > 4.7.5.
---
 tests/syscalls.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/syscalls.scm b/tests/syscalls.scm
index 1b31d87f23..9eb19f9c80 100644
--- a/tests/syscalls.scm
+++ b/tests/syscalls.scm
@@ -146,7 +146,10 @@ (define perform-container-tests?
              (waitpid fork-pid)
              result))))))))
 
-(unless perform-container-tests?
+;; XXX: Skip this test when running Linux > 4.7.5 to work around
+;; <https://bugzilla.kernel.org/show_bug.cgi?id=183461>.
+(when (or (not perform-container-tests?)
+          (version>? (utsname:release (uname)) "4.7.5"))
   (test-skip 1))
 (test-equal "pivot-root"
   #t

From d6aca5835a9b4b2cfb1cf8191faac6628975de8a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 26 Oct 2016 18:15:57 +0200
Subject: [PATCH 02/27] tests: Adjust pypi test to recent importer change.

This is a followup to b5c347ad3d83ee580c111bd14c80b469b0dcb294.

* tests/pypi.scm ("pypi->guix-package"): Expect 'propagated-inputs', not
'inputs'.
("pypi->guix-package, wheels"): Likewise.
---
 tests/pypi.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/pypi.scm b/tests/pypi.scm
index ab4e9c958b..9d2fcc7391 100644
--- a/tests/pypi.scm
+++ b/tests/pypi.scm
@@ -122,7 +122,7 @@ (define test-metadata
                      ('base32
                       (? string? hash)))))
          ('build-system 'python-build-system)
-         ('inputs
+         ('propagated-inputs
           ('quasiquote
            (("python-bar" ('unquote 'python-bar))
             ("python-baz" ('unquote 'python-baz))
@@ -182,7 +182,7 @@ (define test-metadata
                      ('base32
                       (? string? hash)))))
          ('build-system 'python-build-system)
-         ('inputs
+         ('propagated-inputs
           ('quasiquote
            (("python-bar" ('unquote 'python-bar))
             ("python-baz" ('unquote 'python-baz))

From d88767a39986692e4d89d2d4ec8edfc0d4f51782 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 26 Oct 2016 20:04:06 +0200
Subject: [PATCH 03/27] tests: Use #:fallback? #t when building system tests.

* build-aux/run-system-tests.scm (run-system-tests): Pass #:fallback? #t
to 'set-build-options*'.
---
 build-aux/run-system-tests.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/build-aux/run-system-tests.scm b/build-aux/run-system-tests.scm
index 3f3a70e7b4..b582bc5e57 100644
--- a/build-aux/run-system-tests.scm
+++ b/build-aux/run-system-tests.scm
@@ -68,7 +68,8 @@ (define tests
                            (out -> (map derivation->output-path drv)))
         (mbegin %store-monad
           (show-what-to-build* drv)
-          (set-build-options* #:keep-going? #t #:keep-failed? #t)
+          (set-build-options* #:keep-going? #t #:keep-failed? #t
+                              #:fallback? #t)
           (built-derivations* drv)
           (mlet %store-monad ((valid  (filterm (store-lift valid-path?)
                                                out))

From 5479aa2b7cf9164e87a1d1184ec97a9bba5cea92 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 26 Oct 2016 20:04:52 +0200
Subject: [PATCH 04/27] tests: Test installation with store on a separate
 partition.

This is a followup to 0f65f54ebd76324653fd5506a7dab42ee44d9255.

* gnu/tests/install.scm (%separate-store-os, %separate-store-os-source)
(%separate-store-installation-script, %test-separate-store-os): New
variables.
---
 gnu/tests/install.scm | 82 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)

diff --git a/gnu/tests/install.scm b/gnu/tests/install.scm
index 4e79fdb294..0f54935ea8 100644
--- a/gnu/tests/install.scm
+++ b/gnu/tests/install.scm
@@ -33,6 +33,7 @@ (define-module (gnu tests install)
   #:use-module (guix gexp)
   #:use-module (guix utils)
   #:export (%test-installed-os
+            %test-separate-store-os
             %test-encrypted-os))
 
 ;;; Commentary:
@@ -222,6 +223,87 @@ (define %test-installed-os
                       "installed-os")))))
 
 
+;;;
+;;; Separate /gnu/store partition.
+;;;
+
+(define-os-with-source (%separate-store-os %separate-store-os-source)
+  ;; The OS we want to install.
+  (use-modules (gnu) (gnu tests) (srfi srfi-1))
+
+  (operating-system
+    (host-name "liberigilo")
+    (timezone "Europe/Paris")
+    (locale "en_US.UTF-8")
+
+    (bootloader (grub-configuration (device "/dev/vdb")))
+    (kernel-arguments '("console=ttyS0"))
+    (file-systems (cons* (file-system
+                           (device "root-fs")
+                           (title 'label)
+                           (mount-point "/")
+                           (type "ext4"))
+                         (file-system
+                           (device "store-fs")
+                           (title 'label)
+                           (mount-point "/gnu")
+                           (type "ext4")
+                           (needed-for-boot? #t)) ;definitely!
+                         %base-file-systems))
+    (users %base-user-accounts)
+    (services (cons (service marionette-service-type
+                             (marionette-configuration
+                              (imported-modules '((gnu services herd)
+                                                  (guix combinators)))))
+                    %base-services))))
+
+(define %separate-store-installation-script
+  ;; Installation with a separate /gnu partition.
+  "\
+. /etc/profile
+set -e -x
+guix --version
+
+export GUIX_BUILD_OPTIONS=--no-grafts
+guix build isc-dhcp
+parted --script /dev/vdb mklabel gpt \\
+  mkpart primary ext2 1M 3M \\
+  mkpart primary ext2 3M 100M \\
+  mkpart primary ext2 100M 1G \\
+  set 1 boot on \\
+  set 1 bios_grub on
+mkfs.ext4 -L root-fs /dev/vdb2
+mkfs.ext4 -L store-fs /dev/vdb3
+mount /dev/vdb2 /mnt
+mkdir /mnt/gnu
+mount /dev/vdb3 /mnt/gnu
+df -h /mnt
+herd start cow-store /mnt
+mkdir /mnt/etc
+cp /etc/target-config.scm /mnt/etc/config.scm
+guix system init /mnt/etc/config.scm /mnt --no-substitutes
+sync
+reboot\n")
+
+(define %test-separate-store-os
+  (system-test
+   (name "separate-store-os")
+   (description
+    "Test basic functionality of an OS installed like one would do by hand,
+where /gnu lives on a separate partition.")
+   (value
+    (mlet* %store-monad ((image   (run-install %separate-store-os
+                                               %separate-store-os-source
+                                               #:script
+                                               %separate-store-installation-script))
+                         (command (qemu-command/writable-image image)))
+      (run-basic-test %separate-store-os command "separate-store-os")))))
+
+
+;;;
+;;; LUKS-encrypted root file system.
+;;;
+
 (define-os-with-source (%encrypted-root-os %encrypted-root-os-source)
   ;; The OS we want to install.
   (use-modules (gnu) (gnu tests) (srfi srfi-1))

From 30b12678301940a8cf15da22ef327cc7613d5607 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Wed, 26 Oct 2016 19:43:22 -0400
Subject: [PATCH 05/27] gnu: vdirsyncer: Update to 0.14.0.

* gnu/packages/dav.scm (vdirsyncer): Update to 0.14.0.
---
 gnu/packages/dav.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index be6c40f4ba..215ece9ab2 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -52,13 +52,13 @@ (define-public radicale
 (define-public vdirsyncer
   (package
     (name "vdirsyncer")
-    (version "0.13.1")
+    (version "0.14.0")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri name version))
              (sha256
               (base32
-               "1c4kipcc7dx1rn5j1a1x7wckz09mm9ihwakf3ramwn1y78q5zanb"))))
+               "1mbh2gykx9sqsnyfa962ifxksx4afl2lb9rcsbd6rsh3gj2il898"))))
     (build-system python-build-system)
     (arguments
       `(#:phases (modify-phases %standard-phases

From 522fc32ebd34b6cb68bb2aa3156360c06826e106 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Wed, 26 Oct 2016 20:09:19 -0400
Subject: [PATCH 06/27] gnu: shotwell: Update to 0.25.0.

* gnu/packages/gnome.scm (shotwell): Update to 0.25.0.
[inputs]: Add gcr.
---
 gnu/packages/gnome.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 1bd0caccb3..d5995e5d22 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -3841,7 +3841,7 @@ (define-public gexiv2
 (define-public shotwell
   (package
     (name "shotwell")
-    (version "0.23.5")
+    (version "0.25.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -3849,7 +3849,7 @@ (define-public shotwell
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0fgs1rgvkmy79bmpxrsvm5w8rvqml4l1vnwma0xqx5zzm02p8a07"))))
+                "0f3ly7nxy3kqwgs40avsqkxcz98bfmlhlk30n0d7j7ndk67zz57h"))))
     (build-system glib-or-gtk-build-system)
     (propagated-inputs
      `(("dconf" ,dconf)))
@@ -3872,7 +3872,8 @@ (define-public shotwell
        ("libsoup" ,libsoup)
        ("libxml2" ,libxml2)
        ("libgudev" ,libgudev)
-       ("libgphoto2" ,libgphoto2)))
+       ("libgphoto2" ,libgphoto2)
+       ("gcr" ,gcr)))
     (home-page "https://wiki.gnome.org/Apps/Shotwell")
     (synopsis "Photo manager for GNOME 3")
     (description

From 49a531f54541e65a0773452a7e5aaeb734116af0 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Thu, 27 Oct 2016 10:09:10 +0200
Subject: [PATCH 07/27] gnu: python-pathlib2: Add comment.

As suggested by Efraim Flashner.

* gnu/packages/python.scm (python-pathlib2): Add comment.
---
 gnu/packages/python.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index cff9897dd4..459a44c4ca 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8898,6 +8898,9 @@ (define-public python2-pathlib2
                (base32
                 "0p050msg5c8d0kadv702jnfshaxrb0il765cpkgnhn6mq5hakcyy"))))
     (build-system python-build-system)
+    ;; We only need the the Python 2 variant, since for Python 3 our minimum
+    ;; version is 3.4 which already includes this package as part of the
+    ;; standard library.
     (arguments
      `(#:python ,python-2))
     (native-inputs

From e68168eb87cdc95fa97dc5aab0c03bd1633cd67b Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 27 Oct 2016 10:04:48 +0300
Subject: [PATCH 08/27] gnu: valgrind: Update to 3.12.0.

* gnu/packages/valgrind.scm (valgrind): Update to 3.12.0.
---
 gnu/packages/valgrind.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/valgrind.scm b/gnu/packages/valgrind.scm
index ed847c2def..55ae88641c 100644
--- a/gnu/packages/valgrind.scm
+++ b/gnu/packages/valgrind.scm
@@ -30,14 +30,14 @@ (define-module (gnu packages valgrind)
 (define-public valgrind
   (package
     (name "valgrind")
-    (version "3.11.0")
+    (version "3.12.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://valgrind.org/downloads/valgrind-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "0hiv871b9bk689mv42mkhp76za78l5773glszfkdbpf1m1qn4fbc"))
+               "18bnrw9b1d55wi1wnl68n25achsp9w48n51n1xw4fwjjnaal7jk7"))
              (patches (search-patches "valgrind-enable-arm.patch"))))
     (build-system gnu-build-system)
     (arguments

From 5fd84e288cac9a7ddfea9810f6459b02b9f2f86d Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 27 Oct 2016 10:16:39 +0300
Subject: [PATCH 09/27] gnu: valgrind: Use 'modify-phases' syntax.

* gnu/packages/valgrind.scm (valgrind)[arguments]: Use 'modify-phases'
syntax.
---
 gnu/packages/valgrind.scm | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/valgrind.scm b/gnu/packages/valgrind.scm
index 55ae88641c..5f2bef16df 100644
--- a/gnu/packages/valgrind.scm
+++ b/gnu/packages/valgrind.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2013, 2014 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -41,18 +42,18 @@ (define-public valgrind
              (patches (search-patches "valgrind-enable-arm.patch"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:phases (alist-cons-after
-                 'install 'patch-suppression-files
-                 (lambda* (#:key outputs #:allow-other-keys)
-                   ;; Don't assume the FHS.
-                   (let* ((out (assoc-ref outputs "out"))
-                          (dir (string-append out "/lib/valgrind")))
-                     (substitute* (find-files dir "\\.supp$")
-                       (("obj:/lib") "obj:*/lib")
-                       (("obj:/usr/X11R6/lib") "obj:*/lib")
-                       (("obj:/usr/lib") "obj:*/lib"))
-                     #t))
-                 %standard-phases)))
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'patch-suppression-files
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Don't assume the FHS.
+             (let* ((out (assoc-ref outputs "out"))
+                    (dir (string-append out "/lib/valgrind")))
+               (substitute* (find-files dir "\\.supp$")
+                 (("obj:/lib") "obj:*/lib")
+                 (("obj:/usr/X11R6/lib") "obj:*/lib")
+                 (("obj:/usr/lib") "obj:*/lib"))
+               #t))))))
     (inputs `(;; GDB is needed to provide a sane default for `--db-command'.
               ("gdb" ,gdb)))
     (native-inputs `(("perl" ,perl)))

From 8888fe826c44b760783c2a82f140ebcda67bb22d Mon Sep 17 00:00:00 2001
From: ng0 <ng0@we.make.ritual.n0.is>
Date: Sun, 16 Oct 2016 23:00:28 +0000
Subject: [PATCH 10/27] gnu: Add dbacl.

* gnu/packages/textutils.scm (dbacl): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/textutils.scm | 86 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 86 insertions(+)

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index a9725b47d3..2259a16c91 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2016 Jelle Licht <jlicht@fsfe.org>
 ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,7 +33,12 @@ (define-module (gnu packages textutils)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages readline)
+  #:use-module (gnu packages slang)
   #:use-module (gnu packages zip))
 
 (define-public recode
@@ -373,3 +379,83 @@ (define-public utfcpp
     (description "UTF8-CPP is a C++ library for handling UTF-8 encoded text
 in a portable way.")
     (license license:boost1.0)))
+
+(define-public dbacl
+  (package
+    (name "dbacl")
+    (version "1.14")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.lbreyer.com/gpl/"
+                           name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0224g6x71hyvy7jikfxmgcwww1r5lvk0jx36cva319cb9nmrbrq7"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags
+       (list
+        (string-append "-I" (assoc-ref %build-inputs "slang")
+                       "/include/slang")
+        (string-append "-I" (assoc-ref %build-inputs "ncurses")
+                       "/include/ncurses"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'delete-sample6-and-japanese
+           (lambda _
+             (substitute* "doc/Makefile.am"
+               (("sample6.txt") "")
+               (("japanese.txt") ""))
+             (delete-file "doc/sample6.txt")
+             (delete-file "doc/japanese.txt")
+             (substitute* (list "src/tests/Makefile.am"
+                                "src/tests/Makefile.in")
+               (("dbacl-jap.shin") "")
+               (("dbacl-jap.sh") ""))
+             #t))
+         (add-after 'unpack 'delete-test
+           ;; See comments about the license.
+           (lambda _
+             (delete-file "src/tests/dbacl-jap.shin")))
+         (add-after 'delete-sample6-and-japanese 'autoreconf
+           (lambda _
+             (zero? (system* "autoreconf" "-vif"))))
+         (add-after 'unpack 'fix-test-files
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (substitute* (find-files "src/tests/" "\\.shin$")
+                 (("PATH=/bin:/usr/bin")
+                  "#PATH=/bin:/usr/bin")
+                 (("diff") (string-append (which "diff")))
+                 (("tr") (string-append (which "tr"))))
+               #t))))))
+    (inputs
+     `(("ncurses" ,ncurses)
+       ("perl" ,perl)
+       ("readline" ,readline)
+       ("slang" ,slang)))
+    (native-inputs
+     `(("libtool" ,libtool)
+       ("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("pkg-config" ,pkg-config)))
+    (home-page "http://www.lbreyer.com/dbacl.html")
+    (synopsis "Bayesian text and email classifier")
+    (description
+     "dbacl is a fast Bayesian text and email classifier.  It builds a variety
+of language models using maximum entropy (minimum divergence) principles, and
+these can then be used to categorize input data automatically among multiple
+categories.")
+    ;; The software is licensed as GPLv3 or later, but
+    ;; includes various sample texts in the doc dir:
+    ;; - sample1.txt, sample3 and sampe5.txt are in the public domain,
+    ;;   by Mark Twain.
+    ;; - sample2.txt, sample4.txt are in the public domain, by Aristotle.
+    ;; - sample6.txt is a forwarded email, copyright unknown.
+    ;;   Guix does exclude sample6.txt.
+    ;; - japanese.txt is a Japanese unoffical translation of the
+    ;;   GNU General Public License, (c) by the Free Software Foundation.
+    ;;   Guix excludes this file.
+    (license (list license:gpl3+ license:public-domain))))

From a6b256affc94bce215003e52de50ed3fa6fc0106 Mon Sep 17 00:00:00 2001
From: Mike Gerwitz <mtg@gnu.org>
Date: Sat, 22 Oct 2016 12:04:24 -0400
Subject: [PATCH 11/27] gnu: Add pcsc-lite.

* gnu/packages/security-token.scm (pcsc-lite): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/security-token.scm | 38 +++++++++++++++++++++++++++++++--
 1 file changed, 36 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm
index 36ccaa5203..735b2fe0ec 100644
--- a/gnu/packages/security-token.scm
+++ b/gnu/packages/security-token.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 Mike Gerwitz <mtg@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,9 +24,11 @@ (define-module (gnu packages security-token)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
-  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages curl)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages man)
-  #:use-module (gnu packages curl))
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config))
 
 (define-public libyubikey
   (package
@@ -47,6 +50,37 @@ (define-public libyubikey
     (home-page "https://developers.yubico.com/yubico-c/")
     (license license:bsd-2)))
 
+(define-public pcsc-lite
+  (package
+    (name "pcsc-lite")
+    (version "1.8.18")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://alioth.debian.org/frs/download.php/file/4179/"
+                    "pcsc-lite-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "0189s10xsgcmdvc2sixakncwlv47cg6by6m9vdm038gn32q34bdj"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags '("--enable-usbdropdir=/var/lib/pcsc/drivers")))
+    (native-inputs
+     `(("perl" ,perl)                   ; for pod2man
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("libudev" ,eudev)))
+    (home-page "https://pcsclite.alioth.debian.org/pcsclite.html")
+    (synopsis "Middleware to access a smart card using PC/SC")
+    (description
+     "pcsc-lite provides an interface to communicate with smartcards and
+readers using the SCard API.  pcsc-lite is used to connect to the PC/SC daemon
+from a client application and provide access to the desired reader.")
+    (license (list license:bsd-3                ; pcsc-lite
+                   license:expat                ; src/sd-daemon.[ch]
+                   license:isc                  ; src/strlcat.c src/strlcpy.c
+                   license:gpl3+))))            ; src/spy/*
+
 (define-public ykclient
   (package
     (name "ykclient")

From cd9ed6c1cbd9fdcfa38825b8109a646fb968b7a8 Mon Sep 17 00:00:00 2001
From: Mike Gerwitz <mtg@gnu.org>
Date: Sat, 22 Oct 2016 12:06:02 -0400
Subject: [PATCH 12/27] gnu: gnupg: Add support for pcsc-lite.

* gnu/packages/gnupg.scm (gnupg)[inputs]: Add pcsc-lite.
[arguments]: Rename phase 'patch-config-files' to 'patch-paths'.  Patch
`scd/scdaemon.c' with absolute path of libpcsclite.so.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/gnupg.scm | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index 5fcc03a222..60c43abda1 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -9,6 +9,7 @@
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016 Nils Gillmann <ng0@libertad.pw>
 ;;; Copyright © 2016 Christopher Baines <mail@cbaines.net>
+;;; Copyright © 2016 Mike Gerwitz <mtg@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -43,6 +44,7 @@ (define-module (gnu packages gnupg)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages security-token)
   #:use-module (gnu packages tls)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -261,6 +263,7 @@ (define-public gnupg
        ("libksba" ,libksba)
        ("npth" ,npth)
        ("openldap" ,openldap)
+       ("pcsc-lite" ,pcsc-lite)
        ("readline" ,readline)
        ("sqlite" ,sqlite)
        ("zlib" ,zlib)))
@@ -268,10 +271,14 @@ (define-public gnupg
     `(#:configure-flags '("--enable-gpg2-is-gpg")
       #:phases
       (modify-phases %standard-phases
-        (add-before 'configure 'patch-config-files
-          (lambda _
+        (add-before 'configure 'patch-paths
+          (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "tests/openpgp/defs.inc"
               (("/bin/pwd") (which "pwd")))
+            (substitute* "scd/scdaemon.c"
+              (("\"(libpcsclite\\.so[^\"]*)\"" _ name)
+               (string-append "\"" (assoc-ref inputs "pcsc-lite")
+                              "/lib/" name "\"")))
             #t)))))
     (home-page "https://gnupg.org/")
     (synopsis "GNU Privacy Guard")

From 6270769dc216fc6a2f54ca77d3090e3e610ade1c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 27 Oct 2016 09:13:19 +0200
Subject: [PATCH 13/27] gnu: btrfs-progs: Update to 4.8.2.

* gnu/packages/linux.scm (btrfs-progs): Update to 4.8.2.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index c3c84f4a86..45a2cf9799 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -2590,7 +2590,7 @@ (define-public gpm
 (define-public btrfs-progs
   (package
     (name "btrfs-progs")
-    (version "4.8.1")
+    (version "4.8.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://kernel.org/linux/kernel/"
@@ -2598,7 +2598,7 @@ (define-public btrfs-progs
                                   "btrfs-progs-v" version ".tar.xz"))
               (sha256
                (base32
-                "10yv823g92jbd6iq8d70y0bvs716jv956bq7khqmbhdzg9q6svl3"))))
+                "0pswcfmdnfc586770h74abp67gn2xv8fd46vxlimnmn837sj7h41"))))
     (build-system gnu-build-system)
     (outputs '("out"
                "static"))      ; static versions of binaries in "out" (~16MiB!)

From 483b7ce7ae2186a6c0fb4591b4d9308a5da648d8 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 27 Oct 2016 11:02:59 +0200
Subject: [PATCH 14/27] gnu: mcelog: Update to 144.

* gnu/packages/linux.scm (mcelog): Update to 144.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 45a2cf9799..c959f62424 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -2953,14 +2953,14 @@ (define-public module-init-tools
 (define-public mcelog
   (package
     (name "mcelog")
-    (version "143")
+    (version "144")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://git.kernel.org/cgit/utils/cpu/mce/"
                                   "mcelog.git/snapshot/v" version ".tar.gz"))
               (sha256
                (base32
-                "1mn5i1d6ybfxqgr6smlpxcx1wb53h0r2rp90ild7919b9yqxpk0x"))
+                "03jyhsl0s59sfqykj5p6gkb03k4w1h9ay31yxym1dnzis5sq99pa"))
               (file-name (string-append name "-" version ".tar.gz"))
               (modules '((guix build utils)))
               (snippet

From 5d5790ce44667cac4236559caba3516922c99843 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 27 Oct 2016 11:55:57 +0300
Subject: [PATCH 15/27] gnu: Use 'https' for libsdl urls.

* gnu/packages/sdl.scm (sdl, sdl2, sdl-image, sdl-mixer, sdl-net)
(sdl-ttf, sdl2-image, sdl2-ttf)[source]: Use https.
[home-page]: Use https.
---
 gnu/packages/sdl.scm | 27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm
index 161689bf24..aba57c159a 100644
--- a/gnu/packages/sdl.scm
+++ b/gnu/packages/sdl.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015 Alex Kost <alezost@gmail.com>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -47,7 +48,7 @@ (define-public sdl
     (source (origin
              (method url-fetch)
              (uri
-              (string-append "http://libsdl.org/release/SDL-"
+              (string-append "https://libsdl.org/release/SDL-"
                              version ".tar.gz"))
              (sha256
               (base32
@@ -81,7 +82,7 @@ (define-public sdl
     (description "Simple DirectMedia Layer is a cross-platform development
 library designed to provide low level access to audio, keyboard, mouse,
 joystick, and graphics hardware.")
-    (home-page "http://libsdl.org/")
+    (home-page "https://libsdl.org/")
     (license lgpl2.1)))
 
 (define-public sdl2
@@ -91,7 +92,7 @@ (define-public sdl2
     (source (origin
              (method url-fetch)
              (uri
-              (string-append "http://libsdl.org/release/SDL2-"
+              (string-append "https://libsdl.org/release/SDL2-"
                              version ".tar.gz"))
              (sha256
               (base32
@@ -154,7 +155,7 @@ (define-public sdl-image
     (source (origin
              (method url-fetch)
              (uri
-              (string-append "http://www.libsdl.org/projects/SDL_image/release/SDL_image-"
+              (string-append "https://www.libsdl.org/projects/SDL_image/release/SDL_image-"
                              version ".tar.gz"))
              (sha256
               (base32
@@ -180,7 +181,7 @@ (define-public sdl-image
     (description "SDL_image is an image file loading library for SDL that
 supports the following formats: BMP, GIF, JPEG, LBM, PCX, PNG, PNM, TGA, TIFF,
 WEBP, XCF, XPM, and XV.")
-    (home-page "http://www.libsdl.org/projects/SDL_image/")
+    (home-page "https://www.libsdl.org/projects/SDL_image/")
     (license zlib)))
 
 (define-public sdl-mixer
@@ -190,7 +191,7 @@ (define-public sdl-mixer
     (source (origin
               (method url-fetch)
               (uri
-               (string-append "http://www.libsdl.org/projects/SDL_mixer/release/SDL_mixer-"
+               (string-append "https://www.libsdl.org/projects/SDL_mixer/release/SDL_mixer-"
                               version ".tar.gz"))
               (sha256
                (base32
@@ -218,7 +219,7 @@ (define-public sdl-mixer
 It supports any number of simultaneously playing channels of 16 bit stereo
 audio, plus a single channel of music.  Supported format include FLAC, MOD,
 MIDI, Ogg Vorbis, and MP3.")
-    (home-page "http://www.libsdl.org/projects/SDL_mixer/")
+    (home-page "https://www.libsdl.org/projects/SDL_mixer/")
     (license zlib)))
 
 (define-public sdl-net
@@ -228,7 +229,7 @@ (define-public sdl-net
     (source (origin
               (method url-fetch)
               (uri
-               (string-append "http://www.libsdl.org/projects/SDL_net/release/SDL_net-"
+               (string-append "https://www.libsdl.org/projects/SDL_net/release/SDL_net-"
                               version ".tar.gz"))
               (sha256
                (base32
@@ -239,7 +240,7 @@ (define-public sdl-net
     (synopsis "SDL networking library")
     (description "SDL_net is a small, cross-platform networking library for
 SDL.")
-    (home-page "http://www.libsdl.org/projects/SDL_net/")
+    (home-page "https://www.libsdl.org/projects/SDL_net/")
     (license zlib)))
 
 (define-public sdl-ttf
@@ -249,7 +250,7 @@ (define-public sdl-ttf
     (source (origin
              (method url-fetch)
              (uri
-              (string-append "http://www.libsdl.org/projects/SDL_ttf/release/SDL_ttf-"
+              (string-append "https://www.libsdl.org/projects/SDL_ttf/release/SDL_ttf-"
                              version ".tar.gz"))
              (sha256
               (base32
@@ -261,7 +262,7 @@ (define-public sdl-ttf
     (native-inputs `(("pkg-config" ,pkg-config)))
     (synopsis "SDL TrueType font library")
     (description "SDL_ttf is a TrueType font rendering library for SDL.")
-    (home-page "http://www.libsdl.org/projects/SDL_ttf/")
+    (home-page "https://www.libsdl.org/projects/SDL_ttf/")
     (license zlib)))
 
 (define* (sdl-union #:optional (packages (list sdl sdl-gfx sdl-net sdl-ttf
@@ -308,7 +309,7 @@ (define-public sdl2-image
     (source (origin
               (method url-fetch)
               (uri
-               (string-append "http://www.libsdl.org/projects/SDL_image/release/SDL2_image-"
+               (string-append "https://www.libsdl.org/projects/SDL_image/release/SDL2_image-"
                               version ".tar.gz"))
               (sha256
                (base32
@@ -342,7 +343,7 @@ (define-public sdl2-ttf
     (source (origin
              (method url-fetch)
              (uri
-              (string-append "http://www.libsdl.org/projects/SDL_ttf/release/SDL2_ttf-"
+              (string-append "https://www.libsdl.org/projects/SDL_ttf/release/SDL2_ttf-"
                              version ".tar.gz"))
              (modules '((guix build utils)))
              (snippet

From 355d8e873b655b80bad34d283c1ea8cfff4c5d02 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 27 Oct 2016 12:07:35 +0300
Subject: [PATCH 16/27] gnu: sdl2: Update to 2.0.5.

* gnu/packages/sdl.scm (sdl2): Update to 2.0.5.
---
 gnu/packages/sdl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm
index aba57c159a..a942b33302 100644
--- a/gnu/packages/sdl.scm
+++ b/gnu/packages/sdl.scm
@@ -88,7 +88,7 @@ (define-public sdl
 (define-public sdl2
   (package (inherit sdl)
     (name "sdl2")
-    (version "2.0.4")
+    (version "2.0.5")
     (source (origin
              (method url-fetch)
              (uri
@@ -96,7 +96,7 @@ (define-public sdl2
                              version ".tar.gz"))
              (sha256
               (base32
-               "0jqp46mxxbh9lhpx1ih6sp93k752j2smhpc0ad0q4cb3px0famfs"))))
+               "11c75qj1qxmx67iwkvf9z4x69phk301pdn86zzr6jncnap7kh824"))))
     (license bsd-3)))
 
 (define-public libmikmod

From 7d876afdd8648a481fd8736985cd3359086b0dfb Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 27 Oct 2016 12:13:07 +0300
Subject: [PATCH 17/27] gnu: libmikmod: Update to 3.3.10.

* gnu/packages/sdl.scm (libmikmod): Update to 3.3.10.
---
 gnu/packages/sdl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm
index a942b33302..bb4ad1c90b 100644
--- a/gnu/packages/sdl.scm
+++ b/gnu/packages/sdl.scm
@@ -102,14 +102,14 @@ (define-public sdl2
 (define-public libmikmod
   (package
     (name "libmikmod")
-    (version "3.3.7")
+    (version "3.3.10")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/mikmod/libmikmod/"
                                  version "/libmikmod-" version ".tar.gz"))
              (sha256
               (base32
-               "18nrkf5l50hfg0y50yxr7bvik9f002lhn8c00nbcp6dgm5011x2c"))))
+               "0j7g4jpa2zgzw7x6s3rldypa7zlwjvn97rwx0sylx1iihhlzbcq0"))))
     (build-system gnu-build-system)
     (arguments
      ;; By default, libmikmod tries to dlopen libasound etc., which won't work

From 631fda7e90c5327cb365b785b221f37a899e8bce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 27 Oct 2016 11:18:53 +0200
Subject: [PATCH 18/27] gnu: Add mdadm-static.

* gnu/packages/linux.scm (mdadm-static): New variable.
---
 gnu/packages/linux.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index c959f62424..3db3a58a02 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -2374,6 +2374,35 @@ (define-public mdadm
 arrays when needed.")
     (license license:gpl2+)))
 
+(define-public mdadm-static
+  (package
+    (inherit mdadm)
+    (name "mdadm-static")
+    (arguments
+     (substitute-keyword-arguments (package-arguments mdadm)
+       ((#:make-flags flags)
+        `(cons "LDFLAGS = -static" ,flags))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'install 'remove-cruft
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out         (assoc-ref outputs "out"))
+                      (precious?   (lambda (file)
+                                     (member file '("." ".." "sbin"))))
+                      (directories (scandir out (negate precious?))))
+                 (with-directory-excursion out
+                   (for-each delete-file-recursively directories)
+                   (remove-store-references "sbin/mdadm")
+                   (delete-file "sbin/mdmon")
+                   #t))))))
+       ((#:modules modules %gnu-build-system-modules)
+        `((ice-9 ftw) ,@modules))
+       ((#:strip-flags _ '())
+        ''("--strip-all"))                        ;strip a few extra KiB
+       ((#:allowed-references _ '("out"))
+        '("out"))))                               ;refer only self
+    (synopsis "Statically-linked 'mdadm' command for use in an initrd")))
+
 (define-public libaio
   (package
     (name "libaio")

From 4ed2f515d69a199154c272997f4683b89ac0a9b8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 27 Oct 2016 11:20:26 +0200
Subject: [PATCH 19/27] mapped-devices: Use 'mdadm-static' in
 'raid-device-mapping'.

* gnu/system/mapped-devices.scm (open-raid-device, close-raid-device):
Use MDADM-STATIC instead of MDADM.  Use 'file-append'.
---
 gnu/system/mapped-devices.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/system/mapped-devices.scm b/gnu/system/mapped-devices.scm
index 2487638c52..e44f2693a7 100644
--- a/gnu/system/mapped-devices.scm
+++ b/gnu/system/mapped-devices.scm
@@ -24,7 +24,7 @@ (define-module (gnu system mapped-devices)
   #:use-module (gnu services)
   #:use-module (gnu services shepherd)
   #:autoload   (gnu packages cryptsetup) (cryptsetup)
-  #:autoload   (gnu packages linux) (mdadm)
+  #:autoload   (gnu packages linux) (mdadm-static)
   #:use-module (srfi srfi-1)
   #:use-module (ice-9 match)
   #:export (mapped-device
@@ -150,12 +150,14 @@ (define (open-raid-device sources target)
           (sleep 1)
           (loop (+ 1 attempts))))
 
-      (zero? (apply system* (string-append #$mdadm "/sbin/mdadm")
+      ;; Use 'mdadm-static' rather than 'mdadm' to avoid pulling its whole
+      ;; closure (80 MiB) in the initrd when a RAID device is needed for boot.
+      (zero? (apply system* #$(file-append mdadm-static "/sbin/mdadm")
                     "--assemble" #$target sources))))
 
 (define (close-raid-device sources target)
   "Return a gexp that stops the RAID device TARGET."
-  #~(zero? (system* (string-append #$mdadm "/sbin/mdadm")
+  #~(zero? (system* #$(file-append mdadm-static "/sbin/mdadm")
                     "--stop" #$target)))
 
 (define raid-device-mapping

From b800b8da2123fb6877c706a06e531b7266aee507 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 27 Oct 2016 11:21:28 +0200
Subject: [PATCH 20/27] tests: Add #:memory-size parameter for the command to
 run the installed OS.

* gnu/tests/install.scm (qemu-command/writable-image): Add #:memory-size
parameter and honor it.
---
 gnu/tests/install.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/tests/install.scm b/gnu/tests/install.scm
index 0f54935ea8..b3908ec7b2 100644
--- a/gnu/tests/install.scm
+++ b/gnu/tests/install.scm
@@ -191,9 +191,9 @@ (define marionette
 
     (gexp->derivation "installation" install)))
 
-(define (qemu-command/writable-image image)
+(define* (qemu-command/writable-image image #:key (memory-size 256))
   "Return as a monadic value the command to run QEMU on a writable copy of
-IMAGE, a disk image."
+IMAGE, a disk image.  The QEMU VM is has access to MEMORY-SIZE MiB of RAM."
   (mlet %store-monad ((system (current-system)))
     (return #~(let ((image #$image))
                 ;; First we need a writable copy of the image.
@@ -205,7 +205,7 @@ (define (qemu-command/writable-image image)
                   ,@(if (file-exists? "/dev/kvm")
                         '("-enable-kvm")
                         '())
-                  "-no-reboot" "-m" "256"
+                  "-no-reboot" "-m" #$(number->string memory-size)
                   "-drive" "file=disk.img,if=virtio")))))
 
 

From 49baaff4d2995cc4455843d7249894cb7456d8d5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 27 Oct 2016 13:44:13 +0200
Subject: [PATCH 21/27] file-systems: 'disk-partitions' detected partitions
 from mapped devices.

Previously, partitions of mdadm- or cryptsetup-produced block devices
would not be returned by 'disk-partitions'.

* gnu/build/file-systems.scm (disk-partitions)[last-character]: New
procedure.
[partition?]: Add 'name' parameter and rewrite.  Adjust caller.
* gnu/build/file-systems.scm (ENOENT-safe): Silently ignore ENOMEDIUM.
---
 gnu/build/file-systems.scm | 35 +++++++++++++++++++----------------
 1 file changed, 19 insertions(+), 16 deletions(-)

diff --git a/gnu/build/file-systems.scm b/gnu/build/file-systems.scm
index f1fccbdf2e..bfc353ae6b 100644
--- a/gnu/build/file-systems.scm
+++ b/gnu/build/file-systems.scm
@@ -192,15 +192,15 @@ (define (luks-header-uuid header)
 
 (define (disk-partitions)
   "Return the list of device names corresponding to valid disk partitions."
-  (define (partition? major minor)
-    (let ((marker (format #f "/sys/dev/block/~a:~a/partition" major minor)))
-      (catch 'system-error
-        (lambda ()
-          (not (zero? (call-with-input-file marker read))))
-        (lambda args
-          (if (= ENOENT (system-error-errno args))
-              #f
-              (apply throw args))))))
+  (define (last-character str)
+    (string-ref str (- (string-length str) 1)))
+
+  (define (partition? name major minor)
+    ;; Select device names that end in a digit, like libblkid's 'probe_all'
+    ;; function does.  Checking for "/sys/dev/block/MAJOR:MINOR/partition"
+    ;; doesn't work for partitions coming from mapped devices.
+    (and (char-set-contains? char-set:digit (last-character name))
+         (> major 2)))                      ;ignore RAM disks and floppy disks
 
   (call-with-input-file "/proc/partitions"
     (lambda (port)
@@ -217,7 +217,7 @@ (define (partition? major minor)
               (match (string-tokenize line)
                 (((= string->number major) (= string->number minor)
                   blocks name)
-                 (if (partition? major minor)
+                 (if (partition? name major minor)
                      (loop (cons name parts))
                      (loop parts))))))))))
 
@@ -232,12 +232,15 @@ (define (ENOENT-safe proc)
         ;; When running on the hand-made /dev,
         ;; 'disk-partitions' could return partitions for which
         ;; we have no /dev node.  Handle that gracefully.
-        (if (= ENOENT (system-error-errno args))
-            (begin
-              (format (current-error-port)
-                      "warning: device '~a' not found~%" device)
-              #f)
-            (apply throw args))))))
+        (let ((errno (system-error-errno args)))
+          (cond ((= ENOENT errno)
+                 (format (current-error-port)
+                         "warning: device '~a' not found~%" device)
+                 #f)
+                ((= ENOMEDIUM errno)              ;for removable media
+                 #f)
+                (else
+                 (apply throw args))))))))
 
 (define (partition-predicate read field =)
   "Return a predicate that returns true if the FIELD of partition header that

From 245cc5f5d55e8c0931a1a2d2becd78f9805de2df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 27 Oct 2016 13:46:43 +0200
Subject: [PATCH 22/27] tests: Test installation with a RAID root partition.

* gnu/tests/install.scm (%raid-root-os, %raid-root-os-source)
(%raid-root-installation-script, %test-raid-root-os): New variables.
---
 gnu/tests/install.scm | 84 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)

diff --git a/gnu/tests/install.scm b/gnu/tests/install.scm
index b3908ec7b2..98f8649af8 100644
--- a/gnu/tests/install.scm
+++ b/gnu/tests/install.scm
@@ -34,6 +34,7 @@ (define-module (gnu tests install)
   #:use-module (guix utils)
   #:export (%test-installed-os
             %test-separate-store-os
+            %test-raid-root-os
             %test-encrypted-os))
 
 ;;; Commentary:
@@ -299,6 +300,89 @@ (define %test-separate-store-os
                          (command (qemu-command/writable-image image)))
       (run-basic-test %separate-store-os command "separate-store-os")))))
 
+
+;;;
+;;; RAID root device.
+;;;
+
+(define-os-with-source (%raid-root-os %raid-root-os-source)
+  ;; An OS whose root partition is a RAID partition.
+  (use-modules (gnu) (gnu tests))
+
+  (operating-system
+    (host-name "raidified")
+    (timezone "Europe/Paris")
+    (locale "en_US.utf8")
+
+    (bootloader (grub-configuration (device "/dev/vdb")))
+    (kernel-arguments '("console=ttyS0"))
+    (initrd (lambda (file-systems . rest)
+              ;; Add a kernel module for RAID-0 (aka. "stripe").
+              (apply base-initrd file-systems
+                     #:extra-modules '("raid0")
+                     rest)))
+    (mapped-devices (list (mapped-device
+                           (source (list "/dev/vda2" "/dev/vda3"))
+                           (target "/dev/md0")
+                           (type raid-device-mapping))))
+    (file-systems (cons (file-system
+                          (device "root-fs")
+                          (title 'label)
+                          (mount-point "/")
+                          (type "ext4")
+                          (dependencies mapped-devices))
+                        %base-file-systems))
+    (users %base-user-accounts)
+    (services (cons (service marionette-service-type
+                             (marionette-configuration
+                              (imported-modules '((gnu services herd)
+                                                  (guix combinators)))))
+                    %base-services))))
+
+(define %raid-root-installation-script
+  ;; Installation with a separate /gnu partition.  See
+  ;; <https://raid.wiki.kernel.org/index.php/RAID_setup> for more on RAID and
+  ;; mdadm.
+  "\
+. /etc/profile
+set -e -x
+guix --version
+
+export GUIX_BUILD_OPTIONS=--no-grafts
+parted --script /dev/vdb mklabel gpt \\
+  mkpart primary ext2 1M 3M \\
+  mkpart primary ext2 3M 600M \\
+  mkpart primary ext2 600M 1200M \\
+  set 1 boot on \\
+  set 1 bios_grub on
+mdadm --create /dev/md0 --verbose --level=stripe --raid-devices=2 \\
+  /dev/vdb2 /dev/vdb3
+mkfs.ext4 -L root-fs /dev/md0
+mount /dev/md0 /mnt
+df -h /mnt
+herd start cow-store /mnt
+mkdir /mnt/etc
+cp /etc/target-config.scm /mnt/etc/config.scm
+guix system init /mnt/etc/config.scm /mnt --no-substitutes
+sync
+reboot\n")
+
+(define %test-raid-root-os
+  (system-test
+   (name "raid-root-os")
+   (description
+    "Test functionality of an OS installed with a RAID root partition managed
+by 'mdadm'.")
+   (value
+    (mlet* %store-monad ((image   (run-install %raid-root-os
+                                               %raid-root-os-source
+                                               #:script
+                                               %raid-root-installation-script
+                                               #:target-size (* 1300 MiB)))
+                         (command (qemu-command/writable-image image)))
+      (run-basic-test %raid-root-os
+                      `(,@command) "raid-root-os")))))
+
 
 ;;;
 ;;; LUKS-encrypted root file system.

From 6178274d19ed3e637b5365b64a28f298574df81f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 27 Oct 2016 14:03:07 +0100
Subject: [PATCH 23/27] gnu: python-urllib3: Update to 1.18.1.

* gnu/packages/python.scm (python-urllib3): Update to 1.18.1.
[home-page]: Use https URL.
---
 gnu/packages/python.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 459a44c4ca..f33a2fa11f 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7711,14 +7711,14 @@ (define-public python2-promise
 (define-public python-urllib3
   (package
     (name "python-urllib3")
-    (version "1.13.1")
+    (version "1.18.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "urllib3" version))
         (sha256
          (base32
-          "10rrbr6c6k7j5dvfsyj4b2gsgxg9gggnn708qixf6ll57xqivfkf"))))
+          "1wb8aqnq53vzh2amrv8kc66f3h6fx217y0q62y6n30a64p2yqmam"))))
     (build-system python-build-system)
     (arguments `(#:tests? #f))
     (native-inputs
@@ -7733,7 +7733,7 @@ (define-public python-urllib3
        ("python-ndg-httpsclient" ,python-ndg-httpsclient)
        ("python-pyasn1" ,python-pyasn1)
        ("python-pyopenssl" ,python-pyopenssl)))
-    (home-page "http://urllib3.readthedocs.org/")
+    (home-page "https://urllib3.readthedocs.org/")
     (synopsis "HTTP library with thread-safe connection pooling")
     (description
      "Urllib3 supports features left out of urllib and urllib2 libraries.  It

From b5ce25cc0ecd1d8393f89ddca91be7000c0cc2cd Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 27 Oct 2016 16:36:09 +0200
Subject: [PATCH 24/27] gnu: r: Use uname from Guix

* gnu/packages/statistics.scm (r): Use uname from Guix.
---
 gnu/packages/statistics.scm | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 29eaadf394..b15f9cf45e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -118,6 +118,13 @@ (define-public r
                             "/lib/R/lib"))
        #:phases
        (modify-phases %standard-phases
+         (add-before 'configure 'patch-uname
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
+                                             "/bin/uname")))
+               (substitute* "src/scripts/R.sh.in"
+                 (("uname") uname-bin)))
+             #t))
          (add-before
           'configure 'set-default-pager
           ;; Set default pager to "cat", because otherwise it is "false",
@@ -169,6 +176,7 @@ (define-public r
      `(;; We need not only cairo here, but pango to ensure that tests for the
        ;; "cairo" bitmapType plotting backend succeed.
        ("pango" ,pango)
+       ("coreutils" ,coreutils)
        ("curl" ,curl)
        ("tzdata" ,tzdata)
        ("gfortran" ,gfortran)

From 233fbb61022c79ff0c2b11d908f34f3020d7fbbb Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kei@openmailbox.org>
Date: Sun, 23 Oct 2016 11:26:25 -0400
Subject: [PATCH 25/27] gnu: windowmaker: Add support for more image formats.

* gnu/packages/gnustep.scm (windowmaker)[inputs]: Add giflib, libpng,
and libtiff.
---
 gnu/packages/gnustep.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/gnustep.scm b/gnu/packages/gnustep.scm
index f49b25492e..6c365cbbc4 100644
--- a/gnu/packages/gnustep.scm
+++ b/gnu/packages/gnustep.scm
@@ -76,7 +76,10 @@ (define-public windowmaker
        ("libxft" ,libxft)
        ("libx11" ,libx11)
        ("fontconfig" ,fontconfig)
-       ("libjpeg" ,libjpeg)))
+       ("libjpeg" ,libjpeg)
+       ("giflib" ,giflib)
+       ("libpng" ,libpng)
+       ("libtiff" ,libtiff)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (home-page "http://windowmaker.org/")

From 327be74720bff418e611e399f92a4182a98e9750 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 27 Oct 2016 20:14:17 +0300
Subject: [PATCH 26/27] gnu: jasper: Updat eto 1.900.16.

* gnu/packages/image.scm (japer): Update to 1.900.16.
---
 gnu/packages/image.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index acde2d4064..4e1c10f16b 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -781,14 +781,14 @@ (define-public devil
 (define-public jasper
   (package
     (name "jasper")
-    (version "1.900.13")
+    (version "1.900.16")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.ece.uvic.ca/~frodo/jasper"
                                   "/software/jasper-" version ".tar.gz"))
               (sha256
                (base32
-                "0nmy5248gar057s94a30fssvq70m3jy4vdrfcispvn01ih33fa19"))))
+                "0wgrz6970sf8apyld35vrxamzx46fq15l0ipkvjsjlbwfrhj57rl"))))
     (build-system gnu-build-system)
     (arguments
      '(#:make-flags '("CFLAGS=-std=c99"))) ; 1.900.13 added c++ style comments

From 7500e42b3e51fa9ba5fb2ba552f168081b7f044a Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 27 Oct 2016 20:07:05 +0200
Subject: [PATCH 27/27] gnu: Add r-mutationalpatterns.

* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
---
 gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fa35531868..4e9397e14e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7394,6 +7394,39 @@ (define-public rcas-web
 @dfn{RNA-centric annotation system} (RCAS).")
     (license license:agpl3+)))
 
+(define-public r-mutationalpatterns
+  (package
+    (name "r-mutationalpatterns")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MutationalPatterns" version))
+       (sha256
+        (base32
+         "1a3c2bm0xx0q4gf98jiw74msmdf2fr8rbsdysd5ww9kqlzmsbr17"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-iranges" ,r-iranges)
+       ("r-nmf" ,r-nmf)
+       ("r-plyr" ,r-plyr)
+       ("r-pracma" ,r-pracma)
+       ("r-reshape2" ,r-reshape2)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "http://bioconductor.org/packages/MutationalPatterns/")
+    (synopsis "Extract and visualize mutational patterns in genomic data")
+    (description "This package provides an extensive toolset for the
+characterization and visualization of a wide range of mutational patterns
+in SNV base substitution data.")
+    (license license:expat)))
+
 (define-public emboss
   (package
     (name "emboss")