Merge branch 'master' into core-updates

125 files changed, 2984 insertions, 1839 deletions

diff --git a/Makefile.am b/Makefile.am
index af6870cf67..5c8639d665 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -63,9 +63,6 @@ MODULES =					\
   guix/base64.scm				\
   guix/cpio.scm					\
   guix/records.scm				\
-  guix/gcrypt.scm				\
-  guix/hash.scm					\
-  guix/pk-crypto.scm				\
   guix/pki.scm					\
   guix/progress.scm				\
   guix/combinators.scm				\
@@ -207,6 +204,7 @@ MODULES =					\
   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				\
@@ -331,8 +329,6 @@ SCM_TESTS =					\
   tests/base32.scm				\
   tests/base64.scm				\
   tests/cpio.scm				\
-  tests/hash.scm				\
-  tests/pk-crypto.scm				\
   tests/pki.scm					\
   tests/print.scm				\
   tests/sets.scm				\
@@ -414,6 +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)
diff --git a/README b/README
index 348a7ada5f..4c76c4bc43 100644
--- a/README
+++ b/README
@@ -21,7 +21,7 @@ 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
@@ -31,6 +31,7 @@ GNU Guix currently depends on the following packages:
 
 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]]
diff --git a/build-aux/build-self.scm b/build-aux/build-self.scm
index edb7f5d9c5..9e8cc90067 100644
--- a/build-aux/build-self.scm
+++ b/build-aux/build-self.scm
@@ -22,6 +22,7 @@
   #: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 (rnrs io ports)
@@ -72,7 +73,7 @@
                                       (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 +93,6 @@
                                %state-directory
                                %store-database-directory
                                %config-directory
-                               %libgcrypt
                                %libz
                                %gzip
                                %bzip2
@@ -137,9 +137,6 @@
                      (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 +197,54 @@ 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 +257,21 @@ 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))))
+
   (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)
+
                            ,@(source-module-closure `((guix store)
                                                       (guix self)
                                                       (guix derivations)
@@ -237,13 +293,24 @@ person's version identifier."
                            (match %load-path
                              ((front _ ...)
                               (unless (string=? front source) ;already done?
-                                (set! %load-path (list source front)))))))
-
-                        ;; Only load our own modules or those of Guile.
+                                (set! %load-path
+                                  (list source
+                                        (string-append #$guile-gcrypt
+                                                       "/share/guile/site/"
+                                                       (effective-version))
+                                        front)))))))
+
+                        ;; Only load Guile-Gcrypt, our own modules, or those
+                        ;; of Guile.
                         (match %load-compiled-path
                           ((front _ ... sys1 sys2)
-                           (set! %load-compiled-path
-                             (list front sys1 sys2)))))
+                           (unless (string-prefix? #$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)
diff --git a/config-daemon.ac b/config-daemon.ac
index 6cf65bef1d..04f0fde3b2 100644
--- a/config-daemon.ac
+++ b/config-daemon.ac
@@ -48,7 +48,7 @@ if test "x$guix_build_daemon" = "xyes"; then
   esac
 
   case "$LIBGCRYPT_LIBDIR" in
-    no)
+    no | "")
       LIBGCRYPT_LIBS="-lgcrypt"
       ;;
     *)
diff --git a/configure.ac b/configure.ac
index b34f15a77b..c83d4d8a28 100644
--- a/configure.ac
+++ b/configure.ac
@@ -130,6 +130,11 @@ if test "x$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 +218,10 @@ 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
 
diff --git a/doc/guix.texi b/doc/guix.texi
index 307f915dbb..19a497c746 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -147,6 +147,7 @@ Package Management
 * Invoking guix gc::            Running the garbage collector.
 * Invoking guix pull::          Fetching the latest Guix and distribution.
 * Channels::                    Customizing the package collection.
+* Invoking guix describe::      Display information about your Guix revision.
 * Invoking guix pack::          Creating software bundles.
 * Invoking guix archive::       Exporting and importing store files.
 
@@ -620,7 +621,8 @@ GNU Guix depends on the following packages:
 @itemize
 @item @url{http://gnu.org/software/guile/, GNU Guile}, version 2.0.13 or
 later, including 2.2.x;
-@item @url{http://gnupg.org/, GNU libgcrypt};
+@item @url{https://notabug.org/cwebber/guile-gcrypt, Guile-Gcrypt}, version
+0.1.0 or later;
 @item
 @uref{http://gnutls.org/, GnuTLS}, specifically its Guile bindings
 (@pxref{Guile Preparations, how to install the GnuTLS bindings for
@@ -662,6 +664,7 @@ Unless @code{--disable-daemon} was passed to @command{configure}, the
 following packages are also needed:
 
 @itemize
+@item @url{http://gnupg.org/, GNU libgcrypt};
 @item @url{http://sqlite.org, SQLite 3};
 @item @url{http://gcc.gnu.org, GCC's g++}, with support for the
 C++11 standard.
@@ -1696,6 +1699,7 @@ guix package -i emacs-guix
 * Invoking guix gc::            Running the garbage collector.
 * Invoking guix pull::          Fetching the latest Guix and distribution.
 * Channels::                    Customizing the package collection.
+* Invoking guix describe::      Display information about your Guix revision.
 * Invoking guix pack::          Creating software bundles.
 * Invoking guix archive::       Exporting and importing store files.
 @end menu
@@ -1749,7 +1753,7 @@ collected.
 
 @cindex reproducibility
 @cindex reproducible builds
-Finally, Guix takes a @dfn{purely functional} approach to package
+Guix takes a @dfn{purely functional} approach to package
 management, as described in the introduction (@pxref{Introduction}).
 Each @file{/gnu/store} package directory name contains a hash of all the
 inputs that were used to build that package---compiler, libraries, build
@@ -1777,6 +1781,15 @@ a package to quickly set up the right development environment for their
 package, without having to manually install the dependencies of the
 package into their profile (@pxref{Invoking guix environment}).
 
+@cindex replication, of software environments
+@cindex provenance tracking, of software artifacts
+All of Guix and its package definitions is version-controlled, and
+@command{guix pull} allows you to ``travel in time'' on the history of Guix
+itself (@pxref{Invoking guix pull}).  This makes it possible to replicate a
+Guix instance on a different machine or at a later point in time, which in
+turn allows you to @emph{replicate complete software environments}, while
+retaining precise @dfn{provenance tracking} of the software.
+
 @node Invoking guix package
 @section Invoking @command{guix package}
 
@@ -2804,6 +2817,9 @@ Generation 3	Jun 13 2018 23:31:07	(current)
   69 packages upgraded: borg@@1.1.6, cheese@@3.28.0, @dots{}
 @end example
 
+@ref{Invoking guix describe, @command{guix describe}}, for other ways to
+describe the current status of Guix.
+
 This @code{~/.config/guix/current} profile works like any other profile
 created by @command{guix package} (@pxref{Invoking guix package}).  That
 is, you can list generations, roll back to the previous
@@ -2849,6 +2865,13 @@ is provided, the subset of generations that match @var{pattern}.
 The syntax of @var{pattern} is the same as with @code{guix package
 --list-generations} (@pxref{Invoking guix package}).
 
+@ref{Invoking guix describe}, for a way to display information about the
+current generation only.
+
+@item --profile=@var{profile}
+@itemx -p @var{profile}
+Use @var{profile} instead of @file{~/.config/guix/current}.
+
 @item --bootstrap
 Use the bootstrap Guile to build the latest Guix.  This option is only
 useful to Guix developers.
@@ -3017,6 +3040,9 @@ say, on another machine, by providing a channel specification in
        (branch "dd3df5e2c8818760a8fc0bd699e55d3b69fef2bb")))
 @end lisp
 
+The @command{guix describe --format=channels} command can even generate this
+list of channels directly (@pxref{Invoking guix describe}).
+
 At this point the two machines run the @emph{exact same Guix}, with access to
 the @emph{exact same packages}.  The output of @command{guix build gimp} on
 one machine will be exactly the same, bit for bit, as the output of the same
@@ -3028,6 +3054,78 @@ This gives you super powers, allowing you to track the provenance of binary
 artifacts with very fine grain, and to reproduce software environments at
 will---some sort of ``meta reproducibility'' capabilities, if you will.
 
+@node Invoking guix describe
+@section Invoking @command{guix describe}
+
+@cindex reproducibility
+@cindex replicating Guix
+Often you may want to answer questions like: ``Which revision of Guix am I
+using?'' or ``Which channels am I using?''  This is useful information in many
+situations: if you want to @emph{replicate} an environment on a different
+machine or user account, if you want to report a bug or to determine what
+change in the channels you are using caused it, or if you want to record your
+system state for reproducibility purposes.  The @command{guix describe}
+command answers these questions.
+
+When run from a @command{guix pull}ed @command{guix}, @command{guix describe}
+displays the channel(s) that it was built from, including their repository URL
+and commit IDs (@pxref{Channels}):
+
+@example
+$ guix describe
+Generation 10	Sep 03 2018 17:32:44	(current)
+  guix e0fa68c
+    repository URL: https://git.savannah.gnu.org/git/guix.git
+    branch: master
+    commit: e0fa68c7718fffd33d81af415279d6ddb518f727
+@end example
+
+If you're familiar with the Git version control system, this is similar in
+spirit to @command{git describe}; the output is also similar to that of
+@command{guix pull --list-generations}, but limited to the current generation
+(@pxref{Invoking guix pull, the @option{--list-generations} option}).  Because
+the Git commit ID shown above unambiguously refers to a snapshot of Guix, this
+information is all it takes to describe the revision of Guix you're using, and
+also to replicate it.
+
+To make it easier to replicate Guix, @command{guix describe} can also be asked
+to return a list of channels instead of the human-readable description above:
+
+@example
+$ guix describe -f channels
+(list (channel
+        (name 'guix)
+        (url "https://git.savannah.gnu.org/git/guix.git")
+        (commit
+          "e0fa68c7718fffd33d81af415279d6ddb518f727")))
+@end example
+
+@noindent
+You can save this to a file and feed it to @command{guix pull -C} on some
+other machine or at a later point in time, which will instantiate @emph{this
+exact Guix revision} (@pxref{Invoking guix pull, the @option{-C} option}).
+From there on, since you're able to deploy the same revision of Guix, you can
+just as well @emph{replicate a complete software environment}.  We humbly
+think that this is @emph{awesome}, and we hope you'll like it too!
+
+The details of the options supported by @command{guix describe} are as
+follows:
+
+@table @code
+@item --format=@var{format}
+@itemx -f @var{format}
+Produce output in the specified @var{format}, one of:
+
+@table @code
+@item human
+produce human-readable output;
+@item channels
+produce a list of channel specifications that can be passed to @command{guix
+pull -C} or installed as @file{~/.config/guix/channels.scm} (@pxref{Invoking
+guix pull}).
+@end table
+@end table
+
 @node Invoking guix pack
 @section Invoking @command{guix pack}
 
@@ -16823,6 +16921,13 @@ Extension package for @code{hpcguix-web}.
 
 @item @code{menu} (default: @code{'()})
 Additional entry in page @code{menu}.
+
+@item @code{channels} (default: @code{%default-channels})
+List of channels from which the package list is built (@pxref{Channels}).
+
+@item @code{package-list-expiration} (default: @code{(* 12 3600)})
+The expiration time, in seconds, after which the package list is rebuilt from
+the latest instances of the given channels.
 @end table
 
 See the hpcguix-web repository for a
@@ -16846,6 +16951,17 @@ A typical hpcguix-web service declaration looks like this:
                 (menu '(("/about" "ABOUT"))))))))
 @end example
 
+@quotation Note
+The hpcguix-web service periodically updates the package list it publishes by
+pulling channels from Git.  To that end, it needs to access X.509 certificates
+so that it can authenticate Git servers when communicating over HTTPS, and it
+assumes that @file{/etc/ssl/certs} contains those certificates.
+
+Thus, make sure to add @code{nss-certs} or another certificate package to the
+@code{packages} field of your configuration.  @ref{X.509 Certificates}, for
+more information on X.509 certificates.
+@end quotation
+
 @node Certificate Services
 @subsubsection Certificate Services
 
diff --git a/gnu/local.mk b/gnu/local.mk
index 21f0482847..c3cd1d4084 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -729,6 +729,8 @@ dist_patch_DATA =						\
   %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/ghostscript-CVE-2018-10194.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 \
@@ -955,6 +957,7 @@ 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/mes-nyacc-0.86.0.patch			\
   %D%/packages/patches/mesa-skip-disk-cache-test.patch		\
   %D%/packages/patches/meson-for-build-rpath.patch		\
   %D%/packages/patches/metabat-fix-compilation.patch		\
@@ -991,6 +994,7 @@ 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/ocaml-bisect-fix-camlp4-in-another-directory.patch	\
   %D%/packages/patches/ocaml-bitstring-fix-configure.patch \
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index e731569ae1..3b898c024a 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1908,7 +1908,7 @@ lv2-c++-tools.")
 (define-public openal
   (package
     (name "openal")
-    (version "1.18.2")
+    (version "1.19.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1916,7 +1916,7 @@ lv2-c++-tools.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "10kydm8701a2kppiss9sdidn1820cmzhqgx1b2bsa5dsgzic32lz"))))
+                "1mhf5bsb58s1xk6hvxl7ly7rd4rpl9z8h07xl1q94brywykg7bgi"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f  ; no check target
diff --git a/gnu/packages/bash.scm b/gnu/packages/bash.scm
index 46cb13048d..fb4e3f4be3 100644
--- a/gnu/packages/bash.scm
+++ b/gnu/packages/bash.scm
@@ -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)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7e993189d6..a47a5aad05 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -360,17 +360,64 @@ 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 "1.58.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "graph" version))
+              (sha256
+               (base32
+                "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759"))))
+    (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 "3.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0"))))
+         "1cn1hfc3nvsf2n3563lkmvwjxfbiygx7f84zk683p89gy7zi1gyj"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f60fc4c84c..2d5ec6d170 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -51,6 +51,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
+  #:use-module (gnu packages bioconductor)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
@@ -1887,42 +1888,33 @@ other types of unwanted sequence from high-throughput sequencing reads.")
 (define-public libbigwig
   (package
     (name "libbigwig")
-    (version "0.1.4")
+    (version "0.4.2")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/dpryan79/libBigWig/"
-                                  "archive/" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/dpryan79/libBigWig.git")
+                    (commit version)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
+                "0h2smg24v5srdcqzrmz2g23cmlp4va465mgx8r2z571sfz8pv454"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
+       #:tests? #f ; tests require access to the web
        #:make-flags
        (list "CC=gcc"
              (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure)
-         (add-before 'check 'disable-curl-test
-           (lambda _
-             (substitute* "Makefile"
-               (("./test/testRemote.*") ""))
-             #t))
-         ;; This has been fixed with the upstream commit 4ff6959cd8a0, but
-         ;; there has not yet been a release containing this change.
-         (add-before 'install 'create-target-dirs
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (mkdir-p (string-append out "/lib"))
-               (mkdir-p (string-append out "/include"))
-               #t))))))
+         (delete 'configure))))
     (inputs
      `(("zlib" ,zlib)
        ("curl" ,curl)))
     (native-inputs
-     `(("doxygen" ,doxygen)))
+     `(("doxygen" ,doxygen)
+       ;; Need for tests
+       ("python" ,python-2)))
     (home-page "https://github.com/dpryan79/libBigWig")
     (synopsis "C library for handling bigWig files")
     (description
@@ -1933,13 +1925,13 @@ files.")
 (define-public python-pybigwig
   (package
     (name "python-pybigwig")
-    (version "0.2.5")
+    (version "0.3.12")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pyBigWig" version))
               (sha256
                (base32
-                "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
+                "00w4kfnm2c5l7wdwr2nj1z5djv8kzgf7h1zhsgv6njff1rwr26g0"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1955,6 +1947,8 @@ files.")
              (substitute* "setup.py"
                (("libs=\\[") "libs=[\"BigWig\", "))
              #t)))))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)))
     (inputs
      `(("libbigwig" ,libbigwig)
        ("zlib" ,zlib)
@@ -6378,14 +6372,14 @@ exploration of the results.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.22.0")
+    (version "1.22.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65"))))
+         "17kmy7nvpyyj6w5jyrjciw87rydmmmc8q6cnwqjv1j7li9bp09gr"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -6964,13 +6958,13 @@ Bioconductor, CRAN, and Github.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.48.2")
+    (version "1.48.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "01yiafayl1m5704xdd2cn3zjc78rs10dqyz66lr3qkf6d8w66938"))))
+                "1rxvwikqivsgxjjcazlszy8xgz346lfh5rw4llxw6fz38fjgb0k5"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -7183,13 +7177,13 @@ utilities for sequence data management under the ACNUC system.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.14.10")
+    (version "2.14.11")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6"))))
+                "0wz63hysspyjihqadg91dbvllc5a61zzjrsz0b9498lihqc6m1la"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -7263,13 +7257,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.22.2")
+    (version "3.22.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3"))))
+                "0w3jv29n0kkaiig8dbbdqy2dkng8xfaihch82mj9ci5hphrx3nng"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7291,13 +7285,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.26.0")
+    (version "1.26.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7"))))
+                "1r55ki951dj81qvy73knfcy69ik5vzkd56wnk3f6vvf9vngqb8jr"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
@@ -7329,13 +7323,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.36.1")
+    (version "3.36.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm"))))
+                "0iiifszr6hcqih6kszdsbkx3gacfg3d7v8hdx0lbjqnjqgqz7pwk"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7384,13 +7378,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.32.3")
+    (version "1.32.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni"))))
+                "0p58yk2i5gqvjlkx548mnrr49wvs0xfcl06l9rqj2hi6hkkbvnp3"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -7495,13 +7489,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.14.1")
+    (version "1.14.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "00qg1kg2l9qqpyjaw5q910cmf84vwfiw1fhsx3ig784gwinwgj6n"))))
+                "1llb5a62hn4yxpdgqdh2l7i5zd06mjkk8hagsna69cq65wv6iifm"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -7546,13 +7540,13 @@ biological sequences or sets of sequences.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "1.32.0")
+    (version "1.32.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "1s65y5wn4d0x8zsljg2kmhcl6r9884h95kr041j7hp49bmxg3an6"))))
+                "1hpjr22h33pf4fgv0sj83rqzv6l5l7s6fpmmqvchh45ikks1mnhq"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -7590,13 +7584,13 @@ files.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.6.1")
+    (version "0.6.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "0sjwszxdi0vkj2i2di5i46gh9chc660yr3gs5nk9qnqp77713zds"))))
+                "10b03zrnvz5isfh4z55hasya2m71lrfx10l5lm2sdmqs0gwkanrd"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
@@ -7685,13 +7679,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.40.3")
+    (version "1.40.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "0kvsjdaypn1jnxbnsxpycildwdyxwnjkigfq8qm8mlyfc4ahdgy3"))))
+                "1wxxxlyps19dw3i0pw4mlm3kinnswsc35rgvlnbwvpnpjbca6w4l"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -7732,13 +7726,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.32.0")
+    (version "1.32.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "1cqcl72q0k5wylw1brn4g4h7xzys1v06piry19cvp0gjcvm5sp7a"))))
+                "0kfyyg1ib8fkq2hxraal10z4bx3rg8figdskw4yhn1mbh6l42q5f"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -7794,25 +7788,6 @@ extracting the desired features in a convenient format.")
 information about the latest version of the Gene Ontologies.")
     (license license:artistic2.0)))
 
-(define-public r-graph
-  (package
-    (name "r-graph")
-    (version "1.58.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "graph" version))
-              (sha256
-               (base32
-                "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759"))))
-    (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-topgo
   (package
     (name "r-topgo")
@@ -8544,7 +8519,7 @@ paired-end data.")
      `(("r-testthat" ,r-testthat)
        ;; During vignette building knitr checks that "pandoc-citeproc"
        ;; is in the PATH.
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)))
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biomart" ,r-biomart)
@@ -9328,14 +9303,14 @@ unmodeled, or latent sources of noise.")
 (define-public r-seqminer
   (package
     (name "r-seqminer")
-    (version "6.0")
+    (version "6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seqminer" version))
        (sha256
         (base32
-         "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l"))))
+         "15yhg4vfc7jg1jnqb3371j00pgbmbyc9l1xx63hq1l3p34lazq2l"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -9382,14 +9357,14 @@ trait.")
 (define-public r-maldiquant
   (package
     (name "r-maldiquant")
-    (version "1.17")
+    (version "1.18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MALDIquant" version))
        (sha256
         (base32
-         "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z"))))
+         "18nl214xjsxkcpbg79jkmw0yznwm5szyh2qb84n7ip46mm779ha6"))))
     (properties `((upstream-name . "MALDIquant")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/MALDIquant")
@@ -9626,14 +9601,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.6.1")
+    (version "2.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "0zrpx9r93q5ca2zdak5rs2m9sjm0wjdra1xfj3d3sx6p5gzfyg6n"))))
+         "15jhqg02ypmznc0wxksw56yij02csy678vqy531fdv86fsmypwa0"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9708,58 +9683,31 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "2.3.2")
+    (version "2.3.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "1sjpy5rrpvlpm6hs7qy7qpglgbp7zrgfybcsalpmjb51rhxhgcg1"))
-              ;; Delete pre-built jar.
-              (snippet
-               '(begin (delete-file "inst/java/ModularityOptimizer.jar")
-                       #t))))
+                "0l8bv4i9nzz26mirnva10mq6pimibj24vk7vpvfypgn7xk4942hd"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'build-jar
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((classesdir "tmp-classes"))
-               (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
-               (mkdir classesdir)
-               (with-output-to-file "manifest"
-                 (lambda _
-                   (display "Manifest-Version: 1.0
-Main-Class: ModularityOptimizer\n")))
-               (and (zero? (apply system* `("javac" "-d" ,classesdir
-                                            ,@(find-files "java" "\\.java$"))))
-                    (zero? (system* "jar"
-                                    "-cmf" "manifest"
-                                    "inst/java/ModularityOptimizer.jar"
-                                    "-C" classesdir  ".")))))))))
-    (native-inputs
-     `(("jdk" ,icedtea "jdk")))
     (propagated-inputs
      `(("r-ape" ,r-ape)
-       ("r-caret" ,r-caret)
        ("r-cluster" ,r-cluster)
        ("r-cowplot" ,r-cowplot)
-       ("r-diffusionmap" ,r-diffusionmap)
        ("r-dosnow" ,r-dosnow)
        ("r-dplyr" ,r-dplyr)
        ("r-dtw" ,r-dtw)
        ("r-fitdistrplus" ,r-fitdistrplus)
-       ("r-fnn" ,r-fnn)
        ("r-foreach" ,r-foreach)
        ("r-fpc" ,r-fpc)
-       ("r-gdata" ,r-gdata)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggridges" ,r-ggridges)
        ("r-gplots" ,r-gplots)
        ("r-hdf5r" ,r-hdf5r)
        ("r-hmisc" ,r-hmisc)
+       ("r-httr" ,r-httr)
        ("r-ica" ,r-ica)
        ("r-igraph" ,r-igraph)
        ("r-irlba" ,r-irlba)
@@ -9772,7 +9720,6 @@ Main-Class: ModularityOptimizer\n")))
        ("r-pbapply" ,r-pbapply)
        ("r-plotly" ,r-plotly)
        ("r-png" ,r-png)
-       ("r-ranger" ,r-ranger)
        ("r-rann" ,r-rann)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
@@ -9783,11 +9730,8 @@ Main-Class: ModularityOptimizer\n")))
        ("r-rocr" ,r-rocr)
        ("r-rtsne" ,r-rtsne)
        ("r-sdmtools" ,r-sdmtools)
-       ("r-stringr" ,r-stringr)
-       ("r-tclust" ,r-tclust)
        ("r-tidyr" ,r-tidyr)
-       ("r-tsne" ,r-tsne)
-       ("r-vgam" ,r-vgam)))
+       ("r-tsne" ,r-tsne)))
     (home-page "http://www.satijalab.org/seurat")
     (synopsis "Seurat is an R toolkit for single cell genomics")
     (description
@@ -9860,14 +9804,14 @@ distribution.")
 (define-public r-edaseq
   (package
     (name "r-edaseq")
-    (version "2.14.0")
+    (version "2.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EDASeq" version))
        (sha256
         (base32
-         "1832pb3jkim4vrqzb8lajwx9r482bhww5n9nz3s6crvyamlp2dj0"))))
+         "0970w9d5ddqw1qxqqafdidkxh6hmcv9j5djwgnpz3fgl05kmysg8"))))
     (properties `((upstream-name . "EDASeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9987,14 +9931,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.20.0")
+    (version "1.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "1349vidgl9m10l1rbrp3pkwwgi2xcbsw9h9z2xqbvg97lmqc4r8j"))))
+         "1ss0xd5570x570v01r6lp64rr1apjrzp0j62520pvm3g8knjhfvs"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10207,14 +10151,14 @@ the fact that each of these packages implements a select methods.")
 (define-public r-biovizbase
   (package
     (name "r-biovizbase")
-    (version "1.28.0")
+    (version "1.28.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biovizBase" version))
        (sha256
         (base32
-         "0lkiqdr3ics6hgv47lwkykcy761823bbkhffbn4ykyfzyqwl4p67"))))
+         "0wc45j3hfn01i44bkkxjj3n8b8xzbkkcdv35mrkzb1f9yprkf8gq"))))
     (properties `((upstream-name . "biovizBase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10231,6 +10175,7 @@ the fact that each of these packages implements a select methods.")
        ("r-hmisc" ,r-hmisc)
        ("r-iranges" ,r-iranges)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rlang" ,r-rlang)
        ("r-rsamtools" ,r-rsamtools)
        ("r-s4vectors" ,r-s4vectors)
        ("r-scales" ,r-scales)
@@ -10248,14 +10193,14 @@ effort and encourages consistency.")
 (define-public r-ggbio
   (package
     (name "r-ggbio")
-    (version "1.28.0")
+    (version "1.28.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggbio" version))
        (sha256
         (base32
-         "0wszh3w8yia5zw758h837i1q35k99sn444y2hahcxqbdmmlbf7in"))))
+         "19s2v40fycwf44fl3lm791y635xzw67b30sq2g0qq4a6phjik42d"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10278,6 +10223,7 @@ effort and encourages consistency.")
        ("r-iranges" ,r-iranges)
        ("r-organismdbi" ,r-organismdbi)
        ("r-reshape2" ,r-reshape2)
+       ("r-rlang" ,r-rlang)
        ("r-rsamtools" ,r-rsamtools)
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
@@ -10732,14 +10678,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.8.0")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "1l0276qxkhgdxsfck3jmi8jvnsr20g10gjki53g0mqa45wnhm3ck"))))
+         "1s44zgm9jg82bk4b8k3dh7xw7mxychlfm3grs8516mxnw91zpvy5"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10878,13 +10824,13 @@ libraries.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.8.0")
+    (version "1.8.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "0bhpikgz3b9f510dawsay4zry9rlp8vjx5n6zvwbcpwrd94p3903"))))
+                "173lfpas2fqsp4xxsw01wkxd4496c5p8himw9b4r9z4npxkfyv16"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
@@ -10922,14 +10868,14 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.8.2")
+    (version "1.8.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "0nbn5x75gf9d0p18w7vpkbv30cpdqvp5bz8xvila0h7jla7xdyih"))))
+         "17vq9vb9ak7n4mcqpwnm9x3z91vmr7xnsgj8f45b8dbj7m0v126j"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
@@ -12885,8 +12831,8 @@ once.  This package provides tools to perform Drop-seq analyses.")
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-rjson" ,r-rjson)
        ("salmon" ,salmon)
-       ("ghc-pandoc" ,ghc-pandoc-1)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
        ("python-wrapper" ,python-wrapper)
        ("python-pyyaml" ,python-pyyaml)))
     (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
@@ -12947,8 +12893,8 @@ expression report comparing samples in an easily configurable manner.")
        ("macs" ,macs)
        ("multiqc" ,multiqc)
        ("perl" ,perl)
-       ("ghc-pandoc" ,ghc-pandoc-1)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
        ("fastqc" ,fastqc)
        ("bowtie" ,bowtie)
        ("idr" ,idr)
@@ -13009,8 +12955,8 @@ in an easily configurable manner.")
        ("r-bookdown" ,r-bookdown)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggbio" ,r-ggbio)
-       ("ghc-pandoc" ,ghc-pandoc-1)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
        ("python-wrapper" ,python-wrapper)
        ("python-pyyaml" ,python-pyyaml)
        ("snakemake" ,snakemake-4)
@@ -13060,8 +13006,8 @@ methylation and segmentation.")
        ("python-magic" ,python-magic)
        ("python-numpy" ,python-numpy)
        ("python-loompy" ,python-loompy)
-       ("ghc-pandoc" ,ghc-pandoc-1)
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
        ("samtools" ,samtools)
        ("snakemake" ,snakemake-4)
        ("star" ,star)
diff --git a/gnu/packages/ccache.scm b/gnu/packages/ccache.scm
index af06b741a7..af29cee565 100644
--- a/gnu/packages/ccache.scm
+++ b/gnu/packages/ccache.scm
@@ -30,7 +30,7 @@
 (define-public ccache
   (package
     (name "ccache")
-    (version "3.4.2")
+    (version "3.4.3")
     (source
      (origin
       (method url-fetch)
@@ -38,7 +38,7 @@
                           version ".tar.xz"))
       (sha256
        (base32
-        "1qpy6k9f06kpr6bxy26ncdxcszqv1skcncvczcvksgfncx1v3a0q"))))
+        "0jjzq5340qw3jm5gkajjkkb5wd0yqqy1dyjw3mf3jy15cakmazi9"))))
     (build-system gnu-build-system)
     (native-inputs `(("perl" ,perl)     ; for test.sh
                      ("which" ,(@ (gnu packages base) which))))
@@ -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")
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index e26983da3b..067a288004 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -32,6 +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)
@@ -223,39 +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)
diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index be178a5f99..b3fbea0b38 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -211,16 +211,16 @@ COCOMO model or user-provided parameters.")
 (define-public cloc
   (package
     (name "cloc")
-    (version "1.76")
+    (version "1.78")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
-             "https://github.com/AlDanial/cloc/releases/download/v" version
+             "https://github.com/AlDanial/cloc/releases/download/" version
              "/cloc-" version ".tar.gz"))
        (sha256
         (base32
-         "05srlvzwisr7y7ymvzb5yfdsrspja27ysqdmkwhiiivy84mq2gnl"))))
+         "176xklr2qsgxh9zdb565gib6pp4gsm585rz5fvyphgjy4i679wkv"))))
     (build-system gnu-build-system)
     (inputs
      `(("coreutils" ,coreutils)
@@ -651,6 +651,19 @@ 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")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 016d1b1e41..8144391729 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -43,6 +43,25 @@
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web))
 
+(define-public r-clipr
+  (package
+    (name "r-clipr")
+    (version "0.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "clipr" version))
+       (sha256
+        (base32
+         "061x84ildc7g1p91yw5iyj8lpqdf4hqv36as85lw8c6qv9ywbsqv"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/mdlincoln/clipr")
+    (synopsis "Read and write from the system clipboard")
+    (description
+     "This package provides simple utility functions to read from and write to
+the system clipboards.")
+    (license license:gpl3)))
+
 (define-public r-tidyverse
   (package
     (name "r-tidyverse")
@@ -143,20 +162,23 @@ package is a port of the Python package @code{cssselect}.")
 (define-public r-reprex
   (package
     (name "r-reprex")
-    (version "0.1.2")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reprex" version))
        (sha256
         (base32
-         "105d9vsmqfilgpw8psfb2wyiz1hvcycvh4cqhb3ab37lm3rcavvs"))))
+         "1l44pxjiz3g0jkk3v6rg5jps3llihfiah0qyv40s0bxvxa6gm8v9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
+       ("r-clipr" ,r-clipr)
        ("r-knitr" ,r-knitr)
+       ("r-rlang" ,r-rlang)
        ("r-rmarkdown" ,r-rmarkdown)
-       ("r-whisker" ,r-whisker)))
+       ("r-whisker" ,r-whisker)
+       ("r-withr" ,r-withr)))
     (home-page "https://github.com/tidyverse/reprex")
     (synopsis "Prepare reproducible R code examples for sharing")
     (description
@@ -171,17 +193,18 @@ such as copy/paste from an R session.")
 (define-public r-callr
   (package
     (name "r-callr")
-    (version "2.0.4")
+    (version "3.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "callr" version))
        (sha256
         (base32
-         "1053qqq632z94pqq2v5dynjpgyv1b1c8zvidmcllw7zn8zha8gqf"))))
+         "1rxbxy6kn7dj90z9hpppr9cnpvnxzknba2dwrdp0lrk5dh462qz3"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-r6" ,r-r6)
+     `(("r-base64enc" ,r-base64enc)
+       ("r-r6" ,r-r6)
        ("r-processx" ,r-processx)))
     (home-page "https://github.com/r-lib/callr#readme")
     (synopsis "Call R from R")
@@ -369,14 +392,14 @@ colors are provided.")
 (define-public r-glue
   (package
     (name "r-glue")
-    (version "1.2.0")
+    (version "1.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "glue" version))
        (sha256
         (base32
-         "0vi9y8ix95g6hjqdz9c9y4119apbdjcypdv0ag8cl6vaxqs5n9qr"))))
+         "1vhw5497lpfr4m8lcx9bs0fgdp4ax0sycrk6n8yksp33qd25m7kq"))))
     (build-system r-build-system)
     (home-page "https://github.com/tidyverse/glue")
     (synopsis "Interpreted string literals")
@@ -430,14 +453,14 @@ error stream.")
 (define-public r-pls
   (package
     (name "r-pls")
-    (version "2.6-0")
+    (version "2.7-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pls" version))
        (sha256
         (base32
-         "15j59p5x0rkdrk7iqzkipsy50rsyjl31w8zxc4w3v1j5gzxhi1rx"))))
+         "0xaqqgmdvfh7g7v1m4bcwjqzph68b9cq3bn4kjisfsadl54i5p2x"))))
     (build-system r-build-system)
     (home-page "http://mevik.net/work/software/pls.html")
     (synopsis "Partial Least Squares and Principal Component Regression")
@@ -480,6 +503,60 @@ print, summary, plot, update, etc.
 processes.  Most of its code is based on the @code{psutil} Python package.")
     (license license:bsd-3)))
 
+(define-public r-pkgbuild
+  (package
+    (name "r-pkgbuild")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pkgbuild" version))
+       (sha256
+        (base32
+         "10iz8057mixl9j73pq2cbp4ib6dadfsgi3fcsjjm7l3wwb9issd9"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-callr" ,r-callr)
+       ("r-crayon" ,r-crayon)
+       ("r-desc" ,r-desc)
+       ("r-r6" ,r-r6)
+       ("r-rprojroot" ,r-rprojroot)
+       ("r-withr" ,r-withr)))
+    (home-page "https://github.com/r-pkgs/pkgbuild")
+    (synopsis "Find tools needed to build R packages")
+    (description
+     "This package provides functions used to build R packages.  It locates
+compilers needed to build R packages on various platforms and ensures the PATH
+is configured appropriately so R can use them.")
+    (license license:gpl3)))
+
+(define-public r-pkgload
+  (package
+    (name "r-pkgload")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pkgload" version))
+       (sha256
+        (base32
+         "1rjj229nq9fsl4ki4m75ybsavjgpqqhsr1zjzapwicsrxv6212px"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-desc" ,r-desc)
+       ("r-pkgbuild" ,r-pkgbuild)
+       ("r-rlang" ,r-rlang)
+       ("r-rprojroot" ,r-rprojroot)
+       ("r-rstudioapi" ,r-rstudioapi)
+       ("r-withr" ,r-withr)))
+    (home-page "https://github.com/r-lib/pkgload")
+    (synopsis "Simulate package installation and attach")
+    (description
+     "This package simulates the process of installing a package and then
+attaching it.  This is a key part of the @code{devtools} package as it allows
+you to rapidly iterate while developing a package.")
+    (license license:gpl3)))
+
 (define-public r-rcpp
   (package
     (name "r-rcpp")
@@ -1678,14 +1755,14 @@ provided.")
 (define-public r-ipred
   (package
     (name "r-ipred")
-    (version "0.9-6")
+    (version "0.9-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ipred" version))
        (sha256
         (base32
-         "1vrw1pqcpnc04x1r2h9grdfm6bivs358sww5gg90jwlvxcw69lxq"))))
+         "0q53cqs46501wsd4cmfsmr78l8nv1hkbamk9m0ns5qy02df5r254"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)
@@ -1739,22 +1816,23 @@ created using basic graphics.")
 (define-public r-broom
   (package
     (name "r-broom")
-    (version "0.4.5")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "broom" version))
        (sha256
         (base32
-         "1mrrqqw1bmjf2v88ziqwb5y86g29h0a3rsx2jpw0hrzrzb8i5kcb"))))
+         "1r3831vq0fd5sh5841xr844sghg88z7ws91hg4jgnzbbkxfjp4ag"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-dplyr" ,r-dplyr)
+     `(("r-backports" ,r-backports)
+       ("r-dplyr" ,r-dplyr)
        ("r-nlme" ,r-nlme)
-       ("r-plyr" ,r-plyr)
-       ("r-psych" ,r-psych)
+       ("r-purrr" ,r-purrr)
        ("r-reshape2" ,r-reshape2)
        ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
        ("r-tidyr" ,r-tidyr)))
     (home-page "https://github.com/tidyverse/broom")
     (synopsis "Convert statistical analysis objects into tidy data frames")
@@ -1903,20 +1981,72 @@ can be computed between character vectors while taking proper care of encoding
 or between integer vectors representing generic sequences.")
     (license license:gpl3+)))
 
+(define-public r-ucminf
+  (package
+    (name "r-ucminf")
+    (version "1.1-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ucminf" version))
+       (sha256
+        (base32
+         "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/ucminf/")
+    (synopsis "General-purpose unconstrained non-linear optimization")
+    (description
+     "This package provides an implementation of an algorithm for
+general-purpose unconstrained non-linear optimization.  The algorithm is of
+quasi-Newton type with BFGS updating of the inverse Hessian and soft line
+search with a trust region type monitoring of the input to the line search
+algorithm.  The interface of @code{ucminf} is designed for easy interchange
+with the package @code{optim}.")
+    (license license:gpl2+)))
+
+(define-public r-ordinal
+  (package
+    (name "r-ordinal")
+    (version "2018.8-25")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ordinal" version))
+       (sha256
+        (base32
+         "03cv9hcrw8j3lhamzhz8sk2p3ns4cw9z41x49h301k2b3pajv43h"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-numderiv" ,r-numderiv)
+       ("r-ucminf" ,r-ucminf)))
+    (home-page "https://github.com/runehaubo/ordinal")
+    (synopsis "Regression models for ordinal data")
+    (description
+     "This package provides an implementation of cumulative link (mixed)
+models also known as ordered regression models, proportional odds models,
+proportional hazards models for grouped survival times and ordered models.
+Estimation is via maximum likelihood and mixed models are fitted with the
+Laplace approximation and adaptive Gauss-Hermite quadrature.")
+    (license license:gpl2+)))
+
 (define-public r-jomo
   (package
     (name "r-jomo")
-    (version "2.6-3")
+    (version "2.6-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "jomo" version))
        (sha256
         (base32
-         "14s8q0j5zgl1g1pfxg3a4y1jzvs0wl61ir4992wsj7safskj7zvi"))))
+         "05g2rj9g7rgyb22b0gybw042nydyqsqsb31v05hifzavri8ij01x"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lme4" ,r-lme4)
+       ("r-ordinal" ,r-ordinal)
        ("r-survival" ,r-survival)))
     (home-page "https://cran.r-project.org/web/packages/jomo/")
     (synopsis "Multilevel Joint Modelling Multiple Imputation")
@@ -1932,14 +2062,14 @@ impute compatibly with the substantive model.")
 (define-public r-pan
   (package
     (name "r-pan")
-    (version "1.4")
+    (version "1.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pan" version))
        (sha256
         (base32
-         "1p3nigmhrnlch86g89hn7l0wvkifx3k9n59g0psi95yck43kza76"))))
+         "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
     (home-page "https://cran.r-project.org/web/packages/pan/")
@@ -1977,14 +2107,14 @@ analysis of multiply imputed data sets.")
 (define-public r-mice
   (package
     (name "r-mice")
-    (version "3.1.0")
+    (version "3.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mice" version))
        (sha256
         (base32
-         "0xpn215yfzib4hw09cwilnyg9zbvq460njavfvm84mvgwbm25byi"))))
+         "1p0ipbqk5aqdi7iikw3qrjyvdi9sdhpnw1h5mwakwvv0yl0pzbyx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
@@ -2182,17 +2312,16 @@ training models for classification or ranking.")
 (define-public r-xts
   (package
     (name "r-xts")
-    (version "0.10-2")
+    (version "0.11-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xts" version))
        (sha256
         (base32
-         "1i11fczks4lh8rpi6xbm9bm7f3jpcp6xw03kv178g3n3361qhmc1"))))
+         "1v50yn4bsjzdyk7r90isn6dxmpkapillrhpx3gqsshd180vwzqk9"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-zoo" ,r-zoo)))
-    (native-inputs `(("gfortran" ,gfortran)))
     (home-page "https://github.com/joshuaulrich/xts")
     (synopsis "Extensible time series")
     (description
@@ -2669,18 +2798,19 @@ display.")
 (define-public r-pillar
   (package
     (name "r-pillar")
-    (version "1.2.3")
+    (version "1.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pillar" version))
        (sha256
         (base32
-         "1rzhssprqgam1nq3s0f5rzxhxsq02azcghvxf6k8kmsmddf1n7f8"))))
+         "1q6arybmfqxhp5zqj1fri5pb8v7ywcv7bmgf81rrmgl892p4bn5f"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
        ("r-crayon" ,r-crayon)
+       ("r-fansi" ,r-fansi)
        ("r-rlang" ,r-rlang)
        ("r-utf8" ,r-utf8)))
     (home-page "https://github.com/r-lib/pillar")
@@ -2713,14 +2843,14 @@ terminals.")
 (define-public r-tinytex
   (package
     (name "r-tinytex")
-    (version "0.6")
+    (version "0.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tinytex" version))
        (sha256
         (base32
-         "16y9dldaff2kx1fkm92p7zlph0dcrdmlmavpdgf5y9jbhmc8g83f"))))
+         "1bgpr5i5399jf9n6pg2mm4aamisbhppg082ad0wv1j4g0rlxf1gy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-xfun" ,r-xfun)))
@@ -2737,17 +2867,18 @@ automatically.")
 (define-public r-metap
   (package
     (name "r-metap")
-    (version "0.9")
+    (version "1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "metap" version))
        (sha256
         (base32
-         "03vg0mb6q7j2z0pkxykbak0hcp6dcak7zxs1lw9hswz9kqrq5jhz"))))
+         "18rzvqfzyk8fn54gjvy2qd21nk9w69j7ihww477ma3f3ab6i982h"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-lattice" ,r-lattice)))
+     `(("r-lattice" ,r-lattice)
+       ("r-rdpack" ,r-rdpack)))
     (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
     (synopsis "Meta-analysis of significance values")
     (description
@@ -2781,14 +2912,14 @@ supports arbitrary vertex/edge/graph attributes.")
 (define-public r-statnet-common
   (package
     (name "r-statnet-common")
-    (version "4.1.2")
+    (version "4.1.4")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "statnet.common" version))
         (sha256
           (base32
-            "0h3g687214rlycca0fjrpy1lqbqsrginxqhmhl2mb2jinqqxcfgd"))))
+            "14dydm4c4dzc4v6ldxpn04q551nczzfablwibrd8lzgja8x9ksic"))))
     (properties
       `((upstream-name . "statnet.common")))
     (build-system r-build-system)
@@ -3010,21 +3141,20 @@ University Press, 2000.")
 (define-public r-tsa
   (package
     (name "r-tsa")
-    (version "1.01")
+    (version "1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TSA" version))
        (sha256
         (base32
-         "0cm97hwxm6vfgy9mc3kgwq6dnmn86p8a4avnfjbai048qnwrn6hx"))))
+         "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
     (properties `((upstream-name . "TSA")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-leaps" ,r-leaps)
        ("r-locfit" ,r-locfit)
-       ("r-mgcv" ,r-mgcv)
-       ("r-tseries" ,r-tseries)))
+       ("r-mgcv" ,r-mgcv)))
     (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
     (synopsis "Time series analysis")
     (description
@@ -3277,14 +3407,14 @@ exponentiation.")
 (define-public r-heatmaply
   (package
     (name "r-heatmaply")
-    (version "0.14.1")
+    (version "0.15.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "heatmaply" version))
        (sha256
         (base32
-         "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc"))))
+         "0h8s5djzj4mrmaswlcaap6jbwxrkbzc43bbqik3qf8vrqz335w04"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -3633,14 +3763,14 @@ multivariate plot methods.")
 (define-public r-fnn
   (package
     (name "r-fnn")
-    (version "1.1")
+    (version "1.1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "FNN" version))
        (sha256
         (base32
-         "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
+         "1n61jrcmakqif8f827x4qnlhm2jqpj5fgjj65c4p0kdd8lzw8pqp"))))
     (properties `((upstream-name . "FNN")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/FNN")
@@ -3925,14 +4055,14 @@ simple method for converting between file types.")
 (define-public r-maptools
   (package
     (name "r-maptools")
-    (version "0.9-2")
+    (version "0.9-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "maptools" version))
        (sha256
         (base32
-         "075lmb3b62171cw2dg8fv1vwmvfzg39r1ji7jwb8s5k9dz88ry1v"))))
+         "0hxbv01im9zk1qrwgigpc510w6x0kzdzip4gx2jzfqmmwr8m17r8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreign" ,r-foreign)
@@ -3953,14 +4083,14 @@ exchanging spatial objects with other R packages.")
 (define-public r-later
   (package
     (name "r-later")
-    (version "0.7.3")
+    (version "0.7.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "later" version))
        (sha256
         (base32
-         "04j2phymxgkk4hv9pfa5w3s98w5d7fvm11blrdhxmray4n618msw"))))
+         "125zc499gj702x2bch95lsfzk2qb4dzv3604x9afym2i3ylrmm64"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
@@ -4047,33 +4177,6 @@ to the cluster management tool @code{sfCluster}, but can also used without
 it.")
    (license license:gpl2+)))
 
-(define-public r-codedepends
-  (package
-    (name "r-codedepends")
-    (version "0.5-3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "CodeDepends" version))
-       (sha256
-        (base32
-         "03p82s0abca2jimzqvxdzykfzca7c7fhm5xsjxybcksr4gggr5sc"))))
-    (properties `((upstream-name . "CodeDepends")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-codetools" ,r-codetools)
-       ("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-rappdirs
   (package
     (name "r-rappdirs")
@@ -4163,14 +4266,14 @@ obtain a better initial configuration in non-metric MDS.")
 (define-public r-reticulate
   (package
     (name "r-reticulate")
-    (version "1.8")
+    (version "1.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reticulate" version))
        (sha256
         (base32
-         "0zwb4ikf021nw7axdn7qlr6bq4xkph3anfy314idkspy1iil4nmr"))))
+         "0bz3lxbisjwn6cv23090zivpy0bxcncr82g5qja13l37i8xnvqsq"))))
     (build-system r-build-system)
     (inputs `(("python" ,python)))
     (propagated-inputs
@@ -4280,14 +4383,14 @@ and adds the annotation to the plot.")
 (define-public r-ggpubr
   (package
     (name "r-ggpubr")
-    (version "0.1.7")
+    (version "0.1.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggpubr" version))
        (sha256
         (base32
-         "110ny8p41kmbz0a5rl0mv9cqpjkx6yr3ybflp1r0fmcvhwv7cr3i"))))
+         "0psl2zndm4wk6nnj1nv305islpxfvfgd87gjh2ph8yqn4mxpnfi1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cowplot" ,r-cowplot)
@@ -4296,8 +4399,10 @@ and adds the annotation to the plot.")
        ("r-ggrepel" ,r-ggrepel)
        ("r-ggsci" ,r-ggsci)
        ("r-ggsignif" ,r-ggsignif)
+       ("r-glue" ,r-glue)
        ("r-gridextra" ,r-gridextra)
        ("r-magrittr" ,r-magrittr)
+       ("r-polynom" ,r-polynom)
        ("r-purrr" ,r-purrr)
        ("r-scales" ,r-scales)
        ("r-tidyr" ,r-tidyr)))
@@ -4424,6 +4529,27 @@ packages.  It contains also functions for simplifying some clustering analysis
 steps and provides ggplot2-based elegant data visualization.")
     (license license:gpl2)))
 
+(define-public r-fansi
+  (package
+    (name "r-fansi")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fansi" version))
+       (sha256
+        (base32
+         "135qj7bcc3mwn0vg55hiiadf66lx6zaxvkicfmfw9x0zr7ah2r6x"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
+    (home-page "https://github.com/brodieG/fansi")
+    (synopsis "ANSI control sequence aware string functions")
+    (description
+     "This package provides counterparts to R string manipulation functions
+that account for the effects of ANSI text formatting control sequences.")
+    (license license:gpl2+)))
+
 (define-public r-nbclust
   (package
     (name "r-nbclust")
@@ -4495,6 +4621,303 @@ patterned after functions in the Python @code{itertools} module, and others
 patterned after functions in the snow package.")
     (license license:gpl2)))
 
+(define-public r-polynom
+  (package
+    (name "r-polynom")
+    (version "1.3-9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "polynom" version))
+       (sha256
+        (base32
+         "1s4xxv5rvpigawknvq27v9vzvs83phfsj5h8mim2lmf5bj950nnk"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/polynom/")
+    (synopsis "Functions for univariate polynomial manipulations")
+    (description
+     "This package provides a collection of functions to implement a class for
+univariate polynomial manipulations.")
+    (license license:gpl2)))
+
+(define-public r-gbrd
+  (package
+    (name "r-gbrd")
+    (version "0.4-11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gbRd" version))
+       (sha256
+        (base32
+         "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
+    (properties `((upstream-name . "gbRd")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/gbRd/")
+    (synopsis "Utilities for processing Rd objects and files")
+    (description
+     "This package provides utilities for processing Rd objects and files.
+Extract argument descriptions and other parts of the help pages of
+functions.")
+    (license license:gpl2+)))
+
+(define-public r-rdpack
+  (package
+    (name "r-rdpack")
+    (version "0.9-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Rdpack" version))
+       (sha256
+        (base32
+         "067w0w6kza0hkzcnx58danl83yfvl9yjacr47mnid2bg856gdd1b"))))
+    (properties `((upstream-name . "Rdpack")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bibtex" ,r-bibtex)
+       ("r-gbrd" ,r-gbrd)))
+    (home-page "https://github.com/GeoBosh/Rdpack")
+    (synopsis "Update and manipulate Rd documentation objects")
+    (description
+     "This package provides functions for manipulation of R documentation
+objects, including functions @code{reprompt()} and @code{ereprompt()} for
+updating Rd documentation for functions, methods and classes; it also includes
+Rd macros for citations and import of references from bibtex files for use in
+Rd files and roxygen2 comments, as well as many functions for manipulation of
+references and Rd files.")
+    (license license:gpl2+)))
+
+(define-public r-officer
+  (package
+    (name "r-officer")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "officer" version))
+       (sha256
+        (base32
+         "14b6ii9h3fi5g8ja929mfhxps9r7x78flqjdy437y9aygkhmiz2i"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-base64enc" ,r-base64enc)
+       ("r-digest" ,r-digest)
+       ("r-htmltools" ,r-htmltools)
+       ("r-magrittr" ,r-magrittr)
+       ("r-r6" ,r-r6)
+       ("r-rcpp" ,r-rcpp)
+       ("r-uuid" ,r-uuid)
+       ("r-xml2" ,r-xml2)
+       ("r-zip" ,r-zip)))
+    (home-page "https://davidgohel.github.io/officer")
+    (synopsis "Manipulation of Word and PowerPoint documents")
+    (description
+     "This package provides tools to access and manipulate Word and PowerPoint
+documents from R.  The package focuses on tabular and graphical reporting from
+R; it also provides two functions that let users get document content into
+data objects.  A set of functions lets add and remove images, tables and
+paragraphs of text in new or existing documents.  When working with PowerPoint
+presentations, slides can be added or removed; shapes inside slides can also
+be added or removed.  When working with Word documents, a cursor can be used
+to help insert or delete content at a specific location in the document.")
+    (license license:gpl3)))
+
+(define-public r-snakecase
+  (package
+    (name "r-snakecase")
+    (version "0.9.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "snakecase" version))
+       (sha256
+        (base32
+         "1g6xai53dl24ws0mwhqrkcv583ziaq505cv3z8v5dhjgy98kilyj"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-stringi" ,r-stringi)
+       ("r-stringr" ,r-stringr)))
+    (home-page "https://github.com/Tazinho/snakecase")
+    (synopsis "Convert strings into any case")
+    (description
+     "This package provides a consistent, flexible and easy to use tool to
+parse and convert strings into cases like snake or camel among others.")
+    (license license:gpl3)))
+
+(define-public r-prediction
+  (package
+    (name "r-prediction")
+    (version "0.3.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "prediction" version))
+       (sha256
+        (base32
+         "19d7312f5lkqfglfvlgssnvyw7gl161s0xradcry44r1i6qp05j1"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)))
+    (home-page "https://github.com/leeper/prediction")
+    (synopsis "Tidy, type-safe prediction methods")
+    (description
+     "This package provides the @code{prediction()} function, a type-safe
+alternative to @code{predict()} that always returns a data frame.  The package
+currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
+from the @code{stats} package, as well as numerous other model classes from
+other add-on packages.")
+    (license license:expat)))
+
+(define-public r-sjlabelled
+  (package
+    (name "r-sjlabelled")
+    (version "1.0.13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sjlabelled" version))
+       (sha256
+        (base32
+         "0xizj7mrhnbn8kwjgm076si9w68a7lgrx4vj1sbqmv9jx055h8wv"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-broom" ,r-broom)
+       ("r-dplyr" ,r-dplyr)
+       ("r-haven" ,r-haven)
+       ("r-magrittr" ,r-magrittr)
+       ("r-prediction" ,r-prediction)
+       ("r-purrr" ,r-purrr)
+       ("r-rlang" ,r-rlang)
+       ("r-snakecase" ,r-snakecase)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyselect" ,r-tidyselect)))
+    (home-page "https://github.com/strengejacke/sjlabelled")
+    (synopsis "Labelled data utility functions")
+    (description
+     "This package provides a collection of functions dealing with labelled
+data, like reading and writing data between R and other statistical software
+packages.  This includes easy ways to get, set or change value and variable
+label attributes, to convert labelled vectors into factors or numeric (and
+vice versa), or to deal with multiple declared missing values.")
+    (license license:gpl3)))
+
+(define-public r-sjmisc
+  (package
+    (name "r-sjmisc")
+    (version "2.7.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sjmisc" version))
+       (sha256
+        (base32
+         "11cy09k1d2y5wwqvafqxr01hzk4x68ji2pqlwj7fnpw27i3ap4q4"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-broom" ,r-broom)
+       ("r-crayon" ,r-crayon)
+       ("r-dplyr" ,r-dplyr)
+       ("r-haven" ,r-haven)
+       ("r-magrittr" ,r-magrittr)
+       ("r-pillar" ,r-pillar)
+       ("r-purrr" ,r-purrr)
+       ("r-rlang" ,r-rlang)
+       ("r-sjlabelled" ,r-sjlabelled)
+       ("r-stringdist" ,r-stringdist)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)
+       ("r-tidyselect" ,r-tidyselect)))
+    (home-page "https://github.com/strengejacke/sjmisc")
+    (synopsis "Data and variable transformation functions")
+    (description
+     "This package is a collection of miscellaneous utility functions,
+supporting data transformation tasks like recoding, dichotomizing or grouping
+variables, setting and replacing missing values.  The data transformation
+functions also support labelled data, and all integrate seamlessly into a
+tidyverse workflow.")
+    (license license:gpl3)))
+
+(define-public r-nortest
+  (package
+    (name "r-nortest")
+    (version "1.0-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nortest" version))
+       (sha256
+        (base32
+         "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/nortest/")
+    (synopsis "Tests for normality")
+    (description
+     "This package provides five omnibus tests for testing the composite
+hypothesis of normality.")
+    (license license:gpl2+)))
+
+(define-public r-moonbook
+  (package
+    (name "r-moonbook")
+    (version "0.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "moonBook" version))
+       (sha256
+        (base32
+         "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
+    (properties `((upstream-name . "moonBook")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-magrittr" ,r-magrittr)
+       ("r-nortest" ,r-nortest)
+       ("r-purrr" ,r-purrr)
+       ("r-sjmisc" ,r-sjmisc)
+       ("r-stringr" ,r-stringr)
+       ("r-survival" ,r-survival)))
+    (home-page "https://github.com/cardiomoon/moonBook")
+    (synopsis "Functions and datasets for the book by Keon-Woong Moon")
+    (description
+     "This package provides several analysis-related functions for the book
+entitled \"R statistics and graph for medical articles\" (written in Korean),
+version 1, by Keon-Woong Moon with Korean demographic data with several plot
+functions.")
+    (license license:gpl2)))
+
+(define-public r-flextable
+  (package
+    (name "r-flextable")
+    (version "0.4.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "flextable" version))
+       (sha256
+        (base32
+         "09j2y0z7rkc0w1cl9pp1cpk6fnzzfr6245mxa3ca42z9k2cy2jfl"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gdtools" ,r-gdtools)
+       ("r-htmltools" ,r-htmltools)
+       ("r-knitr" ,r-knitr)
+       ("r-officer" ,r-officer)
+       ("r-r6" ,r-r6)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-stringr" ,r-stringr)
+       ("r-xml2" ,r-xml2)))
+    (home-page "https://davidgohel.github.io/flextable")
+    (synopsis "Functions for tabular reporting")
+    (description
+     "This package provides tools to create pretty tables for HTML documents
+and other formats.  Functions are provided to let users create tables, modify
+and format their content.  It extends the @code{officer} package and can be
+used within R markdown documents when rendering to HTML and to Word
+documents.")
+    (license license:gpl3)))
+
 (define-public r-writexl
   (package
     (name "r-writexl")
@@ -4688,14 +5111,14 @@ Group (Non-)Overlap considerations.")
 (define-public r-doby
   (package
     (name "r-doby")
-    (version "4.6-1")
+    (version "4.6-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doBy" version))
        (sha256
         (base32
-         "1y02awzid23bxz8hx6j8pxd6i7jaq8pdw3k60rag8y6m69incrw5"))))
+         "02vbv9nfgywg6lsiialkmfnax5z3rkyb9nr8j9l2cp8xi6ml95mb"))))
     (properties `((upstream-name . "doBy")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4988,3 +5411,156 @@ maximum cycle number.  The @code{r-abcoptim} implements the Artificial bee
 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
   This version is a work-in-progress and is written in R code.")
     (license license:expat)))
+
+(define-public r-abcp2
+  (package
+    (name "r-abcp2")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ABCp2" version))
+       (sha256
+        (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
+    (properties `((upstream-name . "ABCp2")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/ABCp2/")
+    (synopsis "Approximate Bayesian Computational Model for Estimating P2")
+    (description
+     "This package tests the goodness of fit of a distribution of offspring to the Normal,
+Poisson, and Gamma distribution and estimates the proportional paternity of the
+second male (P2) based on the best fit distribution.")
+    (license license:gpl2)))
+
+(define-public r-abcrf
+  (package
+    (name "r-abcrf")
+    (version "1.7.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abcrf" version))
+       (sha256
+        (base32 "06vy3inikrr9hv36q4djhrgzi9zizdfnhz17wpra8kadmr7qj441"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-ranger" ,r-ranger)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-readr" ,r-readr)
+       ("r-stringr" ,r-stringr)))
+    (home-page "https://cran.r-project.org/web/packages/abcrf/")
+    (synopsis "Approximate bayesian computation via random forests")
+    (description
+     "This package performs approximate bayesian computation (ABC) model choice and
+parameter inference via random forests.  This machine learning tool named random
+forests (RF) can conduct selection among the highly complex models covered by
+ABC algorithms.")
+    (license license:gpl2+)))
+
+(define-public r-abctools
+  (package
+    (name "r-abctools")
+    (version "1.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abctools" version))
+       (sha256
+        (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-abc" ,r-abc)
+       ("r-abind" ,r-abind)
+       ("r-hmisc" ,r-hmisc)
+       ("r-plyr" ,r-plyr)))
+    (home-page "https://github.com/dennisprangle/abctools/")
+    (synopsis "Tools for ABC analyses")
+    (description
+     "This @code{r-abctools} package provides tools for approximate Bayesian computation
+including summary statistic selection and assessing coverage.  This includes
+recent dimension reduction algorithms to tune the choice of summary statistics,
+and coverage methods to tune the choice of threshold.")
+    (license license:gpl2+)))
+
+(define-public r-ggstance
+  (package
+    (name "r-ggstance")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggstance" version))
+       (sha256
+        (base32 "0v7f3xdaaridw6d4jvnsfwxmpjrasvx5vl555wsrn50aah17fkvh"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-plyr" ,r-plyr)
+       ("r-rlang" ,r-rlang)
+       ("r-withr" ,r-withr)))
+    (home-page "https://cran.r-project.org/web/packages/ggstance/")
+    (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
+    (description
+     "This package is a @code{r-ggplot2} extension that provides flipped components:
+@enumerate
+@item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
+@item vertical versions of @code{r-ggplot2} positions.
+@end enumerate")
+    (license license:gpl3)))
+
+(define-public r-mosaiccore
+  (package
+    (name "r-mosaiccore")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mosaicCore" version))
+       (sha256
+        (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
+    (properties `((upstream-name . "mosaicCore")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-lazyeval" ,r-lazyeval)
+       ("r-mass" ,r-mass)
+       ("r-rlang" ,r-rlang)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
+    (synopsis "Common utilities for mosaic family packages")
+    (description
+     "Common utilities used in other Mosaic family packages are collected here.")
+    (license license:gpl2+)))
+
+(define-public r-ggformula
+  (package
+    (name "r-ggformula")
+    (version "0.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggformula" version))
+       (sha256
+        (base32 "1pmpdfjfbrc6kcpq70cr1kbj2qy711hw940g2aiis6l443z706kh"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-ggstance" ,r-ggstance)
+       ("r-magrittr" ,r-magrittr)
+       ("r-mosaiccore" ,r-mosaiccore)
+       ("r-rlang" ,r-rlang)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "https://github.com/ProjectMOSAIC/ggformula/")
+    (synopsis "Formula interface for the @code{r-ggplot2}")
+    (description
+     "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
+gf_density(), and so on, bring the formula interface to ggplot().  This captures
+and extends the excellent simplicity of the lattice-graphics formula interface,
+while providing the intuitive capabilities of @code{r-ggplot2}.")
+    (license license:expat)))
diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index e070ef61ac..d9111135e8 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -126,7 +126,7 @@ 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/"
@@ -134,7 +134,7 @@ 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().
diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm
index a0fbd7738a..d4a620f1b3 100644
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@ -51,6 +51,7 @@
   (package
    (name "curl")
    (version "7.61.0")
+   (replacement curl-7.61.1)
    (source (origin
             (method url-fetch)
             (uri (string-append "https://curl.haxx.se/download/curl-"
@@ -141,6 +142,19 @@ tunneling, and so on.")
                                   "See COPYING in the distribution."))
    (home-page "https://curl.haxx.se/")))
 
+(define-public curl-7.61.1
+  (package
+    (inherit curl)
+    (version "7.61.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://curl.haxx.se/download/curl-"
+                            version ".tar.xz"))
+        (sha256
+         (base32
+          "148qv1f32290r9pwg07mccawihz4srznkzsdwdl2xllvlgb16n9x"))))))
+
 (define-public kurly
   (package
     (name "kurly")
diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index 7a80e1bd9b..29c3d9b923 100644
--- a/gnu/packages/dns.scm
+++ b/gnu/packages/dns.scm
@@ -498,14 +498,14 @@ Extensions} (DNSSEC).")
 (define-public knot
   (package
     (name "knot")
-    (version "2.7.1")
+    (version "2.7.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://secure.nic.cz/files/knot-dns/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "108k6x3hjsnyf06pv5rlxqhynjbbz13pzwax1mqff3hgv85f4skx"))
+                "0cc4wgb02ch09x99a1fnr7vsdik8k920q7jafzcamjvy3kpb4w6b"))
               (modules '((guix build utils)))
               (snippet
                '(begin
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 8f0c564f88..1f64a5e84a 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -15,7 +15,7 @@
 ;;; Copyright © 2016, 2017 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2016, 2017, 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
-;;; Copyright © 2016, 2017 Alex Vong <alexvong1995@gmail.com>
+;;; Copyright © 2016, 2017, 2018 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2016, 2017, 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
 ;;; Copyright © 2017, 2018 Mathieu Othacehe <m.othacehe@gmail.com>
@@ -38,6 +38,7 @@
 ;;; Copyright © 2018 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
 ;;; Copyright © 2018 Jack Hill <jackhill@jackhill.us>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
+;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -4123,22 +4124,34 @@ programming language.")
 (define-public emacs-ess
   (package
     (name "emacs-ess")
-    (version "16.10")
+    (version "17.11")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://ess.r-project.org/downloads/ess/ess-"
-                                  version ".tgz"))
+              (uri (string-append "https://github.com/emacs-ess/ESS/archive/v"
+                                  version ".tar.gz"))
               (sha256
                (base32
-                "04m8lwp3ylh2vl7k2bjjs7mxbm64j4sdckqpvnm9k0qhaqf02pjk"))
+                "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (modules '((guix build utils)))
               (snippet
                '(begin
                   ;; Stop ESS from trying to bundle an external julia-mode.el.
                   (substitute* "lisp/Makefile"
                     (("^\tjulia-mode.elc\\\\\n") "")
-                    (("^all: \\$\\(ELC\\) ess-custom.el julia-mode.el")
-                     "all: $(ELC) ess-custom.el"))
+                    (("^dist: all julia-mode.el")
+                     "dist: all"))
+                  ;; No need to build docs in so many formats.  Also, skipping
+                  ;; pdf lets us not pull in texlive.
+                  (substitute* "doc/Makefile"
+                    (("all  : info text html pdf")
+                     "all  : info")
+                    (("install: install-info install-other-docs")
+                     "install: install-info"))
+                  ;; Test fails upstream
+                  (substitute* "test/ess-r-tests.el"
+                    (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()")
+                     "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed"))
                   #t))))
     (build-system gnu-build-system)
     (arguments
@@ -4157,10 +4170,6 @@ programming language.")
                  (("SHELL = /bin/sh")
                   (string-append "SHELL = " (which "sh"))))
                #t))
-           ;; FIXME: the texlive-union insists on regenerating fonts.  It stores
-           ;; them in HOME, so it needs to be writeable.
-           (add-before 'build 'set-HOME
-             (lambda _ (setenv "HOME" "/tmp") #t))
            (replace 'check
              (lambda _
                (invoke "make" "test")))))))
@@ -4169,16 +4178,14 @@ programming language.")
        ("r-minimal" ,r-minimal)))
     (native-inputs
      `(("perl" ,perl)
-       ("texinfo" ,texinfo)
-       ("texlive" ,(texlive-union (list texlive-latex-natbib
-                                        texlive-latex-seminar
-                                        texlive-latex-hyperref
-                                        texlive-tex-texinfo)))))
+       ("texinfo" ,texinfo)))
+    (propagated-inputs
+     `(("emacs-julia-mode" ,emacs-julia-mode)))
     (home-page "https://ess.r-project.org/")
     (synopsis "Emacs mode for statistical analysis programs")
     (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU
 Emacs.  It is designed to support editing of scripts and interaction with
-various statistical analysis programs such as R and OpenBUGS.")
+various statistical analysis programs such as R, Julia, and JAGS.")
     (license license:gpl2+)))
 
 (define-public emacs-smex
@@ -11315,6 +11322,43 @@ e.g. the package dependencies it requires.  See function
 file.")
       (license license:gpl3+))))
 
+(define-public emacs-picpocket
+  (let ((version "20180610.1059") ; taken from melpa
+        (commit "ce4b6ed088384f2414af82e8e4eae5b92c2874bf"))
+    (package
+      (name "emacs-picpocket")
+      (version version)
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/johanclaesson/picpocket")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "15vpbcv83mc4j1pvrk7xic0klh2bl9gzg2xxs7c2lmnix52hy8mv"))))
+      (build-system emacs-build-system)
+      (arguments ; needed for running tests
+       `(#:tests? #t
+         #:emacs ,emacs
+         #:test-command '("emacs" "--batch"
+                          "-l" "picpocket-test.el"
+                          "-f" "ert-run-tests-batch-and-exit")))
+      (home-page "https://github.com/johanclaesson/picpocket")
+      (synopsis "Image viewer for Emacs")
+      (description
+       "Picpocket is an image viewer for GNU Emacs.  It has commands for:
+
+@itemize
+@item File operations on the picture files (delete, move, copy, hardlink).
+@item Scale and rotate the picture.
+@item Associate pictures with tags which are saved to disk.
+@item Filter pictures according to tags.
+@item Customizing keystrokes for quick tagging and file operations.
+@item Undo and browse history of undoable commands.
+@end itemize")
+      (license license:gpl3+))))
+
 (define-public emacs-wgrep-helm
   ;; `emacs-wgrep-helm' was mistakenly added.
   (deprecated-package "emacs-wgrep-helm" emacs-wgrep))
diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index 8e68c676ef..e02339af62 100644
--- a/gnu/packages/emulators.scm
+++ b/gnu/packages/emulators.scm
@@ -117,8 +117,8 @@
 
 ;; Building from recent Git because the official 5.0 release no longer builds.
 (define-public dolphin-emu
-  (let ((commit "806c1ee8f0ed824008185212bfab2658d400b576")
-        (revision "2"))
+  (let ((commit "5f0d825f40b8aabe13eaef32d44ab667ff8e8c28")
+        (revision "3"))
     (package
       (name "dolphin-emu")
       (version (git-version "5.0" revision commit))
@@ -144,7 +144,7 @@
              #t))
          (sha256
           (base32
-           "1sdc7rh6z7gjx4kxg18jrv7srfpx1vgf936zg5y43radnlscrh1j"))))
+           "0dh7mih16aif9ynbgcsn7n10f89g8d232i86xqfp2rijsdggcmzl"))))
       (build-system cmake-build-system)
       (arguments
        '(#:tests? #f
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index d53b25cff9..ee524ec78e 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018 Jonathan Brielmaier <jonathan.brielmaier@web.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -680,24 +681,19 @@ language.")
 (define-public ao
   (deprecated-package "ao-cad" libfive))
 
-;; We use kicad from a git commit, because support for boost 1.61.0 has been
-;; recently added.
 (define-public kicad
-  (let ((commit "5f4599fb56da4dd748845ab10abec02961d477f3")
-        (revision "2"))
     (package
       (name "kicad")
-      (version (string-append "4.0-" revision "."
-                              (string-take commit 7)))
+      (version "5.0.0")
       (source
        (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://git.launchpad.net/kicad")
-               (commit commit)))
+         (method url-fetch)
+         (file-name (string-append name "-" version ".tar.xz"))
+         (uri (string-append
+                "https://launchpad.net/kicad/5.0/" version "/+download/" name
+                "-" version ".tar.xz"))
          (sha256
-          (base32 "1833pln2975gmc5s18xf7s8m9vg834lmxxdjk0wlk3lq7bvjjnff"))
-         (file-name (string-append name "-" version "-checkout"))))
+          (base32 "17nqjszyvd25wi6550j981whlnb1wxzmlanljdjihiki53j84x9p"))))
       (build-system cmake-build-system)
       (arguments
        `(#:out-of-source? #t
@@ -706,8 +702,6 @@ language.")
          #:configure-flags
          (list "-DKICAD_STABLE_VERSION=ON"
                "-DKICAD_REPO_NAME=stable"
-               ,(string-append "-DKICAD_BUILD_VERSION=4.0-"
-                               (string-take commit 7))
                "-DKICAD_SKIP_BOOST=ON"; Use our system's boost library.
                "-DKICAD_SCRIPTING=ON"
                "-DKICAD_SCRIPTING_MODULES=ON"
@@ -754,6 +748,7 @@ language.")
          ("libngspice" ,libngspice)
          ("libsm" ,libsm)
          ("mesa" ,mesa)
+         ("opencascade-oce" ,opencascade-oce)
          ("openssl" ,openssl)
          ("python" ,python-2)
          ("wxwidgets" ,wxwidgets-gtk2)
@@ -764,7 +759,7 @@ language.")
 boards and electrical circuits.  The software has a number of programs that
 perform specific functions, for example, pcbnew (Editing PCB), eeschema (editing
 electrical diagrams), gerbview (viewing Gerber files) and others.")
-      (license license:gpl3+))))
+      (license license:gpl3+)))
 
 (define-public kicad-library
   (let ((version "4.0.7"))
diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index 4d02b4bc62..ce07d3ad4c 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -887,7 +887,7 @@ designed to work well in user interface environments.")
 (define-public font-fira-code
   (package
     (name "font-fira-code")
-    (version "1.204")
+    (version "1.205")
     (source (origin
               (method url-fetch/zipbomb)
               (uri (string-append "https://github.com/tonsky/FiraCode/releases/"
@@ -895,7 +895,7 @@ designed to work well in user interface environments.")
                                   "/FiraCode_" version ".zip"))
               (sha256
                (base32
-                "17wky221b3igrqhmxgmqiyv1xdfn0nw471vzhpkrvv1w2w1w1k18"))))
+                "13bxgf59g6fw5191xclcjzn22hj8jk9k5jjwf7vz07mpjbgadcl5"))))
     (build-system font-build-system)
     (home-page "https://mozilla.github.io/Fira/")
     (synopsis "Monospaced font with programming ligatures")
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 728f763806..2015e3ce47 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -34,6 +34,7 @@
 ;;; Copyright © 2018 okapi <okapi@firemail.cc>
 ;;; Copyright © 2018 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
 ;;; Copyright © 2018 Madalin Ionel-Patrascu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018 Benjamin Slade <slade@jnanam.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -5553,3 +5554,159 @@ open-source FPS of its kind.")
     (license (list license:gpl2+
                    license:bsd-3 ; /source/d0_blind_id folder and others
                    (license:x11-style "" "See file rcon.pl.")))))
+
+(define-public frotz
+  (package
+    (name "frotz")
+    (version "2.44")
+    (source (origin
+              (method url-fetch)
+              (uri (list (string-append
+                          "http://www.ifarchive.org/if-archive/infocom/interpreters/"
+                          name "/" name "-" version ".tar.gz")
+                         (string-append
+                          "ftp://ftp.ifarchive.org/if-archive/infocom/interpreters/"
+                          name "/" name "-" version ".tar.gz")))
+              (sha256
+               (base32
+                "1v735xr3blznac8fnwa27s1vhllx4jpz7kw7qdw1bsfj6kq21v3k"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; there are no tests
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'build 'curses
+           (lambda _
+             (substitute* "Makefile"
+               (("lcurses") "lncurses"))
+             #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (man (string-append out "/share/man/man6")))
+               (install-file "frotz" bin)
+               (mkdir-p man)
+               (install-file "doc/frotz.6" man)
+               #t))))))
+    (inputs `(("libmodplug" ,libmodplug)
+              ("libsamplerate" ,libsamplerate)
+              ("libsndfile" ,libsndfile)
+              ("libvorbis" ,libvorbis)
+              ("ncurses" ,ncurses)))
+    (synopsis "Portable Z-machine interpreter (ncurses version) for text adventure games")
+    (description "Frotz is an interpreter for Infocom games and other Z-machine
+games in the text adventure/interactive fiction genre.  This version of Frotz
+complies with standard 1.0 of Graham Nelson's specification.  It plays all
+Z-code games V1-V8, including V6, with sound support through libao, and uses
+ncurses for text display.")
+    (home-page "http://frotz.sourceforge.net")
+    (license license:gpl2+)))
+
+(define-public frotz-dumb-terminal
+  (package
+    (name "frotz-dumb-terminal")
+    (version "2.44")
+    (source (origin
+              (method url-fetch)
+              (uri (list (string-append
+                          "http://www.ifarchive.org/if-archive/infocom/interpreters/"
+                          "frotz" "/" "frotz" "-" version ".tar.gz")
+                         (string-append
+                          "ftp://ftp.ifarchive.org/if-archive/infocom/interpreters/"
+                          "frotz" "/" "frotz" "-" version ".tar.gz")))
+              (sha256
+               (base32
+                "1v735xr3blznac8fnwa27s1vhllx4jpz7kw7qdw1bsfj6kq21v3k"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; there are no tests
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'build
+           (lambda _
+             (invoke "make" "dumb")))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (man (string-append out "/share/man/man6")))
+               (install-file "dfrotz" bin)
+               (mkdir-p man)
+               (install-file "doc/dfrotz.6" man)
+               #t))))))
+    (synopsis "Portable Z-machine dumb interpreter for text adventure games")
+    (description "Frotz is an interpreter for Infocom games and
+other Z-machine games in the text adventure/interactive fiction genre.
+dfrotz is the dumb interface version.  You get no screen control; everything
+is just printed to the terminal line by line.  The terminal handles all the
+scrolling.  Maybe you'd like to experience what it's like to play Adventure on
+a teletype.  A much cooler use for compiling Frotz with the dumb interface is
+that it can be wrapped in CGI scripting, PHP, and the like to allow people
+to play games on webpages.  It can also be made into a chat bot.")
+    (home-page "http://frotz.sourceforge.net")
+    (license license:gpl2+)))
+
+(define-public frotz-sdl
+  (let* ((commit "4de8c34f2116fff554af6216c30ec9d41bf50b24"))
+    (package
+      (name "frotz-sdl")
+      (version "2.45pre")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://gitlab.com/DavidGriffith/frotz")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "18ms21pcrl7ipcnyqnf8janamkryzx78frsgd9kfk67jvbj0z2k8"))
+                (file-name (git-file-name name version))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                    ; there are no tests
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (add-before 'build 'patch-makefile
+             (lambda _
+               (substitute* "Makefile"
+                 (("lcurses") "lncurses")
+                 (("^BUILD_DATE_TIME =.*$")
+                  "BUILD_DATE_TIME = \"2.45pre-20180907.00000\"\n"))
+               #t))
+           (replace 'build
+             (lambda _
+               (invoke "make" "sdl")))
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (bin (string-append out "/bin"))
+                      (man (string-append out "/share/man/man6")))
+                 (install-file "sfrotz" bin)
+                 (mkdir-p man)
+                 (install-file "doc/sfrotz.6" man)
+                 #t))))))
+      (native-inputs
+       `(("pkg-config" ,pkg-config)
+         ("which" ,which)
+         ("perl" ,perl)))
+      (inputs `(("sdl2" ,sdl2)
+                ("sdl2-mixer" ,sdl2-mixer)
+                ("libmodplug" ,libmodplug)
+                ("libsamplerate" ,libsamplerate)
+                ("libsndfile" ,libsndfile)
+                ("libvorbis" ,libvorbis)
+                ("ncurses" ,ncurses)
+                ("freetype" ,freetype)
+                ("libjpeg-turbo" ,libjpeg-turbo)))
+      (synopsis "Portable Z-machine interpreter (SDL port) for text adventure games")
+      (description "Frotz is an interpreter for Infocom games and other Z-machine
+games in the text adventure/interactive fiction genre.  This version of Frotz
+using SDL fully supports all these versions of the Z-Machine including the
+graphical version 6.  Graphics and sound are created through the use of the SDL
+libraries.  AIFF sound effects and music in MOD and OGG formats are supported
+when packaged in Blorb container files or optionally from individual files.")
+      (home-page "http://frotz.sourceforge.net")
+      (license license:gpl2+))))
diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm
index 520f5cba0b..8207104174 100644
--- a/gnu/packages/gcc.scm
+++ b/gnu/packages/gcc.scm
@@ -668,6 +668,10 @@ as the 'native-search-paths' field."
   (custom-gcc gcc-7 "gfortran" '("fortran")
               %generic-search-paths))
 
+(define-public gfortran-8
+  (custom-gcc gcc-8 "gfortran" '("fortran")
+              %generic-search-paths))
+
 (define-public gfortran
   ;; Note: Update this when GCC changes!  We cannot use
   ;; (custom-gcc gcc "fortran" …) because that would lead to a package object
@@ -728,6 +732,15 @@ as the 'native-search-paths' field."
                      (variable "LIBRARY_PATH")
                      (files '("lib" "lib64"))))))
 
+(define-public gcc-objc-8
+  (custom-gcc gcc-8 "gcc-objc" '("objc")
+              (list (search-path-specification
+                     (variable "OBJC_INCLUDE_PATH")
+                     (files '("include")))
+                    (search-path-specification
+                     (variable "LIBRARY_PATH")
+                     (files '("lib" "lib64"))))))
+
 (define-public gcc-objc gcc-objc-5)
 
 (define-public gcc-objc++-4.8
@@ -775,6 +788,15 @@ as the 'native-search-paths' field."
                      (variable "LIBRARY_PATH")
                      (files '("lib" "lib64"))))))
 
+(define-public gcc-objc++-8
+  (custom-gcc gcc-8 "gcc-objc++" '("obj-c++")
+              (list (search-path-specification
+                     (variable "OBJCPLUS_INCLUDE_PATH")
+                     (files '("include")))
+                    (search-path-specification
+                     (variable "LIBRARY_PATH")
+                     (files '("lib" "lib64"))))))
+
 (define-public gcc-objc++ gcc-objc++-5)
 
 (define (make-libstdc++-doc gcc)
diff --git a/gnu/packages/gdb.scm b/gnu/packages/gdb.scm
index f0c4c8b804..74eb0f8994 100644
--- a/gnu/packages/gdb.scm
+++ b/gnu/packages/gdb.scm
@@ -37,14 +37,14 @@
 (define-public gdb
   (package
     (name "gdb")
-    (version "8.1.1")
+    (version "8.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/gdb/gdb-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0g6hv9xk12aa58w77fydaldqr9a6b0a6bnwsq87jfc6lkcbc7p4p"))))
+               "0fbw6j4z7kmvywwgavn7w3knp860i5i9qnjffc5p52bwkji43963"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; FIXME "make check" fails on single-processor systems.
diff --git a/gnu/packages/ghostscript.scm b/gnu/packages/ghostscript.scm
index cd7cd604fd..3808d81524 100644
--- a/gnu/packages/ghostscript.scm
+++ b/gnu/packages/ghostscript.scm
@@ -7,6 +7,7 @@
 ;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -38,8 +39,10 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix utils)
   #:use-module (guix build-system gnu)
-  #:use-module (guix build-system trivial))
+  #:use-module (guix build-system trivial)
+  #:use-module (srfi srfi-1))
 
 (define-public lcms
   (package
@@ -132,6 +135,7 @@ printing, and psresize, for adjusting page sizes.")
 (define-public ghostscript
   (package
     (name "ghostscript")
+    (replacement ghostscript/fixed)
     (version "9.23")
     (source
       (origin
@@ -251,6 +255,44 @@ output file formats and printers.")
     (home-page "https://www.ghostscript.com/")
     (license license:agpl3+)))
 
+(define-public ghostscript/fixed
+  (hidden-package
+    (package
+      (inherit ghostscript)
+      (version "9.24")
+      (source
+        (origin
+          (inherit (package-source ghostscript))
+          (uri (string-append "https://github.com/ArtifexSoftware/"
+                              "ghostpdl-downloads/releases/download/gs"
+                              (string-delete #\. version)
+                              "/ghostscript-" version ".tar.xz"))
+          (sha256
+           (base32
+            "1mk922rnml93w2g42yxiyn8xqanc50cm65irrgh0b6lp4kgifjfl"))
+          (patches (search-patches "ghostscript-CVE-2018-16509.patch"
+                                   "ghostscript-bug-699708.patch"
+                                   "ghostscript-no-header-creationdate.patch"
+                                   "ghostscript-no-header-id.patch"
+                                   "ghostscript-no-header-uuid.patch"))))
+      (arguments
+       (substitute-keyword-arguments (package-arguments ghostscript)
+         ((#:configure-flags flags)
+          ;; Notice that we removed the 'ghostscript-runpath' patch above.
+          ;; The reason is that it conflicts with an upstream change that
+          ;; takes LDFLAGS into account.
+          `(cons (string-append "LDFLAGS=-Wl,-rpath="
+                                (assoc-ref %outputs "out") "/lib")
+                 ,flags))
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (add-before 'configure 'create-output-directory
+               (lambda* (#:key outputs #:allow-other-keys)
+                 ;; Unfortunately the configure script refuses to function if
+                 ;; the directory specified as -rpath does not already exist.
+                 (mkdir-p (string-append (assoc-ref outputs "out") "/lib"))
+                 #t)))))))))
+
 (define-public ghostscript/x
   (package/inherit ghostscript
     (name (string-append (package-name ghostscript) "-with-x"))
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 659f5dd5d4..2b723e99ee 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -2461,7 +2461,7 @@ libxml to ease remote use of the RESTful API.")
 (define-public libsoup
   (package
     (name "libsoup")
-    (version "2.62.3")
+    (version "2.64.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/libsoup/"
@@ -2469,7 +2469,7 @@ libxml to ease remote use of the RESTful API.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0whi8p03kpbp68kg6fg3vb7rhykjp7wn3nlbzy9j0p298zjss4nk"))))
+                "09z7g3spww3f84y8jmicdd6lqp360mbggpg5h1fq1v4p5ihcjnyr"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (arguments
@@ -2573,6 +2573,7 @@ libxml to ease remote use of the RESTful API.")
        ("libxml2" ,libxml2)))
     (inputs
      `(("glib-networking" ,glib-networking)
+       ("libpsl" ,libpsl)
        ("sqlite" ,sqlite)))
     (home-page "https://live.gnome.org/LibSoup/")
     (synopsis "GLib-based HTTP Library")
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index b393919e66..245ee8f956 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -28,6 +28,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages bioconductor)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cran)
@@ -98,14 +99,14 @@ more.")
 (define-public r-igraph
   (package
     (name "r-igraph")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "igraph" version))
        (sha256
         (base32
-         "1hcr6b1lz030lgay1bz8y8sxaf2j93ds8n8gsqr6qhssz141hd2m"))))
+         "1bggm7b8v3bh7q2589w26qvd7sgs69m4qiij7d0rbm0ykkgxm8lx"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -130,14 +131,14 @@ more.")
 (define-public r-diffusionmap
   (package
     (name "r-diffusionmap")
-    (version "1.1-0")
+    (version "1.1-0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "diffusionMap" version))
        (sha256
         (base32
-         "1l985q2hfc8ss5afajik4p25dx628yikvhdimz5s0pql800q2yv3"))))
+         "11l4kbciawvli5nlsi4qaf8afmgk5xgqiqpdyhvaqri5mx0zhk5j"))))
     (properties `((upstream-name . "diffusionMap")))
     (build-system r-build-system)
     (propagated-inputs
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 3322860d83..7a70239684 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -890,14 +890,7 @@ images onto Cairo surfaces.")
               (sha256
                (base32
                 "1qam447m05sxxv6x8dlzg7qnyfc4dh8apjw1idpfhpns671gfr6m"))
-              (patches (search-patches "guile-present-coding.patch"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  (substitute* "Makefile.in"
-                    (("godir = .*$")
-                     "godir = $(moddir)\n"))
-                  #t))))
+              (patches (search-patches "guile-present-coding.patch"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 8c561b0210..7c88454300 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -866,7 +866,7 @@ for Guile\".")
 (define-public guile-json
   (package
     (name "guile-json")
-    (version "1.1.1")
+    (version "1.2.0")
     (home-page "https://github.com/aconchillo/guile-json")
     (source (origin
               (method url-fetch)
@@ -875,7 +875,7 @@ for Guile\".")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "12jqkn9qgwdlxbasy2n25a2a7apf30dww1nnxqfam5735k3jdngv"))))
+                "02kqv0q98fmchn7i4y7ycmrjlh4b2c93ij0z7k036qwpp204w4gh"))))
     (build-system gnu-build-system)
     (native-inputs `(("autoconf" ,autoconf)
                      ("automake" ,automake)
@@ -893,7 +893,9 @@ specification.  These are the main features:
 @item Unicode support for strings.
 @item Allows JSON pretty printing.
 @end itemize\n")
-    (license license:lgpl3+)))
+
+    ;; Version 1.2.0 switched to GPLv3+ (from LGPLv3+).
+    (license license:gpl3+)))
 
 (define-public guile2.2-json
   (deprecated-package "guile2.2-json" guile-json))
@@ -1581,8 +1583,10 @@ you send to a FIFO file.")
                     (("ac_subst_vars='")
                      "ac_subst_vars='GUILE_EFFECTIVE_VERSION\n"))
                   (substitute* "Makefile.in"
-                    (("/site/2.0")
-                     "/site/@GUILE_EFFECTIVE_VERSION@"))
+                    (("moddir =.*")
+                     "moddir = $(datadir)/guile/site/@GUILE_EFFECTIVE_VERSION@\n")
+                    (("godir =.*")
+                     "godir = $(libdir)/guile/@GUILE_EFFECTIVE_VERSION@/site-ccache\n"))
                   #t))))
     (build-system gnu-build-system)
     (inputs
@@ -1786,6 +1790,20 @@ Note that 8sync is only available for Guile 2.2.")
                (base32
                 "0vjkg72ghgdgphzbjz9ig8al8271rq8974viknb2r1rg4lz92ld0"))))
     (build-system gnu-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-after 'install 'mode-guile-objects
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      ;; .go files are installed to "lib/guile/X.Y/cache".
+                      ;; This phase moves them to "…/site-ccache".
+                      (let* ((out (assoc-ref outputs "out"))
+                             (lib (string-append out "/lib/guile"))
+                             (old (car (find-files lib "^ccache$"
+                                                   #:directories? #t)))
+                             (new (string-append (dirname old)
+                                                 "/site-ccache")))
+                        (rename-file old new)
+                        #t))))))
     (native-inputs
      `(("texinfo" ,texinfo)
        ("pkg-config" ,pkg-config)))
diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index c3ef85f3f0..31407ca259 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -39,7 +39,7 @@
 (define-public ghc-tasty-ant-xml
   (package
     (name "ghc-tasty-ant-xml")
-    (version "1.0.2")
+    (version "1.1.4")
     (source
      (origin
        (method url-fetch)
@@ -49,7 +49,7 @@
              ".tar.gz"))
        (sha256
         (base32
-         "0pgz2lclg2hp72ykljcbxd88pjanfdfk8m5vb2qzcyjr85kwrhxv"))))
+         "0v0gsb90kh6hwlgxbclzawsskywc6yf7n8xhiifia97l4y0yx2m8"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-generic-deriving" ,ghc-generic-deriving)
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a07bb049a2..eb629cf138 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2078,9 +2078,13 @@ literals.")
         (base32
          "1vbzf0awb6zb456xf48za1kl22018646cfzq4frvxgb9ay97vk0d"))))
     (build-system haskell-build-system)
-    ;; Tests require older versions of testy.
-    (arguments `(#:tests? #f))
+    (arguments `(#:configure-flags (list "--allow-newer=tasty")))
     (inputs `(("zlib" ,zlib)))
+    (native-inputs
+     `(("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-hunit" ,ghc-tasty-hunit)
+       ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)))
     (home-page "https://hackage.haskell.org/package/zlib")
     (synopsis
      "Compression and decompression in the gzip and zlib formats")
@@ -4220,7 +4224,7 @@ system.")
 (define-public ghc-base-compat
   (package
     (name "ghc-base-compat")
-    (version "0.10.4")
+    (version "0.9.3")
     (source
      (origin
        (method url-fetch)
@@ -4230,7 +4234,7 @@ system.")
              ".tar.gz"))
        (sha256
         (base32
-         "0ksp990gxs731mq19rzbxrbs43nazfljjc8krlx5bjqblw3kfs8d"))))
+         "0452l6zf6fjhy4kxqwv6i6hhg6yfx4wcg450k3axpyj30l7jnq3x"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)
@@ -5190,6 +5194,8 @@ occurrences of a substring (the first in case of overlaps) with another.")
         (base32
          "1wj8kgjg5bn2yrs4zh9qfjv85cx6w998j9pi39yrbv305944mb9j"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:configure-flags (list "--allow-newer=tasty")))
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-smallcheck" ,ghc-smallcheck)
@@ -10152,4 +10158,29 @@ tools are not needed to actually run Gtk2Hs programs.")
 backends provided by the @code{Cairo} and @code{Diagrams} libraries.")
     (license license:bsd-3)))
 
+(define-public ghc-wcwidth
+  (package
+    (name "ghc-wcwidth")
+    (version "0.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/wcwidth/wcwidth-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "1n1fq7v64b59ajf5g50iqj9sa34wm7s2j3viay0kxpmvlcv8gipz"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-setlocale" ,ghc-setlocale)
+       ("ghc-utf8-string" ,ghc-utf8-string)
+       ("ghc-attoparsec" ,ghc-attoparsec)))
+    (home-page "https://github.com/solidsnack/wcwidth/")
+    (synopsis "Haskell bindings to wcwidth")
+    (description "This package provides Haskell bindings to your system's
+native wcwidth and a command line tool to examine the widths assigned by it.
+The command line tool can compile a width table to Haskell code that assigns
+widths to the Char type.")
+    (license license:bsd-3)))
+
 ;;; haskell.scm ends here
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index c6010f1f56..03f08a614f 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -19,6 +19,7 @@
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -485,6 +486,7 @@ arithmetic ops.")
   (package
     (name "jbig2dec")
     (version "0.14")
+    (replacement jbig2dec-0.15)
     (source
       (origin
         (method url-fetch)
@@ -509,6 +511,21 @@ work.")
     (home-page "https://jbig2dec.com")
     (license license:gpl2+)))
 
+;; This is a bugfix release from an ongoing Ghostscript security audit.
+;; It was released alongside Ghostscript 9.24.
+(define-public jbig2dec-0.15
+  (package
+    (inherit jbig2dec)
+    (version "0.15")
+    (source (origin
+              (inherit (package-source jbig2dec))
+              (uri (string-append "https://github.com/ArtifexSoftware"
+                                  "/ghostpdl-downloads/releases/download/gs924/"
+                                  "jbig2dec-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0m1qwpbjbirgw2fqznbajdhdhh35d6xa2csr64lpjz735pvimykb"))))))
+
 (define-public openjpeg
   (package
     (name "openjpeg")
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index 39e2322739..fb9b0eeedf 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -355,10 +355,12 @@
        ("objconv"
         ,(origin
            (method url-fetch)
-           (uri "http://www.agner.org/optimize/objconv.zip")
+           ;; No versioned URL, see <https://www.agner.org/optimize/> for updates.
+           (uri "https://www.agner.org/optimize/objconv.zip")
+           (file-name "objconv-2018-08-15.zip")
            (sha256
             (base32
-             "1fi7qa2sd9vb35dvkgripjf0fayzg2qmff215f8agfqfiwd1g8qs"))))
+             "09y4pwxfs6fl47cyingbf95i2rxx74wmycl9fd4ldcgvpx9bzdrx"))))
        ("dsfmt"
         ,(origin
            (method url-fetch)
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 14f23db888..fc071a1338 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -399,8 +399,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.5")
-(define %linux-libre-hash "1y52ns34vh9p4pfj08xsycv8p0xywm6dbpdi0wwpkll1xgpqikvf")
+(define %linux-libre-version "4.18.6")
+(define %linux-libre-hash "1l5caid77vbfb54zrfxkk7qj7lrf9ck9kpn96kr45spkwl51wm8m")
 
 (define %linux-libre-4.18-patches
   (list %boot-logo-patch
@@ -430,8 +430,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.18-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.67")
-(define %linux-libre-4.14-hash "050zvdxjy6sc64q75pr1gxsmh49chwav2pwxz8xlif39bvahnrpg")
+(define %linux-libre-4.14-version "4.14.68")
+(define %linux-libre-4.14-hash "05l5y0vbbl60jxdbqglqr9c99a8g8lfsp4mcqfpcx1pkh5br7i3l")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
@@ -440,14 +440,14 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.124"
-                    "0p78gx5jiqvaf2cadf5jp40lzgarrg0m0ybf9w2499v28vjsp30q"
+  (make-linux-libre "4.9.125"
+                    "1saihk61l1kk42jf8yfsfkm77zalq31f0bdlam3c1g7yw702wj9g"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.153"
-                    "195vzkkmjiicqfzd38hgf381rlz665rl06abzf8cww0gbnzvrf72"
+  (make-linux-libre "4.4.154"
+                    "08i9fvrmswkydj538wg6c7ggxmhll0ff0bjkw8rnyslqwilfwr1i"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index a86bdcb5ed..7790e78779 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -560,13 +560,13 @@ I/O.")
 (define-public r-adaptivesparsity
   (package
     (name "r-adaptivesparsity")
-    (version "1.4")
+    (version "1.6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "AdaptiveSparsity" version))
               (sha256
                (base32
-                "1az7isvalf3kmdiycrfl6s9k9xqk22k1mc6rh8v0jmcz402qyq8z"))))
+                "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
     (properties
      `((upstream-name . "AdaptiveSparsity")))
     (build-system r-build-system)
@@ -579,7 +579,9 @@ I/O.")
                (("PKG_LIBS=" prefix)
                 (string-append prefix "-larmadillo"))))))))
     (propagated-inputs
-     `(("r-rcpp" ,r-rcpp)
+     `(("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
        ("r-rcpparmadillo" ,r-rcpparmadillo)))
     (inputs
      `(("armadillo" ,armadillo)))
@@ -594,14 +596,14 @@ geometric models.")
 (define-public r-kernlab
   (package
     (name "r-kernlab")
-    (version "0.9-26")
+    (version "0.9-27")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "kernlab" version))
        (sha256
         (base32
-         "0xv0slf3ggw3sswsi34416lb1g3h1pqkrr2h7r1n1kvgii3l0jcm"))))
+         "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/kernlab")
     (synopsis "Kernel-based machine learning tools")
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 4944dd7622..024e75aaa1 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -1071,7 +1071,7 @@ which can add many functionalities to the base client.")
 (define-public msmtp
   (package
     (name "msmtp")
-    (version "1.6.8")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
@@ -1079,11 +1079,10 @@ which can add many functionalities to the base client.")
                            "/msmtp-" version ".tar.xz"))
        (sha256
         (base32
-         "1ysrnshvwhzwmvb2walw5i9jdzlvmckj7inr0xnvb26q0jirbzsm"))))
+         "1k9wwlapkxk9ql3xq05y6vwn6ziqk9b1v8lyhj1866qd02zhqwxx"))))
     (build-system gnu-build-system)
     (inputs
-     `(("libidn" ,libidn)
-       ("libsecret" ,libsecret)
+     `(("libsecret" ,libsecret)
        ("gnutls" ,gnutls)
        ("zlib" ,zlib)
        ("gsasl" ,gsasl)))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 50c0a320e0..01bd03c600 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -15,7 +15,7 @@
 ;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
-;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
+;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
@@ -1580,7 +1580,7 @@ September 2004}")
 (define-public petsc
   (package
     (name "petsc")
-    (version "3.8.0")
+    (version "3.9.3")
     (source
      (origin
       (method url-fetch)
@@ -1588,7 +1588,9 @@ September 2004}")
       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
                           "petsc-lite-" version ".tar.gz"))
       (sha256
-       (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s"))))
+       (base32 "1fwkbwv4g7zf2lc8fw865xd0bl9anb6jaczfis5dff7h449gwa48"))))
+    (outputs '("out"                    ;libraries and headers
+               "examples"))             ;~30MiB of examples
     (build-system gnu-build-system)
     (native-inputs
      `(("python" ,python-2)))
@@ -1605,11 +1607,7 @@ September 2004}")
        #:configure-flags
        `("--with-mpi=0"
          "--with-openmp=1"
-         "--with-superlu=1"
-         ,(string-append "--with-superlu-include="
-                         (assoc-ref %build-inputs "superlu") "/include")
-         ,(string-append "--with-superlu-lib="
-                         (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
+         "--with-superlu=1")
        #:make-flags
        ;; Honor (parallel-job-count) for build.  Do not use --with-make-np,
        ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
@@ -1662,6 +1660,15 @@ September 2004}")
                           "PETScBuildInternal.cmake"
                           ;; Once installed, should uninstall with Guix
                           "uninstall.py"))
+              #t)))
+        (add-after 'install 'move-examples
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let* ((out (assoc-ref outputs "out"))
+                   (examples (assoc-ref outputs "examples"))
+                   (exdir (string-append out "/share/petsc/examples"))
+                   (exdir' (string-append examples "/share/petsc/examples")))
+              (copy-recursively exdir exdir')
+              (delete-file-recursively exdir)
               #t))))))
     (home-page "http://www.mcs.anl.gov/petsc")
     (synopsis "Library to solve PDEs")
@@ -1685,6 +1692,7 @@ scientific applications modeled by partial differential equations.")
     (name "petsc-openmpi")
     (inputs
      `(("openmpi" ,openmpi)
+       ("hdf5" ,hdf5-parallel-openmpi)
        ,@(package-inputs petsc)))
     (arguments
      (substitute-keyword-arguments (package-arguments petsc)
@@ -1692,7 +1700,21 @@ scientific applications modeled by partial differential equations.")
         ``("--with-mpiexec=mpirun"
            ,(string-append "--with-mpi-dir="
                            (assoc-ref %build-inputs "openmpi"))
-           ,@(delete "--with-mpi=0" ,cf)))))
+           ,(string-append "--with-hdf5-include="
+                           (assoc-ref %build-inputs "hdf5") "/include")
+           ,(string-append "--with-hdf5-lib="
+                           (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
+           ,@(delete "--with-mpi=0" ,cf)))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-before 'check 'set-test-environment
+             (lambda _
+               ;; By default, running the test suite would fail because 'ssh'
+               ;; could not be found in $PATH.  Define this variable to
+               ;; placate Open MPI without adding a dependency on OpenSSH (the
+               ;; agent isn't used anyway.)
+               (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
+               #t))))))
     (synopsis "Library to solve PDEs (with MPI support)")))
 
 (define-public petsc-complex-openmpi
@@ -1738,7 +1760,7 @@ savings are consistently > 5x.")
 (define-public slepc
   (package
     (name "slepc")
-    (version "3.8.2")
+    (version "3.9.2")
     (source
      (origin
        (method url-fetch)
@@ -1746,7 +1768,7 @@ savings are consistently > 5x.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "04zd48p43rnvg68p6cp28zll0px5whglc5v0sc3s6vdj1v920z8y"))))
+         "0gmhdqac8zm3jx43h935z7bflazjnpvqxjv4jh5za2y1z2rqax94"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("python" ,python-2)))
@@ -2824,8 +2846,8 @@ parts of it.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
-                           version))
+       (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
+                           version "%20version.tar.gz"))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
@@ -3231,7 +3253,7 @@ Failure to do so will result in a library with poor performance.")
 (define-public glm
   (package
     (name "glm")
-    (version "0.9.9.0")
+    (version "0.9.9.1")
     (source
      (origin
        (method url-fetch)
@@ -3239,7 +3261,7 @@ Failure to do so will result in a library with poor performance.")
                            version  "/glm-" version ".zip"))
        (sha256
         (base32
-         "0ihjadp2sb8w312a276skfjsljm3y41bjscbxf79wn23gi00giz1"))))
+         "042a23hmxfs429czkmlg5ixf28aikzfbw18780prj2gcd4flgw8h"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("unzip" ,unzip)))
@@ -4027,3 +4049,80 @@ terminal do calculations simply and quickly.  The formula to be calculated can
 be fed to @command{tcalc} through the command line.")
   (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
   (license license:gpl3+)))
+
+(define-public sundials
+  (package
+    (name "sundials")
+    (version "3.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
+                           "sundials-" version ".tar.gz"))
+       (sha256
+        (base32
+         "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("python" ,python-2)))    ;for tests; syntax incompatible with python 3
+    (inputs
+     `(("fortran" ,gfortran)            ;for fcmix
+       ("blas" ,openblas)
+       ("suitesparse" ,suitesparse)))   ;TODO: Add hypre
+    (arguments
+     `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
+                           "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
+                           "-DEXAMPLES_ENABLE_F77:BOOL=ON"
+                           "-DEXAMPLES_ENABLE_F90:BOOL=ON"
+                           "-DEXAMPLES_INSTALL:BOOL=OFF"
+
+                           "-DFCMIX_ENABLE:BOOL=ON"
+
+                           "-DKLU_ENABLE:BOOL=ON"
+                           ,(string-append "-DKLU_INCLUDE_DIR="
+                                           (assoc-ref %build-inputs "suitesparse")
+                                           "/include")
+                           ,(string-append "-DKLU_LIBRARY_DIR="
+                                           (assoc-ref %build-inputs "suitesparse")
+                                           "/lib"))))
+    (home-page "https://computation.llnl.gov/projects/sundials")
+    (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
+    (description "SUNDIALS is a family of software packages implemented with
+the goal of providing robust time integrators and nonlinear solvers that can
+easily be incorporated into existing simulation codes.")
+    (license license:bsd-3)))
+
+(define-public sundials-openmpi
+  (package (inherit sundials)
+    (name "sundials-openmpi")
+    (inputs
+     `(("mpi" ,openmpi)
+       ("petsc" ,petsc-openmpi)         ;support in SUNDIALS requires MPI
+       ,@(package-inputs sundials)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments sundials)
+       ((#:configure-flags flags '())
+        `(cons* "-DMPI_ENABLE:BOOL=ON"
+                "-DPETSC_ENABLE:BOOL=ON"
+                (string-append "-DPETSC_INCLUDE_DIR="
+                               (assoc-ref %build-inputs "petsc")
+                               "/include")
+                (string-append "-DPETSC_LIBRARY_DIR="
+                               (assoc-ref %build-inputs "petsc")
+                               "/lib")
+                ,flags))
+       ((#:phases phases '%standard-phases)
+        `(modify-phases ,phases
+           (add-before 'check 'set-test-environment
+             (lambda _
+               ;; By default, running the test suite would fail because 'ssh'
+               ;; could not be found in $PATH.  Define this variable to
+               ;; placate Open MPI without adding a dependency on OpenSSH (the
+               ;; agent isn't used anyway.)
+               (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
+               ;; Allow oversubscription in case there are less
+               ;; physical cores available in the build environment
+               ;; than SUNDIALS wants while testing.
+               (setenv "OMPI_MCA_rmaps_base_oversubscribe" "yes")
+               #t))))))
+    (synopsis "SUNDIALS with OpenMPI support")))
diff --git a/gnu/packages/mes.scm b/gnu/packages/mes.scm
index 81d4145439..63a8db449a 100644
--- a/gnu/packages/mes.scm
+++ b/gnu/packages/mes.scm
@@ -39,15 +39,15 @@
 (define-public nyacc
   (package
     (name "nyacc")
-    (version "0.83.3")
+    (version "0.86.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://savannah/nyacc/"
                                   name "-" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (patches (search-patches "nyacc-binary-literals.patch"))
               (sha256
                (base32
-                "0120n0mdb6r58c4jc024dhwqy5s8a20waknijfhqjc59a884lrd6"))))
+                "0lkd9lyspvhxlfs0496gsllwinh62jk9wij6gpadvx9gwz6yavd9"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("guile" ,guile-2.2)))
@@ -59,36 +59,24 @@ extensive examples, including parsers for the Javascript and C99 languages.")
     (home-page "https://savannah.nongnu.org/projects/nyacc")
     (license (list gpl3+ lgpl3+))))
 
-(define-public nyacc-for-mes
-  (package
-    (inherit nyacc)
-    (version "0.80.42")
-      (source (origin
-                (method url-fetch)
-                (uri (string-append "https://gitlab.com/janneke/nyacc"
-                                    "/-/archive/v" version
-                                    "/nyacc-" version ".tar.gz"))
-                (sha256
-                 (base32
-                  "0c8c8kxir0h2d4nxr131xbkfs7c80haipmkp2g6677sh14wn0b3y"))))))
-
 (define-public mes
   (let ((triplet "i686-unknown-linux-gnu"))
     (package
       (name "mes")
-      (version "0.17")
+      (version "0.17.1")
       (source (origin
                 (method url-fetch)
                 (uri (string-append "http://alpha.gnu.org/gnu/mes/"
                                     "mes-" version ".tar.gz"))
+                (patches (search-patches "mes-nyacc-0.86.0.patch"))
                 (sha256
                  (base32
-                  "1j32x4zqy2cqjlg9m35f2411mwac2b0p5ch4hm99gddmfbxzgyhg"))))
+                  "02g8zig53ffd0ai8kqhv2zj7bj2366a8hr6ydkwakmi2d1amyrna"))))
       (build-system gnu-build-system)
       (supported-systems '("i686-linux" "x86_64-linux"))
       (propagated-inputs
        `(("mescc-tools" ,mescc-tools)
-         ("nyacc" ,nyacc-for-mes)))
+         ("nyacc" ,nyacc)))
       (native-inputs
        `(("guile" ,guile-2.2)
          ,@(if (not (string-prefix? "i686-linux" (or (%current-target-system)
diff --git a/gnu/packages/mp3.scm b/gnu/packages/mp3.scm
index 579127d06e..c9effbafa3 100644
--- a/gnu/packages/mp3.scm
+++ b/gnu/packages/mp3.scm
@@ -84,7 +84,7 @@ fully implemented.
 
 This package contains the library.")
    (license license:gpl2+)
-   (home-page "http://www.underbit.com/products/mad/")))
+   (home-page "https://www.underbit.com/products/mad/")))
 
 (define-public libid3tag
   (package
@@ -105,7 +105,7 @@ This package contains the library.")
     "Libid3tag is a library for reading ID3 tags, both ID3v1 and the various
 versions of ID3v2.")
    (license license:gpl2+)
-   (home-page "http://www.underbit.com/products/mad/")))
+   (home-page "https://www.underbit.com/products/mad/")))
 
 (define-public id3lib
   (package
@@ -184,7 +184,7 @@ Speex, WavPack TrueAudio, WAV, AIFF, MP4 and ASF files.")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://ibiblio.org"
+                    "https://ibiblio.org"
                     "/pub/linux/apps/sound/mp3-utils/mp3info/mp3info-"
                     version ".tgz"))
               (sha256
@@ -231,7 +231,7 @@ Speex, WavPack TrueAudio, WAV, AIFF, MP4 and ASF files.")
     (inputs
      `(("gtk+" ,gtk+-2)
        ("ncurses" ,ncurses)))
-    (home-page "http://www.ibiblio.org/mp3info/")
+    (home-page "https://www.ibiblio.org/mp3info/")
     (synopsis "MP3 technical info viewer and ID3 1.x tag editor")
     (description
      "MP3Info is a little utility used to read and modify the ID3 tags of MP3
@@ -309,7 +309,7 @@ This package contains the binary.")
               (uri (list (string-append "mirror://sourceforge/mpg123/mpg123/"
                                         version "/mpg123-" version ".tar.bz2")
                          (string-append
-                          "http://www.mpg123.org/download/mpg123-"
+                          "https://www.mpg123.org/download/mpg123-"
                           version ".tar.bz2")))
               (sha256
                (base32
@@ -413,7 +413,7 @@ for album and track information.")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://files.musepack.net/source/libmpcdec-"
+                    "https://files.musepack.net/source/libmpcdec-"
                     version ".tar.bz2"))
               (sha256
                (base32
@@ -424,7 +424,7 @@ for album and track information.")
      "This library supports decoding of the Musepack (MPC) audio compression
 format.")
     (license license:bsd-3)
-    (home-page "http://musepack.net")))
+    (home-page "https://musepack.net")))
 
 (define-public mpc123
   (package
@@ -491,7 +491,7 @@ specifically mp3 files containing ID3 metadata (i.e. song info).  It provides a
 command-line tool (eyeD3) and a Python library (import eyed3) that can be used
 to write your own applications or plugins that are callable from the
 command-line tool.")
-    (home-page "http://eyed3.nicfit.net/")
+    (home-page "https://eyed3.readthedocs.io/en/latest/")
     (license license:gpl2+)))
 
 (define-public chromaprint
diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm
index 2554ec9efd..5c82bf9ba1 100644
--- a/gnu/packages/mpd.scm
+++ b/gnu/packages/mpd.scm
@@ -56,7 +56,7 @@
 (define-public libmpdclient
   (package
     (name "libmpdclient")
-    (version "2.14")
+    (version "2.15")
     (source (origin
               (method url-fetch)
               (uri
@@ -65,7 +65,7 @@
                               "/libmpdclient-" version ".tar.xz"))
               (sha256
                (base32
-                "0whk0qw0lsd3kaimdznz0c45bfym0p4885zf4b7pfc7y3dwy510a"))))
+                "1la60ar6i4ghpscrlgm45kci9b74bvkpsfybhg0ygs4rzpwzdnxl"))))
     (build-system meson-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
diff --git a/gnu/packages/multiprecision.scm b/gnu/packages/multiprecision.scm
index e185a98359..4f5eac16b9 100644
--- a/gnu/packages/multiprecision.scm
+++ b/gnu/packages/multiprecision.scm
@@ -108,7 +108,7 @@ algebra.")
 library for performing multiple-precision, floating-point computations with
 correct rounding.")
    (license lgpl3+)
-   (home-page "http://www.mpfr.org/")))
+   (home-page "https://www.mpfr.org/")))
 
 (define-public mpc
   (package
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index ba21e5da2b..e39478e794 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -786,18 +786,23 @@ interface.  It is implemented as a frontend to @code{klick}.")
 (define-public libgme
   (package
     (name "libgme")
-    (version "0.6.1")
+    (version "0.6.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://bitbucket.org/mpyne/game-music-emu/"
                                   "downloads/game-music-emu-" version
-                                  ".tar.bz2"))
+                                  ".tar.xz"))
               (sha256
                (base32
-                "08fk7zddpn7v93d0fa7fcypx7hvgwx9b5psj9l6m8b87k2hbw4fw"))))
+                "0hkkmxbaas2sirlb5i4r10mgbbiaapjx8pazifabwba23m3wnijh"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f)) ; no check target
+    (native-inputs
+     `(;; Use gcc-4.9 to work around an internal compiler error that happens
+       ;; when using gcc-5.5.0.  FIXME: Try removing this when the default
+       ;; compiler is no longer gcc-5.5.0.
+       ("gcc" ,gcc-4.9)))
     (home-page "https://bitbucket.org/mpyne/game-music-emu")
     (synopsis "Video game music file playback library")
     (description
diff --git a/gnu/packages/musl.scm b/gnu/packages/musl.scm
index ff789b8c6f..357372becd 100644
--- a/gnu/packages/musl.scm
+++ b/gnu/packages/musl.scm
@@ -28,17 +28,17 @@
 (define-public musl
   (package
     (name "musl")
-    (version "1.1.19")
+    (version "1.1.20")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://www.musl-libc.org/releases/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1nf1wh44bhm8gdcfr75ayib29b99vpq62zmjymrq7f96h9bshnfv"))))
+                "0q8dsjxl41dccscv9a0r78bs7jap57mn4mni5pwbbip6s1qqggj4"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f  ; Musl has no tests
+     `(#:tests? #f                      ; Musl has no tests
        #:configure-flags
        (list "--disable-gcc-wrapper")))
     (synopsis "Small C standard library")
diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 61c0ad7fba..abc616de3c 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -580,7 +580,7 @@ of the same name.")
 (define-public wireshark
   (package
     (name "wireshark")
-    (version "2.6.2")
+    (version "2.6.3")
     (source
      (origin
        (method url-fetch)
@@ -588,7 +588,7 @@ of the same name.")
                            version ".tar.xz"))
        (sha256
         (base32
-         "153h6prxamv5a62f3pfadkry0y57696xrgxfy2gfy5xswdg8kcj9"))))
+         "1v538h02y8avwy3cr11xz6wkyf9xd8qva4ng4sl9f2fw4skahn6i"))))
     (build-system gnu-build-system)
     (inputs `(("c-ares" ,c-ares)
               ("glib" ,glib)
@@ -762,52 +762,58 @@ live network and disk I/O bandwidth monitor.")
 (define-public aircrack-ng
   (package
     (name "aircrack-ng")
-    (version "1.2-rc4")
+    (version "1.3")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "http://download.aircrack-ng.org/aircrack-ng-"
+       (uri (string-append "https://download.aircrack-ng.org/aircrack-ng-"
                            version ".tar.gz"))
        (sha256
         (base32
-         "0dpzx9kddxpgzmgvdpl3rxn0jdaqhm5wxxndp1xd7d75mmmc2fnr"))))
+         "1jl30d0kibc82447fr3lgw75arik0l9729k94z76l7vl51y8mq4a"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)
+       ("which" ,which)))
     (inputs
      `(("libgcrypt" ,libgcrypt)
        ("libnl" ,libnl)
+       ("libpcap" ,libpcap)
        ("ethtool" ,ethtool)
        ("pcre" ,pcre)
        ("sqlite" ,sqlite)
        ("zlib" ,zlib)))
     (arguments
-     `(#:make-flags `("sqlite=true"
-                      "gcrypt=true"
-                      "libnl=true"
-                      "pcre=true"
-                      "experimental=true" ;build wesside-ng, etc.
-                      "AVX2FLAG=N" "AVX1FLAG=N"
-                      ,,@(match (%current-system)
-                           ((or "x86_64-linux" "i686-linux")
-                            `("SSEFLAG=Y"))
-                           (_
-                            `("NEWSSE=false")))
-                      ,(string-append "prefix=" %output))
+     `(#:configure-flags
+       (list "--with-experimental=yes"  ; build wesside-ng, etc.
+             "--with-gcrypt")           ; openssl's the default
        #:phases (modify-phases %standard-phases
-                  (delete 'configure)   ;no configure phase
+                  (add-before 'bootstrap 'patch-evalrev
+                    (lambda _
+                      ;; Called by ./autogen.sh below, before the default
+                      ;; ‘patch-shebangs’ phase has had a chance to run.
+                      (substitute* "evalrev"
+                        (("/bin/sh")
+                         (which "sh")))
+                      #t))
+                  (replace 'bootstrap
+                    (lambda _
+                      ;; Patch shebangs in generated files before running
+                      ;; ./configure.
+                      (setenv "NOCONFIGURE" "please")
+                      (invoke "bash" "./autogen.sh")))
                   (add-after 'build 'absolutize-tools
                     (lambda* (#:key inputs #:allow-other-keys)
                       (let ((ethtool (string-append (assoc-ref inputs "ethtool")
                                                     "/sbin/ethtool")))
                         (substitute* "scripts/airmon-ng"
-                          (("\\[ ! -x \"\\$\\(command -v ethtool 2>&1)\" \\]")
-                           (string-append "! " ethtool " --version "
-                                          ">/dev/null 2>&1"))
-                          (("\\$\\(ethtool")
-                           (string-append "$(" ethtool)))
+                          (("ethtool ")
+                           (string-append ethtool " ")))
                         #t))))))
-    (home-page "http://www.aircrack-ng.org")
+    (home-page "https://www.aircrack-ng.org")
     (synopsis "Assess WiFi network security")
     (description
      "Aircrack-ng is a complete suite of tools to assess WiFi network
diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm
index 1cdce999b3..ae39870dd4 100644
--- a/gnu/packages/openldap.scm
+++ b/gnu/packages/openldap.scm
@@ -106,14 +106,14 @@
 (define-public nss-pam-ldapd
   (package
     (name "nss-pam-ldapd")
-    (version "0.9.9")
+    (version "0.9.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://arthurdejong.org/nss-pam-ldapd/"
                                   "nss-pam-ldapd-" version ".tar.gz"))
               (sha256
                (base32
-                "1lj7qkjlg3bshwdc5x5r1ny37rly4wgm1c8b6w6b5f4wa11nmji0"))))
+                "1cqamcr6qpgwxijlr6kg7jspjamjra8w0haan0qssn0yxn95d7c0"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 6c3d245058..06c344e7af 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -101,8 +101,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "0.15.0")
-        (commit "8bbb79cf95a07a40950448a8a09d888254404ed4")
-        (revision 2))
+        (commit "3d43017026f9995ad128915db8ca5eafe061bf75")
+        (revision 3))
     (package
       (name "guix")
 
@@ -118,7 +118,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "0h83l91v2cg9bb78c7vqx9wj71ckz22jbjmm2fy4vqs9216jnvc0"))
+                  "167rzz2h33xmmchkplwzfq94s5jwdn5nabsq2lb84s54ps0sm89m"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
@@ -213,6 +213,7 @@
                         ;; Guile-JSON, and Guile-Git automatically.
                         (let* ((out    (assoc-ref outputs "out"))
                                (guile  (assoc-ref inputs "guile"))
+                               (gcrypt (assoc-ref inputs "guile-gcrypt"))
                                (json   (assoc-ref inputs "guile-json"))
                                (sqlite (assoc-ref inputs "guile-sqlite3"))
                                (git    (assoc-ref inputs "guile-git"))
@@ -220,7 +221,8 @@
                                                   "guile-bytestructures"))
                                (ssh    (assoc-ref inputs "guile-ssh"))
                                (gnutls (assoc-ref inputs "gnutls"))
-                               (deps   (list json sqlite gnutls git bs ssh))
+                               (deps   (list gcrypt json sqlite gnutls
+                                             git bs ssh))
                                (effective
                                 (read-line
                                  (open-pipe* OPEN_READ
@@ -277,6 +279,7 @@
                '())))
       (propagated-inputs
        `(("gnutls" ,gnutls)
+         ("guile-gcrypt" ,guile-gcrypt)
          ("guile-json" ,guile-json)
          ("guile-sqlite3" ,guile-sqlite3)
          ("guile-ssh" ,guile-ssh)
@@ -312,6 +315,7 @@ the Nix package manager.")
     (inputs
      `(("gnutls" ,gnutls)
        ("guile-git" ,guile-git)
+       ("guile-gcrypt" ,guile-gcrypt)
        ,@(fold alist-delete (package-inputs guix)
                '("boot-guile" "boot-guile/i686" "util-linux"))))
 
@@ -562,13 +566,13 @@ transactions from C or Python.")
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "96")
+    (version "100")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri name version))
               (sha256
                (base32
-                "1x66f2x8miy3giff14higpcs70c0zb5d3gj6yn8ac6p183sngl72"))))
+                "0sh7g26i5ndpa8l7xq6rnijbi3jz5izjn0b98zcnm6wpgghszw48"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/patches/ghostscript-CVE-2018-16509.patch b/gnu/packages/patches/ghostscript-CVE-2018-16509.patch
new file mode 100644
index 0000000000..50ffa3cb98
--- /dev/null
+++ b/gnu/packages/patches/ghostscript-CVE-2018-16509.patch
@@ -0,0 +1,193 @@
+Ghostscript 9.24 was released with an incomplete fix for CVE-2018-16509:
+https://nvd.nist.gov/vuln/detail/CVE-2018-16509
+https://bugs.chromium.org/p/project-zero/issues/detail?id=1640#c19
+https://bugs.ghostscript.com/show_bug.cgi?id=699718
+
+The reproducers no longer work after applying these commits:
+
+https://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=5812b1b78fc4d36fdc293b7859de69241140d590
+https://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=e914f1da46e33decc534486598dc3eadf69e6efb
+https://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=3e5d316b72e3965b7968bb1d96baa137cd063ac6
+https://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=643b24dbd002fb9c131313253c307cf3951b3d47
+
+This patch is a "squashed" version of those.
+
+diff --git a/Resource/Init/gs_setpd.ps b/Resource/Init/gs_setpd.ps
+index bba3c8c0e..8fa7c51df 100644
+--- a/Resource/Init/gs_setpd.ps
++++ b/Resource/Init/gs_setpd.ps
+@@ -95,27 +95,41 @@ level2dict begin
+  {	% Since setpagedevice doesn't create new device objects,
+         % we must (carefully) reinstall the old parameters in
+         % the same device.
+-   .currentpagedevice pop //null currentdevice //null .trysetparams
++   .currentpagedevice pop //null currentdevice //null
++   { .trysetparams } .internalstopped
++   {
++     //null
++   } if
+    dup type /booleantype eq
+     { pop pop }
+-    {		% This should never happen!
++    {
+       SETPDDEBUG { (Error in .trysetparams!) = pstack flush } if
+-      cleartomark pop pop pop
++      {cleartomark pop pop pop} .internalstopped pop
++      % if resetting the entire device state failed, at least put back the
++      % security related key
++      currentdevice //null //false mark /.LockSafetyParams
++      currentpagedevice /.LockSafetyParams .knownget not
++      {systemdict /SAFER .knownget not {//false} } if
++      .putdeviceparamsonly
+       /.installpagedevice cvx /rangecheck signalerror
+     }
+    ifelse pop pop
+         % A careful reading of the Red Book reveals that an erasepage
+         % should occur, but *not* an initgraphics.
+    erasepage .beginpage
+- } bind def
++ } bind executeonly def
+ 
+ /.uninstallpagedevice
+- { 2 .endpage { .currentnumcopies //false .outputpage } if
++ {
++   {2 .endpage { .currentnumcopies //false .outputpage } if} .internalstopped pop
+    nulldevice
+  } bind def
+ 
+ (%grestorepagedevice) cvn
+- { .uninstallpagedevice grestore .installpagedevice
++ {
++ .uninstallpagedevice
++ grestore
++ .installpagedevice
+  } bind def
+ 
+ (%grestoreallpagedevice) cvn
+diff --git a/psi/zdevice2.c b/psi/zdevice2.c
+index 0c7080d57..159a0c0d9 100644
+--- a/psi/zdevice2.c
++++ b/psi/zdevice2.c
+@@ -251,8 +251,8 @@ z2currentgstate(i_ctx_t *i_ctx_p)
+ /* ------ Wrappers for operators that reset the graphics state. ------ */
+ 
+ /* Check whether we need to call out to restore the page device. */
+-static bool
+-restore_page_device(const gs_gstate * pgs_old, const gs_gstate * pgs_new)
++static int
++restore_page_device(i_ctx_t *i_ctx_p, const gs_gstate * pgs_old, const gs_gstate * pgs_new)
+ {
+     gx_device *dev_old = gs_currentdevice(pgs_old);
+     gx_device *dev_new;
+@@ -260,9 +260,10 @@ restore_page_device(const gs_gstate * pgs_old, const gs_gstate * pgs_new)
+     gx_device *dev_t2;
+     bool samepagedevice = obj_eq(dev_old->memory, &gs_int_gstate(pgs_old)->pagedevice,
+         &gs_int_gstate(pgs_new)->pagedevice);
++    bool LockSafetyParams = dev_old->LockSafetyParams;
+ 
+     if ((dev_t1 = (*dev_proc(dev_old, get_page_device)) (dev_old)) == 0)
+-        return false;
++        return 0;
+     /* If we are going to putdeviceparams in a callout, we need to */
+     /* unlock temporarily.  The device will be re-locked as needed */
+     /* by putdeviceparams from the pgs_old->pagedevice dict state. */
+@@ -271,23 +272,51 @@ restore_page_device(const gs_gstate * pgs_old, const gs_gstate * pgs_new)
+     dev_new = gs_currentdevice(pgs_new);
+     if (dev_old != dev_new) {
+         if ((dev_t2 = (*dev_proc(dev_new, get_page_device)) (dev_new)) == 0)
+-            return false;
+-        if (dev_t1 != dev_t2)
+-            return true;
++            samepagedevice = true;
++        else if (dev_t1 != dev_t2)
++            samepagedevice = false;
++    }
++
++    if (LockSafetyParams && !samepagedevice) {
++        const int required_ops = 512;
++        const int required_es = 32;
++
++        /* The %grestorepagedevice must complete: the biggest danger
++           is operand stack overflow. As we use get/putdeviceparams
++           that means pushing all the device params onto the stack,
++           pdfwrite having by far the largest number of parameters
++           at (currently) 212 key/value pairs - thus needing (currently)
++           424 entries on the op stack. Allowing for working stack
++           space, and safety margin.....
++         */
++        if (required_ops + ref_stack_count(&o_stack) >= ref_stack_max_count(&o_stack)) {
++           gs_currentdevice(pgs_old)->LockSafetyParams = LockSafetyParams;
++           return_error(gs_error_stackoverflow);
++        }
++        /* We also want enough exec stack space - 32 is an overestimate of
++           what we need to complete the Postscript call out.
++         */
++        if (required_es + ref_stack_count(&e_stack) >= ref_stack_max_count(&e_stack)) {
++           gs_currentdevice(pgs_old)->LockSafetyParams = LockSafetyParams;
++           return_error(gs_error_execstackoverflow);
++        }
+     }
+     /*
+      * The current implementation of setpagedevice just sets new
+      * parameters in the same device object, so we have to check
+      * whether the page device dictionaries are the same.
+      */
+-    return !samepagedevice;
++    return samepagedevice ? 0 : 1;
+ }
+ 
+ /* - grestore - */
+ static int
+ z2grestore(i_ctx_t *i_ctx_p)
+ {
+-    if (!restore_page_device(igs, gs_gstate_saved(igs)))
++    int code = restore_page_device(i_ctx_p, igs, gs_gstate_saved(igs));
++    if (code < 0) return code;
++
++    if (code == 0)
+         return gs_grestore(igs);
+     return push_callout(i_ctx_p, "%grestorepagedevice");
+ }
+@@ -297,7 +326,9 @@ static int
+ z2grestoreall(i_ctx_t *i_ctx_p)
+ {
+     for (;;) {
+-        if (!restore_page_device(igs, gs_gstate_saved(igs))) {
++        int code = restore_page_device(i_ctx_p, igs, gs_gstate_saved(igs));
++        if (code < 0) return code;
++        if (code == 0) {
+             bool done = !gs_gstate_saved(gs_gstate_saved(igs));
+ 
+             gs_grestore(igs);
+@@ -328,11 +359,15 @@ z2restore(i_ctx_t *i_ctx_p)
+     if (code < 0) return code;
+ 
+     while (gs_gstate_saved(gs_gstate_saved(igs))) {
+-        if (restore_page_device(igs, gs_gstate_saved(igs)))
++        code = restore_page_device(i_ctx_p, igs, gs_gstate_saved(igs));
++        if (code < 0) return code;
++        if (code > 0)
+             return push_callout(i_ctx_p, "%restore1pagedevice");
+         gs_grestore(igs);
+     }
+-    if (restore_page_device(igs, gs_gstate_saved(igs)))
++    code = restore_page_device(i_ctx_p, igs, gs_gstate_saved(igs));
++    if (code < 0) return code;
++    if (code > 0)
+         return push_callout(i_ctx_p, "%restorepagedevice");
+ 
+     code = dorestore(i_ctx_p, asave);
+@@ -355,9 +390,12 @@ static int
+ z2setgstate(i_ctx_t *i_ctx_p)
+ {
+     os_ptr op = osp;
++    int code;
+ 
+     check_stype(*op, st_igstate_obj);
+-    if (!restore_page_device(igs, igstate_ptr(op)))
++    code = restore_page_device(i_ctx_p, igs, igstate_ptr(op));
++    if (code < 0) return code;
++    if (code == 0)
+         return zsetgstate(i_ctx_p);
+     return push_callout(i_ctx_p, "%setgstatepagedevice");
+ }
diff --git a/gnu/packages/patches/ghostscript-bug-699708.patch b/gnu/packages/patches/ghostscript-bug-699708.patch
new file mode 100644
index 0000000000..1567be1c6f
--- /dev/null
+++ b/gnu/packages/patches/ghostscript-bug-699708.patch
@@ -0,0 +1,160 @@
+Additional security fix that missed 9.24.
+
+Taken from upstream:
+http://git.ghostscript.com/?p=ghostpdl.git;a=commitdiff;h=fb713b3818b52d8a6cf62c951eba2e1795ff9624
+
+From fb713b3818b52d8a6cf62c951eba2e1795ff9624 Mon Sep 17 00:00:00 2001
+From: Chris Liddell <chris.liddell@artifex.com>
+Date: Thu, 6 Sep 2018 09:16:22 +0100
+Subject: [PATCH] Bug 699708 (part 1): 'Hide' non-replaceable error handlers
+ for SAFER
+
+We already had a 'private' dictionary for non-standard errors: gserrordict.
+
+This now includes all the default error handlers, the dictionary is made
+noaccess and all the prodedures are bound and executeonly.
+
+When running with -dSAFER, in the event of a Postscript error, instead of
+pulling the handler from errordict, we'll pull it from gserrordict - thus
+malicious input cannot trigger problems by the use of custom error handlers.
+
+errordict remains open and writeable, so files such as the Quality Logic tests
+that install their own handlers will still 'work', with the exception that the
+custom error handlers will not be called.
+
+This is a 'first pass', 'sledgehammer' approach: a nice addition would to allow
+an integrator to specify a list of errors that are not to be replaced (for
+example, embedded applications would probably want to ensure that VMerror is
+always handled as they intend).
+---
+ Resource/Init/gs_init.ps | 29 ++++++++++++++++++-----------
+ psi/interp.c             | 30 +++++++++++++++++++++---------
+ 2 files changed, 39 insertions(+), 20 deletions(-)
+
+diff --git a/Resource/Init/gs_init.ps b/Resource/Init/gs_init.ps
+index 071c39205..bc8b7951c 100644
+--- a/Resource/Init/gs_init.ps
++++ b/Resource/Init/gs_init.ps
+@@ -881,7 +881,7 @@ userdict /.currentresourcefile //null put
+        { not exch pop exit } { pop } ifelse
+     }
+    for exch pop .quit
+- } bind def
++ } bind executeonly def
+ /.errorhandler		% <command> <errorname> .errorhandler -
+   {		% Detect an internal 'stopped'.
+     1 .instopped { //null eq { pop pop stop } if } if
+@@ -926,7 +926,7 @@ userdict /.currentresourcefile //null put
+     $error /globalmode get $error /.nosetlocal get and .setglobal
+     $error /.inerror //false put
+     stop
+-  } bind def
++  } bind executeonly def
+ % Define the standard handleerror.  We break out the printing procedure
+ % (.printerror) so that it can be extended for binary output
+ % if the Level 2 facilities are present.
+@@ -976,7 +976,7 @@ userdict /.currentresourcefile //null put
+      ifelse	% newerror
+      end
+      flush
+-    } bind def
++    } bind executeonly def
+   /.printerror_long			% long error printout,
+                                         % $error is on the dict stack
+    {	% Push the (anonymous) stack printing procedure.
+@@ -1053,14 +1053,14 @@ userdict /.currentresourcefile //null put
+         { (Current file position is ) print position = }
+        if
+ 
+-   } bind def
++   } bind executeonly def
+ % Define a procedure for clearing the error indication.
+ /.clearerror
+  { $error /newerror //false put
+    $error /errorname //null put
+    $error /errorinfo //null put
+    0 .setoserrno
+- } bind def
++ } bind executeonly def
+ 
+ % Define $error.  This must be in local VM.
+ .currentglobal //false .setglobal
+@@ -1086,11 +1086,15 @@ end
+ /errordict ErrorNames length 3 add dict
+ .forcedef		% errordict is local, systemdict is global
+ .setglobal		% back to global VM
+-% For greater Adobe compatibility, we put all non-standard errors in a
+-%   separate dictionary, gserrordict.  It does not need to be in local VM,
+-%   because PostScript programs do not access it.
++%  gserrordict contains all the default error handling methods, but unlike
++%  errordict it is noaccess after creation (also it is in global VM).
++%  When running 'SAFER', we'll ignore the contents of errordict, which
++%  may have been tampered with by the running job, and always use gserrordict
++%  gserrordict also contains any non-standard errors, for better compatibility
++%  with Adobe.
++%
+ %   NOTE: the name gserrordict is known to the interpreter.
+-/gserrordict 5 dict def
++/gserrordict ErrorNames length 3 add dict def
+ % Register an error in errordict.  We make this a procedure because we only
+ % register the Level 1 errors here: the rest are registered by "feature"
+ % files.  However, ErrorNames contains all of the error names regardless of
+@@ -1119,8 +1123,11 @@ errordict begin
+  } bind def
+ end		% errordict
+ 
+-% Put non-standard errors in gserrordict.
+-gserrordict /unknownerror errordict /unknownerror get put
++% Put all the default handlers in gserrordict
++gserrordict
++errordict {2 index 3 1 roll put} forall
++noaccess pop
++% remove the non-standard errors from errordict
+ errordict /unknownerror .undef
+ % Define a stable private copy of handleerror that we will always use under
+ % JOBSERVER mode.
+diff --git a/psi/interp.c b/psi/interp.c
+index c27b70dca..d41a9d3f5 100644
+--- a/psi/interp.c
++++ b/psi/interp.c
+@@ -661,16 +661,28 @@ again:
+         return code;
+     if (gs_errorname(i_ctx_p, code, &error_name) < 0)
+         return code;            /* out-of-range error code! */
+-    /*
+-     * For greater Adobe compatibility, only the standard PostScript errors
+-     * are defined in errordict; the rest are in gserrordict.
++
++    /*  If LockFilePermissions is true, we only refer to gserrordict, which
++     *  is not accessible to Postcript jobs
+      */
+-    if (dict_find_string(systemdict, "errordict", &perrordict) <= 0 ||
+-        (dict_find(perrordict, &error_name, &epref) <= 0 &&
+-         (dict_find_string(systemdict, "gserrordict", &perrordict) <= 0 ||
+-          dict_find(perrordict, &error_name, &epref) <= 0))
+-        )
+-        return code;            /* error name not in errordict??? */
++    if (i_ctx_p->LockFilePermissions) {
++        if (((dict_find_string(systemdict, "gserrordict", &perrordict) <= 0 ||
++              dict_find(perrordict, &error_name, &epref) <= 0))
++            )
++            return code;            /* error name not in errordict??? */
++    }
++    else {
++        /*
++         * For greater Adobe compatibility, only the standard PostScript errors
++         * are defined in errordict; the rest are in gserrordict.
++         */
++        if (dict_find_string(systemdict, "errordict", &perrordict) <= 0 ||
++            (dict_find(perrordict, &error_name, &epref) <= 0 &&
++             (dict_find_string(systemdict, "gserrordict", &perrordict) <= 0 ||
++              dict_find(perrordict, &error_name, &epref) <= 0))
++            )
++            return code;            /* error name not in errordict??? */
++    }
+     doref = *epref;
+     epref = &doref;
+     /* Push the error object on the operand stack if appropriate. */
+-- 
+2.18.0
+
diff --git a/gnu/packages/patches/mes-nyacc-0.86.0.patch b/gnu/packages/patches/mes-nyacc-0.86.0.patch
new file mode 100644
index 0000000000..58dfc5a46b
--- /dev/null
+++ b/gnu/packages/patches/mes-nyacc-0.86.0.patch
@@ -0,0 +1,197 @@
+From 9e610736bf779f3295c1192e748cd19cbbe3be28 Mon Sep 17 00:00:00 2001
+From: Jan Nieuwenhuizen <janneke@gnu.org>
+Date: Wed, 5 Sep 2018 20:28:06 +0200
+Subject: [PATCH 1/2] mes: Support Nyacc 0.85.3: Add char-set-copy.
+
+* mes/module/srfi/srfi-14.mes (char-set-copy): New function>
+---
+ mes/module/srfi/srfi-14.mes | 3 +++
+ 1 file changed, 3 insertions(+)
+
+diff --git a/mes/module/srfi/srfi-14.mes b/mes/module/srfi/srfi-14.mes
+index 0be39b1e..a16d16ce 100644
+--- a/mes/module/srfi/srfi-14.mes
++++ b/mes/module/srfi/srfi-14.mes
+@@ -52,3 +52,6 @@
+ 
+ (define (char-whitespace? c)
+   (char-set-contains? char-set:whitespace c))
++
++(define (char-set-copy cs)
++  (map identity cs))
+-- 
+2.18.0
+
+From b952bdf44f11edbfc277600dc35236aae1769b54 Mon Sep 17 00:00:00 2001
+From: Jan Nieuwenhuizen <janneke@gnu.org>
+Date: Wed, 5 Sep 2018 22:14:34 +0200
+Subject: [PATCH 2/2] mes: Support Nyacc 0.85.3: Integrate progress.
+
+* mes/module/nyacc/lang/sx-util.mes: New file.
+* mes/module/nyacc/version.mes: New file.
+* mes/module/nyacc/lang/c99/cpp.mes (nyacc): Include them.
+* mes/module/nyacc/lang/c99/parser.mes (nyacc): Include them.
+* module/mescc/preprocess.scm (need-progress): New function.
+(progress): New function.
+(insert-progress-monitors): Use them to Integrate progress.
+---
+ mes/module/mescc/preprocess.mes      |  1 +
+ mes/module/nyacc/lang/c99/cpp.mes    |  1 +
+ mes/module/nyacc/lang/c99/parser.mes |  1 +
+ mes/module/nyacc/lang/sx-util.mes    | 27 +++++++++++++++++++++
+ mes/module/nyacc/version.mes         | 26 +++++++++++++++++++++
+ module/mescc/preprocess.scm          | 35 ++++++++++++++++++++++++++++
+ 6 files changed, 91 insertions(+)
+ create mode 100644 mes/module/nyacc/lang/sx-util.mes
+ create mode 100644 mes/module/nyacc/version.mes
+
+diff --git a/mes/module/mescc/preprocess.mes b/mes/module/mescc/preprocess.mes
+index c7c5fcaa..022a372c 100644
+--- a/mes/module/mescc/preprocess.mes
++++ b/mes/module/mescc/preprocess.mes
+@@ -24,4 +24,5 @@
+ (mes-use-module (srfi srfi-13))
+ (mes-use-module (srfi srfi-26))
+ (mes-use-module (nyacc lang c99 parser))
++(mes-use-module (nyacc version))
+ (include-from-path "mescc/preprocess.scm")
+diff --git a/mes/module/nyacc/lang/c99/cpp.mes b/mes/module/nyacc/lang/c99/cpp.mes
+index fad1dc55..b25c4a93 100644
+--- a/mes/module/nyacc/lang/c99/cpp.mes
++++ b/mes/module/nyacc/lang/c99/cpp.mes
+@@ -28,5 +28,6 @@
+ 
+ (mes-use-module (nyacc parse))
+ (mes-use-module (nyacc lex))
++(mes-use-module (nyacc lang sx-util))
+ (mes-use-module (nyacc lang util))
+ (include-from-path "nyacc/lang/c99/cpp.scm")
+diff --git a/mes/module/nyacc/lang/c99/parser.mes b/mes/module/nyacc/lang/c99/parser.mes
+index c51552d6..1a9aaf73 100644
+--- a/mes/module/nyacc/lang/c99/parser.mes
++++ b/mes/module/nyacc/lang/c99/parser.mes
+@@ -32,6 +32,7 @@
+ 
+ (mes-use-module (nyacc lex))
+ (mes-use-module (nyacc parse))
++(mes-use-module (nyacc lang sx-util))
+ (mes-use-module (nyacc lang util))
+ (mes-use-module (nyacc lang c99 cpp))
+ 
+diff --git a/mes/module/nyacc/lang/sx-util.mes b/mes/module/nyacc/lang/sx-util.mes
+new file mode 100644
+index 00000000..41ac5b4a
+--- /dev/null
++++ b/mes/module/nyacc/lang/sx-util.mes
+@@ -0,0 +1,27 @@
++;;; -*-scheme-*-
++
++;;; GNU Mes --- Maxwell Equations of Software
++;;; Copyright © 2018 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
++;;;
++;;; This file is part of GNU Mes.
++;;;
++;;; GNU Mes 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 Mes 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 Mes.  If not, see <http://www.gnu.org/licenses/>.
++
++;;; Commentary:
++
++;;; Code:
++
++(mes-use-module (srfi srfi-1))
++(mes-use-module (srfi srfi-16))
++(include-from-path "nyacc/lang/sx-util.scm")
+diff --git a/mes/module/nyacc/version.mes b/mes/module/nyacc/version.mes
+new file mode 100644
+index 00000000..b9db628e
+--- /dev/null
++++ b/mes/module/nyacc/version.mes
+@@ -0,0 +1,26 @@
++;;; -*-scheme-*-
++
++;;; GNU Mes --- Maxwell Equations of Software
++;;; Copyright © 2018 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
++;;;
++;;; This file is part of GNU Mes.
++;;;
++;;; GNU Mes 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 Mes 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 Mes.  If not, see <http://www.gnu.org/licenses/>.
++
++;;; Commentary:
++
++;;; Code:
++
++(include-from-path "nyacc/version.scm")
++(display "nyacc version\n")
+diff --git a/module/mescc/preprocess.scm b/module/mescc/preprocess.scm
+index 9e341cba..c2efb32c 100644
+--- a/module/mescc/preprocess.scm
++++ b/module/mescc/preprocess.scm
+@@ -26,9 +26,44 @@
+   #:use-module (srfi srfi-1)
+   #:use-module (srfi srfi-26)
+   #:use-module (nyacc lang c99 parser)
++  #:use-module (nyacc lang c99 parser)
++  #:use-module (nyacc version)
+   #:use-module (mes guile)
+   #:export (c99-input->ast))
+ 
++(format (current-error-port) "*nyacc-version*=~a\n" *nyacc-version*)
++;; list of which rules you want progress reported
++(define need-progress
++  (assoc-ref
++   '(("0.85.3" (1 2 3))
++     ("0.86.0" (1 2 3)))
++   *nyacc-version*))
++
++(define (progress o)
++  (when (and o (getenv "NYACC_DEBUG"))
++    (display "    :" (current-error-port))
++    (display o (current-error-port))
++    (display "\n" (current-error-port))))
++
++(define (insert-progress-monitors act-v len-v)
++  (let ((n (vector-length act-v)))
++    (let loop ((ix 0))
++      (when (< ix n)
++	(if (memq ix need-progress)
++	    (vector-set
++	     act-v ix
++	     (lambda args
++	       (progress (list-ref args (1- (vector-ref len-v ix))))
++	       (apply (vector-ref act-v ix) args))))
++        (loop (1+ ix))))))
++
++(cond-expand
++ (guile
++  (insert-progress-monitors (@@ (nyacc lang c99 parser) c99-act-v)
++                            (@@ (nyacc lang c99 parser) c99-len-v)))
++ (mes
++  (insert-progress-monitors c99-act-v c99-len-v)))
++
+ (define (logf port string . rest)
+   (apply format (cons* port string rest))
+   (force-output port)
+-- 
+2.18.0
+
diff --git a/gnu/packages/patches/nyacc-binary-literals.patch b/gnu/packages/patches/nyacc-binary-literals.patch
new file mode 100644
index 0000000000..8159d74032
--- /dev/null
+++ b/gnu/packages/patches/nyacc-binary-literals.patch
@@ -0,0 +1,29 @@
+From 6a08014b77bf435f025ecdac08396580b85f159a Mon Sep 17 00:00:00 2001
+From: Jan Nieuwenhuizen <janneke@gnu.org>
+Date: Sat, 8 Sep 2018 20:22:45 +0200
+Subject: [PATCH] fix binary literals.
+
+---
+ module/nyacc/lex.scm | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/module/nyacc/lex.scm b/module/nyacc/lex.scm
+index 2ec9895..b205212 100644
+--- a/module/nyacc/lex.scm
++++ b/module/nyacc/lex.scm
+@@ -345,10 +345,11 @@
+ 	  ((char-numeric? ch) (iter chl '$fixed ba 1 ch))
+ 	  ((char=? #\. ch) (iter (cons ch chl) #f ba 15 (read-char))) 
+ 	  (else #f)))
+-	((10) ;; allow x after 0
++	((10) ;; allow x, b after 0
+ 	 (cond
+ 	  ((eof-object? ch) (iter chl ty ba 5 ch))
+ 	  ((char=? #\x ch) (iter (cons ch chl) ty 16 1 (read-char)))
++          ((char=? #\b ch) (iter (cons ch chl) ty 2 1 (read-char)))
+ 	  (else (iter chl ty ba 1 ch))))
+ 	((15) ;; got `.' only
+ 	 (cond
+-- 
+2.18.0
+
diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 761c5987b0..4792b6fb49 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -153,8 +153,10 @@
                                 (files '("lib/perl5/site_perl")))))
     (synopsis "Implementation of the Perl programming language")
     (description
-     "Perl 5 is a highly capable, feature-rich programming language with over
-24 years of development.")
+     "Perl is a general-purpose programming language originally developed for
+text manipulation and now used for a wide range of tasks including system
+administration, web development, network programming, GUI development, and
+more.")
     (home-page "http://www.perl.org/")
     (license gpl1+)))                          ; or "Artistic"
 
@@ -1369,7 +1371,7 @@ supports XML, YAML, JSON, Apache-style configuration, and Perl code.")
 (define-public perl-config-autoconf
   (package
     (name "perl-config-autoconf")
-    (version "0.315")
+    (version "0.317")
     (source
      (origin
        (method url-fetch)
@@ -1377,7 +1379,7 @@ supports XML, YAML, JSON, Apache-style configuration, and Perl code.")
                            "Config-AutoConf-" version ".tar.gz"))
        (sha256
         (base32
-         "0h39x9rzrhhilpg8yxlzpka269qrzsjg0iy0c1b9xflqlvhx2g2b"))))
+         "1qcwib4yaml5z2283qy5khjcydyibklsnk8zrk9wzdzc5wnv5r01"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-capture-tiny" ,perl-capture-tiny)))
@@ -2140,7 +2142,7 @@ hours, minutes, seconds, and time zones.")
 (define-public perl-datetime
   (package
     (name "perl-datetime")
-    (version "1.49")
+    (version "1.50")
     (source
      (origin
        (method url-fetch)
@@ -2148,7 +2150,7 @@ hours, minutes, seconds, and time zones.")
                            "DateTime-" version ".tar.gz"))
        (sha256
         (base32
-         "0hbw4zq1562slnz7g7hyhfhyq98dzkk3i5g21x3xra5cvfix93kh"))))
+         "165iqk1xvhs5j0kzsipa7aqycx3h37wqsl2r4jl104yqvmqhqszd"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-cpan-meta-check" ,perl-cpan-meta-check)
@@ -3128,7 +3130,7 @@ only about 40% as many lines of code and with zero non-core dependencies.")
 (define-public perl-extutils-installpaths
   (package
     (name "perl-extutils-installpaths")
-    (version "0.011")
+    (version "0.012")
     (source
      (origin
        (method url-fetch)
@@ -3136,7 +3138,7 @@ only about 40% as many lines of code and with zero non-core dependencies.")
                            "ExtUtils-InstallPaths-" version ".tar.gz"))
        (sha256
         (base32
-         "0z06y0fhx9hy9x01abb7s2xdbqrh9x4ps7avmlf4bwfwih2gl2bn"))))
+         "1v9lshfhm9ck4p0v77arj5f7haj1mmkqal62lgzzvcds6wq5www4"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-extutils-config" ,perl-extutils-config)))
@@ -3192,7 +3194,7 @@ XS interface besides the perl one.")
 (define-public perl-extutils-helpers
   (package
     (name "perl-extutils-helpers")
-    (version "0.022")
+    (version "0.026")
     (source
      (origin
        (method url-fetch)
@@ -3200,7 +3202,7 @@ XS interface besides the perl one.")
                            "ExtUtils-Helpers-" version ".tar.gz"))
        (sha256
         (base32
-         "15dalfwmpfmifw312i5pwiai8134pxf7b2804shlqhdk1xqczy6k"))))
+         "05ilqcj1rg5izr09dsqmy5di4fvq6ph4k0chxks7qmd4j1kip46y"))))
     (build-system perl-build-system)
     (home-page "https://metacpan.org/release/ExtUtils-Helpers")
     (synopsis "Various portability utilities for module builders")
@@ -3772,7 +3774,7 @@ single-letter approach, is provided but not enabled by default.")
 (define-public perl-getopt-long-descriptive
   (package
     (name "perl-getopt-long-descriptive")
-    (version "0.102")
+    (version "0.103")
     (source
      (origin
        (method url-fetch)
@@ -3780,7 +3782,7 @@ single-letter approach, is provided but not enabled by default.")
                            "Getopt-Long-Descriptive-" version ".tar.gz"))
        (sha256
         (base32
-         "0ii8xafvlph5vzcqp3dpc83lg7nkg3l1l2hmqdf5382a567vkm4s"))))
+         "1cpl240qxmh7jf85ai9sfkp3nzm99syya4jxidizp7aa83kvmqbh"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-cpan-meta-check" ,perl-cpan-meta-check)
@@ -6324,7 +6326,7 @@ anything that looks like a method.")
 (define-public perl-namespace-clean
   (package
     (name "perl-namespace-clean")
-    (version "0.25")
+    (version "0.27")
     (source
      (origin
        (method url-fetch)
@@ -6332,7 +6334,7 @@ anything that looks like a method.")
                            "namespace-clean-" version ".tar.gz"))
        (sha256
         (base32
-         "016dds70ql1mp18b07chkxiy4drn976ibnbshqc2hmhrh9xjnsll"))))
+         "17dg64pd4bwi2ad3p8ykwys1zha7kg8a8ykvks7wfg8q7qyah44a"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-package-stash" ,perl-package-stash)
@@ -6704,7 +6706,7 @@ checking parameters easier.")
 (define-public perl-params-validate
   (package
     (name "perl-params-validate")
-    (version "1.26")
+    (version "1.29")
     (source
      (origin
        (method url-fetch)
@@ -6712,7 +6714,7 @@ checking parameters easier.")
                            "Params-Validate-" version ".tar.gz"))
        (sha256
         (base32
-         "1vbj78qd46ip09i06dsbb62jfwpzp4bg7yi617v98nvim77w66l2"))))
+         "0cwpf8yxwyxbnwhf6rx4wnaq1q38j38i34a78a005shb8gxqv9j9"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-module-build" ,perl-module-build)
@@ -6897,7 +6899,7 @@ for correctness.")
 (define-public perl-pegex
   (package
    (name "perl-pegex")
-   (version "0.64")
+   (version "0.67")
    (source
     (origin
      (method url-fetch)
@@ -6906,7 +6908,7 @@ for correctness.")
            version ".tar.gz"))
      (sha256
       (base32
-       "1kb7y2cc3nibbn8i8y3vrzz1f9h3892nbf8jj88c5fdgpmj05q17"))))
+       "149015ra2figalxrnj72fz02qc5cm96xg6x8d6kmyanfmrrxzf9w"))))
    (build-system perl-build-system)
    (native-inputs
     `(("perl-file-sharedir-install" ,perl-file-sharedir-install)
diff --git a/gnu/packages/plotutils.scm b/gnu/packages/plotutils.scm
index 0e65cb319f..2a330695c6 100644
--- a/gnu/packages/plotutils.scm
+++ b/gnu/packages/plotutils.scm
@@ -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 © 2015 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016, 2017 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -93,15 +93,7 @@ scientific data.")
                                   "guile-charting-" version ".tar.gz"))
               (sha256
                (base32
-                "0w5qiyv9v0ip5li22x762bm48g8xnw281w66iyw094zdw611pb2m"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; Use the standard location for modules.
-                  (substitute* "Makefile.in"
-                    (("godir = .*$")
-                     "godir = $(moddir)\n"))
-                  #t))))
+                "0w5qiyv9v0ip5li22x762bm48g8xnw281w66iyw094zdw611pb2m"))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)))
     (inputs `(("guile" ,guile-2.2)))
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ed04de7547..56176529c9 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6186,14 +6186,14 @@ printing of sub-tables by specifying a row range.")
 (define-public python-tables
   (package
     (name "python-tables")
-    (version "3.2.2")
+    (version "3.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "tables" version))
        (sha256
         (base32
-         "117s6w7s3yxafpmf3zz3svana7xfrsviw01va1xp7h8ylx8v6r1m"))
+         "0affz7k8babh8wdmsgrz5jxrd569by2w8ffimcxs9wiaf5rw1idx"))
        (modules '((guix build utils)))
        (snippet
         '(begin
diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm
index 6dbe1c4db7..900c8ec686 100644
--- a/gnu/packages/shells.scm
+++ b/gnu/packages/shells.scm
@@ -292,7 +292,7 @@ history mechanism, job control and a C-like syntax.")
 (define-public zsh
   (package
     (name "zsh")
-    (version "5.5.1")
+    (version "5.6")
     (source (origin
               (method url-fetch)
               (uri (list (string-append
@@ -303,7 +303,7 @@ history mechanism, job control and a C-like syntax.")
                            ".tar.xz")))
               (sha256
                (base32
-                "105aqkdfsdxc4531anrj2zis2ywz6icagjam9lsc235yzh48ihz1"))))
+                "1mp6h2452z2029n12mxipjv4b0cc8i8sb72g8p8jklg8275iysvl"))))
     (build-system gnu-build-system)
     (arguments `(#:configure-flags '("--with-tcsetpgrp" "--enable-pcre")
                  #:phases
@@ -336,6 +336,19 @@ history mechanism, job control and a C-like syntax.")
                          (("command -pv") "command -v")
                          (("command -p") "command ")
                          (("'command' -p") "'command' "))
+                       ;; This file is ISO-8859-1 encoded.
+                       (with-fluids ((%default-port-encoding #f))
+                         (substitute* "Test/A05execution.ztst"
+                           ;; Help it find `sh`
+                           (("PATH=/bin:\\$\\{ZTST_testdir\\}/command.tmp/ tstcmd-slashless")
+                            (string-append "PATH=/bin:"
+                                           (assoc-ref %build-inputs "bash") "/bin:"
+                                           "${ZTST_testdir}/command.tmp/ tstcmd-slashless"))
+                           ;; Help it find `echo`
+                           (("PATH=/bin:\\$\\{ZTST_testdir\\}/command.tmp tstcmd-arg")
+                            (string-append "PATH=/bin:"
+                                           (assoc-ref %build-inputs "coreutils") "/bin:"
+                                           "PATH=/bin:${ZTST_testdir}/command.tmp tstcmd-arg"))))
                        #t)))))
     (native-inputs `(("autoconf" ,autoconf)))
     (inputs `(("ncurses" ,ncurses)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 64c331d28c..6e915aa437 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -960,14 +960,14 @@ solution for sending email, including attachments, from within R.")
 (define-public r-stringi
   (package
     (name "r-stringi")
-    (version "1.2.3")
+    (version "1.2.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringi" version))
        (sha256
         (base32
-         "1sgg4krw03qkz1n4dwiya0djggk7giwd0w21qlp0pfjqi0rxq6qx"))))
+         "1y46xab7g1lsjmilp4hbl7pjad6pcxp66hdj8wnfdg9518h0lmq1"))))
     (build-system r-build-system)
     (inputs `(("icu4c" ,icu4c)))
     (native-inputs `(("pkg-config" ,pkg-config)))
@@ -1033,19 +1033,17 @@ using just two functions: melt and dcast (or acast).")
 (define-public r-scales
   (package
     (name "r-scales")
-    (version "0.5.0")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scales" version))
        (sha256
-        (base32 "0zg9wfzmsdjxpbld0nzv7hcpq5r0wazqxmn7grvvif2agj0w1z6v"))))
+        (base32 "0353dkh3d7x78463c6ds80hcml59lrqwr8rlv82a8dnkxla4l7qc"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-dichromat" ,r-dichromat)
-       ("r-labeling" ,r-labeling)
+     `(("r-labeling" ,r-labeling)
        ("r-munsell" ,r-munsell)
-       ("r-plyr" ,r-plyr)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
        ("r-r6" ,r-r6)
@@ -1251,13 +1249,13 @@ for template use among CRAN packages.")
 (define-public r-evaluate
   (package
     (name "r-evaluate")
-    (version "0.10.1")
+    (version "0.11")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "evaluate" version))
               (sha256
                (base32
-                "070vvmnbdlp7sz2zhza7fhd2a6mlwiln8fn4hyzhsiizbn4n79y9"))))
+                "1k8vcd4vsgg0hf7kdz8rlqp1dx4ygvg35aj4n3ay50kdnpzhaj5h"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-stringr" ,r-stringr)))
@@ -1356,13 +1354,13 @@ syntax that can be converted to XHTML or other formats.")
 (define-public r-yaml
   (package
     (name "r-yaml")
-    (version "2.1.19")
+    (version "2.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "yaml" version))
               (sha256
                (base32
-                "04bzrnfgbpk0rhkvzwp3k3ip7jpq26bjxz71bx5mwxmcjdb07nz5"))))
+                "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/yaml/")
     (synopsis "Methods to convert R data to YAML and back")
@@ -1656,14 +1654,14 @@ database.")
 (define-public r-dbplyr
   (package
     (name "r-dbplyr")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dbplyr" version))
        (sha256
         (base32
-         "1nwrls9c3kc9q7405jp6b9sh23642sz13yw55iikgw134shffj5k"))))
+         "0j5w6a1qim972kv4vmvinp3j50yr4idmm9cd3w7y3zsz0nq0nhcx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -1789,17 +1787,17 @@ and fast file reading.")
 (define-public r-xtable
   (package
     (name "r-xtable")
-    (version "1.8-2")
+    (version "1.8-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xtable" version))
        (sha256
         (base32
-         "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn"))))
+         "09f311gq9g7dzf8jdvcx72j11xb7p00jlg066jjbpa6pz3zv1cjk"))))
     (build-system r-build-system)
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     `(("r-knitr" ,r-knitr))) ; for vignettes
     (home-page "http://xtable.r-forge.r-project.org/")
     (synopsis "Export R tables to LaTeX or HTML")
     (description
@@ -1936,14 +1934,14 @@ chain.")
 (define-public r-ade4
   (package
     (name "r-ade4")
-    (version "1.7-11")
+    (version "1.7-13")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "ade4" version))
         (sha256
           (base32
-            "0wm54wcpn87rdh6vyw04cr8vgba899y6jsl61f22bmlvx6d7kkac"))))
+            "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)))
@@ -2237,24 +2235,28 @@ tables, autolinks and strikethrough text.")
 (define-public r-roxygen2
   (package
     (name "r-roxygen2")
-    (version "6.0.1")
+    (version "6.1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "roxygen2" version))
               (sha256
                (base32
-                "0xpzziminf225kjwhyl51kgkzhplyzhk5farhf5s822krl2xqbfj"))))
+                "0ji9k4s1bvfbl8wimfqj1lqr33h1claaz30vb5pgksxyg77j5xaa"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-brew" ,r-brew)
        ("r-commonmark" ,r-commonmark)
        ("r-desc" ,r-desc)
        ("r-digest" ,r-digest)
+       ("r-pkgload" ,r-pkgload)
+       ("r-purrr" ,r-purrr)
        ("r-r6" ,r-r6)
        ("r-rcpp" ,r-rcpp)
        ("r-stringi" ,r-stringi)
        ("r-stringr" ,r-stringr)
        ("r-xml2" ,r-xml2)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
     (home-page "https://github.com/klutometis/roxygen")
     (synopsis "In-source documentation system for R")
     (description
@@ -2320,13 +2322,13 @@ functions make it easy to control additional request components.")
 (define-public r-git2r
   (package
     (name "r-git2r")
-    (version "0.21.0")
+    (version "0.23.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "git2r" version))
               (sha256
                (base32
-                "11xgddmxzh9cy85k8fb90il43qswpvryz0h9r0j1gbclfg2f9004"))))
+                "01250jz255fnyy2ap90nskvzhd8nhlmbhwgpvb43mk1fax077lrz"))))
     (build-system r-build-system)
     ;; This R package contains modified sources of libgit2.  This modified
     ;; version of libgit2 is built as the package is built.  Hence libgit2 is
@@ -2335,6 +2337,8 @@ functions make it easy to control additional request components.")
      `(("libssh2" ,libssh2)
        ("openssl" ,openssl)
        ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
     (home-page "https://github.com/ropensci/git2r")
     (synopsis "Access Git repositories with R")
     (description
@@ -2514,13 +2518,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.8.500.0")
+    (version "0.9.100.5.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1sh36dx6inmb56m40nigy94gxlgjva816qnlmjwg7y2bdvqj8vsi"))))
+                "1iyjqhfjip1nxrkllzh7r1m01jjnx7cahqkf3s557w34p987f2l1"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (native-inputs
@@ -2629,11 +2633,7 @@ certain criterion, e.g., it contains a certain regular file.")
        ("r-stringr" ,r-stringr)
        ("r-tinytex" ,r-tinytex)
        ("r-yaml" ,r-yaml)
-       ;; rmarkdown works with the 2.x release of Pandoc, but with degraded
-       ;; functionality.  For example, tabbed plots do not currently work with
-       ;; Pandoc 2.  The authors of rmarkdown recommend the use of Pandoc 1
-       ;; for the time being.
-       ("ghc-pandoc" ,ghc-pandoc-1)))
+       ("ghc-pandoc" ,ghc-pandoc)))
     (home-page "http://rmarkdown.rstudio.com")
     (synopsis "Convert R Markdown documents into a variety of formats")
     (description
@@ -2799,13 +2799,13 @@ ldap, and also supports cookies, redirects, authentication, etc.")
 (define-public r-xml
   (package
     (name "r-xml")
-    (version "3.98-1.11")
+    (version "3.98-1.16")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "XML" version))
               (sha256
                (base32
-                "18izvlg2x9mzr6yb3yf02ghwbyn00frki3av4lpc44r22m4djnsh"))))
+                "0nl1kk354r8snhj6p9mc74m7awvqc6akmd4y3a46y78yv3g15njp"))))
     (properties
      `((upstream-name . "XML")))
     (build-system r-build-system)
@@ -3281,14 +3281,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
 (define-public r-e1071
   (package
     (name "r-e1071")
-    (version "1.6-8")
+    (version "1.7-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "e1071" version))
        (sha256
         (base32
-         "08n6i26nfckjpxjkzi8phhanc3ahsrirkv5rz38y2jcv7ds031pn"))))
+         "0fk4pw67cw1663d0n9rf1qfdqzz8k5nqkjgp3hi5jr422qp9lsck"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)))
@@ -3459,13 +3459,13 @@ maintenance for package developers.")
 (define-public r-r-utils
   (package
     (name "r-r-utils")
-    (version "2.6.0")
+    (version "2.7.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.utils" version))
               (sha256
                (base32
-                "03j7hrs03kyj9qrjxyp5kqv4lpqqpk6xwbkzx6j15d8928yrjr2x"))))
+                "0cxhn14a57x4gcyrwpfz1d6dw4xh0jcpqkb33hx8imnr340blh7n"))))
     (properties `((upstream-name . "R.utils")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3507,13 +3507,13 @@ persistent (on the file system).")
 (define-public r-r-rsp
   (package
     (name "r-r-rsp")
-    (version "0.42.0")
+    (version "0.43.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.rsp" version))
               (sha256
                (base32
-                "1zcq0hzi0j7fvj2rs796a1i120wbr0387vck17rrd644awwbsbm0"))))
+                "0ax6781kfylx0acz0i3sqnpkxmrq73x29wwfic59ng7vj0ws0gyd"))))
     (properties `((upstream-name . "R.rsp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3558,13 +3558,13 @@ t-probabilities, quantiles, random deviates and densities.")
 (define-public r-matrixstats
   (package
     (name "r-matrixstats")
-    (version "0.53.1")
+    (version "0.54.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "matrixStats" version))
               (sha256
                (base32
-                "0bkiz5fm09d3512mfr2ymj9qsb1b8aic5l5m6fkaf5j7nsgvqw6z"))))
+                "0vx00ldsg2zvdrjn49jxczk2c9iaabgvzgpdka5j02ihh7hv83cg"))))
     (properties `((upstream-name . "matrixStats")))
     (build-system r-build-system)
     (native-inputs
@@ -3739,13 +3739,13 @@ features present in other programming languages.")
 (define-public r-plotly
   (package
     (name "r-plotly")
-    (version "4.7.1")
+    (version "4.8.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotly" version))
               (sha256
                (base32
-                "0wj9lw7w28z8w9ip9vadv6sydjhqyg65kfiai9m3bndzz50b1m3w"))))
+                "19p8pa03q9mw5vaan7r56xgd13d90ssiz0flbrkvpfrir2105ybq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-base64enc" ,r-base64enc)
@@ -3761,8 +3761,10 @@ features present in other programming languages.")
        ("r-jsonlite" ,r-jsonlite)
        ("r-lazyeval" ,r-lazyeval)
        ("r-magrittr" ,r-magrittr)
+       ("r-promises" ,r-promises)
        ("r-purrr" ,r-purrr)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rlang" ,r-rlang)
        ("r-scales" ,r-scales)
        ("r-tibble" ,r-tibble)
        ("r-tidyr" ,r-tidyr)
@@ -3844,14 +3846,14 @@ character vector.")
 (define-public r-googlesheets
   (package
     (name "r-googlesheets")
-    (version "0.2.2")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "googlesheets" version))
        (sha256
         (base32
-         "18q0xmxn09b52rmky7gr5flp0awndcnsgb7zcvkzvkrkvmwad52b"))))
+         "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cellranger" ,r-cellranger)
@@ -3861,6 +3863,7 @@ character vector.")
        ("r-purrr" ,r-purrr)
        ("r-readr" ,r-readr)
        ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
        ("r-tidyr" ,r-tidyr)
        ("r-xml2" ,r-xml2)))
     (home-page "https://github.com/jennybc/googlesheets")
@@ -4088,14 +4091,14 @@ Zurich, including many that are related to graphics.")
 (define-public r-gtools
   (package
     (name "r-gtools")
-    (version "3.5.0")
+    (version "3.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gtools" version))
        (sha256
         (base32
-         "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6"))))
+         "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -4228,13 +4231,13 @@ mechanism.")
 (define-public r-zoo
   (package
     (name "r-zoo")
-    (version "1.8-2")
+    (version "1.8-3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "zoo" version))
               (sha256
                (base32
-                "1lpwigxmi5sc23xrha4gcsccsm4yfsg0sa97y6vac3pg1lliblvx"))))
+                "15jmkgwvq2mm9f09vijgx7sff8pszh90fndcwhk2vw9i0p183di0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -4248,14 +4251,22 @@ series of numeric vectors/matrices and factors.")
 (define-public r-ztable
   (package
     (name "r-ztable")
-    (version "0.1.8")
+    (version "0.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "ztable" version))
               (sha256
                (base32
-                "1hk5k9614n52dpfrhdws06w4gvwhnz8q47x4cwxx88qmrzm8z2m3"))))
+                "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy"))))
     (build-system r-build-system)
+    (propagated-inputs
+     `(("r-flextable" ,r-flextable)
+       ("r-magrittr" ,r-magrittr)
+       ("r-moonbook" ,r-moonbook)
+       ("r-officer" ,r-officer)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-scales" ,r-scales)
+       ("r-stringr" ,r-stringr)))
     (home-page "https://cran.r-project.org/web/packages/ztable")
     (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
     (description
@@ -4350,19 +4361,20 @@ data at that region, and avoids over-plotting.")
 (define-public r-ggthemes
   (package
     (name "r-ggthemes")
-    (version "3.5.0")
+    (version "4.0.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "ggthemes" version))
               (sha256
                (base32
-                "0drbzzb4i5jq1579fx1wmgh87ybnswjn7srak2l8g771ip49xwb8"))))
+                "0y6570wv135sf7pv57l7bqilzw47rziaqx4vsk45pf1w4lmj0w8b"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-assertthat" ,r-assertthat)
-       ("r-colorspace" ,r-colorspace)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-scales" ,r-scales)))
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-purrr" ,r-purrr)
+       ("r-scales" ,r-scales)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)))
     (home-page "https://cran.rstudio.com/web/packages/ggthemes")
     (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
     (description "This package provides extra themes and scales for
@@ -4401,13 +4413,13 @@ dispersion modeling and Tweedie power-law families.")
 (define-public r-rann
   (package
     (name "r-rann")
-    (version "2.5.1")
+    (version "2.6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RANN" version))
               (sha256
                (base32
-                "0il5i99vbcagnxvb15af5n37g04a4q1x96bz73zh3jhki9fpw9vm"))))
+                "1r6rivh9ba4gwnzryip0aiwsbm46zma7nvd9z5y456p2dgzp9lii"))))
     (properties
      `((upstream-name . "RANN")))
     (build-system r-build-system)
@@ -4723,14 +4735,14 @@ can be efficiently implemented directly in the R language.")
 (define-public r-robustbase
   (package
     (name "r-robustbase")
-    (version "0.93-0")
+    (version "0.93-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "robustbase" version))
        (sha256
         (base32
-         "130pzibn5cb8mycv8byc6npzcpddghz8m7jqwk15qmx4g3cj8zgy"))))
+         "1632p73iv9iqqm0v3k9rfv9way0him3fl35si1nly9wi5kpq5ci7"))))
     (build-system r-build-system)
     (inputs
      `(("gfortran" ,gfortran)))
@@ -4999,18 +5011,19 @@ decompositions of such matrices, and solutions of linear systems.")
 (define-public r-modelmetrics
   (package
     (name "r-modelmetrics")
-    (version "1.1.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
         (uri (cran-uri "ModelMetrics" version))
         (sha256
          (base32
-          "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8"))))
+          "1sgdyrf6fbsn18gk8slir4a1yhv133kfhyg2crfs759nff4aw89h"))))
     (properties `((upstream-name . "ModelMetrics")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-rcpp" ,r-rcpp)))
+     `(("r-rcpp" ,r-rcpp)
+       ("r-data-table" ,r-data-table)))
     (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
     (synopsis "Rapid calculation of model metrics")
     (description
diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm
index 45252c933d..2c2767dbbc 100644
--- a/gnu/packages/web-browsers.scm
+++ b/gnu/packages/web-browsers.scm
@@ -86,14 +86,14 @@ older or slower computers and embedded systems.")
 (define-public links
   (package
     (name "links")
-    (version "2.16")
+    (version "2.17")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://links.twibright.com/download/"
                                   name "-" version ".tar.bz2"))
                 (sha256
                (base32
-                "0gsa2gpb1grhssl5jzpc5pa0zi21mxi8g25rh5bacl70slw31w42"))))
+                "0dh2gbzcw8kxy81z4ggsynibnqs56b83vy8qgz7illsag1irff6q"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 001644c195..53d886cf0d 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3823,15 +3823,17 @@ CDF, Atom 0.3, and Atom 1.0 feeds.")
 (define-public r-httpuv
   (package
     (name "r-httpuv")
-    (version "1.4.4.1")
+    (version "1.4.5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httpuv" version))
               (sha256
                (base32
-                "12kwq10xa8glrip7rai9xb4hnpysng00g2l0rw7swfzq5lk4z966"))))
+                "1ddpcarzf694h0gy5pdz7l5glqfv4hr9dmxb4vw7yqd0bga174gi"))))
     (build-system r-build-system)
-    (native-inputs `(("r-rcpp" ,r-rcpp)))
+    (native-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("pkg-config" ,pkg-config)))
     (propagated-inputs
      `(("r-bh" ,r-bh)
        ("r-later" ,r-later)
@@ -6706,10 +6708,11 @@ compressed JSON header blocks.
     (license l:expat)))
 
 (define-public hpcguix-web
-  (let ((commit "87cb51611c0f1fd3863b830614ab1364599cf1ca"))
+  (let ((commit "9ff40fcc77f248901d861756dbbddc80270c380c")
+        (revision "2"))
     (package
       (name "hpcguix-web")
-      (version (git-version "0.0.1" "1" commit))
+      (version (git-version "0.0.1" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -6718,7 +6721,7 @@ compressed JSON header blocks.
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0p66fl8r3v73v13fqg9rbqbzbdzvyznchxbq2s1jwq6qfsn2w3gr"))))
+                  "0lxcj9s3wxrv1l7lrxxx374jwzx7h60gxwkbgr46lzcbgvb3k26s"))))
       (build-system gnu-build-system)
       (arguments
        `(#:modules ((guix build gnu-build-system)
@@ -6739,10 +6742,13 @@ compressed JSON header blocks.
                (let* ((out      (assoc-ref outputs "out"))
                       (guix     (assoc-ref inputs "guix"))
                       (guile    (assoc-ref inputs "guile"))
+                      (gcrypt   (assoc-ref inputs "guile-gcrypt"))
+                      (git      (assoc-ref inputs "guile-git"))
+                      (bs       (assoc-ref inputs "guile-bytestructures"))
                       (json     (assoc-ref inputs "guile-json"))
                       (guile-cm (assoc-ref inputs
                                            "guile-commonmark"))
-                      (deps (list guile guile-cm guix json))
+                      (deps (list guile gcrypt git bs guile-cm guix json))
                       (effective
                        (read-line
                         (open-pipe* OPEN_READ
diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 6b99a3a8a8..aa24811695 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -17,6 +17,7 @@
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2018 Benjamin Slade <slade@jnanam.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -6170,3 +6171,44 @@ and embedded platforms.")
 cursor to any point on the screen with a few key strokes.  It also simulates
 mouse click.  You can do everything mouse can do with a keyboard.")
     (license license:bsd-3)))
+
+(define-public transset-df
+  (package
+    (name "transset-df")
+    (version "6")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://forchheimer.se/" name "/" name "-" version
+                                  ".tar.gz"))
+              (sha256
+               (base32
+                "1vnykwwrv75miigbhmcwxniw8xnhsdyzhqydip2m9crxi2lwhqs5"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'setenv
+           (lambda _
+             (setenv "CC" (which "gcc"))
+             #t))
+         (delete 'configure)
+         (delete 'check)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (install-file "transset-df" bin)
+               #t))))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs `(("libxcomposite" ,libxcomposite)
+              ("libxdamager" ,libxdamage)
+              ("libxrender" ,libxrender)))
+    (synopsis "Set the transparency of X11 windows")
+    (description "The @command{transset-df} command allows you to set the
+opacity of X11 windows.  This patched version of X.Org's @command{transset}
+adds functionality, including: selecting window by clicking (as transset),
+selecting windows by pointing select actual focused X11 window, selecting by
+window name or id, forcing toggle, increase or decrease opacity.")
+    (home-page "http://forchheimer.se/transset-df/")
+    (license license:x11)))
diff --git a/gnu/services.scm b/gnu/services.scm
index 49cf01a4f8..f151bbaa9d 100644
--- a/gnu/services.scm
+++ b/gnu/services.scm
@@ -732,13 +732,23 @@ instantiated; other missing services lead to a
            instances
            (service-type-extensions (service-kind svc))))
 
-  (let ((instances (fold (lambda (service result)
-                           (vhash-consq (service-kind service) service
-                                        result))
-                         vlist-null services)))
-    (fold2 adjust-service-list
-           services instances
-           services)))
+  (let loop ((services services))
+    (define instances
+      (fold (lambda (service result)
+              (vhash-consq (service-kind service) service
+                           result))
+            vlist-null services))
+
+    (define adjusted
+      (fold2 adjust-service-list
+             services instances
+             services))
+
+    ;; If we instantiated services, they might in turn depend on missing
+    ;; services.  Loop until we've reached fixed point.
+    (if (= (length adjusted) (vlist-length instances))
+        adjusted
+        (loop adjusted))))
 
 (define* (fold-services services
                         #:key (target-type system-service-type))
diff --git a/gnu/services/web.scm b/gnu/services/web.scm
index 467656444e..df82a6de61 100644
--- a/gnu/services/web.scm
+++ b/gnu/services/web.scm
@@ -608,16 +608,14 @@ of index files."
                                (default-nginx-config config))
                          #$@args)
                  (match '#$args
-                   (("-s" . _) #t)
+                   (("-s" . _) #f)
                    (_
-                    (let loop ((duration 0))
-                      ;; https://bugs.launchpad.net/ubuntu/+source/nginx/+bug/1581864/comments/7
-                      (sleep duration)
-                      (if (file-exists? #$pid-file)
-                          (let ((pid (call-with-input-file #$pid-file read)))
-                            ;; it could be #<eof>
-                            (if (integer? pid) pid (loop 1)))
-                          (loop 1)))))))))
+                    ;; When FILE is true, we cannot be sure that PID-FILE will
+                    ;; be created, so assume it won't show up.  When FILE is
+                    ;; false, read PID-FILE.
+                    #$(if file
+                          #~#t
+                          #~(read-pid-file #$pid-file))))))))
 
      ;; TODO: Add 'reload' action.
      (list (shepherd-service
@@ -967,7 +965,8 @@ a webserver.")
                  #:user "hpcguix-web"
                  #:group "hpcguix-web"
                  #:environment-variables
-                 (list "XDG_CACHE_HOME=/var/cache")))
+                 (list "XDG_CACHE_HOME=/var/cache"
+                       "SSL_CERT_DIR=/etc/ssl/certs")))
        (stop #~(make-kill-destructor))))))
 
 (define hpcguix-web-service-type
diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm
index b505b0cf6b..91e117b9f3 100644
--- a/gnu/system/vm.scm
+++ b/gnu/system/vm.scm
@@ -32,7 +32,7 @@
   #:use-module (guix modules)
   #:use-module (guix scripts pack)
   #:use-module (guix utils)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix base32)
   #:use-module ((guix self) #:select (make-config.scm))
 
@@ -43,7 +43,7 @@
   #:use-module (gnu packages cdrom)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages guile)
-  #:autoload   (gnu packages gnupg) (libgcrypt)
+  #:autoload   (gnu packages gnupg) (guile-gcrypt)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages less)
@@ -124,10 +124,12 @@
     (('gnu rest ...) #t)
     (rest #f)))
 
-(define guile-sqlite3&co
-  ;; Guile-SQLite3 and its propagated inputs.
-  (cons guile-sqlite3
-        (package-transitive-propagated-inputs guile-sqlite3)))
+(define gcrypt-sqlite3&co
+  ;; Guile-Gcrypt, Guile-SQLite3, and their propagated inputs.
+  (append-map (lambda (package)
+                (cons package
+                      (package-transitive-propagated-inputs package)))
+              (list guile-gcrypt guile-sqlite3)))
 
 (define* (expression->derivation-in-linux-vm name exp
                                              #:key
@@ -164,10 +166,6 @@ based on the size of the closure of REFERENCES-GRAPHS.
 When REFERENCES-GRAPHS is true, it must be a list of file name/store path
 pairs, as for `derivation'.  The files containing the reference graphs are
 made available under the /xchg CIFS share."
-  (define config
-    ;; (guix config) module for consumption by (guix gcrypt).
-    (make-config.scm #:libgcrypt libgcrypt))
-
   (define user-builder
     (program-file "builder-in-linux-vm" exp))
 
@@ -195,12 +193,14 @@ made available under the /xchg CIFS share."
 
     (define builder
       ;; Code that launches the VM that evaluates EXP.
-      (with-extensions guile-sqlite3&co
+      (with-extensions gcrypt-sqlite3&co
         (with-imported-modules `(,@(source-module-closure
                                     '((guix build utils)
                                       (gnu build vm))
                                     #:select? not-config?)
-                                 ((guix config) => ,config))
+
+                                 ;; For consumption by (gnu store database).
+                                 ((guix config) => ,(make-config.scm)))
           #~(begin
               (use-modules (guix build utils)
                            (gnu build vm))
@@ -255,9 +255,6 @@ made available under the /xchg CIFS share."
   "Return a bootable, stand-alone iso9660 image.
 
 INPUTS is a list of inputs (as for packages)."
-  (define config
-    (make-config.scm #:libgcrypt libgcrypt))
-
   (define schema
     (and register-closures?
          (local-file (search-path %load-path
@@ -265,12 +262,12 @@ INPUTS is a list of inputs (as for packages)."
 
   (expression->derivation-in-linux-vm
    name
-   (with-extensions guile-sqlite3&co
+   (with-extensions gcrypt-sqlite3&co
      (with-imported-modules `(,@(source-module-closure '((gnu build vm)
                                                          (guix store database)
                                                          (guix build utils))
                                                        #:select? not-config?)
-                              ((guix config) => ,config))
+                              ((guix config) => ,(make-config.scm)))
        #~(begin
            (use-modules (gnu build vm)
                         (guix store database)
@@ -347,9 +344,6 @@ INPUTS is a list of inputs (as for packages).  When COPY-INPUTS? is true, copy
 all of INPUTS into the image being built.  When REGISTER-CLOSURES? is true,
 register INPUTS in the store database of the image so that Guix can be used in
 the image."
-  (define config
-    (make-config.scm #:libgcrypt libgcrypt))
-
   (define schema
     (and register-closures?
          (local-file (search-path %load-path
@@ -357,13 +351,13 @@ the image."
 
   (expression->derivation-in-linux-vm
    name
-   (with-extensions guile-sqlite3&co
+   (with-extensions gcrypt-sqlite3&co
      (with-imported-modules `(,@(source-module-closure '((gnu build vm)
                                                          (gnu build bootloader)
                                                          (guix store database)
                                                          (guix build utils))
                                                        #:select? not-config?)
-                              ((guix config) => ,config))
+                              ((guix config) => ,(make-config.scm)))
        #~(begin
            (use-modules (gnu build bootloader)
                         (gnu build vm)
@@ -462,10 +456,6 @@ makes sense when you want to build a GuixSD Docker image that has Guix
 installed inside of it.  If you don't need Guix (e.g., your GuixSD Docker
 image just contains a web server that is started by the Shepherd), then you
 should set REGISTER-CLOSURES? to #f."
-  (define config
-    ;; (guix config) module for consumption by (guix gcrypt).
-    (make-config.scm #:libgcrypt libgcrypt))
-
   (define schema
     (and register-closures?
          (local-file (search-path %load-path
@@ -475,8 +465,8 @@ should set REGISTER-CLOSURES? to #f."
                       (name -> (string-append name ".tar.gz"))
                       (graph -> "system-graph"))
     (define build
-      (with-extensions (cons guile-json          ;for (guix docker)
-                             guile-sqlite3&co)   ;for (guix store database)
+      (with-extensions (cons guile-json           ;for (guix docker)
+                             gcrypt-sqlite3&co)   ;for (guix store database)
         (with-imported-modules `(,@(source-module-closure
                                     '((guix docker)
                                       (guix store database)
@@ -484,7 +474,7 @@ should set REGISTER-CLOSURES? to #f."
                                       (guix build store-copy)
                                       (gnu build vm))
                                     #:select? not-config?)
-                                 ((guix config) => ,config))
+                                 ((guix config) => ,(make-config.scm)))
           #~(begin
               (use-modules (guix docker)
                            (guix build utils)
@@ -539,17 +529,42 @@ should set REGISTER-CLOSURES? to #f."
 (define* (operating-system-uuid os #:optional (type 'dce))
   "Compute UUID object with a deterministic \"UUID\" for OS, of the given
 TYPE (one of 'iso9660 or 'dce).  Return a UUID object."
+  ;; Note: For this to be deterministic, we must not hash things that contains
+  ;; (directly or indirectly) procedures, for example.  That rules out
+  ;; anything that contains gexps, thunk or delayed record fields, etc.
+
+  (define service-name
+    (compose service-type-name service-kind))
+
+  (define (file-system-digest fs)
+    ;; Return a hashable digest that does not contain 'dependencies' since
+    ;; this field can contain procedures.
+    (let ((device (file-system-device fs)))
+      (list (file-system-mount-point fs)
+            (file-system-type fs)
+            (cond ((file-system-label? device)
+                   (file-system-label->string device))
+                  ((uuid? device)
+                   (uuid->string device))
+                  ((string? device)
+                   device)
+                  (else #f))
+            (file-system-options fs))))
+
   (if (eq? type 'iso9660)
       (let ((pad (compose (cut string-pad <> 2 #\0)
                           number->string))
-            (h   (hash (operating-system-services os) 3600)))
+            (h   (hash (map service-name (operating-system-services os))
+                       3600)))
         (bytevector->uuid
          (string->iso9660-uuid
           (string-append "1970-01-01-"
                          (pad (hash (operating-system-host-name os) 24)) "-"
                          (pad (quotient h 60)) "-"
                          (pad (modulo h 60)) "-"
-                         (pad (hash (operating-system-file-systems os) 100))))
+                         (pad (hash (map file-system-digest
+                                         (operating-system-file-systems os))
+                                    100))))
          'iso9660))
       (bytevector->uuid
        (uint-list->bytevector
@@ -557,9 +572,9 @@ TYPE (one of 'iso9660 or 'dce).  Return a UUID object."
                     (- (expt 2 32) 1))
               (hash (operating-system-host-name os)
                     (- (expt 2 32) 1))
-              (hash (operating-system-services os)
+              (hash (map service-name (operating-system-services os))
                     (- (expt 2 32) 1))
-              (hash (operating-system-file-systems os)
+              (hash (map file-system-digest (operating-system-file-systems os))
                     (- (expt 2 32) 1)))
         (endianness little)
         4)
diff --git a/gnu/tests/base.scm b/gnu/tests/base.scm
index f27064af85..f97581de33 100644
--- a/gnu/tests/base.scm
+++ b/gnu/tests/base.scm
@@ -42,6 +42,7 @@
   #:use-module (guix monads)
   #:use-module (guix packages)
   #:use-module (srfi srfi-1)
+  #:use-module (ice-9 match)
   #:export (run-basic-test
             %test-basic-os
             %test-halt
@@ -68,6 +69,11 @@ initialization step, such as entering a LUKS passphrase."
      (fold-services (operating-system-services os)
                     #:target-type special-files-service-type)))
 
+  (define guix&co
+    (match (package-transitive-propagated-inputs guix)
+      (((labels packages) ...)
+       (cons guix packages))))
+
   (define test
     (with-imported-modules '((gnu build marionette)
                              (guix build syscalls))
@@ -345,8 +351,14 @@ info --version")
             'success!
             (marionette-eval '(begin
                                 ;; Make sure the (guix …) modules are found.
-                                (add-to-load-path
-                                 #+(file-append guix "/share/guile/site/2.2"))
+                                (eval-when (expand load eval)
+                                  (set! %load-path
+                                    (append (map (lambda (package)
+                                                   (string-append package
+                                                                  "/share/guile/site/"
+                                                                  (effective-version)))
+                                                 '#$guix&co)
+                                            %load-path)))
 
                                 (use-modules (srfi srfi-34) (guix store))
 
diff --git a/guix/channels.scm b/guix/channels.scm
index ec3e05eaf5..cf833db8b9 100644
--- a/guix/channels.scm
+++ b/guix/channels.scm
@@ -48,7 +48,7 @@
 
             latest-channel-instances
             channel-instance-derivations
-            latest-channel-derivations
+            latest-channel-derivation
             channel-instances->manifest))
 
 ;;; Commentary:
@@ -78,7 +78,7 @@
   ;; Default list of channels.
   (list (channel
          (name 'guix)
-         (branch "origin/master")
+         (branch "master")
          (url "https://git.savannah.gnu.org/git/guix.git"))))
 
 (define (guix-channel? channel)
@@ -207,23 +207,20 @@ INSTANCES."
             (guix-channel? (channel-instance-channel instance)))
           instances))
 
+  ;; Guile-Gcrypt is a dependency of CORE-INSTANCE.
+  (define guile-gcrypt
+    (module-ref (resolve-interface '(gnu packages gnupg))
+                'guile-gcrypt))
+
   (mlet %store-monad ((core (build-channel-instance core-instance)))
     (mapm %store-monad
           (lambda (instance)
             (if (eq? instance core-instance)
                 (return core)
                 (build-channel-instance instance
-                                        (list core))))
+                                        (list core guile-gcrypt))))
           instances)))
 
-(define latest-channel-derivations
-  (let ((latest-channel-instances (store-lift latest-channel-instances)))
-    (lambda (channels)
-      "Return, as a monadic value, the list of derivations for the latest
-instances of CHANNELS."
-      (mlet %store-monad ((instances (latest-channel-instances channels)))
-        (channel-instance-derivations instances)))))
-
 (define (whole-package-for-legacy name modules)
   "Return a full-blown Guix package for MODULES, a derivation that builds Guix
 modules in the old ~/.config/guix/latest style."
@@ -290,3 +287,14 @@ channel instances."
                        (entries     (mapm %store-monad instance->entry
                                           (zip instances derivations))))
     (return (manifest entries))))
+
+(define latest-channel-instances*
+  (store-lift latest-channel-instances))
+
+(define* (latest-channel-derivation #:optional (channels %default-channels))
+  "Return as a monadic value the derivation that builds the profile for the
+latest instances of CHANNELS."
+  (mlet* %store-monad ((instances ((store-lift latest-channel-instances)
+                                   channels))
+                       (manifest  (channel-instances->manifest instances)))
+    (profile-derivation manifest)))
diff --git a/guix/derivations.scm b/guix/derivations.scm
index da686e89e2..7afecb10cc 100644
--- a/guix/derivations.scm
+++ b/guix/derivations.scm
@@ -35,7 +35,7 @@
   #:use-module (guix memoization)
   #:use-module (guix combinators)
   #:use-module (guix monads)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix base32)
   #:use-module (guix records)
   #:use-module (guix sets)
diff --git a/guix/describe.scm b/guix/describe.scm
index 3122a762fe..670db63ce7 100644
--- a/guix/describe.scm
+++ b/guix/describe.scm
@@ -21,7 +21,9 @@
   #:use-module (guix profiles)
   #:use-module (srfi srfi-1)
   #:use-module (ice-9 match)
-  #:export (package-path-entries))
+  #:export (current-profile
+            current-profile-entries
+            package-path-entries))
 
 ;;; Commentary:
 ;;;
diff --git a/guix/docker.scm b/guix/docker.scm
index b869901599..0757d3356f 100644
--- a/guix/docker.scm
+++ b/guix/docker.scm
@@ -19,7 +19,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (guix docker)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix base16)
   #:use-module ((guix build utils)
                 #:select (mkdir-p
diff --git a/guix/gcrypt.scm b/guix/gcrypt.scm
deleted file mode 100644
index 1517501751..0000000000
--- a/guix/gcrypt.scm
+++ /dev/null
@@ -1,49 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.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 (guix gcrypt)
-  #:use-module (guix config)
-  #:use-module (system foreign)
-  #:export (gcrypt-version
-            libgcrypt-func))
-
-;;; Commentary:
-;;;
-;;; Common code for the GNU Libgcrypt bindings.  Loading this module
-;;; initializes Libgcrypt as a side effect.
-;;;
-;;; Code:
-
-(define libgcrypt-func
-  (let ((lib (dynamic-link %libgcrypt)))
-    (lambda (func)
-      "Return a pointer to symbol FUNC in libgcrypt."
-      (dynamic-func func lib))))
-
-(define gcrypt-version
-  ;; According to the manual, this function must be called before any other,
-  ;; and it's not clear whether it can be called more than once.  So call it
-  ;; right here from the top level.
-  (let* ((ptr     (libgcrypt-func "gcry_check_version"))
-         (proc    (pointer->procedure '* ptr '(*)))
-         (version (pointer->string (proc %null-pointer))))
-    (lambda ()
-      "Return the version number of libgcrypt as a string."
-      version)))
-
-;;; gcrypt.scm ends here
diff --git a/guix/gexp.scm b/guix/gexp.scm
index 3a600c3830..770b79e012 100644
--- a/guix/gexp.scm
+++ b/guix/gexp.scm
@@ -1417,26 +1417,31 @@ denoting the target file.  Here's an example:
               `((\"hosts\" ,(plain-file \"hosts\"
                                         \"127.0.0.1 localhost\"))
                 (\"bashrc\" ,(plain-file \"bashrc\"
-                                         \"alias ls='ls --color'\"))))
+                                         \"alias ls='ls --color'\"))
+                (\"libvirt/qemu.conf\" ,(plain-file \"qemu.conf\" \"\"))))
 
 This yields an 'etc' directory containing these two files."
   (computed-file name
-                 (gexp
-                  (begin
-                    (mkdir (ungexp output))
-                    (chdir (ungexp output))
-                    (ungexp-splicing
-                     (map (match-lambda
-                            ((target source)
-                             (gexp
-                              (begin
-                                ;; Stat the source to abort early if it does
-                                ;; not exist.
-                                (stat (ungexp source))
-
-                                (symlink (ungexp source)
-                                         (ungexp target))))))
-                          files))))))
+                 (with-imported-modules '((guix build utils))
+                   (gexp
+                    (begin
+                      (use-modules (guix build utils))
+
+                      (mkdir (ungexp output))
+                      (chdir (ungexp output))
+                      (ungexp-splicing
+                       (map (match-lambda
+                              ((target source)
+                               (gexp
+                                (begin
+                                  ;; Stat the source to abort early if it does
+                                  ;; not exist.
+                                  (stat (ungexp source))
+
+                                  (mkdir-p (dirname (ungexp target)))
+                                  (symlink (ungexp source)
+                                           (ungexp target))))))
+                            files)))))))
 
 (define* (directory-union name things
                           #:key (copy? #f) (quiet? #f)
diff --git a/guix/git.scm b/guix/git.scm
index 193e2df111..3d0eb93d9b 100644
--- a/guix/git.scm
+++ b/guix/git.scm
@@ -21,7 +21,7 @@
   #:use-module (git)
   #:use-module (git object)
   #:use-module (guix base32)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module ((guix build utils) #:select (mkdir-p))
   #:use-module (guix store)
   #:use-module (guix utils)
@@ -112,7 +112,7 @@ OID (roughly the commit hash) corresponding to REF."
 
 (define* (update-cached-checkout url
                                  #:key
-                                 (ref '(branch . "origin/master"))
+                                 (ref '(branch . "master"))
                                  (cache-directory
                                   (url-cache-directory
                                    url (%repository-cache-directory))))
@@ -122,6 +122,17 @@ to REF.
 
 REF is pair whose key is [branch | commit | tag] and value the associated
 data, respectively [<branch name> | <sha1> | <tag name>]."
+  (define canonical-ref
+    ;; We used to require callers to specify "origin/" for each branch, which
+    ;; made little sense since the cache should be transparent to them.  So
+    ;; here we append "origin/" if it's missing and otherwise keep it.
+    (match ref
+      (('branch . branch)
+       `(branch . ,(if (string-prefix? "origin/" branch)
+                       branch
+                       (string-append "origin/" branch))))
+      (_ ref)))
+
   (with-libgit2
    (let* ((cache-exists? (openable-repository? cache-directory))
           (repository    (if cache-exists?
@@ -130,7 +141,7 @@ data, respectively [<branch name> | <sha1> | <tag name>]."
      ;; Only fetch remote if it has not been cloned just before.
      (when cache-exists?
        (remote-fetch (remote-lookup repository "origin")))
-     (let ((oid (switch-to-ref repository ref)))
+     (let ((oid (switch-to-ref repository canonical-ref)))
 
        ;; Reclaim file descriptors and memory mappings associated with
        ;; REPOSITORY as soon as possible.
@@ -144,7 +155,7 @@ data, respectively [<branch name> | <sha1> | <tag name>]."
                                    #:key
                                    (cache-directory
                                     (%repository-cache-directory))
-                                   (ref '(branch . "origin/master")))
+                                   (ref '(branch . "master")))
   "Return two values: the content of the git repository at URL copied into a
 store directory and the sha1 of the top level commit in this directory.  The
 reference to be checkout, once the repository is fetched, is specified by REF.
diff --git a/guix/hash.scm b/guix/hash.scm
deleted file mode 100644
index 8d7ba21425..0000000000
--- a/guix/hash.scm
+++ /dev/null
@@ -1,184 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.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 (guix hash)
-  #:use-module (guix gcrypt)
-  #:use-module (rnrs bytevectors)
-  #:use-module (ice-9 binary-ports)
-  #:use-module (system foreign)
-  #:use-module ((guix build utils) #:select (dump-port))
-  #:use-module (srfi srfi-11)
-  #:use-module (srfi srfi-26)
-  #:export (sha1
-            sha256
-            open-sha256-port
-            port-sha256
-            file-sha256
-            open-sha256-input-port))
-
-;;; Commentary:
-;;;
-;;; Cryptographic hashes.
-;;;
-;;; Code:
-
-
-;;;
-;;; Hash.
-;;;
-
-(define-syntax GCRY_MD_SHA256
-  ;; Value as of Libgcrypt 1.5.2.
-  (identifier-syntax 8))
-
-(define-syntax GCRY_MD_SHA1
-  (identifier-syntax 2))
-
-(define bytevector-hash
-  (let ((hash (pointer->procedure void
-                                  (libgcrypt-func "gcry_md_hash_buffer")
-                                  `(,int * * ,size_t))))
-    (lambda (bv type size)
-      "Return the hash TYPE, of SIZE bytes, of BV as a bytevector."
-      (let ((digest (make-bytevector size)))
-        (hash type (bytevector->pointer digest)
-              (bytevector->pointer bv) (bytevector-length bv))
-        digest))))
-
-(define sha1
-  (cut bytevector-hash <> GCRY_MD_SHA1 20))
-
-(define sha256
-  (cut bytevector-hash <> GCRY_MD_SHA256 (/ 256 8)))
-
-(define open-sha256-md
-  (let ((open (pointer->procedure int
-                                  (libgcrypt-func "gcry_md_open")
-                                  `(* ,int ,unsigned-int))))
-    (lambda ()
-      (let* ((md  (bytevector->pointer (make-bytevector (sizeof '*))))
-             (err (open md GCRY_MD_SHA256 0)))
-        (if (zero? err)
-            (dereference-pointer md)
-            (throw 'gcrypt-error err))))))
-
-(define md-write
-  (pointer->procedure void
-                      (libgcrypt-func "gcry_md_write")
-                      `(* * ,size_t)))
-
-(define md-read
-  (pointer->procedure '*
-                      (libgcrypt-func "gcry_md_read")
-                      `(* ,int)))
-
-(define md-close
-  (pointer->procedure void
-                      (libgcrypt-func "gcry_md_close")
-                      '(*)))
-
-
-(define (open-sha256-port)
-  "Return two values: an output port, and a thunk.  When the thunk is called,
-it returns the SHA256 hash (a bytevector) of all the data written to the
-output port."
-  (define sha256-md
-    (open-sha256-md))
-
-  (define digest #f)
-  (define position 0)
-
-  (define (finalize!)
-    (let ((ptr (md-read sha256-md 0)))
-      (set! digest (bytevector-copy (pointer->bytevector ptr 32)))
-      (md-close sha256-md)))
-
-  (define (write! bv offset len)
-    (if (zero? len)
-        (begin
-          (finalize!)
-          0)
-        (let ((ptr (bytevector->pointer bv offset)))
-          (md-write sha256-md ptr len)
-          (set! position (+ position len))
-          len)))
-
-  (define (get-position)
-    position)
-
-  (define (close)
-    (unless digest
-      (finalize!)))
-
-  (values (make-custom-binary-output-port "sha256"
-                                          write! get-position #f
-                                          close)
-          (lambda ()
-            (unless digest
-              (finalize!))
-            digest)))
-
-(define (port-sha256 port)
-  "Return the SHA256 hash (a bytevector) of all the data drained from PORT."
-  (let-values (((out get)
-                (open-sha256-port)))
-    (dump-port port out)
-    (close-port out)
-    (get)))
-
-(define (file-sha256 file)
-  "Return the SHA256 hash (a bytevector) of FILE."
-  (call-with-input-file file port-sha256))
-
-(define (open-sha256-input-port port)
-  "Return an input port that wraps PORT and a thunk to get the hash of all the
-data read from PORT.  The thunk always returns the same value."
-  (define md
-    (open-sha256-md))
-
-  (define (read! bv start count)
-    (let ((n (get-bytevector-n! port bv start count)))
-      (if (eof-object? n)
-          0
-          (begin
-            (unless digest
-              (let ((ptr (bytevector->pointer bv start)))
-                (md-write md ptr n)))
-            n))))
-
-  (define digest #f)
-
-  (define (finalize!)
-    (let ((ptr (md-read md 0)))
-      (set! digest (bytevector-copy (pointer->bytevector ptr 32)))
-      (md-close md)))
-
-  (define (get-hash)
-    (unless digest
-      (finalize!))
-    digest)
-
-  (define (unbuffered port)
-    ;; Guile <= 2.0.9 does not support 'setvbuf' on custom binary input ports.
-    (setvbuf port _IONBF)
-    port)
-
-  (values (unbuffered (make-custom-binary-input-port "sha256" read! #f #f #f))
-          get-hash))
-
-;;; hash.scm ends here
diff --git a/guix/http-client.scm b/guix/http-client.scm
index 3b34d4ffba..07360e6108 100644
--- a/guix/http-client.scm
+++ b/guix/http-client.scm
@@ -34,7 +34,7 @@
   #:use-module (guix ui)
   #:use-module (guix utils)
   #:use-module (guix base64)
-  #:autoload   (guix hash) (sha256)
+  #:autoload   (gcrypt hash) (sha256)
   #:use-module ((guix build utils)
                 #:select (mkdir-p dump-port))
   #:use-module ((guix build download)
diff --git a/guix/import/cpan.scm b/guix/import/cpan.scm
index d0ff64ed05..d4bea84353 100644
--- a/guix/import/cpan.scm
+++ b/guix/import/cpan.scm
@@ -27,7 +27,7 @@
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26)
   #:use-module (json)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix store)
   #:use-module (guix utils)
   #:use-module (guix base32)
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index a5203fe78d..89c84f7037 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -29,7 +29,7 @@
   #:use-module (web uri)
   #:use-module (guix memoization)
   #:use-module (guix http-client)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix store)
   #:use-module (guix base32)
   #:use-module ((guix download) #:select (download-to-store))
diff --git a/guix/import/crate.scm b/guix/import/crate.scm
index 3724a457a4..e0b400d054 100644
--- a/guix/import/crate.scm
+++ b/guix/import/crate.scm
@@ -20,7 +20,7 @@
   #:use-module (guix base32)
   #:use-module (guix build-system cargo)
   #:use-module ((guix download) #:prefix download:)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix http-client)
   #:use-module (guix import json)
   #:use-module (guix import utils)
diff --git a/guix/import/elpa.scm b/guix/import/elpa.scm
index c37afaf8e6..83354d3f04 100644
--- a/guix/import/elpa.scm
+++ b/guix/import/elpa.scm
@@ -32,7 +32,7 @@
   #:use-module (guix http-client)
   #:use-module (guix store)
   #:use-module (guix ui)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix base32)
   #:use-module (guix upstream)
   #:use-module (guix packages)
diff --git a/guix/import/gnu.scm b/guix/import/gnu.scm
index bbb17047f0..29324d7554 100644
--- a/guix/import/gnu.scm
+++ b/guix/import/gnu.scm
@@ -21,7 +21,7 @@
   #:use-module (guix import utils)
   #:use-module (guix utils)
   #:use-module (guix store)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix base32)
   #:use-module (guix upstream)
   #:use-module (srfi srfi-1)
diff --git a/guix/import/hackage.scm b/guix/import/hackage.scm
index 54301de2e8..766a0b53f1 100644
--- a/guix/import/hackage.scm
+++ b/guix/import/hackage.scm
@@ -33,7 +33,7 @@
   #:use-module ((guix import utils) #:select (factorize-uri recursive-import))
   #:use-module (guix import cabal)
   #:use-module (guix store)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix base32)
   #:use-module (guix memoization)
   #:use-module (guix upstream)
diff --git a/guix/import/texlive.scm b/guix/import/texlive.scm
index d4c3714364..791b514485 100644
--- a/guix/import/texlive.scm
+++ b/guix/import/texlive.scm
@@ -26,7 +26,7 @@
   #:use-module (srfi srfi-34)
   #:use-module (web uri)
   #:use-module (guix http-client)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix memoization)
   #:use-module (guix store)
   #:use-module (guix base32)
diff --git a/guix/import/utils.scm b/guix/import/utils.scm
index 0dc8fd5857..516c0cfaa2 100644
--- a/guix/import/utils.scm
+++ b/guix/import/utils.scm
@@ -23,7 +23,7 @@
 (define-module (guix import utils)
   #:use-module (guix base32)
   #:use-module ((guix build download) #:prefix build:)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix http-client)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix utils)
diff --git a/guix/inferior.scm b/guix/inferior.scm
index 05c8d65deb..af37233a03 100644
--- a/guix/inferior.scm
+++ b/guix/inferior.scm
@@ -19,6 +19,7 @@
 (define-module (guix inferior)
   #:use-module (srfi srfi-9)
   #:use-module (srfi srfi-9 gnu)
+  #:use-module ((guix utils) #:select (source-properties->location))
   #:use-module (ice-9 match)
   #:use-module (ice-9 popen)
   #:export (inferior?
@@ -33,7 +34,9 @@
 
             inferior-packages
             inferior-package-synopsis
-            inferior-package-description))
+            inferior-package-description
+            inferior-package-home-page
+            inferior-package-location))
 
 ;;; Commentary:
 ;;;
@@ -198,3 +201,18 @@ TRANSLATE? is true, translate it to the current locale's language."
                           (if translate?
                               '(compose (@ (guix ui) P_) package-description)
                               'package-description)))
+
+(define (inferior-package-home-page package)
+  "Return the home page of PACKAGE."
+  (inferior-package-field package 'package-home-page))
+
+(define (inferior-package-location package)
+  "Return the source code location of PACKAGE, either #f or a <location>
+record."
+  (source-properties->location
+   (inferior-package-field package
+                           '(compose (lambda (loc)
+                                       (and loc
+                                            (location->source-properties
+                                             loc)))
+                                     package-location))))
diff --git a/guix/nar.scm b/guix/nar.scm
index 3556de1379..0495b4a40c 100644
--- a/guix/nar.scm
+++ b/guix/nar.scm
@@ -25,9 +25,9 @@
   #:use-module (guix store)
   #:use-module (guix store database)
   #:use-module (guix ui)                          ; for '_'
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix pki)
-  #:use-module (guix pk-crypto)
+  #:use-module (gcrypt pk-crypto)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-11)
   #:use-module (srfi srfi-26)
diff --git a/guix/pk-crypto.scm b/guix/pk-crypto.scm
deleted file mode 100644
index 55ba7b1bb8..0000000000
--- a/guix/pk-crypto.scm
+++ /dev/null
@@ -1,407 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2017 Ludovic Courtès <ludo@gnu.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 (guix pk-crypto)
-  #:use-module (guix base16)
-  #:use-module (guix gcrypt)
-
-  #:use-module (system foreign)
-  #:use-module (rnrs bytevectors)
-  #:use-module (ice-9 match)
-  #:use-module (ice-9 rdelim)
-  #:export (canonical-sexp?
-            error-source
-            error-string
-            string->canonical-sexp
-            canonical-sexp->string
-            read-file-sexp
-            number->canonical-sexp
-            canonical-sexp-car
-            canonical-sexp-cdr
-            canonical-sexp-nth
-            canonical-sexp-nth-data
-            canonical-sexp-length
-            canonical-sexp-null?
-            canonical-sexp-list?
-            bytevector->hash-data
-            hash-data->bytevector
-            key-type
-            sign
-            verify
-            generate-key
-            find-sexp-token
-            canonical-sexp->sexp
-            sexp->canonical-sexp)
-  #:re-export (gcrypt-version))
-
-
-;;; Commentary:
-;;;
-;;; Public key cryptographic routines from GNU Libgcrypt.
-;;;;
-;;; Libgcrypt uses "canonical s-expressions" to represent key material,
-;;; parameters, and data.  We keep it as an opaque object to map them to
-;;; Scheme s-expressions because (1) Libgcrypt sexps may be stored in secure
-;;; memory, and (2) the read syntax is different.
-;;;
-;;; A 'canonical-sexp->sexp' procedure is provided nevertheless, for use in
-;;; cases where it is safe to move data out of Libgcrypt---e.g., when
-;;; processing ACL entries, public keys, etc.
-;;;
-;;; Canonical sexps were defined by Rivest et al. in the IETF draft at
-;;; <http://people.csail.mit.edu/rivest/Sexp.txt> for the purposes of SPKI
-;;; (see <http://www.ietf.org/rfc/rfc2693.txt>.)
-;;;
-;;; Code:
-
-;; Libgcrypt "s-expressions".
-(define-wrapped-pointer-type <canonical-sexp>
-  canonical-sexp?
-  naked-pointer->canonical-sexp
-  canonical-sexp->pointer
-  (lambda (obj port)
-    ;; Don't print OBJ's external representation: we don't want key material
-    ;; to leak in backtraces and such.
-    (format port "#<canonical-sexp ~a | ~a>"
-            (number->string (object-address obj) 16)
-            (number->string (pointer-address (canonical-sexp->pointer obj))
-                            16))))
-
-(define finalize-canonical-sexp!
-  (libgcrypt-func "gcry_sexp_release"))
-
-(define-inlinable (pointer->canonical-sexp ptr)
-  "Return a <canonical-sexp> that wraps PTR."
-  (let* ((sexp (naked-pointer->canonical-sexp ptr))
-         (ptr* (canonical-sexp->pointer sexp)))
-    ;; Did we already have a <canonical-sexp> object for PTR?
-    (when (equal? ptr ptr*)
-      ;; No, so we can safely add a finalizer (in Guile 2.0.9
-      ;; 'set-pointer-finalizer!' *adds* a finalizer rather than replacing the
-      ;; existing one.)
-      (set-pointer-finalizer! ptr finalize-canonical-sexp!))
-    sexp))
-
-(define error-source
-  (let* ((ptr  (libgcrypt-func "gcry_strsource"))
-         (proc (pointer->procedure '* ptr (list int))))
-    (lambda (err)
-      "Return the error source (a string) for ERR, an error code as thrown
-along with 'gcry-error'."
-      (pointer->string (proc err)))))
-
-(define error-string
-  (let* ((ptr  (libgcrypt-func "gcry_strerror"))
-         (proc (pointer->procedure '* ptr (list int))))
-    (lambda (err)
-      "Return the error description (a string) for ERR, an error code as
-thrown along with 'gcry-error'."
-      (pointer->string (proc err)))))
-
-(define string->canonical-sexp
-  (let* ((ptr  (libgcrypt-func "gcry_sexp_new"))
-         (proc (pointer->procedure int ptr `(* * ,size_t ,int))))
-    (lambda (str)
-      "Parse STR and return the corresponding gcrypt s-expression."
-
-      ;; When STR comes from 'canonical-sexp->string', it may contain
-      ;; characters that are really meant to be interpreted as bytes as in a C
-      ;; 'char *'.  Thus, convert STR to ISO-8859-1 so the byte values of the
-      ;; characters are preserved.
-      (let* ((sexp (bytevector->pointer (make-bytevector (sizeof '*))))
-             (err  (proc sexp (string->pointer str "ISO-8859-1") 0 1)))
-        (if (= 0 err)
-            (pointer->canonical-sexp (dereference-pointer sexp))
-            (throw 'gcry-error 'string->canonical-sexp err))))))
-
-(define-syntax GCRYSEXP_FMT_ADVANCED
-  (identifier-syntax 3))
-
-(define canonical-sexp->string
-  (let* ((ptr  (libgcrypt-func "gcry_sexp_sprint"))
-         (proc (pointer->procedure size_t ptr `(* ,int * ,size_t))))
-    (lambda (sexp)
-      "Return a textual representation of SEXP."
-      (let loop ((len 1024))
-        (let* ((buf  (bytevector->pointer (make-bytevector len)))
-               (size (proc (canonical-sexp->pointer sexp)
-                           GCRYSEXP_FMT_ADVANCED buf len)))
-          (if (zero? size)
-              (loop (* len 2))
-              (pointer->string buf size "ISO-8859-1")))))))
-
-(define (read-file-sexp file)
-  "Return the canonical sexp read from FILE."
-  (call-with-input-file file
-    (compose string->canonical-sexp
-             read-string)))
-
-(define canonical-sexp-car
-  (let* ((ptr  (libgcrypt-func "gcry_sexp_car"))
-         (proc (pointer->procedure '* ptr '(*))))
-    (lambda (lst)
-      "Return the first element of LST, an sexp, if that element is a list;
-return #f if LST or its first element is not a list (this is different from
-the usual Lisp 'car'.)"
-      (let ((result (proc (canonical-sexp->pointer lst))))
-        (if (null-pointer? result)
-            #f
-            (pointer->canonical-sexp result))))))
-
-(define canonical-sexp-cdr
-  (let* ((ptr  (libgcrypt-func "gcry_sexp_cdr"))
-         (proc (pointer->procedure '* ptr '(*))))
-    (lambda (lst)
-      "Return the tail of LST, an sexp, or #f if LST is not a list."
-      (let ((result (proc (canonical-sexp->pointer lst))))
-        (if (null-pointer? result)
-            #f
-            (pointer->canonical-sexp result))))))
-
-(define canonical-sexp-nth
-  (let* ((ptr  (libgcrypt-func "gcry_sexp_nth"))
-         (proc (pointer->procedure '* ptr `(* ,int))))
-    (lambda (lst index)
-      "Return the INDEXth nested element of LST, an s-expression.  Return #f
-if that element does not exist, or if it's an atom.  (Note: this is obviously
-different from Scheme's 'list-ref'.)"
-      (let ((result (proc (canonical-sexp->pointer lst) index)))
-        (if (null-pointer? result)
-            #f
-            (pointer->canonical-sexp result))))))
-
-(define (dereference-size_t p)
-  "Return the size_t value pointed to by P."
-  (bytevector-uint-ref (pointer->bytevector p (sizeof size_t))
-                       0 (native-endianness)
-                       (sizeof size_t)))
-
-(define canonical-sexp-length
-  (let* ((ptr  (libgcrypt-func "gcry_sexp_length"))
-         (proc (pointer->procedure int ptr '(*))))
-    (lambda (sexp)
-      "Return the length of SEXP if it's a list (including the empty list);
-return zero if SEXP is an atom."
-      (proc (canonical-sexp->pointer sexp)))))
-
-(define token-string?
-  (let ((token-cs (char-set-union char-set:digit
-                                  char-set:letter
-                                  (char-set #\- #\. #\/ #\_
-                                            #\: #\* #\+ #\=))))
-    (lambda (str)
-      "Return #t if STR is a token as per Section 4.3 of
-<http://people.csail.mit.edu/rivest/Sexp.txt>."
-      (and (not (string-null? str))
-           (string-every token-cs str)
-           (not (char-set-contains? char-set:digit (string-ref str 0)))))))
-
-(define canonical-sexp-nth-data
-  (let* ((ptr  (libgcrypt-func "gcry_sexp_nth_data"))
-         (proc (pointer->procedure '* ptr `(* ,int *))))
-    (lambda (lst index)
-      "Return as a symbol (for \"sexp tokens\") or a bytevector (for any other
-\"octet string\") the INDEXth data element (atom) of LST, an s-expression.
-Return #f if that element does not exist, or if it's a list."
-      (let* ((size*  (bytevector->pointer (make-bytevector (sizeof '*))))
-             (result (proc (canonical-sexp->pointer lst) index size*)))
-        (if (null-pointer? result)
-            #f
-            (let* ((len (dereference-size_t size*))
-                   (str (pointer->string result len "ISO-8859-1")))
-              ;; The sexp spec speaks of "tokens" and "octet strings".
-              ;; Sometimes these octet strings are actual strings (text),
-              ;; sometimes they're bytevectors, and sometimes they're
-              ;; multi-precision integers (MPIs).  Only the application knows.
-              ;; However, for convenience, we return a symbol when a token is
-              ;; encountered since tokens are frequent (at least in the 'car'
-              ;; of each sexp.)
-              (if (token-string? str)
-                  (string->symbol str)   ; an sexp "token"
-                  (bytevector-copy       ; application data, textual or binary
-                   (pointer->bytevector result len)))))))))
-
-(define (number->canonical-sexp number)
-  "Return an s-expression representing NUMBER."
-  (string->canonical-sexp (string-append "#" (number->string number 16) "#")))
-
-(define* (bytevector->hash-data bv
-                                #:optional
-                                (hash-algo "sha256")
-                                #:key (key-type 'ecc))
-  "Given BV, a bytevector containing a hash of type HASH-ALGO, return an
-s-expression suitable for use as the 'data' argument for 'sign'.  KEY-TYPE
-must be a symbol: 'dsa, 'ecc, or 'rsa."
-  (string->canonical-sexp
-   (format #f "(data (flags ~a) (hash \"~a\" #~a#))"
-           (case key-type
-             ((ecc dsa) "rfc6979")
-             ((rsa)     "pkcs1")
-             (else (error "unknown key type" key-type)))
-           hash-algo
-           (bytevector->base16-string bv))))
-
-(define (key-type sexp)
-  "Return a symbol denoting the type of public or private key represented by
-SEXP--e.g., 'rsa', 'ecc'--or #f if SEXP does not denote a valid key."
-  (case (canonical-sexp-nth-data sexp 0)
-    ((public-key private-key)
-     (canonical-sexp-nth-data (canonical-sexp-nth sexp 1) 0))
-    (else #f)))
-
-(define* (hash-data->bytevector data)
-  "Return two values: the hash value (a bytevector), and the hash algorithm (a
-string) extracted from DATA, an sexp as returned by 'bytevector->hash-data'.
-Return #f if DATA does not conform."
-  (let ((hash (find-sexp-token data 'hash)))
-    (if hash
-        (let ((algo  (canonical-sexp-nth-data hash 1))
-              (value (canonical-sexp-nth-data hash 2)))
-          (values value (symbol->string algo)))
-        (values #f #f))))
-
-(define sign
-  (let* ((ptr  (libgcrypt-func "gcry_pk_sign"))
-         (proc (pointer->procedure int ptr '(* * *))))
-    (lambda (data secret-key)
-      "Sign DATA, a canonical s-expression representing a suitable hash, with
-SECRET-KEY (a canonical s-expression whose car is 'private-key'.)  Note that
-DATA must be a 'data' s-expression, as returned by
-'bytevector->hash-data' (info \"(gcrypt) Cryptographic Functions\")."
-      (let* ((sig (bytevector->pointer (make-bytevector (sizeof '*))))
-             (err (proc sig (canonical-sexp->pointer data)
-                        (canonical-sexp->pointer secret-key))))
-        (if (= 0 err)
-            (pointer->canonical-sexp (dereference-pointer sig))
-            (throw 'gcry-error 'sign err))))))
-
-(define verify
-  (let* ((ptr  (libgcrypt-func "gcry_pk_verify"))
-         (proc (pointer->procedure int ptr '(* * *))))
-    (lambda (signature data public-key)
-      "Verify that SIGNATURE is a signature of DATA with PUBLIC-KEY, all of
-which are gcrypt s-expressions."
-      (zero? (proc (canonical-sexp->pointer signature)
-                   (canonical-sexp->pointer data)
-                   (canonical-sexp->pointer public-key))))))
-
-(define generate-key
-  (let* ((ptr  (libgcrypt-func "gcry_pk_genkey"))
-         (proc (pointer->procedure int ptr '(* *))))
-    (lambda (params)
-      "Return as an s-expression a new key pair for PARAMS.  PARAMS must be an
-s-expression like: (genkey (rsa (nbits 4:2048)))."
-      (let* ((key (bytevector->pointer (make-bytevector (sizeof '*))))
-             (err (proc key (canonical-sexp->pointer params))))
-        (if (zero? err)
-            (pointer->canonical-sexp (dereference-pointer key))
-            (throw 'gcry-error 'generate-key err))))))
-
-(define find-sexp-token
-  (let* ((ptr  (libgcrypt-func "gcry_sexp_find_token"))
-         (proc (pointer->procedure '* ptr `(* * ,size_t))))
-    (lambda (sexp token)
-      "Find in SEXP the first element whose 'car' is TOKEN and return it;
-return #f if not found."
-      (let* ((token (string->pointer (symbol->string token)))
-             (res   (proc (canonical-sexp->pointer sexp) token 0)))
-        (if (null-pointer? res)
-            #f
-            (pointer->canonical-sexp res))))))
-
-(define-inlinable (canonical-sexp-null? sexp)
-  "Return #t if SEXP is the empty-list sexp."
-  (null-pointer? (canonical-sexp->pointer sexp)))
-
-(define (canonical-sexp-list? sexp)
-  "Return #t if SEXP is a list."
-  (or (canonical-sexp-null? sexp)
-      (> (canonical-sexp-length sexp) 0)))
-
-(define (canonical-sexp-fold proc seed sexp)
-  "Fold PROC (as per SRFI-1) over SEXP, a canonical sexp."
-  (if (canonical-sexp-list? sexp)
-      (let ((len (canonical-sexp-length sexp)))
-        (let loop ((index  0)
-                   (result seed))
-          (if (= index len)
-              result
-              (loop (+ 1 index)
-                    ;; XXX: Call 'nth-data' *before* 'nth' to work around
-                    ;; <https://bugs.g10code.com/gnupg/issue1594>, which
-                    ;; affects 1.6.0 and earlier versions.
-                    (proc (or (canonical-sexp-nth-data sexp index)
-                              (canonical-sexp-nth sexp index))
-                          result)))))
-      (error "sexp is not a list" sexp)))
-
-(define (canonical-sexp->sexp sexp)
-  "Return a Scheme sexp corresponding to SEXP.  This is particularly useful to
-compare sexps (since Libgcrypt does not provide an 'equal?' procedure), or to
-use pattern matching."
-  (if (canonical-sexp-list? sexp)
-      (reverse
-       (canonical-sexp-fold (lambda (item result)
-                              (cons (if (canonical-sexp? item)
-                                        (canonical-sexp->sexp item)
-                                        item)
-                                    result))
-                            '()
-                            sexp))
-
-      ;; As of Libgcrypt 1.6.0, there's no function to extract the buffer of a
-      ;; non-list sexp (!), so we first enlist SEXP, then get at its buffer.
-      (let ((sexp (string->canonical-sexp
-                   (string-append "(" (canonical-sexp->string sexp)
-                                  ")"))))
-        (or (canonical-sexp-nth-data sexp 0)
-            (canonical-sexp-nth sexp 0)))))
-
-(define (sexp->canonical-sexp sexp)
-  "Return a canonical sexp equivalent to SEXP, a Scheme sexp as returned by
-'canonical-sexp->sexp'."
-  ;; XXX: This is inefficient, but the Libgcrypt API doesn't allow us to do
-  ;; much better.
-  (string->canonical-sexp
-    (call-with-output-string
-     (lambda (port)
-       (define (write item)
-         (cond ((list? item)
-                (display "(" port)
-                (for-each write item)
-                (display ")" port))
-               ((symbol? item)
-                (format port " ~a" item))
-               ((bytevector? item)
-                (format port " #~a#"
-                        (bytevector->base16-string item)))
-               (else
-                (error "unsupported sexp item type" item))))
-
-       (write sexp)))))
-
-(define (gcrypt-error-printer port key args default-printer)
-  "Print the gcrypt error specified by ARGS."
-  (match args
-    ((proc err)
-     (format port "In procedure ~a: ~a: ~a"
-             proc (error-source err) (error-string err)))))
-
-(set-exception-printer! 'gcry-error gcrypt-error-printer)
-
-;;; pk-crypto.scm ends here
diff --git a/guix/pki.scm b/guix/pki.scm
index 1551425c33..6326e065e9 100644
--- a/guix/pki.scm
+++ b/guix/pki.scm
@@ -18,7 +18,7 @@
 
 (define-module (guix pki)
   #:use-module (guix config)
-  #:use-module (guix pk-crypto)
+  #:use-module (gcrypt pk-crypto)
   #:use-module ((guix utils) #:select (with-atomic-file-output))
   #:use-module ((guix build utils) #:select (mkdir-p))
   #:use-module (ice-9 match)
diff --git a/guix/profiles.scm b/guix/profiles.scm
index f34f4fcff6..8acfcff8c1 100644
--- a/guix/profiles.scm
+++ b/guix/profiles.scm
@@ -286,7 +286,8 @@ file name."
            (manifest-transitive-entries manifest))))
 
 (define* (package->manifest-entry package #:optional (output "out")
-                                  #:key (parent (delay #f)))
+                                  #:key (parent (delay #f))
+                                  (properties '()))
   "Return a manifest entry for the OUTPUT of package PACKAGE."
   ;; For each dependency, keep a promise pointing to its "parent" entry.
   (letrec* ((deps  (map (match-lambda
@@ -305,7 +306,8 @@ file name."
                      (dependencies (delete-duplicates deps))
                      (search-paths
                       (package-transitive-native-search-paths package))
-                     (parent parent))))
+                     (parent parent)
+                     (properties properties))))
     entry))
 
 (define (packages->manifest packages)
diff --git a/guix/scripts/archive.scm b/guix/scripts/archive.scm
index a359f405fe..fb2f61ce30 100644
--- a/guix/scripts/archive.scm
+++ b/guix/scripts/archive.scm
@@ -29,7 +29,7 @@
   #:use-module (guix monads)
   #:use-module (guix ui)
   #:use-module (guix pki)
-  #:use-module (guix pk-crypto)
+  #:use-module (gcrypt pk-crypto)
   #:use-module (guix scripts)
   #:use-module (guix scripts build)
   #:use-module (gnu packages)
diff --git a/guix/scripts/authenticate.scm b/guix/scripts/authenticate.scm
index 8b19dc871b..f1fd8ee895 100644
--- a/guix/scripts/authenticate.scm
+++ b/guix/scripts/authenticate.scm
@@ -19,7 +19,7 @@
 (define-module (guix scripts authenticate)
   #:use-module (guix config)
   #:use-module (guix base16)
-  #:use-module (guix pk-crypto)
+  #:use-module (gcrypt pk-crypto)
   #:use-module (guix pki)
   #:use-module (guix ui)
   #:use-module (ice-9 binary-ports)
diff --git a/guix/scripts/describe.scm b/guix/scripts/describe.scm
new file mode 100644
index 0000000000..fdff07d0e3
--- /dev/null
+++ b/guix/scripts/describe.scm
@@ -0,0 +1,159 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.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 (guix scripts describe)
+  #:use-module ((guix ui) #:hide (display-profile-content))
+  #:use-module (guix scripts)
+  #:use-module (guix describe)
+  #:use-module (guix profiles)
+  #:use-module ((guix scripts pull) #:select (display-profile-content))
+  #:use-module (git)
+  #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-37)
+  #:use-module (ice-9 match)
+  #:autoload   (ice-9 pretty-print) (pretty-print)
+  #:export (guix-describe))
+
+
+;;;
+;;; Command-line options.
+;;;
+
+(define %options
+  ;; Specifications of the command-line options.
+  (list (option '(#\f "format") #t #f
+                (lambda (opt name arg result)
+                  (unless (member arg '("human" "channels"))
+                    (leave (G_ "~a: unsupported output format~%") arg))
+                  (alist-cons 'format 'channels result)))
+        (option '(#\h "help") #f #f
+                (lambda args
+                  (show-help)
+                  (exit 0)))
+        (option '(#\V "version") #f #f
+                (lambda args
+                  (show-version-and-exit "guix describe")))))
+
+(define %default-options
+  ;; Alist of default option values.
+  '((format . human)))
+
+(define (show-help)
+  (display (G_ "Usage: guix describe [OPTION]...
+Display information about the channels currently in use.\n"))
+  (display (G_ "
+  -f, --format=FORMAT    display information in the given FORMAT"))
+  (newline)
+  (display (G_ "
+  -h, --help             display this help and exit"))
+  (display (G_ "
+  -V, --version          display version information and exit"))
+  (newline)
+  (show-bug-report-information))
+
+(define (display-package-search-path fmt)
+  "Display GUIX_PACKAGE_PATH, if it is set, according to FMT."
+  (match (getenv "GUIX_PACKAGE_PATH")
+    (#f #t)
+    (string
+     (match fmt
+       ('human
+        (format #t "~%GUIX_PACKAGE_PATH=\"~a\"~%" string))
+       ('channels
+        (format #t (G_ "~%;; warning: GUIX_PACKAGE_PATH=\"~a\"~%")
+                string))))))
+
+(define (display-checkout-info fmt)
+  "Display information about the current checkout according to FMT, a symbol
+denoting the requested format.  Exit if the current directory does not lie
+within a Git checkout."
+  (let* ((program    (car (command-line)))
+         (directory  (catch 'git-error
+                       (lambda ()
+                         (repository-discover (dirname program)))
+                       (lambda (key err)
+                         (leave (G_ "failed to determine origin~%")))))
+         (repository (repository-open directory))
+         (head       (repository-head repository))
+         (commit     (oid->string (reference-target head))))
+    (match fmt
+      ('human
+       (format #t (G_ "Git checkout:~%"))
+       (format #t (G_ "  repository: ~a~%") (dirname directory))
+       (format #t (G_ "  branch: ~a~%") (reference-shorthand head))
+       (format #t (G_ "  commit: ~a~%") commit))
+      ('channels
+       (pretty-print `(list (channel
+                             (name 'guix)
+                             (url ,(dirname directory))
+                             (commit ,commit))))))
+    (display-package-search-path fmt)))
+
+(define (display-profile-info profile fmt)
+  "Display information about PROFILE, a profile as created by (guix channels),
+in the format specified by FMT."
+  (define number
+    (generation-number profile))
+
+  (match fmt
+    ('human
+     (display-profile-content profile number))
+    ('channels
+     (pretty-print
+      `(list ,@(map (lambda (entry)
+                      (match (assq 'source (manifest-entry-properties entry))
+                        (('source ('repository ('version 0)
+                                               ('url url)
+                                               ('branch branch)
+                                               ('commit commit)
+                                               _ ...))
+                         `(channel (name ',(string->symbol
+                                            (manifest-entry-name entry)))
+                                   (url ,url)
+                                   (commit ,commit)))
+
+                        ;; Pre-0.15.0 Guix does not provide that information,
+                        ;; so there's not much we can do in that case.
+                        (_ '???)))
+
+                    ;; Show most recently installed packages last.
+                    (reverse
+                     (manifest-entries
+                      (profile-manifest (generation-file-name profile
+                                                              number)))))))))
+  (display-package-search-path fmt))
+
+
+;;;
+;;; Entry point.
+;;;
+
+(define (guix-describe . args)
+  (let* ((opts   (args-fold* args %options
+                             (lambda (opt name arg result)
+                               (leave (G_ "~A: unrecognized option~%")
+                                      name))
+                             cons
+                             %default-options))
+         (format (assq-ref opts 'format)))
+    (with-error-handling
+      (match (current-profile)
+        (#f
+         (display-checkout-info format))
+        (profile
+         (display-profile-info profile format))))))
diff --git a/guix/scripts/download.scm b/guix/scripts/download.scm
index 1b99bc62cf..b9162d3449 100644
--- a/guix/scripts/download.scm
+++ b/guix/scripts/download.scm
@@ -20,7 +20,7 @@
   #:use-module (guix ui)
   #:use-module (guix scripts)
   #:use-module (guix store)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix base16)
   #:use-module (guix base32)
   #:use-module ((guix download) #:hide (url-fetch))
diff --git a/guix/scripts/hash.scm b/guix/scripts/hash.scm
index cae5d6bcdf..2bd2ac4a06 100644
--- a/guix/scripts/hash.scm
+++ b/guix/scripts/hash.scm
@@ -20,7 +20,7 @@
 
 (define-module (guix scripts hash)
   #:use-module (guix base32)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix serialization)
   #:use-module (guix ui)
   #:use-module (guix scripts)
@@ -44,7 +44,7 @@
   `((format . ,bytevector->nix-base32-string)))
 
 (define (show-help)
-  (display (G_ "Usage: guix hash [OPTION] FILE
+  (display (G_ "Usage: gcrypt hash [OPTION] FILE
 Return the cryptographic hash of FILE.
 
 Supported formats: 'nix-base32' (default), 'base32', and 'base16' ('hex'
@@ -93,7 +93,7 @@ and 'hexadecimal' can be used as well).\n"))
                   (exit 0)))
         (option '(#\V "version") #f #f
                 (lambda args
-                  (show-version-and-exit "guix hash")))))
+                  (show-version-and-exit "gcrypt hash")))))
 
 
 
diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm
index fb0677de28..1916f3b9d7 100644
--- a/guix/scripts/pack.scm
+++ b/guix/scripts/pack.scm
@@ -41,7 +41,7 @@
   #:use-module (gnu packages guile)
   #:use-module (gnu packages base)
   #:autoload   (gnu packages package-management) (guix)
-  #:autoload   (gnu packages gnupg) (libgcrypt)
+  #:autoload   (gnu packages gnupg) (guile-gcrypt)
   #:autoload   (gnu packages guile) (guile2.0-json guile-json)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-9)
@@ -95,10 +95,12 @@ found."
     (('gnu _ ...) #t)
     (_ #f)))
 
-(define guile-sqlite3&co
-  ;; Guile-SQLite3 and its propagated inputs.
-  (cons guile-sqlite3
-        (package-transitive-propagated-inputs guile-sqlite3)))
+(define gcrypt-sqlite3&co
+  ;; Guile-Gcrypt, Guile-SQLite3, and their propagated inputs.
+  (append-map (lambda (package)
+                (cons package
+                      (package-transitive-propagated-inputs package)))
+              (list guile-gcrypt guile-sqlite3)))
 
 (define* (self-contained-tarball name profile
                                  #:key target
@@ -124,16 +126,14 @@ added to the pack."
                                   "guix/store/schema.sql"))))
 
   (define build
-    (with-imported-modules `(((guix config)
-                              => ,(make-config.scm
-                                   #:libgcrypt libgcrypt))
+    (with-imported-modules `(((guix config) => ,(make-config.scm))
                              ,@(source-module-closure
                                 `((guix build utils)
                                   (guix build union)
                                   (guix build store-copy)
                                   (gnu build install))
                                 #:select? not-config?))
-      (with-extensions guile-sqlite3&co
+      (with-extensions gcrypt-sqlite3&co
         #~(begin
             (use-modules (guix build utils)
                          ((guix build union) #:select (relative-file-name))
@@ -251,22 +251,14 @@ points for virtual file systems (like procfs), and optional symlinks.
 
 SYMLINKS must be a list of (SOURCE -> TARGET) tuples denoting symlinks to be
 added to the pack."
-  (define libgcrypt
-    ;; XXX: Not strictly needed, but pulled by (guix store database).
-    (module-ref (resolve-interface '(gnu packages gnupg))
-                'libgcrypt))
-
-
   (define build
-    (with-imported-modules `(((guix config)
-                              => ,(make-config.scm
-                                   #:libgcrypt libgcrypt))
+    (with-imported-modules `(((guix config) => ,(make-config.scm))
                              ,@(source-module-closure
                                 '((guix build utils)
                                   (guix build store-copy)
                                   (gnu build install))
                                 #:select? not-config?))
-      (with-extensions guile-sqlite3&co
+      (with-extensions gcrypt-sqlite3&co
         #~(begin
             (use-modules (guix build utils)
                          (gnu build install)
@@ -349,32 +341,12 @@ must a be a GNU triplet and it is used to derive the architecture metadata in
 the image."
   (define defmod 'define-module)                  ;trick Geiser
 
-  (define config
-    ;; (guix config) module for consumption by (guix gcrypt).
-    (scheme-file "gcrypt-config.scm"
-                 #~(begin
-                     (#$defmod (guix config)
-                       #:export (%libgcrypt))
-
-                     ;; XXX: Work around <http://bugs.gnu.org/15602>.
-                     (eval-when (expand load eval)
-                       (define %libgcrypt
-                         #+(file-append libgcrypt "/lib/libgcrypt"))))))
-
-  (define json
-    ;; Pick the guile-json package that corresponds to the Guile used to build
-    ;; derivations.
-    (if (string-prefix? "2.0" (package-version (default-guile)))
-        guile2.0-json
-        guile-json))
-
   (define build
-    ;; Guile-JSON is required by (guix docker).
-    (with-extensions (list json)
-      (with-imported-modules `(,@(source-module-closure '((guix docker)
-                                                          (guix build store-copy))
-                                                        #:select? not-config?)
-                               ((guix config) => ,config))
+    ;; Guile-JSON and Guile-Gcrypt are required by (guix docker).
+    (with-extensions (list guile-json guile-gcrypt)
+      (with-imported-modules (source-module-closure '((guix docker)
+                                                      (guix build store-copy))
+                                                    #:select? not-config?)
         #~(begin
             (use-modules (guix docker) (srfi srfi-19) (guix build store-copy))
 
diff --git a/guix/scripts/package.scm b/guix/scripts/package.scm
index b38a55d01c..97bcc699d9 100644
--- a/guix/scripts/package.scm
+++ b/guix/scripts/package.scm
@@ -35,6 +35,7 @@
   #:use-module (guix config)
   #:use-module (guix scripts)
   #:use-module (guix scripts build)
+  #:autoload   (guix describe) (current-profile-entries)
   #:use-module ((guix build utils)
                 #:select (directory-exists? mkdir-p))
   #:use-module (ice-9 format)
@@ -238,7 +239,7 @@ of relevance scores."
     (info (G_ "package '~a' has been superseded by '~a'~%")
           (manifest-entry-name old) (package-name new))
     (manifest-transaction-install-entry
-     (package->manifest-entry new (manifest-entry-output old))
+     (package->manifest-entry* new (manifest-entry-output old))
      (manifest-transaction-remove-pattern
       (manifest-pattern
         (name (manifest-entry-name old))
@@ -261,7 +262,7 @@ of relevance scores."
            (case (version-compare candidate-version version)
              ((>)
               (manifest-transaction-install-entry
-               (package->manifest-entry pkg output)
+               (package->manifest-entry* pkg output)
                transaction))
              ((<)
               transaction)
@@ -274,7 +275,7 @@ of relevance scores."
                          (null? (package-propagated-inputs pkg)))
                     transaction
                     (manifest-transaction-install-entry
-                     (package->manifest-entry pkg output)
+                     (package->manifest-entry* pkg output)
                      transaction))))))))
        (#f
         (warning (G_ "package '~a' no longer exists~%") name)
@@ -570,6 +571,52 @@ upgrading, #f otherwise."
       (output "out")                              ;XXX: wild guess
       (item item))))
 
+(define (package-provenance package)
+  "Return the provenance of PACKAGE as an sexp for use as the 'provenance'
+property of manifest entries, or #f if it could not be determined."
+  (define (entry-source entry)
+    (match (assq 'source
+                 (manifest-entry-properties entry))
+      (('source value) value)
+      (_ #f)))
+
+  (match (and=> (package-location package) location-file)
+    (#f #f)
+    (file
+     (let ((file (if (string-prefix? "/" file)
+                     file
+                     (search-path %load-path file))))
+       (and file
+            (string-prefix? (%store-prefix) file)
+
+            ;; Always store information about the 'guix' channel and
+            ;; optionally about the specific channel FILE comes from.
+            (or (let ((main  (and=> (find (lambda (entry)
+                                            (string=? "guix"
+                                                      (manifest-entry-name entry)))
+                                          (current-profile-entries))
+                                    entry-source))
+                      (extra (any (lambda (entry)
+                                    (let ((item (manifest-entry-item entry)))
+                                      (and (string-prefix? item file)
+                                           (entry-source entry))))
+                                  (current-profile-entries))))
+                  (and main
+                       `(,main
+                         ,@(if extra (list extra) '()))))))))))
+
+(define (package->manifest-entry* package output)
+  "Like 'package->manifest-entry', but attach PACKAGE provenance meta-data to
+the resulting manifest entry."
+  (define (provenance-properties package)
+    (match (package-provenance package)
+      (#f   '())
+      (sexp `((provenance ,@sexp)))))
+
+  (package->manifest-entry package output
+                           #:properties (provenance-properties package)))
+
+
 (define (options->installable opts manifest transaction)
   "Given MANIFEST, the current manifest, and OPTS, the result of 'args-fold',
 return an variant of TRANSACTION that accounts for the specified installations
@@ -590,13 +637,13 @@ and upgrades."
                   (('install . (? package? p))
                    ;; When given a package via `-e', install the first of its
                    ;; outputs (XXX).
-                   (package->manifest-entry p "out"))
+                   (package->manifest-entry* p "out"))
                   (('install . (? string? spec))
                    (if (store-path? spec)
                        (store-item->manifest-entry spec)
                        (let-values (((package output)
                                      (specification->package+output spec)))
-                         (package->manifest-entry package output))))
+                         (package->manifest-entry* package output))))
                   (_ #f))
                 opts))
 
diff --git a/guix/scripts/publish.scm b/guix/scripts/publish.scm
index b5dfdab32f..c5326b33da 100644
--- a/guix/scripts/publish.scm
+++ b/guix/scripts/publish.scm
@@ -44,9 +44,9 @@
   #:use-module (guix base64)
   #:use-module (guix config)
   #:use-module (guix derivations)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix pki)
-  #:use-module (guix pk-crypto)
+  #:use-module (gcrypt pk-crypto)
   #:use-module (guix workers)
   #:use-module (guix store)
   #:use-module ((guix serialization) #:select (write-file))
diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index 18c04f05dd..976e054a84 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -48,7 +48,8 @@
   #:use-module (srfi srfi-37)
   #:use-module (ice-9 match)
   #:use-module (ice-9 vlist)
-  #:export (guix-pull))
+  #:export (display-profile-content
+            guix-pull))
 
 
 ;;;
@@ -80,6 +81,8 @@ Download and deploy the latest version of Guix.\n"))
   -l, --list-generations[=PATTERN]
                          list generations matching PATTERN"))
   (display (G_ "
+  -p, --profile=PROFILE  use PROFILE instead of ~/.config/guix/current"))
+  (display (G_ "
       --bootstrap        use the bootstrap Guile to build the new Guix"))
   (newline)
   (show-build-options-help)
@@ -113,6 +116,10 @@ Download and deploy the latest version of Guix.\n"))
                  (lambda (opt name arg result)
                    (alist-cons 'ref `(branch . ,(string-append "origin/" arg))
                                result)))
+         (option '(#\p "profile") #t #f
+                 (lambda (opt name arg result)
+                   (alist-cons 'profile (canonicalize-profile arg)
+                               result)))
          (option '(#\n "dry-run") #f #f
                  (lambda (opt name arg result)
                    (alist-cons 'dry-run? #t (alist-cons 'graft? #f result))))
@@ -152,15 +159,12 @@ Download and deploy the latest version of Guix.\n"))
                                       #:heading (G_ "New in this revision:\n"))))
     (_ #t)))
 
-(define* (build-and-install instances config-dir
+(define* (build-and-install instances profile
                             #:key verbose?)
-  "Build the tool from SOURCE, and install it in CONFIG-DIR."
+  "Build the tool from SOURCE, and install it in PROFILE."
   (define update-profile
     (store-lift build-and-use-profile))
 
-  (define profile
-    (string-append config-dir "/current"))
-
   (mlet %store-monad ((manifest (channel-instances->manifest instances)))
     (mbegin %store-monad
       (update-profile profile manifest)
@@ -414,7 +418,9 @@ Use '~/.config/guix/channels.scm' instead."))
      (let* ((opts     (parse-command-line args %options
                                           (list %default-options)))
             (cache    (string-append (cache-directory) "/pull"))
-            (channels (channel-list opts)))
+            (channels (channel-list opts))
+            (profile  (or (assoc-ref opts 'profile)
+                          (string-append (config-directory) "/current"))))
 
        (cond ((assoc-ref opts 'query)
               (process-query opts))
@@ -456,7 +462,7 @@ Use '~/.config/guix/channels.scm' instead."))
                                          %bootstrap-guile
                                          (canonical-package guile-2.2)))))
                       (run-with-store store
-                        (build-and-install instances (config-directory)
+                        (build-and-install instances profile
                                            #:verbose?
                                            (assoc-ref opts 'verbose?)))))))))))))
 
diff --git a/guix/scripts/refresh.scm b/guix/scripts/refresh.scm
index a8fe993e33..bcc23bd39c 100644
--- a/guix/scripts/refresh.scm
+++ b/guix/scripts/refresh.scm
@@ -23,7 +23,7 @@
 
 (define-module (guix scripts refresh)
   #:use-module (guix ui)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix scripts)
   #:use-module (guix store)
   #:use-module (guix utils)
diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm
index 7634bb37f6..cd300195d8 100755
--- a/guix/scripts/substitute.scm
+++ b/guix/scripts/substitute.scm
@@ -26,11 +26,11 @@
   #:use-module (guix config)
   #:use-module (guix records)
   #:use-module ((guix serialization) #:select (restore-file))
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix base32)
   #:use-module (guix base64)
   #:use-module (guix cache)
-  #:use-module (guix pk-crypto)
+  #:use-module (gcrypt pk-crypto)
   #:use-module (guix pki)
   #:use-module ((guix build utils) #:select (mkdir-p dump-port))
   #:use-module ((guix build download)
diff --git a/guix/self.scm b/guix/self.scm
index c5da6130bb..733c4a2cc9 100644
--- a/guix/self.scm
+++ b/guix/self.scm
@@ -83,8 +83,8 @@ GUILE-VERSION (\"2.0\" or \"2.2\"), or #f if none of the packages matches."
       ("guile-ssh"  (ref '(gnu packages ssh)   'guile-ssh))
       ("guile-git"  (ref '(gnu packages guile) 'guile-git))
       ("guile-sqlite3" (ref '(gnu packages guile) 'guile-sqlite3))
+      ("guile-gcrypt"  (ref '(gnu packages gnupg) 'guile-gcrypt))
       ("gnutls"     (ref '(gnu packages tls) 'gnutls))
-      ("libgcrypt"  (ref '(gnu packages gnupg) 'libgcrypt))
       ("zlib"       (ref '(gnu packages compression) 'zlib))
       ("gzip"       (ref '(gnu packages compression) 'gzip))
       ("bzip2"      (ref '(gnu packages compression) 'bzip2))
@@ -454,7 +454,6 @@ assumed to be part of MODULES."
                         (name (string-append "guix-" version))
                         (guile-version (effective-version))
                         (guile-for-build (guile-for-build guile-version))
-                        (libgcrypt (specification->package "libgcrypt"))
                         (zlib (specification->package "zlib"))
                         (gzip (specification->package "gzip"))
                         (bzip2 (specification->package "bzip2"))
@@ -481,6 +480,10 @@ assumed to be part of MODULES."
                        "guile-sqlite3"
                        "guile2.0-sqlite3"))
 
+  (define guile-gcrypt
+    (package-for-guile guile-version
+                       "guile-gcrypt"))
+
   (define gnutls
     (package-for-guile guile-version
                        "gnutls" "guile2.0-gnutls"))
@@ -489,7 +492,7 @@ assumed to be part of MODULES."
     (match (append-map (lambda (package)
                          (cons (list "x" package)
                                (package-transitive-propagated-inputs package)))
-                       (list gnutls guile-git guile-json
+                       (list guile-gcrypt gnutls guile-git guile-json
                              guile-ssh guile-sqlite3))
       (((labels packages _ ...) ...)
        packages)))
@@ -513,10 +516,7 @@ assumed to be part of MODULES."
                  ;; rebuilt when the version changes, which in turn means we
                  ;; can have substitutes for it.
                  #:extra-modules
-                 `(((guix config)
-                    => ,(make-config.scm #:libgcrypt
-                                         (specification->package
-                                          "libgcrypt"))))
+                 `(((guix config) => ,(make-config.scm)))
 
                  ;; (guix man-db) is needed at build-time by (guix profiles)
                  ;; but we don't need to compile it; not compiling it allows
@@ -526,6 +526,7 @@ assumed to be part of MODULES."
                    ("guix/store/schema.sql"
                     ,(local-file "../guix/store/schema.sql")))
 
+                 #:extensions (list guile-gcrypt)
                  #:guile-for-build guile-for-build))
 
   (define *extra-modules*
@@ -600,8 +601,7 @@ assumed to be part of MODULES."
                  '()
                  #:extra-modules
                  `(((guix config)
-                    => ,(make-config.scm #:libgcrypt libgcrypt
-                                         #:zlib zlib
+                    => ,(make-config.scm #:zlib zlib
                                          #:gzip gzip
                                          #:bzip2 bzip2
                                          #:xz xz
@@ -684,7 +684,7 @@ assumed to be part of MODULES."
 
 (define %dependency-variables
   ;; (guix config) variables corresponding to dependencies.
-  '(%libgcrypt %libz %xz %gzip %bzip2))
+  '(%libz %xz %gzip %bzip2))
 
 (define %persona-variables
   ;; (guix config) variables that define Guix's persona.
@@ -703,7 +703,7 @@ assumed to be part of MODULES."
                                       (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")
@@ -723,7 +723,6 @@ assumed to be part of MODULES."
                                %state-directory
                                %store-database-directory
                                %config-directory
-                               %libgcrypt
                                %libz
                                %gzip
                                %bzip2
@@ -766,9 +765,6 @@ assumed to be part of MODULES."
                    (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"))))
diff --git a/guix/store.scm b/guix/store.scm
index f41a1e2690..af7f6980cf 100644
--- a/guix/store.scm
+++ b/guix/store.scm
@@ -25,7 +25,7 @@
   #:use-module (guix monads)
   #:use-module (guix base16)
   #:use-module (guix base32)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix profiling)
   #:autoload   (guix build syscalls) (terminal-columns)
   #:use-module (rnrs bytevectors)
diff --git a/guix/store/deduplication.scm b/guix/store/deduplication.scm
index 8c19d7309e..53810c680f 100644
--- a/guix/store/deduplication.scm
+++ b/guix/store/deduplication.scm
@@ -21,7 +21,7 @@
 ;;; timestamps, deduplicating, etc.
 
 (define-module (guix store deduplication)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix build utils)
   #:use-module (guix base16)
   #:use-module (srfi srfi-11)
diff --git a/guix/tests.scm b/guix/tests.scm
index 34e3e0fc2a..06e9f8da0b 100644
--- a/guix/tests.scm
+++ b/guix/tests.scm
@@ -22,7 +22,7 @@
   #:use-module (guix packages)
   #:use-module (guix base32)
   #:use-module (guix serialization)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages bootstrap)
   #:use-module (srfi srfi-34)
diff --git a/m4/guix.m4 b/m4/guix.m4
index a6897be961..da3c65f8f7 100644
--- a/m4/guix.m4
+++ b/m4/guix.m4
@@ -18,24 +18,6 @@ dnl
 dnl You should have received a copy of the GNU General Public License
 dnl along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
-dnl GUIX_ASSERT_LIBGCRYPT_USABLE
-dnl
-dnl Assert that GNU libgcrypt is usable from Guile.
-AC_DEFUN([GUIX_ASSERT_LIBGCRYPT_USABLE],
-  [AC_CACHE_CHECK([whether $LIBGCRYPT can be dynamically loaded],
-    [guix_cv_libgcrypt_usable_p],
-    [GUILE_CHECK([retval],
-      [(dynamic-func \"gcry_md_hash_buffer\" (dynamic-link \"$LIBGCRYPT\"))])
-     if test "$retval" = 0; then
-       guix_cv_libgcrypt_usable_p="yes"
-     else
-       guix_cv_libgcrypt_usable_p="no"
-     fi])
-
-   if test "x$guix_cv_libgcrypt_usable_p" != "xyes"; then
-     AC_MSG_ERROR([GNU libgcrypt does not appear to be usable; see `--with-libgcrypt-prefix' and `README'.])
-   fi])
-
 dnl GUIX_SYSTEM_TYPE
 dnl
 dnl Determine the Guix host system type, and store it in the
diff --git a/po/guix/POTFILES.in b/po/guix/POTFILES.in
index 7f881355e7..2762ea078a 100644
--- a/po/guix/POTFILES.in
+++ b/po/guix/POTFILES.in
@@ -31,6 +31,7 @@ guix/scripts/challenge.scm
 guix/scripts/copy.scm
 guix/scripts/pack.scm
 guix/scripts/weather.scm
+guix/scripts/describe.scm
 guix/gnu-maintenance.scm
 guix/scripts/container.scm
 guix/scripts/container/exec.scm
diff --git a/tests/base32.scm b/tests/base32.scm
index 194f8da96b..134e578633 100644
--- a/tests/base32.scm
+++ b/tests/base32.scm
@@ -17,7 +17,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (test-base32)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix base32)
   #:use-module (guix utils)
   #:use-module (srfi srfi-1)
diff --git a/tests/builders.scm b/tests/builders.scm
index bb9e0fa85b..8b8ef013e7 100644
--- a/tests/builders.scm
+++ b/tests/builders.scm
@@ -25,7 +25,7 @@
   #:use-module (guix utils)
   #:use-module (guix base32)
   #:use-module (guix derivations)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix tests)
   #:use-module ((guix packages)
                 #:select (package-derivation package-native-search-paths))
diff --git a/tests/challenge.scm b/tests/challenge.scm
index 387d205a64..4b13ec278e 100644
--- a/tests/challenge.scm
+++ b/tests/challenge.scm
@@ -18,7 +18,7 @@
 
 (define-module (test-challenge)
   #:use-module (guix tests)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix store)
   #:use-module (guix monads)
   #:use-module (guix derivations)
diff --git a/tests/cpan.scm b/tests/cpan.scm
index 396744e529..189dd027e6 100644
--- a/tests/cpan.scm
+++ b/tests/cpan.scm
@@ -20,7 +20,7 @@
 (define-module (test-cpan)
   #:use-module (guix import cpan)
   #:use-module (guix base32)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix tests)
   #:use-module (guix grafts)
   #:use-module (srfi srfi-64)
diff --git a/tests/crate.scm b/tests/crate.scm
index eb93822bbb..a1dcfd5e52 100644
--- a/tests/crate.scm
+++ b/tests/crate.scm
@@ -21,7 +21,7 @@
   #:use-module (guix import crate)
   #:use-module (guix base32)
   #:use-module (guix build-system cargo)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix tests)
   #:use-module (ice-9 iconv)
   #:use-module (ice-9 match)
diff --git a/tests/derivations.scm b/tests/derivations.scm
index 5d83529183..159a6971b3 100644
--- a/tests/derivations.scm
+++ b/tests/derivations.scm
@@ -23,7 +23,7 @@
   #:use-module (guix grafts)
   #:use-module (guix store)
   #:use-module (guix utils)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix base32)
   #:use-module (guix tests)
   #:use-module (guix tests http)
diff --git a/tests/gem.scm b/tests/gem.scm
index 4220170ff0..a12edb294c 100644
--- a/tests/gem.scm
+++ b/tests/gem.scm
@@ -21,7 +21,7 @@
 (define-module (test-gem)
   #:use-module (guix import gem)
   #:use-module (guix base32)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix tests)
   #:use-module ((guix build utils) #:select (delete-file-recursively))
   #:use-module (srfi srfi-41)
diff --git a/tests/gexp.scm b/tests/gexp.scm
index a0ed34aa6d..380b83509a 100644
--- a/tests/gexp.scm
+++ b/tests/gexp.scm
@@ -1093,6 +1093,24 @@
                                (call-with-input-file out get-string-all))
                      (equal? refs (list guile))))))))
 
+(test-assertm "file-union"
+  (mlet* %store-monad ((union -> (file-union "union"
+                                             `(("a" ,(plain-file "a" "1"))
+                                               ("b/c/d" ,(plain-file "d" "2"))
+                                               ("e" ,(plain-file "e" "3")))))
+                       (drv      (lower-object union))
+                       (out ->   (derivation->output-path drv)))
+    (define (contents=? file str)
+      (string=? (call-with-input-file (string-append out "/" file)
+                  get-string-all)
+                str))
+
+    (mbegin %store-monad
+      (built-derivations (list drv))
+      (return (and (contents=? "a" "1")
+                   (contents=? "b/c/d" "2")
+                   (contents=? "e" "3"))))))
+
 (test-assert "gexp->derivation vs. %current-target-system"
   (let ((mval (gexp->derivation "foo"
                                 #~(begin
diff --git a/tests/guix-describe.sh b/tests/guix-describe.sh
new file mode 100644
index 0000000000..af523f0a0b
--- /dev/null
+++ b/tests/guix-describe.sh
@@ -0,0 +1,47 @@
+# GNU Guix --- Functional package management for GNU
+# Copyright © 2018 Ludovic Courtès <ludo@gnu.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/>.
+
+#
+# Test 'guix describe'.
+#
+
+guix describe --version
+
+tmpfile="t-guix-describe-$$"
+trap "rm -f $tmpfile" EXIT
+rm -f "$tmpfile"
+
+if [ -d "$abs_top_srcdir/.git" ]
+then
+    # Since we're in a Git checkout, we can at least check that these things
+    # work.
+    guix describe | grep -i "checkout"
+    if git --version > /dev/null 2>&1
+    then
+	result="`guix describe | grep commit: | cut -d : -f 2-`"
+	commit="`git log | head -1 | cut -c 7-`"
+	test "x$result" = "x$commit"
+    fi
+    guix describe -f channels
+    case "`guix describe -f channels | grep url`" in
+	*"(url \"$abs_top_srcdir\")") true;;
+	*) false;;
+    esac
+else
+    exit 77
+fi
diff --git a/tests/guix-system.sh b/tests/guix-system.sh
index 36ba5fbd5f..a129efdfcb 100644
--- a/tests/guix-system.sh
+++ b/tests/guix-system.sh
@@ -232,6 +232,14 @@ guix system build "$tmpfile" -d | grep '\.drv$'
 guix system vm "$tmpfile" -d	      # succeeds
 guix system vm "$tmpfile" -d | grep '\.drv$'
 
+# Make sure the behavior is deterministic (<https://bugs.gnu.org/32652>).
+drv1="`guix system vm "$tmpfile" -d`"
+drv2="`guix system vm "$tmpfile" -d`"
+test "$drv1" = "$drv2"
+drv1="`guix system disk-image --file-system-type=iso9660 "$tmpfile" -d`"
+drv2="`guix system disk-image --file-system-type=iso9660 "$tmpfile" -d`"
+test "$drv1" = "$drv2"
+
 make_user_config "group-that-does-not-exist" "users"
 if guix system build "$tmpfile" -n 2> "$errorfile"
 then false
diff --git a/tests/hash.scm b/tests/hash.scm
deleted file mode 100644
index 47dff3915b..0000000000
--- a/tests/hash.scm
+++ /dev/null
@@ -1,128 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2017, 2018 Ludovic Courtès <ludo@gnu.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 (test-hash)
-  #:use-module (guix hash)
-  #:use-module (guix base16)
-  #:use-module (srfi srfi-1)
-  #:use-module (srfi srfi-11)
-  #:use-module (srfi srfi-64)
-  #:use-module (rnrs bytevectors)
-  #:use-module (rnrs io ports))
-
-;; Test the (guix hash) module.
-
-(define %empty-sha256
-  ;; SHA256 hash of the empty string.
-  (base16-string->bytevector
-   "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"))
-
-(define %hello-sha256
-  ;; SHA256 hash of "hello world"
-  (base16-string->bytevector
-   "b94d27b9934d3e08a52e52d7da7dabfac484efe37a5380ee9088f7ace2efcde9"))
-
-
-(test-begin "hash")
-
-(test-equal "sha1, empty"
-  (base16-string->bytevector "da39a3ee5e6b4b0d3255bfef95601890afd80709")
-  (sha1 #vu8()))
-
-(test-equal "sha1, hello"
-  (base16-string->bytevector "2aae6c35c94fcfb415dbe95f408b9ce91ee846ed")
-  (sha1 (string->utf8 "hello world")))
-
-(test-equal "sha256, empty"
-  %empty-sha256
-  (sha256 #vu8()))
-
-(test-equal "sha256, hello"
-  %hello-sha256
-  (sha256 (string->utf8 "hello world")))
-
-(test-equal "open-sha256-port, empty"
-  %empty-sha256
-  (let-values (((port get)
-                (open-sha256-port)))
-    (close-port port)
-    (get)))
-
-(test-equal "open-sha256-port, hello"
-  (list %hello-sha256 (string-length "hello world"))
-  (let-values (((port get)
-                (open-sha256-port)))
-    (put-bytevector port (string->utf8 "hello world"))
-    (force-output port)
-    (list (get) (port-position port))))
-
-(test-assert "port-sha256"
-  (let* ((file     (search-path %load-path "ice-9/psyntax.scm"))
-         (size     (stat:size (stat file)))
-         (contents (call-with-input-file file get-bytevector-all)))
-    (equal? (sha256 contents)
-            (call-with-input-file file port-sha256))))
-
-(test-equal "open-sha256-input-port, empty"
-  `("" ,%empty-sha256)
-  (let-values (((port get)
-                (open-sha256-input-port (open-string-input-port ""))))
-    (let ((str (get-string-all port)))
-      (list str (get)))))
-
-(test-equal "open-sha256-input-port, hello"
-  `("hello world" ,%hello-sha256)
-  (let-values (((port get)
-                (open-sha256-input-port
-                 (open-bytevector-input-port
-                  (string->utf8 "hello world")))))
-    (let ((str (get-string-all port)))
-      (list str (get)))))
-
-(test-equal "open-sha256-input-port, hello, one two"
-  (list (string->utf8 "hel") (string->utf8 "lo")
-        (base16-string->bytevector                ; echo -n hello | sha256sum
-         "2cf24dba5fb0a30e26e83b2ac5b9e29e1b161e5c1fa7425e73043362938b9824")
-        " world")
-  (let-values (((port get)
-                (open-sha256-input-port
-                 (open-bytevector-input-port (string->utf8 "hello world")))))
-    (let* ((one   (get-bytevector-n port 3))
-           (two   (get-bytevector-n port 2))
-           (hash  (get))
-           (three (get-string-all port)))
-      (list one two hash three))))
-
-(test-equal "open-sha256-input-port, hello, read from wrapped port"
-  (list (string->utf8 "hello")
-        (base16-string->bytevector                ; echo -n hello | sha256sum
-         "2cf24dba5fb0a30e26e83b2ac5b9e29e1b161e5c1fa7425e73043362938b9824")
-        " world")
-  (let*-values (((wrapped)
-                 (open-bytevector-input-port (string->utf8 "hello world")))
-                ((port get)
-                 (open-sha256-input-port wrapped)))
-    (let* ((hello (get-bytevector-n port 5))
-           (hash  (get))
-
-           ;; Now read from WRAPPED to make sure its current position is
-           ;; correct.
-           (world (get-string-all wrapped)))
-      (list hello hash world))))
-
-(test-end)
diff --git a/tests/inferior.scm b/tests/inferior.scm
index 5e0f8ae66e..ff5cad4210 100644
--- a/tests/inferior.scm
+++ b/tests/inferior.scm
@@ -45,9 +45,11 @@
 
 (test-equal "inferior-packages"
   (take (sort (fold-packages (lambda (package lst)
-                               (alist-cons (package-name package)
+                               (cons (list (package-name package)
                                            (package-version package)
-                                           lst))
+                                           (package-home-page package)
+                                           (package-location package))
+                                     lst))
                              '())
               (lambda (x y)
                 (string<? (car x) (car y))))
@@ -56,14 +58,18 @@
                                   #:command "scripts/guix"))
          (packages (inferior-packages inferior)))
     (and (every string? (map inferior-package-synopsis packages))
-         (begin
+         (let ()
+           (define result
+             (take (sort (map (lambda (package)
+                                (list (inferior-package-name package)
+                                      (inferior-package-version package)
+                                      (inferior-package-home-page package)
+                                      (inferior-package-location package)))
+                              packages)
+                         (lambda (x y)
+                           (string<? (car x) (car y))))
+                   10))
            (close-inferior inferior)
-           (take (sort (map (lambda (package)
-                              (cons (inferior-package-name package)
-                                    (inferior-package-version package)))
-                            packages)
-                       (lambda (x y)
-                         (string<? (car x) (car y))))
-                 10)))))
+           result))))
 
 (test-end "inferior")
diff --git a/tests/nar.scm b/tests/nar.scm
index 9b5fb984b4..d610ea53f7 100644
--- a/tests/nar.scm
+++ b/tests/nar.scm
@@ -21,7 +21,7 @@
   #:use-module (guix nar)
   #:use-module (guix serialization)
   #:use-module (guix store)
-  #:use-module ((guix hash)
+  #:use-module ((gcrypt hash)
                 #:select (open-sha256-port open-sha256-input-port))
   #:use-module ((guix packages)
                 #:select (base32))
diff --git a/tests/opam.scm b/tests/opam.scm
index 26832174a8..a1320abfdc 100644
--- a/tests/opam.scm
+++ b/tests/opam.scm
@@ -19,7 +19,7 @@
 (define-module (test-opam)
   #:use-module (guix import opam)
   #:use-module (guix base32)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix tests)
   #:use-module ((guix build utils) #:select (delete-file-recursively mkdir-p which))
   #:use-module (srfi srfi-64)
diff --git a/tests/packages.scm b/tests/packages.scm
index 65ccb14889..237feb7aba 100644
--- a/tests/packages.scm
+++ b/tests/packages.scm
@@ -28,7 +28,7 @@
                 #:renamer (lambda (name)
                             (cond ((eq? name 'location) 'make-location)
                                   (else name))))
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix derivations)
   #:use-module (guix packages)
   #:use-module (guix grafts)
diff --git a/tests/pk-crypto.scm b/tests/pk-crypto.scm
deleted file mode 100644
index fe33a6f7b5..0000000000
--- a/tests/pk-crypto.scm
+++ /dev/null
@@ -1,290 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2017 Ludovic Courtès <ludo@gnu.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 (test-pk-crypto)
-  #:use-module (guix pk-crypto)
-  #:use-module (guix utils)
-  #:use-module (guix base16)
-  #:use-module (guix hash)
-  #:use-module (srfi srfi-1)
-  #:use-module (srfi srfi-11)
-  #:use-module (srfi srfi-26)
-  #:use-module (srfi srfi-64)
-  #:use-module (rnrs bytevectors)
-  #:use-module (rnrs io ports)
-  #:use-module (ice-9 match))
-
-;; Test the (guix pk-crypto) module.
-
-(define %key-pair
-  ;; RSA key pair that was generated with:
-  ;;   (generate-key (string->canonical-sexp "(genkey (rsa (nbits 4:1024)))"))
-  ;; which takes a bit of time.
-  "(key-data
-    (public-key
-     (rsa
-      (n #00C1F764069F54FFE93A126B02328903E984E4AE3AF6DF402B5B6B3907911B88C385F1BA76A002EC9DEA109A5228EF0E62EE31A06D1A5861CAB474F6C857AC66EB65A1905F25BBA1869579E73A3B7FED13AF5A1667326F88CDFC2FF24B03C14FD1384AA7E73CA89572880B606E3A974E15347963FC7B6378574936A47580DBCB45#)
-      (e #010001#)))
-    (private-key
-     (rsa
-      (n #00C1F764069F54FFE93A126B02328903E984E4AE3AF6DF402B5B6B3907911B88C385F1BA76A002EC9DEA109A5228EF0E62EE31A06D1A5861CAB474F6C857AC66EB65A1905F25BBA1869579E73A3B7FED13AF5A1667326F88CDFC2FF24B03C14FD1384AA7E73CA89572880B606E3A974E15347963FC7B6378574936A47580DBCB45#)
-      (e #010001#)
-      (d #58CAD84653D0046A8EC3F9AA82D9C829B145422109FC3F12DA01A694B92FA296E70D366FB166454D30E632CEE3A033B4C41781BA10325F69FCDC0250CA19C8EEB352FA085992494098DB133E682ED38A931701F0DED1A1E508F4341A4FB446A04F019427C7CB3C44F251EEA9D386100DA80F125E0FD5CE1B0DFEC6D21516EACD#)
-      (p #00D47F185147EC39393CCDA4E7323FFC20FC8B8073E2A54DD63BA392A66975E4204CA48572496A9DFD7522436B852C07472A5AB25B7706F7C14E6F33FBC420FF3B#)
-      (q #00E9AD22F158060BC9AE3601DA623AFC60FFF3058795802CA92371C00097335CF9A23D7782DE353C9DBA93D7BB99E6A24A411107605E722481C5C191F80D7EB77F#)
-      (u #59B45B95AE01A7A7370FAFDB08FE73A4793CE37F228961B09B1B1E7DDAD9F8D3E28F5C5E8B4B067E6B8E0BBF3F690B42991A79E46108DDCDA2514323A66964DE#))))")
-
-(define %ecc-key-pair
-  ;; Ed25519 key pair generated with:
-  ;;   (generate-key (string->canonical-sexp "(genkey (ecdsa (curve Ed25519) (flags rfc6979 transient)))"))
-  "(key-data
-      (public-key
-        (ecc
-          (curve Ed25519)
-          (q #94869C1B9E69DB8DD910B7F7F4D6E56A63A964A59AE8F90F6703ACDDF6F50C81#)))
-      (private-key
-        (ecc
-          (curve Ed25519)
-          (q #94869C1B9E69DB8DD910B7F7F4D6E56A63A964A59AE8F90F6703ACDDF6F50C81#)
-          (d #6EFB32D0B4EC6B3237B523539F1979379B82726AAA605EB2FBA6775B2B777B78#))))")
-
-(test-begin "pk-crypto")
-
-(test-assert "version"
-  (gcrypt-version))
-
-(let ((sexps '("(foo bar)"
-
-               ;; In Libgcrypt 1.5.3 the following integer is rendered as
-               ;; binary, whereas in 1.6.0 it's rendered as is (hexadecimal.)
-               ;;"#C0FFEE#"
-
-               "(genkey \n (rsa \n  (nbits \"1024\")\n  )\n )")))
-  (test-equal "string->canonical-sexp->string"
-    sexps
-    (let ((sexps (map string->canonical-sexp sexps)))
-      (and (every canonical-sexp? sexps)
-           (map (compose string-trim-both canonical-sexp->string) sexps)))))
-
-(gc)                                              ; stress test!
-
-(let ((sexps `(("(foo bar)" foo -> "(foo bar)")
-               ("(foo (bar (baz 3:123)))" baz -> "(baz \"123\")")
-               ("(foo (bar 3:123))" baz -> #f))))
-  (test-equal "find-sexp-token"
-    (map (match-lambda
-          ((_ _ '-> expected)
-           expected))
-         sexps)
-    (map (match-lambda
-          ((input token '-> _)
-           (let ((sexp (find-sexp-token (string->canonical-sexp input) token)))
-             (and sexp
-                  (string-trim-both (canonical-sexp->string sexp))))))
-         sexps)))
-
-(gc)
-
-(test-equal "canonical-sexp-length"
-  '(0 1 2 4 0 0)
-  (map (compose canonical-sexp-length string->canonical-sexp)
-       '("()" "(a)" "(a b)" "(a #616263# b #C001#)" "a" "#123456#")))
-
-(test-equal "canonical-sexp-list?"
-  '(#t #f #t #f)
-  (map (compose canonical-sexp-list? string->canonical-sexp)
-       '("()" "\"abc\"" "(a b c)" "#123456#")))
-
-(gc)
-
-(test-equal "canonical-sexp-car + cdr"
-  '("(b \n (c xyz)\n )")
-  (let ((lst (string->canonical-sexp "(a (b (c xyz)))")))
-    (map (lambda (sexp)
-           (and sexp (string-trim-both (canonical-sexp->string sexp))))
-         ;; Note: 'car' returns #f when the first element is an atom.
-         (list (canonical-sexp-car (canonical-sexp-cdr lst))))))
-
-(gc)
-
-(test-equal "canonical-sexp-nth"
-  '("(b pqr)" "(c \"456\")" "(d xyz)" #f #f)
-
-  (let ((lst (string->canonical-sexp "(a (b 3:pqr) (c 3:456) (d 3:xyz))")))
-    ;; XXX: In Libgcrypt 1.5.3, (canonical-sexp-nth lst 0) returns LST, whereas in
-    ;; 1.6.0 it returns #f.
-    (map (lambda (sexp)
-           (and sexp (string-trim-both (canonical-sexp->string sexp))))
-         (unfold (cut > <> 5)
-                 (cut canonical-sexp-nth lst <>)
-                 1+
-                 1))))
-
-(gc)
-
-(test-equal "canonical-sexp-nth-data"
-  `(Name Otto Meier #f ,(base16-string->bytevector "123456") #f)
-  (let ((lst (string->canonical-sexp
-              "(Name Otto Meier (address Burgplatz) #123456#)")))
-    (unfold (cut > <> 5)
-            (cut canonical-sexp-nth-data lst <>)
-            1+
-            0)))
-
-(let ((bv (base16-string->bytevector
-           "5eff0b55c9c5f5e87b4e34cd60a2d5654ca1eb78c7b3c67c3179fed1cff07b4c")))
-  (test-equal "hash corrupt due to restrictive locale encoding"
-    bv
-
-    ;; In Guix up to 0.6 included this test would fail because at some point
-    ;; the hash value would be cropped to ASCII.  In practice 'guix
-    ;; authenticate' would produce invalid signatures that would fail
-    ;; signature verification.  See <http://bugs.gnu.org/17312>.
-    (let ((locale (setlocale LC_ALL)))
-     (dynamic-wind
-       (lambda ()
-         (setlocale LC_ALL "C"))
-       (lambda ()
-         (hash-data->bytevector
-          (string->canonical-sexp
-           (canonical-sexp->string
-            (bytevector->hash-data bv "sha256")))))
-       (lambda ()
-         (setlocale LC_ALL locale))))))
-
-(gc)
-
-;; XXX: The test below is typically too long as it needs to gather enough entropy.
-
-;; (test-assert "generate-key"
-;;   (let ((key (generate-key (string->canonical-sexp
-;;                             "(genkey (rsa (nbits 3:128)))"))))
-;;     (and (canonical-sexp? key)
-;;          (find-sexp-token key 'key-data)
-;;          (find-sexp-token key 'public-key)
-;;          (find-sexp-token key 'private-key))))
-
-(test-assert "bytevector->hash-data->bytevector"
-  (let* ((bv   (sha256 (string->utf8 "Hello, world.")))
-         (data (bytevector->hash-data bv "sha256")))
-    (and (canonical-sexp? data)
-         (let-values (((value algo) (hash-data->bytevector data)))
-           (and (string=? algo "sha256")
-                (bytevector=? value bv))))))
-
-(test-equal "key-type"
-  '(rsa ecc)
-  (map (compose key-type
-                (cut find-sexp-token <> 'public-key)
-                string->canonical-sexp)
-       (list %key-pair %ecc-key-pair)))
-
-(test-assert "sign + verify"
-  (let* ((pair   (string->canonical-sexp %key-pair))
-         (secret (find-sexp-token pair 'private-key))
-         (public (find-sexp-token pair 'public-key))
-         (data   (bytevector->hash-data
-                  (sha256 (string->utf8 "Hello, world."))
-                  #:key-type (key-type public)))
-         (sig    (sign data secret)))
-    (and (verify sig data public)
-         (not (verify sig
-                      (bytevector->hash-data
-                       (sha256 (string->utf8 "Hi!"))
-                       #:key-type (key-type public))
-                      public)))))
-
-;; Ed25519 appeared in libgcrypt 1.6.0.
-(test-skip (if (version>? (gcrypt-version) "1.6.0") 0 1))
-(test-assert "sign + verify, Ed25519"
-  (let* ((pair   (string->canonical-sexp %ecc-key-pair))
-         (secret (find-sexp-token pair 'private-key))
-         (public (find-sexp-token pair 'public-key))
-         (data   (bytevector->hash-data
-                  (sha256 (string->utf8 "Hello, world."))))
-         (sig    (sign data secret)))
-    (and (verify sig data public)
-         (not (verify sig
-                      (bytevector->hash-data
-                       (sha256 (string->utf8 "Hi!")))
-                      public)))))
-
-(gc)
-
-(test-equal "canonical-sexp->sexp"
-  `((data
-     (flags pkcs1)
-     (hash sha256
-           ,(base16-string->bytevector
-             "2749f0ea9f26c6c7be746a9cff8fa4c2f2a02b000070dba78429e9a11f87c6eb")))
-
-    (public-key
-     (rsa
-      (n ,(base16-string->bytevector
-           (string-downcase
-            "00C1F764069F54FFE93A126B02328903E984E4AE3AF6DF402B5B6B3907911B88C385F1BA76A002EC9DEA109A5228EF0E62EE31A06D1A5861CAB474F6C857AC66EB65A1905F25BBA1869579E73A3B7FED13AF5A1667326F88CDFC2FF24B03C14FD1384AA7E73CA89572880B606E3A974E15347963FC7B6378574936A47580DBCB45")))
-      (e ,(base16-string->bytevector
-           "010001")))))
-
-  (list (canonical-sexp->sexp
-         (string->canonical-sexp
-          "(data
-             (flags pkcs1)
-             (hash \"sha256\"
-                   #2749f0ea9f26c6c7be746a9cff8fa4c2f2a02b000070dba78429e9a11f87c6eb#))"))
-
-        (canonical-sexp->sexp
-         (find-sexp-token (string->canonical-sexp %key-pair)
-                          'public-key))))
-
-
-(let ((lst
-       `((data
-          (flags pkcs1)
-          (hash sha256
-                ,(base16-string->bytevector
-                  "2749f0ea9f26c6c7be746a9cff8fa4c2f2a02b000070dba78429e9a11f87c6eb")))
-
-         (public-key
-          (rsa
-           (n ,(base16-string->bytevector
-                (string-downcase
-                 "00C1F764069F54FFE93A126B02328903E984E4AE3AF6DF402B5B6B3907911B88C385F1BA76A002EC9DEA109A5228EF0E62EE31A06D1A5861CAB474F6C857AC66EB65A1905F25BBA1869579E73A3B7FED13AF5A1667326F88CDFC2FF24B03C14FD1384AA7E73CA89572880B606E3A974E15347963FC7B6378574936A47580DBCB45")))
-           (e ,(base16-string->bytevector
-                "010001"))))
-
-         ,(base16-string->bytevector
-           "2749f0ea9f26c6c7be746a9cff8fa4c2f2a02b000070dba78429e9a11f87c6eb"))))
-  (test-equal "sexp->canonical-sexp->sexp"
-    lst
-    (map (compose canonical-sexp->sexp sexp->canonical-sexp)
-         lst)))
-
-(let ((sexp `(signature
-              (public-key
-               (rsa
-                (n ,(make-bytevector 1024 1))
-                (e ,(base16-string->bytevector "010001")))))))
-  (test-equal "https://bugs.g10code.com/gnupg/issue1594"
-    ;; The gcrypt bug above was primarily affecting our uses in
-    ;; 'canonical-sexp->sexp', typically when applied to a signature sexp (in
-    ;; 'guix authenticate -verify') with a "big" RSA key, such as 4096 bits.
-    sexp
-    (canonical-sexp->sexp (sexp->canonical-sexp sexp))))
-
-(test-end)
diff --git a/tests/pki.scm b/tests/pki.scm
index 876ad98d73..d6a6b476c7 100644
--- a/tests/pki.scm
+++ b/tests/pki.scm
@@ -18,8 +18,8 @@
 
 (define-module (test-pki)
   #:use-module (guix pki)
-  #:use-module (guix pk-crypto)
-  #:use-module (guix hash)
+  #:use-module (gcrypt pk-crypto)
+  #:use-module (gcrypt hash)
   #:use-module (rnrs io ports)
   #:use-module (srfi srfi-64))
 
diff --git a/tests/publish.scm b/tests/publish.scm
index 1ed8308076..0e793c1ee5 100644
--- a/tests/publish.scm
+++ b/tests/publish.scm
@@ -25,7 +25,7 @@
   #:use-module (guix tests)
   #:use-module (guix config)
   #:use-module (guix utils)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix store)
   #:use-module (guix derivations)
   #:use-module (guix gexp)
@@ -33,7 +33,7 @@
   #:use-module (guix base64)
   #:use-module ((guix records) #:select (recutils->alist))
   #:use-module ((guix serialization) #:select (restore-file))
-  #:use-module (guix pk-crypto)
+  #:use-module (gcrypt pk-crypto)
   #:use-module ((guix pki) #:select (%public-key-file %private-key-file))
   #:use-module (guix zlib)
   #:use-module (web uri)
diff --git a/tests/pypi.scm b/tests/pypi.scm
index 310c6c8f29..616ec191f5 100644
--- a/tests/pypi.scm
+++ b/tests/pypi.scm
@@ -20,7 +20,7 @@
 (define-module (test-pypi)
   #:use-module (guix import pypi)
   #:use-module (guix base32)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix tests)
   #:use-module (guix build-system python)
   #:use-module ((guix build utils) #:select (delete-file-recursively which))
diff --git a/tests/services.scm b/tests/services.scm
index b146a0dec2..1ad577e601 100644
--- a/tests/services.scm
+++ b/tests/services.scm
@@ -138,6 +138,31 @@
          (equal? (list s1 s2)
                  (instantiate-missing-services (list s1 s2))))))
 
+(test-assert "instantiate-missing-services, indirect"
+  (let* ((t1 (service-type (name 't1) (extensions '())
+                           (default-value 'dflt)
+                           (compose concatenate)
+                           (extend cons)))
+         (t2 (service-type (name 't2) (extensions '())
+                           (default-value 'dflt2)
+                           (compose concatenate)
+                           (extend cons)
+                           (extensions
+                            (list (service-extension t1 list)))))
+         (t3 (service-type (name 't3)
+                           (extensions
+                            (list (service-extension t2 list)))))
+         (s1 (service t1))
+         (s2 (service t2))
+         (s3 (service t3 42))
+         (== (cut lset= equal? <...>)))
+    (and (== (list s1 s2 s3)
+             (instantiate-missing-services (list s3)))
+         (== (list s1 s2 s3)
+             (instantiate-missing-services (list s1 s3)))
+         (== (list s1 s2 s3)
+             (instantiate-missing-services (list s2 s3))))))
+
 (test-assert "instantiate-missing-services, no default value"
   (let* ((t1 (service-type (name 't1) (extensions '())))
          (t2 (service-type (name 't2)
diff --git a/tests/store-deduplication.scm b/tests/store-deduplication.scm
index 4ca2ec0f61..e438aa84c6 100644
--- a/tests/store-deduplication.scm
+++ b/tests/store-deduplication.scm
@@ -19,7 +19,7 @@
 (define-module (test-store-deduplication)
   #:use-module (guix tests)
   #:use-module (guix store deduplication)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module ((guix utils) #:select (call-with-temporary-directory))
   #:use-module (guix build utils)
   #:use-module (rnrs bytevectors)
diff --git a/tests/store.scm b/tests/store.scm
index 47fab0df18..2858369706 100644
--- a/tests/store.scm
+++ b/tests/store.scm
@@ -21,7 +21,7 @@
   #:use-module (guix store)
   #:use-module (guix utils)
   #:use-module (guix monads)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix base32)
   #:use-module (guix packages)
   #:use-module (guix derivations)
@@ -45,6 +45,9 @@
 (define %store
   (open-connection-for-tests))
 
+(define %shell
+  (or (getenv "SHELL") (getenv "CONFIG_SHELL")))
+
 
 (test-begin "store")
 
@@ -220,7 +223,8 @@
     ("./foo/c" directory #t)
     ("./foo/c/p" regular "file p")
     ("./foo/c/q" directory #t)
-    ("./foo/c/q/x" regular "#!/bin/sh\nexit 42")
+    ("./foo/c/q/x" regular
+     ,(string-append "#!" %shell "\nexit 42"))
     ("./foo/c/q/y" symlink "..")
     ("./foo/c/q/z" directory #t))
   (let* ((tree  `("file-tree" directory
@@ -231,7 +235,7 @@
                     ("p" regular (data ,(string->utf8 "file p")))
                     ("q" directory
                      ("x" executable
-                      (data "#!/bin/sh\nexit 42"))
+                      (data ,(string-append "#!" %shell "\nexit 42")))
                      ("y" symlink "..")
                      ("z" directory))))
                   ("bar" directory)))
diff --git a/tests/substitute.scm b/tests/substitute.scm
index 0ad6247954..964a57f30b 100644
--- a/tests/substitute.scm
+++ b/tests/substitute.scm
@@ -20,9 +20,9 @@
 (define-module (test-substitute)
   #:use-module (guix scripts substitute)
   #:use-module (guix base64)
-  #:use-module (guix hash)
+  #:use-module (gcrypt hash)
   #:use-module (guix serialization)
-  #:use-module (guix pk-crypto)
+  #:use-module (gcrypt pk-crypto)
   #:use-module (guix pki)
   #:use-module (guix config)
   #:use-module (guix base32)