gx-download (DRAFT)

.dir-locals.el

@@ -45,7 +45,6 @@
    (eval . (put 'manifest-pattern 'scheme-indent-function 0))
    (eval . (put 'substitute-keyword-arguments 'scheme-indent-function 1))
    (eval . (put 'with-store 'scheme-indent-function 1))
-   (eval . (put 'with-external-store 'scheme-indent-function 1))
    (eval . (put 'with-error-handling 'scheme-indent-function 0))
    (eval . (put 'with-mutex 'scheme-indent-function 1))
    (eval . (put 'with-atomic-file-output 'scheme-indent-function 1))

.gitignore

@@ -90,7 +90,7 @@
 /nix/config.h.in
 /nix/nix-daemon/nix-daemon.cc
 /nix/nix-setuid-helper/nix-setuid-helper.cc
-/nix/scripts/authenticate
+/nix/scripts/guix-authenticate
 /nix/scripts/list-runtime-roots
 /nix/scripts/offload
 /nix/scripts/substitute

Makefile.am

@@ -12,7 +12,6 @@
 # Copyright © 2018 Nils Gillmann <ng0@n0.is>
 # Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
 # Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-# Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 #
 # This file is part of GNU Guix.
 #
@@ -62,9 +61,7 @@ MODULES =					\
   guix/base16.scm				\
   guix/base32.scm				\
   guix/base64.scm				\
-  guix/ci.scm					\
   guix/cpio.scm					\
-  guix/docker.scm	   			\
   guix/records.scm				\
   guix/pki.scm					\
   guix/progress.scm				\
@@ -77,7 +74,6 @@ MODULES =					\
   guix/discovery.scm				\
   guix/git-download.scm				\
   guix/hg-download.scm				\
-  guix/swh.scm					\
   guix/monads.scm				\
   guix/monad-repl.scm				\
   guix/gexp.scm					\
@@ -104,7 +100,6 @@ MODULES =					\
   guix/build-system/android-ndk.scm		\
   guix/build-system/ant.scm			\
   guix/build-system/cargo.scm			\
-  guix/build-system/clojure.scm			\
   guix/build-system/cmake.scm			\
   guix/build-system/dub.scm			\
   guix/build-system/emacs.scm			\
@@ -177,8 +172,6 @@ MODULES =					\
   guix/build/syscalls.scm                       \
   guix/build/gremlin.scm			\
   guix/build/debug-link.scm			\
-  guix/build/clojure-build-system.scm		\
-  guix/build/clojure-utils.scm			\
   guix/build/emacs-utils.scm			\
   guix/build/java-utils.scm			\
   guix/build/lisp-utils.scm			\
@@ -188,24 +181,16 @@ MODULES =					\
   guix/build/make-bootstrap.scm			\
   guix/search-paths.scm				\
   guix/packages.scm				\
-  guix/import/cabal.scm				\
-  guix/import/cpan.scm				\
-  guix/import/cran.scm				\
-  guix/import/crate.scm				\
-  guix/import/elpa.scm   			\
-  guix/import/gem.scm				\
-  guix/import/github.scm   			\
-  guix/import/gnome.scm				\
-  guix/import/gnu.scm				\
-  guix/import/hackage.scm			\
-  guix/import/json.scm				\
-  guix/import/opam.scm				\
   guix/import/print.scm				\
-  guix/import/pypi.scm				\
-  guix/import/snix.scm				\
-  guix/import/stackage.scm			\
-  guix/import/texlive.scm   			\
   guix/import/utils.scm				\
+  guix/import/gnu.scm				\
+  guix/import/snix.scm				\
+  guix/import/cabal.scm				\
+  guix/import/cran.scm				\
+  guix/import/hackage.scm			\
+  guix/import/elpa.scm				\
+  guix/import/texlive.scm			\
+  guix/import/gopkg.scm				\
   guix/scripts.scm				\
   guix/scripts/download.scm			\
   guix/scripts/perform-download.scm		\
@@ -217,7 +202,6 @@ MODULES =					\
   guix/scripts/hash.scm				\
   guix/scripts/pack.scm				\
   guix/scripts/pull.scm				\
-  guix/scripts/processes.scm			\
   guix/scripts/substitute.scm			\
   guix/scripts/authenticate.scm			\
   guix/scripts/refresh.scm			\
@@ -227,29 +211,47 @@ MODULES =					\
   guix/scripts/system/search.scm		\
   guix/scripts/lint.scm				\
   guix/scripts/challenge.scm			\
-  guix/scripts/import/crate.scm			\
   guix/scripts/import/cran.scm			\
-  guix/scripts/import/elpa.scm  		\
-  guix/scripts/import/gem.scm			\
   guix/scripts/import/gnu.scm			\
-  guix/scripts/import/hackage.scm		\
-  guix/scripts/import/json.scm  		\
   guix/scripts/import/nix.scm			\
-  guix/scripts/import/opam.scm			\
-  guix/scripts/import/pypi.scm			\
-  guix/scripts/import/stackage.scm		\
-  guix/scripts/import/texlive.scm  		\
+  guix/scripts/import/hackage.scm		\
+  guix/scripts/import/elpa.scm			\
+  guix/scripts/import/texlive.scm		\
+  guix/scripts/import/gopkg.scm			\
   guix/scripts/environment.scm			\
   guix/scripts/publish.scm			\
   guix/scripts/edit.scm				\
   guix/scripts/size.scm				\
   guix/scripts/graph.scm			\
-  guix/scripts/weather.scm			\
   guix/scripts/container.scm			\
   guix/scripts/container/exec.scm		\
   guix.scm					\
   $(GNU_SYSTEM_MODULES)
 
+if HAVE_GUILE_JSON
+
+MODULES +=					\
+  guix/ci.scm					\
+  guix/docker.scm	   			\
+  guix/import/cpan.scm				\
+  guix/import/crate.scm				\
+  guix/import/gem.scm				\
+  guix/import/github.scm   			\
+  guix/import/gnome.scm				\
+  guix/import/json.scm				\
+  guix/import/opam.scm				\
+  guix/import/pypi.scm				\
+  guix/import/stackage.scm			\
+  guix/scripts/import/crate.scm			\
+  guix/scripts/import/gem.scm			\
+  guix/scripts/import/json.scm  		\
+  guix/scripts/import/opam.scm			\
+  guix/scripts/import/pypi.scm			\
+  guix/scripts/import/stackage.scm		\
+  guix/scripts/weather.scm
+
+endif
+
 if HAVE_GUILE_SSH
 
 MODULES +=					\
@@ -279,10 +281,10 @@ dist_noinst_DATA = guix/tests.scm guix/tests/http.scm
 # Auxiliary files for packages.
 AUX_FILES =						\
   gnu/packages/aux-files/emacs/guix-emacs.el		\
-  gnu/packages/aux-files/linux-libre/4.19-arm.conf	\
-  gnu/packages/aux-files/linux-libre/4.19-arm64.conf	\
-  gnu/packages/aux-files/linux-libre/4.19-i686.conf	\
-  gnu/packages/aux-files/linux-libre/4.19-x86_64.conf	\
+  gnu/packages/aux-files/linux-libre/4.18-arm.conf	\
+  gnu/packages/aux-files/linux-libre/4.18-arm64.conf	\
+  gnu/packages/aux-files/linux-libre/4.18-i686.conf	\
+  gnu/packages/aux-files/linux-libre/4.18-x86_64.conf	\
   gnu/packages/aux-files/linux-libre/4.14-arm.conf	\
   gnu/packages/aux-files/linux-libre/4.14-i686.conf	\
   gnu/packages/aux-files/linux-libre/4.14-x86_64.conf	\
@@ -329,10 +331,7 @@ SCM_TESTS =					\
   tests/base16.scm				\
   tests/base32.scm				\
   tests/base64.scm				\
-  tests/cpan.scm				\
   tests/cpio.scm				\
-  tests/crate.scm				\
-  tests/gem.scm					\
   tests/pki.scm					\
   tests/print.scm				\
   tests/sets.scm				\
@@ -346,7 +345,6 @@ SCM_TESTS =					\
   tests/ui.scm					\
   tests/status.scm				\
   tests/records.scm				\
-  tests/processes.scm				\
   tests/upstream.scm				\
   tests/combinators.scm				\
   tests/discovery.scm				\
@@ -386,22 +384,28 @@ SCM_TESTS =					\
   tests/services.scm				\
   tests/scripts-build.scm			\
   tests/containers.scm				\
-  tests/opam.scm				\
   tests/pack.scm				\
-  tests/pypi.scm				\
   tests/import-utils.scm			\
   tests/store-database.scm			\
   tests/store-deduplication.scm
 
+if HAVE_GUILE_JSON
+
+SCM_TESTS += 					\
+  tests/pypi.scm				\
+  tests/opam.scm				\
+  tests/cpan.scm				\
+  tests/gem.scm					\
+  tests/crate.scm
+
+endif
+
 SH_TESTS =					\
   tests/guix-build.sh				\
-  tests/guix-build-branch.sh			\
   tests/guix-download.sh			\
   tests/guix-gc.sh				\
   tests/guix-hash.sh				\
   tests/guix-pack.sh				\
-  tests/guix-pack-localstatedir.sh		\
-  tests/guix-pack-relocatable.sh		\
   tests/guix-package.sh				\
   tests/guix-package-net.sh			\
   tests/guix-system.sh				\
@@ -458,9 +462,8 @@ check-system: $(GOBJECTS)
 
 # Public key used to sign substitutes from hydra.gnu.org & co.
 dist_pkgdata_DATA =				\
-  etc/substitutes/hydra.gnu.org.pub		\
-  etc/substitutes/berlin.guixsd.org.pub		\
-  etc/substitutes/ci.guix.info.pub
+  hydra.gnu.org.pub				\
+  berlin.guixsd.org.pub
 
 # Bash completion file.
 dist_bashcompletion_DATA = etc/completion/bash/guix	\
@@ -592,17 +595,18 @@ AM_DISTCHECK_CONFIGURE_FLAGS =			\
   --enable-daemon				\
   ac_cv_guix_test_root="$(GUIX_TEST_ROOT)"
 
-# The self-contained tarball.
+# The self-contained tarball.  Add 'glibc-utf8-locales' along with glibc just
+# so 'etc/profile' defines 'GUIX_LOCPATH' pointing to a valid set of locales.
 guix-binary.%.tar.xz:
 	$(AM_V_GEN)GUIX_PACKAGE_PATH=					\
 	tarball=`$(top_builddir)/pre-inst-env guix pack -K -C xz	\
-	  -s "$*" --localstatedir --profile-name=current-guix guix` ;	\
+	  -s "$*" --localstatedir guix glibc-utf8-locales		\
+	  -e  '(@@ (gnu packages commencement) glibc-final)'` ;		\
 	cp "$$tarball" "$@.tmp" ; mv "$@.tmp" "$@"
 
 
 dist-hook: $(distdir)/ChangeLog gen-AUTHORS gen-tarball-version
 dist-hook: assert-no-store-file-names
-dist-hook: doc-po-update
 
 distcheck-hook: assert-binaries-available assert-final-inputs-self-contained
 
@@ -763,7 +767,7 @@ assert-no-store-file-names: $(distdir)/ChangeLog
 	  exit 1 ;								\
 	fi
 
-# Make sure important substitutes are available.
+# Make sure hydra.gnu.org has the important binaries.
 assert-binaries-available: $(GOBJECTS)
 	$(AM_V_at)$(top_builddir)/pre-inst-env "$(GUILE)"			\
 	  "$(top_srcdir)/build-aux/check-available-binaries.scm"

NEWS

@@ -11,109 +11,15 @@ Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 
 Please send Guix bug reports to bug-guix@gnu.org.
 
-* Changes in 0.16.0 (since 0.15.0)
+* Changes since 0.15.0
 
 ** Package management
 
-*** Default substitute URL changed to https://ci.guix.info
-*** ‘guix pull -l’ lists new and upgraded packages
-*** ‘guix pull’ now supports channels via ~/.config/guix/channels.scm
-*** New ‘--profile’ or ‘-p’ option for ‘guix pull’
-*** ~/.config/guix/current is now a symlink to /var/guix/profiles
-*** New ‘guix describe’ command
-*** ‘guix package’ no longer shows build logs by default
-*** ‘guix’ commands now produce colored output by default
-*** User interface now reports grafts separately
-*** Manifests can now refer to arbitrary Guix commits using “inferiors”
-*** New ‘--with-branch’ and ‘--with-commit’ package transformation options
-*** ‘guix build -f’ now accepts any kind of “file-like object”
-*** Git checkouts may now be fetched from Software Heritage
-*** New ‘guix repl’ command for use by inferiors
-*** New ‘guix processes’ command
-*** ‘guix pack’ now honors ‘--localstatedir’ for all its backends
-*** New ‘opam’ importer for ‘guix import’
 *** ‘guix import pypi’ has a new ‘--recursive’ option
 *** ‘guix import hackage’ has a new ‘--recursive’ option
 *** ‘guix import stackage’ has a new ‘--recursive’ option
 The short option for ‘--lts-version’ is now ‘-l’ (used to be ‘-r’).
-*** ‘guix refresh’ now stores upstream keys in ~/.config/guix/upstream
-*** Guix now depends on Guile-Gcrypt
-*** Guix now requires Guile-JSON
 
-** Distribution
-
-*** Rust is now bootstrapped from mrustc
-*** The GNU Shepherd was upgraded to 0.5.0
-*** ‘guix system reconfigure’ now loads Shepherd service replacements
-*** ‘herd schedule mcron’ now displays mcron’s job schedule
-*** ‘herd statistics nscd’ now displays nscd statistics
-*** ‘herd invalidate nscd TABLE’ instructs nscd to invalidate TABLE
-*** New services
-
-ddclient, gitolite, iptables, pcscd, prometheus-node-exporter, varnish
-
-*** 985 new packages
-
-*** 1945 package updates
-
-Noteworthy updates:
-bash 4.4.23, binutils 2.31.1, cups 2.2.8, enlightenment 0.22.4, gcc 8.2.0,
-gdb 8.2, ghc 8.4.3, gimp 2.10.6, glibc 2.28, gnupg 2.2.11, go 1.11.1,
-guile 2.2.4, icecat 60.3.0-gnu1, icedtea 3.7.0, libreoffice 6.1.3.2,
-linux-libre 4.19.6, ocaml 4.07.1, octave 4.4.1, perl 5.28.0,
-python2 2.7.15, python 3.7.0, racket 7.0, rust 1.28.0, r 3.5.1,
-sbcl 1.4.13, shepherd 0.5.0, xorg-server 1.20.3
-
-** Programming interfaces
-
-*** New (guix channels) module, see “Channels” in the manual
-*** New (guix inferior) module, see “Inferiors” in the manual
-*** New (guix describe) module, used by ‘guix describe’
-*** New (guix status) module, for build progress reporting
-*** ‘packages->manifest’ now accepts inferior packages
-*** New build systems: ‘clojure’, ‘guile’
-*** New ‘git-checkout’ record constructor in (guix git)
-*** Shepherd services can now declare custom actions
-*** More of the (gnu system …) APIs are now non-monadic
-*** New ‘add-file-tree-to-store’ procedure in (guix store)
-*** New (guix swh) module to access Software Heritage
-*** New (guix build debug-link) module, for ELF ‘.gnu_debuglink’ sections
-
-** Noteworthy bug fixes
-
-*** Fix GCC crashes caused by a patch of ours (<https://bugs.gnu.org/31708>)
-*** ‘guix import hackage’ now supports ‘custom-setup’ field
-    (<https://bugs.gnu.org/23961>)
-*** ‘guix-daemon’ taken from ‘guix pull’ looks up ‘guix’ in the right place
-    (<https://bugs.gnu.org/32183>)
-*** Try several file names when looking up kernel modules
-    (<https://bugs.gnu.org/31714>)
-*** ‘file-system-*’ services are now always started after ‘udev’
-    (<https://bugs.gnu.org/32313>)
-*** Racket now ignores bytecode checksums for files in the store
-    (<https://bugs.gnu.org/30680>)
-*** Grafting now updates CRCs in ‘.gnu_debuglink’ ELF sections
-    (<https://bugs.gnu.org/19973>)
-*** UUID computation for VMs is now deterministic (<https://bugs.gnu.org/32652>)
-*** ‘git-predicate’ from (guix git) now uses Guile-Git, which fixes corner cases
-    (<https://bugs.gnu.org/27925>)
-*** (guix store database) registers each store item only once
-    (<https://bugs.gnu.org/32600>)
-*** The File > Open dialog in LibreOffice no longer triggers a crash
-    (<https://bugs.gnu.org/30642>)
-*** Account home directory is always honored (<https://bugs.gnu.org/33422>)
-
-** Native language support
-
-*** The manual is now partially translated into German, in addition to French
-
-To read the German manual, just type “info guix.de” or read it on-line at
-<https://gnu.org/s/guix/manual/de/html_node>.  Consider translating the manual
-to your native language by joining the Translation Project:
-<https://translationproject.org/domain/guix-manual.html>.
-
-*** Updated translations:
-*** New translations:
 
 * Changes in 0.15.0 (since 0.14.0)
 

README

@@ -24,10 +24,10 @@ GNU Guix currently depends on the following packages:
   - [[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/guile-sqlite3/guile-sqlite3][Guile-SQLite3]], version 0.1.0 or later
+  - [[https://notabug.org/civodul/guile-sqlite3][Guile-SQLite3]], version 0.1.0 or later
   - [[https://gitlab.com/guile-git/guile-git][Guile-Git]]
   - [[http://www.zlib.net/][zlib]]
-  - [[https://savannah.nongnu.org/projects/guile-json/][Guile-JSON]]
+  - optionally [[https://savannah.nongnu.org/projects/guile-json/][Guile-JSON]], for the 'guix import pypi' command
 
 Unless `--disable-daemon' was passed, the following packages are needed:
 

build-aux/build-self.scm

@@ -374,15 +374,10 @@ interface (FFI) of Guile.")
 ;; The procedure below is our return value.
 (define* (build source
                 #:key verbose? (version (date-version-string)) system
+                (guile-version (match ((@ (guile) version))
+                                 ("2.2.2" "2.2.2")
+                                 (_       (effective-version))))
                 (pull-version 0)
-
-                ;; For the standalone Guix, default to Guile 2.2.  For old
-                ;; versions of 'guix pull' (pre-0.15.0), we have to use the
-                ;; same Guile as the current one.
-                (guile-version (if (> pull-version 0)
-                                   "2.2"
-                                   (effective-version)))
-
                 #:allow-other-keys
                 #:rest rest)
   "Return a derivation that unpacks SOURCE into STORE and compiles Scheme

build-aux/check-available-binaries.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -17,7 +17,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 ;;;
-;;; Check whether important binaries are available.
+;;; Check whether important binaries are available at hydra.gnu.org.
 ;;;
 
 (use-modules (guix store)

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

@@ -17,7 +17,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 ;;;
-;;; Check whether important binaries are available.
+;;; Check whether important binaries are available at hydra.gnu.org.
 ;;;
 
 (use-modules (guix store)

build-aux/update-NEWS.scm

@@ -30,7 +30,6 @@
              (ice-9 match)
              (ice-9 rdelim)
              (ice-9 regex)
-             (ice-9 vlist)
              (ice-9 pretty-print))
 
 (define %header-rx
@@ -99,60 +98,31 @@ paragraph."
                              (lambda (match port)
                                (let ((stars (match:substring match 1)))
                                  (format port
-                                         "~a ~a new packages~%~%"
-                                         stars (length added)))))))))
+                                         "~a ~a new packages~%~%~a~%~%"
+                                         stars (length added)
+                                         (enumeration->paragraph added)))))))))
 
 (define (write-packages-updates news-file old new)
   "Write to NEWS-FILE the list of packages upgraded between OLD and NEW."
-  (define important
-    '("gcc" "glibc" "binutils" "gdb"                   ;toolchain
-      "shepherd" "linux-libre" "xorg-server" "cups"    ;OS
-      "gnome" "xfce" "enlightenment" "lxde" "mate"     ;desktop env.
-      "guile" "bash" "python" "python2" "perl"         ;languages
-      "ghc" "rust" "go" "julia" "r" "ocaml"
-      "icedtea" "openjdk" "clojure" "sbcl" "racket"
-      "emacs" "gimp" "inkscape" "libreoffice"          ;applications
-      "octave" "icecat" "gnupg"))
-
-  (let* ((table    (fold (lambda (package table)
-                           (match package
-                             ((name . version)
-                              (vhash-cons name version table))))
-                         vlist-null
-                         new))
-         (latest   (lambda (name)
-                     (let ((versions (vhash-fold* cons '() name table)))
-                       (match (sort versions version>?)
-                         ((latest . _) latest)))))
-         (upgraded (filter-map (match-lambda
-                                 ((package . new-version)
-                                  (match (assoc package old)
-                                    ((_ . old-version)
-                                     (and (string=? new-version
-                                                    (latest package))
-                                          (version>? new-version old-version)
-                                          (cons package new-version)))
-                                    (_ #f))))
-                               new))
-         (noteworthy (filter (match-lambda
-                               ((package . version)
-                                (member package important)))
-                             upgraded)))
+  (let ((upgraded (filter-map (match-lambda
+                                ((package . new-version)
+                                 (match (assoc package old)
+                                   ((_ . old-version)
+                                    (and (version>? new-version old-version)
+                                         (string-append package "@"
+                                                        new-version)))
+                                   (_ #f))))
+                              new)))
     (with-atomic-file-replacement news-file
       (lambda (input output)
         (rewrite-org-section input output
                              (make-regexp "^(\\*+) (.*) package updates")
                              (lambda (match port)
-                               (let ((stars (match:substring match 1))
-                                     (lst   (map (match-lambda
-                                                   ((package . version)
-                                                    (string-append package " "
-                                                                   version)))
-                                                 noteworthy)))
+                               (let ((stars (match:substring match 1)))
                                  (format port
-                                         "~a ~a package updates~%~%Noteworthy updates:~%~a~%~%"
+                                         "~a ~a package updates~%~%~a~%~%"
                                          stars (length upgraded)
-                                         (enumeration->paragraph lst)))))))))
+                                         (enumeration->paragraph upgraded)))))))))
 
 
 (define (main . args)
@@ -168,8 +138,6 @@ paragraph."
 
        (let-values (((previous-version new-version)
                      (call-with-input-file news-file NEWS->versions)))
-         (format (current-error-port) "Updating NEWS for ~a to ~a...~%"
-                 previous-version new-version)
          (let* ((old (call-with-input-file (package-file previous-version)
                        read))
                 (new (fold-packages (lambda (p r)

config-daemon.ac

@@ -120,7 +120,15 @@ if test "x$guix_build_daemon" = "xyes"; then
 
   dnl Determine the appropriate default list of substitute URLs (GnuTLS
   dnl is required so we can default to 'https'.)
-  guix_substitute_urls="https://ci.guix.info"
+  case "x$host_cpu" in
+    xaarch64)
+      # Currently only berlin.guixsd.org provides aarch64 binaries.
+      guix_substitute_urls="https://berlin.guixsd.org"
+      ;;
+    *)
+      guix_substitute_urls="https://mirror.hydra.gnu.org"
+      ;;
+  esac
 
   AC_MSG_CHECKING([for default substitute URLs])
   AC_MSG_RESULT([$guix_substitute_urls])
@@ -155,8 +163,8 @@ if test "x$guix_build_daemon" = "xyes"; then
     [chmod +x nix/scripts/download])
   AC_CONFIG_FILES([nix/scripts/substitute],
     [chmod +x nix/scripts/substitute])
-  AC_CONFIG_FILES([nix/scripts/authenticate],
-    [chmod +x nix/scripts/authenticate])
+  AC_CONFIG_FILES([nix/scripts/guix-authenticate],
+    [chmod +x nix/scripts/guix-authenticate])
   AC_CONFIG_FILES([nix/scripts/offload],
     [chmod +x nix/scripts/offload])
 fi

configure.ac

@@ -122,11 +122,9 @@ if test "x$have_guile_git" != "xyes"; then
   AC_MSG_ERROR([Guile-Git is missing; please install it.])
 fi
 
-dnl Check for Guile-JSON.
+dnl Guile-JSON is used in various places.
 GUILE_MODULE_AVAILABLE([have_guile_json], [(json)])
-if test "x$have_guile_json" != "xyes"; then
-  AC_MSG_ERROR([Guile-JSON is missing; please install it.])
-fi
+AM_CONDITIONAL([HAVE_GUILE_JSON], [test "x$have_guile_json" = "xyes"])
 
 dnl Guile-Sqlite3 is used by the (guix store ...) modules.
 GUIX_CHECK_GUILE_SQLITE3

doc/contributing.de.texi

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

doc/contributing.fr.texi

@@ -110,15 +110,14 @@ changement localement sans les installer pour de vrai.  Pour pouvoir
 distinguer votre rôle « d'utilisateur final » de celui parfois haut en
 couleur de « développeur ».
 
-Pour cela, tous les outils en ligne de commande sont utilisables même sans
-avoir lancé @code{make install}.  Pour cela, vous devez d'abord avoir un
-environnement avec toutes les dépendances disponibles (@pxref{Construire depuis Git}), puis préfixer chaque commande par @command{./pre-inst-env} (le script
-@file{pre-inst-env} se trouve dans le répertoire de plus haut niveau de
-l'arborescence des sources de Guix ; il est généré par
-@command{./configure}) comme cela@footnote{L'option @option{-E} de
-@command{sudo} garantie que @code{GUILE_LOAD_PATH} est bien paramétré pour
-@command{guix-daemon} et pour que les outils qu'il utilise puissent trouver
-les modules Guile dont ils ont besoin.} :
+To that end, all the command-line tools can be used even if you have not run
+@code{make install}.  To do that, you first need to have an environment with
+all the dependencies available (@pxref{Construire depuis Git}), and then simply
+prefix each command with @command{./pre-inst-env} (the @file{pre-inst-env}
+script lives in the top build tree of Guix), as in@footnote{The @option{-E}
+flag to @command{sudo} guarantees that @code{GUILE_LOAD_PATH} is correctly
+set such that @command{guix-daemon} and the tools it uses can find the Guile
+modules they need.}:
 
 @example
 $ sudo -E ./pre-inst-env guix-daemon --build-users-group=guixbuild
@@ -214,13 +213,12 @@ variables @var{yas-snippet-dirs} d'Emacs.
   (add-to-list 'yas-snippet-dirs "~/src/guix/etc/snippets"))
 @end lisp
 
-Les extraits de messages de commit dépendent de @url{https://magit.vc/,
-Magit} pour afficher les fichiers sélectionnés.  Lors de la modification
-d'un message de commit, tapez @code{add} suivi de @kbd{TAB} pour insérer un
-modèle de message de commit pour ajouter un paquet ; tapez @code{update}
-suivi de @kbd{TAB} pour insérer un modèle pour la mise à jour d'un paquet ;
-tapez @code{https} suivi de @kbd{TAB} pour insérer un modèle pour le
-changement à HTTPS de l'URI de la page d'accueil.
+The commit message snippets depend on @url{https://magit.vc/, Magit} to
+display staged files.  When editing a commit message type @code{add}
+followed by @kbd{TAB} to insert a commit message template for adding a
+package; type @code{update} followed by @kbd{TAB} to insert a template for
+updating a package; type @code{https} followed by @kbd{TAB} to insert a
+template for changing the home page URI of a package to HTTPS.
 
 L'extrait principal pour @code{scheme-mode} est lancé en tapant
 @code{package…} suivi par @kbd{TAB}.  Cet extrait insère aussi la chaîne de
@@ -489,13 +487,6 @@ Suivez nos règles de formatage de code, éventuellement en lançant le script
 @command{et/indent-code.el} pour le faire automatiquement (@pxref{Formatage
 du code}).
 
-@item
-Si possible, utilisez des miroirs dans l'URL des sources (@pxref{Invoquer guix download}).  Utilisez des URL stable, pas des URL générées.  Par
-exemple, les archives GitHub ne sont pas nécessairement identiques d'une
-génération à la suivante, donc il vaut mieux dans ce cas cloner le dépôt.
-N'utilisez pas le champ @command{name} dans l'URL : ce n'est pas très utile
-et si le nom change, l'URL sera probablement erronée.
-
 @end enumerate
 
 Lorsque vous envoyez un correctif à la liste de diffusion, utilisez

doc/contributing.texi

@@ -112,8 +112,7 @@ run @code{make install}.  To do that, you first need to have an environment
 with all the dependencies available (@pxref{Building from Git}), and then
 simply prefix each command with
 @command{./pre-inst-env} (the @file{pre-inst-env} script lives in the
-top build tree of Guix; it is generated by @command{./configure}),
-as in@footnote{The @option{-E} flag to
+top build tree of Guix), as in@footnote{The @option{-E} flag to
 @command{sudo} guarantees that @code{GUILE_LOAD_PATH} is correctly set
 such that @command{guix-daemon} and the tools it uses can find the Guile
 modules they need.}:
@@ -443,7 +442,7 @@ as timestamps or randomly-generated output in the build result.
 
 Another option is to use @command{guix challenge} (@pxref{Invoking guix
 challenge}).  You may run it once the package has been committed and
-built by @code{@value{SUBSTITUTE-SERVER}} to check whether it obtains the same
+built by @code{hydra.gnu.org} to check whether it obtains the same
 result as you did.  Better yet: Find another machine that can build it
 and run @command{guix publish}.  Since the remote build machine is
 likely different from yours, this can catch non-determinism issues

doc/local.mk

@@ -22,8 +22,7 @@
 # along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 info_TEXINFOS = %D%/guix.texi \
-  %D%/guix.fr.texi \
-  %D%/guix.de.texi
+  %D%/guix.fr.texi
 
 %C%_guix_TEXINFOS = \
   %D%/contributing.texi \
@@ -55,9 +54,7 @@ OS_CONFIG_EXAMPLES_TEXI =			\
   %D%/os-config-lightweight-desktop.texi
 
 TRANSLATED_INFO = \
-  %D%/guix.de.texi \
   %D%/guix.fr.texi \
-  %D%/contributing.de.texi \
   %D%/contributing.fr.texi
 
 # Bundle this file so that makeinfo finds it in out-of-source-tree builds.

etc/completion/bash/guix

@@ -1,5 +1,5 @@
 # GNU Guix --- Functional package management for GNU
-# Copyright © 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+# Copyright © 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 #
 # This file is part of GNU Guix.
 #
@@ -172,8 +172,6 @@ _guix_complete ()
                 if _guix_is_dash_L
                 then
                     _guix_complete_file
-		else
-		    _guix_complete_available_package "$word_at_point"
                 fi
 	    elif _guix_is_command "download"
 	    then

etc/guix-daemon.conf.in

@@ -7,4 +7,4 @@ start on runlevel [2345]
 
 stop on runlevel [016]
 
-exec @localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix-daemon --build-users-group=guixbuild
+exec @localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix-daemon --build-users-group=guixbuild

etc/guix-daemon.service.in

@@ -6,8 +6,8 @@
 Description=Build daemon for GNU Guix
 
 [Service]
-ExecStart=@localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix-daemon --build-users-group=guixbuild
-Environment=GUIX_LOCPATH=@localstatedir@/guix/profiles/per-user/root/guix-profile/lib/locale
+ExecStart=@localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix-daemon --build-users-group=guixbuild
+Environment=GUIX_LOCPATH=/root/.guix-profile/lib/locale
 RemainAfterExit=yes
 StandardOutput=syslog
 StandardError=syslog

etc/guix-install.sh

@@ -269,13 +269,12 @@ sys_create_store()
     fi
 
     _msg "${INF}Linking the root user's profile"
-    mkdir -p "${ROOT_HOME}/.config/guix"
-    ln -sf /var/guix/profiles/per-user/root/current-guix \
-       "${ROOT_HOME}/.config/guix/current"
+    ln -sf /var/guix/profiles/per-user/root/guix-profile \
+       "${ROOT_HOME}/.guix-profile"
 
-    GUIX_PROFILE="${ROOT_HOME}/.config/guix/current"
+    GUIX_PROFILE="${ROOT_HOME}/.guix-profile"
     source "${GUIX_PROFILE}/etc/profile"
-    _msg "${PAS}activated root profile at ${ROOT_HOME}/.config/guix/current"
+    _msg "${PAS}activated root profile at /root/.guix-profile"
 }
 
 sys_create_build_user()
@@ -318,18 +317,18 @@ sys_enable_guix_daemon()
 
     info_path="/usr/local/share/info"
     local_bin="/usr/local/bin"
-    var_guix="/var/guix/profiles/per-user/root/current-guix"
+    var_guix="/var/guix/profiles/per-user/root/guix-profile"
 
     case "$INIT_SYS" in
         upstart)
             { initctl reload-configuration;
-              cp "${ROOT_HOME}/.config/guix/current/lib/upstart/system/guix-daemon.conf" \
+              cp "${ROOT_HOME}/.guix-profile/lib/upstart/system/guix-daemon.conf" \
                  /etc/init/ &&
                   start guix-daemon; } &&
                 _msg "${PAS}enabled Guix daemon via upstart"
             ;;
         systemd)
-            { cp "${ROOT_HOME}/.config/guix/current/lib/systemd/system/guix-daemon.service" \
+            { cp "${ROOT_HOME}/.guix-profile/lib/systemd/system/guix-daemon.service" \
                  /etc/systemd/system/;
               chmod 664 /etc/systemd/system/guix-daemon.service;
               systemctl daemon-reload &&
@@ -339,7 +338,7 @@ sys_enable_guix_daemon()
             ;;
         NA|*)
             _msg "${ERR}unsupported init system; run the daemon manually:"
-            echo "  ${ROOT_HOME}/.config/guix/current/bin/guix-daemon --build-users-group=guixbuild"
+            echo "  ${ROOT_HOME}/.guix-profile/bin/guix-daemon --build-users-group=guixbuild"
             ;;
     esac
 
@@ -359,10 +358,10 @@ sys_authorize_build_farms()
     while true; do
         read -p "Permit downloading pre-built package binaries from the project's build farms? (yes/no) " yn
         case $yn in
-            [Yy]*) guix archive --authorize < "${ROOT_HOME}/.config/guix/current/share/guix/hydra.gnu.org.pub" &&
+            [Yy]*) guix archive --authorize < "${ROOT_HOME}/.guix-profile/share/guix/hydra.gnu.org.pub" &&
                          _msg "${PAS}Authorized public key for hydra.gnu.org";
-                   guix archive --authorize < "${ROOT_HOME}/.config/guix/current/share/guix/ci.guix.info.pub" &&
-                       _msg "${PAS}Authorized public key for ci.guix.info";
+                   guix archive --authorize < "${ROOT_HOME}/.guix-profile/share/guix/berlin.guixsd.org.pub" &&
+                       _msg "${PAS}Authorized public key for berlin.guixsd.org";
                    break;;
             [Nn]*) _msg "${INF}Skipped authorizing build farm public keys"
                    break;;

etc/guix-publish.conf.in

@@ -9,4 +9,4 @@ stop on runlevel [016]
 
 task
 
-exec @localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix publish --user=nobody --port=8181
+exec @localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix publish --user=nobody --port=8181

etc/guix-publish.service.in

@@ -6,8 +6,8 @@
 Description=Publish the GNU Guix store
 
 [Service]
-ExecStart=@localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix publish --user=nobody --port=8181
-Environment=GUIX_LOCPATH=@localstatedir@/guix/profiles/per-user/root/guix-profile/lib/locale
+ExecStart=@localstatedir@/guix/profiles/per-user/root/guix-profile/bin/guix publish --user=nobody --port=8181
+Environment=GUIX_LOCPATH=/root/.guix-profile/lib/locale
 RemainAfterExit=yes
 StandardOutput=syslog
 StandardError=syslog

etc/substitutes/ci.guix.info.pub

@@ -1 +0,0 @@
-berlin.guixsd.org.pub

gnu/artwork.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -33,7 +33,7 @@
     (origin
       (method git-fetch)
       (uri (git-reference
-             (url "https://git.savannah.gnu.org/git/guix/guix-artwork.git")
+             (url "git://git.savannah.gnu.org/guix/guix-artwork.git")
              (commit commit)))
       (file-name (string-append "guix-artwork-" (string-take commit 7)
                                 "-checkout"))

gnu/bootloader/extlinux.scm

@@ -19,8 +19,12 @@
 
 (define-module (gnu bootloader extlinux)
   #:use-module (gnu bootloader)
+  #:use-module (gnu system)
+  #:use-module (gnu build bootloader)
   #:use-module (gnu packages bootloaders)
   #:use-module (guix gexp)
+  #:use-module (guix monads)
+  #:use-module (guix records)
   #:use-module (guix utils)
   #:export (extlinux-bootloader
             extlinux-bootloader-gpt))
@@ -74,7 +78,7 @@ TIMEOUT ~a~%"
                       (format port "~%"))
                    #~())))))
 
-  (computed-file "extlinux.conf" builder))
+  (gexp->derivation "extlinux.conf" builder))
 
 
 

gnu/bootloader/grub.scm

@@ -20,18 +20,26 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu bootloader grub)
+  #:use-module (guix store)
+  #:use-module (guix packages)
+  #:use-module (guix derivations)
   #:use-module (guix records)
-  #:use-module ((guix utils) #:select (%current-system))
+  #:use-module (guix monads)
   #:use-module (guix gexp)
+  #:use-module (guix download)
   #:use-module (gnu artwork)
+  #:use-module (gnu system)
   #:use-module (gnu bootloader)
   #:use-module (gnu system uuid)
   #:use-module (gnu system file-systems)
   #:autoload   (gnu packages bootloaders) (grub)
+  #:autoload   (gnu packages compression) (gzip)
   #:autoload   (gnu packages gtk) (guile-cairo guile-rsvg)
+  #:autoload   (gnu packages guile) (guile-2.2)
   #:use-module (ice-9 match)
   #:use-module (ice-9 regex)
   #:use-module (srfi srfi-1)
+  #:use-module (rnrs bytevectors)
   #:export (grub-image
             grub-image?
             grub-image-aspect-ratio
@@ -113,14 +121,14 @@ otherwise."
 
 (define* (svg->png svg #:key width height)
   "Build a PNG of HEIGHT x WIDTH from SVG."
-  (computed-file "grub-image.png"
-                 (with-imported-modules '((gnu build svg))
-                   (with-extensions (list guile-rsvg guile-cairo)
-                     #~(begin
-                         (use-modules (gnu build svg))
-                         (svg->png #+svg #$output
-                                   #:width #$width
-                                   #:height #$height))))))
+  (gexp->derivation "grub-image.png"
+                    (with-imported-modules '((gnu build svg))
+                      (with-extensions (list guile-rsvg guile-cairo)
+                        #~(begin
+                            (use-modules (gnu build svg))
+                            (svg->png #+svg #$output
+                                      #:width #$width
+                                      #:height #$height))))))
 
 (define* (grub-background-image config #:key (width 1024) (height 768))
   "Return the GRUB background image defined in CONFIG with a ratio of
@@ -130,13 +138,15 @@ WIDTH/HEIGHT, or #f if none was found."
                         (= (grub-image-aspect-ratio image) ratio))
                       (grub-theme-images
                        (bootloader-theme config)))))
-    (and image
-         (svg->png (grub-image-file image)
-                   #:width width #:height height))))
+    (if image
+        (svg->png (grub-image-file image)
+                  #:width width #:height height)
+        (with-monad %store-monad
+          (return #f)))))
 
 (define* (eye-candy config store-device store-mount-point
                     #:key system port)
-  "Return a gexp that writes to PORT (a port-valued gexp) the
+  "Return in %STORE-MONAD a gexp that writes to PORT (a port-valued gexp) the
 'grub.cfg' part concerned with graphics mode, background images, colors, and
 all that.  STORE-DEVICE designates the device holding the store, and
 STORE-MOUNT-POINT is its mount point; these are used to determine where the
@@ -184,11 +194,9 @@ fi~%" #$font-file)
     (strip-mount-point store-mount-point
                        (file-append grub "/share/grub/unicode.pf2")))
 
-  (define image
-    (grub-background-image config))
-
-  (and image
-       #~(format #$port "
+  (mlet* %store-monad ((image (grub-background-image config)))
+    (return (and image
+                 #~(format #$port "
 function setup_gfxterm {~a}
 
 # Set 'root' to the partition that contains /gnu/store.
@@ -205,14 +213,14 @@ else
   set menu_color_normal=cyan/blue
   set menu_color_highlight=white/blue
 fi~%"
-                 #$setup-gfxterm-body
-                 #$(grub-root-search store-device font-file)
-                 #$(setup-gfxterm config font-file)
-                 #$(grub-setup-io config)
+                           #$setup-gfxterm-body
+                           #$(grub-root-search store-device font-file)
+                           #$(setup-gfxterm config font-file)
+                           #$(grub-setup-io config)
 
-                 #$(strip-mount-point store-mount-point image)
-                 #$(theme-colors grub-theme-color-normal)
-                 #$(theme-colors grub-theme-color-highlight))))
+                           #$(strip-mount-point store-mount-point image)
+                           #$(theme-colors grub-theme-color-normal)
+                           #$(theme-colors grub-theme-color-highlight))))))
 
 
 ;;;
@@ -323,36 +331,36 @@ entries corresponding to old generations of the system."
                   #$(grub-root-search device kernel)
                   #$kernel (string-join (list #$@arguments))
                   #$initrd))))
-  (define sugar
-    (eye-candy config
-               (menu-entry-device (first all-entries))
-               (menu-entry-device-mount-point (first all-entries))
-               #:system system
-               #:port #~port))
-
-  (define builder
-    #~(call-with-output-file #$output
-        (lambda (port)
-          (format port
-                  "# This file was generated from your GuixSD configuration.  Any changes
+  (mlet %store-monad ((sugar (eye-candy config
+                                        (menu-entry-device
+                                         (first all-entries))
+                                        (menu-entry-device-mount-point
+                                         (first all-entries))
+                                        #:system system
+                                        #:port #~port)))
+    (define builder
+      #~(call-with-output-file #$output
+          (lambda (port)
+            (format port
+                    "# This file was generated from your GuixSD configuration.  Any changes
 # will be lost upon reconfiguration.
 ")
-          #$sugar
-          (format port "
+            #$sugar
+            (format port "
 set default=~a
 set timeout=~a~%"
-                  #$(bootloader-configuration-default-entry config)
-                  #$(bootloader-configuration-timeout config))
-          #$@(map menu-entry->gexp all-entries)
+                    #$(bootloader-configuration-default-entry config)
+                    #$(bootloader-configuration-timeout config))
+            #$@(map menu-entry->gexp all-entries)
 
-          #$@(if (pair? old-entries)
-                 #~((format port "
+            #$@(if (pair? old-entries)
+                   #~((format port "
 submenu \"GNU system, old configurations...\" {~%")
-                    #$@(map menu-entry->gexp old-entries)
-                    (format port "}~%"))
-                 #~()))))
+                      #$@(map menu-entry->gexp old-entries)
+                      (format port "}~%"))
+                   #~()))))
 
-  (computed-file "grub.cfg" builder))
+    (gexp->derivation "grub.cfg" builder)))
 
 
 

gnu/bootloader/u-boot.scm

@@ -20,8 +20,13 @@
 (define-module (gnu bootloader u-boot)
   #:use-module (gnu bootloader extlinux)
   #:use-module (gnu bootloader)
+  #:use-module (gnu system)
+  #:use-module (gnu build bootloader)
   #:use-module (gnu packages bootloaders)
   #:use-module (guix gexp)
+  #:use-module (guix monads)
+  #:use-module (guix records)
+  #:use-module (guix utils)
   #:export (u-boot-bootloader
             u-boot-a20-olinuxino-lime-bootloader
             u-boot-a20-olinuxino-lime2-bootloader
@@ -32,7 +37,6 @@
             u-boot-nintendo-nes-classic-edition-bootloader
             u-boot-novena-bootloader
             u-boot-pine64-plus-bootloader
-            u-boot-pinebook-bootloader
             u-boot-puma-rk3399-bootloader
             u-boot-wandboard-bootloader))
 
@@ -169,11 +173,6 @@
    (inherit u-boot-allwinner64-bootloader)
    (package u-boot-pine64-plus)))
 
-(define u-boot-pinebook-bootloader
-  (bootloader
-   (inherit u-boot-allwinner64-bootloader)
-   (package u-boot-pinebook)))
-
 (define u-boot-puma-rk3399-bootloader
   (bootloader
    (inherit u-boot-bootloader)

gnu/build/activation.scm

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

gnu/build/install.scm

@@ -18,6 +18,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu build install)
+  #:use-module (guix store database)
   #:use-module (guix build utils)
   #:use-module (guix build store-copy)
   #:use-module (srfi srfi-26)
@@ -26,7 +27,6 @@
             evaluate-populate-directive
             populate-root-file-system
             register-closure
-            install-database-and-gc-roots
             populate-single-profile-directory))
 
 ;;; Commentary:
@@ -141,53 +141,41 @@ includes /etc, /var, /run, /bin/sh, etc., and all the symlinks to SYSTEM."
                 (try))
               (apply throw args)))))))
 
-(define %root-profile
-  "/var/guix/profiles/per-user/root")
-
-(define* (install-database-and-gc-roots root database profile
-                                        #:key (profile-name "guix-profile"))
-  "Install DATABASE, the store database, under directory ROOT.  Create
-PROFILE-NAME and have it link to PROFILE, a store item."
-  (define (scope file)
-    (string-append root "/" file))
-
-  (define (mkdir-p* dir)
-    (mkdir-p (scope dir)))
-
-  (define (symlink* old new)
-    (symlink old (scope new)))
-
-  (install-file database (scope "/var/guix/db/"))
-  (chmod (scope "/var/guix/db/db.sqlite") #o644)
-  (mkdir-p* "/var/guix/profiles")
-  (mkdir-p* "/var/guix/gcroots")
-  (symlink* "/var/guix/profiles" "/var/guix/gcroots/profiles")
-
-  ;; Make root's profile, which makes it a GC root.
-  (mkdir-p* %root-profile)
-  (symlink* profile
-            (string-append %root-profile "/" profile-name "-1-link"))
-  (symlink* (string-append profile-name "-1-link")
-            (string-append %root-profile "/" profile-name)))
+(define* (register-closure prefix closure
+                           #:key
+                           (deduplicate? #t) (reset-timestamps? #t)
+                           (schema (sql-schema)))
+  "Register CLOSURE in PREFIX, where PREFIX is the directory name of the
+target store and CLOSURE is the name of a file containing a reference graph as
+produced by #:references-graphs..  As a side effect, if RESET-TIMESTAMPS? is
+true, reset timestamps on store files and, if DEDUPLICATE? is true,
+deduplicates files common to CLOSURE and the rest of PREFIX."
+  (let ((items (call-with-input-file closure read-reference-graph)))
+    (register-items items
+                    #:prefix prefix
+                    #:deduplicate? deduplicate?
+                    #:reset-timestamps? reset-timestamps?
+                    #:registration-time %epoch
+                    #:schema schema)))
 
 (define* (populate-single-profile-directory directory
                                             #:key profile closure
-                                            (profile-name "guix-profile")
-                                            database)
+                                            deduplicate?
+                                            register? schema)
   "Populate DIRECTORY with a store containing PROFILE, whose closure is given
 in the file called CLOSURE (as generated by #:references-graphs.)  DIRECTORY
 is initialized to contain a single profile under /root pointing to PROFILE.
-
-When DATABASE is true, copy it to DIRECTORY/var/guix/db and create
-DIRECTORY/var/guix/gcroots and friends.
-
-PROFILE-NAME is the name of the profile being created under
-/var/guix/profiles, typically either \"guix-profile\" or \"current-guix\".
+When REGISTER? is true, initialize DIRECTORY/var/guix/db to reflect the
+contents of the store; DEDUPLICATE? determines whether to deduplicate files in
+the store.
 
 This is used to create the self-contained tarballs with 'guix pack'."
   (define (scope file)
     (string-append directory "/" file))
 
+  (define %root-profile
+    "/var/guix/profiles/per-user/root")
+
   (define (mkdir-p* dir)
     (mkdir-p (scope dir)))
 
@@ -197,20 +185,25 @@ This is used to create the self-contained tarballs with 'guix pack'."
   ;; Populate the store.
   (populate-store (list closure) directory)
 
-  (when database
-    (install-database-and-gc-roots directory database profile
-                                   #:profile-name profile-name))
+  (when register?
+    (register-closure (canonicalize-path directory) closure
+                      #:deduplicate? deduplicate?
+                      #:schema schema)
 
-  (match profile-name
-    ("guix-profile"
-     (mkdir-p* "/root")
-     (symlink* (string-append %root-profile "/guix-profile")
-               "/root/.guix-profile"))
-    ("current-guix"
-     (mkdir-p* "/root/.config/guix")
-     (symlink* (string-append %root-profile "/current-guix")
-               "/root/.config/guix/current"))
-    (_
-     #t)))
+    (mkdir-p* "/var/guix/profiles")
+    (mkdir-p* "/var/guix/gcroots")
+    (symlink* "/var/guix/profiles"
+              "/var/guix/gcroots/profiles"))
+
+  ;; Make root's profile, which makes it a GC root.
+  (mkdir-p* %root-profile)
+  (symlink* profile
+            (string-append %root-profile "/guix-profile-1-link"))
+  (symlink* (string-append %root-profile "/guix-profile-1-link")
+            (string-append %root-profile "/guix-profile"))
+
+  (mkdir-p* "/root")
+  (symlink* (string-append %root-profile "/guix-profile")
+            "/root/.guix-profile"))
 
 ;;; install.scm ends here

gnu/build/linux-initrd.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -72,23 +72,11 @@ COMPRESS? is true, compress it using GZIP.  On success, return OUTPUT."
                                #:file->header cpio:file->cpio-header*)))
 
   (or (not compress?)
-
-      ;; Gzip insists on adding a '.gz' suffix and does nothing if the input
-      ;; file already has that suffix.  Shuffle files around to placate it.
-      (let* ((gz-suffix? (string-suffix? ".gz" output))
-             (sans-gz    (if gz-suffix?
-                             (string-drop-right output 3)
-                             output)))
-        (when gz-suffix?
-          (rename-file output sans-gz))
-        ;; Use '--no-name' so that gzip records neither a file name nor a time
-        ;; stamp in its output.
-        (and (zero? (system* gzip "--best" "--no-name" sans-gz))
-             (begin
-               (unless gz-suffix?
-                 (rename-file (string-append output ".gz") output))
-               output)))
-
+      ;; Use '--no-name' so that gzip records neither a file name nor a time
+      ;; stamp in its output.
+      (and (zero? (system* gzip "--best" "--no-name" output))
+           (rename-file (string-append output ".gz")
+                        output))
       output))
 
 (define (cache-compiled-file-name file)
@@ -151,12 +139,6 @@ REFERENCES-GRAPHS."
 
     (write-cpio-archive output "." #:gzip gzip))
 
-  ;; Make sure directories are writable so we can delete files.
-  (for-each make-file-writable
-            (find-files "contents"
-                        (lambda (file stat)
-                          (eq? 'directory (stat:type stat)))
-                        #:directories? #t))
   (delete-file-recursively "contents"))
 
 ;;; linux-initrd.scm ends here

gnu/build/vm.scm

@@ -25,7 +25,7 @@
   #:use-module (guix build utils)
   #:use-module (guix build store-copy)
   #:use-module (guix build syscalls)
-  #:use-module (guix store database)
+  #:use-module ((guix store database) #:select (reset-timestamps))
   #:use-module (gnu build linux-boot)
   #:use-module (gnu build install)
   #:use-module (gnu system uuid)
@@ -191,23 +191,6 @@ the #:references-graphs parameter of 'derivation'."
           (mkdir output)
           (copy-recursively "xchg" output)))))
 
-(define* (register-closure prefix closure
-                           #:key
-                           (deduplicate? #t) (reset-timestamps? #t)
-                           (schema (sql-schema)))
-  "Register CLOSURE in PREFIX, where PREFIX is the directory name of the
-target store and CLOSURE is the name of a file containing a reference graph as
-produced by #:references-graphs..  As a side effect, if RESET-TIMESTAMPS? is
-true, reset timestamps on store files and, if DEDUPLICATE? is true,
-deduplicates files common to CLOSURE and the rest of PREFIX."
-  (let ((items (call-with-input-file closure read-reference-graph)))
-    (register-items items
-                    #:prefix prefix
-                    #:deduplicate? deduplicate?
-                    #:reset-timestamps? reset-timestamps?
-                    #:registration-time %epoch
-                    #:schema schema)))
-
 
 ;;;
 ;;; Partitions.
@@ -477,11 +460,6 @@ GRUB configuration and OS-DRV as the stuff in it."
                 "mnt=/tmp/root/mnt"
                 "-path-list" "-"
                 "--"
-
-                ;; XXX: Add padding to avoid I/O errors on i686:
-                ;; <https://bugs.gnu.org/33639>.
-                "-padding" "10m"
-
                 "-volid" (string-upcase volume-id)
                 (if volume-uuid
                     `("-volume_date" "uuid"

gnu/local.mk

@@ -19,7 +19,6 @@
 # Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
 # Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
 # Copyright © 2018 Stefan Stefanović <stefanx2ovic@gmail.com>
-# Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 #
 # This file is part of GNU Guix.
 #
@@ -61,7 +60,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/android.scm			\
   %D%/packages/animation.scm			\
   %D%/packages/anthy.scm			\
-  %D%/packages/antivirus.scm			\
   %D%/packages/apl.scm				\
   %D%/packages/apr.scm				\
   %D%/packages/aspell.scm			\
@@ -101,7 +99,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/chez.scm				\
   %D%/packages/ci.scm				\
   %D%/packages/cinnamon.scm			\
-  %D%/packages/clojure.scm			\
   %D%/packages/cluster.scm			\
   %D%/packages/cmake.scm			\
   %D%/packages/cobol.scm			\
@@ -237,7 +234,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/imagemagick.scm			\
   %D%/packages/inklingreader.scm		\
   %D%/packages/inkscape.scm			\
-  %D%/packages/ipfs.scm			\
   %D%/packages/irc.scm  			\
   %D%/packages/iso-codes.scm			\
   %D%/packages/java.scm				\
@@ -348,7 +344,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/perl-check.scm			\
   %D%/packages/perl-web.scm			\
   %D%/packages/photo.scm			\
-  %D%/packages/phabricator.scm 			\
   %D%/packages/php.scm				\
   %D%/packages/pkg-config.scm			\
   %D%/packages/plotutils.scm			\
@@ -575,7 +570,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/aegis-test-fixup-1.patch            	\
   %D%/packages/patches/aegis-test-fixup-2.patch            	\
   %D%/packages/patches/aegisub-icu59-include-unistr.patch	\
-  %D%/packages/patches/aegisub-boost68.patch                    \
   %D%/packages/patches/agg-am_c_prototype.patch			\
   %D%/packages/patches/amule-crypto-6.patch			\
   %D%/packages/patches/ansible-wrap-program-hack.patch		\
@@ -600,32 +594,25 @@ dist_patch_DATA =						\
   %D%/packages/patches/bash-completion-directories.patch	\
   %D%/packages/patches/bastet-change-source-of-unordered_set.patch	\
   %D%/packages/patches/bazaar-CVE-2017-14176.patch		\
-  %D%/packages/patches/beets-python-3.7-fix.patch		\
   %D%/packages/patches/beignet-correct-file-names.patch		\
+  %D%/packages/patches/binutils-aarch64-symbol-relocation.patch	\
   %D%/packages/patches/binutils-loongson-workaround.patch	\
   %D%/packages/patches/blast+-fix-makefile.patch		\
-  %D%/packages/patches/blender-newer-ffmpeg.patch		\
   %D%/packages/patches/boost-fix-icu-build.patch		\
   %D%/packages/patches/borg-respect-storage-quota.patch		\
   %D%/packages/patches/byobu-writable-status.patch		\
   %D%/packages/patches/cairo-CVE-2016-9082.patch			\
-  %D%/packages/patches/cairo-setjmp-wrapper.patch		\
   %D%/packages/patches/calibre-no-updates-dialog.patch		\
   %D%/packages/patches/calibre-use-packaged-feedparser.patch	\
-  %D%/packages/patches/casync-renameat2-declaration.patch	\
   %D%/packages/patches/catdoc-CVE-2017-11110.patch		\
   %D%/packages/patches/cdparanoia-fpic.patch			\
   %D%/packages/patches/cdrtools-3.01-mkisofs-isoinfo.patch 	\
-  %D%/packages/patches/ceph-detect-rocksdb.patch		\
   %D%/packages/patches/ceph-disable-cpu-optimizations.patch	\
+  %D%/packages/patches/ceph-rocksdb-compat.patch		\
   %D%/packages/patches/ceph-skip-collect-sys-info-test.patch	\
   %D%/packages/patches/ceph-skip-unittest_blockdev.patch	\
-  %D%/packages/patches/ceph-volume-respect-PATH.patch		\
   %D%/packages/patches/chmlib-inttypes.patch			\
-  %D%/packages/patches/clamav-config-llvm-libs.patch		\
-  %D%/packages/patches/clamav-system-tomsfastmath.patch		\
   %D%/packages/patches/clang-3.5-libc-search-path.patch		\
-  %D%/packages/patches/clang-3.5-libsanitizer-ustat-fix.patch	\
   %D%/packages/patches/clang-3.8-libc-search-path.patch		\
   %D%/packages/patches/clang-6.0-libc-search-path.patch		\
   %D%/packages/patches/clang-runtime-asan-build-fixes.patch	\
@@ -647,6 +634,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/cracklib-fix-buffer-overflow.patch	\
   %D%/packages/patches/crawl-upgrade-saves.patch		\
   %D%/packages/patches/crda-optional-gcrypt.patch		\
+  %D%/packages/patches/crossmap-allow-system-pysam.patch	\
   %D%/packages/patches/clucene-contribs-lib.patch               \
   %D%/packages/patches/cube-nocheck.patch			\
   %D%/packages/patches/cursynth-wave-rand.patch			\
@@ -655,6 +643,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/datamash-arm-tests.patch			\
   %D%/packages/patches/dbus-helper-search-path.patch		\
   %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch	\
+  %D%/packages/patches/delly-use-system-libraries.patch		\
   %D%/packages/patches/dfu-programmer-fix-libusb.patch		\
   %D%/packages/patches/diffutils-gets-undeclared.patch		\
   %D%/packages/patches/diffutils-getopt.patch			\
@@ -662,6 +651,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/doc++-include-directives.patch		\
   %D%/packages/patches/doc++-segfault-fix.patch			\
   %D%/packages/patches/dovecot-trees-support-dovecot-2.3.patch	\
+  %D%/packages/patches/doxygen-gcc-ice.patch			\
   %D%/packages/patches/doxygen-test.patch			\
   %D%/packages/patches/dropbear-CVE-2018-15599.patch		\
   %D%/packages/patches/dvd+rw-tools-add-include.patch 		\
@@ -669,13 +659,12 @@ dist_patch_DATA =						\
   %D%/packages/patches/elogind-glibc-2.27.patch			\
   %D%/packages/patches/einstein-build.patch			\
   %D%/packages/patches/emacs-exec-path.patch			\
+  %D%/packages/patches/emacs-exwm-fix-fullscreen-issue.patch	\
   %D%/packages/patches/emacs-fix-scheme-indent-function.patch	\
   %D%/packages/patches/emacs-json-reformat-fix-tests.patch	\
   %D%/packages/patches/emacs-highlight-stages-add-gexp.patch	\
-  %D%/packages/patches/emacs-pdf-tools-poppler.patch		\
   %D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch	\
   %D%/packages/patches/emacs-source-date-epoch.patch		\
-  %D%/packages/patches/emacs-realgud-fix-configure-ac.patch	\
   %D%/packages/patches/enlightenment-fix-setuid-path.patch	\
   %D%/packages/patches/erlang-man-path.patch			\
   %D%/packages/patches/eudev-rules-directory.patch		\
@@ -694,9 +683,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/fcgi-2.4.0-poll.patch			\
   %D%/packages/patches/fifo-map-fix-flags-for-gcc.patch		\
   %D%/packages/patches/fifo-map-remove-catch.hpp.patch		\
-  %D%/packages/patches/findutils-gnulib-libio.patch		\
   %D%/packages/patches/findutils-localstatedir.patch		\
-  %D%/packages/patches/findutils-makedev.patch			\
   %D%/packages/patches/findutils-test-xargs.patch		\
   %D%/packages/patches/flann-cmake-3.11.patch			\
   %D%/packages/patches/flint-ldconfig.patch			\
@@ -706,6 +693,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/freeimage-CVE-2016-5684.patch		\
   %D%/packages/patches/freeimage-fix-build-with-gcc-5.patch	\
   %D%/packages/patches/freeimage-unbundle.patch		\
+  %D%/packages/patches/freetype-CVE-2018-6942.patch		\
   %D%/packages/patches/fuse-overlapping-headers.patch				\
   %D%/packages/patches/gawk-shell.patch				\
   %D%/packages/patches/gcc-arm-bug-71399.patch			\
@@ -715,9 +703,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gcc-fix-texi2pod.patch			\
   %D%/packages/patches/gcc-4.8-libsanitizer-fix.patch		\
   %D%/packages/patches/gcc-4.9-libsanitizer-fix.patch		\
-  %D%/packages/patches/gcc-4.9-libsanitizer-ustat.patch		\
   %D%/packages/patches/gcc-libsanitizer-fix.patch		\
-  %D%/packages/patches/gcc-libsanitizer-ustat.patch		\
   %D%/packages/patches/gcc-libvtv-runpath.patch			\
   %D%/packages/patches/gcc-strmov-store-file-names.patch	\
   %D%/packages/patches/gcc-4-compile-with-gcc-5.patch		 \
@@ -738,15 +724,16 @@ dist_patch_DATA =						\
   %D%/packages/patches/gd-fix-tests-on-i686.patch		\
   %D%/packages/patches/gd-freetype-test-failure.patch		\
   %D%/packages/patches/gdm-CVE-2018-14424.patch			\
+  %D%/packages/patches/gemma-intel-compat.patch			\
   %D%/packages/patches/geoclue-config.patch			\
   %D%/packages/patches/ghc-8.0-fall-back-to-madv_dontneed.patch \
   %D%/packages/patches/ghc-dont-pass-linker-flags-via-response-files.patch	\
-  %D%/packages/patches/ghc-haddock-library-unbundle.patch		\
   %D%/packages/patches/ghostscript-CVE-2018-16509.patch		\
   %D%/packages/patches/ghostscript-bug-699708.patch		\
   %D%/packages/patches/ghostscript-no-header-id.patch		\
   %D%/packages/patches/ghostscript-no-header-uuid.patch		\
   %D%/packages/patches/ghostscript-no-header-creationdate.patch \
+  %D%/packages/patches/ghostscript-runpath.patch		\
   %D%/packages/patches/giflib-make-reallocarray-private.patch	\
   %D%/packages/patches/glib-networking-ssl-cert-file.patch	\
   %D%/packages/patches/glib-tests-timer.patch			\
@@ -769,7 +756,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/glibc-vectorized-strcspn-guards.patch	\
   %D%/packages/patches/glibc-versioned-locpath.patch		\
   %D%/packages/patches/glibc-2.27-git-fixes.patch		\
-  %D%/packages/patches/glibc-2.28-git-fixes.patch		\
   %D%/packages/patches/glusterfs-use-PATH-instead-of-hardcodes.patch		\
   %D%/packages/patches/glog-gcc-5-demangling.patch		\
   %D%/packages/patches/gmp-arm-asm-nothumb.patch		\
@@ -789,7 +775,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/grep-timing-sensitive-test.patch		\
   %D%/packages/patches/groff-source-date-epoch.patch		\
   %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch	\
-  %D%/packages/patches/grub-binutils-compat.patch		\
   %D%/packages/patches/grub-check-error-efibootmgr.patch	\
   %D%/packages/patches/gsl-test-i686.patch			\
   %D%/packages/patches/gspell-dash-test.patch			\
@@ -809,6 +794,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch \
   %D%/packages/patches/gtkglext-disable-disable-deprecated.patch \
   %D%/packages/patches/gzdoom-search-in-installed-share.patch	\
+  %D%/packages/patches/handbrake-pkg-config-path.patch		\
   %D%/packages/patches/haskell-mode-unused-variables.patch	\
   %D%/packages/patches/haskell-mode-make-check.patch		\
   %D%/packages/patches/hdf4-architectures.patch 		\
@@ -825,9 +811,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/higan-remove-march-native-flag.patch	\
   %D%/packages/patches/hubbub-sort-entities.patch		\
   %D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch        \
-  %D%/packages/patches/hplip-remove-imageprocessor.patch	\
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
   %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
+  %D%/packages/patches/icecat-CVE-2018-12383.patch		\
   %D%/packages/patches/icecat-use-system-graphite2+harfbuzz.patch	\
   %D%/packages/patches/icecat-use-system-media-libs.patch	\
   %D%/packages/patches/icedtea-6-hotspot-gcc-segfault-workaround.patch  \
@@ -847,8 +833,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/java-xerces-bootclasspath.patch	\
   %D%/packages/patches/java-xerces-build_dont_unzip.patch	\
   %D%/packages/patches/java-xerces-xjavac_taskdef.patch	\
+  %D%/packages/patches/jemalloc-arm-address-bits.patch		\
   %D%/packages/patches/jbig2dec-ignore-testtest.patch		\
   %D%/packages/patches/json-glib-fix-tests-32bit.patch		\
+  %D%/packages/patches/jq-CVE-2015-8863.patch			\
   %D%/packages/patches/kdbusaddons-kinit-file-name.patch	\
   %D%/packages/patches/khmer-use-libraries.patch                \
   %D%/packages/patches/libziparchive-add-includes.patch		\
@@ -890,18 +878,18 @@ dist_patch_DATA =						\
   %D%/packages/patches/libevent-2.1-skip-failing-test.patch	\
   %D%/packages/patches/libexif-CVE-2016-6328.patch		\
   %D%/packages/patches/libexif-CVE-2017-7544.patch		\
-  %D%/packages/patches/libgcrypt-make-yat2m-reproducible.patch	\
   %D%/packages/patches/libgit2-mtime-0.patch			\
-  %D%/packages/patches/libgit2-oom-test.patch			\
   %D%/packages/patches/libgdata-fix-tests.patch			\
   %D%/packages/patches/libgdata-glib-duplicate-tests.patch	\
   %D%/packages/patches/libgnome-encoding.patch			\
   %D%/packages/patches/libgnomeui-utf8.patch			\
+  %D%/packages/patches/libgpg-error-aarch64-logging-fix.patch	\
+  %D%/packages/patches/libgxps-CVE-2017-11590.patch		\
   %D%/packages/patches/libffi-3.2.1-complex-alpha.patch		\
   %D%/packages/patches/libjxr-fix-function-signature.patch	\
   %D%/packages/patches/libjxr-fix-typos.patch			\
-  %D%/packages/patches/libopenshot-tests-with-system-libs.patch	\
   %D%/packages/patches/libotr-test-auth-fix.patch		\
+  %D%/packages/patches/liblxqt-include.patch			\
   %D%/packages/patches/libmad-armv7-thumb-pt1.patch		\
   %D%/packages/patches/libmad-armv7-thumb-pt2.patch		\
   %D%/packages/patches/libmad-frame-length.patch		\
@@ -939,7 +927,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/lierolibre-try-building-other-arch.patch	\
   %D%/packages/patches/linux-pam-no-setfsuid.patch		\
   %D%/packages/patches/lirc-localstatedir.patch			\
-  %D%/packages/patches/lirc-reproducible-build.patch		\
   %D%/packages/patches/llvm-3.5-fix-clang-build-with-gcc5.patch	\
   %D%/packages/patches/llvm-for-extempore.patch			\
   %D%/packages/patches/lm-sensors-hwmon-attrs.patch		\
@@ -955,8 +942,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/lvm2-static-link.patch			\
   %D%/packages/patches/lxsession-use-gapplication.patch         \
   %D%/packages/patches/lyx-2.2.3-fix-test.patch			\
+  %D%/packages/patches/mailutils-uninitialized-memory.patch	\
   %D%/packages/patches/make-glibc-compat.patch			\
   %D%/packages/patches/make-impure-dirs.patch			\
+  %D%/packages/patches/mariadb-gcc-ice.patch			\
   %D%/packages/patches/mariadb-client-test-32bit.patch		\
   %D%/packages/patches/mars-install.patch			\
   %D%/packages/patches/mars-sfml-2.3.patch			\
@@ -967,7 +956,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/mcrypt-CVE-2012-4409.patch			\
   %D%/packages/patches/mcrypt-CVE-2012-4426.patch			\
   %D%/packages/patches/mcrypt-CVE-2012-4527.patch			\
-  %D%/packages/patches/meandmyshadow-define-paths-earlier.patch	\
   %D%/packages/patches/mesa-skip-disk-cache-test.patch		\
   %D%/packages/patches/meson-for-build-rpath.patch		\
   %D%/packages/patches/metabat-fix-compilation.patch		\
@@ -977,7 +965,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/module-init-tools-moduledir.patch	\
   %D%/packages/patches/monero-use-system-miniupnpc.patch			\
   %D%/packages/patches/mongodb-support-unknown-linux-distributions.patch	\
-  %D%/packages/patches/mono-mdoc-timestamping.patch		\
   %D%/packages/patches/mozjs17-aarch64-support.patch		\
   %D%/packages/patches/mozjs24-aarch64-support.patch		\
   %D%/packages/patches/mozjs38-pkg-config-version.patch		\
@@ -990,7 +977,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/mupen64plus-ui-console-notice.patch	\
   %D%/packages/patches/mupen64plus-video-z64-glew-correct-path.patch    \
   %D%/packages/patches/mutt-store-references.patch		\
-  %D%/packages/patches/m4-gnulib-libio.patch			\
+  %D%/packages/patches/myrepos-CVE-2018-7032.patch		\
   %D%/packages/patches/net-tools-bitrot.patch			\
   %D%/packages/patches/netcdf-date-time.patch			\
   %D%/packages/patches/netcdf-tst_h_par.patch			\
@@ -1007,7 +994,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/nvi-db4.patch				\
   %D%/packages/patches/nyacc-binary-literals.patch		\
   %D%/packages/patches/nyx-show-header-stats-with-python3.patch	\
-  %D%/packages/patches/oath-toolkit-glibc-compat.patch		\
   %D%/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch	\
   %D%/packages/patches/ocaml-bitstring-fix-configure.patch \
   %D%/packages/patches/ocaml-CVE-2015-8869.patch		\
@@ -1024,6 +1010,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/openocd-nrf52.patch			\
   %D%/packages/patches/opensmtpd-fix-crash.patch		\
   %D%/packages/patches/openssl-runpath.patch			\
+  %D%/packages/patches/openssl-1.0.2-CVE-2018-0495.patch	\
+  %D%/packages/patches/openssl-1.0.2-CVE-2018-0732.patch	\
   %D%/packages/patches/openssl-1.1-c-rehash-in.patch		\
   %D%/packages/patches/openssl-c-rehash-in.patch		\
   %D%/packages/patches/orpheus-cast-errors-and-includes.patch	\
@@ -1033,11 +1021,13 @@ dist_patch_DATA =						\
   %D%/packages/patches/p7zip-CVE-2016-9296.patch		\
   %D%/packages/patches/p7zip-CVE-2017-17969.patch		\
   %D%/packages/patches/p7zip-remove-unused-code.patch		\
-  %D%/packages/patches/parted-glibc-compat.patch		\
   %D%/packages/patches/patchelf-page-size.patch			\
   %D%/packages/patches/patchelf-rework-for-arm.patch		\
-  %D%/packages/patches/patchutils-test-perms.patch		\
+  %D%/packages/patches/patchutils-xfail-gendiff-tests.patch	\
   %D%/packages/patches/patch-hurd-path-max.patch		\
+  %D%/packages/patches/perf-gcc-ice.patch			\
+  %D%/packages/patches/perl-archive-tar-CVE-2018-12015.patch	\
+  %D%/packages/patches/perl-file-path-CVE-2017-6512.patch	\
   %D%/packages/patches/perl-autosplit-default-time.patch	\
   %D%/packages/patches/perl-deterministic-ordering.patch	\
   %D%/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch \
@@ -1056,15 +1046,12 @@ dist_patch_DATA =						\
   %D%/packages/patches/pinball-missing-separators.patch		\
   %D%/packages/patches/pinball-src-deps.patch			\
   %D%/packages/patches/pinball-system-ltdl.patch		\
-  %D%/packages/patches/pinentry-efl.patch			\
   %D%/packages/patches/pingus-sdl-libs-config.patch		\
   %D%/packages/patches/pius.patch       			\
   %D%/packages/patches/pixman-CVE-2016-5296.patch		\
   %D%/packages/patches/plink-1.07-unclobber-i.patch		\
   %D%/packages/patches/plink-endian-detection.patch		\
   %D%/packages/patches/plotutils-libpng-jmpbuf.patch		\
-  %D%/packages/patches/podofo-cmake-3.12.patch			\
-  %D%/packages/patches/poppler-CVE-2018-19149.patch		\
   %D%/packages/patches/portaudio-audacity-compat.patch		\
   %D%/packages/patches/portmidi-modular-build.patch		\
   %D%/packages/patches/potrace-tests.patch			\
@@ -1082,8 +1069,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/pygpgme-disable-problematic-tests.patch  \
   %D%/packages/patches/pyqt-configure.patch			\
   %D%/packages/patches/pyqt-public-sip.patch			\
-  %D%/packages/patches/python2-CVE-2018-14647.patch		\
-  %D%/packages/patches/python2-CVE-2018-1000802.patch		\
   %D%/packages/patches/python-2-deterministic-build-info.patch	\
   %D%/packages/patches/python-2.7-adjust-tests.patch		\
   %D%/packages/patches/python-2.7-search-paths.patch		\
@@ -1092,17 +1077,18 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-3-deterministic-build-info.patch	\
   %D%/packages/patches/python-3-search-paths.patch		\
   %D%/packages/patches/python-3-fix-tests.patch			\
-  %D%/packages/patches/python-CVE-2018-14647.patch		\
   %D%/packages/patches/python-axolotl-AES-fix.patch		\
   %D%/packages/patches/python-cairocffi-dlopen-path.patch	\
-  %D%/packages/patches/python-cffi-x87-stack-clean.patch	\
   %D%/packages/patches/python-fix-tests.patch			\
   %D%/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch \
+  %D%/packages/patches/python-networkx2-reproducible-build.patch	\
+  %D%/packages/patches/python-pillow-fix-failing-tests.patch	\
   %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch	\
+  %D%/packages/patches/python-scikit-learn-fix-test-non-determinism.patch	\
   %D%/packages/patches/python-configobj-setuptools.patch	\
   %D%/packages/patches/python-faker-fix-build-32bit.patch	\
   %D%/packages/patches/python-mox3-python3.6-compat.patch	\
-  %D%/packages/patches/python-testtools.patch			\
+  %D%/packages/patches/python-paste-remove-website-test.patch	\
   %D%/packages/patches/python-paste-remove-timing-test.patch	\
   %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch	\
   %D%/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \
@@ -1115,14 +1101,12 @@ dist_patch_DATA =						\
   %D%/packages/patches/qt4-ldflags.patch			\
   %D%/packages/patches/qtbase-use-TZDIR.patch			\
   %D%/packages/patches/qtscript-disable-tests.patch		\
-  %D%/packages/patches/qt-5-renameat2.patch			\
   %D%/packages/patches/quagga-reproducible-build.patch          \
   %D%/packages/patches/quickswitch-fix-dmenu-check.patch	\
   %D%/packages/patches/quilt-test-fix-regex.patch		\
-  %D%/packages/patches/quilt-getopt-nondigit-param.patch	\
-  %D%/packages/patches/quilt-getopt-second-separator.patch	\
+  %D%/packages/patches/quilt-compat-getopt-fix-second-separator.patch	\
+  %D%/packages/patches/quilt-compat-getopt-fix-option-with-nondigit-param.patch	\
   %D%/packages/patches/qtwebkit-pbutils-include.patch		\
-  %D%/packages/patches/randomjungle-disable-static-build.patch	\
   %D%/packages/patches/rapicorn-isnan.patch			\
   %D%/packages/patches/raptor2-heap-overflow.patch		\
   %D%/packages/patches/ratpoison-shell.patch			\
@@ -1146,14 +1130,12 @@ dist_patch_DATA =						\
   %D%/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch \
   %D%/packages/patches/rust-bootstrap-stage0-test.patch		\
   %D%/packages/patches/rust-coresimd-doctest.patch		\
-  %D%/packages/patches/rust-reproducible-builds.patch		 \
   %D%/packages/patches/rxvt-unicode-escape-sequences.patch	\
   %D%/packages/patches/scheme48-tests.patch			\
   %D%/packages/patches/scotch-test-threading.patch		\
   %D%/packages/patches/scotch-build-parallelism.patch		\
   %D%/packages/patches/scotch-graph-diam-64.patch		\
   %D%/packages/patches/scotch-graph-induce-type-64.patch	\
-  %D%/packages/patches/scribus-poppler.patch			\
   %D%/packages/patches/sdl-libx11-1.6.patch			\
   %D%/packages/patches/seq24-rename-mutex.patch			\
   %D%/packages/patches/sharutils-CVE-2018-1000097.patch		\
@@ -1163,14 +1145,11 @@ dist_patch_DATA =						\
   %D%/packages/patches/slim-sigusr1.patch			\
   %D%/packages/patches/slim-reset.patch				\
   %D%/packages/patches/slim-login.patch				\
-  %D%/packages/patches/snappy-add-O2-flag-in-CmakeLists.txt.patch	\
   %D%/packages/patches/sooperlooper-build-with-wx-30.patch 	\
-  %D%/packages/patches/soundconverter-remove-gconf-dependency.patch	\
   %D%/packages/patches/soundtouch-CVE-2018-14044-14045.patch 	\
   %D%/packages/patches/soundtouch-CVE-2018-1000223.patch 	\
   %D%/packages/patches/steghide-fixes.patch			\
   %D%/packages/patches/superlu-dist-scotchmetis.patch		\
-  %D%/packages/patches/swig-guile-gc.patch			\
   %D%/packages/patches/swish-e-search.patch			\
   %D%/packages/patches/swish-e-format-security.patch		\
   %D%/packages/patches/synfigstudio-fix-ui-with-gtk3.patch 	\
@@ -1184,9 +1163,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/tcsh-fix-out-of-bounds-read.patch	\
   %D%/packages/patches/teensy-loader-cli-help.patch		\
   %D%/packages/patches/teeworlds-use-latest-wavpack.patch	\
-  %D%/packages/patches/texinfo-perl-compat.patch		\
-  %D%/packages/patches/texinfo-5-perl-compat.patch		\
-  %D%/packages/patches/telegram-purple-adjust-test.patch	\
   %D%/packages/patches/texi2html-document-encoding.patch	\
   %D%/packages/patches/texi2html-i18n.patch			\
   %D%/packages/patches/thefuck-test-environ.patch		\
@@ -1197,16 +1173,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/tk-find-library.patch			\
   %D%/packages/patches/ttf2eot-cstddef.patch			\
   %D%/packages/patches/ttfautohint-source-date-epoch.patch	\
-  %D%/packages/patches/tomsfastmath-constness.patch		\
+  %D%/packages/patches/tophat-build-with-later-seqan.patch	\
   %D%/packages/patches/totem-meson-easy-codec.patch		\
   %D%/packages/patches/tuxpaint-stamps-path.patch		\
   %D%/packages/patches/twinkle-include-qregexpvalidator.patch	\
-  %D%/packages/patches/u-boot-pinebook-a64-update-dts.patch	\
-  %D%/packages/patches/u-boot-pinebook-mmc-calibration.patch	\
-  %D%/packages/patches/u-boot-pinebook-r_i2c-controller.patch	\
-  %D%/packages/patches/u-boot-pinebook-dts.patch		\
-  %D%/packages/patches/u-boot-pinebook-syscon-node.patch	\
-  %D%/packages/patches/u-boot-pinebook-video-bridge.patch	\
   %D%/packages/patches/unrtf-CVE-2016-10091.patch		\
   %D%/packages/patches/unzip-CVE-2014-8139.patch		\
   %D%/packages/patches/unzip-CVE-2014-8140.patch		\
@@ -1256,8 +1226,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/wpa-supplicant-fix-zeroed-keys.patch	\
   %D%/packages/patches/wpa-supplicant-fix-nonce-reuse.patch	\
   %D%/packages/patches/wpa-supplicant-krack-followups.patch	\
-  %D%/packages/patches/x265-arm-flags.patch			\
-  %D%/packages/patches/x265-detect512-all-arches.patch		\
+  %D%/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch	\
+  %D%/packages/patches/x265-arm-asm-primitives.patch		\
+  %D%/packages/patches/xapian-revert-5489fb2f8.patch		\
   %D%/packages/patches/xboing-CVE-2004-0149.patch		\
   %D%/packages/patches/xf86-video-ark-remove-mibstore.patch	\
   %D%/packages/patches/xf86-video-geode-glibc-2.20.patch	\
@@ -1273,6 +1244,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/xinetd-fix-fd-leak.patch			\
   %D%/packages/patches/xinetd-CVE-2013-4342.patch		\
   %D%/packages/patches/xmodmap-asprintf.patch 			\
+  %D%/packages/patches/zathura-pdf-mupdf-link-to-jpeg-libraries.patch \
   %D%/packages/patches/zathura-plugindir-environment-variable.patch
 
 MISC_DISTRO_FILES =				\

gnu/packages/admin.scm

@@ -9,7 +9,7 @@
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Peter Feigl <peter.feigl@nexoid.at>
 ;;; Copyright © 2016 John J. Foerch <jjfoerch@earthlink.net>
 ;;; Copyright © 2016, 2017 Nils Gillmann <ng0@n0.is>
@@ -45,7 +45,6 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system cmake)
-  #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
@@ -126,9 +125,7 @@
      `(("libgcrypt" ,libgcrypt)
        ("libgpg-error" ,libgpg-error)
        ("libmhash" ,libmhash)
-       ("pcre:static" ,pcre "static")
        ("pcre" ,pcre)
-       ("zlib:static" ,zlib "static")
        ("zlib" ,zlib)))
     (synopsis "File and directory integrity checker")
     (description
@@ -228,15 +225,13 @@ interface and is based on GNU Guile.")
        (modify-phases %standard-phases
          (add-after 'unpack 'chdir
            (lambda _
-             (chdir ,(string-append name "-" version))
-             #t))
+             (chdir ,(string-append  name "-" version))))
          (delete 'configure)
          (add-before 'build 'patch
            (lambda _
              (substitute* "src/error.h"
                (("extern int errno;")
-                "#include <errno.h>"))
-             #t))
+                "#include <errno.h>"))))
          (replace 'build
            (lambda _
              (invoke "package/compile")))
@@ -246,8 +241,7 @@ interface and is based on GNU Guile.")
                     (bin (string-append out "/bin")))
                (for-each (lambda (file)
                            (install-file file bin))
-                         (find-files "command")))
-             #t)))))
+                         (find-files "command"))))))))
     (synopsis "Tools for managing UNIX style services")
     (description
      "@code{daemontools} is a collection of tools for managing UNIX
@@ -969,7 +963,7 @@ at once based on a Perl regular expression.")
                       #t))
                   (add-after 'install 'install-info
                     (lambda _
-                      (invoke "make" "install-info"))))))
+                      (zero? (system* "make" "install-info")))))))
     (native-inputs `(("texinfo" ,texinfo)
                      ("util-linux" ,util-linux))) ; for 'cal'
     (home-page "https://www.gnu.org/software/rottlog/")
@@ -985,7 +979,7 @@ system administrator.")
 (define-public sudo
   (package
     (name "sudo")
-    (version "1.8.26")
+    (version "1.8.25p1")
     (source (origin
               (method url-fetch)
               (uri
@@ -995,7 +989,7 @@ system administrator.")
                                     version ".tar.gz")))
               (sha256
                (base32
-                "1qpyyfga8rs02p3186sns8qvh2bzwa48ka845nrcqh83dyd23nj0"))
+                "0nqri46d4dpycj96zin2f2wszmhm7q9mr68hhj9sp81pgmx9rjcx"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1100,8 +1094,7 @@ commands and their arguments.")
       CFLAGS += $(shell pkg-config libnl-3.0 --cflags)
       CONFIG_LIBNL32=y
       CONFIG_READLINE=y\n" port)
-               (close-port port))
-             #t))
+               (close-port port))))
          (add-after 'install 'install-man-pages
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out  (assoc-ref outputs "out"))
@@ -1240,10 +1233,11 @@ This package provides the 'wpa_supplicant' daemon and the 'wpa_cli' command.")
                ;; It's an old configure script that doesn't understand
                ;; the extra options we pass.
                (setenv "CONFIG_SHELL" (which "bash"))
-               (invoke "./configure"
-                       (string-append "--prefix=" out)
-                       (string-append "--mandir=" out
-                                      "/share/man"))))))
+               (zero?
+                (system* "./configure"
+                         (string-append "--prefix=" out)
+                         (string-append "--mandir=" out
+                                        "/share/man")))))))
        #:tests? #f))
     (home-page "https://www.kernel.org") ; really, no home page
     (synopsis "Send a wake-on-LAN packet")
@@ -1345,30 +1339,25 @@ system is under heavy load.")
 (define-public detox
   (package
     (name "detox")
-    (version "1.3.0")
+    (version "1.2.0")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/dharple/detox.git")
-                    (commit (string-append "v" version))))
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/detox/detox/" version
+                                  "/detox-" version ".tar.bz2"))
               (sha256
                (base32
-                "1dd608c7g65s5lj02cddvani3q9kzirddgkjqa22ap9d4f8b9xgr"))))
+                "1y6vvjqsg54kl49cry73jbfhr04s7wjs779vrr9zrq6kww7dkymb"))))
     (build-system gnu-build-system)
-    (native-inputs
-     `(("autoconf" ,autoconf)
-       ("automake" ,automake)
-       ("flex" ,flex)))
+    ;; Both flex and popt are used in this case for their runtime libraries
+    ;; (libfl and libpopt).
+    (inputs
+     `(("flex" ,flex)
+       ("popt" ,popt)))
     (arguments
-     `(#:tests? #f                    ;no 'check' target
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'delete-configure
-                    ;; The "configure" script is present, but otherwise the
-                    ;; project is not bootstrapped: missing install-sh and
-                    ;; Makefile.in, so delete it so the bootstrap phase will
-                    ;; take over.
-                    (lambda _ (delete-file "configure") #t)))))
-    (home-page "https://github.com/dharple/detox")
+     `(#:configure-flags `(,(string-append "--with-popt="
+                                           (assoc-ref %build-inputs "popt")))
+       #:tests? #f))                    ;no 'check' target
+    (home-page "http://detox.sourceforge.net")
     (synopsis "Clean up file names")
     (description
      "Detox is a program that renames files to make them easier to work with
@@ -1600,14 +1589,14 @@ of supported upstream metrics systems simultaneously.")
 (define-public ansible
   (package
     (name "ansible")
-    (version "2.7.4")
+    (version "2.5.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ansible" version))
        (sha256
         (base32
-         "0p1n6yyc632522fl2r247p0jg4mncc7z4hqngzbh1zxq3dcb12s9"))
+         "0wbsjjx3xjlm8g50a9j9c6p9rn23jx32yn1234bf5rmj1qgy3p85"))
        (patches (search-patches "ansible-wrap-program-hack.patch"))))
     (build-system python-build-system)
     (native-inputs
@@ -1633,34 +1622,6 @@ ad hoc task execution, and multinode orchestration---including trivializing
 things like zero-downtime rolling updates with load balancers.")
     (license license:gpl3+)))
 
-(define-public emacs-ansible-doc
-  (let ((commit "86083a7bb2ed0468ca64e52076b06441a2f8e9e0"))
-    (package
-      (name "emacs-ansible-doc")
-      (version (git-version "0.4" "1" commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/lunaryorn/ansible-doc.el")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "0lap404ch74w99n3xip176jr42b38xhyzkfnkyqg0g3wk2cd3aq8"))))
-      (build-system emacs-build-system)
-      ;; Unmaintained by upstream.
-      (home-page "https://github.com/lunaryorn/ansible-doc.el")
-      (synopsis "Ansible documentation for Emacs")
-      (description
-       "This package provides an Ansible documentation for GNU Emacs.
-
-@code{ansible-doc} allows you to view the documentation of an Ansible
-module and @code{ansible-doc-mode} minor mode adds documentation
-lookup to YAML Mode.  You could enable the mode with @code{(add-hook
-'yaml-mode-hook #'ansible-doc-mode)}.")
-      (license license:gpl3+))))
-
 (define-public cpulimit
   (package
     (name "cpulimit")
@@ -1678,18 +1639,20 @@ lookup to YAML Mode.  You could enable the mode with @code{(add-hook
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (delete 'configure)
-                  (replace 'build
-                    (lambda _
-                      (invoke "make" "CC=gcc" "-Csrc")))
-                  (replace 'check
-                    (lambda _
-                      (invoke "make" "CC=gcc" "-Ctests")))
-                  (replace 'install
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      (let* ((out (assoc-ref outputs "out"))
-                             (bin (string-append out "/bin")))
-                        (install-file "src/cpulimit" bin))
-                      #t)))))
+                  (replace
+                   'build
+                   (lambda _
+                     (zero? (system* "make" "CC=gcc" "-Csrc"))))
+                  (replace
+                   'check
+                   (lambda _
+                     (zero? (system* "make" "CC=gcc" "-Ctests"))))
+                  (replace
+                   'install
+                   (lambda* (#:key outputs #:allow-other-keys)
+                     (let* ((out (assoc-ref outputs "out"))
+                            (bin (string-append out "/bin")))
+                       (install-file "src/cpulimit" bin)))))))
     (home-page "https://github.com/opsengine/cpulimit")
     (synopsis "Limit CPU usage")
     (description
@@ -1898,9 +1861,10 @@ done with the @code{auditctl} utility.")
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (define (make out . args)
-               (apply invoke "make"
-                      (string-append "prefix=" out)
-                      args))
+               (unless (zero? (apply system* "make"
+                                     (string-append "prefix=" out)
+                                     args))
+                 (error "make failed")))
              (define (python-path dir)
                (string-append dir "/lib/python2.7/site-packages"))
              (let ((out (assoc-ref outputs "out"))
@@ -1914,14 +1878,13 @@ done with the @code{auditctl} utility.")
                (make ndiff "install-ndiff")
                (wrap-program (string-append ndiff "/bin/ndiff")
                  `("PYTHONPATH" prefix
-                   (,(python-path ndiff)))))
-             #t))
+                   (,(python-path ndiff)))))))
          ;; These are the tests that do not require network access.
          (replace 'check
-           (lambda _ (invoke "make"
-                             "check-nse"
-                             "check-ndiff"
-                             "check-dns"))))
+           (lambda _ (zero? (system* "make"
+                                     "check-nse"
+                                     "check-ndiff"
+                                     "check-dns")))))
        ;; Nmap can't cope with out-of-source building.
        #:out-of-source? #f))
     (home-page "https://nmap.org/")
@@ -2227,15 +2190,15 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.")
              #t))
          (replace 'build
            (lambda* (#:key make-flags #:allow-other-keys)
-             (apply invoke "make" "tools" "misc" make-flags)))
+             (zero? (apply system* "make" "tools" "misc" make-flags))))
          (add-after 'build 'build-armhf
            (lambda* (#:key make-flags #:allow-other-keys)
              (setenv "LIBRARY_PATH" #f)
-             (apply invoke "make" "target-tools" make-flags)))
+             (zero? (apply system* "make" "target-tools" make-flags))))
          (replace 'install
            (lambda* (#:key make-flags #:allow-other-keys)
-             (apply invoke "make" "install-all" "install-misc"
-                    make-flags))))))
+             (zero? (apply system* "make" "install-all" "install-misc"
+                           make-flags)))))))
     (home-page "https://github.com/linux-sunxi/sunxi-tools")
     (synopsis "Hardware management tools for Allwinner computers")
     (description "This package contains tools for Allwinner devices:
@@ -2489,20 +2452,26 @@ make it a perfect utility on modern distros.")
     (version "1.7.2")
     (source
      (origin
-      (method git-fetch)
-      (uri (git-reference
-             (url "https://github.com/01org/thermal_daemon")
-             (commit (string-append "v" version))))
-      (file-name (git-file-name name version))
-      (sha256
-       (base32
-        "1cs2pq8xvfnsvrhg2bxawk4kn3z1qmfrnpnhs178pvfbglzh15hc"))))
+      (method url-fetch)
+      (uri (string-append "https://github.com/01org/thermal_daemon/archive/v"
+                          version ".tar.gz"))
+      (file-name (string-append name "-" version ".tar.gz"))
+      (sha256 (base32
+               "15a6vb67y5wsmf0irrq7sxam18yqpz64130k83ryf24mp40h661b"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:configure-flags
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'bootstrap
+           (lambda _
+             (invoke "sh" "autogen.sh")
+             #t)))
+       #:configure-flags
        (let ((out      (assoc-ref %outputs "out")))
          (list (string-append "--sysconfdir="
                               out "/etc")
+               (string-append "--with-udev-dir="
+                              out "/lib/udev")
                (string-append "--with-dbus-sys-dir="
                               out "/etc/dbus-1/system.d")
                "--localstatedir=/var"))))
@@ -2874,82 +2843,3 @@ support forum.  It runs with the @code{/exec} command in most IRC clients.")
     (description "This package provides tools to manage clients of the
 Logitech Unifying Receiver.")
     (license license:gpl2)))
-
-(define-public lynis
-  (package
-    (name "lynis")
-    (version "2.7.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/CISOfy/lynis")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "0rzc0y8lk22bymf56249jzmllki2lh0rz5in4lkrc5fkmp29c2wv"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           ;; Remove proprietary plugins. As of now, all plugins supplied with
-           ;; lynis are proprietary. In the future, if free plugins are
-           ;; provided, whitelist them from deletion.
-           (for-each delete-file (find-files "plugins"))
-           #t))))
-    (build-system gnu-build-system)
-    (native-inputs
-     `(;; For tests
-       ("lynis-sdk"
-        ,(origin
-           (method git-fetch)
-           (uri (git-reference
-                 (url "https://github.com/CISOfy/lynis-sdk")
-                 (commit "3310aef4f2b3dd97d166c96ad0253c89c4ad390d")))
-           (file-name (git-file-name "lynis-sdk" version))
-           (sha256
-            (base32
-             "0sqsrm5wal742yrwps8bqb8a8lxd93n4b93n3kkm1b30nbs25g7y"))))))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'configure
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (substitute* "lynis"
-               (("/usr/share/lynis")
-                (string-append (assoc-ref outputs "out") "/share/lynis")))
-             (substitute* "include/functions"
-               (("/usr/local/etc/lynis")
-                (string-append (assoc-ref outputs "out") "/etc/lynis")))
-             #t))
-         (delete 'build)
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (install-file "lynis" (string-append out "/bin/"))
-               (install-file "default.prf" (string-append out "/etc/lynis"))
-               (for-each
-                (lambda (dir)
-                  (copy-recursively dir (string-append out "/share/lynis/" dir)))
-                (list "db" "include" "plugins"))
-               (install-file "lynis.8" (string-append out "/share/man/man8"))
-               #t)))
-         (replace 'check
-           (lambda* (#:key inputs #:allow-other-keys)
-             (copy-recursively (assoc-ref inputs "lynis-sdk") "../lynis-sdk")
-             (setenv "LANG" "en_US.UTF-8")
-             (let ((lynis-dir (getcwd)))
-               (with-directory-excursion "../lynis-sdk"
-                 (substitute* "config"
-                   (("\\.\\./lynis") lynis-dir))
-                 (substitute* "unit-tests/tests-language-translations.sh"
-                   (("\\.\\./lynis") lynis-dir))
-                 (invoke "sh" "lynis-devkit" "run" "unit-tests"))))))))
-    (home-page "https://cisofy.com/lynis/")
-    (synopsis "Security auditing tool")
-    (description "Lynis is a security auditing tool.  It performs an in-depth
-security scan and runs on the system itself.  The primary goal is to test
-security defenses and provide tips for further system hardening.  It will also
-scan for general system information, vulnerable software packages, and
-possible configuration issues.")
-    (license license:gpl3+)))

gnu/packages/agda.scm

@@ -1,7 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Alex ter Weele <alex.ter.weele@gmail.com>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -86,7 +85,6 @@
            (lambda* (#:key outputs inputs tests? (configure-flags '())
                      #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
-                    (name-version (strip-store-file-name out))
                     (input-dirs (match inputs
                                   (((_ . dir) ...)
                                    dir)
@@ -97,7 +95,8 @@
                                     `(,(string-append "--bindir=" out "/bin"))
                                     `(,(string-append
                                         "--docdir=" out
-                                        "/share/doc/" name-version))
+                                        "/share/doc/" ((@@ (guix build haskell-build-system)
+                                                           package-name-version) out)))
                                     '("--libsubdir=$compiler/$pkg-$version")
                                     '("--package-db=../package.conf.d")
                                     '("--global")

gnu/packages/algebra.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017, 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
@@ -179,7 +179,7 @@ PARI is also available as a C library to allow for faster computations.")
 (define-public gp2c
   (package
    (name "gp2c")
-   (version "0.0.11pl1")
+   (version "0.0.11")
    (source (origin
             (method url-fetch)
             (uri (string-append
@@ -187,7 +187,7 @@ PARI is also available as a C library to allow for faster computations.")
                   version ".tar.gz"))
             (sha256
               (base32
-                "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s"))))
+                "1z69xj2dpd8yyi8108rz26c50xpv0k2j8qnk0bzy1c5lw3pd1adm"))))
    (build-system gnu-build-system)
    (native-inputs `(("perl" ,perl)))
    (inputs `(("pari-gp" ,pari-gp)))
@@ -210,40 +210,10 @@ GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
    (license license:gpl2)
    (home-page "https://pari.math.u-bordeaux.fr/")))
 
-(define-public cmh
-  (package
-   (name "cmh")
-   (version "1.0")
-   (source (origin
-            (method url-fetch)
-            (uri (string-append
-                  "https://gforge.inria.fr/frs/download.php/33497/cmh-"
-                  version ".tar.gz"))
-            (sha256
-             (base32
-              "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
-   (build-system gnu-build-system)
-   (inputs
-     `(("gmp" ,gmp)
-       ("mpfr" ,mpfr)
-       ("mpc" ,mpc)
-       ("mpfrcx" ,mpfrcx)
-       ("fplll" ,fplll)
-       ("pari-gp"  ,pari-gp)))
-   (synopsis "Igusa class polynomial computations")
-   (description
-    "The CMH software computes Igusa (genus 2) class polynomials, which
-parameterize the CM points in the moduli space of 2-dimensional abelian
-varieties, i.e. Jacobians of hyperelliptic curves.
-It can also be used to compute theta constants at arbitrary
-precision.")
-   (license license:gpl3+)
-   (home-page "http://cmh.gforge.inria.fr/")))
-
 (define-public giac-xcas
   (package
     (name "giac-xcas")
-    (version "1.5.0-19")
+    (version "1.4.9-59")
     (source (origin
               (method url-fetch)
               ;; "~parisse/giac" is not used because the maintainer regularly
@@ -255,48 +225,16 @@ precision.")
                                   "source/giac_" version ".tar.gz"))
               (sha256
                (base32
-                "0ds1zh712sr20qh0fih8jnm4nlv90andllp8n263qs7rlhblz551"))))
+                "0dv5p5y6gkrsmz3xa7fw87rjyabwdwk09mqb09kb7gai9n9dgayk"))))
     (build-system gnu-build-system)
-    (outputs '("out" "doc"))            ;77MiB of documentation
     (arguments
-     `(#:modules ((ice-9 ftw)
-                  (guix build utils)
-                  (guix build gnu-build-system))
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-bin-cp
-           ;; Some Makefiles contain hard-coded "/bin/cp".
            (lambda _
+             ;; Some Makefiles contain hard-coded "/bin/cp".
              (substitute* (find-files "doc" "^Makefile")
                (("/bin/cp") (which "cp")))
-             #t))
-         (add-after 'unpack 'disable-failing-test
-           ;; FIXME: Test failing.  Not sure why.
-           (lambda _
-             (substitute* "check/Makefile.in"
-               (("chk_fhan11") ""))
-             #t))
-         (add-after 'install 'install-doc
-           ;; Setting --docdir to "doc" output isn't sufficient as
-           ;; documentation and examples are scattered throughout the source.
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (doc (assoc-ref outputs "doc"))
-                    (docdir (string-append doc
-                                           "/share/doc/"
-                                           (string-append ,name "-" ,version))))
-               ;; For some reason, the install process moves
-               ;; "share/giac/examples" instead of "share/giac/doc" to
-               ;; "$(docdir)".  Clean up the mess and start over.
-               (delete-file-recursively (string-append doc "/share"))
-               (mkdir-p docdir)
-               (with-directory-excursion out
-                 (for-each (lambda (f)
-                             (unless (member f '("." ".."))
-                               (copy-recursively (string-append "share/giac/" f)
-                                                 (string-append docdir "/" f))))
-                           (scandir "share/giac"))
-                 (delete-file-recursively "share/giac")))
              #t)))))
     (inputs
      `(("fltk" ,fltk)
@@ -376,47 +314,47 @@ fast arithmetic.")
 
 (define-public arb
   (package
-    (name "arb")
-    (version "2.14.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/fredrik-johansson/arb.git")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1ndxg7h4xvccjgp5l9z2f8b66dsff6fhf86bn5n7f75a1ksd7554"))))
-    (build-system gnu-build-system)
-    (propagated-inputs
-     `(("flint" ,flint)))               ; flint.h is included by arf.h
-    (inputs
-     `(("gmp" ,gmp)
-       ("mpfr" ,mpfr)))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'configure
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out"))
-                   (flint (assoc-ref inputs "flint"))
-                   (gmp (assoc-ref inputs "gmp"))
-                   (mpfr (assoc-ref inputs "mpfr")))
-               ;; do not pass "--enable-fast-install", which makes the
-               ;; homebrew configure process fail
-               (invoke "./configure"
-                       (string-append "--prefix=" out)
-                       (string-append "--with-flint=" flint)
-                       (string-append "--with-gmp=" gmp)
-                       (string-append "--with-mpfr=" mpfr))))))))
-    (synopsis "Arbitrary precision floating-point ball arithmetic")
-    (description
-     "Arb is a C library for arbitrary-precision floating-point ball
+   (name "arb")
+   (version "2.14.0")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://github.com/fredrik-johansson/arb/archive/"
+                  version ".tar.gz"))
+            (file-name (string-append name "-" version ".tar.gz"))
+            (sha256
+              (base32
+                "0ncr27nd20xxi18nj30cvpa6r52v59nq7gbi34x3l4xym3p8mlmx"))))
+   (build-system gnu-build-system)
+   (propagated-inputs
+    `(("flint" ,flint))) ; flint.h is included by arf.h
+   (inputs
+    `(("gmp" ,gmp)
+      ("mpfr" ,mpfr)))
+   (arguments
+    `(#:phases
+      (modify-phases %standard-phases
+        (replace 'configure
+          (lambda* (#:key inputs outputs #:allow-other-keys)
+            (let ((out (assoc-ref outputs "out"))
+                  (flint (assoc-ref inputs "flint"))
+                  (gmp (assoc-ref inputs "gmp"))
+                  (mpfr (assoc-ref inputs "mpfr")))
+              ;; do not pass "--enable-fast-install", which makes the
+              ;; homebrew configure process fail
+              (invoke "./configure"
+                      (string-append "--prefix=" out)
+                      (string-append "--with-flint=" flint)
+                      (string-append "--with-gmp=" gmp)
+                      (string-append "--with-mpfr=" mpfr))))))))
+   (synopsis "Arbitrary precision floating-point ball arithmetic")
+   (description
+    "Arb is a C library for arbitrary-precision floating-point ball
 arithmetic.  It supports efficient high-precision computation with
 polynomials, power series, matrices and special functions over the
 real and complex numbers, with automatic, rigorous error control.")
-    (license license:lgpl2.1+)
-    (home-page "http://fredrikj.net/arb/")))
+   (license license:lgpl2.1+)
+   (home-page "http://fredrikj.net/arb/")))
 
 (define-public ntl
   (package
@@ -568,14 +506,13 @@ syntax is similar to that of C, so basic usage is familiar.  It also includes
     (name "kiss-fft-for-extempore")
     (version "1.3.0")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/extemporelang/kiss_fft.git")
-                    (commit version)))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append "https://github.com/extemporelang/kiss_fft/archive/"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
+                "0hkp9l6l4c92fb1l2sh6a6zv1hynpvb2s4d03vd8vxyvybc0l4pv"))))
     (build-system cmake-build-system)
     (arguments `(#:tests? #f)) ; no tests included
     ;; Extempore refuses to build on architectures other than x86_64
@@ -591,14 +528,14 @@ a C program.")
 (define-public fftw
   (package
     (name "fftw")
-    (version "3.3.8")
+    (version "3.3.7")
     (source (origin
              (method url-fetch)
              (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
                                  version".tar.gz"))
              (sha256
               (base32
-               "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
+               "0wsms8narnbhfsa8chdflv2j9hzspvflblnqdn7hw8x5xdzrnq1v"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags

gnu/packages/android.scm

@@ -108,7 +108,7 @@ use their packages mostly unmodified in our Android NDK build system.")
 ;; Big thanks to them for laying the groundwork.
 
 ;; The version tag is consistent between all repositories.
-(define (android-platform-version) "7.1.2_r36")
+(define (android-platform-version) "7.1.2_r6")
 
 (define (android-platform-system-core version)
   (origin
@@ -120,7 +120,7 @@ use their packages mostly unmodified in our Android NDK build system.")
                               version "-checkout"))
     (sha256
      (base32
-      "1krnc2b9zfkzpdgs1dcbji59nszlx2qr723pg89m52622czc06hg"))
+      "0xc2n7jxrf1iw9cc278pijdfjix2fkiig5ws27f6rwp40zg5mrgg"))
     (patches
      (search-patches "libbase-use-own-logging.patch"
                      "libbase-fix-includes.patch"
@@ -151,7 +151,7 @@ use their packages mostly unmodified in our Android NDK build system.")
                               version "-checkout"))
     (sha256
      (base32
-      "15r4s20d7vw022f8vrc3jbghmqwdcqzprl7i2bfvdkz8z76wc1ps"))))
+      "0n9wkz3ynqw39if1ss9n32m66iga14nndf29hpm7g1aqn4wvvgzk"))))
 
 (define (android-platform-external version subdirectory checksum)
   (origin
@@ -339,13 +339,6 @@ various Android core host applications.")
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-source
            (lambda _ (chdir "adb") #t))
-         (add-after 'enter-source 'glibc-compat
-           (lambda _
-             ;; Include sysmacros.h for "major" and "minor" in Glibc 2.28.
-             (substitute* "usb_linux.cpp"
-               (("#include <sys/types.h>" all)
-                (string-append all "\n#include <sys/sysmacros.h>\n")))
-             #t))
          (add-after 'enter-source 'make-libs-available
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (substitute* "Android.mk"

gnu/packages/antivirus.scm

@@ -1,156 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
-
-(define-module (gnu packages antivirus)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix utils)
-  #:use-module (gnu packages)
-  #:use-module (gnu packages autotools)
-  #:use-module (gnu packages bison)
-  #:use-module (gnu packages check)
-  #:use-module (gnu packages compression)
-  #:use-module (gnu packages curl)
-  #:use-module (gnu packages cyrus-sasl)
-  #:use-module (gnu packages flex)
-  #:use-module (gnu packages llvm)
-  #:use-module (gnu packages multiprecision)
-  #:use-module (gnu packages ncurses)
-  #:use-module (gnu packages pcre)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages tls)
-  #:use-module (gnu packages web)
-  #:use-module (gnu packages xml))
-
-(define-public clamav
-  (package
-    (name "clamav")
-    (version "0.100.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://www.clamav.net/downloads/production/"
-                                  "clamav-" version ".tar.gz"))
-              (sha256
-               (base32
-                "1mkd41sxbjkfjinpx5b9kb85q529gj2s3d0klysssqhysh64ybja"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  (for-each delete-file-recursively
-                            '("win32"              ;unnecessary
-                              "libclamav/c++/llvm" ;use system llvm
-                              "libclamunrar"))))   ;non-free license
-              (patches
-               (search-patches "clamav-system-tomsfastmath.patch"
-                               "clamav-config-llvm-libs.patch"))))
-    (build-system gnu-build-system)
-    (native-inputs
-     `(("bison" ,bison)
-       ("check" ,check)                 ;for tests
-       ("flex" ,flex)
-       ("pkg-config" ,pkg-config)
-       ;; The tomsfastmath patch touches configure.ac and Makefile.am
-       ("autoconf" ,autoconf)
-       ("automake" ,automake)
-       ("libtool" ,libtool)))
-    (inputs
-     `(("bzip2" ,bzip2)
-       ("libcurl" ,curl)
-       ("libjson" ,json-c)
-       ("libltdl" ,libltdl)
-       ("libmspack" ,libmspack)
-       ("llvm" ,llvm-3.6)               ;requires <3.7, for JIT/verifier
-       ("ncurses" ,ncurses)
-       ("openssl" ,libressl)
-       ("pcre" ,pcre "bin")             ;for pcre-config
-       ("sasl" ,cyrus-sasl)             ;for linking curl with libtool
-       ("tomsfastmath" ,tomsfastmath)
-       ("xml" ,libxml2)
-       ("zlib" ,zlib)))
-    (arguments
-     `(#:configure-flags
-       (let-syntax ((with (syntax-rules ()
-                            ((_ name)
-                             (string-append "--with-" name "="
-                                            (assoc-ref %build-inputs name))))))
-         (list "--disable-unrar"
-               "--enable-llvm"
-               "--with-system-llvm"
-               "--with-system-libmspack"
-               "--without-included-ltdl"
-               (with "xml")
-               (with "openssl")
-               (with "libjson")
-               (with "pcre")
-               (with "zlib")
-               (with "libcurl")
-               ;; For sanity, specifying --enable-* flags turns
-               ;; "support unavailable" warnings into errors.
-               "--enable-bzip2"
-               "--enable-check"
-               "--sysconfdir=/etc/clamav"
-               ;; Default database directory needs to be writeable
-               "--with-dbdir=/var/db/clamav"))
-       ;; install sample .conf files to %output/etc rather than /etc/clamav
-       #:make-flags (list (string-append "sysconfdir=" %output "/etc"))
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'reconf
-                    (lambda _ (zero? (system* "autoreconf" "-vfi"))))
-                  (add-before 'configure 'patch-llvm-config
-                    (lambda _
-                      (substitute* '("libclamav/c++/detect.cpp"
-                                     "libclamav/c++/ClamBCRTChecks.cpp"
-                                     "libclamav/c++/bytecode2llvm.cpp")
-                        (("llvm/Config/config.h") "llvm/Config/llvm-config.h"))
-                      ;; `llvm-config --libfiles` inappropriately lists lib*.a
-                      ;; libraries, rather than the lib*.so's that our llvm
-                      ;; contains.  They're used only for listing extra build
-                      ;; dependencies, so ignore them until that's fixed.
-                      (substitute* "libclamav/c++/Makefile.in"
-                        (("@LLVMCONFIG_LIBFILES@") ""))
-                      #t))
-                  (add-before 'check 'skip-clamd-tests
-                    ;; XXX: The check?_clamd tests fail inside the build
-                    ;; chroot, but pass outside.
-                    (lambda _
-                      (substitute* "unit_tests/Makefile"
-                        (("check2_clamd.sh.*check4_clamd.sh") ""))
-                      #t)))))
-    (home-page "https://www.clamav.net")
-    (synopsis "Antivirus engine")
-    (description
-     "Clam AntiVirus is an anti-virus toolkit, designed especially for e-mail
-scanning on mail gateways.  It provides a number of utilities including a
-flexible and scalable multi-threaded daemon, a command line scanner, and
-advanced tool for automatic database updates.  The core of the package is an
-anti-virus engine available in the form of a shared library.")
-    (license (list license:gpl2+        ;ClamAV itself
-                   license:lgpl2.1      ;libclamav/mspack.[ch]
-                   license:public-domain ;libclamav/7z/*, libclamav/rijndael.[ch], etc...
-                   (package-license bzip2) ;modified bzip2 source in libclamav/nsis
-                   license:bsd-2        ;several files in libclamav
-                   license:bsd-3        ;libclamav/{regex,qsort.c,swf.[ch]
-                   license:ncsa         ;libclamav/c++/PointerTracking.cpp
-                   license:zlib         ;libclamav/inf*.h
-                   license:x11          ;libclamav/lzw
-                   (license:non-copyleft "libclamav/strlcat.c") ;"OpenBSD" license
-                   license:asl2.0       ;libclamav/yara*
-                   license:expat))))    ;shared/getopt.[ch]

gnu/packages/audio.scm

@@ -14,9 +14,6 @@
 ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2018 Brett Gilio <brettg@posteo.net>
-;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2018 Thorsten Wilms <t_w_@freenet.de>
-;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -429,46 +426,6 @@ and editing digital audio.  It features digital effects and spectrum analysis
 tools.")
     (license license:gpl2+)))
 
-(define-public autotalent
-  (package
-    (name "autotalent")
-    (version "0.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "http://tombaran.info/autotalent-"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "1n04qm66f14195ly6gsy3ra7v2j7zad5n19d8dwfmh0qs6h9hphh"))))
-    (build-system gnu-build-system)
-    (arguments
-     `(#:tests? #f ; no check target
-       #:phases
-       (modify-phases %standard-phases
-         ;; no configure script
-         (delete 'configure)
-         (add-before 'install 'prepare-target-directory
-           (lambda* (#:key outputs #:allow-other-keys)
-             (mkdir-p (string-append (assoc-ref outputs "out") "/lib/ladspa"))
-             #t))
-         (add-after 'unpack 'override-target-directory
-           (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* "Makefile"
-               (("/usr/lib64/ladspa")
-                (string-append (assoc-ref outputs "out") "/lib/ladspa")))
-             #t)))))
-    (inputs
-     `(("ladspa" ,ladspa)))
-    (home-page "http://tombaran.info/autotalent.html")
-    (synopsis "Pitch-correction LADSPA audio plugin")
-    (description
-     "Autotalent is a LADSPA plugin for real-time pitch-correction.  Among its
-controls are allowable notes, strength of correction, LFO for vibrato and
-formant warp.")
-    ;; All code except the FFT routine is licensed under GPLv2+.
-    ;; The FFT routine is under BSD-3.
-    (license license:gpl2+)))
-
 (define-public azr3
   (package
     (name "azr3")
@@ -556,47 +513,6 @@ tools (analyzer, mono/stereo tools, crossovers).")
     ;; The plugins are released under LGPLv2.1+
     (license (list license:lgpl2.1+ license:gpl2+))))
 
-(define-public caps-plugins-lv2
-  (package
-    (name "caps-plugins-lv2")
-    (version "0.9.24") ; version that has been ported.
-    (source
-     (origin
-       ;; The Github project hasn't tagged a release.
-       (method git-fetch)
-       (uri (git-reference
-             ;; Actually https://github.com/moddevices/caps-lv2.git, but it's
-             ;; missing fixes for newer glibc, so using the origin of a pull
-             ;; request regarding this issue:
-             (url "https://github.com/jujudusud/caps-lv2.git")
-             (commit "9c9478b7fbd8f9714f552ebe2a6866398b0babfb")))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "1idfnazin3cca41zw1a8vwgnxjnkrap7bxxjamjqvgpmvydgcam1"))))
-    (build-system gnu-build-system)
-    (arguments
-     `(#:tests? #f ; no check target
-       #:phases
-       (modify-phases %standard-phases
-         ;; no configure script
-         (delete 'configure)
-         (add-after 'unpack 'override-target-directory
-           (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* (find-files "plugins" "Makefile")
-               (("/usr/local")(assoc-ref outputs "out")))
-             #t)))))
-    (inputs
-     `(("lv2" ,lv2)))
-    ;; home-page of the original LADSPA version: http://quitte.de/dsp/caps.html
-    (home-page "https://github.com/moddevices/caps-lv2")
-    (synopsis "LV2 port of the CAPS audio plugin colection")
-    (description
-     "LV2 port of CAPS, a collection of audio plugins comprising basic virtual
-guitar amplification and a small range of classic effects, signal processors and
-generators of mostly elementary and occasionally exotic nature.")
-    (license license:gpl3+)))
-
 (define-public espeak
   (package
     (name "espeak")
@@ -655,14 +571,13 @@ based on human speech recordings.")
     (name "infamous-plugins")
     (version "0.2.04")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/ssj71/infamousPlugins.git")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append "https://github.com/ssj71/infamousPlugins/"
+                                  "archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0hmqk80w4qxq09iag7b7srf2g0wigkyhzq0ywxvhz2iz0hq9k0dh"))))
+                "1n6rhqsmvad7692w2h01niw5gqg5yk7a09wxl5ivs77zyp93vf7z"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests
@@ -694,14 +609,13 @@ envelope follower, distortion effects, tape effects and more.")
     (name "swh-plugins-lv2")
     (version "1.0.16")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/swh/lv2.git")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append "https://github.com/swh/"
+                                  "lv2/archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0y7nnww864mm4k6ayy2lhcws3wlbhb2gkyjbrwk921fvc18qk9mz"))))
+                "0j1mih0lp4fds07knp5i32in515sh0df1qi6694pmyz2wqnm295w"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no check target
@@ -739,14 +653,14 @@ emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.")
     (name "csound")
     (version "6.11.0")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/csound/csound.git")
-                    (commit version)))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/csound/csound/archive/"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1hlkrnv3gghx4v382nl6v6k2k1dzm5ddk35m5g3q6pzc959726s7"))))
+                "072pk5h9w0vhw0ncc9dn90haw1yv18v04iwwjn8nsp6930w7dvxd"))))
     (build-system cmake-build-system)
     (inputs
      `(("alsa-lib" ,alsa-lib)
@@ -798,8 +712,7 @@ language and software synthesizer.")
            (lambda _
              (symlink "libclalsadrv.so"
                       (string-append (assoc-ref %outputs "out")
-                                     "/lib/libclalsadrv.so.2"))
-             #t))
+                                     "/lib/libclalsadrv.so.2"))))
          ;; no configure script
          (delete 'configure))))
     (inputs
@@ -1128,7 +1041,7 @@ follower.")
 (define-public fluidsynth
   (package
     (name "fluidsynth")
-    (version "2.0.2")
+    (version "1.1.11")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1137,7 +1050,7 @@ follower.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "02vs5sfsyh1dl7wlcvgs4w3x0qcmsl7vi000qgp99ynwh3wjb274"))))
+                "0n75jq3xgq46hfmjkaaxz3gic77shs4fzajq40c8gk043i84xbdh"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f                      ; no check target
@@ -1169,22 +1082,6 @@ device.  It is the software analogue of a MIDI synthesizer.  FluidSynth can
 also play midifiles using a Soundfont.")
     (license license:lgpl2.1+)))
 
-;; gzdoom@3.3.0 and lmms@1.1.3 requires this version.  Remove once no longer
-;; needed.
-(define-public fluidsynth-1
-  (package
-    (inherit fluidsynth)
-    (version "1.1.11")
-    (source (origin
-              (inherit (package-source fluidsynth))
-              (uri (git-reference
-                    (url "https://github.com/FluidSynth/fluidsynth")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name "fluidsynth" version))
-              (sha256
-               (base32
-                "0n75jq3xgq46hfmjkaaxz3gic77shs4fzajq40c8gk043i84xbdh"))))))
-
 (define-public faad2
   (package
     (name "faad2")
@@ -1260,15 +1157,19 @@ PS, and DAB+.")
 (define-public faust-2
   (package
     (inherit faust)
-    (version "2.5.23")
+    (version "2.1.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/grame-cncm/faust/"
-                                  "releases/download/" version
-                                  "/faust-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/grame-cncm/faust.git")
+                    (commit (string-append "v"
+                                           (string-map (lambda (c)
+                                                         (if (char=? c #\.) #\- c))
+                                                       version)))))
+              (file-name (string-append "faust-" version "-checkout"))
               (sha256
                (base32
-                "1yz5jnr76hh7rmxkpdi7gyrw1wp4gyqfpq8zyl97qdi5ga5gjznq"))))
+                "06km0ygwxxwgw1lqldccqidxhmjfz8ck0wnbd95qk5sg8sbpc068"))))
     (build-system gnu-build-system)
     (arguments
      (substitute-keyword-arguments (package-arguments faust)
@@ -1276,7 +1177,7 @@ PS, and DAB+.")
         `(list (string-append "prefix=" (assoc-ref %outputs "out"))
                "world"))))
     (native-inputs
-     `(("llvm" ,llvm-3.8)
+     `(("llvm" ,llvm-with-rtti)
        ("which" ,which)
        ("xxd" ,xxd)
        ("ctags" ,emacs-minimal)  ; for ctags
@@ -1568,8 +1469,7 @@ synchronous execution of all clients, and low latency operation.")
               ((".*CFLAGS.*-Wall.*" m)
                (string-append m
                               "    conf.env.append_unique('LINKFLAGS',"
-                              "'-Wl,-rpath=" %output "/lib')\n")))
-            #t))
+                              "'-Wl,-rpath=" %output "/lib')\n")))))
          (add-after 'install 'wrap-python-scripts
           (lambda* (#:key inputs outputs #:allow-other-keys)
             ;; Make sure 'jack_control' runs with the correct PYTHONPATH.
@@ -1605,7 +1505,6 @@ synchronous execution of all clients, and low latency operation.")
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f ; no check target
-       #:python ,python-2
        #:phases
        (modify-phases %standard-phases
          (add-before
@@ -1653,20 +1552,19 @@ plugin function as a JACK application.")
     (arguments
      `(#:tests? #f  ; the "test" target is a listening test only
        #:phases
-       (modify-phases %standard-phases
-         (replace 'configure
-           (lambda* (#:key inputs outputs #:allow-other-keys #:rest args)
-             (chdir "src")
-             (let ((out (assoc-ref outputs "out")))
-               (substitute* "makefile"
-                 (("/usr/lib/ladspa/") (string-append out "/lib/ladspa/"))
-                 (("/usr/include/")    (string-append out "/include/"))
-                 (("/usr/bin/")        (string-append out "/bin/"))
-                 (("-mkdirhier")       "mkdir -p")
-                 (("^CC.*")            "CC = gcc\n")
-                 (("^CPP.*")           "CPP = g++\n")))
-             #t))
-         (delete 'build))))
+       (alist-replace
+        'configure
+        (lambda* (#:key inputs outputs #:allow-other-keys #:rest args)
+          (chdir "src")
+          (let ((out (assoc-ref outputs "out")))
+            (substitute* "makefile"
+              (("/usr/lib/ladspa/") (string-append out "/lib/ladspa/"))
+              (("/usr/include/")    (string-append out "/include/"))
+              (("/usr/bin/")        (string-append out "/bin/"))
+              (("-mkdirhier")       "mkdir -p")
+              (("^CC.*")            "CC = gcc\n")
+              (("^CPP.*")           "CPP = g++\n"))))
+        (alist-delete 'build %standard-phases))))
     ;; Since the home page is gone, we provide a link to the archived version.
     (home-page
      "https://web.archive.org/web/20140729190945/http://www.ladspa.org/")
@@ -1881,8 +1779,6 @@ significantly faster and have minimal dependencies.")
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f  ; no check target
-       ;; XXX: The bundled waf does not work with Python 3.7.
-       #:python ,python-2
        #:configure-flags '("--no-plugins")))
     (inputs
      ;; Leaving off cairo and gtk+-2.0 which are needed for example plugins
@@ -1966,14 +1862,14 @@ software.")
     (name "lvtk")
     (version "1.2.0")
     (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                   (url "https://github.com/lvtk/lvtk.git")
-                   (commit version)))
-             (file-name (git-file-name name version))
+             (method url-fetch)
+             (uri (string-append "https://github.com/lvtk/lvtk/archive/"
+                                 version
+                                 ".tar.gz"))
+             (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
-               "1b01zvzl70ana6l1kn8fgyr7msnn3c7x61cgw7fdpp50322352p8"))))
+               "03nbj2cqcklqwh50zj2gwm07crh5iwqbpxbpzwbg5hvgl4k4rnjd"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f  ; no check target
@@ -2014,7 +1910,7 @@ lv2-c++-tools.")
 (define-public openal
   (package
     (name "openal")
-    (version "1.19.1")
+    (version "1.19.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2022,7 +1918,7 @@ lv2-c++-tools.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1sdjhkz2gd6lbnwphi1b6aw3br4wv2lik5vnqh6mxfc8a7zqfbsw"))))
+                "1mhf5bsb58s1xk6hvxl7ly7rd4rpl9z8h07xl1q94brywykg7bgi"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f  ; no check target
@@ -2181,7 +2077,7 @@ background file post-processing.")
 (define-public supercollider
   (package
     (name "supercollider")
-    (version "3.9.3")
+    (version "3.9.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2190,7 +2086,7 @@ background file post-processing.")
                     "/SuperCollider-" version "-Source-linux.tar.bz2"))
               (sha256
                (base32
-                "1d8ixfl100jvlialxdizp8wqsl1mp5pi2bam25vp97bhjd59cfdr"))))
+                "0d3cb6dw8jz7ijriqn3rlwin24gffczp69hl17pzxj1d5w57yj44"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags '("-DSYSTEM_BOOST=on" "-DSYSTEM_YAMLCPP=on"
@@ -2359,32 +2255,36 @@ tempo and pitch of an audio recording independently of one another.")
     (name "rtmidi")
     (version "2.1.0")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/powertab/rtmidi.git")
-                    (commit version)))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri
+               (string-append "https://github.com/powertab/rtmidi/archive/"
+                              version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "106v177y3nrjv2l1yskch4phpqd8h97b67zj0jiq9pc3c69jr1ay"))))
+                "0d49lapnmdgmjxh4vw57h6xk74nn5r0zwysv7jbd7m8kqhpq5rjj"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'fix-makefile
-           (lambda _
-             (substitute* "Makefile"
-               (("/bin/ln") "ln")
-               (("RtMidi.h RtError.h") "RtMidi.h"))
-             #t))
-         (add-before 'install 'make-target-dirs
-           (lambda _
-             (let ((out (assoc-ref %outputs "out")))
-               (mkdir-p (string-append out "/bin"))
-               (mkdir (string-append out "/lib"))
-               (mkdir (string-append out "/include")))
-             #t)))))
+       #:phases (modify-phases %standard-phases
+                  (add-after
+                   'unpack 'autoconf
+                   (lambda _ (invoke "autoreconf" "-vfi")))
+                  (add-before
+                   'build 'fix-makefile
+                   (lambda _
+                     (substitute* "Makefile"
+                       (("/bin/ln") "ln")
+                       (("RtMidi.h RtError.h") "RtMidi.h"))
+                     #t))
+                  (add-before
+                   'install 'make-target-dirs
+                   (lambda _
+                     (let ((out (assoc-ref %outputs "out")))
+                       (mkdir-p (string-append out "/bin"))
+                       (mkdir (string-append out "/lib"))
+                       (mkdir (string-append out "/include")))
+                     #t)))))
     (inputs
      `(("jack" ,jack-1)
        ("alsa-lib" ,alsa-lib)))
@@ -2441,7 +2341,6 @@ the Turtle syntax.")
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f ; no check target
-       #:python ,python-2 ;XXX: The bundled waf does not work with Python 3.7.0.
        #:configure-flags
        '("CXXFLAGS=-std=gnu++11")))
     (inputs
@@ -2590,8 +2489,7 @@ analysis plugins or audio feature extraction plugins.")
             (symlink
              (string-append (assoc-ref inputs "automake") "/share/automake-"
                             ,(package-version automake) "/ar-lib")
-             "ar-lib")
-            #t)))))
+             "ar-lib"))))))
     (home-page "http://sbsms.sourceforge.net/")
     (synopsis "Library for time stretching and pitch scaling of audio")
     (description
@@ -2836,14 +2734,20 @@ portions of LAME.")
      ;; TODO: Add ASIHPI.
      `(("alsa-lib" ,alsa-lib)
        ("jack" ,jack-1)))
-    ;; Autoreconf is necessary because the audacity-compat patch modifies .in
-    ;; files.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
        ("libtool" ,libtool)
        ("pkg-config" ,pkg-config)))
-    (arguments '(#:tests? #f))                    ;no 'check' target
+    (arguments
+     '(#:phases
+       ;; Autoreconf is necessary because the audacity-compat patch modifies
+       ;; .in files.
+       (modify-phases %standard-phases
+         (add-after 'unpack 'autoreconf
+           (lambda _
+             (invoke "autoreconf" "-vif"))))
+       #:tests? #f))                    ;no 'check' target
     (home-page "http://www.portaudio.com/")
     (synopsis "Audio I/O library")
     (description
@@ -2855,7 +2759,7 @@ interface.")
 (define-public qsynth
   (package
     (name "qsynth")
-    (version "0.5.3")
+    (version "0.5.2")
     (source
      (origin
        (method url-fetch)
@@ -2863,7 +2767,7 @@ interface.")
                            "/qsynth-" version ".tar.gz"))
        (sha256
         (base32
-         "1jghczmmva7cyavg1q0j8nr3hmjpzzglzi5ckg92ax4ji8gpks9c"))))
+         "1rfkaxq1pyc4hv3l0i6wicianbcbm1wp53kh9i5d4jsljgisd1dv"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no "check" phase
@@ -2889,13 +2793,12 @@ synthesizer written in C++.")
     (version "1.1")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/Themaister/RSound.git")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (string-append "https://github.com/Themaister/RSound/archive/v"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version))
        (sha256
-        (base32 "0gspmr3klwnq98h17p5hc6ifygya4p80g4g8r7a1qavm3mv19waf"))))
+        (base32 "1wzs40c0k5zpkmm5ffl6c17xmr399sxli7ys0fbb9ib0fd334knx"))))
     (build-system gnu-build-system)
     (inputs
      `(("alsa-lib" ,alsa-lib)
@@ -2928,14 +2831,14 @@ with a much different focus than most other audio daemons.")
     (name "xjackfreak")
     (version "1.0")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/johnhldavis/xjackfreak.git")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/johnhldavis/xjackfreak/archive/v"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "18c546qidbrj0f5wfiq5llii2192xpln0ab3r4vpr7i3wybxqjfz"))))
+                "0xj6gpxfnw9jbdgwgm0x23xgfvj2kwmwb1nk0drw8lxgcchkq7d9"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
@@ -2987,14 +2890,12 @@ result.")
              (substitute* "libs/Makefile"
                (("ldconfig") "true")
                (("^LIBDIR =.*") "LIBDIR = lib\n"))
-             (chdir "libs")
-             #t))
+             (chdir "libs") #t))
          (add-after 'install 'install-symlink
            (lambda _
              (symlink "libzita-convolver.so"
                       (string-append (assoc-ref %outputs "out")
-                                     "/lib/libzita-convolver.so.3"))
-             #t))
+                                     "/lib/libzita-convolver.so.3"))))
          ;; no configure script
          (delete 'configure))))
     (inputs `(("fftwf" ,fftwf)))
@@ -3044,8 +2945,7 @@ engine.")
           (lambda _
             (symlink "libzita-resampler.so"
                      (string-append (assoc-ref %outputs "out")
-                                    "/lib/libzita-resampler.so.1"))
-            #t))
+                                    "/lib/libzita-resampler.so.1"))))
          ;; no configure script
          (delete 'configure))))
     (home-page "https://kokkinizita.linuxaudio.org/linuxaudio/zita-resampler/resampler.html")
@@ -3086,8 +2986,7 @@ provide high-quality sample rate conversion.")
            (lambda _
              (symlink "libzita-alsa-pcmi.so"
                       (string-append (assoc-ref %outputs "out")
-                                     "/lib/libzita-alsa-pcmi.so.0"))
-             #t))
+                                     "/lib/libzita-alsa-pcmi.so.0"))))
           ;; no configure script
           (delete 'configure))))
     (inputs
@@ -3107,16 +3006,15 @@ point audio data.")
     (name "cuetools")
     (version "1.4.1")
     (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                   (url "https://github.com/svend/cuetools.git")
-                   (commit version)))
-             (file-name (git-file-name name version))
+             (method url-fetch)
+             (uri (string-append "https://github.com/svend/cuetools/archive/"
+                                 version ".tar.gz"))
+             (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
-               "02ksv1ahf1v4cr2xbclsfv5x17m9ivzbssb5r8xjm97yh8a7spa3"))))
+               "01xi3rvdmil9nawsha04iagjylqr1l9v9vlzk99scs8c207l58i4"))))
     (build-system gnu-build-system)
-    ;; The source checkout is not bootstrapped.
+    ;; The source tarball is not bootstrapped.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
@@ -3157,14 +3055,13 @@ use them split WAVE data into multiple files.")
     (name "dcadec")
     (version "0.2.0")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/foo86/dcadec.git")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append "https://github.com/foo86/dcadec/archive/v"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "07nd0ajizrp1w02bsyfcv18431r8m8rq8gjfmz9wmckpg7cxj2hs"))))
+                "0i0dpypgqkhhi4v1fmsp2way6w9kbcix3c7q79pmg39yvrzj17gd"))))
     (build-system gnu-build-system)
     (arguments
      ;; Test files are missing: https://github.com/foo86/dcadec/issues/53
@@ -3191,7 +3088,7 @@ with support for HD extensions.")
 (define-public bs1770gain
   (package
     (name "bs1770gain")
-    (version "0.5.1")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
@@ -3199,7 +3096,7 @@ with support for HD extensions.")
                            version "/bs1770gain-" version ".tar.gz"))
        (sha256
         (base32
-         "0r4fbajgfmnwgl63hcm56f1j8m5f135q6j5jkzdvrrhpcj39yx06"))))
+         "0vd7320k7s2zcn2vganclxbr1vav18ghld27rcwskvcc3dm8prii"))))
     (build-system gnu-build-system)
     (inputs `(("ffmpeg" ,ffmpeg)
               ("sox" ,sox)))
@@ -3272,8 +3169,7 @@ code, used in @code{libtoxcore}.")
                (mkdir-p (string-append out "/man/man1"))
                (mkdir-p (string-append out "/man/man3"))
                (mkdir-p (string-append out "/bin"))
-               (mkdir-p (string-append out "/lib")))
-             #t))
+               (mkdir-p (string-append out "/lib")))))
          (add-after 'install 'post-install
            (lambda _
              (let ((out (assoc-ref %outputs "out")))
@@ -3281,8 +3177,7 @@ code, used in @code{libtoxcore}.")
                             (string-append out "/include"))
                (mkdir-p (string-append out "/include/gsm"))
                (copy-recursively "inc"
-                                 (string-append out "/include/gsm")))
-             #t))
+                                 (string-append out "/include/gsm")))))
          (delete 'configure))))         ; no configure script
     (synopsis "GSM 06.10 lossy speech compression library")
     (description "This C library provides an encoder and a decoder for the GSM
@@ -3471,14 +3366,13 @@ the following features:
     (version "1.6")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/dpayne/cli-visualizer.git")
-             (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (string-append "https://github.com/dpayne/cli-visualizer/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0mirp8bk398di5xyq95iprmdyvplfghxqmrfj7jdnpy554vx7ppc"))))
+         "07zkm87f2fr8kc6531zrkya7q81sdanm6813y2f54mg13g41y6hi"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("which" ,which)))
@@ -3526,14 +3420,14 @@ representations.")
     (name "cava")
     (version "0.6.1")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/karlstav/cava.git")
-                    (commit version)))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/karlstav/cava/archive/"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1kvhqgijs29909w3sq9m0bslx2zxxn4b3i07kdz4hb0dqkppxpjy"))))
+                "13d72swnjs894llf0paandmhf1lf90dz6ygkcdw4bv84wzkq1f4q"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -3558,16 +3452,14 @@ representations.")
              (invoke "sh" "autogen.sh")))
          (add-before 'build 'make-cava-ldflags
            (lambda* (#:key outputs #:allow-other-keys)
-             (mkdir-p (string-append (assoc-ref outputs "out") "/lib"))
-             #t))
+             (mkdir-p (string-append (assoc-ref outputs "out") "/lib"))))
          (add-after 'install 'data
            (lambda* (#:key outputs #:allow-other-keys)
              (for-each (lambda (file)
                          (install-file file
                                        (string-append (assoc-ref outputs "out")
                                                       "/share/doc/examples")))
-                       (find-files "example_files"))
-             #t)))))
+                       (find-files "example_files")))))))
     (home-page "https://karlstav.github.io/cava/")
     (synopsis "Console audio visualizer for ALSA, MPD, and PulseAudio")
     (description "C.A.V.A. is a bar audio spectrum visualizer for the terminal
@@ -3606,72 +3498,3 @@ using ALSA, MPD, PulseAudio, or a FIFO buffer as its input.")
       (synopsis "Pro-quality GM soundfont")
       (description "Fluid-3 is Frank Wen's pro-quality GM soundfont.")
       (license license:expat))))
-
-(define-public libfdk
-  (let ((commit "2326faaf8f2cdf2c3a9108ccdaf1d7551aec543e")
-        (revision "0"))
-    (package
-      (name "libfdk")
-      ;; The latest upstream revision, with many bug fixes.
-      (version (git-version "0.1.6" revision commit))
-      (source
-        (origin
-          (method git-fetch)
-          (uri (git-reference
-                 (url "https://github.com/mstorsjo/fdk-aac")
-                 (commit commit)))
-          (file-name (git-file-name name version))
-          (sha256
-           (base32
-            "0yy6ndd9d61bwl283vl1r5kva2a4acc0f4r9g0sza156f2abr9ws"))))
-      (build-system gnu-build-system)
-      (native-inputs
-       `(("autoconf" ,autoconf)
-         ("automake" ,automake)
-         ("libtool" ,libtool)))
-      (home-page "https://github.com/mstorsjo/fdk-aac")
-      (synopsis "Fraunhofer FDK AAC library")
-      (description "FDK is a library for encoding and decoding Advanced Audio
-Coding (AAC) format audio, developed by Fraunhofer IIS, and included as part of
-Android.  It supports several Audio Object Types including MPEG-2 and MPEG-4 AAC
-LC, HE-AAC (AAC LC + SBR), HE-AACv2 (LC + SBR + PS) as well AAC-LD (low delay)
-and AAC-ELD (enhanced low delay) for real-time communication.  The encoding
-library supports sample rates up to 96 kHz and up to eight channels (7.1
-surround).")
-      (license (license:fsf-free "https://github.com/mstorsjo/fdk-aac/blob/master/NOTICE"
-                                 "https://www.gnu.org/licenses/license-list.html#fdk")))))
-
-(define-public libopenshot-audio
-  (package
-    (name "libopenshot-audio")
-    (version "0.1.7")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/OpenShot/libopenshot-audio")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "08a8wbi28kwrdz4h0rs1b9vsr28ldfi8g75q54rj676y1vwg3qys"))))
-    (build-system cmake-build-system)
-    (inputs
-     `(("alsa-lib" ,alsa-lib)
-       ;; The following are for JUCE GUI components:
-       ("libx11" ,libx11)
-       ("freetype" ,freetype)
-       ("libxrandr" ,libxrandr)
-       ("libxinerama" ,libxinerama)
-       ("libxcursor" ,libxcursor)))
-    (arguments
-     `(#:tests? #f                      ;there are no tests
-       #:configure-flags
-       (list (string-append "-DCMAKE_CXX_FLAGS=-I"
-                            (assoc-ref %build-inputs "freetype")
-                            "/include/freetype2"))))
-    (home-page "https://openshot.org")
-    (synopsis "Audio editing and playback for OpenShot")
-    (description "OpenShot Audio Library (libopenshot-audio) allows
-high-quality editing and playback of audio, and is based on the JUCE
-library.")
-    (license license:lgpl3+)))

gnu/packages/authentication.scm

@@ -17,7 +17,6 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages authentication)
-  #:use-module (gnu packages)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages pkg-config)
   #:use-module (guix build-system gnu)
@@ -36,7 +35,6 @@
        (method url-fetch)
        (uri (string-append "https://download.savannah.nongnu.org/releases/"
                            name "/" name "-" version ".tar.gz"))
-       (patches (search-patches "oath-toolkit-glibc-compat.patch"))
        (sha256
         (base32 "182ah8vfbg0yhv6mh1b6ap944d0na6x7lpfkwkmzb6jl9gx4cd5h"))))
     (build-system gnu-build-system)

gnu/packages/backup.scm

@@ -11,7 +11,6 @@
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -31,7 +30,6 @@
 (define-module (gnu packages backup)
   #:use-module (guix packages)
   #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix git-download)
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
@@ -134,18 +132,22 @@ spying and/or modification by the server.")
     (name "par2cmdline")
     (version "0.8.0")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/Parchive/par2cmdline.git")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append "https://github.com/Parchive/par2cmdline/archive/v"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0f1jsd5sw2wynjzi7yjqjaf13yhyjfdid91p8yh0jn32y03kjyrz"))))
+                "1jpshmmcr81mxly0md2rr231qz9c8c680bbvcmhh100dg9i4a6s6"))))
     (native-inputs
      `(("automake" ,automake)
        ("autoconf" ,autoconf)))
     (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'autoreconf
+           (lambda _ (invoke "autoreconf" "-vfi"))))))
     (synopsis "File verification and repair tools")
     (description "Par2cmdline uses Reed-Solomon error-correcting codes to
 generate and verify PAR2 recovery files.  These files can be distributed
@@ -887,7 +889,6 @@ is like a time machine for your data. ")
                                         ,version)
                ;; Disable 'restic self-update'.  It makes little sense in Guix.
                (substitute* "build.go" (("selfupdate") ""))
-               (setenv "HOME" (getcwd)) ; for $HOME/.cache/go-build
                (invoke "go" "run" "build.go"))))
 
          (replace 'check

gnu/packages/base.scm

@@ -102,15 +102,6 @@ command-line arguments, multiple languages, and so on.")
    (arguments
     `(#:phases
       (modify-phases %standard-phases
-        (add-before 'check 'disable-failing-tests
-          (lambda _
-            ;; These tests are expected to fail due to a glibc bug which has
-            ;; been fixed in 2.28, so they are unexpectedly passing.  They
-            ;; should be fixed for grep versions > 3.1.
-            (substitute* "tests/Makefile.in"
-              (("^[[:blank:]]+backref-alt[[:blank:]]+\\\\") "\\")
-              (("^[[:blank:]]+triple-backref[[:blank:]]+\\\\") "\\"))
-            #t))
         (add-after 'install 'fix-egrep-and-fgrep
           ;; Patch 'egrep' and 'fgrep' to execute 'grep' via its
           ;; absolute file name instead of searching for it in $PATH.
@@ -298,9 +289,7 @@ interactive means to merge two files.")
              (base32
               "178nn4dl7wbcw499czikirnkniwnx36argdnqgz4ik9i6zvwkm6y"))
             (patches (search-patches
-                      "findutils-gnulib-libio.patch"
                       "findutils-localstatedir.patch"
-                      "findutils-makedev.patch"
                       "findutils-test-xargs.patch"))
             (modules '((guix build utils)))
             (snippet
@@ -337,14 +326,14 @@ used to apply commands with arbitrarily long arguments.")
 (define-public coreutils
   (package
    (name "coreutils")
-   (version "8.30")
+   (version "8.29")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/coreutils/coreutils-"
                                 version ".tar.xz"))
             (sha256
              (base32
-              "0mxhw43d4wpqmvg0l4znk1vm10fy92biyh90lzdnqjcic2lb6cg8"))))
+              "0plm1zs9il6bb5mk881qvbghq4glc8ybbgakk2lfzb0w64fgml4j"))))
    (build-system gnu-build-system)
    (inputs `(("acl"  ,acl)                        ; TODO: add SELinux
              ("gmp"  ,gmp)                        ;bignums in 'expr', yay!
@@ -375,17 +364,7 @@ used to apply commands with arbitrarily long arguments.")
                      (substitute* (find-files "gnulib-tests" "\\.c$")
                        (("/bin/sh") (which "sh")))
                      (substitute* (find-files "tests" "\\.sh$")
-                       (("#!/bin/sh") (string-append "#!" (which "sh"))))
-                     #t))
-                 (add-before 'check 'disable-broken-test
-                   (lambda _
-                     ;; This test hits the 127 character shebang limit in the build
-                     ;; environment due to the way "env -S" splits arguments into
-                     ;; shebangs.  Note that "env-S-script.sh" works around this
-                     ;; specific issue, but "env-S.pl" is not adjusted for build
-                     ;; environments with long prefixes (/tmp/guix-build-...).
-                     (substitute* "Makefile"
-                       (("^.*tests/misc/env-S.pl.*$") ""))
+                       (("#!/bin/sh") (which "sh")))
                      #t)))
 
       ;; Work around a cross-compilation bug whereby libcoreutils.a would
@@ -456,14 +435,14 @@ change.  GNU make offers many powerful extensions over the standard utility.")
 (define-public binutils
   (package
    (name "binutils")
-   (version "2.31.1")
+   (version "2.30")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/binutils/binutils-"
                                 version ".tar.bz2"))
             (sha256
              (base32
-              "1l34hn1zkmhr1wcrgf0d4z7r3najxnw3cx2y2fk7v55zjlk3ik7z"))
+              "028cklfqaab24glva1ks2aqa1zxa6w6xmc8q34zs1sb7h22dxspg"))
             (patches (search-patches "binutils-loongson-workaround.patch"))))
    (build-system gnu-build-system)
 
@@ -501,6 +480,17 @@ included.")
    (license gpl3+)
    (home-page "https://www.gnu.org/software/binutils/")))
 
+(define-public binutils/fixed
+  ;; TODO: Incorporate this in binutils during the next rebuild cycle.
+  (hidden-package
+   (package
+     (inherit binutils)
+     (source (origin
+               (inherit (package-source binutils))
+               (patches (append (origin-patches (package-source binutils))
+                                (search-patches
+                                 "binutils-aarch64-symbol-relocation.patch"))))))))
+
 (define* (make-ld-wrapper name #:key
                           (target (const #f))
                           binutils
@@ -577,20 +567,18 @@ store.")
 
 (export make-ld-wrapper)
 
-(define-public glibc
-  ;; This is the GNU C Library, used on GNU/Linux and GNU/Hurd.  Prior to
-  ;; version 2.28, GNU/Hurd used a different glibc branch.
+(define-public glibc/linux
   (package
    (name "glibc")
    ;; Note: Always use a dot after the minor version since various places rely
    ;; on "version-major+minor" to determine where locales are found.
-   (version "2.28")
+   (version "2.27")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/glibc/glibc-" version ".tar.xz"))
             (sha256
              (base32
-              "10iha5ynvdj5m62vgpgqbq4cwvc2yhyl2w9yyyjgfxmdmx8h145i"))
+              "0wpwq7gsm7sd6ysidv0z575ckqdg13cr2njyfgrbgh4f65adwwji"))
             (snippet
              ;; Disable 'ldconfig' and /etc/ld.so.cache.  The latter is
              ;; required on LFS distros to avoid loading the distro's libc.so
@@ -602,7 +590,7 @@ store.")
                 #t))
             (modules '((guix build utils)))
             (patches (search-patches "glibc-ldd-x86_64.patch"
-                                     "glibc-2.28-git-fixes.patch"
+                                     "glibc-2.27-git-fixes.patch"
                                      "glibc-hidden-visibility-ldconfig.patch"
                                      "glibc-versioned-locpath.patch"
                                      "glibc-allow-kernel-2.6.32.patch"
@@ -610,13 +598,8 @@ store.")
    (build-system gnu-build-system)
 
    ;; Glibc's <limits.h> refers to <linux/limit.h>, for instance, so glibc
-   ;; users should automatically pull Linux headers as well.  On GNU/Hurd,
-   ;; libc provides <hurd.h>, which includes a bunch of Hurd and Mach headers,
-   ;; so both should be propagated.
-   (propagated-inputs
-    (if (hurd-target?)
-        `(("hurd-core-headers" ,hurd-core-headers))
-        `(("kernel-headers" ,linux-libre-headers))))
+   ;; users should automatically pull Linux headers as well.
+   (propagated-inputs `(("kernel-headers" ,linux-libre-headers)))
 
    (outputs '("out" "debug"
               "static"))                          ;9 MiB of .a files
@@ -671,13 +654,7 @@ store.")
             ;; Use our Bash instead of /bin/sh.
             (string-append "BASH_SHELL="
                            (assoc-ref %build-inputs "bash")
-                           "/bin/bash")
-
-            ;; On GNU/Hurd we get discarded-qualifiers warnings for
-            ;; 'device_write_inband' among other things.  Ignore them.
-            ,@(if (hurd-target?)
-                  '("--disable-werror")
-                  '()))
+                           "/bin/bash"))
 
       #:tests? #f                                 ; XXX
       #:phases (modify-phases %standard-phases
@@ -782,18 +759,7 @@ store.")
                                  (filter linker-script?
                                          (map (cut string-append slib "/" <>)
                                               files)))
-                       #t)))
-
-                 ,@(if (hurd-target?)
-                       '((add-after 'install 'augment-libc.so
-                           (lambda* (#:key outputs #:allow-other-keys)
-                             (let* ((out (assoc-ref outputs "out")))
-                               (substitute* (string-append out "/lib/libc.so")
-                                 (("/[^ ]+/lib/libc.so.0.3")
-                                  (string-append out "/lib/libc.so.0.3"
-                                                 " libmachuser.so libhurduser.so"))))
-                             #t)))
-                       '()))))
+                       #t))))))
 
    (inputs `(("static-bash" ,static-bash)))
 
@@ -802,12 +768,7 @@ store.")
    (native-inputs `(("texinfo" ,texinfo)
                     ("perl" ,perl)
                     ("bison" ,bison)
-                    ("gettext" ,gettext-minimal)
-
-                    ,@(if (hurd-target?)
-                          `(("mig" ,mig)
-                            ("perl" ,perl))
-                          '())))
+                    ("gettext" ,gettext-minimal)))
 
    (native-search-paths
     ;; Search path for packages that provide locale data.  This is useful
@@ -829,25 +790,108 @@ with the Linux kernel.")
    (license lgpl2.0+)
    (home-page "https://www.gnu.org/software/libc/")))
 
-;; Below are old libc versions, which we use mostly to build locale data in
-;; the old format (which the new libc cannot cope with.)
+(define-public glibc/hurd
+  ;; The Hurd's libc variant.
+  (package (inherit glibc/linux)
+    (name "glibc-hurd")
+    (version "2.23")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://alpha.gnu.org/gnu/hurd/glibc-"
+                                  version "-hurd+libpthread-20161218" ".tar.gz"))
+              (sha256
+               (base32
+                "0vpdv05j6j3ria5bw8gp468i64gij94cslxkxj9xkfgi6p615b8p"))))
 
-(define-public glibc-2.27
+    ;; Libc provides <hurd.h>, which includes a bunch of Hurd and Mach headers,
+    ;; so both should be propagated.
+    (propagated-inputs `(("hurd-core-headers" ,hurd-core-headers)))
+    (native-inputs
+     `(,@(package-native-inputs glibc/linux)
+       ("mig" ,mig)
+       ("perl" ,perl)))
+
+    (arguments
+     (substitute-keyword-arguments (package-arguments glibc/linux)
+       ((#:phases original-phases)
+        ;; Add libmachuser.so and libhurduser.so to libc.so's search path.
+        ;; See <http://lists.gnu.org/archive/html/bug-hurd/2015-07/msg00051.html>.
+        `(modify-phases ,original-phases
+           (add-after 'install 'augment-libc.so
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out")))
+                 (substitute* (string-append out "/lib/libc.so")
+                   (("/[^ ]+/lib/libc.so.0.3")
+                    (string-append out "/lib/libc.so.0.3" " libmachuser.so" " libhurduser.so"))))
+               #t))
+           (add-after 'pre-configure 'pre-configure-set-pwd
+             (lambda _
+               ;; Use the right 'pwd'.
+               (substitute* "configure"
+                 (("/bin/pwd") "pwd"))
+               #t))
+           (replace 'build
+             (lambda _
+               ;; Force mach/hurd/libpthread subdirs to build first in order to avoid
+               ;; linking errors.
+               ;; See <https://lists.gnu.org/archive/html/bug-hurd/2016-11/msg00045.html>
+               (let ((flags (list "-j" (number->string (parallel-job-count)))))
+                 (define (make target)
+                   (apply invoke "make" target flags))
+                 (make "mach/subdir_lib")
+                 (make "hurd/subdir_lib")
+                 (make "libpthread/subdir_lib")
+                 (apply invoke "make" flags))))))
+        ((#:configure-flags original-configure-flags)
+        `(append (list "--host=i586-pc-gnu"
+
+                       ;; We need this to get a working openpty() function.
+                       "--enable-pt_chown"
+
+                       ;; <https://lists.gnu.org/archive/html/bug-hurd/2016-10/msg00033.html>
+                       "--disable-werror"
+
+                       ;; nscd fails to build for GNU/Hurd:
+                       ;; <https://lists.gnu.org/archive/html/bug-hurd/2014-07/msg00006.html>.
+                       ;; Disable it.
+                       "--disable-nscd")
+                 (filter (lambda (flag)
+                           (not (string-prefix? "--enable-kernel=" flag)))
+                         ,original-configure-flags)))))
+    (synopsis "The GNU C Library (GNU Hurd variant)")
+    (supported-systems %hurd-systems)))
+
+(define* (glibc-for-target #:optional
+                           (target (or (%current-target-system)
+                                       (%current-system))))
+  "Return the glibc for TARGET, GLIBC/LINUX for a Linux host or
+GLIBC/HURD for a Hurd host"
+  (match target
+    ((or "i586-pc-gnu" "i586-gnu") glibc/hurd)
+    (_ glibc/linux)))
+
+(define-syntax glibc
+  (identifier-syntax (glibc-for-target)))
+
+;; The "next" libc.  Useful for populating locale data before reconfiguring the
+;; entire system on it.  Will be the default in the next rebuild cycle.
+(define-public glibc-2.28
   (package
     (inherit glibc)
-    (version "2.27")
+    (version "2.28")
     (source (origin
               (inherit (package-source glibc))
               (uri (string-append "mirror://gnu/glibc/glibc-" version ".tar.xz"))
               (sha256
                (base32
-                "0wpwq7gsm7sd6ysidv0z575ckqdg13cr2njyfgrbgh4f65adwwji"))
-              (patches (search-patches "glibc-ldd-x86_64.patch"
-                                       "glibc-2.27-git-fixes.patch"
+                "10iha5ynvdj5m62vgpgqbq4cwvc2yhyl2w9yyyjgfxmdmx8h145i"))
+              (patches (search-patches "glibc-allow-kernel-2.6.32.patch"
+                                       "glibc-ldd-x86_64.patch"
                                        "glibc-hidden-visibility-ldconfig.patch"
-                                       "glibc-versioned-locpath.patch"
-                                       "glibc-allow-kernel-2.6.32.patch"
-                                       "glibc-reinstate-prlimit64-fallback.patch"))))))
+                                       "glibc-versioned-locpath.patch"))))))
+
+;; Below are old libc versions, which we use mostly to build locale data in
+;; the old format (which the new libc cannot cope with.)
 
 (define-public glibc-2.26
   (package
@@ -1067,17 +1111,18 @@ command.")
     (license gpl3+))) ; some files are under GPLv2+
 
 (define-public glibc/hurd-headers
-  (package (inherit glibc)
+  (package (inherit glibc/hurd)
     (name "glibc-hurd-headers")
     (outputs '("out"))
     (propagated-inputs `(("gnumach-headers" ,gnumach-headers)
                          ("hurd-headers" ,hurd-headers)))
     (arguments
-     (substitute-keyword-arguments (package-arguments glibc)
+     (substitute-keyword-arguments (package-arguments glibc/hurd)
        ;; We just pass the flags really needed to build the headers.
        ((#:configure-flags _)
         `(list "--enable-add-ons"
-               "--host=i586-pc-gnu"))
+               "--host=i586-pc-gnu"
+               "--enable-obsolete-rpc"))
        ((#:phases _)
         '(modify-phases %standard-phases
            (replace 'install
@@ -1092,7 +1137,13 @@ command.")
                   (open-output-file
                    (string-append out "/include/gnu/stubs.h"))))
                #t))
-           (delete 'build)))))))                  ; nothing to build
+           (delete 'build)              ; nothing to build
+           (add-before 'configure 'patch-configure-script
+             (lambda _
+               ;; Use the right 'pwd'.
+               (substitute* "configure"
+                 (("/bin/pwd") "pwd"))
+               #t))))))))
 
 (define-public tzdata
   (package

gnu/packages/bash.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2017 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -79,11 +79,7 @@
    (16 "1cgi1y6mifm8hsgv4avj5ih76535js3qba1sqwbfvp7si76927sh")
    (17 "0w6jpj2giakji1ir83rpkx1y7n7xqppah3j748m6dm38hywr0gvp")
    (18 "1k58h4wxbsg7r4rwhrvzx5hfbapba2nxjysbhh6qp6ki5ys99i2v")
-   (19 "07n1i5610lbs672x1s8g82qn3qfj06s0ip3z80sri0g8vxp0s5r7")
-   (20 "0b2jk5n1af1vh590qfc52hv65mafb4vl1xv26s8j5a3byb5y4h0q")
-   (21 "1hblcd2xmqqlp0idnavw66570n7m0yv5rbbr873c2gkn982mk3xx")
-   (22 "0yfbjzr79vzjs2hyi5m8iy2b38fq7vikdfa4zqdvjsp36q4iycs5")
-   (23 "1dlism6qdx60nvzj0v7ndr7lfahl4a8zmzckp13hqgdx7xpj7v2g")))
+   (19 "07n1i5610lbs672x1s8g82qn3qfj06s0ip3z80sri0g8vxp0s5r7")))
 
 (define (download-patches store count)
   "Download COUNT Bash patches into store.  Return a list of

gnu/packages/bdw-gc.scm

@@ -30,14 +30,14 @@
 (define-public libgc
   (package
    (name "libgc")
-   (version "7.6.6")
+   (version "7.6.4")
    (source (origin
             (method url-fetch)
-            (uri (string-append "https://github.com/ivmai/bdwgc/releases"
-                                "/download/v" version "/gc-" version ".tar.gz"))
+            (uri (string-append "http://www.hboehm.info/gc/gc_source/gc-"
+                                version ".tar.gz"))
             (sha256
              (base32
-              "1p1r015a7jbpvkkbgzv1y8nxrbbp6dg0mq3ksi6ji0qdz3wfss79"))))
+              "076dzsqqyxd3nlzs0z277vvhqjp8nv5dqi763s0m90zr6ljiyk5r"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags
@@ -91,7 +91,7 @@ C or C++ programs, though that is not its primary goal.")
 (define-public libatomic-ops
   (package
     (name "libatomic-ops")
-    (version "7.6.6")
+    (version "7.6.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -99,7 +99,7 @@ C or C++ programs, though that is not its primary goal.")
                     version "/libatomic_ops-" version ".tar.gz"))
               (sha256
                (base32
-                "0x7071z707msvyrv9dmgahd1sghbkw8fpbagvcag6xs8yp2spzlr"))))
+                "0knxncsjhbknlyy6lx7ycxhpzfk3sykhvicgxyp0rmsxd1d3v0jv"))))
     (build-system gnu-build-system)
     (outputs '("out" "debug"))
     (synopsis "Accessing hardware atomic memory update operations")

gnu/packages/benchmark.scm

@@ -35,14 +35,14 @@
 (define-public fio
   (package
     (name "fio")
-    (version "3.11")
+    (version "3.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://brick.kernel.dk/snaps/"
-                                  "fio-" version ".tar.bz2"))
+                                  "fio-" version ".tar.gz"))
               (sha256
                (base32
-                "0s8m0wcz5j6sa1hblj80wk3syy5b4shg7y3gabvm9xa3wj0lzasa"))))
+                "0rw9jf2ikm19lq4jizavdvvp3vfvlm3annq7jsxl2y5nf1pi2qr7"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"

gnu/packages/bioconductor.scm

@@ -201,14 +201,14 @@ genomes and gene ID formats, largely based on the UCSC table browser.")
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.24.0")
+    (version "1.22.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
+         "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/hpar/")
     (synopsis "Human Protein Atlas in R")
@@ -219,24 +219,23 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.14.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
+         "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-genomeinfodb" ,r-genomeinfodb)
+     `(("r-memoise" ,r-memoise)
        ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-memoise" ,r-memoise)
+       ("r-bsgenome" ,r-bsgenome)
        ("r-rtracklayer" ,r-rtracklayer)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-iranges" ,r-iranges)
        ("r-s4vectors" ,r-s4vectors)))
     (home-page "https://bioconductor.org/packages/regioneR/")
     (synopsis "Association analysis of genomic regions")
@@ -248,14 +247,14 @@ region sets and other genomic features.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "2.10.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
+         "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (inputs
@@ -293,14 +292,14 @@ occupancy (overlap) analysis and plotting functions.")
 (define-public r-ripseeker
   (package
     (name "r-ripseeker")
-    (version "1.22.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RIPSeeker" version))
        (sha256
         (base32
-         "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
+         "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
     (properties `((upstream-name . "RIPSeeker")))
     (build-system r-build-system)
     (propagated-inputs
@@ -326,14 +325,14 @@ processing to visualization and annotation.")
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.38.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
+         "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-survival" ,r-survival)
@@ -364,13 +363,13 @@ expressed genes in DNA microarray experiments.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.60.0")
+    (version "1.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
+                "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))
@@ -411,19 +410,18 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.16.0")
+    (version "3.14.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3"))))
+         "13rksc65lxxzyw11galh6xzvgzp5ii0gwiwpvrm395v2r17rhwsc"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
        ("r-biostrings" ,r-biostrings)
        ("r-delayedarray" ,r-delayedarray)
        ("r-go-db" ,r-go-db)
@@ -439,6 +437,7 @@ determining dependencies between variables, code improvement suggestions.")
        ("r-multtest" ,r-multtest)
        ("r-rbgl" ,r-rbgl)
        ("r-graph" ,r-graph)
+       ("r-biocinstaller" ,r-biocinstaller)
        ("r-regioner" ,r-regioner)
        ("r-dbi" ,r-dbi)
        ("r-ensembldb" ,r-ensembldb)
@@ -466,12 +465,12 @@ enrichedGO (addGeneIDs).")
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.60.0")
+    (version "1.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
+               (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-limma" ,r-limma)))
@@ -485,12 +484,12 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.42.0")
+   (version "1.40.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
+             (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
@@ -505,12 +504,12 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.44.0")
+   (version "2.42.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
+             (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
@@ -528,12 +527,12 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.18.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
+               (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -560,14 +559,14 @@ respectively.")
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.16.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
+         "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -586,14 +585,14 @@ more complex hypotheses) via empirical Bayesian methods.")
 (define-public r-chipcomp
   (package
     (name "r-chipcomp")
-    (version "1.12.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPComp" version))
        (sha256
         (base32
-         "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
+         "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
     (properties `((upstream-name . "ChIPComp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -620,14 +619,14 @@ datasets.")
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.12.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
+         "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
@@ -659,14 +658,14 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.16.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
+         "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -687,14 +686,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
 (define-public r-interactionset
   (package
     (name "r-interactionset")
-    (version "1.10.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
+         "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
@@ -719,14 +718,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.16.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
+         "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -758,14 +757,14 @@ information and producing various plots and statistics.")
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.56.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
+         "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-amap" ,r-amap)))
     (home-page "https://bioconductor.org/packages/ctc/")
@@ -778,14 +777,14 @@ trees and clusters to other programs.")
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.34.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "1401x0jn5f8hqc12r3gd1wammp1nxir3is1k5ldd03ln97x00i7a"))))
+         "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -804,14 +803,14 @@ defined categories which are over/under represented in RNA-seq data.")
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "1.10.0")
+    (version "1.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "0cbsi6g8k1whkh21jxfn22sj7wry2g3rshiracf5nyvrl2fnl947"))))
+         "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s"))))
     (properties `((upstream-name . "Glimma")))
     (build-system r-build-system)
     (propagated-inputs
@@ -831,14 +830,14 @@ information.")
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.10.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5"))))
+         "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -855,14 +854,14 @@ in omics data.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.12.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "0b671x5v2wyq5np2flq2m1fnjz32f303yjlw64a1inwc9k2w2pz2"))))
+         "1gk0pwyimkswrvgb2xr3c2zy4myi448a2shr5ap65rq9pcpp0l8p"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -891,14 +890,14 @@ modeling the rates that determines changes in mature mRNA levels.")
 (define-public r-dnabarcodes
   (package
     (name "r-dnabarcodes")
-    (version "1.12.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNABarcodes" version))
        (sha256
         (base32
-         "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
+         "0xhna7f0kr7pp2hqwara5i57m9mdr65shflfxiyw6yy3g90pgb5x"))))
     (properties `((upstream-name . "DNABarcodes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -914,157 +913,3 @@ can be analyzed regarding their minimal, maximal and average distances between
 barcodes.  Finally, reads that start with a (possibly mutated) barcode can be
 demultiplexed, i.e. assigned to their original reference barcode.")
     (license license:gpl2)))
-
-(define-public r-ruvseq
-  (package
-    (name "r-ruvseq")
-    (version "1.16.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "RUVSeq" version))
-       (sha256
-        (base32
-         "0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m"))))
-    (properties `((upstream-name . "RUVSeq")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-edaseq" ,r-edaseq)
-       ("r-edger" ,r-edger)
-       ("r-mass" ,r-mass)))
-    (home-page "https://github.com/drisso/RUVSeq")
-    (synopsis "Remove unwanted variation from RNA-Seq data")
-    (description
-     "This package implements methods to @dfn{remove unwanted variation} (RUV)
-of Risso et al. (2014) for the normalization of RNA-Seq read counts between
-samples.")
-    (license license:artistic2.0)))
-
-(define-public r-biocneighbors
-  (package
-    (name "r-biocneighbors")
-    (version "1.0.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "BiocNeighbors" version))
-       (sha256
-        (base32
-         "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
-    (properties `((upstream-name . "BiocNeighbors")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcppannoy" ,r-rcppannoy)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://bioconductor.org/packages/BiocNeighbors")
-    (synopsis "Nearest Neighbor Detection for Bioconductor packages")
-    (description
-     "This package implements exact and approximate methods for nearest
-neighbor detection, in a framework that allows them to be easily switched
-within Bioconductor packages or workflows.  The exact algorithm is implemented
-using pre-clustering with the k-means algorithm.  Functions are also provided
-to search for all neighbors within a given distance.  Parallelization is
-achieved for all methods using the BiocParallel framework.")
-    (license license:gpl3)))
-
-(define-public r-destiny
-  (package
-    (name "r-destiny")
-    (version "2.12.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "destiny" version))
-       (sha256
-        (base32
-         "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-fnn" ,r-fnn)
-       ("r-ggthemes" ,r-ggthemes)
-       ("r-hmisc" ,r-hmisc)
-       ("r-igraph" ,r-igraph)
-       ("r-matrix" ,r-matrix)
-       ("r-proxy" ,r-proxy)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rcppeigen" ,r-rcppeigen)
-       ("r-scales" ,r-scales)
-       ("r-scatterplot3d" ,r-scatterplot3d)
-       ("r-smoother" ,r-smoother)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-vim" ,r-vim)))
-    (home-page "https://bioconductor.org/packages/destiny/")
-    (synopsis "Create and plot diffusion maps")
-    (description "This package provides tools to create and plot diffusion
-maps.")
-    ;; Any version of the GPL
-    (license license:gpl3+)))
-
-(define-public r-savr
-  (package
-    (name "r-savr")
-    (version "1.20.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "savR" version))
-       (sha256
-        (base32
-         "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
-    (properties `((upstream-name . "savR")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-ggplot2" ,r-ggplot2)
-       ("r-gridextra" ,r-gridextra)
-       ("r-reshape2" ,r-reshape2)
-       ("r-scales" ,r-scales)
-       ("r-xml" ,r-xml)))
-    (home-page "https://github.com/bcalder/savR")
-    (synopsis "Parse and analyze Illumina SAV files")
-    (description
-     "This package provides tools to parse Illumina Sequence Analysis
-Viewer (SAV) files, access data, and generate QC plots.")
-    (license license:agpl3+)))
-
-(define-public r-chipexoqual
-  (package
-    (name "r-chipexoqual")
-    (version "1.6.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ChIPexoQual" version))
-       (sha256
-        (base32
-         "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
-    (properties `((upstream-name . "ChIPexoQual")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-biovizbase" ,r-biovizbase)
-       ("r-broom" ,r-broom)
-       ("r-data-table" ,r-data-table)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-hexbin" ,r-hexbin)
-       ("r-iranges" ,r-iranges)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rmarkdown" ,r-rmarkdown)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-viridis" ,r-viridis)))
-    (home-page "https://github.com/keleslab/ChIPexoQual")
-    (synopsis "Quality control pipeline for ChIP-exo/nexus data")
-    (description
-     "This package provides a quality control pipeline for ChIP-exo/nexus
-sequencing data.")
-    (license license:gpl2+)))

gnu/packages/bison.scm

@@ -1,6 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2015 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,7 +29,7 @@
 (define-public bison
   (package
     (name "bison")
-    (version "3.0.5")
+    (version "3.0.4")
     (source
      (origin
       (method url-fetch)
@@ -38,10 +37,10 @@
                           version ".tar.xz"))
       (sha256
        (base32
-        "0f7kjygrckkx8vas2nm673592jif0a9mw5g8207f6hj6h4pfyp07"))))
+        "1qbgf6q1n2z17k8g33444m0q68kf3fbiq65q7jlrzpvvj73jh957"))))
     (build-system gnu-build-system)
     (native-inputs `(("perl" ,perl)
-                     ;; m4 is not present in PATH when cross-building.
+                     ;; m4 is not present in PATH when cross-building
                      ("m4" ,m4)))
     (inputs `(("flex" ,flex)))
     (propagated-inputs `(("m4" ,m4)))
@@ -53,3 +52,15 @@ deterministic or generalized LR parser from an annotated, context-free
 grammar.  It is versatile enough to have many applications, from parsers for
 simple tools through complex programming languages.")
     (license gpl3+)))
+
+(define-public bison-2.7
+  (package (inherit bison)
+    (version "2.7")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (string-append "mirror://gnu/bison/bison-"
+                          version ".tar.xz"))
+      (sha256
+       (base32
+        "1zd77ilmpv5mi3kr55jrj6ncqlcnyhpianhrwzak2q28cv2cbn23"))))))

gnu/packages/bittorrent.scm

@@ -1,14 +1,13 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017, 2018 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016, 2018 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
-;;; Copyright © 2018 Nam Nguyen <namn@berkeley.edu>
-;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -43,7 +42,6 @@
   #:use-module (gnu packages cyrus-sasl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages file)
-  #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
@@ -56,7 +54,6 @@
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
-  #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages tls)
@@ -217,14 +214,14 @@ Transmission BitTorrent daemon.")
     (name "transmission-remote-cli")
     (version "1.7.1")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/fagga/transmission-remote-cli.git")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append "https://github.com/fagga/"
+                                  "transmission-remote-cli/archive/v"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "09w9f8vrm61lapin8fmq4rgahr95y3c6wss10g0fgd0kl16f895v"))))
+                "1y0hkpcjf6jw9xig8yf484hbhy63nip0pkchx401yxj81m25l4z9"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2 ; only supports Python 2
@@ -341,14 +338,13 @@ downloads, download scheduling, download rate limiting.")
     (name "mktorrent")
     (version "1.1")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/Rudde/mktorrent.git")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (file-name (string-append name "-" version ".tar.gz"))
+              (uri (string-append "https://github.com/Rudde/mktorrent/archive/v"
+                                  version ".tar.gz"))
               (sha256
                (base32
-                "17pdc5mandl739f8q26n5is8ga56s83aqcrwhlnnplbxwx2inidr"))))
+                "1j9qc4fxa9isnaygqk6jazsiklqywl2wcs95b8dx01963407bx6h"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -375,17 +371,17 @@ and will take advantage of multiple processor cores where possible.")
 (define-public libtorrent-rasterbar
   (package
     (name "libtorrent-rasterbar")
-    (version "1.1.11")
+    (version "1.1.8")
     (source (origin
               (method url-fetch)
               (uri
                (string-append
-                "https://github.com/arvidn/libtorrent/releases/download/libtorrent_"
+                "https://github.com/arvidn/libtorrent/releases/download/libtorrent-"
                 (string-join (string-split version #\.) "_")
                 "/libtorrent-rasterbar-" version ".tar.gz"))
               (sha256
                (base32
-                "0isqidr11fnhybr0wvk0qxd97jaikmh8fx9h89b84yd2gyxdw8vw"))))
+                "0pcdy26l5ivcs78y2bqh2qca83ikzjfchw5815xh69qf8g88zgvb"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -397,18 +393,7 @@ and will take advantage of multiple processor cores where possible.")
              "CXXFLAGS=-std=c++11")     ; Use std::chrono instead of boost
        #:make-flags (list
                      (string-append "LDFLAGS=-Wl,-rpath="
-                                    (assoc-ref %outputs "out") "/lib"))
-       #:phases (modify-phases %standard-phases
-           (add-after 'unpack 'compile-python-c++11
-             (lambda _
-               ;; Make sure the Python bindings are compiled in C++ mode to
-               ;; avoid undefined references as mentioned in
-               ;; <https://github.com/qbittorrent/qBittorrent/issues/638>.
-               ;; XXX: This can be removed for 1.2+.
-               (substitute* "bindings/python/setup.py"
-                 (("\\+ target_specific\\(\\)\\,")
-                  "+ target_specific() + ['-std=c++11'],"))
-               #t)))))
+                                    (assoc-ref %outputs "out") "/lib"))))
     (inputs `(("boost" ,boost)
               ("openssl" ,openssl)))
     (native-inputs `(("python" ,python-2)
@@ -463,40 +448,3 @@ It aims to be a good alternative to all other BitTorrent clients out there.
 qBittorrent is fast, stable and provides unicode support as well as many
 features.")
     (license l:gpl2+)))
-
-(define-public deluge
-  (package
-    (name "deluge")
-    (version "1.3.15")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "http://download.deluge-torrent.org/source/deluge-"
-             version ".tar.xz"))
-       (sha256
-        (base32
-         "0b7rri4x0wrcj7rjghrnw1kfrsd5i7i6aq85dsg5dg1w1qa0ar59"))))
-    (build-system python-build-system)
-    (inputs
-     `(("libtorrent" ,libtorrent-rasterbar)
-       ("python2-chardet" ,python2-chardet)
-       ("python2-pygtk" ,python2-pygtk)
-       ("python2-pyopenssl" ,python2-pyopenssl)
-       ("python2-pyxdg" ,python2-pyxdg)
-       ("python2-service-identity" ,python2-service-identity)
-       ("python2-twisted" ,python2-twisted)))
-    (native-inputs
-     `(("intltool" ,intltool)))
-    (arguments
-     `(#:python ,python-2))
-    (home-page "https://www.deluge-torrent.org/")
-    (synopsis  "Fully-featured cross-platform ​BitTorrent client")
-    (description
-     "Deluge contains the common features to BitTorrent clients such as
-Protocol Encryption, DHT, Local Peer Discovery (LSD), Peer Exchange
-(PEX), UPnP, NAT-PMP, Proxy support, Web seeds, global and per-torrent
-speed limits.  Deluge heavily utilises the ​libtorrent library.  It is
-designed to run as both a normal standalone desktop application and as a
-​client-server.")
-    (license l:gpl3+)))

gnu/packages/boost.scm

@@ -9,7 +9,6 @@
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
-;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,7 +27,6 @@
 
 (define-module (gnu packages boost)
   #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix utils)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -45,7 +43,7 @@
 (define-public boost
   (package
     (name "boost")
-    (version "1.68.0")
+    (version "1.66.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -54,7 +52,7 @@
                     ".tar.bz2"))
               (sha256
                (base32
-                "1dyqsr9yb01y0nnjdq9b8q5s2kvhxbayk34832k5cpzn7jy30qbz"))
+                "1aaw48cmimsskzgiclwn0iifp62a5iw9cbqrhfari876af1828ap"))
               (patches (search-patches "boost-fix-icu-build.patch"))))
     (build-system gnu-build-system)
     (inputs `(("icu4c" ,icu4c)
@@ -80,6 +78,7 @@
                    (out (assoc-ref outputs "out")))
                (substitute* '("libs/config/configure"
                               "libs/spirit/classic/phoenix/test/runtest.sh"
+                              "tools/build/doc/bjam.qbk"
                               "tools/build/src/engine/execunix.c"
                               "tools/build/src/engine/Jambase"
                               "tools/build/src/engine/jambase.c")
@@ -101,18 +100,7 @@
                     make-flags)))
          (replace 'install
            (lambda* (#:key make-flags #:allow-other-keys)
-             (apply invoke "./b2" "install" make-flags)))
-         (add-after 'install 'provide-libboost_python
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               ;; Boost can build support for both Python 2 and Python 3 since
-               ;; version 1.67.0, and suffixes each library with the Python
-               ;; version.  Many consumers only check for libboost_python
-               ;; however, so we provide it here as suggested in
-               ;; <https://github.com/boostorg/python/issues/203>.
-               (with-directory-excursion (string-append out "/lib")
-                 (symlink "libboost_python27.so" "libboost_python.so"))
-               #t))))))
+             (apply invoke "./b2" "install" make-flags))))))
 
     (home-page "https://www.boost.org")
     (synopsis "Peer-reviewed portable C++ source libraries")
@@ -136,15 +124,6 @@ across a broad spectrum of applications.")
               (sha256
                (base32
                 "1jj1aai5rdmd72g90a3pd8sw9vi32zad46xv5av8fhnr48ir6ykj"))))
-    (arguments (substitute-keyword-arguments (package-arguments boost)
-      ((#:phases phases)
-       `(modify-phases ,phases
-          ;; This was removed after boost-1.67.
-          (add-before 'configure 'more-bin-sh-patching
-            (lambda _
-              (substitute* "tools/build/doc/bjam.qbk"
-                (("/bin/sh") (which "sh")))))
-          (delete 'provide-libboost_python)))))
     (properties '((hidden? . #t)))))
 
 (define-public boost-sync
@@ -182,14 +161,14 @@ Boost.Thread.")
 (define-public mdds
   (package
     (name "mdds")
-    (version "1.4.3")
+    (version "1.3.1")
     (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://kohei.us/files/mdds/src/mdds-" version ".tar.bz2"))
              (sha256
               (base32
-               "10cw6irdm6d15nxnys2v5akp8yz52qijpcjvw0frwq7nz5d3vki5"))))
+               "18g511z1lgfxrga2ld9yr95phmyfbd3ymbv4q5g5lyjn4ljcvf6w"))))
     (build-system gnu-build-system)
     (propagated-inputs
       `(("boost" ,boost))) ; inclusion of header files

gnu/packages/bootloaders.scm

@@ -34,7 +34,6 @@
   #:use-module (gnu packages bison)
   #:use-module (gnu packages cdrom)
   #:use-module (gnu packages check)
-  #:use-module (gnu packages compression)
   #:use-module (gnu packages cross-base)
   #:use-module (gnu packages disk)
   #:use-module (gnu packages firmware)
@@ -87,8 +86,7 @@
              (sha256
               (base32
                "03vvdfhdmf16121v7xs8is2krwnv15wpkhkf16a4yf8nsfc3f2w1"))
-             (patches (search-patches "grub-check-error-efibootmgr.patch"
-                                      "grub-binutils-compat.patch"))))
+             (patches (search-patches "grub-check-error-efibootmgr.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -362,7 +360,7 @@ tree binary files.  These are board description files used by Linux and BSD.")
 (define u-boot
   (package
     (name "u-boot")
-    (version "2018.11")
+    (version "2018.09")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -370,13 +368,12 @@ tree binary files.  These are board description files used by Linux and BSD.")
                     "u-boot-" version ".tar.bz2"))
               (sha256
                (base32
-                "0znkwljfwwn4y7j20pzz4ilqw8znphrfxns0x1lwdzh3xbr96z3k"))))
+                "0s122kyz1svvs2yjzj4j9qravl3ra4vn0fjqgski7rlczqyg56w3"))))
     (native-inputs
      `(("bc" ,bc)
        ("bison" ,bison)
        ("dtc" ,dtc)
        ("flex" ,flex)
-       ("lz4" ,lz4)
        ("openssl" ,openssl)
        ("python-2" ,python-2)
        ("python2-coverage" ,python2-coverage)
@@ -555,8 +552,8 @@ board-independent tools.")))
 (define-public u-boot-beagle-bone-black
   (make-u-boot-package "am335x_boneblack" "arm-linux-gnueabihf"))
 
-(define-public (make-u-boot-sunxi64-package board triplet)
-  (let ((base (make-u-boot-package board triplet)))
+(define-public u-boot-pine64-plus
+  (let ((base (make-u-boot-package "pine64_plus" "aarch64-linux-gnu")))
     (package
       (inherit base)
       (arguments
@@ -574,28 +571,9 @@ board-independent tools.")))
                     )
                   #t))))))
       (native-inputs
-       `(("firmware" ,arm-trusted-firmware-sun50i-a64)
+       `(("firmware" ,arm-trusted-firmware-pine64-plus)
          ,@(package-native-inputs base))))))
 
-(define-public u-boot-pine64-plus
-  (make-u-boot-sunxi64-package "pine64_plus" "aarch64-linux-gnu"))
-
-(define-public u-boot-pinebook
-  (let ((base (make-u-boot-sunxi64-package "pinebook" "aarch64-linux-gnu")))
-    (package
-      (inherit base)
-      (source (origin
-              (inherit (package-source u-boot))
-              (patches (search-patches
-                        ;; Add patches to enable Pinebook support from sunxi
-                        ;; maintainer tree: git://git.denx.de/u-boot-sunxi.git
-                        "u-boot-pinebook-a64-update-dts.patch"
-                        "u-boot-pinebook-syscon-node.patch"
-                        "u-boot-pinebook-mmc-calibration.patch"
-                        "u-boot-pinebook-video-bridge.patch"
-                        "u-boot-pinebook-r_i2c-controller.patch"
-                        "u-boot-pinebook-dts.patch")))))))
-
 (define-public u-boot-bananapi-m2-ultra
   (make-u-boot-package "Bananapi_M2_Ultra" "arm-linux-gnueabihf"))
 

gnu/packages/build-tools.scm

@@ -1,11 +1,9 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Corentin Bocquillon <corentin@nybble.fr>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
-;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -31,7 +29,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages lua)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
@@ -42,30 +39,33 @@
 (define-public bam
   (package
     (name "bam")
-    (version "0.5.1")
+    (version "0.4.0")
     (source (origin
-              ;; do not use auto-generated tarballs
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/matricks/bam.git")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append "http://github.com/downloads/matricks/"
+                                  "bam/bam-" version ".tar.bz2"))
               (sha256
                (base32
-                "13br735ig7lygvzyfd15fc2rdygrqm503j6xj5xkrl1r7w2wipq6"))))
+                "0z90wvyd4nfl7mybdrv9dsd4caaikc6fxw801b72gqi1m9q0c0sn"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:make-flags `("CC=gcc"
-                      ,(string-append "INSTALL_PREFIX="
-                                      (assoc-ref %outputs "out")))
-       #:test-target "test"
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
-         (delete 'configure))))
+         (delete 'configure)
+         (replace 'build
+           (lambda _
+             (zero? (system* "bash" "make_unix.sh"))))
+         (replace 'check
+           (lambda _
+             (zero? (system* "python" "scripts/test.py"))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+               (mkdir-p bin)
+               (install-file "bam" bin)
+               #t))))))
     (native-inputs
      `(("python" ,python-2)))
-    (inputs
-     `(("lua" ,lua)))
     (home-page "https://matricks.github.io/bam/")
     (synopsis "Fast and flexible build system")
     (description "Bam is a fast and flexible build system.  Bam uses Lua to
@@ -98,67 +98,10 @@ it is easy to re-run the compilation with alternate programs.  Bear is used to
 generate such a compilation database.")
     (license license:gpl3+)))
 
-(define-public gn
-  (let ((commit "f73698ebb33e26a0bf120e2b55d12528fd1dbe7d")
-        (revision "1481"))          ;as returned by `git describe`, used below
-    (package
-      (name "gn")
-      (version (git-version "0.0" revision commit))
-      (home-page "https://gn.googlesource.com/gn")
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference (url home-page) (commit commit)))
-                (sha256
-                 (base32
-                  "078ydwak4424bkqh3hd7q955zxp2c3qlw44lsb29i8jqap140f9d"))
-                (file-name (git-file-name name version))))
-      (build-system gnu-build-system)
-      (arguments
-       `(#:tests? #f                    ;FIXME: How to run?
-         #:phases (modify-phases %standard-phases
-                    (add-before 'configure 'set-build-environment
-                      (lambda _
-                        (setenv "CC" "gcc") (setenv "CXX" "g++")
-                        (setenv "AR" "ar")
-                        #t))
-                    (replace 'configure
-                      (lambda _
-                        (invoke "python" "build/gen.py" "--no-sysroot"
-                                "--no-last-commit-position")))
-                    (add-after 'configure 'create-last-commit-position
-                      (lambda _
-                        ;; Create "last_commit_position.h" to avoid a dependency
-                        ;; on 'git' (and the checkout..).
-                        (call-with-output-file "out/last_commit_position.h"
-                          (lambda (port)
-                            (format port
-                                    "#define LAST_COMMIT_POSITION \"~a (~a)\"\n"
-                                    ,revision ,(string-take commit 8))
-                            #t))))
-                    (replace 'build
-                      (lambda _
-                        (invoke "ninja" "-C" "out" "gn"
-                                "-j" (number->string (parallel-job-count)))))
-                    (replace 'install
-                      (lambda* (#:key outputs #:allow-other-keys)
-                        (let ((out (assoc-ref outputs "out")))
-                          (install-file "out/gn" (string-append out "/bin"))
-                          #t))))))
-      (native-inputs
-       `(("ninja" ,ninja)
-         ("python" ,python-2)))
-      (synopsis "Generate Ninja build files")
-      (description
-       "GN is a tool that collects information about a project from @file{.gn}
-files and generates build instructions for the Ninja build system.")
-      ;; GN is distributed as BSD-3, but bundles some files from ICU using the
-      ;; X11 license.
-      (license (list license:bsd-3 license:x11)))))
-
 (define-public meson
   (package
     (name "meson")
-    (version "0.47.2")
+    (version "0.47.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/mesonbuild/meson/"
@@ -166,7 +109,7 @@ files and generates build instructions for the Ninja build system.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1swmycf6p9p0ag6yiywyyri42ffkxxj38r2ic7in24km47cszn4j"))))
+                "19mdap2ncvczajx220bd73xmwhd8x906382y18cn9c5syxwxwwyn"))))
     (build-system python-build-system)
     (arguments
      `(;; FIXME: Tests require many additional inputs, a fix for the RUNPATH

gnu/packages/c.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
@@ -160,7 +160,8 @@ standard.")
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _ (invoke "make" "-C" "cc/cpp" "test") #t)))))
+           (lambda _
+             (zero? (system* "make" "-C" "cc/cpp" "test")))))))
     (native-inputs
      `(("bison" ,bison)
        ("flex" ,flex)))
@@ -177,53 +178,16 @@ compiler while still keeping it small, simple, fast and understandable.")
 (define-public libbytesize
   (package
     (name "libbytesize")
-    (version "1.4")
+    (version "1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "https://github.com/storaged-project/libbytesize/releases/"
-                    "download/" version "/libbytesize-" version ".tar.gz"))
+                    "https://github.com/storaged-project/libbytesize/releases/download/1.3/libbytesize-"
+                    version ".tar.gz"))
               (sha256
                (base32
-                "0bbqzln1nhjxl71aydq9k4jg3hvki9lqsb4w10s1i27jgibxqkdv"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; This Makefile hard-codes MSGMERGE et al. instead of
-                  ;; honoring what 'configure' detected.  Fix that.
-                  (substitute* "po/Makefile.in"
-                    (("^MSGMERGE = msgmerge")
-                     "MSGMERGE = @MSGMERGE@\n"))
-                  #t))))
+                "1l7mxm2vq2h6137fyfa46v9r4lydp9dvmsixkd64xr3ylqk1g6fi"))))
     (build-system gnu-build-system)
-    (arguments
-     ;; When running "make", the POT files are built with the build time as
-     ;; their "POT-Creation-Date".  Later on, "make" notices that .pot
-     ;; files were updated and goes on to run "msgmerge"; as a result, the
-     ;; non-deterministic POT-Creation-Date finds its way into .po files,
-     ;; and then in .gmo files.  To avoid that, simply make sure 'msgmerge'
-     ;; never runs.  See <https://bugs.debian.org/792687>.
-     '(#:configure-flags '("ac_cv_path_MSGMERGE=true")
-
-       #:phases (modify-phases %standard-phases
-                  (add-after 'configure 'create-merged-po-files
-                    (lambda _
-                      ;; Create "merged PO" (.mpo) files so that 'msgmerge'
-                      ;; doesn't need to run.
-                      (for-each (lambda (po-file)
-                                  (let ((merged-po
-                                         (string-append (dirname po-file) "/"
-                                                        (basename po-file
-                                                                  ".po")
-                                                        ".mpo")))
-                                    (copy-file po-file merged-po)))
-                                (find-files "po" "\\.po$"))
-                      #t)))
-
-       ;; One test fails because busctl (systemd only?) and python2-pocketlint
-       ;; are missing.  Should we fix it, we would need the "python-2" ,
-       ;; "python2-polib" and "python2-six" native-inputs.
-       #:tests? #f))
     (native-inputs
      `(("gettext" ,gettext-minimal)
        ("pkg-config" ,pkg-config)
@@ -231,6 +195,10 @@ compiler while still keeping it small, simple, fast and understandable.")
     (inputs
      `(("mpfr" ,mpfr)
        ("pcre" ,pcre)))
+    ;; One test fails because busctl (systemd only?) and python2-pocketlint
+    ;; are missing.  Should we fix it, we would need the "python-2" ,
+    ;; "python2-polib" and "python2-six" native-inputs.
+    (arguments `(#:tests? #f))
     (home-page "https://github.com/storaged-project/libbytesize")
     (synopsis "Tiny C library for working with arbitrary big sizes in bytes")
     (description

gnu/packages/calcurse.scm

@@ -34,7 +34,7 @@
     (source
      (origin
       (method url-fetch)
-      (uri (string-append "https://calcurse.org/files/calcurse-"
+      (uri (string-append "http://calcurse.org/files/calcurse-"
                           version ".tar.gz"))
       (sha256
        (base32
@@ -57,7 +57,7 @@
                       (setenv "TZDIR"   ;for test/ical-007.sh
                               (string-append (assoc-ref inputs "tzdata")
                                              "/share/zoneinfo")))))))
-    (home-page "https://www.calcurse.org")
+    (home-page "http://www.calcurse.org")
     (synopsis "Text-based calendar and scheduling")
     (description
      "Calcurse is a text-based calendar and scheduling application.  It helps

gnu/packages/calendar.scm

@@ -48,7 +48,7 @@
 (define-public libical
   (package
     (name "libical")
-    (version "3.0.4")
+    (version "3.0.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -56,7 +56,7 @@
                     version "/libical-" version ".tar.gz"))
               (sha256
                (base32
-                "0ifisnh42cw5z53hp9p52l3ggc7k877zlqk0n06gdhrk0bhidckj"))))
+                "0hcjyf35b8rrvy8xziqxc4imi28mmkixb09gknisvp6jsa5fp4av"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; test suite appears broken

gnu/packages/ccache.scm

@@ -30,7 +30,7 @@
 (define-public ccache
   (package
     (name "ccache")
-    (version "3.5")
+    (version "3.4.3")
     (source
      (origin
       (method url-fetch)
@@ -38,9 +38,9 @@
                           version ".tar.xz"))
       (sha256
        (base32
-        "04n0xram2416pv98qrd7pi5lfsk0bjqyz7zgvvia41j5mrr4pm5x"))))
+        "0jjzq5340qw3jm5gkajjkkb5wd0yqqy1dyjw3mf3jy15cakmazi9"))))
     (build-system gnu-build-system)
-    (native-inputs `(("perl" ,perl)     ; for test/run
+    (native-inputs `(("perl" ,perl)     ; for test.sh
                      ("which" ,(@ (gnu packages base) which))))
     (inputs `(("zlib" ,zlib)))
     (arguments

gnu/packages/cdrom.scm

@@ -11,7 +11,6 @@
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,7 +29,6 @@
 
 (define-module (gnu packages cdrom)
   #:use-module (guix download)
-  #:use-module (guix git-download)
   #:use-module (guix packages)
   #:use-module ((guix licenses) #:select (lgpl2.1+ gpl2 gpl2+ gpl3+ cddl1.0))
   #:use-module (guix build-system cmake)
@@ -293,26 +291,17 @@ images.")
      `(#:tests? #f ; No tests.
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'fix-glibc-compatability
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; We use sed --in-place because substitute* cannot handle the
-             ;; character encoding used by growisofs.c.
-             (invoke "sed" "-i" "-e"
-                     (string-append
-                       "s,<sys/stat.h>,"
-                       "<sys/stat.h>\\\n#include <sys/sysmacros.h>,")
-                     "growisofs.c")))
          (replace 'configure
            (lambda _ (setenv "prefix" (assoc-ref %outputs "out")) #t))
          (add-before 'build 'embed-mkisofs
-           (lambda* (#:key inputs #:allow-other-keys)
+           (lambda*  (#:key inputs #:allow-other-keys)
              ;; We use sed --in-place because substitute* cannot handle the
              ;; character encoding used by growisofs.c.
-             (invoke "sed" "-i" "-e"
-                     (string-append
-                       "s,\"mkisofs\","
-                       "\"" (which "mkisofs") "\",")
-                     "growisofs.c"))))))
+             (zero? (system* "sed" "-i" "-e"
+                             (string-append
+                              "s,\"mkisofs\","
+                              "\"" (which "mkisofs") "\",")
+                             "growisofs.c")))))))
     (home-page "http://fy.chalmers.se/~appro/linux/DVD+RW/")
     (synopsis "DVD and Blu-ray Disc burning tools")
     (description "dvd+rw-tools, mostly known for its command
@@ -432,14 +421,14 @@ graphical interface.")
     (name "libcue")
     (version "2.2.1")
     (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                   (url "https://github.com/lipnitsk/libcue.git")
-                   (commit (string-append "v" version))))
-             (file-name (git-file-name name version))
+             (method url-fetch)
+             (uri (string-append
+                   "https://github.com/lipnitsk/libcue/archive/v"
+                   version ".tar.gz"))
+             (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
-               "1iqw4n01rv2jyk9lksagyxj8ml0kcfwk67n79zy1r6zv1xfp5ywm"))))
+               "000j5xqp7cc7njwlixr9byahz9kn8pcfdgm76afwv4p8nbmw6yzj"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")))

gnu/packages/check.scm

@@ -26,7 +26,7 @@
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -51,7 +51,6 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages llvm)
   #:use-module (gnu packages golang)
-  #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages time)
@@ -251,7 +250,7 @@ a multi-paradigm automated test framework for C++ and Objective-C.")
              ;; the build environment. Hence assuming-failure test fails.
              (delete-file "yarn.tests/assuming-failure.script")
              (delete-file "yarn.tests/assuming-failure.stdout")
-             (invoke "python" "setup.py" "check"))))))
+             (zero? (system* "python" "setup.py" "check")))))))
     (native-inputs
      `(("python2-coverage-test-runner" ,python2-coverage-test-runner)))
     (propagated-inputs
@@ -294,13 +293,13 @@ format.")
 (define-public cppcheck
   (package
     (name "cppcheck")
-    (version "1.85")
+    (version "1.84")
     (source (origin
       (method url-fetch)
       (uri (string-append "https://github.com/danmar/cppcheck/archive/"
                           version ".tar.gz"))
       (sha256
-       (base32 "18qlddf1i9bk5nnvy1v2nfxjd46y8wvp3rqz2hrfxjxsyvrfq5yw"))
+       (base32 "1ibz07dgs1dpfb8bmjh3qsma37wl5p6s6b4qlv5ccpshj4yjk9ma"))
       (file-name (string-append name "-" version ".tar.gz"))))
     (build-system cmake-build-system)
     (home-page "http://cppcheck.sourceforge.net")
@@ -620,14 +619,14 @@ standard library.")
 (define-public python-pytest
   (package
     (name "python-pytest")
-    (version "3.8.0")
+    (version "3.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest" version))
        (sha256
         (base32
-         "17grcfvd6ggvvqmprwv5y8g319nayam70hr43ssjwj40ws27z858"))))
+         "1q832zd07zak2lyxbycxjydh0jp7y3hvawjqzlvra6aghz8r3r7s"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -643,11 +642,9 @@ standard library.")
                 (string-append "@pytest.mark.skip"
                                "(reason=\"Assumes that /usr exists.\")\n    "
                                line)))
-             #t))
-         (replace 'check (lambda _ (invoke "pytest" "-vv"))))))
+             #t)))))
     (propagated-inputs
-     `(("python-atomicwrites" ,python-atomicwrites)
-       ("python-attrs" ,python-attrs-bootstrap)
+     `(("python-attrs" ,python-attrs-bootstrap)
        ("python-more-itertools" ,python-more-itertools)
        ("python-pluggy" ,python-pluggy)
        ("python-py" ,python-py)
@@ -658,7 +655,6 @@ standard library.")
        ("python-hypothesis" ,python-hypothesis)
        ("python-nose" ,python-nose)
        ("python-mock" ,python-mock)
-       ("python-pytest" ,python-pytest-bootstrap)
        ("python-setuptools-scm" ,python-setuptools-scm)))
     (home-page "http://pytest.org")
     (synopsis "Python testing library")
@@ -676,7 +672,6 @@ and many external plugins.")
       (inherit pytest)
       (propagated-inputs
        `(("python2-funcsigs" ,python2-funcsigs)
-         ("python2-pathlib2" ,python2-pathlib2)
          ,@(package-propagated-inputs pytest))))))
 
 (define-public python-pytest-bootstrap
@@ -693,20 +688,19 @@ and many external plugins.")
     (package (inherit pytest)
              (propagated-inputs
               `(("python2-funcsigs" ,python2-funcsigs-bootstrap)
-                ("python2-pathlib2" ,python2-pathlib2-bootstrap)
                 ,@(package-propagated-inputs pytest))))))
 
 (define-public python-pytest-cov
   (package
     (name "python-pytest-cov")
-    (version "2.5.1")
+    (version "2.4.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pytest-cov" version))
         (sha256
          (base32
-          "0bbfpwdh9k3636bxc88vz9fa7vf4akchgn513ql1vd0xy4n7bah3"))))
+          "03c2qc42r4bczyw93gd7n0qi1h1jfhw7fnbhi33c3vp1hs81gm2k"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -716,8 +710,8 @@ and many external plugins.")
             ;; options taken from tox.ini
             ;; TODO: make "--restructuredtext" tests pass. They currently fail
             ;; with "Duplicate implicit target name"
-            (invoke "python" "./setup.py" "check"
-                    "--strict" "--metadata"))))))
+            (zero? (system* "python" "./setup.py" "check"
+                            "--strict" "--metadata")))))))
     (propagated-inputs
      `(("python-coverage" ,python-coverage)
        ("python-pytest" ,python-pytest)))
@@ -735,15 +729,26 @@ supports coverage of subprocesses.")
 (define-public python-pytest-runner
   (package
     (name "python-pytest-runner")
-    (version "4.2")
+    (version "2.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-runner" version))
        (sha256
         (base32
-         "1gkpyphawxz38ni1gdq1fmwyqcg02m7ypzqvv46z06crwdxi2gyj"))))
+         "1cw978kqqcq916b9gfns1qjqvg33c5ail5jhw9054dsynkm32flq"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; The fancy way of setting the version with setuptools_scm does not
+         ;; seem to work here.
+         (add-after 'unpack 'set-version
+          (lambda _
+            (substitute* "docs/conf.py"
+              (("version = setuptools_scm\\.get_version\\(root='\\.\\.')")
+               (string-append "version = \"" ,version "\"")))
+            #t)))))
     (native-inputs
      `(("python-pytest" ,python-pytest-bootstrap)
        ("python-setuptools-scm" ,python-setuptools-scm)))
@@ -760,14 +765,14 @@ supports coverage of subprocesses.")
 (define-public python-pytest-mock
   (package
     (name "python-pytest-mock")
-    (version "1.10.0")
+    (version "1.6.3")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pytest-mock" version))
         (sha256
          (base32
-          "1h6lgpmsvs9s8j2s80v06f9f3iaw1n1rc51mbrxk1f12sw4q56nq"))))
+          "075v7b2wm5f839r1a30n21wfk5rfqp3d05q7zb9jlb2wmxki23cj"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-setuptools-scm" ,python-setuptools-scm)))
@@ -880,8 +885,7 @@ subprocess and see the output as well as any file modifications.")
        (uri (pypi-uri "testtools" version))
        (sha256
         (base32
-         "0n8519lk8aaa91vymz842831181wf7fss98hyllhygi3z1nfq9sq"))
-       (patches (search-patches "python-testtools.patch"))))
+         "0n8519lk8aaa91vymz842831181wf7fss98hyllhygi3z1nfq9sq"))))
     (build-system python-build-system)
     (arguments '(#:tests? #f))
     (propagated-inputs
@@ -1101,8 +1105,8 @@ python-fixtures package instead.")
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (invoke "python" "-m" "testtools.run"
-                     "fixtures.test_suite"))))))
+             (zero? (system* "python" "-m" "testtools.run"
+                             "fixtures.test_suite")))))))
     (propagated-inputs
      ;; Fixtures uses pbr at runtime to check versions, etc.
      `(("python-pbr" ,python-pbr)
@@ -1342,20 +1346,20 @@ the last py.test invocation.")
 (define-public python-pytest-localserver
   (package
     (name "python-pytest-localserver")
-    (version "0.5.0")
+    (version "0.4.1")
     (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "pytest-localserver" version))
-              (sha256
-               (base32
-                "1hpgpxrpfq5c731ndnsay2lc0y9nh2wy9fn1f83s3z8xkn82fm1s"))))
+             (method url-fetch)
+             (uri (pypi-uri "pytest-localserver" version))
+             (sha256
+              (base32
+               "08f06rvj31wqf0vgmd1waya87r7vy6x8ck48lxl3dxy83q5gcam7"))))
     (build-system python-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
+      `(#:phases (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (invoke "py.test" "-v"))))))
+             (zero? (system* "py.test" "--genscript=runtests.py"))
+             (zero? (system* "py.test")))))))
     (native-inputs
      `(("python-pytest" ,python-pytest)
        ("python-requests" ,python-requests)
@@ -1417,17 +1421,16 @@ normally the case.")
 (define-public python-hypothesis
   (package
     (name "python-hypothesis")
-    (version "3.70.3")
+    (version "3.52.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "hypothesis" version))
               (sha256
                (base32
-                "1rshs1japfmwgar98yrkq4hg4z2q76hlnq7w2n3lfbjnscn1jd9b"))))
+                "0g54cypfi5qj6cgxfr7l1nb41r1cqhhngx4qxn4ga9h720rcsbr8"))))
     (build-system python-build-system)
     (native-inputs
-     `(;; FIXME: Change to python-flake8 in the next rebuild cycle.
-       ("python-flake8" ,python-flake8-3.5)
+     `(("python-flake8" ,python-flake8)
        ("python-pytest" ,python-pytest-bootstrap)))
     (propagated-inputs
      `(("python-attrs" ,python-attrs-bootstrap)
@@ -1524,7 +1527,7 @@ failures.")
              ;; It's easier to run tests after install.
              ;; Make installed package available for running the tests
              (add-installed-pythonpath inputs outputs)
-             (invoke "py.test" "-vv"))))))
+             (zero? (system* "py.test" "-vv")))))))
     (native-inputs
      `(("python-coverage" ,python-coverage)
        ("python-pytest" ,python-pytest)
@@ -1561,7 +1564,7 @@ failures.")
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (invoke "./testrun"))))))
+             (zero? (system* "./testrun")))))))
     (propagated-inputs
      `(("python2-coverage" ,python2-coverage)))
     (home-page "https://liw.fi/coverage-test-runner/")
@@ -1607,9 +1610,9 @@ statements in the module it tests.")
                               (string-append (getenv "PYTHONPATH") ":" work))
                       (copy-recursively "." work)
                       (with-directory-excursion "/tmp"
-                        (invoke "python" "-m" "unittest" "discover"
-                                "-s" (string-append work "/pylint/test")
-                                "-p" "*test_*.py"))))))))
+                        (zero? (system* "python" "-m" "unittest" "discover"
+                                        "-s" (string-append work "/pylint/test")
+                                        "-p" "*test_*.py")))))))))
     (home-page "https://github.com/PyCQA/pylint")
     (synopsis "Python source code analyzer which looks for coding standard
 errors")
@@ -1842,8 +1845,7 @@ tests written in a natural language style, backed up by Python code.")
            (lambda _
              (substitute* "setup.py"
                (("'wheel'") "")                ; We don't use it.
-               (("'ordereddict==1.1'") ""))    ; Python >= 2.7 has it built-in.
-             #t)))))
+               (("'ordereddict==1.1'") ""))))))) ; Python >= 2.7 has it built-in.
     (propagated-inputs
      `(("behave" ,behave)
        ("python-requests" ,python-requests)))
@@ -2089,42 +2091,3 @@ aspects of UnitTest++.  UnitTest++ is mostly standard C++ and makes minimal use
 of advanced library and language features, which means it should be easily
 portable to just about any platform.")
     (license license:expat)))
-
-(define-public libfaketime
-  (package
-    (name "libfaketime")
-    (version "0.9.7")
-    (home-page "https://github.com/wolfcw/libfaketime")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url home-page)
-                    (commit (string-append "v" version))))
-              (sha256
-               (base32
-                "1cin1pqwpsswcv7amiwijirvcg3x1zf2l00s1x84nxc5602fzr5c"))
-              (file-name (git-file-name name version))))
-    (build-system gnu-build-system)
-    (arguments
-     '(#:phases (modify-phases %standard-phases
-                  (replace 'configure
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      (let ((out (assoc-ref outputs "out")))
-                        (setenv "CC" "gcc")
-                        (setenv "PREFIX" out)
-                        #t)))
-                  (add-before 'check 'pre-check
-                    (lambda _
-                      (substitute* "test/functests/test_exclude_mono.sh"
-                        (("/bin/bash") (which "bash")))
-                      #t)))
-       #:test-target "test"))
-    (native-inputs
-     `(("perl" ,perl)))                           ;for tests
-    (synopsis "Fake the system time for single applications")
-    (description
-     "The libfaketime library allows users to modify the system time that an
-application \"sees\".  It is meant to be loaded using the dynamic linker's
-@code{LD_PRELOAD} environment variable.  The @command{faketime} command
-provides a simple way to achieve this.")
-    (license license:gpl2)))

gnu/packages/chez.scm

@@ -85,7 +85,6 @@
        ("xorg-rgb" ,xorg-rgb)
        ("nanopass" ,nanopass)
        ("zlib" ,zlib)
-       ("zlib:static" ,zlib "static")
        ("stex" ,stex)))
     (native-inputs
      `(("texlive" ,texlive)
@@ -129,7 +128,6 @@
                    (nanopass (assoc-ref inputs "nanopass"))
                    (stex (assoc-ref inputs "stex"))
                    (zlib (assoc-ref inputs "zlib"))
-                   (zlib-static (assoc-ref inputs "zlib:static"))
                    (unpack (assoc-ref %standard-phases 'unpack))
                    (patch-source-shebangs
                     (assoc-ref %standard-phases 'patch-source-shebangs)))
@@ -150,7 +148,7 @@
                  (("\\$\\{Kernel\\}: \\$\\{kernelobj\\} \\.\\./zlib/libz\\.a")
                   "${Kernel}: ${kernelobj}")
                  (("ld ([-a-zA-Z0-9_${} ]+) \\.\\./zlib/libz\\.a" all args)
-                  (string-append "ld " args " " zlib-static "/lib/libz.a"))
+                  (string-append "ld " args " " zlib "/lib/libz.a"))
                  (("\\(cd \\.\\./zlib; ([-a-zA-Z0-9=./ ]+))")
                   (which "true")))
                (substitute* (find-files "mats" "Mf-.*")

gnu/packages/ci.scm

@@ -186,8 +186,8 @@ their dependencies.")
       (license l:gpl3+))))
 
 (define-public cuirass
-  (let ((commit "0b40dca734468e8b12b3ff58e3e779679f17d38e")
-        (revision "21"))
+  (let ((commit "fe2b73c2353d106431ed0659345391f14ed64600")
+        (revision "20"))
     (package
       (name "cuirass")
       (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -199,7 +199,7 @@ their dependencies.")
                 (file-name (string-append name "-" version))
                 (sha256
                  (base32
-                  "1kdxs8dzdyldfs4wsz5hb64hprkbrnq5ljdll631f3bj8pbvvvc1"))))
+                  "00ldbig2p14qpwrl2i2hnhb9idgbbf0kqnlh4n79rmz96blm7463"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)

gnu/packages/clojure.scm

@@ -1,293 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
-
-(define-module (gnu packages clojure)
-  #:use-module (gnu packages)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix git-download)
-  #:use-module (guix build-system ant)
-  #:use-module (guix build-system clojure)
-  #:use-module (ice-9 match))
-
-(define-public clojure
-  (let* ((lib (lambda (prefix version hash)
-                (origin (method url-fetch)
-                        (uri (string-append "https://github.com/clojure/"
-                                            prefix version ".tar.gz"))
-                        (sha256 (base32 hash)))))
-         ;; The libraries below are needed to run the tests.
-         (libraries
-          `(("core-specs-alpha-src"
-             ,(lib "core.specs.alpha/archive/core.specs.alpha-"
-                   "0.1.24"
-                   "0v2a0svf1ar2y42ajxwsjr7zmm5j7pp2zwrd2jh3k7xzd1p9x1fv"))
-            ("data-generators-src"
-             ,(lib "data.generators/archive/data.generators-"
-                   "0.1.2"
-                   "0kki093jp4ckwxzfnw8ylflrfqs8b1i1wi9iapmwcsy328dmgzp1"))
-            ("spec-alpha-src"
-             ,(lib "spec.alpha/archive/spec.alpha-"
-                   "0.1.143"
-                   "00alf0347licdn773w2jarpllyrbl52qz4d8mw61anjksacxylzz"))
-            ("test-check-src"
-             ,(lib "test.check/archive/test.check-"
-                   "0.9.0"
-                   "0p0mnyhr442bzkz0s4k5ra3i6l5lc7kp6ajaqkkyh4c2k5yck1md"))
-            ("test-generative-src"
-             ,(lib "test.generative/archive/test.generative-"
-                   "0.5.2"
-                   "1pjafy1i7yblc7ixmcpfq1lfbyf3jaljvkgrajn70sws9xs7a9f8"))
-            ("tools-namespace-src"
-             ,(lib "tools.namespace/archive/tools.namespace-"
-                   "0.2.11"
-                   "10baak8v0hnwz2hr33bavshm7y49mmn9zsyyms1dwjz45p5ymhy0"))))
-         (library-names (match libraries
-                          (((library-name _) ...)
-                           library-name))))
-
-    (package
-      (name "clojure")
-      (version "1.9.0")
-      (source
-       (origin
-         (method url-fetch)
-         (uri
-          (string-append "https://github.com/clojure/clojure/archive/clojure-"
-                         version ".tar.gz"))
-         (sha256
-          (base32 "0xjbzcw45z32vsn9pifp7ndysjzqswp5ig0jkjpivigh2ckkdzha"))))
-      (build-system ant-build-system)
-      (arguments
-       `(#:imported-modules ((guix build clojure-utils)
-                             (guix build guile-build-system)
-                             ,@%ant-build-system-modules)
-         #:modules ((guix build ant-build-system)
-                    (guix build clojure-utils)
-                    (guix build java-utils)
-                    (guix build utils)
-                    (srfi srfi-26))
-         #:test-target "test"
-         #:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'unpack-library-sources
-             (lambda* (#:key inputs #:allow-other-keys)
-               (define (extract-library name)
-                 (mkdir-p name)
-                 (with-directory-excursion name
-                   (invoke "tar"
-                           "--extract"
-                           "--verbose"
-                           "--file" (assoc-ref inputs name)
-                           "--strip-components=1"))
-                 (copy-recursively (string-append name "/src/main/clojure/")
-                                   "src/clj/"))
-               (for-each extract-library ',library-names)
-               #t))
-           (add-after 'unpack-library-sources 'fix-manifest-classpath
-             (lambda _
-               (substitute* "build.xml"
-                 (("<attribute name=\"Class-Path\" value=\".\"/>") ""))
-               #t))
-           (add-after 'build 'build-javadoc ant-build-javadoc)
-           (replace 'install (install-jars "./"))
-           (add-after 'install-license-files 'install-doc
-             (cut install-doc #:doc-dirs '("doc/clojure/") <...>))
-           (add-after 'install-doc 'install-javadoc
-             (install-javadoc "target/javadoc/")))))
-      (native-inputs libraries)
-      (home-page "https://clojure.org/")
-      (synopsis "Lisp dialect running on the JVM")
-      (description "Clojure is a dynamic, general-purpose programming language,
-combining the approachability and interactive development of a scripting
-language with an efficient and robust infrastructure for multithreaded
-programming.  Clojure is a compiled language, yet remains completely dynamic
-– every feature supported by Clojure is supported at runtime.  Clojure
-provides easy access to the Java frameworks, with optional type hints and type
-inference, to ensure that calls to Java can avoid reflection.
-
-Clojure is a dialect of Lisp, and shares with Lisp the code-as-data philosophy
-and a powerful macro system.  Clojure is predominantly a functional programming
-language, and features a rich set of immutable, persistent data structures.
-When mutable state is needed, Clojure offers a software transactional memory
-system and reactive Agent system that ensure clean, correct, multithreaded
-designs.")
-      ;; Clojure is licensed under EPL1.0
-      ;; ASM bytecode manipulation library is licensed under BSD-3
-      ;; Guava Murmur3 hash implementation is licensed under APL2.0
-      ;; src/clj/repl.clj is licensed under CPL1.0
-
-      ;; See readme.html or readme.txt for details.
-      (license (list license:epl1.0
-                     license:bsd-3
-                     license:asl2.0
-                     license:cpl1.0)))))
-
-(define-public clojure-algo-generic
-  (package
-    (name "clojure-algo-generic")
-    (version "0.1.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/clojure/algo.generic/archive"
-                       "/algo.generic-" version ".tar.gz"))
-       (sha256
-        (base32 "12w9681i545gp1af4576z1qbixwps1j13c16fmcc7zsb0bd1zr7w"))))
-    (build-system clojure-build-system)
-    (arguments
-     '(#:source-dirs '("src/main/clojure/")
-       #:test-dirs '("src/test/clojure/")
-       #:doc-dirs '()))
-    (synopsis "Generic versions of common functions")
-    (description
-     "Generic versions of commonly used functions, implemented as multimethods
-that can be implemented for any data type.")
-    (home-page "https://github.com/clojure/algo.generic")
-    (license license:epl1.0)))
-
-(define-public clojure-algo-monads
-  (package
-    (name "clojure-algo-monads")
-    (version "0.1.6")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/clojure/algo.monads/archive"
-                       "/algo.monads-" version ".tar.gz"))
-       (sha256
-        (base32 "14gbvfgmrda990h45yn7zag83vp1kdkz4f4yzmyvkr0sjihlgdmq"))))
-    (build-system clojure-build-system)
-    (arguments
-     '(#:source-dirs '("src/main/clojure/")
-       #:test-dirs '("src/test/clojure/")
-       #:doc-dirs '()))
-    (native-inputs
-     `(("clojure-tools-macro" ,clojure-tools-macro)))
-    (synopsis
-     "Monad Macros and Definitions")
-    (description
-     "This library contains the most commonly used monads as well as macros for
-defining and using monads and useful monadic functions.")
-    (home-page "https://github.com/clojure/algo.monads")
-    (license license:epl1.0)))
-
-(define-public clojure-core-match
-  (let ((commit "1837ffbd4a150e8f3953b2d9ed5cf4a4ad3720a7")
-        (revision "1")) ; this is the 1st commit buildable with clojure 1.9
-    (package
-      (name "clojure-core-match")
-      (version (git-version "0.3.0-alpha5" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/clojure/core.match.git")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "04bdlp5dgkrqzrz0lw3mfwmygj2218qnm1cz3dkb9wy4m0238s4d"))))
-      (build-system clojure-build-system)
-      (arguments
-       '(#:source-dirs '("src/main/clojure")
-         #:test-dirs '("src/test/clojure")
-         #:doc-dirs '()))
-      (synopsis "Optimized pattern matching for Clojure")
-      (description
-       "An optimized pattern matching library for Clojure.
-It supports Clojure 1.5.1 and later as well as ClojureScript.")
-      (home-page "https://github.com/clojure/core.match")
-      (license license:epl1.0))))
-
-(define-public clojure-instaparse
-  (let ((commit "dcfffad5b065e750f0f5835f017cdd8188b8ca2e")
-        (version "1.4.9")) ; upstream forget to tag this release
-    (package
-      (name "clojure-instaparse")
-      (version version)
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/Engelberg/instaparse.git")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "002mrgin4z3dqy88r1lak7smd0m7x8d22vmliw0m6w6mh5pa17lk"))))
-      (build-system clojure-build-system)
-      (arguments
-       '(#:doc-dirs '("docs/")))
-      (synopsis "No grammar left behind")
-      (description
-       "Instaparse aims to be the simplest way to build parsers in Clojure.
-
-@itemize
-@item Turns @emph{standard EBNF or ABNF notation} for context-free grammars
-into an executable parser that takes a string as an input and produces a parse
-tree for that string.
-
-@item @dfn{No Grammar Left Behind}: Works for @emph{any} context-free grammar,
-including @emph{left-recursive}, @emph{right-recursive}, and @emph{ambiguous}
-grammars.
-
-@item Extends the power of context-free grammars with PEG-like syntax for
-lookahead and negative lookahead.
-
-@item Supports both of Clojure's most popular tree formats (hiccup and enlive)
-as output targets
-
-@item Detailed reporting of parse errors.
-
-@item Optionally produces lazy sequence of all parses (especially useful for
-diagnosing and debugging ambiguous grammars).
-
-@item ``Total parsing'' mode where leftover string is embedded in the parse
-tree.
-
-@item Optional combinator library for building grammars programmatically.
-
-@item Performant.
-@end itemize")
-      (home-page "https://github.com/Engelberg/instaparse")
-      (license license:epl1.0))))
-
-(define-public clojure-tools-macro
-  (package
-    (name "clojure-tools-macro")
-    (version "0.1.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/clojure/tools.macro/archive"
-                       "/tools.macro-" version ".tar.gz"))
-       (sha256
-        (base32 "0fs64a0g63xx6g7sj6vrsqknhl90s0isf6k053nw8vv5prfzc7v6"))))
-    (build-system clojure-build-system)
-    (arguments
-     '(#:source-dirs '("src/main/clojure/")
-       #:test-dirs '("src/test/clojure/")
-       #:doc-dirs '()))
-    (synopsis "Utilities for macro writers")
-    (description "Tools for writing macros.")
-    (home-page "https://github.com/clojure/tools.macro")
-    (license license:epl1.0)))

gnu/packages/cmake.scm

@@ -7,7 +7,6 @@
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -44,7 +43,7 @@
 (define-public cmake
   (package
     (name "cmake")
-    (version "3.12.2")
+    (version "3.11.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.cmake.org/files/v"
@@ -52,7 +51,7 @@
                                   "/cmake-" version ".tar.gz"))
               (sha256
                (base32
-                "19410mxgcyvk5q42phaclb1hz6rl08z4yj8iriq706p5k5bli5qg"))
+                "0sv5k9q6braa8hhw0y3w19avqn0xn5czv5jf5fz5blnlf7ivw4y3"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -87,13 +86,6 @@
            " --exclude-regex ^\\(" (string-join skipped-tests "\\|") "\\)$")))
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'split-package
-           ;; Remove files that have been packaged in other package recipes.
-           (lambda _
-             (delete-file "Auxiliary/cmake-mode.el")
-             (substitute* "Auxiliary/CMakeLists.txt"
-               ((".*cmake-mode.el.*") ""))
-             #t))
          (add-before 'configure 'patch-bin-sh
            (lambda _
              ;; Replace "/bin/sh" by the right path in... a lot of

gnu/packages/code.scm

@@ -211,16 +211,16 @@ COCOMO model or user-provided parameters.")
 (define-public cloc
   (package
     (name "cloc")
-    (version "1.80")
+    (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
-         "0rqxnaskg5b736asyzfda1113zvpkajyqjf49vl9wgzf1r9m6bq8"))))
+         "1j9lwy9xf43kpv1csqdxzch6y1hnsv881ddqd357f8v58dhr4s68"))))
     (build-system gnu-build-system)
     (inputs
      `(("coreutils" ,coreutils)
@@ -231,8 +231,8 @@ COCOMO model or user-provided parameters.")
        ("perl-regexp-common" ,perl-regexp-common)))
     (arguments
      `(#:phases (modify-phases %standard-phases
-                  (delete 'configure)   ; nothing to configure
-                  (delete 'build)       ; nothing to build
+                  (delete 'configure)
+                  (delete 'build)
                   (replace 'install
                     (lambda* (#:key inputs outputs #:allow-other-keys)
                       (let* ((out (assoc-ref outputs "out")))
@@ -540,20 +540,18 @@ independent targets.")
 (define-public uncrustify
   (package
     (name "uncrustify")
-    (version "0.68.1")
+    (version "0.67")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/uncrustify/uncrustify/")
-                    (commit (string-append name "-" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/uncrustify/uncrustify/archive/"
+                    "uncrustify-" version ".zip"))
               (sha256
                (base32
-                "0gf6vjcfy8pl7idvwsd500ffj9hri62q0n79kpb6cnfprrqpbgf4"))))
+                "0n13kq0nsm35fxhdp0f275n4x0w88hdv3bdjy0hgvv42x0dx5zyp"))))
     (build-system cmake-build-system)
     (native-inputs
-     `(("unzip" ,unzip)
-       ("python" ,python-wrapper)))
+     `(("unzip" ,unzip)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases

gnu/packages/commencement.scm

@@ -186,25 +186,12 @@
                     ,cf)))))
      (inputs %boot0-inputs))))
 
-;; Use a "fixed" package source for this early libstdc++ variant so we can
-;; update GCC 4.9 without triggering a full rebuild.
-(define gcc-for-libstdc++
-  (package
-    (inherit gcc-4.9)
-    (source (origin
-              (inherit (package-source gcc-4.9))
-              (patches (search-patches "gcc-4.9-libsanitizer-fix.patch"
-                                       "gcc-arm-bug-71399.patch"
-                                       "gcc-asan-missing-include.patch"
-                                       "gcc-libvtv-runpath.patch"
-                                       "gcc-fix-texi2pod.patch"))))))
-
 (define libstdc++-boot0
   ;; GCC's libcc1 is always built as a shared library (the top-level
   ;; 'Makefile.def' forcefully adds --enable-shared) and thus needs to refer
   ;; to libstdc++.so.  We cannot build libstdc++-5.3 because it relies on
   ;; C++14 features missing in some of our bootstrap compilers.
-  (let ((lib (package-with-bootstrap-guile (make-libstdc++ gcc-for-libstdc++))))
+  (let ((lib (package-with-bootstrap-guile (make-libstdc++ gcc-4.9))))
     (package
       (inherit lib)
       (name "libstdc++-boot0")

gnu/packages/compression.scm

@@ -7,7 +7,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
-;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2016 Danny Milosavljevic <dannym@scratchpost.org>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -85,7 +85,6 @@
        (base32
         "18dighcs333gsvajvvgqp8l4cx7h1x7yx9gd5xacnk80spyykrf3"))))
     (build-system gnu-build-system)
-    (outputs '("out" "static"))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -100,15 +99,7 @@
                      `((setenv "CHOST" ,(%current-target-system)))
                      '())
                (invoke "./configure"
-                       (string-append "--prefix=" out)))))
-         (add-after 'install 'move-static-library
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out"))
-                   (static (assoc-ref outputs "static")))
-               (with-directory-excursion (string-append out "/lib")
-                 (install-file "libz.a" (string-append static "/lib"))
-                 (delete-file "libz.a")
-                 #t)))))))
+                       (string-append "--prefix=" out))))))))
     (home-page "https://zlib.net/")
     (synopsis "Compression library")
     (description
@@ -133,7 +124,10 @@ in compression.")
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-source
-           (lambda _ (chdir "contrib/minizip") #t)))))
+           (lambda _ (chdir "contrib/minizip") #t))
+         (add-after 'enter-source 'autoreconf
+           (lambda _
+             (invoke "autoreconf" "-vif"))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
@@ -185,7 +179,12 @@ utility.  Instead of being written in Java, FastJar is written in C.")
               "02cihzl77ia0dcz7z2cga2412vyhhs5pa2355q4wpwbyga2lrwjh"))
             (patches (search-patches "libtar-CVE-2013-4420.patch"))))
    (build-system gnu-build-system)
-   (arguments `(#:tests? #f)) ; no "check" target
+   (arguments
+    `(#:tests? #f ;no "check" target
+      #:phases
+      (modify-phases %standard-phases
+        (add-after 'unpack 'autoconf
+          (lambda _ (invoke "sh" "autoreconf" "-vfi"))))))
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
@@ -217,21 +216,6 @@ adding and extracting files to/from a tar archive.")
     '(#:tests? #f
       #:phases
       (modify-phases %standard-phases
-        (add-after 'unpack 'patch-for-glibc-2.28
-          (lambda _
-            ;; Adjust the bundled gnulib to work with glibc 2.28.  See e.g.
-            ;; "m4-gnulib-libio.patch".  This is a phase rather than patch
-            ;; or snippet to work around <https://bugs.gnu.org/32347>.
-            (substitute* (find-files "lib" "\\.c$")
-              (("#if defined _IO_ftrylockfile")
-               "#if defined _IO_EOF_SEEN"))
-            (substitute* "lib/stdio-impl.h"
-              (("^/\\* BSD stdio derived implementations")
-               (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n"
-                              "# define _IO_IN_BACKUP 0x100\n"
-                              "#endif\n\n"
-                              "/* BSD stdio derived implementations")))
-            #t))
         (add-after 'unpack 'use-absolute-name-of-gzip
           (lambda* (#:key outputs #:allow-other-keys)
             (substitute* "gunzip.in"
@@ -264,7 +248,6 @@ file; as a result, it is often used in conjunction with \"tar\", resulting in
     (arguments
      `(#:modules ((guix build gnu-build-system)
                   (guix build utils)
-                  (ice-9 ftw)
                   (srfi srfi-1))
        #:phases
        (modify-phases %standard-phases
@@ -293,32 +276,25 @@ file; as a result, it is often used in conjunction with \"tar\", resulting in
              ;; it create all the (un)versioned symlinks, so we handle it here.
              (let* ((out    (assoc-ref outputs "out"))
                     (libdir (string-append out "/lib"))
-                    (soname "libbz2.so")
-                    ;; Locate the built library (e.g. "libbz2.so.1.0.6").
-                    (lib (car (scandir "."
-                                       (lambda (file)
-                                         (and (string-prefix? soname file)
-                                              (eq? 'regular
-                                                   (stat:type (lstat file))))))))
-                    (soversion (string-drop lib (+ 1 (string-length soname)))))
+                    ;; Find the actual library (e.g. "libbz2.so.1.0.6").
+                    (lib (string-drop
+                          (car (find-files
+                                "."
+                                (lambda (file stat)
+                                  (and (string-prefix? "./libbz2.so" file)
+                                       (eq? 'regular (stat:type stat))))))
+                          2))
+                    (soversion (string-drop lib (string-length "libbz2.so."))))
                (install-file lib libdir)
                (with-directory-excursion libdir
                  ;; Create symlinks libbz2.so.1 -> libbz2.so.1.0, etc.
-                 (let loop ((base soname)
+                 (let loop ((base "libbz2.so")
                             (numbers (string-split soversion #\.)))
                    (unless (null? numbers)
                      (let ((so-file (string-append base "." (car numbers))))
                        (symlink so-file base)
                        (loop so-file (cdr numbers))))))
                #t)))
-         (add-after 'install-shared-lib 'move-static-lib
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out"))
-                   (static (assoc-ref outputs "static")))
-               (with-directory-excursion (string-append out "/lib")
-                 (install-file "libbz2.a" (string-append static "/lib"))
-                 (delete-file "libbz2.a")
-                 #t))))
          (add-after 'install-shared-lib 'patch-scripts
            (lambda* (#:key outputs inputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out")))
@@ -333,7 +309,6 @@ file; as a result, it is often used in conjunction with \"tar\", resulting in
        ,@(if (%current-target-system)
              '(#:tests? #f)
              '())))
-    (outputs '("out" "static"))
     (synopsis "High-quality data compression program")
     (description
      "bzip2 is a freely available, patent free (see below), high-quality data
@@ -355,20 +330,7 @@ decompression.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1sahaqc5bw4i0iyri05syfza4ncf5cml89an033fspn97klmxis6"))
-             (modules '((guix build utils)))
-             (snippet
-              '(begin
-                 (substitute* (find-files "lib" "\\.c$")
-                   (("#if defined _IO_ftrylockfile")
-                    "#if defined _IO_EOF_SEEN"))
-                 (substitute* "lib/stdio-impl.h"
-                   (("^/\\* BSD stdio derived implementations")
-                    (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n"
-                                   "# define _IO_IN_BACKUP 0x100\n"
-                                   "#endif\n\n"
-                                   "/* BSD stdio derived implementations")))
-                 #t))))
+                "1sahaqc5bw4i0iyri05syfza4ncf5cml89an033fspn97klmxis6"))))
     (build-system gnu-build-system)
     (synopsis "Parallel bzip2 compression utility")
     (description
@@ -414,7 +376,7 @@ compressed with pbzip2 can be decompressed with bzip2).")
 (define-public xz
   (package
    (name "xz")
-   (version "5.2.4")
+   (version "5.2.3")
    (source (origin
             (method url-fetch)
             (uri (list (string-append "http://tukaani.org/xz/xz-" version
@@ -423,7 +385,7 @@ compressed with pbzip2 can be decompressed with bzip2).")
                                       version ".tar.gz")))
             (sha256
              (base32
-              "0ibi2zsfaz6l756spjwc5rayf4ckgc9hwmy8qinppcyk4svz64mm"))))
+              "1jr8pxnz55ifc8cvp3ivgl79ph9iik5aypsc9cma228aglsqp4ki"))))
    (build-system gnu-build-system)
    (synopsis "General-purpose data compression")
    (description
@@ -589,20 +551,7 @@ decompressors when faced with corrupted input.")
       (patches (search-patches "sharutils-CVE-2018-1000097.patch"))
       (sha256
        (base32
-        "16isapn8f39lnffc3dp4dan05b7x6mnc76v6q5nn8ysxvvvwy19b"))
-      (modules '((guix build utils)))
-      (snippet
-       '(begin
-          (substitute* (find-files "lib" "\\.c$")
-            (("#if defined _IO_ftrylockfile")
-             "#if defined _IO_EOF_SEEN"))
-          (substitute* "lib/stdio-impl.h"
-            (("^/\\* BSD stdio derived implementations")
-             (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n"
-                            "# define _IO_IN_BACKUP 0x100\n"
-                            "#endif\n\n"
-                            "/* BSD stdio derived implementations")))
-          #t))))
+        "16isapn8f39lnffc3dp4dan05b7x6mnc76v6q5nn8ysxvvvwy19b"))))
     (build-system gnu-build-system)
     (inputs
      `(("which" ,which)))
@@ -696,13 +645,13 @@ sfArk file format to the uncompressed sf2 format.")
   (package
     (name "libmspack")
     (home-page "https://cabextract.org.uk/libmspack/")
-    (version "0.9.1")
+    (version "0.7.1")
     (source
      (origin
       (method url-fetch)
       (uri (string-append home-page name "-" version "alpha.tar.gz"))
       (sha256
-       (base32 "0h1f5w8rjnq7dcqpqm1mpx5m8q80691kid6f7npqlqwqqzckd8v2"))))
+       (base32 "0zn4vwzk5ankgd0l88cipan19pzbzv0sm3fba17lvqwka3dp1acp"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--disable-static")))
@@ -760,8 +709,7 @@ INCLUDE = ~a/include
 LIB = ~:*~a/lib
 OLD_ZLIB = False
 GZIP_OS_CODE = AUTO_DETECT"
-                                 (assoc-ref inputs "zlib"))))
-                     #t)))))
+                                 (assoc-ref inputs "zlib")))))))))
     (home-page "https://metacpan.org/release/Compress-Raw-Zlib")
     (synopsis "Low-level interface to zlib compression library")
     (description "This module provides a Perl interface to the zlib
@@ -894,16 +842,8 @@ the LZ4 frame format.")
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
-           (lambda _
-             (chdir "squashfs-tools")
-             #t))
-         (add-after 'unpack 'fix-glibc-compatability
-           (lambda _
-             (substitute* '("squashfs-tools/mksquashfs.c"
-                            "squashfs-tools/unsquashfs.c")
-               (("<sys/sysinfo.h>")
-                "<sys/sysinfo.h>\n#include <sys/sysmacros.h>"))
-             #t)))))
+                  (lambda _
+                    (chdir "squashfs-tools"))))))
     (inputs
      `(("lz4" ,lz4)
        ("lzo" ,lzo)
@@ -1085,13 +1025,13 @@ smaller than those produced by @code{Xdelta}.")
  (package
    (name "cabextract")
    (home-page "https://cabextract.org.uk/")
-   (version "1.9")
+   (version "1.7")
    (source (origin
               (method url-fetch)
               (uri (string-append home-page name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1hf4zhjxfdgq9x172r5zfdnafma9q0zf7372syn8hcn7hcypkg0v"))
+                "1g86wmb8lkjiv2jarfz979ngbgg7d3si8x5il4g801604v406wi9"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1099,27 +1039,11 @@ smaller than those produced by @code{Xdelta}.")
                   (delete-file-recursively "mspack")
                   #t))))
     (build-system gnu-build-system)
-    (arguments
-     '(#:configure-flags '("--with-external-libmspack")
-       #:phases
-       (modify-phases %standard-phases
-         ;; cabextract needs some of libmspack's header files.
-         ;; These are located in the "mspack" directory of libmspack.
-         (add-before 'build 'unpack-libmspack
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((dir-name "libmspack-src"))
-               (mkdir dir-name)
-               (invoke "tar" "-xvf" (assoc-ref inputs "libmspack-source")
-                       "-C" dir-name "--strip-components" "1")
-               (rename-file (string-append dir-name "/mspack")
-                            "mspack")
-               (delete-file-recursively dir-name)
-               #t))))))
+    (arguments '(#:configure-flags '("--with-external-libmspack")))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (inputs
-     `(("libmspack" ,libmspack)
-       ("libmspack-source" ,(package-source libmspack))))
+     `(("libmspack" ,libmspack)))
     (synopsis "Tool to unpack Cabinet archives")
     (description "Extracts files out of Microsoft Cabinet (.cab) archives")
     ;; Some source files specify gpl2+, lgpl2+, however COPYING is gpl3.
@@ -1131,14 +1055,13 @@ smaller than those produced by @code{Xdelta}.")
     (version "3.1.0")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/jmacd/xdelta.git")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (string-append "https://github.com/jmacd/xdelta/archive/v"
+                           version ".tar.gz"))
        (sha256
         (base32
-         "09mmsalc7dwlvgrda56s2k927rpl3a5dzfa88aslkqcjnr790wjy"))
+         "17g2pbbqy6h20qgdjq7ykib7kg5ajh8fwbsfgyjqg8pwg19wy5bm"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (snippet
         ;; This file isn't freely distributable and has no effect on building.
         '(begin
@@ -1152,7 +1075,9 @@ smaller than those produced by @code{Xdelta}.")
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-build-directory
-           (lambda _ (chdir "xdelta3") #t)))))
+           (lambda _ (chdir "xdelta3") #t))
+         (add-after 'enter-build-directory 'autoconf
+           (lambda _ (invoke "autoreconf" "-vfi"))))))
     (home-page "http://xdelta.org")
     (synopsis "Delta encoder for binary files")
     (description "xdelta encodes only the differences between two binary files
@@ -1202,30 +1127,16 @@ well as bzip2.")
 (define-public bitshuffle
   (package
     (name "bitshuffle")
-    (version "0.3.5")
+    (version "0.3.4")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "bitshuffle" version))
               (sha256
                (base32
-                "1823x61kyax4dc2hjmc1xraskxi1193y8lvxd03vqv029jrj8cjy"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; Remove generated Cython files.
-                  (delete-file "bitshuffle/h5.c")
-                  (delete-file "bitshuffle/ext.c")
-                  #t))))
+                "0ydawb01ghsvmw0lraczhrgvkjj97bpg98f1qqs1cnfp953mdd5v"))))
     (build-system python-build-system)
     (arguments
-     `(#:tests? #f             ; fail: https://github.com/h5py/h5py/issues/769
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'dont-build-native
-           (lambda _
-             (substitute* "setup.py"
-               (("'-march=native', ") ""))
-             #t)))))
+     `(#:tests? #f))           ; fail: https://github.com/h5py/h5py/issues/769
     (inputs
      `(("numpy" ,python-numpy)
        ("h5py" ,python-h5py)
@@ -1243,15 +1154,14 @@ algorithm within the Numpy framework.")
   (package
     (name "snappy")
     (version "1.1.7")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/google/snappy/archive/"
-                           version ".tar.gz"))
-       (file-name (string-append "snappy-" version ".tar.gz"))
-       (sha256
-        (base32 "1m7rcdqzkys5lspj8jcsaah8w33zh28s771bw0ga2lgzfgl05yix"))
-       (patches (search-patches "snappy-add-O2-flag-in-CmakeLists.txt.patch"))))
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/google/snappy/archive/"
+                                  version ".tar.gz"))
+              (file-name (string-append "snappy-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1m7rcdqzkys5lspj8jcsaah8w33zh28s771bw0ga2lgzfgl05yix"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")))
@@ -1361,8 +1271,7 @@ install: libbitshuffle.so
          (add-after 'build-jni 'copy-jni
            (lambda _
              (copy-recursively "src/main/resources/org/xerial/snappy/native"
-                               "build/classes/org/xerial/snappy/native")
-             #t))
+                               "build/classes/org/xerial/snappy/native")))
          (add-before 'check 'fix-failing
            (lambda _
              (with-directory-excursion "src/test/java/org/xerial/snappy"
@@ -1480,8 +1389,7 @@ compressor/decompressor.")
                        class))
              (invoke "ant" "compile-tests")
              (test "org.iq80.snappy.SnappyFramedStreamTest")
-             (test "org.iq80.snappy.SnappyStreamTest")
-             #t))
+             (test "org.iq80.snappy.SnappyStreamTest")))
          (add-before 'build 'remove-hadoop-dependency
            (lambda _
              ;; We don't have hadoop
@@ -1786,14 +1694,14 @@ or junctions, and always follows hard links.")
 (define-public zstd
   (package
     (name "zstd")
-    (version "1.3.7")
+    (version "1.3.6")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/facebook/zstd/releases/download/"
                            "v" version "/zstd-" version ".tar.gz"))
        (sha256
-        (base32 "0gapsdzqfsfqqddzv22592iwa0008xjyi15f06pfv9hcvwvg4xrj"))))
+        (base32 "1525b31jmbiczjj1n58nckdzky4cdnbwcsil3zgy4cx03v0a0cp8"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -1836,7 +1744,7 @@ speed.")
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-subdirectory
-           (lambda _ (chdir "contrib/pzstd") #t))
+           (lambda _ (chdir "contrib/pzstd")))
          (delete 'configure)            ; no configure script
          (add-before 'check 'compile-tests
            (lambda* (#:key make-flags #:allow-other-keys)
@@ -2118,16 +2026,14 @@ type by using either Perl modules, or command-line tools on your system.")
            (lambda _
              ;; Our build system enters the first directory in the archive, but
              ;; the package is not contained in a subdirectory
-             (chdir "..")
-             #t))
+             (chdir "..")))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Do we want to install *Demo.jar?
              (install-file "build/jar/xz.jar"
                            (string-append
                              (assoc-ref outputs "out")
-                             "/share/java/xz.jar"))
-             #t)))))
+                             "/share/java/xz.jar")))))))
     (native-inputs
      `(("unzip" ,unzip)))
     (home-page "https://tukaani.org")

gnu/packages/cross-base.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
@@ -356,7 +356,7 @@ target that libc."
              ,@(package-arguments glibc/hurd-headers))
          ((#:phases phases)
           `(modify-phases ,phases
-             (add-after 'unpack 'set-cross-headers-path
+             (add-before 'pre-configure 'set-cross-headers-path
                (lambda* (#:key inputs #:allow-other-keys)
                  (let* ((mach (assoc-ref inputs "gnumach-headers"))
                         (hurd (assoc-ref inputs "hurd-headers"))
@@ -426,9 +426,17 @@ target that libc."
                      (xheaders (cross-kernel-headers target)))
   "Return a libc cross-built for TARGET, a GNU triplet.  Use XGCC and
 XBINUTILS and the cross tool chain."
+  (define (cross-libc-for-target target)
+    "Return libc depending on TARGET."
+    (match target
+      ((or "i586-pc-gnu" "i586-gnu") glibc/hurd)
+      (_ glibc/linux)))
+
+  ;; Use (cross-libc-for-target ...) to determine the correct libc to use.
+
   (if (cross-newlib? target)
       (native-libc target)
-      (let ((libc glibc))
+      (let ((libc (cross-libc-for-target target)))
         (package (inherit libc)
           (name (string-append "glibc-cross-" target))
           (arguments
@@ -449,9 +457,7 @@ XBINUTILS and the cross tool chain."
                  ,@(package-arguments libc))
              ((#:configure-flags flags)
               `(cons ,(string-append "--host=" target)
-                     ,(if (hurd-triplet? target)
-                          `(cons "--disable-werror" ,flags)
-                          flags)))
+                   ,flags))
              ((#:phases phases)
               `(modify-phases ,phases
                  (add-before 'configure 'set-cross-kernel-headers-path

gnu/packages/crypto.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 David Thompson <davet@gnu.org>
-;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -10,7 +10,6 @@
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
-;;; Copyright © 2018 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -94,7 +93,7 @@ communication, encryption, decryption, signatures, etc.")
 (define-public libmd
   (package
     (name "libmd")
-    (version "1.0.1")
+    (version "1.0.0")
     (source (origin
             (method url-fetch)
             (uri
@@ -105,7 +104,7 @@ communication, encryption, decryption, signatures, etc.")
                              version ".tar.xz")))
             (sha256
              (base32
-              "0waclg2d5qin3r26gy5jvy4584ik60njc8pqbzwk0lzq3j9ynkp1"))))
+              "1iv45npzv0gncjgcpx5m081861zdqxw667ysghqb8721yrlyl6pj"))))
     (build-system gnu-build-system)
     (synopsis "Message Digest functions from BSD systems")
     (description
@@ -164,31 +163,34 @@ OpenBSD tool of the same name.")
                                           "See base64.c in the distribution for
                                            the license from IBM.")))))
 
+
 (define-public opendht
   (package
     (name "opendht")
     (version "0.6.1")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/savoirfairelinux/opendht.git")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  (delete-file-recursively "src/argon2")
-                  (substitute* "src/Makefile.am"
-                    (("./argon2/libargon2.la") "")
-                    (("SUBDIRS = argon2") ""))
-                  (substitute* "src/crypto.cpp"
-                    (("argon2/argon2.h") "argon2.h"))
-                  (substitute* "configure.ac"
-                    (("src/argon2/Makefile") ""))
-                  #t))
-              (sha256
-               (base32
-                "1akk613f18rc8kqs0cxdm34iq7wwc9kffhgp5rng09arwlw8gw3w"))))
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append
+         "https://github.com/savoirfairelinux/" name
+         "/archive/" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (delete-file-recursively "src/argon2")
+           (substitute* "src/Makefile.am"
+             (("./argon2/libargon2.la") "")
+             (("SUBDIRS = argon2") ""))
+           (substitute* "src/crypto.cpp"
+             (("argon2/argon2.h") "argon2.h"))
+           (substitute* "configure.ac"
+             (("src/argon2/Makefile") ""))
+           #t))
+       (sha256
+        (base32
+         "09yvkmbqbym3b5md4n96qc1s9sf2n8ji404hagih45rmsj49599x"))))
     (build-system gnu-build-system)
     (inputs
      `(("gnutls" ,gnutls)
@@ -203,7 +205,11 @@ OpenBSD tool of the same name.")
        ("automake" ,automake)
        ("libtool" ,libtool)))
     (arguments
-     `(#:configure-flags '("--disable-tools" "--disable-python")))
+     `(#:configure-flags '("--disable-tools" "--disable-python")
+       #:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'autoconf
+                    (lambda _
+                      (zero? (system* "autoreconf" "-vfi")))))))
     (home-page "https://github.com/savoirfairelinux/opendht/")
     (synopsis "Distributed Hash Table (DHT) library")
     (description "OpenDHT is a Distributed Hash Table (DHT) library.  It may
@@ -848,36 +854,3 @@ public-key cryptography.  Asignify is designed to be portable and self-contained
 with zero external dependencies.  Asignify can verify OpenBSD signatures, but it
 cannot sign messages in OpenBSD format yet.")
       (license license:bsd-2))))
-
-(define-public enchive
-  (package
-    (name "enchive")
-    (version "3.4")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/skeeto/" name "/archive/"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "17hrxpp4cpn10bk48sfvfjc8hghky34agsnypam1v9f36kbalqfk"))
-              (file-name (string-append name "-" version ".tar.gz"))))
-    (build-system gnu-build-system)
-    (arguments
-     '(#:tests? #f                      ; no check target         '
-       #:make-flags (list "CC=gcc" "PREFIX=$(out)")
-       #:phases (modify-phases %standard-phases
-                  (delete 'configure)
-                  (add-after 'install 'post-install
-                    (lambda _
-                      (let* ((out (assoc-ref %outputs "out"))
-                             (lisp (string-append out "/share/emacs/site-lisp")))
-                        (install-file "enchive-mode.el" lisp)
-                        #t))))))
-    (synopsis "Encrypted personal archives")
-    (description
-     "Enchive is a tool to encrypt files to yourself for long-term
-archival.  It's a focused, simple alternative to more complex solutions such as
-GnuPG or encrypted filesystems.  Enchive has no external dependencies and is
-trivial to build for local use.  Portability is emphasized over performance.")
-    (home-page "https://github.com/skeeto/enchive")
-    (license license:unlicense)))

gnu/packages/cups.scm

@@ -53,7 +53,7 @@
 (define-public cups-filters
   (package
     (name "cups-filters")
-    (version "1.21.0")
+    (version "1.20.1")
     (source(origin
               (method url-fetch)
               (uri
@@ -61,7 +61,7 @@
                               "cups-filters-" version ".tar.xz"))
               (sha256
                (base32
-                "0fs90xx9i4h8gbpligf5kkh21llv4kf5g3bgfbx4z272xkm7bsfi"))
+                "0qix1whz5n4ijnl6d44f1v8nzkpv99wqjyrby8vx6xnpskw5hsxk"))
               (modules '((guix build utils)))
               (snippet
                ;; install backends, banners and filters to cups-filters output
@@ -176,7 +176,8 @@ filters for the PDF-centric printing workflow introduced by OpenPrinting.")
 (define-public cups-minimal
   (package
     (name "cups-minimal")
-    (version "2.2.8")
+    (replacement cups-minimal-2.2.8)
+    (version "2.2.6")
     (source
      (origin
        (method url-fetch)
@@ -184,7 +185,7 @@ filters for the PDF-centric printing workflow introduced by OpenPrinting.")
                            version "/cups-" version "-source.tar.gz"))
        (sha256
         (base32
-         "1r7r7b3nqpzc1a9dczqpj2mr8rkcwf01676v11sp4j7w4qfzqs1r"))))
+         "16qn41b84xz6khrr2pa2wdwlqxr29rrrkjfi618gbgdkq9w5ff20"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -236,8 +237,21 @@ describe printer capabilities and features, and a wide variety of generic and
 device-specific programs to convert and print many types of files.")
     (license license:gpl2)))
 
+(define-public cups-minimal-2.2.8
+  (package
+    (inherit cups-minimal)
+    (version "2.2.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/apple/cups/releases/download/v"
+                           version "/cups-" version "-source.tar.gz"))
+       (sha256
+        (base32
+         "1r7r7b3nqpzc1a9dczqpj2mr8rkcwf01676v11sp4j7w4qfzqs1r"))))))
+
 (define-public cups
-  (package (inherit cups-minimal)
+  (package/inherit cups-minimal
     (name "cups")
     (arguments
      `(;; Three tests fail:
@@ -382,27 +396,23 @@ device-specific programs to convert and print many types of files.")
 (define-public hplip
   (package
     (name "hplip")
-    (version "3.18.9")
+    (version "3.18.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/hplip/hplip/" version
                                   "/hplip-" version ".tar.gz"))
               (sha256
                (base32
-                "0g3q5mm2crjyc1z4z6gv4lam6sc5d3diz704djrnpqadk4q3h290"))
+                "0zbv6cp9n3xypf2fg4j6fpz8zkvl0z08lyc1vq1gd04ln1l3xkqf"))
               (modules '((guix build utils)))
-              (patches (search-patches "hplip-remove-imageprocessor.patch"))
               (snippet
+               ;; Fix type mismatch.
                '(begin
-                  ;; Delete non-free blobs
-                  (for-each delete-file (find-files "." "\\.so$"))
-                  (delete-file "prnt/hpcups/ImageProcessor.h")
-                  ;; Fix type mismatch.
                   (substitute* "prnt/hpcups/genPCLm.cpp"
                     (("boolean") "bool"))
                   #t))))
     (build-system gnu-build-system)
-    (home-page "https://developers.hp.com/hp-linux-imaging-and-printing")
+    (home-page "http://hplipopensource.com/")
     (synopsis "HP printer drivers")
     (description
      "Hewlett-Packard printer drivers and PostScript Printer Descriptions
@@ -418,8 +428,6 @@ device-specific programs to convert and print many types of files.")
        `("--disable-network-build"
          ,(string-append "--prefix=" (assoc-ref %outputs "out"))
          ,(string-append "--sysconfdir=" (assoc-ref %outputs "out") "/etc")
-         ,(string-append "LDFLAGS=-Wl,-rpath="
-                         (assoc-ref %outputs "out") "/lib")
          ;; Disable until mime.types merging works (FIXME).
          "--disable-fax-build"
          "--enable-hpcups-install"

gnu/packages/curl.scm

@@ -50,15 +50,15 @@
 (define-public curl
   (package
    (name "curl")
-   (version "7.61.1")
-   (replacement curl-7.62.0)
+   (version "7.59.0")
+   (replacement curl-7.61.1)
    (source (origin
             (method url-fetch)
             (uri (string-append "https://curl.haxx.se/download/curl-"
                                 version ".tar.xz"))
             (sha256
              (base32
-              "148qv1f32290r9pwg07mccawihz4srznkzsdwdl2xllvlgb16n9x"))))
+              "1z310hrjm2vmbcpkyp81dcmj9rk127zkjyawpy2pah0nz6yslkp4"))))
    (build-system gnu-build-system)
    (outputs '("out"
               "doc"))                             ;1.2 MiB of man3 pages
@@ -85,8 +85,7 @@
            (separator #f)                         ;single entry
            (files '("etc/ssl/certs/ca-certificates.crt")))))
    (arguments
-    `(#:configure-flags '("--with-gnutls" "--with-gssapi"
-                          "--disable-static")
+    `(#:configure-flags '("--with-gnutls" "--with-gssapi")
       ;; Add a phase to patch '/bin/sh' occurances in tests/runtests.pl
       #:phases
       (modify-phases %standard-phases
@@ -142,10 +141,10 @@ tunneling, and so on.")
                                   "See COPYING in the distribution."))
    (home-page "https://curl.haxx.se/")))
 
-(define-public curl-7.62.0
+(define-public curl-7.61.1
   (package
     (inherit curl)
-    (version "7.62.0")
+    (version "7.61.1")
     (source
       (origin
         (method url-fetch)
@@ -153,7 +152,7 @@ tunneling, and so on.")
                             version ".tar.xz"))
         (sha256
          (base32
-          "1hbm29r3pirhn4gkcnd94ylc4jzgn3v3v7qbay9awxg7bwx69dfs"))))))
+          "148qv1f32290r9pwg07mccawihz4srznkzsdwdl2xllvlgb16n9x"))))))
 
 (define-public kurly
   (package

gnu/packages/databases.scm

@@ -153,7 +153,7 @@
        (modify-phases %standard-phases
          (add-after 'unpack 'generate-configure
            (lambda _
-             (invoke "sh" "autogen.sh"))))))
+             (zero? (system* "sh" "autogen.sh")))))))
     ;; http://www.4store.org has been down for a while now.
     (home-page "https://github.com/4store/4store")
     (synopsis "Clustered RDF storage and query engine")
@@ -164,14 +164,14 @@ either single machines or networked clusters.")
 (define-public gdbm
   (package
     (name "gdbm")
-    (version "1.18")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/gdbm/gdbm-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1kimnv12bzjjhaqk4c8w2j6chdj9c6bg21lchaf7abcyfss2r0mq"))))
+                "0pxwz3jlwvglq2mrbxvrjgr8pa0aj73p3v9sxmdlj570zw0gzknd"))))
     (arguments `(#:configure-flags '("--enable-libgdbm-compat")))
     (build-system gnu-build-system)
     (home-page "http://www.gnu.org.ua/software/gdbm")
@@ -207,16 +207,14 @@ and provides interfaces to the traditional file format.")
          (delete 'reset-gzip-timestamps)
          (add-before 'check 'start-mongodb
            (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (with-directory-excursion "src/gopkg.in/mgo.v2"
-                 (invoke "make" "startdb")))
-             #t))
+             (or (not tests?)
+                 (with-directory-excursion "src/gopkg.in/mgo.v2"
+                   (invoke "make" "startdb")))))
          (add-after 'check 'stop'mongodb
            (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (with-directory-excursion "src/gopkg.in/mgo.v2"
-                 (invoke "make" "stopdb")))
-             #t)))))
+             (or (not tests?)
+                 (with-directory-excursion "src/gopkg.in/mgo.v2"
+                   (invoke "make" "stopdb"))))))))
     (native-inputs
      `(("go-gopkg.in-check.v1" ,go-gopkg.in-check.v1)
        ("mongodb" ,mongodb)
@@ -505,35 +503,37 @@ applications.")
                #t))
            (replace 'build
              (lambda _
-               (apply invoke `("scons"
+               (zero? (apply system*
+                             `("scons"
                                ,@common-options
-                               "mongod" "mongo" "mongos"))))
+                               "mongod" "mongo" "mongos")))))
            (replace 'check
              (lambda* (#:key tests? inputs #:allow-other-keys)
                (setenv "TZDIR"
                        (string-append (assoc-ref inputs "tzdata")
                                       "/share/zoneinfo"))
-               (when tests?
-                 ;; Note that with the tests, especially the unittests, the
-                 ;; build can take up to ~45GB of space, as many tests are
-                 ;; individual executable files, with some being hundreds of
-                 ;; megabytes in size.
-                 (apply invoke `("scons" ,@common-options "dbtest" "unittests"))
-                 (substitute* "build/unittests.txt"
-                   ;; TODO: Don't run the async_stream_test, as it hangs
-                   (("^build\\/opt\\/mongo\\/executor\\/async\\_stream\\_test\n$")
-                    "")
-                   ;; TODO: This test fails
-                   ;; Expected 0UL != disks.size() (0 != 0) @src/mongo/util/procparser_test.cpp:476
-                   (("^build\\/opt\\/mongo\\/util\\/procparser\\_test\n$")
-                    ""))
-                 (invoke "python" "buildscripts/resmoke.py"
-                         "--suites=dbtest,unittests"
-                         (format #f  "--jobs=~a" (parallel-job-count))))
-               #t))
+               (or (not tests?)
+                   ;; Note that with the tests, especially the unittests, the
+                   ;; build can take up to ~45GB of space, as many tests are
+                   ;; individual executable files, with some being hundreds of
+                   ;; megabytes in size.
+                   (begin
+                     (apply
+                       invoke `("scons" ,@common-options "dbtest" "unittests"))
+                     (substitute* "build/unittests.txt"
+                       ;; TODO: Don't run the async_stream_test, as it hangs
+                       (("^build\\/opt\\/mongo\\/executor\\/async\\_stream\\_test\n$")
+                        "")
+                       ;; TODO: This test fails
+                       ;; Expected 0UL != disks.size() (0 != 0) @src/mongo/util/procparser_test.cpp:476
+                       (("^build\\/opt\\/mongo\\/util\\/procparser\\_test\n$")
+                        ""))
+                     (invoke "python" "buildscripts/resmoke.py"
+                             "--suites=dbtest,unittests"
+                             (format #f  "--jobs=~a" (parallel-job-count)))))))
            (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+             (lambda _
+               (let ((bin  (string-append (assoc-ref %outputs "out") "/bin")))
                  (install-file "mongod" bin)
                  (install-file "mongos" bin)
                  (install-file "mongo" bin))
@@ -621,7 +621,7 @@ Language.")
 (define-public mariadb
   (package
     (name "mariadb")
-    (version "10.1.37")
+    (version "10.1.35")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://downloads.mariadb.org/f/"
@@ -629,20 +629,14 @@ Language.")
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0ijdmdn9mcciwv361zfmja6b1h6qpbdqgrnnq6kkdapplyq1dmcc"))
-              (patches (search-patches "mariadb-client-test-32bit.patch"))
+                "0k9walaglwmwdwmkq48ir17g98n83vliyyg5wck22rjgxn2xk4cy"))
+              (patches (search-patches "mariadb-gcc-ice.patch"
+                                       "mariadb-client-test-32bit.patch"))
               (modules '((guix build utils)))
               (snippet
                '(begin
                   ;; Delete bundled snappy and xz.
                   (delete-file-recursively "storage/tokudb/PerconaFT/third_party")
-                  (substitute* "storage/tokudb/PerconaFT/CMakeLists.txt"
-                    ;; This file checks that the bundled sources are present and
-                    ;; declares build procedures for them.
-                    (("^include\\(TokuThirdParty\\)") ""))
-                  (substitute* "storage/tokudb/PerconaFT/ft/CMakeLists.txt"
-                    ;; Don't attempt to use the procedures we just removed.
-                    ((" build_lzma build_snappy") ""))
 
                   ;; Preserve CMakeLists.txt for these.
                   (for-each (lambda (file)
@@ -686,7 +680,7 @@ Language.")
          "-DINSTALL_SHAREDIR=share")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'fix-pcre-detection
+         (add-after 'unpack 'unbundle
            (lambda _
              ;; The bundled PCRE in MariaDB has a patch that was upstreamed
              ;; in version 8.34.  Unfortunately the upstream patch behaves
@@ -695,6 +689,16 @@ Language.")
              ;; XXX: Consider patching PCRE instead.
              (substitute* "cmake/pcre.cmake"
                ((" OR NOT PCRE_STACK_SIZE_OK") ""))
+
+             (substitute* "storage/tokudb/PerconaFT/ft/CMakeLists.txt"
+               ;; Remove dependency on these CMake targets.
+               ((" build_lzma build_snappy") ""))
+
+             (substitute* "storage/tokudb/PerconaFT/CMakeLists.txt"
+               ;; This file checks that the bundled sources are present and
+               ;; declares build procedures for them.  We don't need that.
+               (("^include\\(TokuThirdParty\\)") ""))
+
              #t))
          (add-after 'unpack 'adjust-tests
            (lambda _
@@ -704,7 +708,6 @@ Language.")
                       ;; See <https://jira.mariadb.org/browse/MDEV-7761>.
                       "main.join_cache"
                       "main.explain_non_select"
-                      "main.stat_tables_innodb"
                       "roles.acl_statistics"
 
                       ;; FIXME: This test fails on i686:
@@ -770,8 +773,8 @@ Language.")
                 (for-each delete-file-recursively
                           '("data" "mysql-test" "sql-bench"
                             "share/man/man1/mysql-test-run.pl.1"))
-                ;; Delete huge and unnecessary executables.
-                (for-each delete-file (find-files "bin" "(test|embedded)"))
+                ;; Delete huge mysqltest executables.
+                (for-each delete-file (find-files "bin" "test"))
                 ;; And static libraries.
                 (for-each delete-file (find-files "lib" "\\.a$")))
               #t))))))
@@ -783,13 +786,11 @@ Language.")
        ("libaio" ,libaio)
        ("libxml2" ,libxml2)
        ("ncurses" ,ncurses)
+       ("openssl" ,openssl)
        ("pcre" ,pcre)
        ("snappy" ,snappy)
        ("xz" ,xz)
        ("zlib" ,zlib)))
-    (propagated-inputs
-     ;; mariadb.pc says -lssl -lcrypto, so propagate it.
-     `(("openssl" ,openssl)))
     ;; The test suite is very resource intensive and can take more than three
     ;; hours on a x86_64 system.  Give slow and busy machines some leeway.
     (properties '((timeout . 64800)))        ;18 hours
@@ -804,14 +805,14 @@ as a drop-in replacement of MySQL.")
 (define-public postgresql
   (package
     (name "postgresql")
-    (version "10.6")
+    (version "10.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "0jv26y3f10svrjxzsgqxg956c86b664azyk2wppzpa5x11pjga38"))))
+                "04a07jkvc5s6zgh6jr78149kcjmsxclizsqabjw44ld4j5n633kc"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-uuid=e2fs")
@@ -849,14 +850,14 @@ pictures, sounds, or video.")
   (package
     (inherit postgresql)
     (name "postgresql")
-    (version "9.6.11")
+    (version "9.6.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "0c55akrkzqd6p6a8hr0338wk246hl76r9j16p4zn3s51d7f0l99q"))))))
+                "0biy8j69dbvdmrag55pdszpc0702agzqhhcwdx21xp02mzim4ydr"))))))
 
 (define-public python-pymysql
   (package
@@ -923,23 +924,7 @@ organized in a hash table or B+ tree.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0cdwa4094x3yx7vn98xykvnlp9rngvd58d19vs3vh5hrvggccg93"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; Adjust the bundled gnulib to work with glibc 2.28.  See e.g.
-                  ;; "m4-gnulib-libio.patch".  This is a phase rather than patch
-                  ;; or snippet to work around <https://bugs.gnu.org/32347>.
-                  (substitute* (find-files "lib" "\\.c$")
-                    (("#if defined _IO_ftrylockfile")
-                     "#if defined _IO_EOF_SEEN"))
-                  (substitute* "lib/stdio-impl.h"
-                    (("^/\\* BSD stdio derived implementations")
-                     (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n"
-                                    "# define _IO_IN_BACKUP 0x100\n"
-                                    "#endif\n\n"
-                                    "/* BSD stdio derived implementations")))
-                  #t))))
+                "0cdwa4094x3yx7vn98xykvnlp9rngvd58d19vs3vh5hrvggccg93"))))
     (build-system gnu-build-system)
 
     ;; Running tests in parallel leads to test failures and crashes in
@@ -989,16 +974,15 @@ types are supported, as is encryption.")
 (define-public rocksdb
   (package
     (name "rocksdb")
-    (version "5.15.10")
+    (version "5.12.4")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/facebook/rocksdb")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
+              (method url-fetch)
+              (uri (string-append "https://github.com/facebook/rocksdb"
+                                  "/archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0q26frbj9pykarcfa0yxgwncxlvsqhjkby0jrbfs1a8srja688r4"))
+                "1jcwgsjhk4hdfr2wf549blkgb89vwcdb5i2ahhqs6zf3mm20i3bf"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1119,8 +1103,7 @@ data in a single database.  RocksDB is partially based on @code{LevelDB}.")
            (lambda _
              (substitute* "Makefile"
                (("^gitrev :=.*$")
-                (string-append "gitrev = \"v" ,version "\"")))
-             #t))
+                (string-append "gitrev = \"v" ,version "\"")))))
          ;; The install phase of the Makefile assumes $PREFIX/usr/local/bin.
          ;; This replacement does the same thing, except for using $PREFIX/bin
          ;; instead.
@@ -1129,13 +1112,14 @@ data in a single database.  RocksDB is partially based on @code{LevelDB}.")
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin")))
                (install-file "sparql-query" bin)
-               (symlink (string-append bin "/sparql-query")
-                        (string-append bin "/sparql-update")))
-             #t))
+               (system* "ln" "--symbolic"
+                        (string-append bin "/sparql-query")
+                        (string-append bin "/sparql-update")))))
          (replace 'check
            (lambda* (#:key make-flags #:allow-other-keys)
-             (apply invoke "make" `(,@make-flags "scan-test"))
-             (invoke "./scan-test"))))))
+             (and
+              (zero? (apply system* "make" `(,@make-flags "scan-test")))
+              (zero? (system "./scan-test"))))))))
     (home-page "https://github.com/tialaramex/sparql-query/")
     (synopsis "Command-line tool for accessing SPARQL endpoints over HTTP")
     (description "Sparql-query is a command-line tool for accessing SPARQL
@@ -1183,7 +1167,7 @@ changes.")
 (define-public sqlite
   (package
    (name "sqlite")
-   (version "3.24.0")
+   (version "3.23.0")
    (source (origin
             (method url-fetch)
             (uri (let ((numeric-version
@@ -1199,7 +1183,7 @@ changes.")
                                   numeric-version ".tar.gz")))
             (sha256
              (base32
-              "0jmprv2vpggzhy7ma4ynmv1jzn3pfiwzkld0kkg6hvgvqs44xlfr"))))
+              "0jbf78g3cm5wq77k7sfg8fb6rz44hnp9hs7p5d66fwd000c1lwdp"))))
    (build-system gnu-build-system)
    (inputs `(("readline" ,readline)))
    (arguments
@@ -1228,18 +1212,6 @@ is in the public domain.")
        ((#:configure-flags flags)
         `(cons "--enable-fts5" ,flags))))))
 
-;; This is used by Qt.
-(define-public sqlite-with-column-metadata
-  (package (inherit sqlite)
-    (name "sqlite-with-column-metadata")
-    (arguments
-     (substitute-keyword-arguments (package-arguments sqlite)
-       ((#:configure-flags flags)
-        `(list (string-append "CFLAGS=-O2 -DSQLITE_SECURE_DELETE "
-                              "-DSQLITE_ENABLE_UNLOCK_NOTIFY "
-                              "-DSQLITE_ENABLE_DBSTAT_VTAB "
-                              "-DSQLITE_ENABLE_COLUMN_METADATA")))))))
-
 (define-public tdb
   (package
     (name "tdb")
@@ -1260,8 +1232,8 @@ is in the public domain.")
              (let ((out (assoc-ref outputs "out")))
                ;; The 'configure' script is a wrapper for Waf and
                ;; doesn't recognize things like '--enable-fast-install'.
-               (invoke "./configure"
-                       (string-append "--prefix=" out))))))))
+               (zero? (system* "./configure"
+                               (string-append "--prefix=" out)))))))))
     (native-inputs
      `(;; TODO: Build the documentation.
        ;; ("docbook-xsl" ,docbook-xsl)
@@ -1626,7 +1598,7 @@ valid SQL query.")
 (define-public unixodbc
   (package
    (name "unixodbc")
-   (version "2.3.7")
+   (version "2.3.6")
    (source (origin
             (method url-fetch)
             (uri
@@ -1634,7 +1606,7 @@ valid SQL query.")
               "ftp://ftp.unixodbc.org/pub/unixODBC/unixODBC-"
               version ".tar.gz"))
             (sha256
-             (base32 "0xry3sg497wly8f7715a7gwkn2k36bcap0mvzjw74jj53yx6kwa5"))))
+             (base32 "0sads5b8cmmj526gyjba7ccknl1vbhkslfqshv1yqln08zv3gdl8"))))
    (build-system gnu-build-system)
    (synopsis "Data source abstraction library")
    (description "Unixodbc is a library providing an API with which to access
@@ -1796,32 +1768,19 @@ trees (LSM), for sustained throughput under random insert workloads.")
     ;; configure.ac: WiredTiger requires a 64-bit build.
     (supported-systems '("x86_64-linux" "mips64el-linux" "aarch64-linux"))))
 
-(define-public wiredtiger-3
-  (package
-    (inherit wiredtiger)
-    (name "wiredtiger")
-    (version "3.1.0")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "http://source.wiredtiger.com/releases/wiredtiger-"
-                                  version ".tar.bz2"))
-              (sha256
-               (base32
-                "014awypv579ascg4jbx4pndj2wld337m79yyzrzyr7hxrff139jx"))))))
-
 (define-public guile-wiredtiger
   (package
     (name "guile-wiredtiger")
-    (version "0.7.0")
+    (version "0.6.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://framagit.org/a-guile-mind/guile-wiredtiger.git")
-                    (commit "340ad4bc2ff4dcc6216a2f5c6f9172ca320ac66b")))
+                    (commit "070ed68139d99c279f058a6c293f00292d35dbd7")))
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "15j36bvxxzil7qpwlmh1rffqpva3ynvrcpqhhqbj2c9208ayz595"))))
+                "14rna97wsylajzxfif95wnblq85csgcfc666gh5dl0ssgd7x8llh"))))
     (build-system gnu-build-system)
     (arguments
      '(#:parallel-tests? #f  ;; tests can't be run in parallel, yet.
@@ -1829,19 +1788,21 @@ trees (LSM), for sustained throughput under random insert workloads.")
        (list (string-append "--with-libwiredtiger-prefix="
                             (assoc-ref %build-inputs "wiredtiger")))
        #:make-flags '("GUILE_AUTO_COMPILE=0")))
+    ;; TODO: Remove microkanren.scm when we have a separate package
+    ;; for it.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
        ("pkg-config" ,pkg-config)))
     (inputs
-     `(("wiredtiger" ,wiredtiger-3)
+     `(("wiredtiger" ,wiredtiger)
        ("guile" ,guile-2.2)))
     (propagated-inputs
-     `(("guile-bytestructures" ,guile-bytestructures)))
+     `(("guile-lib" ,guile-lib)))                 ;for (htmlprag)
     (synopsis "WiredTiger bindings for GNU Guile")
     (description
      "This package provides Guile bindings to the WiredTiger ``NoSQL''
-database.")
+database.  Various higher level database abstractions.")
     (home-page "https://framagit.org/a-guile-mind/guile-wiredtiger")
     (license license:gpl3+)))
 
@@ -1980,14 +1941,14 @@ can autogenerate peewee models using @code{pwiz}, a model generator.")
 (define-public sqlcipher
   (package
     (name "sqlcipher")
-    (version "3.4.2")
+    (version "3.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/sqlcipher/" name
                            "/archive/v" version ".tar.gz"))
        (sha256
-        (base32 "1nxarwbci8jx99f1d0y1ivxcv25s78l1p7q6qy28lkpkcx8pm2b9"))
+        (base32 "1gv58dlbpzrmznly52yqbxgvii0ib88zr3aszla1bsypwjr6flff"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system gnu-build-system)
     (inputs
@@ -2010,7 +1971,8 @@ can autogenerate peewee models using @code{pwiz}, a model generator.")
            (assoc-ref %standard-phases 'check))
          (replace 'check
            (lambda _
-             (invoke "./testfixture" "test/crypto.test"))))))
+             (zero?
+              (system* "./testfixture" "test/crypto.test")))))))
     (home-page "https://www.zetetic.net/sqlcipher/")
     (synopsis
      "Library providing transparent encryption of SQLite database files")
@@ -2087,14 +2049,13 @@ for ODBC.")
     (version "0.7.1")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/brianb/mdbtools.git")
-             (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (string-append "https://github.com/brianb/mdbtools/archive/"
+                           version ".tar.gz"))
        (sha256
         (base32
-         "0gwcpp9y09xhs21g7my2fs8ncb8i6ahlyixcx8jd3q97jbzj441l"))))
+         "05hbmxcq173kzb899gdi3bz2qcc1vi3n1qbbkwpsvrq7ggf11wyw"))
+       (file-name (string-append name "-" version ".tar.gz"))))
     (build-system gnu-build-system)
     (inputs
      `(("glib" ,glib)))
@@ -2105,6 +2066,12 @@ for ODBC.")
        ("pkg-config" ,pkg-config)
        ("txt2man" ,txt2man)
        ("which" ,which)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'autoreconf
+           (lambda _
+             (zero? (system* "autoreconf" "-vfi")))))))
     (home-page "http://mdbtools.sourceforge.net/")
     (synopsis "Read Microsoft Access databases")
     (description "MDB Tools is a set of tools and applications to read the
@@ -2266,6 +2233,9 @@ and web services platform functionality.")
      `(("pkg-config" ,pkg-config)))
     (inputs
      `(("mariadb" ,mariadb)
+       ;; FIXME: This should be propagated from MariaDB, but add it here
+       ;; for now to prevent a large rebuild.
+       ("openssl" ,openssl)
        ("zlib" ,zlib)))
     (propagated-inputs
      `(("r-dbi" ,r-dbi)))
@@ -2334,7 +2304,7 @@ Database API 2.0T.")
 (define-public python-sqlalchemy
   (package
     (name "python-sqlalchemy")
-    (version "1.2.11")
+    (version "1.0.12")
     (source
      (origin
       (method url-fetch)
@@ -2342,7 +2312,7 @@ Database API 2.0T.")
                           "SQLAlchemy/SQLAlchemy-" version ".tar.gz"))
       (sha256
        (base32
-        "094mmbs4igrxplfyqd59j90jb83ixpbbzqc0w49yw81m82nnjrgg"))))
+        "1l8qclhd0s90w3pvwhi5mjxdwr5j7gw7cjka2fx6f2vqmq7f4yb6"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-cython" ,python-cython) ;for c extensions
@@ -2352,7 +2322,7 @@ Database API 2.0T.")
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _ (invoke "py.test"))))))
+           (lambda _ (zero? (system* "py.test")))))))
     (home-page "http://www.sqlalchemy.org")
     (synopsis "Database abstraction library")
     (description
@@ -2419,14 +2389,14 @@ You might also want to install the following optional dependencies:
 (define-public python-alembic
   (package
     (name "python-alembic")
-    (version "1.0.2")
+    (version "0.9.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "alembic" version))
        (sha256
         (base32
-         "0asqz9mwc4w8bsar1icv3ik9jslxrj3gv3yxgmhc6nc6r9qbkg04"))))
+         "0cm73vabrqj92v7a0wwvldj8j7bc7dwv358kvkk7p87gx7mm2a04"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-mock" ,python-mock)
@@ -2744,13 +2714,13 @@ reasonable substitute.")
 (define-public python-rq
   (package
     (name "python-rq")
-    (version "0.12.0")
+    (version "0.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "rq" version))
        (sha256
-        (base32 "16d8kni57xlnah2hawy4xgw21xrv3f64j5q5shyp3zxx4yd9iibs"))))
+        (base32 "0gaq5pnh0zy46r8jvygi0ifbvz3pq6i7xla78ijcgjw0x77qzsdh"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-click" ,python-click)
@@ -2805,7 +2775,7 @@ is designed to have a low barrier to entry.")
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _ (invoke "py.test"))))))
+           (lambda _ (zero? (system* "py.test")))))))
     (native-inputs
      `(("python-pytest" ,python-pytest)))
     (home-page "https://github.com/andialbrecht/sqlparse")
@@ -2872,46 +2842,41 @@ transforms idiomatic python function calls to well-formed SQL queries.")
            (delete 'install-source)
            (replace 'build
              (lambda _
-               (for-each (lambda (tool)
-                           (let ((command
-                                  `("go" "build"
-                                    ;; This is where the tests expect to find the
-                                    ;; executables
-                                    "-o" ,(string-append
-                                           "src/github.com/mongodb/mongo-tools/bin/"
-                                           tool)
-                                    "-v"
-                                    "-tags=\"ssl sasl\""
-                                    "-ldflags"
-                                    "-extldflags=-Wl,-z,now,-z,relro"
-                                    ,(string-append
-                                      "src/github.com/mongodb/mongo-tools/"
-                                      tool "/main/" tool ".go"))))
-                             (simple-format #t "build: running ~A\n"
-                                            (string-join command))
-                             (apply invoke command)))
-                         all-tools)
-               #t))
+               (every (lambda (tool)
+                        (let ((command
+                               `("go" "build"
+                                 ;; This is where the tests expect to find the
+                                 ;; executables
+                                 "-o" ,(string-append
+                                        "src/github.com/mongodb/mongo-tools/bin/"
+                                        tool)
+                                 "-v"
+                                 "-tags=\"ssl sasl\""
+                                 "-ldflags"
+                                 "-extldflags=-Wl,-z,now,-z,relro"
+                                 ,(string-append
+                                   "src/github.com/mongodb/mongo-tools/"
+                                   tool "/main/" tool ".go"))))
+                          (simple-format #t "build: running ~A\n"
+                                         (string-join command))
+                          (apply invoke command)))
+                      all-tools)))
            (replace 'check
              (lambda _
                (with-directory-excursion "src"
-                 (for-each (lambda (tool)
-                             (invoke
-                              "go" "test" "-v"
-                              (string-append "github.com/mongodb/mongo-tools/"
-                                             tool)))
-                           all-tools))
-               #t))
+                 (every (lambda (tool)
+                          (invoke
+                           "go" "test" "-v"
+                           (string-append "github.com/mongodb/mongo-tools/" tool)))
+                        all-tools))))
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
                (for-each (lambda (tool)
                            (install-file
-                            (string-append "src/github.com/mongodb/mongo-tools/bin/"
-                                           tool)
+                            (string-append "src/github.com/mongodb/mongo-tools/bin/" tool)
                             (string-append (assoc-ref outputs "out")
                                            "/bin")))
-                         all-tools)
-               #t))))))
+                         all-tools)))))))
     (native-inputs
      `(("go-github.com-howeyc-gopass" ,go-github.com-howeyc-gopass)
        ("go-github.com-jessevdk-go-flags" ,go-github.com-jessevdk-go-flags)

gnu/packages/datastructures.scm

@@ -1,7 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -49,29 +48,6 @@ binary trees, binary search trees, red-black trees, 2D arrays, permutations
 and heaps.")
     (license license:gpl2+)))
 
-(define-public marisa
-  (package
-    (name "marisa")
-    (version "0.2.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/s-yata/marisa-trie"
-                           "/releases/download/v" version "/" name "-"
-                           version ".tar.gz"))
-       (sha256
-        (base32 "19ifrcmnbr9whaaf4ly3s9ndyiq9sjqhnfkrxbz9zsb44w2n36hf"))))
-    (build-system gnu-build-system)
-    (home-page "https://github.com/s-yata/marisa-trie")
-    (synopsis "Trie data structure C++ library")
-    (description "Matching Algorithm with Recursively Implemented
-StorAge (MARISA) is a static and space-efficient trie data structure C++
-library.")
-
-    ;; Dual-licensed, according to docs/readme.en.html (source files lack
-    ;; copyright/license headers.)
-    (license (list license:bsd-2 license:lgpl2.1+))))
-
 (define-public sparsehash
   (package
     (name "sparsehash")

gnu/packages/dav.scm

@@ -30,13 +30,13 @@
 (define-public radicale
   (package
     (name "radicale")
-    (version "1.1.6")
+    (version "1.1.2")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "Radicale" version))
              (sha256
               (base32
-               "0ay90nj6fmr2aq8imi0mbjl4m2rzq7a83ikj8qs9gxsylj71j1y0"))))
+               "1g20p3998f46ywda7swv0py63wjbrhvk0nrafajlbb6wgzxjmqpb"))))
     (build-system python-build-system)
     (arguments
      '(#:tests? #f)) ; The tests are not distributed in the PyPi release.

gnu/packages/debian.scm

@@ -27,22 +27,21 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gnupg)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages wget))
 
 (define-public debian-archive-keyring
   (package
     (name "debian-archive-keyring")
-    (version "2018.1")
+    (version "2017.7")
     (source
       (origin
-        (method git-fetch)
-        (uri (git-reference
-              (url "https://salsa.debian.org/release-team/debian-archive-keyring.git")
-              (commit version)))
-        (file-name (git-file-name name version))
+        (method url-fetch)
+        (uri (string-append "mirror://debian/pool/main/d/" name "/"
+                            name "_" version ".tar.xz"))
         (sha256
          (base32
-          "136vr5dj7w0dz563qdghsndcfcqm2m8d4j1dyiq9dzx5vd0rcpcw"))))
+          "1pdwgipfi0y4svhxlw8arhq792f1g3vlmw4raphizy7sa65vd4ca"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "verify-results"
@@ -117,7 +116,7 @@ contains the archive keys used for that.")
 (define-public debootstrap
   (package
     (name "debootstrap")
-    (version "1.0.111")
+    (version "1.0.106")
     (source
       (origin
         (method git-fetch)
@@ -127,7 +126,7 @@ contains the archive keys used for that.")
         (file-name (git-file-name name version))
         (sha256
          (base32
-          "1b8s00a2kvaajqhjlms3q2dk3gqv6g4yq9h843jal1pm66zsx19n"))))
+          "1fm5bgllcwgwizrqi4sn8p4fpbzhbzgwprrfppfq9hqdzbmlfmnv"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -136,57 +135,46 @@ contains the archive keys used for that.")
          (add-after 'unpack 'patch-source
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out    (assoc-ref outputs "out"))
-                   (tzdata (assoc-ref inputs "tzdata"))
+                   (coreutils (assoc-ref inputs "coreutils"))
+                   (wget   (assoc-ref inputs "wget"))
                    (debian (assoc-ref inputs "debian-keyring"))
                    (ubuntu (assoc-ref inputs "ubuntu-keyring")))
                (substitute* "Makefile"
                  (("/usr") "")
                  (("-o root -g root") "")
                  (("chown root.*") "\n"))
-               (substitute* '("scripts/etch"
-                              "scripts/potato"
-                              "scripts/sarge"
-                              "scripts/sid"
-                              "scripts/woody"
-                              "scripts/woody.buildd")
+               (substitute* "scripts/sid"
                  (("/usr") debian))
                (substitute* "scripts/gutsy"
                  (("/usr") ubuntu))
                (substitute* "debootstrap"
+                 (("chroot ") (string-append coreutils "/bin/chroot "))
                  (("=/usr") (string-append "=" out)))
-               (substitute* (find-files "scripts" ".")
-                 (("/usr/share/zoneinfo") (string-append tzdata "/share/zoneinfo")))
+               (substitute* "functions"
+                 (("wget ") (string-append wget "/bin/wget ")))
                #t)))
          (add-after 'install 'install-man-file
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))
                (install-file "debootstrap.8"
                              (string-append out "/share/man/man8"))
-               #t)))
-         (add-after 'install 'wrap-executable
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((debootstrap (string-append (assoc-ref outputs "out")
-                                               "/sbin/debootstrap"))
-                   (path        (getenv "PATH")))
-               (wrap-program debootstrap
-                             `("PATH" ":" prefix (,path)))
                #t))))
        #:make-flags (list (string-append "DESTDIR=" (assoc-ref %outputs "out")))
        #:tests? #f)) ; no tests
     (inputs
-     `(("debian-keyring" ,debian-archive-keyring)
+     `(("coreutils" ,coreutils)
+       ("debian-keyring" ,debian-archive-keyring)
        ("ubuntu-keyring" ,ubuntu-keyring)
-       ("tzdata" ,tzdata)))
-    (native-inputs
-     `(("perl" ,perl)))
+       ("wget" ,wget)))
+    ;; The following are required for debootstrap to work correctly
+    (propagated-inputs
+     `(("binutils" ,binutils)
+       ("gnupg" ,gnupg)
+       ("perl" ,perl)))
     (home-page "https://tracker.debian.org/pkg/debootstrap")
     (synopsis "Bootstrap a basic Debian system")
     (description "Debootstrap is used to create a Debian base system from
 scratch, without requiring the availability of @code{dpkg} or @code{apt}.
 It does this by downloading .deb files from a mirror site, and carefully
-unpacking them into a directory which can eventually be chrooted into.
-
-It is recommended to run @code{debootstrap --foreign --arch=...} and then
-@code{chroot} into the directory, set the PATH and run @code{debootstrap
---second-stage} after.")
+unpacking them into a directory which can eventually be chrooted into.")
     (license license:gpl2)))

gnu/packages/dictionaries.scm

@@ -222,7 +222,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
         (base32
          "11byjs3ggdhia5f4vyfqfvbbczsfqimll98h98g7hlsrm7vrifb0"))))
     (build-system python-build-system)
-    (home-page "https://grammalecte.net")
+    (home-page "https://www.dicollecte.org")
     (synopsis  "French spelling and grammar checker")
     (description "Grammalecte is a grammar checker dedicated to the French
 language, derived from Lightproof.

gnu/packages/disk.scm

@@ -76,7 +76,6 @@
               (method url-fetch)
               (uri (string-append "mirror://gnu/parted/parted-"
                                   version ".tar.xz"))
-              (patches (search-patches "parted-glibc-compat.patch"))
               (sha256
                (base32
                 "1r3qpg3bhz37mgvp9chsaa3k0csby3vayfvz8ggsqz194af5i2w5"))))

gnu/packages/django.scm

@@ -265,41 +265,6 @@ account authentication.")
 (define-public python2-django-allauth
   (package-with-python2 python-django-allauth))
 
-(define-public python-django-debug-toolbar
-  (package
-    (name "python-django-debug-toolbar")
-    (version "1.10.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/jazzband/django-debug-toolbar/archive/"
-             version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1rww056hyzks8spbgf4h7kf6ybxlc5p08a2b6gn1nqrrzs4yx9sy"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-sqlparse" ,python-sqlparse)
-       ("python-django" ,python-django)))
-    (native-inputs
-     `(("python-django-jinja" ,python-django-jinja)
-       ("python-html5lib" ,python-html5lib)))
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (invoke "make" "test"))))))
-    (home-page
-     "https://github.com/jazzband/django-debug-toolbar")
-    (synopsis "Toolbar to help with developing Django applications")
-    (description
-     "A configurable set of panels that display information about the current
-request and response as a toolbar on the rendered page.")
-    (license license:bsd-3)))
-
 (define-public python-django-gravatar2
   (package
     (name "python-django-gravatar2")
@@ -373,47 +338,6 @@ merging, minifying and compiling CSS and Javascript files.")
 (define-public python2-django-assets
   (package-with-python2 python-django-assets))
 
-(define-public python-django-jinja
-  (package
-    (name "python-django-jinja")
-    (version "2.4.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/niwinz/django-jinja/archive/"
-             version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "0bzrb4m6wx9ph5cpvz7wpvg5k6ksvj0dnxlg0nhhqskhvp46brs1"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-django" ,python-django)
-       ("python-jinja2" ,python-jinja2)
-       ("python-pytz" ,python-pytz)
-       ("python-django-pipeline" ,python-django-pipeline)))
-    (arguments
-     '(;; TODO Tests currently fail due to issues with the configuration for
-       ;; django-pipeline
-       #:tests? #f
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (or
-              (not tests?)
-              (with-directory-excursion "testing"
-                (invoke "python" "runtests.py"))))))))
-    (home-page
-     "https://niwinz.github.io/django-jinja/latest/")
-    (synopsis "Simple jinja2 templating backend for Django")
-    (description
-     "This package provides a templating backend for Django, using Jinja2.  It
-provides certain advantages over the builtin Jinja2 backend in Django, for
-example, explicit calls to callables from templates and better performance.")
-    (license license:bsd-3)))
-
 (define-public python-django-jsonfield
   (package
     (name "python-django-jsonfield")
@@ -594,46 +518,6 @@ project.")
 (define-public python2-django-overextends
   (package-with-python2 python-django-overextends))
 
-(define-public python-django-pipeline
-  (package
-    (name "python-django-pipeline")
-    (version "1.6.14")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "django-pipeline" version))
-       (sha256
-        (base32
-         "1a207y71r7za033ira0qmh2yrgp5rq0l04gw2fg9b8jri7sslrzg"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-source
-           (lambda _
-             (substitute* "tests/tests/test_compiler.py"
-               (("\\/usr\\/bin\\/env")
-                (which "env")))))
-         (replace 'check
-           (lambda*(#:key tests? #:allow-other-keys)
-             (or
-              (not tests?)
-              (begin
-                (setenv "DJANGO_SETTINGS_MODULE" "tests.settings")
-                (invoke "django-admin" "test" "tests"))))))))
-    (propagated-inputs
-     `(("python-django" ,python-django)
-       ("python-slimit" ,python-slimit)
-       ("python-jsmin" ,python-jsmin)))
-    (home-page
-     "https://github.com/jazzband/django-pipeline")
-    (synopsis "Asset packaging library for Django")
-    (description
-     "Pipeline is an asset packaging library for Django, providing both CSS
-and JavaScript concatenation and compression, built-in JavaScript template
-support, and optional data-URI image and font embedding.")
-    (license license:expat)))
-
 (define-public python-django-redis
   (package
     (name "python-django-redis")

gnu/packages/dns.scm

@@ -58,7 +58,6 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
-  #:use-module (guix git-download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial))
@@ -66,7 +65,7 @@
 (define-public dnsmasq
   (package
     (name "dnsmasq")
-    (version "2.80")
+    (version "2.79")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -74,7 +73,7 @@
                     version ".tar.xz"))
               (sha256
                (base32
-                "1fv3g8vikj3sn37x1j6qsywn09w1jipvlv34j3q5qrljbrwa5ayd"))))
+                "07w6cw706yyahwvbvslhkrbjf2ynv567cgy9pal8bz8lrbsp9bbq"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -364,7 +363,7 @@ to result in system-wide compromise.")
 (define-public unbound
   (package
     (name "unbound")
-    (version "1.8.1")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
@@ -372,7 +371,7 @@ to result in system-wide compromise.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0p9w6spar5dfi7fplxjcq4394wldabaws0ns30cqq6sxqfwv6qn3"))))
+         "0gxqc4ynd2g1a5dwaazqh9n8injh49a7dz0l9bbxqgv47dnrvxvq"))))
     (build-system gnu-build-system)
     (outputs '("out" "python"))
     (native-inputs
@@ -570,14 +569,14 @@ Extensions} (DNSSEC).")
 (define-public knot
   (package
     (name "knot")
-    (version "2.7.3")
+    (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
-                "1pwjcv7hzhqawisibybma160k77a6f1v94xw6ay9c7j49vrw05w7"))
+                "0cc4wgb02ch09x99a1fnr7vsdik8k920q7jafzcamjvy3kpb4w6b"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -728,56 +727,3 @@ The client supports both dynamic and (near) static services, as well as MX
 record and alternative name management.  It caches the address, and only
 attempts the update when it has changed.")
     (license license:gpl2+)))
-
-(define-public hnsd
-  ;; There have been no releases yet, hence this commit.
-  (let ((revision "0")
-        (commit "895d89c25d316d18df9d374fe78aae3902bc89fb"))
-   (package
-     (name "hnsd")
-     (version (git-version "0.0" revision commit))
-     (source (origin
-               (method git-fetch)
-               (uri (git-reference
-                     (url "https://github.com/handshake-org/hnsd")
-                     (commit commit)))
-               (sha256
-                (base32
-                 "0704y73sddn24jga9csw4gxyfb3pnrfnk0vdcph84n1h38490l16"))
-               (file-name (git-file-name name version))
-               (modules '((guix build utils)))
-               (snippet
-                '(begin
-                   ;; Delete the bundled copy of libuv.
-                   (delete-file-recursively "uv")
-                   (substitute* "configure.ac"
-                     (("AC_CONFIG_SUBDIRS\\(\\[uv\\]\\)") ""))
-                   (substitute* "Makefile.am"
-                     (("SUBDIRS = uv") "\n")
-                     (("\\$\\(top_builddir\\)/uv/libuv.la") "-luv")
-
-                     ;; Make sure the 'hnsd' binary is installed and
-                     ;; dynamically-linked.
-                     (("noinst_PROGRAMS") "bin_PROGRAMS")
-                     (("hnsd_LDFLAGS = -static") ""))
-
-                   ;; This script tries to chdir to "uv" and doesn't do more
-                   ;; than "autoreconf" so remove it.
-                   (delete-file "autogen.sh")
-                   #t))))
-     (build-system gnu-build-system)
-     (arguments
-      '(#:configure-flags '("--disable-static"))) ;no need for libhsk.a
-     (native-inputs
-      `(("autoconf" ,autoconf)
-        ("automake" ,automake)
-        ("libtool" ,libtool)))
-     (inputs
-      `(("unbound" ,unbound)
-        ("libuv" ,libuv)))
-     (home-page "https://www.handshake.org/")
-     (synopsis "Resolver daemon for the Handshake naming protocol")
-     (description
-      "@command{hnsd} is a @dfn{host name resolver} for the Handshake Naming
-System (HNS) peer-to-peer network.")
-     (license license:expat))))

gnu/packages/docbook.scm

@@ -138,15 +138,11 @@ by no means limited to these applications.)  This package provides XML DTDs.")
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/docbook/docbook-xsl/"
                                   version "/docbook-xsl-" version ".tar.bz2"))
+              ;; Note: If removing all patches, the XZ dependency is no longer needed.
               (patches (search-patches "docbook-xsl-nonrecursive-string-subst.patch"))
               (sha256
                (base32
-                "0s59lihif2fr7rznckxr2kfyrvkirv76r1zvidp9b5mj28p4apvj"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  (for-each delete-file (find-files "." "\\.jar$"))
-                  #t))))
+                "0s59lihif2fr7rznckxr2kfyrvkirv76r1zvidp9b5mj28p4apvj"))))
     (build-system trivial-build-system)
     (arguments
      `(#:builder (let ((name-version (string-append ,name "-" ,version)))
@@ -172,7 +168,7 @@ by no means limited to these applications.)  This package provides XML DTDs.")
                      #t))
        #:modules ((guix build utils))))
     (native-inputs `(("bzip2" ,bzip2)
-                     ("xz" ,xz)         ;needed for repacked tarballs
+                     ("xz" ,xz)
                      ("tar" ,tar)))
     (home-page "http://docbook.org")
     (synopsis "DocBook XSL style sheets for document authoring")

gnu/packages/documentation.scm

@@ -139,10 +139,23 @@ markup) can be customized and extended by the user.")
        ("libxml2" ,libxml2) ; provides xmllint for the tests
        ("python" ,python-2))) ; for creating the documentation
     (inputs
-     `(("bash" ,bash-minimal)))
+     `(("bash" ,bash-minimal)
+       ,@(if (string-prefix? "armhf-" (%current-system))
+             `(("gcc-ice-patch" ,@(search-patches "doxygen-gcc-ice.patch")))
+             '())))
     (arguments
      `(#:test-target "tests"
        #:phases (modify-phases %standard-phases
+                  ;; Work around an ICE that shows up on native compiles for
+                  ;; armhf-linux.
+                  ,@(if (string-prefix? "armhf-" (%current-system))
+                        `((add-after 'unpack 'apply-gcc-patch
+                            (lambda* (#:key inputs #:allow-other-keys)
+                              (let ((patch (assoc-ref inputs "gcc-ice-patch")))
+                                (invoke "patch" "-p1" "--force"
+                                        "--input" patch)))))
+                        '())
+
                   (add-before 'configure 'patch-sh
                               (lambda* (#:key inputs #:allow-other-keys)
                                 (substitute* "src/portable.cpp"

gnu/packages/education.scm

@@ -243,17 +243,17 @@ easy.")
 (define-public snap
   (package
     (name "snap")
-    (version "4.2.2.2")
+    (version "4.2.1.4")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/jmoenig/Snap.git")
+             (url "https://github.com/jmoenig/Snap--Build-Your-Own-Blocks.git")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0bay08yr58qj8wzpjg33gdj78rfhyskfzidknpdl3cr1jrj6i4p9"))))
+         "0yc0w0cdhvi0nwqqrann2v3y0n7shxh7irgixqvlavp4k49d7aqj"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))
@@ -265,7 +265,7 @@ easy.")
                 (share (string-append out "/share/snap")))
            (copy-recursively source share)
            ;; Replace the sole minified file in the package.
-           (with-directory-excursion (string-append share "/src")
+           (with-directory-excursion share
              (delete-file "FileSaver.min.js")
              (symlink (string-append (assoc-ref %build-inputs "js-filesaver")
                                      "/share/javascript/FileSaver.min.js")

gnu/packages/electronics.scm

@@ -123,7 +123,7 @@ as simple logic analyzer and/or oscilloscope hardware.")
 (define-public libsigrok
   (package
     (name "libsigrok")
-    (version "0.5.1")
+    (version "0.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -131,17 +131,19 @@ as simple logic analyzer and/or oscilloscope hardware.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "171b553dir5gn6w4f7n37waqk62nq2kf1jykx4ifjacdz5xdw3z4"))))
+                "197kr5ip98lxn7rv10zs35d1w0j7265s0xvckx0mq2l8kdvqd32c"))))
     (outputs '("out" "doc"))
     (arguments
-     `(#:tests? #f                      ; tests need USB access
+     `(#:tests? #f ; tests need usb access
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'change-udev-group
            (lambda _
-             (substitute* (find-files "contrib" "\\.rules$")
-               (("plugdev") "dialout"))
-             #t))
+             (let ((file "contrib/z60_libsigrok.rules"))
+               (substitute* file
+                 (("plugdev") "dialout"))
+               (rename-file file "contrib/60-libsigrok.rules")
+               #t)))
          (add-after 'build 'build-doc
            (lambda _
              (invoke "doxygen")))
@@ -153,12 +155,11 @@ as simple logic analyzer and/or oscilloscope hardware.")
              #t))
          (add-after 'install-doc 'install-udev-rules
            (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out   (assoc-ref outputs "out"))
-                    (rules (string-append out "/lib/udev/rules.d/")))
-               (for-each (lambda (file)
-                           (install-file file rules))
-                         (find-files "contrib" "\\.rules$"))
-               #t)))
+             (install-file "contrib/60-libsigrok.rules"
+                           (string-append
+                            (assoc-ref outputs "out")
+                            "/lib/udev/rules.d/"))
+             #t))
          (add-after 'install-udev-rules 'install-fw
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((fx2lafw (assoc-ref inputs "sigrok-firmware-fx2lafw"))
@@ -166,6 +167,7 @@ as simple logic analyzer and/or oscilloscope hardware.")
                     (dir-suffix "/share/sigrok-firmware/")
                     (input-dir (string-append fx2lafw dir-suffix))
                     (output-dir (string-append out dir-suffix)))
+               (mkdir-p output-dir)
                (for-each
                 (lambda (file)
                   (install-file file output-dir))
@@ -202,7 +204,7 @@ format support.")
 (define-public sigrok-cli
   (package
     (name "sigrok-cli")
-    (version "0.7.1")
+    (version "0.7.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -210,7 +212,7 @@ format support.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "15vpn1psriadcbl6v9swwgws7dva85ld03yv6g1mgm27kx11697m"))))
+                "072ylscp0ppgii1k5j07hhv7dfmni4vyhxnsvxmgqgfyq9ldjsan"))))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (inputs
@@ -226,7 +228,7 @@ format support.")
 (define-public pulseview
   (package
     (name "pulseview")
-    (version "0.4.1")
+    (version "0.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -234,20 +236,9 @@ format support.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0bvgmkgz37n2bi9niskpl05hf7rsj1lj972fbrgnlz25s4ywxrwy"))))
-    (build-system cmake-build-system)
+                "1f8f2342d5yam98mmcb8f9g2vslcwv486bmi4x45pxn68l82ky3q"))))
     (arguments
-     `(#:configure-flags '("-DENABLE_TESTS=y")
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'install 'remove-empty-doc-directory
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (with-directory-excursion (string-append out "/share")
-                 ;; Use RMDIR to never risk silently deleting files.
-                 (rmdir "doc/pulseview")
-                 (rmdir "doc"))
-               #t))))))
+     `(#:configure-flags '("-DCMAKE_CXX_FLAGS=-fext-numeric-literals")))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (inputs
@@ -258,6 +249,7 @@ format support.")
        ("libsigrokdecode" ,libsigrokdecode)
        ("qtbase" ,qtbase)
        ("qtsvg" ,qtsvg)))
+    (build-system cmake-build-system)
     (home-page "https://www.sigrok.org/wiki/PulseView")
     (synopsis "Qt based logic analyzer, oscilloscope and MSO GUI for sigrok")
     (description "PulseView is a Qt based logic analyzer, oscilloscope and MSO GUI

gnu/packages/elf.scm

@@ -95,14 +95,14 @@ Executable and Linkable Format (@dfn{ELF}).  This includes @command{ld},
   (package
     (name "libabigail")
     (home-page "https://sourceware.org/libabigail/")
-    (version "1.5")
+    (version "1.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://sourceware.org/pub/" name
                                   "/" name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0srfnkbm386sl2n85686nl28da6ksbs7jgnfks9k0n61c772aas4"))))
+                "17r8i60lxykvdd9pdidmnvkzgf9k8zman0c1czl3zbx0znhlx497"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--disable-static"

gnu/packages/embedded.scm

@@ -321,6 +321,12 @@ languages are C and C++.")
          ("pkg-config" ,pkg-config)))
       (inputs
        `(("libusb" ,libusb)))
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'autoreconf
+             (lambda _
+               (zero? (system* "autoreconf" "-vfi")))))))
       (home-page "http://repo.or.cz/w/libjaylink.git")
       (synopsis "Library to interface Segger J-Link devices")
       (description "libjaylink is a shared library written in C to access
@@ -398,9 +404,9 @@ language.")
                       "presto" "openjtag")))
        #:phases
        (modify-phases %standard-phases
-         ;; Required because of patched sources.
          (add-before 'configure 'autoreconf
-           (lambda _ (invoke "autoreconf" "-vfi") #t))
+           (lambda _
+             (zero? (system* "autoreconf" "-vfi"))))
          (add-after 'autoreconf 'change-udev-group
            (lambda _
              (substitute* "contrib/60-openocd.rules"
@@ -411,8 +417,7 @@ language.")
              (install-file "contrib/60-openocd.rules"
                            (string-append
                             (assoc-ref outputs "out")
-                            "/lib/udev/rules.d/"))
-             #t)))))
+                            "/lib/udev/rules.d/")))))))
     (home-page "http://openocd.org")
     (synopsis "On-Chip Debugger")
     (description "OpenOCD provides on-chip programming and debugging support

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 "2c57e709d0f9e4010a4415de4192de887e37f187")
-        (revision "5"))
+  (let ((commit "5f0d825f40b8aabe13eaef32d44ab667ff8e8c28")
+        (revision "3"))
     (package
       (name "dolphin-emu")
       (version (git-version "5.0" revision commit))
@@ -144,7 +144,7 @@
              #t))
          (sha256
           (base32
-           "0aszfdfvs7yg4bmrd3qxwsiz7hx3mrj29f4aw86bz7h9j7hkh57f"))))
+           "0dh7mih16aif9ynbgcsn7n10f89g8d232i86xqfp2rijsdggcmzl"))))
       (build-system cmake-build-system)
       (arguments
        '(#:tests? #f
@@ -153,8 +153,7 @@
            (add-before 'configure 'fixgcc7
              (lambda _
                (unsetenv "C_INCLUDE_PATH")
-               (unsetenv "CPLUS_INCLUDE_PATH")
-               #t))
+               (unsetenv "CPLUS_INCLUDE_PATH")))
            (add-before 'configure 'generate-fonts&hardcore-libvulkan-path
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let ((fontfile
@@ -196,7 +195,7 @@
          ("bluez" ,bluez)
          ("curl" ,curl)
          ("eudev" ,eudev)
-         ("ffmpeg" ,ffmpeg)
+         ("ffmpeg" ,ffmpeg-3.4)
          ("font-wqy-microhei" ,font-wqy-microhei)
          ("freetype" ,freetype)
          ("glew" ,glew)
@@ -1186,7 +1185,7 @@ play them on systems for which they were never designed!")
 (define-public mame
   (package
     (name "mame")
-    (version "0.203")
+    (version "0.202")
     (source
      (origin
        (method git-fetch)
@@ -1196,7 +1195,7 @@ play them on systems for which they were never designed!")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "19ccqc00024fbjyk0k5d9xljhwq7wsrp7phwm2jmn0h77mgdj844"))
+         "1v9gm124p65nbj678gfkcvwphp9qc15ky2p12ca6g3rllma94di5"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled libraries.

gnu/packages/engineering.scm

@@ -717,13 +717,6 @@ language.")
                "-DBUILD_GITHUB_PLUGIN=OFF")
          #:phases
          (modify-phases %standard-phases
-           (add-after 'unpack 'adjust-boost-include
-             (lambda _
-               ;; The location of this header changed in Boost 1.66.
-               (substitute* "3d-viewer/3d_cache/3d_cache.cpp"
-                 (("boost/uuid/sha1\\.hpp")
-                  "boost/uuid/detail/sha1.hpp"))
-               #t))
            (add-after 'install 'wrap-program
              ;; Ensure correct Python at runtime.
              (lambda* (#:key inputs outputs #:allow-other-keys)

gnu/packages/enlightenment.scm

@@ -58,8 +58,7 @@
   #:use-module (gnu packages tls)
   #:use-module (gnu packages video)
   #:use-module (gnu packages xdisorg)
-  #:use-module (gnu packages xorg)
-  #:use-module (ice-9 match))
+  #:use-module (gnu packages xorg))
 
 (define-public efl
   (package
@@ -140,16 +139,12 @@
     (arguments
      `(#:configure-flags '("--disable-silent-rules"
                            "--disable-systemd"
-                           "--with-profile=release"
                            "--enable-liblz4"
                            "--enable-xinput22"
                            "--enable-image-loader-webp"
                            "--enable-multisense"
-                           ,@(match (%current-system)
-                               ("armhf-linux"
-                                '("--with-opengl=es" "--with-egl"))
-                               (_
-                                '("--with-opengl=full")))
+                           "--with-opengl=es"
+                           "--enable-egl"
                            "--enable-harfbuzz"
                            ;; for wayland
                            "--enable-wayland"
@@ -183,7 +178,7 @@ removable devices or support for multimedia.")
 (define-public terminology
   (package
     (name "terminology")
-    (version "1.3.0")
+    (version "1.2.1")
     (source (origin
               (method url-fetch)
               (uri
@@ -191,9 +186,10 @@ removable devices or support for multimedia.")
                               "terminology/terminology-" version ".tar.xz"))
               (sha256
                (base32
-                "07vw28inkimi9avp16j0rqcfqjq16081554qsv29pcqhz18xp59r"))
+                "1ii8332bl88l8md3gvz5dhi9bjpm6shyf14ck9kfyy7d56hp71mc"))
               (modules '((guix build utils)))
               ;; Remove the bundled fonts.
+              ;; TODO: Remove bundled lz4.
               (snippet
                '(begin
                   (delete-file-recursively "data/fonts")
@@ -275,8 +271,7 @@ Libraries with some extra bells and whistles.")
              (let ((xkeyboard (assoc-ref inputs "xkeyboard-config"))
                    (setxkbmap (assoc-ref inputs "setxkbmap"))
                    (utils     (assoc-ref inputs "util-linux"))
-                   (libc      (assoc-ref inputs "libc"))
-                   (efl       (assoc-ref inputs "efl")))
+                   (libc      (assoc-ref inputs "libc")))
                ;; We need to patch the path to 'base.lst' to be able
                ;; to switch the keyboard layout in E.
                (substitute* (list "src/modules/xkbswitch/e_mod_parse.c"
@@ -291,9 +286,6 @@ Libraries with some extra bells and whistles.")
                                   "src/modules/conf_intl/e_int_config_intl.c"
                                   "src/modules/wizard/page_010.c")
                  (("locale -a") (string-append libc "/bin/locale -a")))
-               (substitute* "src/bin/e_import_config_dialog.c"
-                 (("%s/edje_cc -v %s %s %s\", e_prefix_bin_get\\(\\)")
-                  (string-append efl "/bin/edje_cc -v %s %s %s\"")))
                (substitute* "src/modules/everything/evry_plug_apps.c"
                  (("/usr/bin/") ""))
                (substitute* "configure"

gnu/packages/file-systems.scm

@@ -2,7 +2,6 @@
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24,7 +23,6 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
-  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix utils)
   #:use-module (gnu packages)
@@ -109,7 +107,7 @@ single file can be mounted.")
 (define-public disorderfs
   (package
     (name "disorderfs")
-    (version "0.5.5")
+    (version "0.5.4")
     (source
      (origin
        (method git-fetch)
@@ -119,7 +117,7 @@ single file can be mounted.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "18c32qcdzbxrzg7srnqnw1ls9yqqxyk9b996yxr6w2znw6x6n8v4"))))
+         "1mw4ix9h17ikki8p2rxdvzp87rcm1c7by5lvfn5gxlxr7hlj9f8g"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -128,7 +126,7 @@ single file can be mounted.")
        ("attr" ,attr)))
     (arguments
      `(#:phases (modify-phases %standard-phases
-                  (delete 'configure))  ; no configure script
+                  (delete 'configure))
        #:make-flags (let ((out (assoc-ref %outputs "out")))
                       (list (string-append "PREFIX=" out)))
        #:test-target "test"
@@ -247,50 +245,3 @@ All of this is accomplished without a centralized metadata server.")
     (description
      "This is a file system client based on the FTP File Transfer Protocol.")
     (license license:gpl2+)))
-
-(define-public apfs-fuse
-  (let ((commit "c7036a3030d128bcecefc1eabc47c039ccfdcec9")
-        (revision "0"))
-    (package
-      (name "apfs-fuse")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/sgan81/apfs-fuse")
-                       (recursive? #t) ; for lzfse
-                       (commit commit)))
-         (sha256
-          (base32
-           "1akd4cx1f9cyq6sfk9ybv4chhjwjlnqi8ic4z5ajnd5x0g76nz3r"))
-         (file-name (git-file-name name version))))
-      (build-system cmake-build-system)
-      (arguments
-       `(#:tests? #f ; No test suite
-         #:phases
-         (modify-phases %standard-phases
-           ;; No 'install' target in CMakeLists.txt
-           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let* ((out (assoc-ref outputs "out"))
-                      (bin (string-append out "/bin"))
-                      (lib (string-append out "/lib"))
-                      (doc (string-append out "/share/doc/"
-                                          (string-append ,name "-" ,version))))
-                 (install-file "apfs-dump" bin)
-                 (install-file "apfs-dump-quick" bin)
-                 (install-file "apfs-fuse" bin)
-                 (install-file "libapfs.a" lib)
-                 (install-file "../source/LICENSE" doc)
-                 #t))))))
-      (inputs
-       `(("bzip2" ,bzip2)
-         ("fuse" ,fuse)
-         ("zlib" ,zlib)))
-      (synopsis "Read-only FUSE driver for the APFS filesystem")
-      (description "APFS-FUSE is a read-only FUSE driver for the @dfn{Apple File
-System} (APFS).  It is currently in an experimental state — it may not be able
-to read all files, and it does not support all the compression methods in
-APFS.")
-      (home-page "https://github.com/sgan81/apfs-fuse")
-      (license license:gpl2+))))

gnu/packages/file.scm

@@ -2,7 +2,6 @@
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,14 +28,14 @@
 (define-public file
   (package
     (name "file")
-    (version "5.33")
+    (version "5.32")
     (source (origin
               (method url-fetch)
               (uri (string-append "ftp://ftp.astron.com/pub/file/file-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1iipnwjkag7q04zjkaqic41r9nlw0ml6mhqian6qkkbisb1whlhw"))))
+                "0l1bfa0icng9vdwya00ff48fhvjazi5610ylbhl35qi13d6xqfc6"))))
    (build-system gnu-build-system)
 
    ;; When cross-compiling, this package depends upon a native install of

gnu/packages/finance.scm

@@ -165,13 +165,6 @@ line client and a client based on Qt.")
        #:make-flags (list "ARGS=-E BaselineTest_cmd-org")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'boost-compat
-           (lambda _
-             (substitute* "src/utils.h"
-               ;; This library moved in Boost 1.66.  Remove for Ledger
-               ;; versions > 3.1.1.
-               (("boost/uuid/sha1.hpp") "boost/uuid/detail/sha1.hpp"))
-             #t))
          (add-before 'configure 'install-examples
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((examples (string-append (assoc-ref outputs "out")
@@ -847,7 +840,7 @@ Luhn and family of ISO/IEC 7064 check digit algorithms. ")
 (define-public python-duniterpy
   (package
     (name "python-duniterpy")
-    (version "0.50.0")
+    (version "0.43.7")
     (source
      (origin
        (method git-fetch)
@@ -858,14 +851,10 @@ Luhn and family of ISO/IEC 7064 check digit algorithms. ")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0f24ihglmzphy30pgc49w0rxmsjc76mgcggg078cfsz7xrrk13gf"))))
+         "19m36z98361bqxjdb65597j2kxbly491927c6p9z47s1vxc3raaq"))))
     (build-system python-build-system)
-    (arguments
-     ;; Tests fail with "AttributeError: module 'attr' has no attribute 's'".
-     `(#:tests? #f))
     (propagated-inputs
      `(("python-aiohttp" ,python-aiohttp)
-       ("python-attr" ,python-attr)
        ("python-base58" ,python-base58)
        ("python-jsonschema" ,python-jsonschema)
        ("python-libnacl" ,python-libnacl)
@@ -886,7 +875,7 @@ main features are:
 (define-public silkaj
   (package
     (name "silkaj")
-    (version "0.6.0")
+    (version "0.5.0")
     (source
      (origin
        (method git-fetch)
@@ -896,10 +885,30 @@ main features are:
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "02n028rz1pshgh7w0af3b291r8lwvhzskm1q98d991gr8rscvad2"))))
+         "0xy25lpgz04nxikjvxlnlckrc9xmsxyiz2qm0bsiid8cnbdqcn12"))))
     (build-system python-build-system)
     (arguments
-     `(#:tests? #f))                    ;no test
+     `(#:tests? #f                      ;no test
+       #:phases
+       (modify-phases %standard-phases
+         ;; The program is just a bunch of Python files in "src/" directory.
+         ;; Many phases are useless.  However, `python-build-system' correctly
+         ;; sets PYTHONPATH and patches Python scripts.
+         (delete 'configure)
+         (delete 'build)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (share (string-append out "/share/silkaj"))
+                    (executable (string-append share "/silkaj.py"))
+                    (bin (string-append out "/bin")))
+               ;; Install data.
+               (copy-recursively "src" share)
+               ;; Install executable.
+               (mkdir-p bin)
+               (with-directory-excursion bin
+                 (symlink executable "silkaj")))
+             #t)))))
     (inputs
      `(("python-commandlines" ,python-commandlines)
        ("python-ipaddress" ,python-ipaddress)

gnu/packages/firmware.scm

@@ -446,26 +446,25 @@ such as:
     (license (list license:bsd-3
                    license:bsd-2)))) ; libfdt
 
-(define-public arm-trusted-firmware-sun50i-a64
-  (let ((base (make-arm-trusted-firmware "sun50i_a64"))
-        ;; Use unreleased version which enables additional features needed for
-        ;; LCD support
-        (commit "cabe0a31801e99e7abb84d2114ded6bb56f3c71e")
+(define-public arm-trusted-firmware-pine64-plus
+  (let ((base (make-arm-trusted-firmware "sun50iw1p1"))
+        ;; Vendor's arm trusted firmware branch hasn't been upstreamed yet.
+        (commit "ae78724247a01560164d607ed66db111c74d8df0")
         (revision "1"))
     (package
       (inherit base)
-      (name "arm-trusted-firmware-sun50i-a64")
-      (version (git-version "2.0" revision commit))
+      (name "arm-trusted-firmware-pine64-plus")
+      (version (string-append "1.2-" revision "." (string-take commit 7)))
       (source
         (origin
           (method git-fetch)
           (uri (git-reference
-                 (url "https://github.com/ARM-software/arm-trusted-firmware.git")
+                 (url "https://github.com/apritzel/arm-trusted-firmware.git")
                  (commit commit)))
           (file-name (git-file-name name version))
           (sha256
            (base32
-            "0srw2zj3vn5d2fwzjpwa5h70d5bwvb79jnpdvmd395npv0gxshdz")))))))
+            "0r4xnlq7v9khjfcg6gqp7nmrmnw4z1r8bipwdr07png1dcbb8214")))))))
 
 (define-public arm-trusted-firmware-puma-rk3399
   (let ((base (make-arm-trusted-firmware "rk3399"))

gnu/packages/flex.scm

@@ -45,10 +45,22 @@
     (build-system gnu-build-system)
     (inputs
      (let ((bison-for-tests
+            ;; Work around an incompatibility with Bison 3.0:
+            ;; <http://lists.gnu.org/archive/html/bug-bison/2013-09/msg00014.html>.
             (package
               (inherit bison)
-              ;; Disable tests, since they require flex.
-              (arguments '(#:tests? #f))
+              (version "2.7.1")
+              (source (origin
+                        (method url-fetch)
+                        (uri (string-append
+                              "mirror://gnu/bison/"
+                              "bison-" version ".tar.xz"))
+                        (sha256
+                         (base32
+                          "1yx7isx67sdmyijvihgyra1f59fwdz7sqriginvavfj5yb5ss2dl"))))
+
+              ;; Unlike Bison 3.0, this version did not need Flex for its
+              ;; tests, so it allows us to break the cycle.
               (inputs (alist-delete "flex" (package-inputs bison))))))
        `(("bison" ,bison-for-tests)
          ("indent" ,indent))))

gnu/packages/fltk.scm

@@ -115,12 +115,6 @@ UI builder called FLUID that can be used to create applications in minutes.")
        #:configure-flags '("--enable-gl")
        #:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'setup-waf
-          (lambda* (#:key inputs #:allow-other-keys)
-            (let ((waf (assoc-ref inputs "waf")))
-              (delete-file "waf")
-              (copy-file (string-append waf "/bin/waf") "waf"))
-            #t))
          (add-before 'configure 'set-ldflags
            (lambda* (#:key outputs #:allow-other-keys)
              (setenv "LDFLAGS"
@@ -129,8 +123,7 @@ UI builder called FLUID that can be used to create applications in minutes.")
              #t)))))
     (inputs
      `(("libjpeg" ,libjpeg)
-       ("glu" ,glu)
-       ("waf" ,python-waf)))
+       ("glu" ,glu)))
     ;; ntk.pc lists "x11" and "xft" in Requires.private, and "cairo" in
     ;; Requires.
     (propagated-inputs