Merge branch 'staging'

Conflicts:
	gnu/packages/admin.scm
	gnu/packages/commencement.scm
	gnu/packages/gdb.scm
	gnu/packages/llvm.scm
	gnu/packages/package-management.scm
	gnu/packages/tls.scm

.gitignore

@@ -74,6 +74,7 @@
 /etc/guix-publish.conf
 /etc/guix-publish.service
 /etc/init.d/guix-daemon
+/etc/openrc/guix-daemon
 /guix-daemon
 /guix/config.scm
 /libformat.a

.guix-authorizations

@@ -1,5 +1,5 @@
-;; This is the list of OpenPGP keys currently authorized to sign commits in
+;; This file, which is best viewed as -*- Scheme -*-, lists the OpenPGP keys
-;; this repository.
+;; currently authorized to sign commits in this repository.
 
 (authorizations
  (version 0)
@@ -84,6 +84,8 @@
    (name "lfam"))
   ("2AE3 1395 932B E642 FC0E  D99C 9BED 6EDA 32E5 B0BC"
    (name "lsl88"))
+  ("8887 84C4 1459 ACCB 83E7  E84C 634C 6E89 79FA BEC2"
+   (name "m1gu3l"))
   ("CBF5 9755 CBE7 E7EF EF18  3FB1 DD40 9A15 D822 469D"
    (name "marusich"))
   ("BBB0 2DDF 2CEA F6A8 0D1D  E643 A2A0 6DF2 A33A 54FA"

Makefile.am

@@ -47,6 +47,18 @@ scripts/guix: scripts/guix.in Makefile
 	$(AM_V_GEN)$(do_subst) < "$(srcdir)/$@.in" > "$@-t"
 	$(AM_V_at)chmod a+x,a-w "$@-t" && mv -f "$@-t" "$@"
 
+# This is our variant of the 'guile' executable, one that doesn't complain
+# about locales.
+pkglibexec_PROGRAMS = guile
+guile_SOURCES = gnu/packages/aux-files/guile-launcher.c
+guile_LDADD   = $(GUILE_LIBS)
+guile_CFLAGS  = $(GUILE_CFLAGS)
+
+# Have the 'guix' command refer to our 'guile'.
+install-exec-hook:
+	$(SED) -i "$(DESTDIR)$(bindir)/guix"				\
+	       -e 's,^#![[:graph:]]\+,#!$(pkglibexecdir)/guile,g'
+
 nodist_noinst_SCRIPTS =				\
   pre-inst-env					\
   test-env
@@ -394,6 +406,7 @@ SCM_TESTS =					\
   tests/base16.scm				\
   tests/base32.scm				\
   tests/base64.scm				\
+  tests/boot-parameters.scm			\
   tests/bournish.scm				\
   tests/builders.scm				\
   tests/build-utils.scm			\
@@ -570,6 +583,7 @@ EXTRA_DIST +=						\
   build-aux/hydra/guix-modular.scm			\
   build-aux/cuirass/gnu-system.scm			\
   build-aux/cuirass/guix-modular.scm			\
+  build-aux/cuirass/hurd-manifest.scm			\
   build-aux/cuirass/hydra-to-cuirass.scm		\
   build-aux/check-final-inputs-self-contained.scm	\
   build-aux/check-channel-news.scm			\
@@ -832,9 +846,8 @@ release: dist-with-updated-version
 	      -v1 --no-grafts --fallback
 	for system in $(GUIX_SYSTEM_SUPPORTED_SYSTEMS) ; do				\
 	  image=`$(top_builddir)/pre-inst-env						\
-	    guix system disk-image							\
+	    guix system disk-image -t iso9660                                           \
-	    --file-system-type=iso9660							\
+	    --label="GUIX_$${system}_$(VERSION)"					\
-	    --label="GUIX_$${system}_$(VERSION)"						\
             --system=$$system --fallback						\
 	    gnu/system/install.scm` ;							\
 	  if [ ! -f "$$image" ] ; then							\

build-aux/cuirass/hurd-manifest.scm

@@ -0,0 +1,74 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;;
+;;; This file defines a manifest with a selection of packages for Cuirass to
+;;; build for GNU/Hurd.
+;;;
+;;; Code:
+
+(use-modules (gnu)
+             (gnu system hurd)
+             (guix packages)
+             (guix utils)
+             (ice-9 match)
+             (srfi srfi-1))
+
+(use-package-modules
+ base commencement compression file gawk gdb gettext guile
+ hurd less m4 package-management python ssh version-control)
+
+(define (input->package input)
+  "Return the INPUT as package, or #f."
+  (match input
+    ((label (and (? package?) package))
+     package)
+    ((label (and (? package?) package . output))
+     (cons package output))
+    (_ #f)))
+
+(define guix-dependencies
+  (filter-map input->package
+              (fold alist-delete (package-direct-inputs guix)
+                    '("glibc-utf8-locales" "graphviz" "po4a"))))
+
+(define (package-without-tests p)
+  (package/inherit p
+    (arguments
+     (substitute-keyword-arguments (package-arguments p)
+       ((#:tests? _ #f) #f)))))
+
+(packages->manifest
+ (cons*
+  ;; where it all starts
+  hello
+
+  ;; development utililities
+  diffutils file findutils gawk grep gzip less m4 openssh-sans-x tar xz
+
+  ;; development packages
+  gcc-toolchain gdb-minimal git-minimal gnu-make
+
+  ;; guix environment guix --without-tests=python-minimal --without-tests=gettext-minimal
+  (package-without-tests gettext-minimal)
+  (package-without-tests python-minimal)
+
+  (append
+   guix-dependencies
+   (delete guile-3.0 %base-packages/hurd))))

build-aux/hydra/guix-modular.scm

@@ -43,17 +43,25 @@ for SYSTEM.  Use VERSION as the version identifier."
     (define build
       (primitive-load (string-append source "/build-aux/build-self.scm")))
 
-    `((derivation . ,(derivation-file-name
+    (let ((drv (run-with-store store
-                      (run-with-store store
+                 (build source #:version version #:system system
-                        (build source #:version version #:system system
+                        #:pull-version 1
-                               #:pull-version 1
+                        #:guile-version "2.2"))))
-                               #:guile-version "2.2")))) ;the latest 2.2.x
+      `((derivation . ,(derivation-file-name drv)) ;the latest 2.2.x
-      (description . "Modular Guix")
+        (log . ,(log-file store (derivation-file-name drv)))
-      (long-description
+        (outputs . ,(filter-map (lambda (res)
-       . "This is the modular Guix package as produced by 'guix pull'.")
+                                  (match res
-      (license . ,license:gpl3+)
+                                    ((name . path)
-      (home-page . ,%guix-home-page-url)
+                                     `(,name . ,path))))
-      (maintainers . (,%guix-bug-report-address)))))
+                                (derivation->output-paths drv)))
+        (nix-name . ,(derivation-name drv))
+        (system . ,(derivation-system drv))
+        (description . "Modular Guix")
+        (long-description
+         . "This is the modular Guix package as produced by 'guix pull'.")
+        (license . ,license:gpl3+)
+        (home-page . ,%guix-home-page-url)
+        (maintainers . (,%guix-bug-report-address))))))
 
 (define (hydra-jobs store arguments)
   "Return Hydra jobs."

configure.ac

@@ -105,6 +105,9 @@ if test "x$GUILE_EFFECTIVE_VERSION" = "x2.2"; then
   PKG_CHECK_MODULES([GUILE], [guile-2.2 >= 2.2.3])
 fi
 
+dnl Get CFLAGS and LDFLAGS for libguile.
+GUILE_FLAGS
+
 dnl Installation directories for .scm and .go files.
 guilemoduledir="${datarootdir}/guile/site/$GUILE_EFFECTIVE_VERSION"
 guileobjectdir="${libdir}/guile/$GUILE_EFFECTIVE_VERSION/site-ccache"

doc/build.scm

@@ -33,6 +33,7 @@
              (guix utils)
              (git)
              (gnu packages base)
+             (gnu packages compression)
              (gnu packages gawk)
              (gnu packages gettext)
              (gnu packages guile)
@@ -40,7 +41,10 @@
              (gnu packages iso-codes)
              (gnu packages texinfo)
              (gnu packages tex)
+             (ice-9 match)
+             (srfi srfi-1)
              (srfi srfi-19)
+             (srfi srfi-26)
              (srfi srfi-71))
 
 (define file-append*
@@ -204,9 +208,168 @@ content=\"width=device-width, initial-scale=1\" />"))
                (setenv "XFAIL_TESTS" "htmlprag.scm")
                #t))))))))
 
+(define (normalize-language-code language)        ;XXX: deduplicate
+  ;; Normalize LANGUAGE.  For instance, "zh_CN" becomes "zh-cn".
+  (string-map (match-lambda
+                (#\_ #\-)
+                (chr chr))
+              (string-downcase language)))
+
+(define* (html-manual-identifier-index manual base-url
+                                       #:key
+                                       (name "html-manual-identifier-index"))
+  "Return an index of all the identifiers that appear in MANUAL, a
+makeinfo-generated manual.  The index is a file that contains an alist; each
+key is an identifier and the associated value is the URL reference pointing to
+that identifier.  The URL is constructed by concatenating BASE-URL to the
+actual file name."
+  (define build
+    (with-extensions (list guile-lib/htmlprag-fixed)
+      (with-imported-modules '((guix build utils))
+        #~(begin
+            (use-modules (guix build utils)
+                         (htmlprag)
+                         (srfi srfi-1)
+                         (srfi srfi-26)
+                         (ice-9 ftw)
+                         (ice-9 match)
+                         (ice-9 threads)
+                         (ice-9 pretty-print))
+
+            (define file-url
+              (let ((prefix (string-append #$manual "/")))
+                (lambda (file)
+                  ;; Return the URL for FILE.
+                  (let ((file (string-drop file (string-length prefix)))
+                        (base #$base-url))
+                    (if (string-null? base)
+                        file
+                        (string-append base "/" file))))))
+
+            (define (underscore-decode str)
+              ;; Decode STR, an "underscore-encoded" string as produced by
+              ;; makeinfo for indexes, such as "_0025base_002dservices" for
+              ;; "%base-services".
+              (let loop ((str str)
+                         (result '()))
+                (match (string-index str #\_)
+                  (#f
+                   (string-concatenate-reverse (cons str result)))
+                  (index
+                   (let ((char (string->number
+                                (substring str (+ index 1) (+ index 5))
+                                16)))
+                     (loop (string-drop str (+ index 5))
+                           (append (list (string (integer->char char))
+                                         (string-take str index))
+                                   result)))))))
+
+            (define (anchor-id->key id)
+              ;; Convert ID, an anchor ID such as
+              ;; "index-pam_002dlimits_002dservice" to the corresponding key,
+              ;; "pam-limits-service" in this example.  Drop the suffix of
+              ;; duplicate anchor IDs like "operating_002dsystem-1".
+              (let ((id (if (any (cut string-suffix? <> id)
+                                 '("-1" "-2" "-3" "-4" "-5"))
+                            (string-drop-right id 2)
+                            id)))
+                (underscore-decode
+                 (string-drop id (string-length "index-")))))
+
+            (define* (collect-anchors file #:optional (anchors '()))
+              ;; Collect the anchors that appear in FILE, a makeinfo-generated
+              ;; file.  Grab those from <dt> tags, which corresponds to
+              ;; Texinfo @deftp, @defvr, etc.  Return ANCHORS augmented with
+              ;; more name/reference pairs.
+              (define string-or-entity?
+                (match-lambda
+                  ((? string?) #t)
+                  (('*ENTITY* _ ...) #t)
+                  (_ #f)))
+
+              (define (worthy-entry? lst)
+                ;; Attempt to match:
+                ;;   Scheme Variable: <strong>x</strong>
+                ;; but not:
+                ;;   <code>cups-configuration</code> parameter: …
+                (let loop ((lst lst))
+                  (match lst
+                    (((? string-or-entity?) rest ...)
+                     (loop rest))
+                    ((('strong _ ...) _ ...)
+                     #t)
+                    (_ #f))))
+
+              (let ((shtml (call-with-input-file file html->shtml)))
+                (let loop ((shtml shtml)
+                           (anchors anchors))
+                  (match shtml
+                    (('dt ('@ ('id id)) rest ...)
+                     (if (and (string-prefix? "index-" id)
+                              (worthy-entry? rest))
+                         (alist-cons (anchor-id->key id)
+                                     (string-append (file-url file)
+                                                    "#" id)
+                                     anchors)
+                         anchors))
+                    ((tag ('@ _ ...) body ...)
+                     (fold loop anchors body))
+                    ((tag body ...)
+                     (fold loop anchors body))
+                    (_ anchors)))))
+
+            (define (html-files directory)
+              ;; Return the list of HTML files under DIRECTORY.
+              (map (cut string-append directory "/" <>)
+                   (scandir #$manual (lambda (file)
+                                       (string-suffix? ".html" file)))))
+
+            (define anchors
+              (sort (concatenate
+                     (n-par-map (parallel-job-count)
+                                (cut collect-anchors <>)
+                                (html-files #$manual)))
+                    (match-lambda*
+                      (((key1 . url1) (key2 . url2))
+                       (if (string=? key1 key2)
+                           (string<? url1 url2)
+                           (string<? key1 key2))))))
+
+            (call-with-output-file #$output
+              (lambda (port)
+                (display ";; Identifier index for the manual.\n\n"
+                         port)
+                (pretty-print anchors port)))))))
+
+  (computed-file name build))
+
+(define* (html-identifier-indexes manual directory-suffix
+                                  #:key (languages %languages)
+                                  (manual-name %manual)
+                                  (base-url (const "")))
+  (map (lambda (language)
+         (let ((language (normalize-language-code language)))
+           (list language
+                 (html-manual-identifier-index
+                  (file-append manual "/" language directory-suffix)
+                  (base-url language)
+                  #:name (string-append manual-name "-html-index-"
+                                        language)))))
+       languages))
+
 (define* (syntax-highlighted-html input
                                   #:key
                                   (name "highlighted-syntax")
+                                  (languages %languages)
+                                  (mono-node-indexes
+                                   (html-identifier-indexes input ""
+                                                            #:languages
+                                                            languages))
+                                  (split-node-indexes
+                                   (html-identifier-indexes input
+                                                            "/html_node"
+                                                            #:languages
+                                                            languages))
                                   (syntax-css-url
                                    "/static/base/css/code.css"))
   "Return a derivation called NAME that processes all the HTML files in INPUT
@@ -341,78 +504,6 @@ its <pre class=\"lisp\"> blocks (as produced by 'makeinfo --html')."
                   ((? string? str)
                    str))))
 
-            (define (underscore-decode str)
-              ;; Decode STR, an "underscore-encoded" string as produced by
-              ;; makeinfo for indexes, such as "_0025base_002dservices" for
-              ;; "%base-services".
-              (let loop ((str str)
-                         (result '()))
-                (match (string-index str #\_)
-                  (#f
-                   (string-concatenate-reverse (cons str result)))
-                  (index
-                   (let ((char (string->number
-                                (substring str (+ index 1) (+ index 5))
-                                16)))
-                     (loop (string-drop str (+ index 5))
-                           (append (list (string (integer->char char))
-                                         (string-take str index))
-                                   result)))))))
-
-            (define (anchor-id->key id)
-              ;; Convert ID, an anchor ID such as
-              ;; "index-pam_002dlimits_002dservice" to the corresponding key,
-              ;; "pam-limits-service" in this example.  Drop the suffix of
-              ;; duplicate anchor IDs like "operating_002dsystem-1".
-              (let ((id (if (any (cut string-suffix? <> id)
-                                 '("-1" "-2" "-3" "-4" "-5"))
-                            (string-drop-right id 2)
-                            id)))
-                (underscore-decode
-                 (string-drop id (string-length "index-")))))
-
-            (define* (collect-anchors file #:optional (vhash vlist-null))
-              ;; Collect the anchors that appear in FILE, a makeinfo-generated
-              ;; file.  Grab those from <dt> tags, which corresponds to
-              ;; Texinfo @deftp, @defvr, etc.  Return VHASH augmented with
-              ;; more name/reference pairs.
-              (define string-or-entity?
-                (match-lambda
-                  ((? string?) #t)
-                  (('*ENTITY* _ ...) #t)
-                  (_ #f)))
-
-              (define (worthy-entry? lst)
-                ;; Attempt to match:
-                ;;   Scheme Variable: <strong>x</strong>
-                ;; but not:
-                ;;   <code>cups-configuration</code> parameter: …
-                (let loop ((lst lst))
-                  (match lst
-                    (((? string-or-entity?) rest ...)
-                     (loop rest))
-                    ((('strong _ ...) _ ...)
-                     #t)
-                    (_ #f))))
-
-              (let ((shtml (call-with-input-file file html->shtml)))
-                (let loop ((shtml shtml)
-                           (vhash vhash))
-                  (match shtml
-                    (('dt ('@ ('id id)) rest ...)
-                     (if (and (string-prefix? "index-" id)
-                              (worthy-entry? rest))
-                         (vhash-cons (anchor-id->key id)
-                                     (string-append (basename file)
-                                                    "#" id)
-                                     vhash)
-                         vhash))
-                    ((tag ('@ _ ...) body ...)
-                     (fold loop vhash body))
-                    ((tag body ...)
-                     (fold loop vhash body))
-                    (_ vhash)))))
-
             (define (process-html file anchors)
               ;; Parse FILE and perform syntax highlighting for its Scheme
               ;; snippets.  Install the result to #$output.
@@ -444,38 +535,59 @@ its <pre class=\"lisp\"> blocks (as produced by 'makeinfo --html')."
             (define (html? file stat)
               (string-suffix? ".html" file))
 
+            (define language+node-anchors
+              (match-lambda
+                ((language files ...)
+                 (cons language
+                       (fold (lambda (file vhash)
+                               (let ((alist (call-with-input-file file read)))
+                                 ;; Use 'fold-right' so that the first entry
+                                 ;; wins (e.g., "car" from "Pairs" rather than
+                                 ;; from "rnrs base" in the Guile manual).
+                                 (fold-right (match-lambda*
+                                               (((key . value) vhash)
+                                                (vhash-cons key value vhash)))
+                                             vhash
+                                             alist)))
+                             vlist-null
+                             files)))))
+
+            (define mono-node-anchors
+              ;; List of language/vhash pairs, where each vhash maps an
+              ;; identifier to the corresponding URL in a single-page manual.
+              (map language+node-anchors '#$mono-node-indexes))
+
+            (define multi-node-anchors
+              ;; Likewise for split-node manuals.
+              (map language+node-anchors '#$split-node-indexes))
+
             ;; Install a UTF-8 locale so we can process UTF-8 files.
             (setenv "GUIX_LOCPATH"
                     #+(file-append glibc-utf8-locales "/lib/locale"))
             (setlocale LC_ALL "en_US.utf8")
 
             ;; First process the mono-node 'guix.html' files.
-            (n-par-for-each (parallel-job-count)
+            (for-each (match-lambda
-                            (lambda (mono)
+                        ((language . anchors)
-                              (let ((anchors (collect-anchors mono)))
+                         (let ((files (find-files
-                                (process-html mono anchors)))
+                                       (string-append #$input "/" language)
-                            (find-files
+                                       "^guix(-cookbook|)(\\.[a-zA-Z_-]+)?\\.html$")))
-                             #$input
+                           (n-par-for-each (parallel-job-count)
-                             "^guix(-cookbook|)(\\.[a-zA-Z_-]+)?\\.html$"))
+                                           (cut process-html <> anchors)
+                                           files))))
+                      mono-node-anchors)
 
-            ;; Next process the multi-node HTML files in two phases: (1)
+            ;; Process the multi-node HTML files.
-            ;; collect the list of anchors, and (2) perform
+            (for-each (match-lambda
-            ;; syntax-highlighting.
+                        ((language . anchors)
-            (let* ((multi   (find-files #$input "^html_node$"
+                         (let ((files (find-files
-                                        #:directories? #t))
+                                       (string-append #$input "/" language
-                   (anchors (n-par-map (parallel-job-count)
+                                                      "/html_node")
-                                       (lambda (multi)
+                                       "\\.html$")))
-                                         (cons multi
+                           (n-par-for-each (parallel-job-count)
-                                               (fold collect-anchors vlist-null
+                                           (cut process-html <> anchors)
-                                                     (find-files multi html?))))
+                                           files))))
-                                       multi)))
+                      multi-node-anchors)
-              (n-par-for-each (parallel-job-count)
-                              (lambda (file)
-                                (let ((anchors (assoc-ref anchors (dirname file))))
-                                  (process-html file anchors)))
-                              (append-map (lambda (multi)
-                                            (find-files multi html?))
-                                          multi)))
 
             ;; Last, copy non-HTML files as is.
             (for-each copy-as-is
@@ -486,6 +598,8 @@ its <pre class=\"lisp\"> blocks (as produced by 'makeinfo --html')."
 (define* (html-manual source #:key (languages %languages)
                       (version "0.0")
                       (manual %manual)
+                      (mono-node-indexes (map list languages))
+                      (split-node-indexes (map list languages))
                       (date 1)
                       (options %makeinfo-html-options))
   "Return the HTML manuals built from SOURCE for all LANGUAGES, with the given
@@ -574,6 +688,8 @@ makeinfo OPTIONS."
   (let* ((name   (string-append manual "-html-manual"))
          (manual (computed-file name build)))
     (syntax-highlighted-html manual
+                             #:mono-node-indexes mono-node-indexes
+                             #:split-node-indexes split-node-indexes
                              #:name (string-append name "-highlighted"))))
 
 (define* (pdf-manual source #:key (languages %languages)
@@ -920,6 +1036,8 @@ languages:\n"
                           #:key (languages %languages)
                           (version "0.0")
                           (date (time-second (current-time time-utc)))
+                          (mono-node-indexes (map list %languages))
+                          (split-node-indexes (map list %languages))
                           (manual %manual))
   "Return the union of the HTML and PDF manuals, as well as the indexes."
   (directory-union (string-append manual "-manual")
@@ -930,7 +1048,12 @@ languages:\n"
                                 #:version version
                                 #:manual manual))
                         (list html-manual-indexes
-                              html-manual pdf-manual))
+                              (lambda (source . args)
+                                (apply html-manual source
+                                       #:mono-node-indexes mono-node-indexes
+                                       #:split-node-indexes split-node-indexes
+                                       args))
+                              pdf-manual))
                    #:copy? #t))
 
 (define (latest-commit+date directory)
@@ -943,18 +1066,144 @@ commit date (an integer)."
     ;; TODO: Use (git describe) when it's widely available.
     (values (oid->string oid) (commit-time commit))))
 
+
+;;;
+;;; Guile manual.
+;;;
+
+(define guile-manual
+  ;; The Guile manual as HTML, including both the mono-node "guile.html" and
+  ;; the split-node "html_node" directory.
+  (let ((guile guile-3.0-latest))
+    (computed-file (string-append "guile-manual-" (package-version guile))
+                   (with-imported-modules '((guix build utils))
+                     #~(begin
+                         (use-modules (guix build utils)
+                                      (ice-9 match))
+
+                         (setenv "PATH"
+                                 (string-append #+tar "/bin:"
+                                                #+xz "/bin:"
+                                                #+texinfo "/bin"))
+                         (invoke "tar" "xf" #$(package-source guile))
+                         (mkdir-p (string-append #$output "/en/html_node"))
+
+                         (let* ((texi (find-files "." "^guile\\.texi$"))
+                                (documentation (match texi
+                                                 ((file) (dirname file)))))
+                           (with-directory-excursion documentation
+                             (invoke "makeinfo" "--html" "--no-split"
+                                     "-o" (string-append #$output
+                                                         "/en/guile.html")
+                                     "guile.texi")
+                             (invoke "makeinfo" "--html" "-o" "split"
+                                     "guile.texi")
+                             (copy-recursively
+                              "split"
+                              (string-append #$output "/en/html_node")))))))))
+
+(define %guile-manual-base-url
+  "https://www.gnu.org/software/guile/manual")
+
+(define (for-all-languages index)
+  (map (lambda (language)
+         (list language index))
+       %languages))
+
+(define guile-mono-node-indexes
+  ;; The Guile manual is only available in English so use the same index in
+  ;; all languages.
+  (for-all-languages
+   (html-manual-identifier-index (file-append guile-manual "/en")
+                                 %guile-manual-base-url
+                                 #:name "guile-html-index-en")))
+
+(define guile-split-node-indexes
+  (for-all-languages
+   (html-manual-identifier-index (file-append guile-manual "/en/html_node")
+                                 (string-append %guile-manual-base-url
+                                                "/html_node")
+                                 #:name "guile-html-index-en")))
+
+(define (merge-index-alists alist1 alist2)
+  "Merge ALIST1 and ALIST2, both of which are list of tuples like:
+
+  (LANGUAGE INDEX1 INDEX2 ...)
+
+where LANGUAGE is a string like \"en\" and INDEX1 etc. are indexes as returned
+by 'html-identifier-indexes'."
+  (let ((languages (delete-duplicates
+                    (append (match alist1
+                              (((languages . _) ...)
+                               languages))
+                            (match alist2
+                              (((languages . _) ...)
+                               languages))))))
+    (map (lambda (language)
+           (cons language
+                 (append (or (assoc-ref alist1 language) '())
+                         (or (assoc-ref alist2 language) '()))))
+         languages)))
+
 
 (let* ((root (canonicalize-path
               (string-append (current-source-directory) "/..")))
-       (commit date (latest-commit+date root)))
+       (commit date (latest-commit+date root))
+       (version (or (getenv "GUIX_MANUAL_VERSION")
+                    (string-take commit 7)))
+       (select? (let ((vcs? (git-predicate root)))
+                  (lambda (file stat)
+                    (and (vcs? file stat)
+                         ;; Filter out this file.
+                         (not (string=? (basename file) "build.scm"))))))
+       (source (local-file root "guix" #:recursive? #t
+                           #:select? select?)))
+
+  (define guix-manual
+    (html-manual source
+                 #:manual "guix"
+                 #:version version
+                 #:date date))
+
+  (define guix-mono-node-indexes
+    ;; Alist of indexes for GUIX-MANUAL, where each key is a language code and
+    ;; each value is a file-like object containing the identifier index.
+    (html-identifier-indexes guix-manual ""
+                             #:manual-name "guix"
+                             #:base-url (if (string=? %manual "guix")
+                                            (const "")
+                                            (cut string-append "/manual/" <>))
+                             #:languages %languages))
+
+  (define guix-split-node-indexes
+    ;; Likewise for the split-node variant of GUIX-MANUAL.
+    (html-identifier-indexes guix-manual "/html_node"
+                             #:manual-name "guix"
+                             #:base-url (if (string=? %manual "guix")
+                                            (const "")
+                                            (cut string-append "/manual/" <>
+                                                 "/html_node"))
+                             #:languages %languages))
+
+  (define mono-node-indexes
+    (merge-index-alists guix-mono-node-indexes guile-mono-node-indexes))
+
+  (define split-node-indexes
+    (merge-index-alists guix-split-node-indexes guile-split-node-indexes))
+
   (format (current-error-port)
           "building manual from work tree around commit ~a, ~a~%"
           commit
           (let* ((time (make-time time-utc 0 date))
                  (date (time-utc->date time)))
             (date->string date "~e ~B ~Y")))
-  (pdf+html-manual (local-file root "guix" #:recursive? #t
+
-                               #:select? (git-predicate root))
+  (pdf+html-manual source
-                   #:version (or (getenv "GUIX_MANUAL_VERSION")
+                   ;; Always use the identifier indexes of GUIX-MANUAL and
-                                 (string-take commit 7))
+                   ;; GUILE-MANUAL.  Both "guix" and "guix-cookbook" can
+                   ;; contain links to definitions that appear in either of
+                   ;; these two manuals.
+                   #:mono-node-indexes mono-node-indexes
+                   #:split-node-indexes split-node-indexes
+                   #:version version
                    #:date date))

doc/contributing.texi

@@ -121,8 +121,9 @@ more information.
 Then, run @command{./configure} as usual.  Make sure to pass
 @code{--localstatedir=@var{directory}} where @var{directory} is the
 @code{localstatedir} value used by your current installation (@pxref{The
-Store}, for information about this).  We recommend to use the value
+Store}, for information about this), usually @file{/var}.  Note that you
-@code{/var}.
+will probably not run @command{make install} at the end (you don't have
+to) but it's still important to pass the right @code{localstatedir}.
 
 Finally, you have to invoke @code{make check} to run tests
 (@pxref{Running the Test Suite}).  If anything
@@ -159,13 +160,11 @@ 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}).
-An example@footnote{The @option{-E} flag to
+As an example, here is how you would build the @code{hello} package as
-@command{sudo} guarantees that @code{GUILE_LOAD_PATH} is correctly set
+defined in your working tree (this assumes @command{guix-daemon} is
-such that @command{guix-daemon} and the tools it uses can find the Guile
+already running on your system; it's OK if it's a different version):
-modules they need.}:
 
 @example
-$ sudo -E ./pre-inst-env guix-daemon --build-users-group=guixbuild
 $ ./pre-inst-env guix build hello
 @end example
 
@@ -200,6 +199,17 @@ scheme@@(guile-user)> (length snakes)
 $1 = 361
 @end example
 
+If you are hacking on the daemon and its supporting code or if
+@command{guix-daemon} is not already running on your system, you can
+launch it straight from the build tree@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
+@end example
+
 The @command{pre-inst-env} script sets up all the environment variables
 necessary to support this, including @env{PATH} and @env{GUILE_LOAD_PATH}.
 
@@ -353,7 +363,7 @@ Once your package builds correctly, please send us a patch
 (@pxref{Submitting Patches}).  Well, if you need help, we will be happy to
 help you too.  Once the patch is committed in the Guix repository, the
 new package automatically gets built on the supported platforms by
-@url{@value{SUBSTITUTE-SERVER}, our continuous integration system}.
+@url{@value{SUBSTITUTE-URL}, our continuous integration system}.
 
 @cindex substituter
 Users can obtain the new package definition simply by running
@@ -1016,7 +1026,7 @@ changes).  This branch is intended to be merged in @code{master} every
 6 months or so.
 @end table
 
-All these branches are @uref{@value{SUBSTITUTE-SERVER},
+All these branches are @uref{@value{SUBSTITUTE-URL},
 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

doc/guix-cookbook.texi

@@ -128,8 +128,9 @@ REPL.
 @item
 Scheme syntax boils down to a tree of expressions (or @emph{s-expression} in
 Lisp lingo).  An expression can be a literal such as numbers and strings, or a
-compound which is a parenthesized list of compounds and literals.  @code{#t}
+compound which is a parenthesized list of compounds and literals.  @code{#true}
-and @code{#f} stand for the Booleans ``true'' and ``false'', respectively.
+and @code{#false} (abbreviated @code{#t} and @code{#f}) stand for the
+Booleans ``true'' and ``false'', respectively.
 
 Examples of valid expressions:
 
@@ -249,8 +250,10 @@ definitions.
 @end lisp
 
 @item
-The keyword syntax is @code{#:}; it is used to create unique identifiers.
+@dfn{Keywords} are typically used to identify the named parameters of a
-@pxref{Keywords,,, guile, GNU Guile Reference Manual}.
+procedure.  They are prefixed by @code{#:} (hash, colon) followed by
+alphanumeric characters: @code{#:like-this}.
+@xref{Keywords,,, guile, GNU Guile Reference Manual}.
 
 @item
 The percentage @code{%} is typically used for read-only global variables in
@@ -791,11 +794,11 @@ another, more sophisticated package (slightly modified from the source):
                 (snippet '(begin
                             ;; Remove bundled software.
                             (delete-file-recursively "deps")
-                            #t))))
+                            #true))))
       (build-system cmake-build-system)
       (outputs '("out" "debug"))
       (arguments
-       `(#:tests? #t                            ; Run the test suite (this is the default)
+       `(#:tests? #true                         ; Run the test suite (this is the default)
          #:configure-flags '("-DUSE_SHA1DC=ON") ; SHA-1 collision detection
          #:phases
          (modify-phases %standard-phases
@@ -806,12 +809,12 @@ another, more sophisticated package (slightly modified from the source):
                (substitute* "tests/clar/fs.h"
                  (("/bin/cp") (which "cp"))
                  (("/bin/rm") (which "rm")))
-               #t))
+               #true))
            ;; Run checks more verbosely.
            (replace 'check
              (lambda _ (invoke "./libgit2_clar" "-v" "-Q")))
            (add-after 'unpack 'make-files-writable-for-tests
-               (lambda _ (for-each make-file-writable (find-files "." ".*")))))))
+             (lambda _ (for-each make-file-writable (find-files "." ".*")))))))
       (inputs
        `(("libssh2" ,libssh2)
          ("http-parser" ,http-parser)
@@ -1029,7 +1032,7 @@ If you want to know more about what happens during those phases, consult the
 associated procedures.
 
 For instance, as of this writing the definition of @code{unpack} for the GNU build
-system is
+system is:
 
 @lisp
 (define* (unpack #:key source #:allow-other-keys)
@@ -1044,13 +1047,13 @@ working directory."
         ;; Preserve timestamps (set to the Epoch) on the copied tree so that
         ;; things work deterministically.
         (copy-recursively source "."
-                          #:keep-mtime? #t))
+                          #:keep-mtime? #true))
       (begin
         (if (string-suffix? ".zip" source)
             (invoke "unzip" source)
             (invoke "tar" "xvf" source))
         (chdir (first-subdirectory "."))))
-  #t)
+  #true)
 @end lisp
 
 Note the @code{chdir} call: it changes the working directory to where the source was
@@ -1066,16 +1069,16 @@ the following forms:
 
 @itemize
 @item
-@code{(add-before PHASE NEW-PHASE PROCEDURE)}: Run @code{PROCEDURE} named @code{NEW-PHASE} before @code{PHASE}.
+@code{(add-before @var{phase} @var{new-phase} @var{procedure})}: Run @var{procedure} named @var{new-phase} before @var{phase}.
 @item
-@code{(add-after PHASE NEW-PHASE PROCEDURE)}: Same, but afterwards.
+@code{(add-after @var{phase} @var{new-phase} @var{procedure})}: Same, but afterwards.
 @item
-@code{(replace PHASE PROCEDURE)}.
+@code{(replace @var{phase} @var{procedure})}.
 @item
-@code{(delete PHASE)}.
+@code{(delete @var{phase})}.
 @end itemize
 
-The @code{PROCEDURE} supports the keyword arguments @code{inputs} and @code{outputs}.  Each
+The @var{procedure} supports the keyword arguments @code{inputs} and @code{outputs}.  Each
 input (whether @emph{native}, @emph{propagated} or not) and output directory is referenced
 by their name in those variables.  Thus @code{(assoc-ref outputs "out")} is the store
 directory of the main output of the package.  A phase procedure may look like
@@ -1083,16 +1086,16 @@ this:
 
 @lisp
 (lambda* (#:key inputs outputs #:allow-other-keys)
-  (let (((bash-directory (assoc-ref inputs "bash"))
+  (let ((bash-directory (assoc-ref inputs "bash"))
-         (output-directory (assoc-ref outputs "out"))
+        (output-directory (assoc-ref outputs "out"))
-         (doc-directory (assoc-ref outputs "doc"))
+        (doc-directory (assoc-ref outputs "doc")))
-  ; ...
+    ;; ...
-  #t)
+    #true))
 @end lisp
 
-The procedure must return @code{#t} on success.  It's brittle to rely on the return
+The procedure must return @code{#true} on success.  It's brittle to rely on the return
 value of the last expression used to tweak the phase because there is no
-guarantee it would be a @code{#t}.  Hence the trailing @code{#t} to ensure the right value
+guarantee it would be a @code{#true}.  Hence the trailing @code{#true} to ensure the right value
 is returned on success.
 
 @subsubsection Code staging
@@ -1118,7 +1121,7 @@ Some of those functions can be found in
 @samp{$GUIX_CHECKOUT/guix/guix/build/utils.scm}.  Most of them mirror the behaviour
 of the traditional Unix system commands:
 
-@table @asis
+@table @code
 @item which
 Like the @samp{which} system command.
 @item find-files
@@ -1142,6 +1145,9 @@ then restore the previous working directory.
 A ``@command{sed}-like'' function.
 @end table
 
+@xref{Build Utilities,,, guix, GNU Guix Reference Manual}, for more
+information on these utilities.
+
 @subsubsection Module prefix
 
 The license in our last example needs a prefix: this is because of how the
@@ -1352,6 +1358,7 @@ reference.
 * Running Guix on a Linode Server:: Running Guix on a Linode Server
 * Setting up a bind mount:: Setting up a bind mount in the file-systems definition.
 * Getting substitutes from Tor:: Configuring Guix daemon to get substitutes through Tor.
+* Setting up NGINX with Lua:: Configuring NGINX web-server to load Lua modules.
 @end menu
 
 @node Customizing the Kernel
@@ -1384,8 +1391,8 @@ creates a package.
                            #:key
                            ;; A function that takes an arch and a variant.
                            ;; See kernel-config for an example.
-                           (extra-version #f)
+                           (extra-version #false)
-                           (configuration-file #f)
+                           (configuration-file #false)
                            (defconfig "defconfig")
                            (extra-options %default-extra-linux-options)
                            (patches (list %boot-logo-patch)))
@@ -1428,7 +1435,7 @@ the @code{make-linux-libre} package definition:
       (begin
         (copy-file config ".config")
         (chmod ".config" #o666))
-      (invoke "make" ,defconfig))
+      (invoke "make" ,defconfig)))
 @end lisp
 
 Below is a sample kernel package.  The @code{linux-libre} package is nothing
@@ -1459,7 +1466,7 @@ it:
 @lisp
 (define %default-extra-linux-options
   `(;; https://lists.gnu.org/archive/html/guix-devel/2014-04/msg00039.html
-   ("CONFIG_DEVPTS_MULTIPLE_INSTANCES" . #t)
+   ("CONFIG_DEVPTS_MULTIPLE_INSTANCES" . #true)
    ;; Modules required for initrd:
    ("CONFIG_NET_9P" . m)
    ("CONFIG_NET_9P_VIRTIO" . m)
@@ -1476,9 +1483,9 @@ it:
   (string-join (map (match-lambda
                       ((option . 'm)
                        (string-append option "=m"))
-                      ((option . #t)
+                      ((option . #true)
                        (string-append option "=y"))
-                      ((option . #f)
+                      ((option . #false)
                        (string-append option "=n")))
                     options)
                "\n"))
@@ -1494,7 +1501,7 @@ And in the custom configure script from the `make-linux-libre` package:
   (display extra-configuration port)
   (close-port port))
 
-(invoke "make" "oldconfig"))))
+(invoke "make" "oldconfig")
 @end lisp
 
 So by not providing a configuration-file the @file{.config} starts blank, and
@@ -1865,7 +1872,7 @@ is below. Save the resulting file as @file{guix-config.scm}.
                (bootloader
                 (bootloader
                  (inherit grub-bootloader)
-                 (installer #~(const #t))))))
+                 (installer #~(const #true))))))
   (file-systems (cons (file-system
                         (device "/dev/sda")
                         (mount-point "/")
@@ -1897,7 +1904,7 @@ is below. Save the resulting file as @file{guix-config.scm}.
              (service openssh-service-type
                       (openssh-configuration
                        (openssh openssh-sans-x)
-                       (password-authentication? #f)
+                       (password-authentication? #false)
                        (authorized-keys
                         `(("janedoe" ,(local-file "janedoe_rsa.pub"))
                           ("root" ,(local-file "janedoe_rsa.pub"))))))
@@ -2113,6 +2120,63 @@ sudo herd set-http-proxy guix-daemon http://localhost:9250
 guix build --substitute-urls=https://bp7o7ckwlewr4slm.onion …
 @end example
 
+@node Setting up NGINX with Lua
+@section Setting up NGINX with Lua
+@cindex nginx, lua, openresty, resty
+
+NGINX could be extended with Lua scripts.
+
+Guix provides NGINX service with ability to load Lua module and specific
+Lua packages, and reply to requests by evaluating Lua scripts.
+
+The following example demonstrates system definition with configuration
+to evaluate @file{index.lua} Lua script on HTTP request to
+@uref{http://localhost/hello} endpoint:
+
+@example
+local shell = require "resty.shell"
+
+local stdin = ""
+local timeout = 1000  -- ms
+local max_size = 4096  -- byte
+
+local ok, stdout, stderr, reason, status =
+   shell.run([[/run/current-system/profile/bin/ls /tmp]], stdin, timeout, max_size)
+
+ngx.say(stdout)
+@end example
+
+@lisp
+(use-modules (gnu))
+(use-service-modules #;… web)
+(use-package-modules #;… lua)
+(operating-system
+  ;; …
+  (services
+   ;; …
+   (service nginx-service-type
+            (nginx-configuration
+             (modules
+              (list
+               (file-append nginx-lua-module "/etc/nginx/modules/ngx_http_lua_module.so")))
+             (lua-package-path (list lua-resty-core
+                                     lua-resty-lrucache
+                                     lua-resty-signal
+                                     lua-tablepool
+                                     lua-resty-shell))
+             (lua-package-cpath (list lua-resty-signal))
+             (server-blocks
+              (list (nginx-server-configuration
+                     (server-name '("localhost"))
+                     (listen '("80"))
+                     (root "/etc")
+                     (locations (list
+                                 (nginx-location-configuration
+                                  (uri "/hello")
+                                  (body (list #~(format #f "content_by_lua_file ~s;"
+                                                        #$(local-file "index.lua"))))))))))))))
+@end lisp
+
 @c *********************************************************************
 @node Advanced package management
 @chapter Advanced package management

etc/committer.scm.in

@@ -175,8 +175,8 @@ corresponding to the top-level definition containing the staged changes."
               (let ((old-values (get-values old field))
                     (new-values (get-values new field)))
                 (or (equal? old-values new-values)
-                    (let ((removed (lset-difference eq? old-values new-values))
+                    (let ((removed (lset-difference equal? old-values new-values))
-                          (added (lset-difference eq? new-values old-values)))
+                          (added (lset-difference equal? new-values old-values)))
                       (format port
                               "[~a]: ~a~%" field
                               (match (list (map symbol->string removed)

etc/completion/bash/guix

@@ -27,8 +27,9 @@ _guix_complete_command ()
     if [ -z "$_guix_commands" ]
     then
 	# Cache the list of commands to speed things up.
-	_guix_commands="$(guix --help 2> /dev/null \
+	_guix_commands="$(guix --help 2> /dev/null  \
-                                     | grep '^  ' | cut -c 2-)"
+                                     | grep '^    ' \
+				     | sed '-es/^ *\([a-z-]\+\).*$/\1/g')"
     fi
     COMPREPLY=($(compgen -W "$_guix_commands" -- "$word_at_point"))
 }
@@ -181,7 +182,7 @@ _guix_complete ()
 	*)
 	    if _guix_is_command "package"
 	    then
-		if _guix_is_dash_L || _guix_is_dash_m
+		if _guix_is_dash_L || _guix_is_dash_m || _guix_is_dash_p
 		then
 		    _guix_complete_file
 		elif _guix_is_removing

etc/guix-install.sh

@@ -4,6 +4,8 @@
 # Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 # Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 # Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+# Copyright © 2020 Morgan Smith <Morgan.J.Smith@outlook.com>
+# Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
 #
 # This file is part of GNU Guix.
 #
@@ -53,6 +55,7 @@ REQUIRE=(
 
 PAS=$'[ \033[32;1mPASS\033[0m ] '
 ERR=$'[ \033[31;1mFAIL\033[0m ] '
+WAR=$'[ \033[33;1mWARN\033[0m ] '
 INF="[ INFO ] "
 
 DEBUG=0
@@ -150,6 +153,10 @@ chk_init_sys()
         _msg "${INF}init system is: sysv-init"
         INIT_SYS="sysv-init"
         return 0
+    elif [[ $(openrc --version 2>/dev/null) =~ \(OpenRC\) ]]; then
+        _msg "${INF}init system is: OpenRC"
+        INIT_SYS="openrc"
+        return 0
     else
         INIT_SYS="NA"
         _err "${ERR}Init system could not be detected."
@@ -194,6 +201,19 @@ chk_sys_arch()
     ARCH_OS="${arch}-${os}"
 }
 
+chk_sys_nscd()
+{ # Check if nscd is up and suggest to start it or install it
+    if [ "$(type -P pidof)" ]; then
+        if [ ! "$(pidof nscd)" ]; then
+            _msg "${WAR}We recommend installing and/or starting your distribution 'nscd' service"
+            _msg "${WAR}Please read 'info guix \"Application Setup\"' about \"Name Service Switch\""
+        fi
+    else
+        _msg "${INF}We cannot determine if your distribution 'nscd' service is running"
+        _msg "${INF}Please read 'info guix \"Application Setup\"' about \"Name Service Switch\""
+    fi
+}
+
 # ------------------------------------------------------------------------------
 #+MAIN
 
@@ -212,7 +232,7 @@ guix_get_bin_list()
         | sort -Vu)")
 
     latest_ver="$(echo "$bin_ver_ls" \
-                       | grep -oP "([0-9]{1,2}\.){2}[0-9]{1,2}" \
+                       | grep -oE "([0-9]{1,2}\.){2}[0-9]{1,2}" \
                        | tail -n1)"
 
     default_ver="guix-binary-${latest_ver}.${ARCH_OS}"
@@ -268,8 +288,7 @@ sys_create_store()
     _debug "--- [ $FUNCNAME ] ---"
 
     cd "$tmp_path"
-    tar --warning=no-timestamp \
+    tar --extract \
-        --extract \
         --file "$pkg" &&
     _msg "${PAS}unpacked archive"
 
@@ -384,6 +403,16 @@ sys_enable_guix_daemon()
                   service guix-daemon start; } &&
                 _msg "${PAS}enabled Guix daemon via sysv"
             ;;
+        openrc)
+            { mkdir -p /etc/init.d;
+              cp "${ROOT_HOME}/.config/guix/current/etc/openrc/guix-daemon" \
+                 /etc/init.d/guix-daemon;
+              chmod 775 /etc/init.d/guix-daemon;
+
+              rc-update add guix-daemon default &&
+                  rc-service guix-daemon start; } &&
+                _msg "${PAS}enabled Guix daemon via OpenRC"
+            ;;
         NA|*)
             _msg "${ERR}unsupported init system; run the daemon manually:"
             echo "  ${ROOT_HOME}/.config/guix/current/bin/guix-daemon --build-users-group=guixbuild"
@@ -445,6 +474,26 @@ export XDG_DATA_DIRS="$GUIX_PROFILE/share:${XDG_DATA_DIRS:-/usr/local/share/:/us
 EOF
 }
 
+sys_create_shell_completion()
+{ # Symlink supported shell completions system-wide
+
+    var_guix=/var/guix/profiles/per-user/root/current-guix
+    bash_completion=/etc/bash_completion.d
+    zsh_completion=/usr/share/zsh/site-functions
+    fish_completion=/usr/share/fish/vendor_completions.d
+
+    { # Just in case
+        for dir_shell in $bash_completion $zsh_completion $fish_completion; do
+            [ -d "$dir_shell" ] || mkdir -p $dir_shell
+        done;
+
+        ln -sf ${var_guix}/etc/bash_completion.d/* "$bash_completion";
+        ln -sf ${var_guix}/share/zsh/site-functions/* "$zsh_completion";
+        ln -sf ${var_guix}/share/fish/vendor_completions.d/* "$fish_completion"; } &&
+        _msg "${PAS}installed shell completion"
+}
+
+
 welcome()
 {
     cat<<"EOF"
@@ -488,6 +537,7 @@ main()
     chk_gpg_keyring
     chk_init_sys
     chk_sys_arch
+    chk_sys_nscd
 
     _msg "${INF}system is ${ARCH_OS}"
 
@@ -502,6 +552,7 @@ main()
     sys_enable_guix_daemon
     sys_authorize_build_farms
     sys_create_init_profile
+    sys_create_shell_completion
 
     _msg "${INF}cleaning up ${tmp_path}"
     rm -r "${tmp_path}"

etc/news.scm

@@ -2,6 +2,11 @@
 ;;
 ;; Copyright © 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+;; Copyright © 2019, 2020 Miguel Ángel Arruga Vivas <rosen644835@gmail.com>
+;; Copyright © 2019, 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
+;; Copyright © 2019, 2020 Julien Lepiller <julien@lepiller.eu>
+;; Copyright © 2019, 2020 Florian Pelz <pelzflorian@pelzflorian.de>
+;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
 ;; Copyright © 2020 Mathieu Othacehe <m.othacehe@gmail.com>
 ;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@@ -13,8 +18,297 @@
 (channel-news
  (version 0)
 
+ (entry (commit "abd7a474615353149a44f4504f0b4b248dcc0716")
+        (title (en "New @option{--with-c-toolchain} package transformation option")
+               (de "Neue Paketumwandlungsoption @option{--with-c-toolchain}")
+               (fr "Nouvelle option de transformation @option{--with-c-toolchain}"))
+        (body
+         (en "The new @option{--with-c-toolchain} package transformation
+options provides an easy way for developers to rebuild their favorite packages
+with the C/C++ tool chain of their choice instead of the default one.
+
+For example, the following command rebuilds the @code{fftw} and @code{fftwf}
+packages as well as every package that depends on them, up to and including
+@code{octave-cli}, using GCC version 10 (currently GCC 7.5 is used by
+default):
+
+@example
+guix build octave-cli \\
+  --with-c-toolchain=fftw=gcc-toolchain@@10 \\
+  --with-c-toolchain=fftwf=gcc-toolchain@@10
+@end example
+
+Run @command{info \"(guix) Package Transformation Options\"} for more info.")
+         (de "Die neue Paketumwandlungsoption @option{--with-c-toolchain}
+bietet Entwicklern die Möglichkeit, leicht ihre Lieblingspakete mit der
+selbstgewählten Toolchain für C/C++ anstelle der vorgegebenen neu zu
+erstellen.
+
+Zum Beispiel werden mit folgendem Befehl die Pakete @code{fftw} und
+@code{fftwf} sowie alle davon abhängigen Pakete bis einschließlich
+@code{octave-cli} mit Version 10 der GCC erstellt (vorgegeben wäre zurzeit,
+GCC 7.5 zu benutzen):
+
+@example
+guix build octave-cli \\
+  --with-c-toolchain=fftw=gcc-toolchain@@10 \\
+  --with-c-toolchain=fftwf=gcc-toolchain@@10
+@end example
+
+Führen Sie für mehr Informationen @command{info \"(guix.de)
+Paketumwandlungsoptionen\"} aus.")
+         (fr "La nouvelle option de transformation de paquets
+@option{--with-c-toolchain} permet aux développeur·euses de recompiler leurs
+paquets préférés avec la chaîne d'outils C/C++ de leur choix à la place de
+celle par défaut.
+
+Par exemple, la commande ci-dessous recompile @code{fftw}, @code{fftwf} et
+tous les paquets qui en dépendent, jusqu'à @code{octave-cli} inclus, avec GCC
+10 (actuellement c'est GCC 7.5 qui est utilisé par défaut):
+
+@example
+guix build octave-cli \\
+  --with-c-toolchain=fftw=gcc-toolchain@@10 \\
+  --with-c-toolchain=fftwf=gcc-toolchain@@10
+@end example
+
+Voir @command{info \"(guix.fr) Options de transformation de paquets\"} pour
+plus de détails.")))
+
+ (entry (commit "8e1907a72430aa989125b053573ef0897c480697")
+        (title (en "Package transformation options now recorded in profiles")
+               (es "Las opciones de transformación de paquetes ahora se
+quedan registradas en el perfil")
+               (de "Paketumwandlungsoptionen werden nun in Profilen gesichert")
+               (fr "Options de transformation sauvegardées dans les profils"))
+        (body
+         (en "When installing packages in a profile, package transformation
+options such as @option{--with-input} are now recorded in the profile.  When
+you eventually run @command{guix upgrade}, those transformations will be
+automatically applied to the upgraded packages.
+
+Run @command{info \"(guix) Package Transformation Options\"} for more info.")
+         (es "Si durante la instalación de paquetes en un perfil se utilizaron
+opciones de transformación de paquetes, como por ejemplo
+@option{--with-input}, éstas se registran en el perfil. Cuando vuelva a
+ejecutar @command{guix upgrade}, dichas transformaciones se aplicarán
+automáticamente a los paquetes actualizados.
+
+Ejecute @command{info \"(guix.es) Opciones de transformación de paquetes\"}
+para obtener más información.")
+         (de "Wenn Sie ein Paket in ein Profil installieren, werden nun
+Paketumwandlungsoptionen wie @option{--with-input} im Profil gespeichert.
+Sobald Sie später @command{guix upgrade} ausführen, werden dieselben
+Umwandlungen automatisch auf die aktualisierten Pakete angewandt.
+
+Führen Sie für mehr Informationen @command{info \"(guix.de)
+Paketumwandlungsoptionen\"} aus.")
+         (fr "Lorsqu'on installe des paquets dans un profil, les options de
+transformation telles que @option{--with-input} sont désormais enregistrées
+dans le profil.  Quand on le met plus tard à jour avec @command{guix upgrade},
+ces transformations sont automatiquement appliquées aux nouveaux paquets.
+
+Voir @command{info \"(guix.fr) Options de transformation de paquets\"} pour
+plus de détails.")))
+
+ (entry (commit "313f492657f1d0863c641fa5ee7f5b7028e27c94")
+        (title (en "New @option{--image-type} option for @command{guix system disk-image}.")
+               (es "Nueva opción @option{--image-type} para @command{guix system disk-image}.")
+               (de "Neue Option @option{--image-type} für @command{guix system disk-image}.")
+               (fr "Nouvelle option @option{--image-type} pour @command{guix system disk-image}."))
+        (body
+         (en "The @option{--file-system-type} option for @command{guix system
+disk-image} command has been replaced by the new @option{--image-type} option.
+By default, @code{raw} disk images are produced, but @code{hurd-qcow2},
+@code{hurd-raw}, @code{uncompressed-iso9660} and @code{iso9660} image types
+are also available.
+
+The @option{--list-image-types} option lists all the available image types.")
+         (es "La opción @option{--file-system-type} de @command{guix system
+disk-image} se ha sustituido por la nueva opción @option{--image-type}.  De
+manera predeterminada se producen imágenes en formato crudo (@code{raw}) pero
+también están disponibles los tipos de imagen @code{hurd-qcow2},
+@code{hurd-raw}, @code{uncompressed-iso9660} y @code{iso9660}.
+
+La opción @option{--list-image-types} muestra una lista con todos los tipos
+de imagen disponibles.")
+         (de "Anstelle der Befehlszeilenoption @option{--file-system-type} für
+@command{guix system disk-image} gibt es nun die neue Option
+@option{--image-type}.  In der Vorgabeeinstellung @code{raw} werden rohe
+Disk-Images erzeugt, aber es können auch die Abbildtypen @code{hurd-qcow2},
+@code{hurd-raw}, @code{uncompressed-iso9660} und @code{iso9660} ausgewählt
+werden.
+
+Mit der Option @option{--list-image-types} werden alle verfügbaren Abbildtypen
+aufgelistet.")
+         (fr "L'option @option{--file-system-type} pour la commande
+@command{guix system disk-image} a été remplacée par la nouvelle option
+@option{--image-type}. Par défaut, l'option @code{raw}, produisant des images
+disque brutes est sélectionnée. Les options @code{hurd-qcow2},
+@code{hurd-raw}, @code{uncompressed-iso9660} et @code{iso9660} sont également
+disponibles.
+
+La nouvelle option @option{--list-image-types} énumère les types d'image
+disponibles.")))
+
+ (entry (commit "8819551c8d2a12cd4e84e09b51e434d05a012c9d")
+        (title (en "Package transformations now apply to implicit inputs")
+               (es "Las transformaciones de paquetes ahora afectan también
+a las dependencias implícitas")
+               (de "Paketumwandlungen betreffen jetzt auch implizite Eingaben")
+               (fr "Les transformations de paquets s'appliquent aux
+dépendances implicites"))
+        (body
+         (en "Package transformation options such as @option{--with-branch},
+@option{--with-input}, and so on now apply to implicit inputs---previously
+only a package's explicit inputs would be affected.  This allows for things
+such as replacing the Python dependency of a package that uses
+@code{python-build-system}:
+
+@example
+guix install --with-input=python=python2 python-itsdangerous
+@end example
+
+Another example is grafting a different version of the GNU C
+Library (@code{glibc} is an implicit input of almost all the packages and is
+``deep down'' in the dependency graph):
+
+@example
+guix build --with-graft=glibc=glibc@@2.31 hello
+@end example
+
+Run @command{info \"(guix) Package Transformation Options\"} for more
+info.")
+         (es "Las opciones de transformación de paquetes como
+@option{--with-branch}, @option{--with-input}, etcétera, ahora también
+influyen en las entradas implícitas---antes únicamente las entradas explícitas
+del paquete se veían afectadas. Esto permite, por ejemplo, sustituir la
+dependencia en python de un paquete que use @code{python-build-system}:
+
+@example
+guix install --with-input=python=python2 python-itsdangerous
+@end example
+
+Otro ejemplo podría ser el injerto de una versión diferente de la biblioteca
+de C de GNU (@code{glibc} es una entrada implícita de casi todos los paquetes
+y ``muy abajo'' en el grafo de dependencias):
+
+@example
+guix build --with-graft=glibc=glibc@@2.31 hello
+@end example
+
+Ejecute @command{info \"(guix.es) Opciones de transformación de paquetes\"}
+para obtener más información.")
+         (de "Paketumwandlungsoptionen wie @option{--with-branch},
+@option{--with-input} und so weiter betreffen nun auch implizite Eingaben —
+zuvor haben sie sich nur auf die expliziten Eingaben eines Pakets
+ausgewirkt. Dadurch kann jetzt zum Beispiel die Python-Abhängigkeit eines
+Pakets, welches @code{python-build-system} benutzt, ersetzt werden:
+
+@example
+guix install --with-input=python=python2 python-itsdangerous
+@end example
+
+Ein weiteres Beispiel ist, mit einer anderen Version der GNU-C-Bibliothek zu
+veredeln (@code{glibc} ist eine implizite Eingabe fast aller Pakete und steckt
+„ganz tief“ im Abhängigkeitsgraphen):
+
+@example
+guix build --with-graft=glibc=glibc@@2.31 hello
+@end example
+
+Führen Sie für mehr Informationen @command{info \"(guix.de)
+Paketumwandlungsoptionen\"} aus.")
+         (fr "Les options de transformation de paquets telles que
+@option{--with-branch} et @option{--with-input} s'appliquent désormais aux
+dépendances implicites — jusque là seules les dépendances explicites des
+paquets étaient prises en compte.  Cela permet certaines choses telles que
+remplacer la dépendance sur Python d'un paquet utilisant
+@code{python-build-system} :
+
+@example
+guix install --with-input=python=python2 python-itsdangerous
+@end example
+
+Un autre exemple est la possibilité de greffer une version différente de la
+bibliothèque C GNU (la @code{glibc} est une dépendance implicite de tous les
+paquets et se trouve « tout en bas » du graphe de dépendance) :
+
+@example
+guix build --with-graft=glibc=glibc@@2.31 hello
+@end example
+
+Voir @command{info \"(guix.fr) Options de transformation de paquets\"} pour
+plus de détails.")))
+
+ (entry (commit "f458cfbcc54ed87b1a87dd9e150ea276f17eab74")
+        (title (en "New @option{--without-tests} transformation option")
+               (es "Nueva opción de transformación @option{--without-tests}")
+               (de "Neue Paketumwandlungsoption @option{--without-tests}")
+               (fr "Nouvelle option de transformation @option{--without-tests}"))
+        (body
+         (en "The new @option{--without-tests} package transformation option
+instructs Guix to skip the test suite of a given package.  In the example
+below, @code{guile-gcrypt} is built using a variant of @code{automake} itself
+built without running its (lengthy) test suite:
+
+@example
+guix build guile-gcrypt --without-tests=automake
+@end example
+
+This is primarily useful as a way to speed up development cycles, or to work
+around flaky test suites---skipping tests can hide real issues, so use with
+care.  Run @command{info \"(guix) Package Transformation Options\"} for more
+info.")
+         (es "La nueva opción de transformación de paquetes
+@option{--without-tests} indica a Guix que omita la batería de pruebas del
+paquete proporcionado. En el siguiente ejemplo @code{guile-gcrypt} se
+construye usando una variación de @code{automake}, la cual se ha construido
+sin ejecutar su (larga) batería de pruebas:
+
+@example
+guix build guile-gcrypt --without-tests=automake
+@end example
+
+Esto es principalmente útil como una forma de acelerar ciclos de desarrollo o
+de omitir temporalmente baterías de pruebas problemáticas---omitir las pruebas
+puede ocultar problemas reales, por lo que debe usarse con precaución.
+Ejecute @command{info \"(guix.es) Opciones de transformación de paquetes\"}
+para obtener más información.")
+         (de "Mit der neuen Paketumwandlungsoption @option{--without-tests}
+wird Guix angewiesen, den Testkatalog des angegebenen Pakets zu
+überspringen. Im folgenden Beispiel wird @code{guile-gcrypt} mit einer
+Variante von @code{automake} erstellt, die wiederum ohne Durchlauf ihres (viel
+Zeit in Anspruch nehmenden) Testkatalogs erstellt wird:
+
+@example
+guix build guile-gcrypt --without-tests=automake
+@end example
+
+Der hauptsächliche Nutzen liegt in der Beschleunigung von Entwicklungszyklen
+oder im Umgehen unzuverlässiger Testkataloge. Allerdings kann das Überspringen
+dazu führen, dass echte Probleme verborgen bleiben. Setzen Sie es mit Bedacht
+ein. Führen Sie @command{info \"(guix.de) Paketumwandlungsoptionen\"} aus, um
+mehr Informationen zu erhalten.")
+         (fr "La nouvelle option de transformation de paquets
+@option{--without-tests} demande à Guix de sauter la suite de tests d'un
+paquet.  Dans l'exemple ci-dessous, @code{guile-gcrypt} est construit en
+utilisant une variante de @code{automake} construite sans lancer sa suite de
+tests :
+
+@example
+guix build guile-gcrypt --without-tests=automake
+@end example
+
+Cette option est surtout intéressante pour raccourcir le cycle de
+développement ou pour contourner une suite de tests qui n'est pas
+fiable — sauter les tests peut cacher des vrais problèmes, à utiliser avec
+précaution donc.  Voir @command{info \"(guix.fr) Options de transformation de
+paquets\"} pour plus de détails.")))
+
  (entry (commit "a98712785e0b042a290420fd74e5a4a5da4fc68f")
         (title (en "New @command{guix git authenticate} command")
+               (es "Nueva orden @command{guix git authenticate}")
                (de "Neuer Befehl @command{guix git authenticate}")
                (fr "Nouvelle commande @command{guix git authenticate}"))
         (body
@@ -30,6 +324,20 @@ to allow people to authenticate code fetched from your repository.
 Run @command{info \"(guix) Invoking guix git authenticate\"} for more info,
 and see @uref{https://guix.gnu.org/blog/2020/securing-updates/} for details on
 these mechanisms.")
+         (es "La nueva orden @command{guix git authenticate} comprueba la
+validez de un repositorio git verificando las firmas de las revisiones y
+comprobando que todas las firmas están autorizadas, exactamente igual que
+@command{guix pull}.
+
+Esta orden es principalmente útil para desarrolladoras de canales. Permite
+asegurar, antes de subir nada al repositorio remoto, que el canal contiene
+únicamente revisiones firmadas por claves autorizadas. No obstante esta orden
+es útil siempre que use git y quiera que otras personas puedan verificar el
+código obtenido de su repositorio.
+
+Ejecute @command{info \"(guix.es) Invocación de guix git authenticate\"}
+para obtener más información y vea detalles sobre estos mecanismos en
+ @uref{https://guix.gnu.org/blog/2020/securing-updates/}.")
          (de "Mit dem neuen Befehl @command{guix git authenticate} können Sie
 ein Git-Repository authentifizieren. Dazu werden alle Commit-Signaturen
 verifiziert und geprüft, dass jede von einer autorisierten Quelle kommt, genau
@@ -62,6 +370,7 @@ pour en savoir plus sur ces mécanismes.")))
 
  (entry (commit "43badf261f4688c8a7a7a9004a4bff8acb205835")
         (title (en "@command{guix pull} authenticates channels")
+               (es "@command{guix pull} verifica los canales")
                (de "@command{guix pull} authentifiziert Kanäle")
                (fr "@command{guix pull} authentifie les canaux"))
         (body
@@ -74,6 +383,16 @@ repository and from attempts to ship malicious code to users.
 
 This feature is currently limited to the @code{guix} channel but will soon be
 available to third-party channel authors.")
+         (es "Las ordenes @command{guix pull} y @command{guix time-machine}
+ahora verifican el código fuente que obtienen, a menos que se proporcione la
+opción @option{--disable-authentication}. Lo que esto significa es que Guix se
+asegura de que cada revisión que recibe está firmada criptográficamente por
+una desarrolladora autorizada. Esto le protege de intentos de modificación del
+repositorio de Guix y de entregas de código con malas intenciones sobre las
+usuarias.
+
+Esta característica está limitada actualmente al canal @code{guix} pero pronto
+estará disponible para autoras de canales independientes.")
          (de "Die Befehle @command{guix pull} und @command{guix time-machine}
 prüfen nun die Authentizität des heruntergeladenen Quellcodes, außer wenn die
 neue Befehlszeilenoption @option{--disable-authentication} angegeben
@@ -97,6 +416,7 @@ Cette fonctionnalité n'est actuellement disponible que pour le canal
 
  (entry (commit "c924e541390f9595d819edc33c19d979917c15ec")
         (title (en "@command{guix repl} adds support for running Guile scripts")
+               (es "@command{guix repl} puede ejecutar guiones de Guile")
                (de "@command{guix repl} kann Guile-Skripte ausführen")
                (fr "@command{guix repl} permet d'exécuter des scripts en langage Guile"))
         (body
@@ -110,6 +430,18 @@ guix repl -- my-script,scm --option1 --option2=option-arg arg1 arg2
 @end example
 
 Run @command{info \"(guix) Invoking guix repl\"} for more information.")
+         (es "La orden @command{guix repl} ahora se puede usar para
+ejecutar guiones de Guile. En comparación con únicamente la ejecución
+de la orden @command{guile}, @command{guix repl} garantiza que todos
+los módulos de Guix y sus dependencias están disponibles en la ruta
+ de búsqueda. Los guiones se ejecutan de este modo:
+
+@example
+guix repl -- mi-guion.scm --opcion1 --opcion2=param-op2 param1 param2
+@end example
+
+Ejecute @command{info \"(guix.es) Invocación de guix repl\"} para obtener
+más información.")
          (de "Der Befehl @command{guix repl} kann jetzt zur Ausführung von
 Guile-Skripten verwendet werden.  Im Vergleich zum Befehl
 @command{guile} garantiert @command{guix repl}, dass alle Guix-Module und
@@ -136,6 +468,7 @@ Exécutez @command{info \"(guix.fr) Invoquer guix repl\"} pour plus d'informatio
 
  (entry (commit "b460ba7992a0b4af2ddb5927dcf062784539ef7b")
         (title (en "Add support to boot from a Btrfs subvolume")
+               (es "Implementado el arranque desde un subvolumen de Btrfs")
                (de "Unterstützung für Systemstart von einem
 Btrfs-Unterlaufwerk hinzugefügt")
                (fr "Ajout du support pour démarrer depuis un sous-volume Btrfs")
@@ -146,6 +479,11 @@ operating system declaration now takes into account the use of a Btrfs
 subvolume for the partition holding @file{/gnu/store}.  Run the command
 @command{info \"(guix) Btrfs file system\"} for more information and
 examples.")
+         (es "El fichero de configuración de GRUB producido por la
+declaración de sistema operativo ahora tiene en cuenta el uso de
+subvolúmenes de Btrfs en la partición que contiene @file{/gnu/store}.
+Ejecute la orden @command{info \"(guix.es) Sistema de ficheros Btrfs\"}
+ para obtener más información y ejemplos.")
          (de "Für die Erzeugung einer GRUB-Konfigurationsdatei aus einer
 Betriebssystemdeklaration kann jetzt ein Btrfs-Unterlaufwerk („Subvolume“) für
 die Partition mit @file{/gnu/store} angegeben werden.  Führen Sie
@@ -165,6 +503,8 @@ voorbeelden.")))
  (entry (commit "6456232164890dbf5aa20394ee24637feb4b7b9e")
         (title (en "@command{guix pack -RR} introduces a new execution
 engine")
+               (es "@command{guix pack -RR} introduce un nuevo motor
+de ejecución")
                (de "@command{guix pack -RR} führt neuen Ausführungstreiber
 ein"))
         (body
@@ -185,6 +525,26 @@ export GUIX_EXECUTION_ENGINE
 @end example
 
 Run @command{info \"(guix) Invoking guix pack\"} for more information.")
+         (es "La orden @command{guix pack -RR} le permite crear un
+archivador tar que contiene @dfn{binarios reposicionables}. Hasta ahora
+dichos binarios dependían o bien de los ``espacios de nombres de usuarias
+sin privilegios'' de Linux o en PRoot, cuando estos no estaban
+implementados. No obstante, PRoot introduce una sobrecarga significativa
+en algunos escenarios de trabajo.
+
+Para estos casos @command{guix pack -RR} introduce una tercera opción
+basada en una extensión al enlazador de tiempo de ejecución de GNU (ld.so)
+y en Fakechroot, lo que conlleva muy poca sobrecarga. Puede seleccionar
+la opción más rápida cuando ejecute un binario reposicionable de esta
+manera:
+
+@example
+GUIX_EXECUTION_ENGINE=performance
+export GUIX_EXECUTION_ENGINE
+@end example
+
+Ejecute @command{info \"(guix.es) Invocación de guix pack\"} para
+obtener más información.")
          (de "Mit dem Befehl @command{guix pack -RR} können Sie einen Tarball
 mit @dfn{verschieblichen Binärdateien} erzeugen (englisch „Relocatable
 Binaries“).  Bisher wurden diese entweder in „unprivilegierten
@@ -209,6 +569,7 @@ mehr wissen wollen.")))
 
  (entry (commit "88a96c568c47c97d05d883ada5afbc4e1200b10f")
         (title (en "New @option{--path} option for @command{guix graph}")
+               (es "Nueva opción @option{--path} para @command{guix graph}")
                (de "Neue Option @option{--path} für @command{guix graph}"))
         (body
          (en "The @command{guix graph} command has a new @option{--path}
@@ -221,6 +582,18 @@ guix graph --path libreoffice libunistring
 @end example
 
 Run @code{info \"(guix) Invoking guix graph\"} for more information.")
+         (es "La orden @command{guix graph} tiene una nueva opción
+@option{--path} que le indica que debe mostrar la ruta más corta entre dos
+paquetes, derivaciones o elementos del almacén. Por ejemplo, la siguiente
+orden muestra la ruta más corta desde el paquete @code{libreoffice} hasta
+@code{libunistring}:
+
+@example
+guix graph --path libreoffice libunistring
+@end example
+
+Ejecute @code{info \"(guix.es) Invocación de guix graph\"} para obtener más
+información.")
          (de "Der Befehl @command{guix graph} verfügt über eine neue
 Befehlszeilenoption @option{--path}, die ihn den kürzesten Pfad zwischen zwei
 Paketen, Ableitungen oder Store-Objekten ausgeben lässt.  Zum Beispiel zeigt

etc/openrc/guix-daemon.in

@@ -0,0 +1,28 @@
+#!/sbin/openrc-run
+# GNU Guix --- Functional package management for GNU
+# Copyright © 2020 Morgan Smith <Morgan.J.Smith@outlook.com>
+#
+# 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/>.
+
+export GUIX_LOCPATH=@localstatedir@/guix/profiles/per-user/root/guix-profile/lib/locale
+export LC_ALL=en_US.utf8
+command="@localstatedir@/guix/profiles/per-user/root/current-guix/bin/guix-daemon"
+command_args="--build-users-group=guixbuild"
+command_background="yes"
+pidfile="/var/run/guix-daemon.pid"
+
+output_log="/var/log/guix-daemon-stdout.log"
+error_log="/var/log/guix-daemon-stderr.log"

etc/release-manifest.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2020 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -53,6 +54,7 @@ TARGET."
   (append (map specification->package
                '("xorg-server" "xfce" "gnome" "mate" "enlightenment"
                  "openbox" "awesome" "i3-wm" "ratpoison"
+                 "emacs" "emacs-exwm" "emacs-desktop-environment"
                  "xlockmore" "slock" "libreoffice"
                  "connman" "network-manager" "network-manager-applet"
                  "openssh" "ntp" "tor"

gnu/bootloader/grub.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017, 2020 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2019, 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2019 Miguel Ángel Arruga Vivas <rosen644835@gmail.com>
 ;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2020 Stefan <stefan-guix@vodafonemail.de>
 ;;;
@@ -23,14 +24,17 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu bootloader grub)
+  #:use-module (guix build union)
   #:use-module (guix records)
-  #:use-module ((guix utils) #:select (%current-system))
+  #:use-module (guix store)
+  #:use-module (guix utils)
   #:use-module (guix gexp)
   #:use-module (gnu artwork)
   #:use-module (gnu bootloader)
   #:use-module (gnu system uuid)
   #:use-module (gnu system file-systems)
   #:use-module (gnu system keyboard)
+  #:use-module (gnu system locale)
   #:use-module (gnu packages bootloaders)
   #:autoload   (gnu packages gtk) (guile-cairo guile-rsvg)
   #:autoload   (gnu packages xorg) (xkeyboard-config)
@@ -46,8 +50,11 @@
             grub-theme-color-highlight
             grub-theme-gfxmode
 
+            install-grub-efi-netboot
+
             grub-bootloader
             grub-efi-bootloader
+            grub-efi-netboot-bootloader
             grub-mkrescue-bootloader
             grub-minimal-bootloader
 
@@ -297,9 +304,11 @@ code."
                  (file-system-label->string label)))
         ((? (lambda (device)
               (and (string? device) (string-contains device ":/"))) nfs-uri)
-         ;; This assumes that if your root file system is on NFS, then
+         ;; If the device is an NFS share, then we assume that the expected
-         ;; you also want to load your grub extra files, kernel and initrd
+         ;; file on that device (e.g. the GRUB background image or the kernel)
-         ;; from there.
+         ;; has to be loaded over the network.  Otherwise we would need an
+         ;; additional device information for some local disk to look for that
+         ;; file, which we do not have.
          ;;
          ;; We explicitly set "root=(tftp)" here even though if grub.cfg
          ;; had been loaded via TFTP, Grub would have set "root=(tftp)"
@@ -327,6 +336,7 @@ code."
 
 (define* (grub-configuration-file config entries
                                   #:key
+                                  (locale #f)
                                   (system (%current-system))
                                   (old-entries '())
                                   store-directory-prefix)
@@ -391,6 +401,20 @@ menuentry ~s {
                  #:store-directory-prefix store-directory-prefix
                  #:port #~port)))
 
+  (define locale-config
+    #~(let ((locale #$(and locale
+                           (locale-definition-source
+                            (locale-name->definition locale)))))
+        (when locale
+          (format port "\
+# Localization configuration.
+if search --file --set boot_partition /grub/grub.cfg; then
+    set locale_dir=(${boot_partition})/grub/locale
+else
+    set locale_dir=/boot/grub/locale
+fi
+set lang=~a~%" locale))))
+
   (define keyboard-layout-config
     (let* ((layout (bootloader-configuration-keyboard-layout config))
            (grub   (bootloader-package
@@ -415,6 +439,7 @@ keymap ~a~%" #$keymap))))
 # will be lost upon reconfiguration.
 ")
           #$(sugar)
+          #$locale-config
           #$keyboard-layout-config
           (format port "
 set default=~a
@@ -528,6 +553,99 @@ fi~%"))))
                       "--bootloader-id=Guix"
                       "--efi-directory" target-esp))))
 
+(define (install-grub-efi-netboot subdir)
+  "Define a grub-efi-netboot bootloader installer for installation in SUBDIR,
+which is usually efi/Guix or efi/boot."
+  (let* ((system (string-split (nix-system->gnu-triplet
+                                (or (%current-target-system)
+                                    (%current-system)))
+                               #\-))
+         (arch (first system))
+         (boot-efi-link (match system
+                          ;; These are the supportend systems and the names
+                          ;; defined by the UEFI standard for removable media.
+                          (("i686" _ ...)        "/bootia32.efi")
+                          (("x86_64" _ ...)      "/bootx64.efi")
+                          (("arm" _ ...)         "/bootarm.efi")
+                          (("aarch64" _ ...)     "/bootaa64.efi")
+                          (("riscv" _ ...)       "/bootriscv32.efi")
+                          (("riscv64" _ ...)     "/bootriscv64.efi")
+                          ;; Other systems are not supported, although defined.
+                          ;; (("riscv128" _ ...) "/bootriscv128.efi")
+                          ;; (("ia64" _ ...)     "/bootia64.efi")
+                          ((_ ...)               #f)))
+         (core-efi (string-append
+                    ;; This is the arch dependent file name of GRUB, e.g.
+                    ;; i368-efi/core.efi or arm64-efi/core.efi.
+                    (match arch
+                      ("i686"    "i386")
+                      ("aarch64" "arm64")
+                      ("riscv"   "riscv32")
+                      (_         arch))
+                    "-efi/core.efi")))
+    (with-imported-modules
+     '((guix build union))
+     #~(lambda (bootloader target mount-point)
+         "Install the BOOTLOADER, which must be the package grub, as e.g.
+bootx64.efi or bootaa64.efi into SUBDIR, which is usually efi/Guix or efi/boot,
+below the directory TARGET for the system whose root is mounted at MOUNT-POINT.
+
+MOUNT-POINT is the last argument in 'guix system init /etc/config.scm mnt/point'
+or '/' for other 'guix system' commands.
+
+TARGET is the target argument given to the bootloader-configuration in
+
+(operating-system
+ (bootloader (bootloader-configuration
+              (target \"/boot\")
+              …))
+ …)
+
+TARGET is required to be an absolute directory name, usually mounted via NFS,
+and finally needs to be provided by a TFTP server as the TFTP root directory.
+
+GRUB will load tftp://server/SUBDIR/grub.cfg and this file will instruct it to
+load more files from the store like tftp://server/gnu/store/…-linux…/Image.
+
+To make this possible two symlinks will be created. The first symlink points
+relatively form MOUNT-POINT/TARGET/SUBDIR/grub.cfg to
+MOUNT-POINT/boot/grub/grub.cfg, and the second symlink points relatively from
+MOUNT-POINT/TARGET/%store-prefix to MOUNT-POINT/%store-prefix.
+
+It is important to note that these symlinks need to be relativ, as the absolute
+paths on the TFTP server side are unknown.
+
+It is also important to note that both symlinks will point outside the TFTP root
+directory and that the TARGET/%store-prefix symlink makes the whole store
+accessible via TFTP. Possibly the TFTP server must be configured
+to allow accesses outside its TFTP root directory. This may need to be
+considered for security aspects."
+         (use-modules ((guix build union) #:select (symlink-relative)))
+         (let* ((net-dir (string-append mount-point target "/"))
+                (sub-dir (string-append net-dir #$subdir "/"))
+                (store (string-append mount-point (%store-prefix)))
+                (store-link (string-append net-dir (%store-prefix)))
+                (grub-cfg (string-append mount-point "/boot/grub/grub.cfg"))
+                (grub-cfg-link (string-append sub-dir (basename grub-cfg)))
+                (boot-efi-link (string-append sub-dir #$boot-efi-link)))
+           ;; Prepare the symlink to the store.
+           (mkdir-p (dirname store-link))
+           (false-if-exception (delete-file store-link))
+           (symlink-relative store store-link)
+           ;; Prepare the symlink to the grub.cfg, which points into the store.
+           (mkdir-p (dirname grub-cfg-link))
+           (false-if-exception (delete-file grub-cfg-link))
+           (symlink-relative grub-cfg grub-cfg-link)
+           ;; Install GRUB, which refers to the grub.cfg, with support for
+           ;; encrypted partitions,
+           (setenv "GRUB_ENABLE_CRYPTODISK" "y")
+           (invoke/quiet (string-append bootloader "/bin/grub-mknetdir")
+                         (string-append "--net-directory=" net-dir)
+                         (string-append "--subdir=" #$subdir))
+           ;; Prepare the bootloader symlink, which points to core.efi of GRUB.
+           (false-if-exception (delete-file boot-efi-link))
+           (symlink #$core-efi boot-efi-link))))))
+
 
 
 ;;;
@@ -560,6 +678,12 @@ fi~%"))))
    (name 'grub-efi)
    (package grub-efi)))
 
+(define grub-efi-netboot-bootloader
+  (bootloader
+   (inherit grub-efi-bootloader)
+   (name 'grub-efi-netboot-bootloader)
+   (installer (install-grub-efi-netboot "efi/Guix"))))
+
 (define grub-mkrescue-bootloader
   (bootloader
    (inherit grub-efi-bootloader)

gnu/bootloader/u-boot.scm

@@ -45,7 +45,7 @@
             u-boot-wandboard-bootloader))
 
 (define install-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (if bootloader
         (error "Failed to install U-Boot"))))
 
@@ -56,74 +56,74 @@
   ;; the MLO and is expected at 0x60000.  Write both first stage ("MLO") and
   ;; second stage ("u-boot.img") images, read in BOOTLOADER directory, to the
   ;; specified DEVICE.
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((mlo (string-append bootloader "/libexec/MLO"))
             (u-boot (string-append bootloader "/libexec/u-boot.img")))
         (write-file-on-device mlo (* 256 512)
-                              device (* 256 512))
+                              image (* 256 512))
         (write-file-on-device u-boot (* 1024 512)
-                              device (* 768 512)))))
+                              image (* 768 512)))))
 
 (define install-allwinner-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((u-boot (string-append bootloader
                                    "/libexec/u-boot-sunxi-with-spl.bin")))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 8 1024)))))
+                              image (* 8 1024)))))
 
 (define install-allwinner64-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((spl (string-append bootloader "/libexec/spl/sunxi-spl.bin"))
             (u-boot (string-append bootloader "/libexec/u-boot.itb")))
         (write-file-on-device spl (stat:size (stat spl))
-                              device (* 8 1024))
+                              image (* 8 1024))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 40 1024)))))
+                              image (* 40 1024)))))
 
 (define install-imx-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((spl (string-append bootloader "/libexec/SPL"))
             (u-boot (string-append bootloader "/libexec/u-boot.img")))
         (write-file-on-device spl (stat:size (stat spl))
-                              device (* 1 1024))
+                              image (* 1 1024))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 69 1024)))))
+                              image (* 69 1024)))))
 
 (define install-puma-rk3399-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((spl (string-append bootloader "/libexec/u-boot-spl.rksd"))
             (u-boot (string-append bootloader "/libexec/u-boot.itb")))
         (write-file-on-device spl (stat:size (stat spl))
-                              device (* 64 512))
+                              image (* 64 512))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 512 512)))))
+                              image (* 512 512)))))
 
 (define install-firefly-rk3399-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((idb (string-append bootloader "/libexec/idbloader.img"))
             (u-boot (string-append bootloader "/libexec/u-boot.itb")))
         (write-file-on-device idb (stat:size (stat idb))
-                              device (* 64 512))
+                              image (* 64 512))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 16384 512)))))
+                              image (* 16384 512)))))
 
 (define install-rock64-rk3328-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((idb (string-append bootloader "/libexec/idbloader.img"))
             (u-boot (string-append bootloader "/libexec/u-boot.itb")))
         (write-file-on-device idb (stat:size (stat idb))
-                              device (* 64 512))
+                              image (* 64 512))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 16384 512)))))
+                              image (* 16384 512)))))
 
 (define install-rockpro64-rk3399-u-boot
-  #~(lambda (bootloader device mount-point)
+  #~(lambda (bootloader root-index image)
       (let ((idb (string-append bootloader "/libexec/idbloader.img"))
             (u-boot (string-append bootloader "/libexec/u-boot.itb")))
         (write-file-on-device idb (stat:size (stat idb))
-                              device (* 64 512))
+                              image (* 64 512))
         (write-file-on-device u-boot (stat:size (stat u-boot))
-                              device (* 16384 512)))))
+                              image (* 16384 512)))))
 
 (define install-pinebook-pro-rk3399-u-boot install-rockpro64-rk3399-u-boot)
 
@@ -138,28 +138,29 @@
    (inherit extlinux-bootloader)
    (name 'u-boot)
    (package #f)
-   (installer install-u-boot)))
+   (installer #f)
+   (disk-image-installer install-u-boot)))
 
 (define u-boot-beaglebone-black-bootloader
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-am335x-boneblack)
-   (installer install-beaglebone-black-u-boot)))
+   (disk-image-installer install-beaglebone-black-u-boot)))
 
 (define u-boot-allwinner-bootloader
   (bootloader
    (inherit u-boot-bootloader)
-   (installer install-allwinner-u-boot)))
+   (disk-image-installer install-allwinner-u-boot)))
 
 (define u-boot-allwinner64-bootloader
   (bootloader
    (inherit u-boot-bootloader)
-   (installer install-allwinner64-u-boot)))
+   (disk-image-installer install-allwinner64-u-boot)))
 
 (define u-boot-imx-bootloader
   (bootloader
    (inherit u-boot-bootloader)
-   (installer install-imx-u-boot)))
+   (disk-image-installer install-imx-u-boot)))
 
 (define u-boot-nintendo-nes-classic-edition-bootloader
   (bootloader
@@ -196,7 +197,7 @@
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-firefly-rk3399)
-   (installer install-firefly-rk3399-u-boot)))
+   (disk-image-installer install-firefly-rk3399-u-boot)))
 
 (define u-boot-mx6cuboxi-bootloader
   (bootloader
@@ -232,25 +233,25 @@
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-puma-rk3399)
-   (installer install-puma-rk3399-u-boot)))
+   (disk-image-installer install-puma-rk3399-u-boot)))
 
 (define u-boot-rock64-rk3328-bootloader
   ;; SD and eMMC use the same format
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-rock64-rk3328)
-   (installer install-rock64-rk3328-u-boot)))
+   (disk-image-installer install-rock64-rk3328-u-boot)))
 
 (define u-boot-rockpro64-rk3399-bootloader
   ;; SD and eMMC use the same format
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-rockpro64-rk3399)
-   (installer install-rockpro64-rk3399-u-boot)))
+   (disk-image-installer install-rockpro64-rk3399-u-boot)))
 
 (define u-boot-pinebook-pro-rk3399-bootloader
   ;; SD and eMMC use the same format
   (bootloader
    (inherit u-boot-bootloader)
    (package u-boot-pinebook-pro-rk3399)
-   (installer install-pinebook-pro-rk3399-u-boot)))
+   (disk-image-installer install-pinebook-pro-rk3399-u-boot)))

gnu/build/bootloader.scm

@@ -22,6 +22,8 @@
   #:use-module (guix utils)
   #:use-module (ice-9 binary-ports)
   #:use-module (ice-9 format)
+  #:use-module (rnrs io ports)
+  #:use-module (rnrs io simple)
   #:export (write-file-on-device
             install-efi-loader))
 
@@ -35,11 +37,14 @@
   (call-with-input-file file
     (lambda (input)
       (let ((bv (get-bytevector-n input size)))
-        (call-with-output-file device
+        (call-with-port
-          (lambda (output)
+         (open-file-output-port device
-            (seek output offset SEEK_SET)
+                                (file-options no-truncate no-create)
-            (put-bytevector output bv))
+                                (buffer-mode block)
-          #:binary #t)))))
+                                (native-transcoder))
+         (lambda (output)
+           (seek output offset SEEK_SET)
+           (put-bytevector output bv)))))))
 
 
 ;;;

gnu/build/hurd-boot.scm

@@ -211,6 +211,9 @@ set."
       ("dev/vcs"     ("/hurd/console"))
       ("dev/tty"     ("/hurd/magic"    "tty")               #o666)
 
+      ;; 'fd_to_filename' in libc expects it.
+      ("dev/fd"      ("/hurd/magic"    "--directory" "fd")  #o555)
+
       ("dev/tty1"    ("/hurd/term"     "/dev/tty1" "hurdio" "/dev/vcs/1/console")
                                                             #o666)
       ("dev/tty2"    ("/hurd/term"     "/dev/tty2" "hurdio" "/dev/vcs/2/console")
@@ -240,10 +243,10 @@ set."
   (for-each scope-set-translator devices)
 
   (false-if-EEXIST (symlink "/dev/random" (scope "dev/urandom")))
-  (mkdir* "dev/fd")
   (false-if-EEXIST (symlink "/dev/fd/0" (scope "dev/stdin")))
   (false-if-EEXIST (symlink "/dev/fd/1" (scope "dev/stdout")))
   (false-if-EEXIST (symlink "/dev/fd/2" (scope "dev/stderr")))
+  (false-if-EEXIST (symlink "crash-dump-core" (scope "servers/crash")))
 
   ;; Make sure /etc/mtab is a symlink to /proc/mounts.
   (false-if-exception (delete-file (scope "etc/mtab")))

gnu/build/image.scm

@@ -37,6 +37,7 @@
   #:use-module (srfi srfi-34)
   #:use-module (srfi srfi-35)
   #:export (make-partition-image
+            convert-disk-image
             genimage
             initialize-efi-partition
             initialize-root-partition
@@ -120,13 +121,22 @@ ROOT directory to populate the image."
       (format (current-error-port)
               "Unsupported partition type~%.")))))
 
-(define* (genimage config target)
+(define (convert-disk-image image format output)
+  "Convert IMAGE to OUTPUT according to the given FORMAT."
+  (case format
+    ((compressed-qcow2)
+     (begin
+       (invoke "qemu-img" "convert" "-c" "-f" "raw"
+               "-O" "qcow2" image output)))
+    (else
+     (copy-file image output))))
+
+(define* (genimage config)
   "Use genimage to generate in TARGET directory, the image described in the
 given CONFIG file."
   ;; genimage needs a 'root' directory.
   (mkdir "root")
-  (invoke "genimage" "--config" config
+  (invoke "genimage" "--config" config))
-          "--outputpath" target))
 
 (define* (register-closure prefix closure
                            #:key

gnu/build/linux-container.scm

@@ -170,7 +170,8 @@ for the process."
     (pivot-root root put-old)
     (chdir "/")
     (umount "real-root" MNT_DETACH)
-    (rmdir "real-root")))
+    (rmdir "real-root")
+    (chmod "/" #o755)))
 
 (define* (initialize-user-namespace pid host-uids
                                     #:key (guest-uid 0) (guest-gid 0))

gnu/build/secret-service.scm

@@ -35,44 +35,86 @@
 ;;;
 ;;; Code:
 
-(define* (secret-service-send-secrets port secret-root #:key (retry 60))
+(define-syntax log
-  "Copy all files under SECRET-ROOT using TCP to secret-service listening at
+  (lambda (s)
-local PORT.  If connect fails, sleep 1s and retry RETRY times."
+    "Log the given message."
+    (syntax-case s ()
+      ((_ fmt args ...)
+       (with-syntax ((fmt (string-append "secret service: "
+                                         (syntax->datum #'fmt))))
+         ;; Log to the current output port.  That way, when
+         ;; 'secret-service-send-secrets' is called from shepherd, output goes
+         ;; to syslog.
+         #'(format (current-output-port) fmt args ...))))))
 
+(define* (secret-service-send-secrets port secret-root
+                                      #:key (retry 60)
+                                      (handshake-timeout 120))
+  "Copy all files under SECRET-ROOT using TCP to secret-service listening at
+local PORT.  If connect fails, sleep 1s and retry RETRY times; once connected,
+wait for at most HANDSHAKE-TIMEOUT seconds for handshake to complete.  Return
+#f on failure."
   (define (file->file+size+mode file-name)
     (let ((stat (stat file-name))
           (target (substring file-name (string-length secret-root))))
       (list target (stat:size stat) (stat:mode stat))))
 
-  (format (current-error-port) "sending secrets to ~a~%" port)
+  (define (send-files sock)
-  (let ((sock (socket AF_INET SOCK_STREAM 0))
-        (addr (make-socket-address AF_INET INADDR_LOOPBACK port)))
-    ;; connect to wait for port
-    (let loop ((retry retry))
-      (catch 'system-error
-        (cute connect sock addr)
-        (lambda (key . args)
-          (when (zero? retry)
-            (apply throw key args))
-          (format (current-error-port) "retrying connection~%")
-          (sleep 1)
-          (loop (1- retry)))))
-
-    (format (current-error-port) "connected!  sending files in ~s %~"
-            secret-root)
     (let* ((files (if secret-root (find-files secret-root) '()))
            (files-sizes-modes (map file->file+size+mode files))
            (secrets `(secrets
                       (version 0)
                       (files ,files-sizes-modes))))
       (write secrets sock)
-      (for-each (compose (cute dump-port <> sock)
+      (for-each (lambda (file)
-                         (cute open-input-file <>))
+                  (call-with-input-file file
-                files))))
+                    (lambda (input)
+                      (dump-port input sock))))
+                files)))
+
+  (log "sending secrets to ~a~%" port)
+  (let ((sock (socket AF_INET SOCK_STREAM 0))
+        (addr (make-socket-address AF_INET INADDR_LOOPBACK port)))
+    ;; Connect to QEMU on the forwarded port.  The 'connect' call succeeds as
+    ;; soon as QEMU is ready, even if there's no server listening on the
+    ;; forward port inside the guest.
+    (let loop ((retry retry))
+      (catch 'system-error
+        (cute connect sock addr)
+        (lambda (key . args)
+          (when (zero? retry)
+            (apply throw key args))
+          (log "retrying connection [~a attempts left]~%"
+               (- retry 1))
+          (sleep 1)
+          (loop (1- retry)))))
+
+    (log "connected; waiting for handshake...~%")
+
+    ;; Wait for "hello" message from the server.  This is the only way to know
+    ;; that we're really connected to the server inside the guest.
+    (match (select (list sock) '() '() handshake-timeout)
+      (((_) () ())
+       (match (read sock)
+         (('secret-service-server ('version version ...))
+          (log "sending files from ~s...~%" secret-root)
+          (send-files sock)
+          (log "done sending files to port ~a~%" port)
+          (close-port sock)
+          secret-root)
+         (x
+          (log "invalid handshake ~s~%" x)
+          (close-port sock)
+          #f)))
+      ((() () ())                                 ;timeout
+       (log "timeout while sending files to ~a~%" port)
+       (close-port sock)
+       #f))))
 
 (define (secret-service-receive-secrets port)
   "Listen to local PORT and wait for a secret service client to send secrets.
-Write them to the file system."
+Write them to the file system.  Return the list of files installed on success,
+and #f otherwise."
 
   (define (wait-for-client port)
     ;; Wait for a TCP connection on PORT.  Note: We cannot use the
@@ -81,16 +123,26 @@ Write them to the file system."
     (let ((sock (socket AF_INET SOCK_STREAM 0)))
       (bind sock AF_INET INADDR_ANY port)
       (listen sock 1)
-      (format (current-error-port)
+      (log "waiting for secrets on port ~a...~%" port)
-              "waiting for secrets on port ~a...~%"
+      (match (select (list sock) '() '() 60)
-              port)
+        (((_) () ())
-      (match (accept sock)
+         (match (accept sock)
-        ((client . address)
+           ((client . address)
-         (format (current-error-port) "client connection from ~a~%"
+            (log "client connection from ~a~%"
                  (inet-ntop (sockaddr:fam address)
                             (sockaddr:addr address)))
+
+            ;; Send a "hello" message.  This allows the client running on the
+            ;; host to know that it's now actually connected to server running
+            ;; in the guest.
+            (write '(secret-service-server (version 0)) client)
+            (force-output client)
+            (close-port sock)
+            client)))
+        ((() () ())
+         (log "did not receive any secrets; time out~%")
          (close-port sock)
-         client))))
+         #f))))
 
   ;; TODO: Remove when (@ (guix build utils) dump-port) has a 'size'
   ;; parameter.
@@ -115,23 +167,24 @@ Write them to the file system."
       (('secrets ('version 0)
                  ('files ((files sizes modes) ...)))
        (for-each (lambda (file size mode)
-                   (format (current-error-port)
+                   (log "installing file '~a' (~a bytes)...~%"
-                           "installing file '~a' (~a bytes)...~%"
+                        file size)
-                           file size)
                    (mkdir-p (dirname file))
                    (call-with-output-file file
                      (lambda (output)
                        (dump port output size)
                        (chmod file mode))))
-                 files sizes modes))
+                 files sizes modes)
+       (log "received ~a secret files~%" (length files))
+       files)
       (_
-       (format (current-error-port)
+       (log "invalid secrets received~%")
-               "invalid secrets received~%")
        #f)))
 
-  (let* ((port (wait-for-client port))
+  (let* ((port   (wait-for-client port))
-         (result (read-secrets port)))
+         (result (and=> port read-secrets)))
-    (close-port port)
+    (when port
+      (close-port port))
     result))
 
 ;;; secret-service.scm ends here

gnu/build/shepherd.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020 Mathieu Othacehe <othacehe@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -196,11 +197,16 @@ namespace, in addition to essential bind-mounts such /proc."
                                       #:allow-other-keys
                                       #:rest args)
   "This is a variant of 'fork+exec-command' procedure, that joins the
-namespaces of process PID beforehand."
+namespaces of process PID beforehand.  If there is no support for containers,
-  (container-excursion* pid
+on Hurd systems for instance, fallback to direct forking."
-    (lambda ()
+  (let ((container-support?
-      (apply fork+exec-command command
+         (file-exists? "/proc/self/ns"))
-             (strip-keyword-arguments '(#:pid) args)))))
+        (fork-proc (lambda ()
+                     (apply fork+exec-command command
+                            (strip-keyword-arguments '(#:pid) args)))))
+    (if container-support?
+        (container-excursion* pid fork-proc)
+        (fork-proc))))
 
 ;; Local Variables:
 ;; eval: (put 'container-excursion* 'scheme-indent-function 1)

gnu/ci.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2017, 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2018, 2019 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2020 Julien Lepiller <julien@lepiller.eu>
 ;;;
@@ -56,6 +56,7 @@
   #:use-module (gnu system vm)
   #:use-module (gnu system install)
   #:use-module (gnu system images hurd)
+  #:use-module (gnu system images pine64)
   #:use-module (gnu tests)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26)
@@ -75,28 +76,36 @@
                          #:optional (package-derivation package-derivation))
   "Convert PACKAGE to an alist suitable for Hydra."
   (parameterize ((%graft? #f))
-    `((derivation . ,(derivation-file-name
+    (let ((drv (package-derivation store package system
-                      (package-derivation store package system
+                                   #:graft? #f)))
-                                          #:graft? #f)))
+      `((derivation . ,(derivation-file-name drv))
-      (description . ,(package-synopsis package))
+        (log . ,(log-file store (derivation-file-name drv)))
-      (long-description . ,(package-description package))
+        (outputs . ,(filter-map (lambda (res)
+                                  (match res
+                                    ((name . path)
+                                     `(,name . ,path))))
+                                (derivation->output-paths drv)))
+        (nix-name . ,(derivation-name drv))
+        (system . ,(derivation-system drv))
+        (description . ,(package-synopsis package))
+        (long-description . ,(package-description package))
 
-      ;; XXX: Hydra ignores licenses that are not a <license> structure or a
+        ;; XXX: Hydra ignores licenses that are not a <license> structure or a
-      ;; list thereof.
+        ;; list thereof.
-      (license . ,(let loop ((license (package-license package)))
+        (license . ,(let loop ((license (package-license package)))
-                    (match license
+                      (match license
-                      ((? license?)
+                        ((? license?)
-                       (license-name license))
+                         (license-name license))
-                      ((lst ...)
+                        ((lst ...)
-                       (map loop license)))))
+                         (map loop license)))))
 
-      (home-page . ,(package-home-page package))
+        (home-page . ,(package-home-page package))
-      (maintainers . ("bug-guix@gnu.org"))
+        (maintainers . ("bug-guix@gnu.org"))
-      (max-silent-time . ,(or (assoc-ref (package-properties package)
+        (max-silent-time . ,(or (assoc-ref (package-properties package)
-                                         'max-silent-time)
+                                           'max-silent-time)
-                              3600))              ;1 hour by default
+                                3600))              ;1 hour by default
-      (timeout . ,(or (assoc-ref (package-properties package) 'timeout)
+        (timeout . ,(or (assoc-ref (package-properties package) 'timeout)
-                      72000)))))                  ;20 hours by default
+                        72000))))))                  ;20 hours by default
 
 (define (package-job store job-name package system)
   "Return a job called JOB-NAME that builds PACKAGE on SYSTEM."
@@ -195,12 +204,21 @@ SYSTEM."
   '("x86_64-linux" "i686-linux"))
 
 (define %guix-system-images
-  (list hurd-barebones-disk-image))
+  (list hurd-barebones-qcow2-image
+        pine64-barebones-raw-image))
 
 (define (image-jobs store system)
   "Return a list of jobs that build images for SYSTEM."
   (define (->alist drv)
     `((derivation . ,(derivation-file-name drv))
+      (log . ,(log-file store (derivation-file-name drv)))
+      (outputs . ,(filter-map (lambda (res)
+                                (match res
+                                  ((name . path)
+                                   `(,name . ,path))))
+                              (derivation->output-paths drv)))
+      (nix-name . ,(derivation-name drv))
+      (system . ,(derivation-system drv))
       (description . "Stand-alone image of the GNU system")
       (long-description . "This is a demo stand-alone image of the GNU
 system.")
@@ -304,6 +322,14 @@ system.")
             (system-test-value test))))
 
       `((derivation . ,(derivation-file-name drv))
+        (log . ,(log-file store (derivation-file-name drv)))
+        (outputs . ,(filter-map (lambda (res)
+                                  (match res
+                                    ((name . path)
+                                     `(,name . ,path))))
+                                (derivation->output-paths drv)))
+        (nix-name . ,(derivation-name drv))
+        (system . ,(derivation-system drv))
         (description . ,(format #f "Guix '~a' system test"
                                 (system-test-name test)))
         (long-description . ,(system-test-description test))
@@ -333,6 +359,14 @@ system.")
   "Return Hydra jobs to build the self-contained Guix binary tarball."
   (define (->alist drv)
     `((derivation . ,(derivation-file-name drv))
+      (log . ,(log-file store (derivation-file-name drv)))
+      (outputs . ,(filter-map (lambda (res)
+                                (match res
+                                  ((name . path)
+                                   `(,name . ,path))))
+                              (derivation->output-paths drv)))
+      (nix-name . ,(derivation-name drv))
+      (system . ,(derivation-system drv))
       (description . "Stand-alone binary Guix tarball")
       (long-description . "This is a tarball containing binaries of Guix and
 all its dependencies, and ready to be installed on \"foreign\" distributions.")
@@ -511,20 +545,16 @@ Return #f if no such checkout is found."
                              (cross-jobs store system)))
                     ((hello)
                      ;; Build hello package only.
-                     (if (string=? system (%current-system))
+                     (let ((hello (specification->package "hello")))
-                         (let ((hello (specification->package "hello")))
+                       (list (package-job store (job-name hello) hello system))))
-                           (list (package-job store (job-name hello) hello system)))
-                         '()))
                     ((list)
                      ;; Build selected list of packages only.
-                     (if (string=? system (%current-system))
+                     (let* ((names (assoc-ref arguments 'subset))
-                         (let* ((names (assoc-ref arguments 'subset))
+                            (packages (map specification->package names)))
-                                (packages (map specification->package names)))
+                       (map (lambda (package)
-                           (map (lambda (package)
+                              (package-job store (job-name package)
-                                    (package-job store (job-name package)
+                                           package system))
-                                                 package system))
+                            packages)))
-                                  packages))
-                         '()))
                     ((manifests)
                      ;; Build packages in the list of manifests.
                      (let* ((manifests (arguments->manifests arguments))

gnu/image.scm

@@ -39,7 +39,14 @@
             image-partitions
             image-compression?
             image-volatile-root?
-            image-substitutable?))
+            image-substitutable?
+
+            image-type
+            image-type?
+            image-type-name
+            image-type-constructor
+
+            os->image))
 
 
 ;;;
@@ -84,3 +91,23 @@
                       (default #t))
   (substitutable?     image-substitutable? ;boolean
                       (default #t)))
+
+
+;;;
+;;; Image type.
+;;;
+
+(define-record-type* <image-type>
+  image-type make-image-type
+  image-type?
+  (name           image-type-name) ;symbol
+  (constructor    image-type-constructor)) ;<operating-system> -> <image>
+
+
+;;;
+;;; Image creation.
+;;;
+
+(define* (os->image os #:key type)
+  (let ((constructor (image-type-constructor type)))
+    (constructor os)))

gnu/installer.scm

@@ -71,7 +71,7 @@
     (_ #f)))
 
 (define* (build-compiled-file name locale-builder)
-  "Return a file-like object that evalutes the gexp LOCALE-BUILDER and store
+  "Return a file-like object that evaluates the gexp LOCALE-BUILDER and store
 its result in the scheme file NAME. The derivation will also build a compiled
 version of this file."
   (define set-utf8-locale
@@ -308,7 +308,8 @@ selected keymap."
     ;; translated.
     #~(begin
         (bindtextdomain "guix" (string-append #$guix "/share/locale"))
-        (textdomain "guix")))
+        (textdomain "guix")
+        (setlocale LC_ALL "")))
 
   (define set-installer-path
     ;; Add the specified binary to PATH for later use by the installer.

gnu/installer/connman.scm

@@ -180,7 +180,7 @@ Return the corresponding association list of '((KEY . VALUE) (KEY2 . VALUE2)
 (define (connman-state)
   "Return the state of connman. The nominal states are 'offline, 'idle,
 'ready, 'oneline.  If an unexpected state is read, 'unknown is
-returned. Finally, an error is raised if the comman output could not be
+returned. Finally, an error is raised if the connman output could not be
 parsed, usually because the connman daemon is not responding."
   (let* ((output (connman "state"))
          (state-keys (parse-keys output)))

gnu/installer/newt.scm

@@ -107,7 +107,7 @@ problem. The backtrace is displayed below. Please report it by email to \
   (run-user-page))
 
 (define (partition-page)
-  (run-partioning-page))
+  (run-partitioning-page))
 
 (define (services-page)
   (run-services-page))

gnu/installer/newt/locale.scm

@@ -106,7 +106,7 @@ symbol.")
 territory, codeset and modifier. Use SUPPORTED-LOCALES as the list of glibc
 available locales. ISO639-LANGUAGES is an association list associating a
 locale code to a locale name. ISO3166-TERRITORIES is an association list
-associating a territory code with a territory name. The formated locale, under
+associating a territory code with a territory name. The formatted locale, under
 glibc format is returned."
 
   (define (break-on-locale-found locales)

gnu/installer/newt/partition.scm

@@ -32,7 +32,7 @@
   #:use-module (srfi srfi-35)
   #:use-module (newt)
   #:use-module (parted)
-  #:export (run-partioning-page))
+  #:export (run-partitioning-page))
 
 (define (button-exit-action)
   "Raise the &installer-step-abort condition."
@@ -725,7 +725,7 @@ by pressing the Exit button.~%~%")))
           (run-disk-page result-disks new-user-partitions
                          #:guided? guided?)))))
 
-(define (run-partioning-page)
+(define (run-partitioning-page)
   "Run a page asking the user for a partitioning method."
   (define (run-page devices)
     (let* ((items

gnu/installer/newt/services.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -40,7 +41,7 @@ choose the one to use on the log-in screen.")
      #:items items
      #:selection (map system-service-recommended? items)
      #:item->text system-service-name             ;no i18n for DE names
-     #:checkbox-tree-height 8
+     #:checkbox-tree-height 9
      #:exit-button-callback-procedure
      (lambda ()
        (raise

gnu/installer/parted.scm

@@ -1201,13 +1201,13 @@ the FS-TYPE field set to 'swap, return the empty list if none found."
           user-partitions))
 
 (define (start-swapping user-partitions)
-  "Start swaping on <user-partition> records with FS-TYPE equal to 'swap."
+  "Start swapping on <user-partition> records with FS-TYPE equal to 'swap."
   (let* ((swap-user-partitions (find-swap-user-partitions user-partitions))
          (swap-devices (map user-partition-file-name swap-user-partitions)))
     (for-each swapon swap-devices)))
 
 (define (stop-swapping user-partitions)
-  "Stop swaping on <user-partition> records with FS-TYPE equal to 'swap."
+  "Stop swapping on <user-partition> records with FS-TYPE equal to 'swap."
   (let* ((swap-user-partitions (find-swap-user-partitions user-partitions))
          (swap-devices (map user-partition-file-name swap-user-partitions)))
     (for-each swapoff swap-devices)))

gnu/installer/services.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -82,6 +83,11 @@
       (name "ratpoison")
       (packages '((specification->package "ratpoison")
                   (specification->package "xterm"))))
+     (desktop-environment
+      (name "Emacs EXWM")
+      (packages '((specification->package "emacs")
+                  (specification->package "emacs-exwm")
+                  (specification->package "emacs-desktop-environment"))))
 
      ;; Networking.
      (system-service

gnu/installer/steps.scm

@@ -88,7 +88,7 @@
                               (rewind-strategy 'previous)
                               (menu-proc (const #f)))
   "Run the COMPUTE procedure of all <installer-step> records in STEPS
-sequencially. If the &installer-step-abort condition is raised, fallback to a
+sequentially.  If the &installer-step-abort condition is raised, fallback to a
 previous install-step, accordingly to the specified REWIND-STRATEGY.
 
 REWIND-STRATEGY possible values are 'previous, 'menu and 'start.  If 'previous

gnu/local.mk

@@ -144,6 +144,8 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/cppi.scm				\
   %D%/packages/cran.scm				\
   %D%/packages/crates-io.scm			\
+  %D%/packages/crates-graphics.scm		\
+  %D%/packages/crates-gtk.scm			\
   %D%/packages/cross-base.scm			\
   %D%/packages/crypto.scm			\
   %D%/packages/cryptsetup.scm			\
@@ -646,6 +648,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/system/vm.scm				\
 						\
   %D%/system/images/hurd.scm			\
+  %D%/system/images/pine64.scm			\
 						\
   %D%/machine.scm				\
 						\
@@ -858,6 +861,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/clang-7.0-libc-search-path.patch		\
   %D%/packages/patches/clang-9.0-libc-search-path.patch		\
   %D%/packages/patches/clang-10.0-libc-search-path.patch	\
+  %D%/packages/patches/clang-11.0-libc-search-path.patch	\
   %D%/packages/patches/clang-runtime-asan-build-fixes.patch	\
   %D%/packages/patches/clang-runtime-esan-build-fixes.patch	\
   %D%/packages/patches/clang-runtime-9-libsanitizer-mode-field.patch	\
@@ -894,7 +898,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/dbus-c++-gcc-compat.patch		\
   %D%/packages/patches/dbus-c++-threading-mutex.patch		\
   %D%/packages/patches/dbxfs-remove-sentry-sdk.patch		\
-  %D%/packages/patches/dconf-meson-0.52.patch			\
   %D%/packages/patches/debops-constants-for-external-program-names.patch \
   %D%/packages/patches/debops-debops-defaults-fall-back-to-less.patch \
   %D%/packages/patches/dee-vapi.patch			\
@@ -969,6 +972,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/foomatic-filters-CVE-2015-8560.patch	\
   %D%/packages/patches/fontconfig-hurd-path-max.patch		\
   %D%/packages/patches/fpc-reproducibility.patch		\
+  %D%/packages/patches/fplll-std-fenv.patch     		\
   %D%/packages/patches/freedink-engine-fix-sdl-hints.patch	\
   %D%/packages/patches/freeimage-unbundle.patch		\
   %D%/packages/patches/fuse-overlapping-headers.patch				\
@@ -1069,6 +1073,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gmp-faulty-test.patch			\
   %D%/packages/patches/gnome-shell-theme.patch			\
   %D%/packages/patches/gnome-shell-disable-test.patch		\
+  %D%/packages/patches/gnome-settings-daemon-gc.patch		\
   %D%/packages/patches/gnome-todo-delete-esource-duplicate.patch \
   %D%/packages/patches/gnome-tweaks-search-paths.patch		\
   %D%/packages/patches/gnupg-default-pinentry.patch		\
@@ -1084,6 +1089,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gpsbabel-qstring.patch     		\
   %D%/packages/patches/grantlee-merge-theme-dirs.patch		\
   %D%/packages/patches/grep-timing-sensitive-test.patch		\
+  %D%/packages/patches/grim-revert-output-rotation.patch	\
   %D%/packages/patches/grocsvs-dont-use-admiral.patch		\
   %D%/packages/patches/gromacs-tinyxml2.patch			\
   %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch	\
@@ -1132,6 +1138,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/hubbub-sort-entities.patch		\
   %D%/packages/patches/hurd-cross.patch				\
   %D%/packages/patches/hurd-xattr.patch				\
+  %D%/packages/patches/hplip-fix-bug-1898438.patch		\
   %D%/packages/patches/hplip-remove-imageprocessor.patch	\
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
   %D%/packages/patches/icecat-makeicecat.patch			\
@@ -1155,8 +1162,14 @@ dist_patch_DATA =						\
   %D%/packages/patches/json-c-0.13-CVE-2020-12762.patch	\
   %D%/packages/patches/json-c-0.12-CVE-2020-12762.patch	\
   %D%/packages/patches/jacal-fix-texinfo.patch			\
+  %D%/packages/patches/jamvm-1.5.1-aarch64-support.patch	\
+  %D%/packages/patches/jamvm-1.5.1-armv7-support.patch	\
+  %D%/packages/patches/jamvm-2.0.0-aarch64-support.patch	\
   %D%/packages/patches/jamvm-2.0.0-disable-branch-patching.patch	\
-  %D%/packages/patches/jamvm-arm.patch				\
+  %D%/packages/patches/jamvm-2.0.0-opcode-guard.patch		\
+  %D%/packages/patches/java-antlr4-Add-standalone-generator.patch	\
+  %D%/packages/patches/java-antlr4-fix-code-too-large.java	\
+  %D%/packages/patches/java-tunnelvisionlabs-antlr-code-too-large.patch	\
   %D%/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch	\
   %D%/packages/patches/java-commons-collections-fix-java8.patch \
   %D%/packages/patches/java-jeromq-fix-tests.patch		\
@@ -1198,7 +1211,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/kodi-increase-test-timeout.patch		\
   %D%/packages/patches/kodi-set-libcurl-ssl-parameters.patch		\
   %D%/packages/patches/kodi-skip-test-449.patch		\
-  %D%/packages/patches/konversation-Fix-build-with-Qt-5.11.patch	\
   %D%/packages/patches/laby-make-install.patch			\
   %D%/packages/patches/lcalc-default-parameters-1.patch		\
   %D%/packages/patches/lcalc-default-parameters-2.patch		\
@@ -1219,14 +1231,14 @@ dist_patch_DATA =						\
   %D%/packages/patches/libbase-use-own-logging.patch		\
   %D%/packages/patches/libbonobo-activation-test-race.patch	\
   %D%/packages/patches/libcanberra-sound-theme-freedesktop.patch \
-  %D%/packages/patches/libdrm-realpath-virtio.patch		\
+  %D%/packages/patches/libcanberra-wayland-crash.patch \
+  %D%/packages/patches/libcyaml-libyaml-compat.patch		\
   %D%/packages/patches/libgeotiff-adapt-test-script-for-proj-6.2.patch		\
   %D%/packages/patches/libgit2-mtime-0.patch			\
   %D%/packages/patches/libgnome-encoding.patch			\
   %D%/packages/patches/libgnomeui-utf8.patch			\
   %D%/packages/patches/libjxr-fix-function-signature.patch	\
   %D%/packages/patches/libjxr-fix-typos.patch			\
-  %D%/packages/patches/liblouisutdml-fix-tests.patch		\
   %D%/packages/patches/libofa-ftbfs-1.diff		\
   %D%/packages/patches/libofa-curl.diff		\
   %D%/packages/patches/libofa-ftbfs-2.diff		\
@@ -1244,10 +1256,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/libmygpo-qt-missing-qt5-modules.patch	\
   %D%/packages/patches/libqalculate-3.8.0-libcurl-ssl-fix.patch	\
   %D%/packages/patches/libquicktime-ffmpeg.patch 		\
-  %D%/packages/patches/libsndfile-armhf-type-checks.patch	\
-  %D%/packages/patches/libsndfile-CVE-2017-8361-8363-8365.patch	\
-  %D%/packages/patches/libsndfile-CVE-2017-8362.patch		\
-  %D%/packages/patches/libsndfile-CVE-2017-12562.patch		\
   %D%/packages/patches/libtar-CVE-2013-4420.patch 		\
   %D%/packages/patches/libtgvoip-disable-sse2.patch 		\
   %D%/packages/patches/libtgvoip-disable-webrtc.patch 		\
@@ -1283,6 +1291,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/lm-sensors-hwmon-attrs.patch		\
   %D%/packages/patches/lrcalc-includes.patch    		\
   %D%/packages/patches/lrzip-CVE-2017-8842.patch		\
+  %D%/packages/patches/lsh-fix-x11-forwarding.patch		\
   %D%/packages/patches/lua-CVE-2014-5461.patch                      \
   %D%/packages/patches/lua-pkgconfig.patch                      \
   %D%/packages/patches/lua51-liblua-so.patch                    \
@@ -1291,8 +1300,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/luajit-no_ldconfig.patch			\
   %D%/packages/patches/luit-posix.patch				\
   %D%/packages/patches/lvm2-static-link.patch			\
+  %D%/packages/patches/mailutils-fix-uninitialized-variable.patch	\
   %D%/packages/patches/make-impure-dirs.patch			\
-  %D%/packages/patches/mariadb-client-test-32bit.patch		\
   %D%/packages/patches/mars-install.patch			\
   %D%/packages/patches/mars-sfml-2.3.patch			\
   %D%/packages/patches/maxima-defsystem-mkdir.patch		\
@@ -1351,9 +1360,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/nfs4-acl-tools-0.3.7-fixpaths.patch	\
   %D%/packages/patches/ngircd-handle-zombies.patch		\
   %D%/packages/patches/network-manager-plugin-path.patch	\
+  %D%/packages/patches/nginx-socket-cloexec.patch		\
   %D%/packages/patches/nsis-env-passthru.patch			\
   %D%/packages/patches/nss-increase-test-timeout.patch		\
-  %D%/packages/patches/nss-pkgconfig.patch			\
+  %D%/packages/patches/nss-3.56-pkgconfig.patch			\
   %D%/packages/patches/ntfs-3g-CVE-2019-9755.patch		\
   %D%/packages/patches/nvi-assume-preserve-path.patch		\
   %D%/packages/patches/nvi-dbpagesize-binpower.patch		\
@@ -1400,6 +1410,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/pango-skip-libthai-test.patch		\
   %D%/packages/patches/pciutils-hurd-configure.patch		\
   %D%/packages/patches/ppsspp-disable-upgrade-and-gold.patch		\
+  %D%/packages/patches/samba-fix-fcntl-hint-detection.patch		\
   %D%/packages/patches/sdl-pango-api_additions.patch		\
   %D%/packages/patches/sdl-pango-blit_overflow.patch		\
   %D%/packages/patches/sdl-pango-fillrect_crash.patch		\
@@ -1407,6 +1418,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/sdl-pango-matrix_declarations.patch	\
   %D%/packages/patches/sdl-pango-sans-serif.patch		\
   %D%/packages/patches/sqlite-hurd.patch			\
+  %D%/packages/patches/sunxi-tools-remove-sys-io.patch	\
   %D%/packages/patches/patchutils-test-perms.patch		\
   %D%/packages/patches/patch-hurd-path-max.patch		\
   %D%/packages/patches/perl-autosplit-default-time.patch	\
@@ -1421,6 +1433,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/perl-module-pluggable-search.patch	\
   %D%/packages/patches/perl-reproducible-build-date.patch	\
   %D%/packages/patches/perl-www-curl-remove-symbol.patch	\
+  %D%/packages/patches/picard-fix-id3-rename-test.patch		\
   %D%/packages/patches/picprog-non-intel-support.patch		\
   %D%/packages/patches/pidgin-add-search-path.patch		\
   %D%/packages/patches/pidgin-libnm.patch			\
@@ -1481,7 +1494,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch \
   %D%/packages/patches/python-configobj-setuptools.patch	\
   %D%/packages/patches/python-flask-restful-werkzeug-compat.patch	\
-  %D%/packages/patches/python-gst-fix-build-with-python-3.8.patch	\
   %D%/packages/patches/python-keras-integration-test.patch	\
   %D%/packages/patches/python-pep8-stdlib-tokenize-compat.patch \
   %D%/packages/patches/python-pyfakefs-remove-bad-test.patch	\
@@ -1506,6 +1518,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-unittest2-remove-argparse.patch	\
   %D%/packages/patches/python-waitress-fix-tests.patch		\
   %D%/packages/patches/pypy3-7.3.1-fix-tests.patch		\
+  %D%/packages/patches/qemu-build-info-manual.patch		\
   %D%/packages/patches/qemu-glibc-2.27.patch 			\
   %D%/packages/patches/qrcodegen-cpp-make-install.patch		\
   %D%/packages/patches/qt4-ldflags.patch			\
@@ -1555,7 +1568,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/rust-reproducible-builds.patch		 \
   %D%/packages/patches/rust-openssl-sys-no-vendor.patch	\
   %D%/packages/patches/rxvt-unicode-escape-sequences.patch	\
-  %D%/packages/patches/sbcl-graph-asdf-definitions.patch	\
   %D%/packages/patches/scalapack-blacs-mpi-deprecations.patch	\
   %D%/packages/patches/scheme48-tests.patch			\
   %D%/packages/patches/scotch-build-parallelism.patch		\
@@ -1625,6 +1637,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ucx-tcp-iface-ioctl.patch		\
   %D%/packages/patches/udiskie-no-appindicator.patch		\
   %D%/packages/patches/ungoogled-chromium-system-nspr.patch	\
+  %D%/packages/patches/unison-fix-ocaml-4.08.patch		\
   %D%/packages/patches/unknown-horizons-python-3.8-distro.patch	\
   %D%/packages/patches/unzip-CVE-2014-8139.patch		\
   %D%/packages/patches/unzip-CVE-2014-8140.patch		\
@@ -1688,6 +1701,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/xplanet-1.3.1-libimage_gif.c.patch	\
   %D%/packages/patches/xplanet-1.3.1-xpUtil-Add2017LeapSecond.cpp.patch	\
   %D%/packages/patches/xpra-4.0.1-systemd-run.patch	\
+  %D%/packages/patches/xpra-4.0.4-norequests.patch	\
   %D%/packages/patches/xsane-fix-memory-leak.patch		\
   %D%/packages/patches/xsane-fix-pdf-floats.patch		\
   %D%/packages/patches/xsane-fix-snprintf-buffer-length.patch	\

gnu/machine/ssh.scm

@@ -480,6 +480,8 @@ an environment type of 'managed-host."
                                  (raise roll-back-failure)))
                        (entries -> (map boot-parameters->menu-entry
                                         (list (second boot-parameters))))
+                       (locale -> (boot-parameters-locale
+                                   (second boot-parameters)))
                        (old-entries -> (map boot-parameters->menu-entry
                                             (drop boot-parameters 2)))
                        (bootloader -> (operating-system-bootloader
@@ -489,6 +491,7 @@ an environment type of 'managed-host."
                                    (bootloader-configuration-bootloader
                                     bootloader))
                                   bootloader entries
+                                  #:locale locale
                                   #:old-entries old-entries)))
                        (remote-result (machine-remote-eval machine remote-exp)))
     (when (eqv? 'error remote-result)

gnu/packages/abduco.scm

@@ -19,6 +19,7 @@
 
 (define-module (gnu packages abduco)
   #:use-module (guix build-system gnu)
+  #:use-module (guix utils)
   #:use-module (guix download)
   #:use-module (guix licenses)
   #:use-module (guix packages))
@@ -37,7 +38,7 @@
               "1x1m58ckwsprljgmdy93mvgjyg9x3cqrzdf3mysp0mx97zhhj2f9"))))
    (build-system gnu-build-system)
    (arguments
-    `(#:make-flags (list "CC=gcc"
+    `(#:make-flags (list (string-append "CC=" ,(cc-for-target))
                          (string-append "PREFIX=" (assoc-ref %outputs "out")))
       #:phases (modify-phases %standard-phases
                  (delete 'configure)

gnu/packages/accessibility.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Andrew Miloradovsky <andrew@interpretmath.pw>
+;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -272,7 +273,7 @@ available to help to click.")
        `(("hidapi" ,hidapi)))
       (arguments
        `(#:tests? #f ; no tests
-         #:make-flags (list "CC=gcc")
+         #:make-flags (list (string-append "CC=" ,(cc-for-target)))
          #:phases (modify-phases %standard-phases
                     (delete 'configure)
                     ;; Install target in the Makefile does not work for Guix
@@ -308,7 +309,7 @@ devices have vendorId:productId = 0c45:7403 or 0c45:7404.")
     (arguments
      `(#:tests? #f ; none included
        #:make-flags
-       (list "CC=gcc"
+       (list (string-append "CC=" ,(cc-for-target))
              (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
        (modify-phases %standard-phases

gnu/packages/acl.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,6 +26,7 @@
   #:use-module (guix licenses)
   #:use-module (gnu packages attr)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages hurd)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages perl)
   #:use-module (guix packages)
@@ -49,6 +51,7 @@
      `(#:modules ((ice-9 ftw)
                   ,@%gnu-build-system-modules)
        #:configure-flags '("--disable-static")
+       #:tests? ,(not (hurd-target?))
        #:phases
        (modify-phases %standard-phases
          ;; XXX After repacking the sources the timestamps are reset to the

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, 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 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 Nikita <nikita@n0.is>
@@ -443,7 +443,7 @@ graphs and can export its output to different formats.")
 (define-public facter
   (package
     (name "facter")
-    (version "4.0.35")
+    (version "4.0.43")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -452,7 +452,7 @@ graphs and can export its output to different formats.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1f203g2hp96cp8w4x1myhqdj5j09z9s23kylwkrxr69fjhn0vhnb"))))
+                "0ppzr7vsl6iw8x82c4g60mx1vz06nzwcy8byablhg0n0g6qa3pb0"))))
     (build-system ruby-build-system)
     (arguments
      `(#:phases
@@ -514,7 +514,7 @@ or via the @code{facter} Ruby library.")
 (define-public htop
   (package
     (name "htop")
-    (version "3.0.1")
+    (version "3.0.2")
     (source
      (origin
        (method git-fetch)
@@ -522,7 +522,7 @@ or via the @code{facter} Ruby library.")
              (url "https://github.com/htop-dev/htop")
              (commit version)))
        (sha256
-        (base32 "0kjlphdvwwbj91kk91s4ksc954d3c2bznddzx2223jmb1bn9rcsa"))
+        (base32 "1qmqhbnc5yw4brd24yrp85k09770c1c00nl03mkv5pdz2bvqivk7"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (inputs
@@ -834,7 +834,7 @@ would need and has several interesting built-in capabilities.")
 (define-public netcat-openbsd
   (package
     (name "netcat-openbsd")
-    (version "1.217-1")
+    (version "1.217-2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -843,12 +843,12 @@ would need and has several interesting built-in capabilities.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0kcvi3pav2fdx5c22psjv5dggk4cmrqiaq2cklhqngsk4a7vrjan"))))
+                "19sr52ix14w344pv13ppb0c1wyg5dxhic1fw2q0s3qfmx57b9hhp"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no test suite
        #:make-flags
-       (list "CC=gcc")
+       (list (string-append "CC=" ,(cc-for-target)))
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
@@ -1404,7 +1404,7 @@ system administrator.")
 (define-public sudo
   (package
     (name "sudo")
-    (version "1.9.2")
+    (version "1.9.3p1")
     (source (origin
               (method url-fetch)
               (uri
@@ -1414,25 +1414,19 @@ system administrator.")
                                     version ".tar.gz")))
               (sha256
                (base32
-                "05432672iilb7s52j9l9xzrlambb1wg3k7qvf5973i41y40x563w"))
+                "17mldsg5d08s23cskmjxfa81ibnqw3slgf3l4023j72ywi9xxffw"))
               (modules '((guix build utils)))
               (snippet
                '(begin
                   (delete-file-recursively "lib/zlib")
                   #t))))
     (build-system gnu-build-system)
-    (outputs (list "out" "python"))
+    (outputs (list "out"))
     (arguments
      `(#:configure-flags
        (list (string-append "--docdir=" (assoc-ref %outputs "out")
                             "/share/doc/" ,name "-" ,version)
 
-             ;; XXX: Disable Python support when cross-compiling because
-             ;; 'configure' tries to run 'python', which fails.
-             ,(if (%current-target-system)
-                  "--disable-python"
-                  "--enable-python")              ; for plug-ins written in ~
-
              "--with-logpath=/var/log/sudo.log"
              "--with-rundir=/var/run/sudo" ; must be cleaned up at boot time
              "--with-vardir=/var/db/sudo"
@@ -1479,34 +1473,19 @@ system administrator.")
              (substitute* "plugins/sudoers/Makefile.in"
                (("^pre-install:" match)
                 (string-append match "\ndisabled-" match)))
-             #t))
+             #t)))
-         (add-after 'install 'separate-python-output
-           (lambda* (#:key target outputs #:allow-other-keys)
-             (let ((out        (assoc-ref outputs "out"))
-                   (out:python (assoc-ref outputs "python")))
-               (if target
-                   (mkdir-p (string-append out:python "/empty"))
-                   (for-each
-                    (lambda (file)
-                      (let ((old (string-append out "/" file))
-                            (new (string-append out:python "/" file)))
-                        (mkdir-p (dirname new))
-                        (rename-file old new)))
-                    (list "libexec/sudo/python_plugin.so"
-                          "libexec/sudo/python_plugin.la")))
-               #t))))
 
        ;; XXX: The 'testsudoers' test series expects user 'root' to exist, but
        ;; the chroot's /etc/passwd doesn't have it.  Turn off the tests.
        #:tests? #f))
     (native-inputs
-     `(("groff" ,groff)))
+     ;; XXX TODO: Remove on next rebuild cycle.
+     (if (hurd-target?)
+         '()
+         `(("groff" ,groff))))
     (inputs
      `(("coreutils" ,coreutils)
        ("linux-pam" ,linux-pam)
-       ,@(if (%current-target-system)
-             '()
-             `(("python" ,python)))
        ("zlib" ,zlib)))
     (home-page "https://www.sudo.ws/")
     (synopsis "Run commands as root")
@@ -1837,21 +1816,24 @@ network, which causes enabled computers to power on.")
 (define-public dmidecode
   (package
     (name "dmidecode")
-    (version "3.2")
+    (version "3.3")
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              (uri (string-append
+       (method url-fetch)
-                    "mirror://savannah/dmidecode/dmidecode-"
+       (uri (string-append "mirror://savannah/dmidecode/dmidecode-"
-                    version ".tar.xz"))
+                           version ".tar.xz"))
-              (sha256
+       (sha256
-               (base32
+        (base32 "0m8lzg9rf1qssasiix672bxk5qwms90561g8hfkkhk31h2kkgiw2"))))
-                "1pcfhcgs2ifdjwp7amnsr3lq95pgxpr150bjhdinvl505px0cw07"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:phases (modify-phases %standard-phases (delete 'configure))
+     `(#:tests? #f                                ; no 'check' target
-       #:tests? #f                                ; no 'check' target
+       #:make-flags
-       #:make-flags (list (string-append "prefix="
+       (list (string-append "CC=" ,(cc-for-target))
-                                         (assoc-ref %outputs "out")))))
+             (string-append "prefix="
+                            (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))))                   ; no configure script
     (home-page "https://www.nongnu.org/dmidecode/")
     (synopsis "Read hardware information from the BIOS")
     (description
@@ -2613,14 +2595,14 @@ done with the @code{auditctl} utility.")
 (define-public nmap
   (package
     (name "nmap")
-    (version "7.80")
+    (version "7.91")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nmap.org/dist/nmap-" version
                                   ".tar.bz2"))
               (sha256
                (base32
-                "1aizfys6l9f9grm82bk878w56mg0zpkfns3spzj157h98875mypw"))
+                "001kb5xadqswyw966k2lqi6jr6zz605jpp9w4kmm272if184pk0q"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -2698,7 +2680,7 @@ advanced netcat implementation (ncat), a utility for comparing scan
 results (ndiff), and a packet generation and response analysis tool (nping).")
     ;; This package uses nmap's bundled versions of libdnet and liblinear, which
     ;; both use a 3-clause BSD license.
-    (license (list license:nmap license:bsd-3))))
+    (license (list license:npsl license:bsd-3))))
 
 (define-public dstat
   (package
@@ -2718,9 +2700,8 @@ results (ndiff), and a packet generation and response analysis tool (nping).")
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no make check
-       #:make-flags (let ((out (assoc-ref %outputs "out")))
+       #:make-flags
-                      (list (string-append "DESTDIR=" out)
+       (list (string-append "prefix=" (assoc-ref %outputs "out")))
-                            "prefix=/"))
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'fix-python3-DeprecationWarning
@@ -2952,6 +2933,8 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.")
              (commit (string-append "v" version))))
        (sha256
         (base32 "04f3jqg8ww4jxsf9c6ddcdgy2xbhkyp0b3l5f1hvvbv94p81rjxd"))
+       (patches
+        (search-patches "sunxi-tools-remove-sys-io.patch"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove binaries contained in the tarball which are only for the
@@ -3595,7 +3578,7 @@ Python loading in HPC environments.")
   (let ((real-name "inxi"))
     (package
       (name "inxi-minimal")
-      (version "3.1.06-1")
+      (version "3.1.07-1")
       (source
        (origin
          (method git-fetch)
@@ -3604,7 +3587,7 @@ Python loading in HPC environments.")
                (commit version)))
          (file-name (git-file-name real-name version))
          (sha256
-          (base32 "0h65n03q9kdsv0i1q5f88i11iv79ca7fqq97rdkzkmiqb4whhnm2"))))
+          (base32 "0hs4m2vmfc6srscaz72r6zpkn6n7msgzlps376ks38gj1l103xfn"))))
       (build-system trivial-build-system)
       (inputs
        `(("bash" ,bash-minimal)
@@ -4105,3 +4088,44 @@ the system configuration; hosts only works when using the Guix package manager
 on a foreign distro.  @command{hosts} works with existing hosts files and
 entries, providing commands to add, remove, comment, and search.")
     (license license:expat)))
+
+(define-public nmrpflash
+  (package
+    (name "nmrpflash")
+    (version "0.9.14")
+    (source
+     (origin
+       (method git-fetch)
+       (uri
+        (git-reference
+         (url "https://github.com/jclehner/nmrpflash.git")
+         (commit (string-append "v" version))))
+       (sha256
+        (base32 "1fdjrxhjs96rdclbkld57xarf592slhkp79h46z833npxpn12ck1"))
+       (file-name (git-file-name name version))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("libnl" ,libnl)
+       ("libpcap" ,libpcap)))
+    (arguments
+     `(#:tests? #f ; None exist
+       #:make-flags
+       (list (string-append "CC=" ,(cc-for-target))
+             (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'install 'prepare-install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
+             #t)))))
+    (home-page "https://github.com/jclehner/nmrpflash")
+    (synopsis "Netgear unbrick utility")
+    (description "This package provides a utility to flash a new firmware
+image to a Netgear device.  It has been tested on Netgear EX2700, EX6120,
+EX6150v2, DNG3700v2, R6100, R6220, R7000, D7000, WNR3500, R6400, R6800,
+R8000, R8500, WNDR3800, but is likely to be compatible with many other
+Netgear devices.")
+    (license license:gpl3+)))

gnu/packages/algebra.scm

@@ -48,6 +48,7 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages multiprecision)
+  #:use-module (gnu packages ocaml)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
@@ -123,15 +124,15 @@ greatest common divisor operations.")
 (define-public cm
   (package
    (name "cm")
-   (version "0.3")
+   (version "0.3.1")
    (source (origin
             (method url-fetch)
             (uri (string-append
-                  "http://www.multiprecision.org/cm/download/cm-"
+                  "http://www.multiprecision.org/downloads/cm-"
                   version ".tar.gz"))
             (sha256
              (base32
-              "1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc"))))
+              "0qq6b1kwb1byj8ws33ya5awq0ilkpm32037pi1l4cf2737fg9m42"))))
    (build-system gnu-build-system)
    (propagated-inputs
      `(("mpfrcx" ,mpfrcx)
@@ -151,12 +152,7 @@ line applications.")
 (define-public fplll
   (package
     (name "fplll")
-    ;; The most recent version 5.3.3 fails in the configure phase:
+    (version "5.3.3")
-    ;; ./configure: line 12956: syntax error near unexpected token `LIBQD,'
-    ;; ./configure: line 12956: `  PKG_CHECK_MODULES(LIBQD, qd, have_libqd="yes",'
-    ;; The error disappears when adding qd as an input; but this is
-    ;; supposed to be an optional input.
-    (version "5.3.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -165,13 +161,15 @@ line applications.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "00iyz218ywspizjiimrjdcqvdqmrsb2367zyy3vkmypnf9i9l680"))))
+                "06nyfidagp8pc2kfcw88ldgb2b1xm0a8z31n0sln7j72ihlmd8zj"))
+              (patches (search-patches "fplll-std-fenv.patch"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
-       ("libtool" ,libtool)))
+       ("libtool" ,libtool)
-    (inputs
+       ("pkg-config" ,pkg-config)))
+    (propagated-inputs ; header files pulled in by fplll/defs.h
      `(("gmp" ,gmp)
        ("mpfr" ,mpfr)))
     (home-page "https://github.com/fplll/fplll")
@@ -357,7 +355,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "1.6.0-7")
+    (version "1.6.0-25")
     (source
      (origin
        (method url-fetch)
@@ -369,7 +367,7 @@ precision.")
                            "~parisse/debian/dists/stable/main/source/"
                            "giac_" version ".tar.gz"))
        (sha256
-        (base32 "1pvgp137zcl0rbhdn1j41xxfml7fp771a7x4ph8qrhhlx0hxzn3p"))))
+        (base32 "11kik2csdg9wy0npiih21kaag0nc89i9ldgk7ak7gvf9ycddm6mh"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
@@ -380,7 +378,8 @@ precision.")
          (add-after 'unpack 'patch-bin-cp
            ;; Some Makefiles contain hard-coded "/bin/cp".
            (lambda _
-             (substitute* (find-files "doc" "^Makefile")
+             (substitute* (cons "micropython-1.12/xcas/Makefile"
+                                (find-files "doc" "^Makefile"))
                (("/bin/cp") (which "cp")))
              #t))
          (add-after 'unpack 'disable-failing-test
@@ -409,7 +408,7 @@ precision.")
                (delete-file (string-append out "/bin/xcasnew"))
                #t))))))
     (inputs
-;;; TODO: Add libnauty.
+     ;; TODO: Add libnauty, unbundle "libmicropython.a".
      `(("fltk" ,fltk)
        ("glpk" ,glpk)
        ("gmp" ,gmp)
@@ -433,6 +432,8 @@ precision.")
     (native-inputs
      `(("bison" ,bison)
        ("flex" ,flex)
+       ("hevea" ,hevea)
+       ("python" ,python-wrapper)
        ("readline" ,readline)
        ("texlive" ,texlive-tiny)))
     (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
@@ -1554,7 +1555,7 @@ structure constants of Schubert polynomials.")
          "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
     (build-system gnu-build-system)
     (inputs
-     `(("gmp", gmp)
+     `(("gmp" ,gmp)
        ("cblas" ,openblas))) ; or any other BLAS library; the documentation
                              ; mentions ATLAS in particular
     (arguments

gnu/packages/antivirus.scm

@@ -44,14 +44,14 @@
 (define-public clamav
   (package
     (name "clamav")
-    (version "0.102.4")
+    (version "0.103.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.clamav.net/downloads/production/"
                                   "clamav-" version ".tar.gz"))
               (sha256
                (base32
-                "06rrzyrhnr0rswryijpbbzywr6387rv8qjq8sb8cl3h2d1m45ggf"))
+                "0ih5x1rscg2m64y0z20njj7435q8k7ss575cfw7aipdzfx979a9j"))
               (modules '((guix build utils)))
               (snippet
                '(begin

gnu/packages/aspell.scm

@@ -9,6 +9,8 @@
 ;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
 ;;; Copyright © 2020 Timotej Lazar <timotej.lazar@araneo.si>
 ;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl>
+;;; Copyright © 2020 Jonathan Brielmaier <jonathan.brielmaier@web.de>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -33,7 +35,9 @@
   #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (ice-9 match))
 
@@ -457,3 +461,50 @@ under permissive licensing terms.  See the 'Copyright' file."))))
 (define-word-list-dictionary hunspell-dict-en-us
   "en_US"
   (synopsis "Hunspell dictionary for United States English"))
+
+(define-public ispell
+  (package
+    (name "ispell")
+    (version "3.4.00")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://www.cs.hmc.edu/~geoff/tars/ispell-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1hmfnz55qzfpz7lz0r3m4kkv31smir92ks9s5l1iiwimhr2jxi2x"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:parallel-build? #f
+       #:tests? #f ; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Based on local.h.linux
+             (let* ((grep (assoc-ref inputs "grep"))
+                    (out (assoc-ref outputs "out")))
+               (call-with-output-file "local.h"
+                 (lambda (port)
+                   (format port "#define MINIMENU~%")
+                   (format port "#define USG~%")
+                   (format port "#define HAS_RENAME~%")
+                   (format port "#define CC \"gcc\"~%")
+                   (format port "#define POUNDBANG \"#!~a\"~%" (which "sh"))
+                   (format port "#define EGREPCMD \"~a/bin/grep -Ei\"~%" grep)
+                   (format port "#define BINDIR \"~a/bin\"~%" out)
+                   (format port "#define LIBDIR \"~a/lib/ispell\"~%" out)
+                   (format port "#define MAN1DIR \"~a/share/man/man1\"~%" out)
+                   (format port "#define MAN45DIR \"~a/share/man/man5\"~%" out))))
+             #t)))))
+    (inputs
+     `(("grep" ,grep)
+       ("ncurses" ,ncurses)))
+    (native-inputs
+     `(("bison" ,bison)))
+    (synopsis "Interactive spell-checking tool for Unix")
+    (description "Ispell is an interactive spell-checking tool supporting many
+European languages.")
+    (home-page "https://www.cs.hmc.edu/~geoff/ispell.html")
+    (license bsd-3)))

gnu/packages/astronomy.scm

@@ -159,7 +159,7 @@ programs for the manipulation and analysis of astronomical data.")
 (define-public stellarium
   (package
     (name "stellarium")
-    (version "0.20.2")
+    (version "0.20.3")
     (source
      (origin
        (method url-fetch)
@@ -167,7 +167,7 @@ programs for the manipulation and analysis of astronomical data.")
                            "/releases/download/v" version
                            "/stellarium-" version ".tar.gz"))
        (sha256
-        (base32 "16symz212vjvhfabh39a68qf7d0rm574c6djlibj2qd1q9jgj3j0"))))
+        (base32 "0z5r7b1ac43l330xphxnw54xg7jm87ajix8yl4hkq82cs5ja7097"))))
     (build-system cmake-build-system)
     (inputs
      `(("qtbase" ,qtbase)
@@ -328,7 +328,7 @@ Mechanics, Astrometry and Astrodynamics library.")
        ("freetype" ,freetype)
        ("pango" ,pango)
        ("giflib" ,giflib)
-       ("libjpeg", libjpeg-turbo)
+       ("libjpeg" ,libjpeg-turbo)
        ("libpng" ,libpng)
        ("libtiff" ,libtiff)
        ("netpbm" ,netpbm)

gnu/packages/audio.scm

@@ -33,6 +33,7 @@
 ;;; Copyright © 2020 Jonathan Frederickson <jonathan@terracrypt.net>
 ;;; Copyright © 2020 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1046,7 +1047,7 @@ tools (analyzer, mono/stereo tools, crossovers).")
      `(("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")
+    (synopsis "LV2 port of the CAPS audio plugin collection")
     (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
@@ -1631,7 +1632,7 @@ follower.")
 (define-public fluidsynth
   (package
     (name "fluidsynth")
-    (version "2.1.4")
+    (version "2.1.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1640,7 +1641,7 @@ follower.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1r3khwyw57ybg5m4x0rvdzq7hgw2484sd52k6bm19akbw8yicfna"))))
+                "0ccpq4p1h1g53ng3961g3lh590qnwvpzwdzpl6ai4j6iazq0bh73"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f                      ; no check target
@@ -2030,7 +2031,7 @@ synchronous execution of all clients, and low latency operation.")
 (define-public jack-2
   (package (inherit jack-1)
     (name "jack2")
-    (version "1.9.13")
+    (version "1.9.14")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/jackaudio/jack2/releases/"
@@ -2039,7 +2040,7 @@ synchronous execution of all clients, and low latency operation.")
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
-               "1d1d403jn4366mqig6g8ghr8057b3rn7gs26b5p3rkal34j20qw2"))))
+               "0z11hf55a6mi8h50hfz5wry9pshlwl4mzfwgslghdh40cwv342m2"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f  ; no check target
@@ -2049,6 +2050,10 @@ synchronous execution of all clients, and low latency operation.")
        (modify-phases %standard-phases
          (add-before 'configure 'set-linkflags
            (lambda _
+             ;; Ensure -lstdc++ is the tail of LDFLAGS or the simdtests.cpp
+             ;; will not link with undefined reference to symbol
+             ;; '__gxx_personality_v0@@CXXABI_1.3'
+             (setenv "LDFLAGS" "-lstdc++")
              ;; Add $libdir to the RUNPATH of all the binaries.
              (substitute* "wscript"
                ((".*CFLAGS.*-Wall.*" m)
@@ -2676,20 +2681,21 @@ different audio devices such as ALSA or PulseAudio.")
 (define-public qjackctl
   (package
     (name "qjackctl")
-    (version "0.5.9")
+    (version "0.6.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/qjackctl/qjackctl/"
                                   version "/qjackctl-" version ".tar.gz"))
               (sha256
                (base32
-                "1saywsda9m124rmjp7i3n0llryaliabjxhqhvqr6dm983qy7pypk"))))
+                "0zbb4jlx56qvcqyhx34mbagkqf3wbxgj84hk0ppf5cmcrxv67d4x"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f))                    ; no check target
     (inputs
      `(("jack" ,jack-1)
        ("alsa-lib" ,alsa-lib)
+       ("portaudio" ,portaudio)
        ("qtbase" ,qtbase)
        ("qtx11extras" ,qtx11extras)))
     (native-inputs
@@ -3054,6 +3060,32 @@ that toolkit will work in all hosts that use Suil automatically.
 Suil currently supports every combination of Gtk, Qt, and X11.")
     (license license:isc)))
 
+(define-public libebur128
+  (package
+    (name "libebur128")
+    (version "1.2.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/jiixyj/libebur128")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0n81rnm8dm1zmibkr2v3q79rsd609y0dbbsrbay18njcjva88p0g"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(;; Tests require proprietary .wav files. See
+       ;; https://github.com/jiixyj/libebur128/issues/82.
+       #:tests? #f
+       #:configure-flags '("-DBUILD_STATIC_LIBS=OFF")))
+    (home-page "https://github.com/jiixyj/libebur128")
+    (synopsis "Library implementing the EBU R 128 loudness standard")
+    (description
+     "@code{libebur128} is a C library that implements the EBU R 128 standard
+for loudness normalisation.")
+    (license license:expat)))
+
 (define-public timidity++
   (package
     (name "timidity++")
@@ -3298,7 +3330,7 @@ Tracker 3 S3M and Impulse Tracker IT files.")
 (define-public soundtouch
   (package
     (name "soundtouch")
-    (version "2.1.2")
+    (version "2.2")
     (source
      (origin
        (method git-fetch)
@@ -3307,7 +3339,7 @@ Tracker 3 S3M and Impulse Tracker IT files.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "174wgm3s0inmbnkrlnspxjwm2014qhjhkbdqa5r8rbfi0nzqxzsz"))))
+        (base32 "12i6yg8vvqwyk412lxl2krbfby6hnxld8qxy0k4m5xp4g94jiq4p"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -3959,10 +3991,31 @@ mixers.")
 (define-public python2-pyalsaaudio
   (package-with-python2 python-pyalsaaudio))
 
+(define-public ldacbt
+  (package
+    (name "ldacbt")
+    (version "2.0.2.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/EHfive/ldacBT"
+                                  "/releases/download/v" version
+                                  "/ldacBT-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1d65dms4klzql29abi15i90f41h523kl6mxrz9hi6p5vg37fxn2b"))))
+    (build-system cmake-build-system)
+    (arguments `(#:tests? #f)) ; no check target
+    (home-page "https://github.com/EHfive/ldacBT/")
+    (synopsis "LDAC Bluetooth encoder and ABR library")
+    (description "This package provides an encoder for the LDAC
+high-resolution Bluetooth audio streaming codec for streaming at up to 990
+kbps at 24 bit/96 kHz.")
+    (license license:asl2.0)))
+
 (define-public bluez-alsa
   (package
     (name "bluez-alsa")
-    (version "2.0.0")
+    (version "3.0.0")
     (source (origin
               ;; The tarballs are mere snapshots and don't contain a
               ;; bootstrapped build system.
@@ -3973,11 +4026,12 @@ mixers.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "08mppgnjf1j2733bk9yf0cny6rfxxwiys0s62lz2zd2lpdl6d9lz"))))
+                "1jlsgxyqfhncfhx1sy3ry0dp6p95kd4agh7g2b7g51h0c4cv74h8"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
-       (list (string-append "--with-alsaplugindir="
+       (list "--enable-ldac"
+             (string-append "--with-alsaplugindir="
                             (assoc-ref %outputs "out")
                             "/lib/alsa-lib")
              (string-append "--with-dbusconfdir="
@@ -3993,6 +4047,7 @@ mixers.")
        ("bluez" ,bluez)
        ("dbus" ,dbus)
        ("glib" ,glib)
+       ("ldacbt" ,ldacbt)
        ("libbsd" ,libbsd)
        ("ncurses" ,ncurses)
        ("ortp" ,ortp)
@@ -4464,6 +4519,36 @@ supports both of ID3v1/v2 and APEv2 tags.")
     (home-page "http://tausoft.org/")
     (license license:gpl2+)))
 
+(define-public libsoundio
+  (package
+    (name "libsoundio")
+    (version "2.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/andrewrk/libsoundio")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "12l4rvaypv87vigdrmjz48d4d6sq4gfxf5asvnc4adyabxb73i4x"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f)) ;no tests included
+    (inputs
+     `(("alsa-lib" ,alsa-lib)
+       ("jack" ,jack-1)
+       ("pulseaudio" ,pulseaudio)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://libsound.io")
+    (synopsis "C library for real-time audio input and output")
+    (description "@code{libsoundio} is a C library providing audio input and
+output.  The API is suitable for real-time software such as digital audio
+workstations as well as consumer software such as music players.")
+    (license license:expat)))
+
 (define-public redkite
   (package
     (name "redkite")
@@ -4483,7 +4568,7 @@ supports both of ID3v1/v2 and APEv2 tags.")
     (inputs
      `(("cairo" ,cairo)))
     (native-inputs
-     `(("pkg-config", pkg-config)))
+     `(("pkg-config" ,pkg-config)))
     (synopsis "Small GUI toolkit")
     (description "Redkite is a small GUI toolkit developed in C++17 and
 inspired from other well known GUI toolkits such as Qt and GTK.  It is
@@ -4629,7 +4714,7 @@ in the package.")
     `(("libsamplerate" ,libsamplerate)
       ("libsndfile" ,libsndfile)))
    (native-inputs
-     `(("pkg-config", pkg-config)))
+     `(("pkg-config" ,pkg-config)))
    (synopsis "Library for reading and resampling audio files")
    (description "libaudec is a wrapper library over ffmpeg, sndfile and
 libsamplerate for reading and resampling audio files, based on Robin Gareus'
@@ -4657,11 +4742,11 @@ libsamplerate for reading and resampling audio files, based on Robin Gareus'
        `("-Delf-tests=true" ; for checking symbol visibility
          "-Donline-tests=true"))) ; for checking URI existence
     (inputs
-      `(("curl", curl)
+      `(("curl" ,curl)
-        ("libelf", libelf)
+        ("libelf" ,libelf)
-        ("lilv", lilv)))
+        ("lilv" ,lilv)))
     (native-inputs
-      `(("pkg-config", pkg-config)))
+      `(("pkg-config" ,pkg-config)))
     (synopsis "LV2 plugin lint tool")
     (description "lv2lint is an LV2 lint-like tool that checks whether a
 given plugin and its UI(s) match up with the provided metadata and adhere
@@ -4692,11 +4777,11 @@ to well-known best practices.")
       (modify-phases %standard-phases
         (delete 'configure))))
     (inputs
-      `(("jalv", jalv)
+      `(("jalv" ,jalv)
-        ("lilv", lilv)))
+        ("lilv" ,lilv)))
     (native-inputs
-      `(("help2man", help2man)
+      `(("help2man" ,help2man)
-        ("pkg-config", pkg-config)))
+        ("pkg-config" ,pkg-config)))
     (synopsis "Documentation generator for LV2 plugins")
     (description
       "lv2toweb allows the user to create an xhtml page with information

gnu/packages/aux-files/guile-launcher.c

@@ -0,0 +1,46 @@
+/* GNU Guix --- Functional package management for GNU
+   Copyright 1996-1997,2000-2001,2006,2008,2011,2013,2018
+      Free Software Foundation, Inc.
+   Copyright (C) 2020 Ludovic Courtès <ludo@gnu.org>
+
+   This file is part of GNU Guix.
+
+   GNU Guix is free software; you can redistribute it and/or modify it
+   under the terms of the GNU General Public License as published by
+   the Free Software Foundation; either version 3 of the License, or (at
+   your option) any later version.
+
+   GNU Guix is distributed in the hope that it will be useful, but
+   WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.  */
+
+/* This file implements a variant of the 'guile' executable that does not
+   complain about locale issues.  */
+
+#include <locale.h>
+#include <libguile.h>
+
+static void
+inner_main (void *unused, int argc, char **argv)
+{
+  scm_shell (argc, argv);
+}
+
+int
+main (int argc, char **argv)
+{
+  /* Try to install the current locale; remain silent if it fails.  */
+  if (setlocale (LC_ALL, "") == NULL)
+    /* The 'guix pull'-provided 'guix' includes at least en_US.utf8 so use
+       that.  That gives us UTF-8 support for 'scm_to_locale_string', etc.,
+       which is always preferable over the C locale.  */
+    setlocale (LC_ALL, "en_US.utf8");
+
+  scm_install_gmp_memory_functions = 1;
+  scm_boot_guile (argc, argv, inner_main, 0);
+  return 0; /* never reached */
+}

gnu/packages/aux-files/linux-libre/4.19-arm.conf

@@ -1023,7 +1023,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 CONFIG_NET_KEY_MIGRATE=y
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/aux-files/linux-libre/4.19-arm64.conf

@@ -966,7 +966,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 CONFIG_NET_KEY_MIGRATE=y
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/aux-files/linux-libre/4.19-i686.conf

@@ -1053,7 +1053,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 # CONFIG_NET_KEY_MIGRATE is not set
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/aux-files/linux-libre/4.19-x86_64.conf

@@ -1063,7 +1063,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 # CONFIG_NET_KEY_MIGRATE is not set
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/aux-files/linux-libre/5.4-arm.conf

@@ -1034,7 +1034,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 CONFIG_NET_KEY_MIGRATE=y
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/aux-files/linux-libre/5.4-arm64.conf

@@ -1008,7 +1008,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 CONFIG_NET_KEY_MIGRATE=y
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/aux-files/linux-libre/5.4-i686.conf

@@ -1027,7 +1027,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 # CONFIG_NET_KEY_MIGRATE is not set
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/aux-files/linux-libre/5.4-x86_64.conf

@@ -1044,7 +1044,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 # CONFIG_NET_KEY_MIGRATE is not set
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/aux-files/linux-libre/5.8-arm.conf

@@ -1056,7 +1056,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 CONFIG_NET_KEY_MIGRATE=y
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/aux-files/linux-libre/5.8-arm64.conf

@@ -1048,7 +1048,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 CONFIG_NET_KEY_MIGRATE=y
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/aux-files/linux-libre/5.8-i686.conf

@@ -1035,7 +1035,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 # CONFIG_NET_KEY_MIGRATE is not set
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/aux-files/linux-libre/5.8-x86_64.conf

@@ -1061,7 +1061,8 @@ CONFIG_XFRM_IPCOMP=m
 CONFIG_NET_KEY=m
 # CONFIG_NET_KEY_MIGRATE is not set
 # CONFIG_SMC is not set
-# CONFIG_XDP_SOCKETS is not set
+CONFIG_XDP_SOCKETS=y
+CONFIG_XDP_SOCKETS_DIAG=m
 CONFIG_INET=y
 CONFIG_IP_MULTICAST=y
 CONFIG_IP_ADVANCED_ROUTER=y

gnu/packages/avahi.scm

@@ -74,7 +74,7 @@
        ("expat" ,expat)
        ("gdbm" ,gdbm)
        ("glib" ,glib)
-       ("libcap" ,libcap)            ;to enable chroot support in avahi-daemon
+       ("libcap" ,libcap-2.31)       ;to enable chroot support in avahi-daemon
        ("libdaemon" ,libdaemon)
        ("libevent" ,libevent)))
     (native-inputs

gnu/packages/axoloti.scm

@@ -527,7 +527,7 @@ patcher application.")))
                (install-file "dist/Axoloti.jar" share)
 
                ;; Install old firmware
-               (let ((target (string-append share "/old_firmware/"))
+               (let ((target (string-append share "/old_firmware/firmware-1.0.12"))
                      (old-firmware
                       (string-append (assoc-ref inputs "axoloti-runtime")
                                      "/share/axoloti/firmware/")))
@@ -557,7 +557,7 @@ patcher application.")))
                                         toolchain
                                         "/arm-none-eabi/include:"
                                         toolchain
-                                        "/arm-none-eabi/include/arm-none-eabi/armv7e-m")))
+                                        "/arm-none-eabi/include/arm-none-eabi/thumb/v7e-m")))
                        (display
                         (string-append "#!" (which "sh") "\n"
                                        "export CROSS_CPATH=" includes "\n"

gnu/packages/backup.scm

@@ -569,13 +569,13 @@ detection, and lossless compression.")
 (define-public borg
   (package
     (name "borg")
-    (version "1.1.13")
+    (version "1.1.14")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "borgbackup" version))
        (sha256
-        (base32 "089q3flmwbz7dc28zlscwylf64kgck3jf1n6lqpwww8hlrk8cjhn"))
+        (base32 "1fpdj73cgp96xwasdcifxl7q2pr1my2f4vfdjpv771llri3hgfvx"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -606,7 +606,7 @@ detection, and lossless compression.")
            #t))))
     (build-system python-build-system)
     (arguments
-     `(#:modules ((srfi srfi-26) ; for cut
+     `(#:modules ((srfi srfi-26)        ; for cut
                   (guix build utils)
                   (guix build python-build-system))
        #:phases
@@ -1066,7 +1066,7 @@ other storage medium.  Subsequent incremental backups can then be layered on
 top of the full backup.  The restore command performs the inverse function of
 dump; it can restore a full backup of a file system.  Single files and
 directory subtrees may also be restored from full or partial backups in
-interractive mode.")
+interactive mode.")
     (license license:bsd-3)))
 
 (define-public burp
@@ -1103,7 +1103,7 @@ interractive mode.")
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
-       ("check" ,check)
+       ("check" ,check-0.14)
        ("pkg-config" ,pkg-config)))
     (home-page "https://burp.grke.org")
     (synopsis "Differential backup and restore")

gnu/packages/base.scm

@@ -339,7 +339,7 @@ used to apply commands with arbitrarily long arguments.")
              ,@(if (and (not (%current-target-system))
                         (member (%current-system)
                                 (package-supported-systems libcap)))
-             `(("libcap" ,libcap))  ;capability support in 'ls', etc.
+             `(("libcap" ,libcap-2.31))        ;capability support in 'ls', etc.
              '())))
    (native-inputs
     ;; Perl is needed to run tests in native builds, and to run the bundled
@@ -1238,7 +1238,7 @@ command.")
 (define-public tzdata
   (package
     (name "tzdata")
-    (version "2020a")
+    (version "2020b")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -1246,7 +1246,7 @@ command.")
                    version ".tar.gz"))
              (sha256
               (base32
-               "18lrp0zh8m931jjlrv8lvjas4ka5dfkzdbwnbw5lwd2dlbn62wal"))))
+               "02g88pbw82zr36x9dz5ib4sq6bfq253yx5hbhnfyhp143naky1cv"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f
@@ -1296,7 +1296,7 @@ command.")
                                 version ".tar.gz"))
                           (sha256
                            (base32
-                            "0sfnlqw1p93r7klny69rwr94fh22mz632h52phgzfgg01q9gfakx"))))))
+                            "1nj3zvqpy5lm6w365p9ynz4i5arq4fiy8ldq55v4z9p49nagivs7"))))))
     (home-page "https://www.iana.org/time-zones")
     (synopsis "Database of current and historical time zones")
     (description "The Time Zone Database (often called tz or zoneinfo)

gnu/packages/benchmark.scm

@@ -46,14 +46,14 @@
 (define-public fio
   (package
     (name "fio")
-    (version "3.22")
+    (version "3.23")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://brick.kernel.dk/snaps/"
                                   "fio-" version ".tar.bz2"))
               (sha256
                (base32
-                "0f2x917600y6k0xs34ixgfjm4v1ylbh8svpkqi07xy3474g5s2rv"))))
+                "0cy32431hv0i84yrryna5byj4r610n6i1rm8nfflnrznbf051axs"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"

gnu/packages/bioconductor.scm

@@ -4,6 +4,8 @@
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
+;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1113,7 +1115,7 @@ how the coverage distributed across the genome.")
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-biocgenerics" ,r-biocgenerics)
-      ("r-fastcluster", r-fastcluster)
+      ("r-fastcluster" ,r-fastcluster)
       ("r-ggplot2" ,r-ggplot2)
       ("r-gviz" ,r-gviz)
       ("r-plyr" ,r-plyr)
@@ -1607,14 +1609,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "2.16.0")
+    (version "2.16.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5"))))
+         "11y9kigdikqcd0cnksh306nsaadak0kgivk7773mv3yszrxxwzj1"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (inputs
@@ -1795,14 +1797,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.22.3")
+    (version "3.22.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y"))))
+         "0wxgjdikinkqj7jvs2725ak0291q6zhikyf1c93w8cngwvd9i1gq"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2705,13 +2707,13 @@ gene and isoform level using RNA-seq data")
 (define-public r-karyoploter
   (package
     (name "r-karyoploter")
-    (version "1.14.0")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "karyoploteR" version))
               (sha256
                (base32
-                "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs"))))
+                "1wlnzkq58baqj9854nzf5rbglchb2xy4wsp3s0q8xfq8v0p3baxf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -2734,7 +2736,7 @@ gene and isoform level using RNA-seq data")
     (home-page "https://bioconductor.org/packages/karyoploteR/")
     (synopsis "Plot customizable linear genomes displaying arbitrary data")
     (description "This package creates karyotype plots of arbitrary genomes and
-offers a complete set of functions to plot arbitrary data on them.  It mimicks
+offers a complete set of functions to plot arbitrary data on them.  It mimics
 many R base graphics functions coupling them with a coordinate change function
 automatically mapping the chromosome and data coordinates into the plot
 coordinates.")
@@ -3626,14 +3628,14 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.14.1")
+    (version "2.14.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln"))))
+         "02r7m1x6g8bb7q8l0hpvakdzdv5v1nplhx5lbiy798a7c3xg895b"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3672,7 +3674,7 @@ sets of GO terms, gene products and gene clusters.")
     (description
      "Genome wide studies of translational control is emerging as a tool to
 study various biological conditions.  The output from such analysis is both
-the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
+the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
 involved in translation (the actively translating mRNA level) for each mRNA.
 The standard analysis of such data strives towards identifying differential
 translational between two or more sample classes - i.e.  differences in
@@ -4362,14 +4364,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.12.4")
+    (version "1.12.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh"))))
+         "1103daz82k97vzmxjmf7jwm2nd3w8i0jwplrsi9996bkih11qwbf"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4841,7 +4843,7 @@ a more complex way than the simple GC content.  Instead, the base types (A, T,
 G or C) at each position along the probe determine the affinity of each probe.
 The parameters of the position-specific base contributions to the probe
 affinity is estimated in an NSB experiment in which only NSB but no
-gene-specific bidning is expected.")
+gene-specific binding is expected.")
     ;; Any version of the LGPL
     (license license:lgpl2.1+)))
 
@@ -5060,14 +5062,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.10.1")
+    (version "3.10.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "1aa11gy1v7kkamv3hsnvdx715q8f1saw9p664j6wifyjj0hx13kn"))))
+         "0sk53jcl7sjrpw2ncdpl8sw1b1j9mizlrj517rinr1qrbm6lsn8f"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -7159,14 +7161,14 @@ data.")
 (define-public r-activedriverwgs
   (package
     (name "r-activedriverwgs")
-    (version "1.1.0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActiveDriverWGS" version))
        (sha256
         (base32
-         "0l6h0f54zjvcx19ngq3kp01dypsjqf28vssjm8yzccmpyacfypag"))))
+         "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
     (properties
      `((upstream-name . "ActiveDriverWGS")))
     (build-system r-build-system)
@@ -7245,14 +7247,14 @@ gene expression.")
 (define-public r-bgx
   (package
     (name "r-bgx")
-    (version "1.54.0")
+    (version "1.54.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bgx" version))
        (sha256
         (base32
-         "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx"))))
+         "0a10fg9n5p024jrmbis102gqpbz23sc6vdn1sal2697hlxikzb46"))))
     (properties `((upstream-name . "bgx")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7476,7 +7478,7 @@ networks and estimated fluxes can be visualized with hypergraphs.")
 safety and convenience features to the @code{filebacked.big.matrix} class from
 the @code{bigmemory} package.  @code{BigMatrix} protects against segfaults by
 monitoring and gracefully restoring the connection to on-disk data and it also
-protects against accidental data modification with a filesystem-based
+protects against accidental data modification with a file-system-based
 permissions system.  Utilities are provided for using @code{BigMatrix}-derived
 classes as @code{assayData} matrices within the @code{Biobase} package's
 @code{eSet} family of classes.  @code{BigMatrix} provides some optimizations
@@ -8185,14 +8187,14 @@ truncated data.")
 (define-public r-interval
   (package
     (name "r-interval")
-    (version "1.1-0.1")
+    (version "1.1-0.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "interval" version))
        (sha256
         (base32
-         "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8"))))
+         "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
     (properties `((upstream-name . "interval")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8212,14 +8214,14 @@ plot them, and perform logrank or Wilcoxon type tests.")
 (define-public r-fhtest
   (package
     (name "r-fhtest")
-    (version "1.4")
+    (version "1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "FHtest" version))
        (sha256
         (base32
-         "1wsn0j9ydpp9nfswiqg21p09kgkvaq8fh0y0h8syqgizah7i8vs2"))))
+         "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
     (properties `((upstream-name . "FHtest")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8242,3 +8244,483 @@ with:
 @end itemize
 ")
     (license license:gpl2+)))
+
+(define-public r-fourcseq
+  (package
+    (name "r-fourcseq")
+    (version "1.22.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "FourCSeq" version))
+       (sha256
+        (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
+    (properties `((upstream-name . "FourCSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biostrings" ,r-biostrings)
+       ("r-deseq2" ,r-deseq2)
+       ("r-fda" ,r-fda)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggbio" ,r-ggbio)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gtools" ,r-gtools)
+       ("r-lsd" ,r-lsd)
+       ("r-matrix" ,r-matrix)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page
+     "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
+    (synopsis "Analysis of multiplexed 4C sequencing data")
+    (description
+     "This package is an R package dedicated to the analysis of (multiplexed)
+4C sequencing data.  @code{r-fourcseq} provides a pipeline to detect specific
+interactions between DNA elements and identify differential interactions
+between conditions.  The statistical analysis in R starts with individual bam
+files for each sample as inputs.  To obtain these files, the package contains
+a Python script to demultiplex libraries and trim off primer sequences.  With
+a standard alignment software the required bam files can be then be
+generated.")
+    (license license:gpl3+)))
+
+(define-public r-preprocesscore
+  (package
+    (name "r-preprocesscore")
+    (version "1.50.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "preprocessCore" version))
+       (sha256
+        (base32
+         "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
+    (properties
+     `((upstream-name . "preprocessCore")))
+    (build-system r-build-system)
+    (home-page "https://github.com/bmbolstad/preprocessCore")
+    (synopsis "Collection of pre-processing functions")
+    (description
+     "This package provides a library of core pre-processing and normalization
+routines.")
+    (license license:lgpl2.0+)))
+
+;; This is a CRAN package, but it depends on preprocessorcore, which is a
+;; Bioconductor package.
+(define-public r-wgcna
+  (package
+    (name "r-wgcna")
+    (version "1.69")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "WGCNA" version))
+       (sha256
+        (base32
+         "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
+    (properties `((upstream-name . "WGCNA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-doparallel" ,r-doparallel)
+       ("r-dynamictreecut" ,r-dynamictreecut)
+       ("r-fastcluster" ,r-fastcluster)
+       ("r-foreach" ,r-foreach)
+       ("r-go-db" ,r-go-db)
+       ("r-hmisc" ,r-hmisc)
+       ("r-impute" ,r-impute)
+       ("r-rcpp" ,r-rcpp)
+       ("r-survival" ,r-survival)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-preprocesscore" ,r-preprocesscore)))
+    (home-page
+     "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
+    (synopsis "Weighted correlation network analysis")
+    (description
+     "This package provides functions necessary to perform Weighted
+Correlation Network Analysis on high-dimensional data.  It includes functions
+for rudimentary data cleaning, construction and summarization of correlation
+networks, module identification and functions for relating both variables and
+modules to sample traits.  It also includes a number of utility functions for
+data manipulation and visualization.")
+    (license license:gpl2+)))
+
+(define-public r-rgraphviz
+  (package
+    (name "r-rgraphviz")
+    (version "2.32.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rgraphviz" version))
+       (sha256
+        (base32
+         "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
+    (properties `((upstream-name . "Rgraphviz")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-reproducible
+           (lambda _
+             ;; The replacement value is taken from src/graphviz/builddate.h
+             (substitute* "src/graphviz/configure"
+               (("VERSION_DATE=.*")
+                "VERSION_DATE=20200427.2341\n"))
+             #t)))))
+    ;; FIXME: Rgraphviz bundles the sources of an older variant of
+    ;; graphviz.  It does not build with the latest version of graphviz, so
+    ;; we do not add graphviz to the inputs.
+    (inputs `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-graph" ,r-graph)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://bioconductor.org/packages/Rgraphviz")
+    (synopsis "Plotting capabilities for R graph objects")
+    (description
+     "This package interfaces R with the graphviz library for plotting R graph
+objects from the @code{graph} package.")
+    (license license:epl1.0)))
+
+(define-public r-fithic
+  (package
+    (name "r-fithic")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "FitHiC" version))
+              (sha256
+               (base32
+                "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
+    (properties `((upstream-name . "FitHiC")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)
+       ("r-fdrtool" ,r-fdrtool)
+       ("r-rcpp" ,r-rcpp)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/FitHiC")
+    (synopsis "Confidence estimation for intra-chromosomal contact maps")
+    (description
+     "Fit-Hi-C is a tool for assigning statistical confidence estimates to
+intra-chromosomal contact maps produced by genome-wide genome architecture
+assays such as Hi-C.")
+    (license license:gpl2+)))
+
+(define-public r-hitc
+  (package
+    (name "r-hitc")
+    (version "1.32.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "HiTC" version))
+              (sha256
+               (base32
+                "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
+    (properties `((upstream-name . "HiTC")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rtracklayer" ,r-rtracklayer)))
+    (home-page "https://bioconductor.org/packages/HiTC")
+    (synopsis "High throughput chromosome conformation capture analysis")
+    (description
+     "The HiTC package was developed to explore high-throughput \"C\" data
+such as 5C or Hi-C.  Dedicated R classes as well as standard methods for
+quality controls, normalization, visualization, and further analysis are also
+provided.")
+    (license license:artistic2.0)))
+
+(define-public r-hdf5array
+  (package
+    (name "r-hdf5array")
+    (version "1.16.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "HDF5Array" version))
+       (sha256
+        (base32
+         "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
+    (properties `((upstream-name . "HDF5Array")))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-rhdf5lib" ,r-rhdf5lib)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/HDF5Array")
+    (synopsis "HDF5 back end for DelayedArray objects")
+    (description "This package provides an array-like container for convenient
+access and manipulation of HDF5 datasets.  It supports delayed operations and
+block processing.")
+    (license license:artistic2.0)))
+
+(define-public r-rhdf5lib
+  (package
+    (name "r-rhdf5lib")
+    (version "1.10.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rhdf5lib" version))
+       (sha256
+        (base32
+         "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Delete bundled binaries
+           (delete-file-recursively "src/wininclude/")
+           (delete-file-recursively "src/winlib-4.9.3/")
+           (delete-file-recursively "src/winlib-8.3.0/")
+           (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
+           #t))))
+    (properties `((upstream-name . "Rhdf5lib")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-use-bundled-hdf5
+           (lambda* (#:key inputs #:allow-other-keys)
+             (for-each delete-file '("configure" "configure.ac"))
+             ;; Do not make other packages link with the proprietary libsz.
+             (substitute* "R/zzz.R"
+               ((" \"%s/libsz.a\"") ""))
+             (with-directory-excursion "src"
+               (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
+               (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
+                            "hdf5")
+               ;; Remove timestamp and host system information to make
+               ;; the build reproducible.
+               (substitute* "hdf5/src/libhdf5.settings.in"
+                 (("Configured on: @CONFIG_DATE@")
+                  "Configured on: Guix")
+                 (("Uname information:.*")
+                  "Uname information: Linux\n")
+                 ;; Remove unnecessary store reference.
+                 (("C Compiler:.*")
+                  "C Compiler: GCC\n"))
+               (rename-file "Makevars.in" "Makevars")
+               (substitute* "Makevars"
+                 (("@ZLIB_LIB@") "-lz")
+                 (("@ZLIB_INCLUDE@") "")
+                 (("HDF5_CXX_LIB=.*")
+                  (string-append "HDF5_CXX_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
+                 (("HDF5_LIB=.*")
+                  (string-append "HDF5_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
+                 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
+                 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
+                 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
+                 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
+                 (("HDF5_HL_LIB=.*")
+                  (string-append "HDF5_HL_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
+                 (("HDF5_HL_CXX_LIB=.*")
+                  (string-append "HDF5_HL_CXX_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
+                 ;; szip is non-free software
+                 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
+                 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("hdf5" ,hdf5-1.10)))
+    (native-inputs
+     `(("hdf5-source" ,(package-source hdf5-1.10))
+       ("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/Rhdf5lib")
+    (synopsis "HDF5 library as an R package")
+    (description "This package provides C and C++ HDF5 libraries for use in R
+packages.")
+    (license license:artistic2.0)))
+
+(define-public r-beachmat
+  (package
+    (name "r-beachmat")
+    (version "2.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "beachmat" version))
+       (sha256
+        (base32
+         "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-matrix" ,r-matrix)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/beachmat")
+    (synopsis "Compiling Bioconductor to handle each matrix type")
+    (description "This package provides a consistent C++ class interface for a
+variety of commonly used matrix types, including sparse and HDF5-backed
+matrices.")
+    (license license:gpl3)))
+
+(define-public r-singlecellexperiment
+  (package
+    (name "r-singlecellexperiment")
+    (version "1.10.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "SingleCellExperiment" version))
+       (sha256
+        (base32
+         "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
+    (properties
+     `((upstream-name . "SingleCellExperiment")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/SingleCellExperiment")
+    (synopsis "S4 classes for single cell data")
+    (description "This package defines an S4 class for storing data from
+single-cell experiments.  This includes specialized methods to store and
+retrieve spike-in information, dimensionality reduction coordinates and size
+factors for each cell, along with the usual metadata for genes and
+libraries.")
+    (license license:gpl3)))
+
+(define-public r-scater
+  (package
+    (name "r-scater")
+    (version "1.16.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "scater" version))
+              (sha256
+               (base32
+                "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocneighbors" ,r-biocneighbors)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biocsingular" ,r-biocsingular)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+       ("r-ggbeeswarm" ,r-ggbeeswarm)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rlang" ,r-rlang)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-viridis" ,r-viridis)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/davismcc/scater")
+    (synopsis "Single-cell analysis toolkit for gene expression data in R")
+    (description "This package provides a collection of tools for doing
+various analyses of single-cell RNA-seq gene expression data, with a focus on
+quality control.")
+    (license license:gpl2+)))
+
+(define-public r-scran
+  (package
+    (name "r-scran")
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scran" version))
+       (sha256
+        (base32
+         "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-bh" ,r-bh)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocneighbors" ,r-biocneighbors)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biocsingular" ,r-biocsingular)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+       ("r-dqrng" ,r-dqrng)
+       ("r-edger" ,r-edger)
+       ("r-igraph" ,r-igraph)
+       ("r-iranges" ,r-iranges)
+       ("r-limma" ,r-limma)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scater" ,r-scater)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-statmod" ,r-statmod)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/scran")
+    (synopsis "Methods for single-cell RNA-Seq data analysis")
+    (description "This package implements a variety of low-level analyses of
+single-cell RNA-seq data.  Methods are provided for normalization of
+cell-specific biases, assignment of cell cycle phase, and detection of highly
+variable and significantly correlated genes.")
+    (license license:gpl3)))
+
+(define-public r-delayedmatrixstats
+  (package
+    (name "r-delayedmatrixstats")
+    (version "1.10.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DelayedMatrixStats" version))
+       (sha256
+        (base32
+         "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
+    (properties
+     `((upstream-name . "DelayedMatrixStats")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-hdf5array" ,r-hdf5array)
+       ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
+    (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
+    (description
+     "This package provides a port of the @code{matrixStats} API for use with
+@code{DelayedMatrix} objects from the @code{DelayedArray} package.  It
+contains high-performing functions operating on rows and columns of
+@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
+@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}.  Functions
+are optimized per data type and for subsetted calculations such that both
+memory usage and processing time is minimized.")
+    (license license:expat)))

gnu/packages/bioinformatics.scm

@@ -11,7 +11,7 @@
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
-;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
@@ -4225,6 +4225,13 @@ performance.")
                (base32
                 "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0"))))
     (build-system gnu-build-system)
+    ;; Let htslib translate "gs://" and "s3://" to regular https links with
+    ;; "--enable-gcs" and "--enable-s3". For these options to work, we also
+    ;; need to set "--enable-libcurl".
+    (arguments
+     `(#:configure-flags '("--enable-gcs"
+                           "--enable-libcurl"
+                           "--enable-s3")))
     (inputs
      `(("curl" ,curl)
        ("openssl" ,openssl)))
@@ -4496,7 +4503,7 @@ sequencing tag position and orientation.")
 (define-public mafft
   (package
     (name "mafft")
-    (version "7.394")
+    (version "7.471")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4505,7 +4512,7 @@ sequencing tag position and orientation.")
               (file-name (string-append name "-" version ".tgz"))
               (sha256
                (base32
-                "0bacjkxfg944p5khhyh5rd4y7wkjc9qk4v2jjj442sqlq0f8ar7b"))))
+                "0r1973fx2scq4712zdqfy67wkzqj0c0bhrdy4jxhvq40mdxyry30"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no automated tests, though there are tests in the read me
@@ -4568,7 +4575,7 @@ sequencing tag position and orientation.")
        ("gawk" ,gawk)
        ("grep" ,grep)
        ("coreutils" ,coreutils)))
-    (home-page "http://mafft.cbrc.jp/alignment/software/")
+    (home-page "https://mafft.cbrc.jp/alignment/software/")
     (synopsis "Multiple sequence alignment program")
     (description
      "MAFFT offers a range of multiple alignment methods for nucleotide and
@@ -4576,7 +4583,7 @@ protein sequences.  For instance, it offers L-INS-i (accurate; for alignment
 of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
 sequences).")
     (license (license:non-copyleft
-              "http://mafft.cbrc.jp/alignment/software/license.txt"
+              "https://mafft.cbrc.jp/alignment/software/license.txt"
               "BSD-3 with different formatting"))))
 
 (define-public mash
@@ -7539,13 +7546,13 @@ also known as views, in a controlled vocabulary.")
 (define-public r-biocstyle
   (package
     (name "r-biocstyle")
-    (version "2.16.0")
+    (version "2.16.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "07rjl2n4sazdg581zh7w3yykzphgr2gpz41ba4ryqs7347vh9nbf"))))
+                "09sz2bnbfbj8wz16k0q8xrvag9fldxqyp5vbg9pvd9skh28hv7c7"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
@@ -8848,13 +8855,13 @@ of gene-level counts.")
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.32.2")
+    (version "2.32.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "1v6ygi0avh3gmaj2ld2nr7vww4ipw39b5kqci9w27i3ja985lb8j"))))
+                "0fnx60dpf6s2qwq48lg98g18g8k7wgm66pw0kamlbb7l2hnwycvf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rhdf5lib" ,r-rhdf5lib)))
@@ -10272,14 +10279,14 @@ interval to data view, mismatch pileup, and several splicing summaries.")
 (define-public r-gqtlbase
   (package
     (name "r-gqtlbase")
-    (version "1.20.0")
+    (version "1.20.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gQTLBase" version))
        (sha256
         (base32
-         "06xvzp4fn3qfa46ggg8kxi267gbyd821vvx4040173xkqxpr0g5j"))))
+         "1ly14vhhqxjpbxjypi6ppd37dycabdhf4ny4nsvp9969k418zv41"))))
     (properties `((upstream-name . "gQTLBase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10599,343 +10606,6 @@ EMBL-EBI GWAS catalog.")
 visualizations for publication-quality multi-panel figures.")
     (license license:gpl2+)))
 
-(define-public r-fithic
-  (package
-    (name "r-fithic")
-    (version "1.14.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "FitHiC" version))
-              (sha256
-               (base32
-                "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
-    (properties `((upstream-name . "FitHiC")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-data-table" ,r-data-table)
-       ("r-fdrtool" ,r-fdrtool)
-       ("r-rcpp" ,r-rcpp)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/FitHiC")
-    (synopsis "Confidence estimation for intra-chromosomal contact maps")
-    (description
-     "Fit-Hi-C is a tool for assigning statistical confidence estimates to
-intra-chromosomal contact maps produced by genome-wide genome architecture
-assays such as Hi-C.")
-    (license license:gpl2+)))
-
-(define-public r-hitc
-  (package
-    (name "r-hitc")
-    (version "1.32.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "HiTC" version))
-              (sha256
-               (base32
-                "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
-    (properties `((upstream-name . "HiTC")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rtracklayer" ,r-rtracklayer)))
-    (home-page "https://bioconductor.org/packages/HiTC")
-    (synopsis "High throughput chromosome conformation capture analysis")
-    (description
-     "The HiTC package was developed to explore high-throughput \"C\" data
-such as 5C or Hi-C.  Dedicated R classes as well as standard methods for
-quality controls, normalization, visualization, and further analysis are also
-provided.")
-    (license license:artistic2.0)))
-
-(define-public r-hdf5array
-  (package
-    (name "r-hdf5array")
-    (version "1.16.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "HDF5Array" version))
-       (sha256
-        (base32
-         "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
-    (properties `((upstream-name . "HDF5Array")))
-    (build-system r-build-system)
-    (inputs
-     `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-rhdf5" ,r-rhdf5)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://bioconductor.org/packages/HDF5Array")
-    (synopsis "HDF5 back end for DelayedArray objects")
-    (description "This package provides an array-like container for convenient
-access and manipulation of HDF5 datasets.  It supports delayed operations and
-block processing.")
-    (license license:artistic2.0)))
-
-(define-public r-rhdf5lib
-  (package
-    (name "r-rhdf5lib")
-    (version "1.10.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "Rhdf5lib" version))
-       (sha256
-        (base32
-         "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           ;; Delete bundled binaries
-           (delete-file-recursively "src/wininclude/")
-           (delete-file-recursively "src/winlib-4.9.3/")
-           (delete-file-recursively "src/winlib-8.3.0/")
-           (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
-           #t))))
-    (properties `((upstream-name . "Rhdf5lib")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'do-not-use-bundled-hdf5
-           (lambda* (#:key inputs #:allow-other-keys)
-             (for-each delete-file '("configure" "configure.ac"))
-             ;; Do not make other packages link with the proprietary libsz.
-             (substitute* "R/zzz.R"
-               ((" \"%s/libsz.a\"") ""))
-             (with-directory-excursion "src"
-               (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
-               (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
-                            "hdf5")
-               ;; Remove timestamp and host system information to make
-               ;; the build reproducible.
-               (substitute* "hdf5/src/libhdf5.settings.in"
-                 (("Configured on: @CONFIG_DATE@")
-                  "Configured on: Guix")
-                 (("Uname information:.*")
-                  "Uname information: Linux\n")
-                 ;; Remove unnecessary store reference.
-                 (("C Compiler:.*")
-                  "C Compiler: GCC\n"))
-               (rename-file "Makevars.in" "Makevars")
-               (substitute* "Makevars"
-                 (("@ZLIB_LIB@") "-lz")
-                 (("@ZLIB_INCLUDE@") "")
-                 (("HDF5_CXX_LIB=.*")
-                  (string-append "HDF5_CXX_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
-                 (("HDF5_LIB=.*")
-                  (string-append "HDF5_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
-                 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
-                 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
-                 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
-                 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
-                 (("HDF5_HL_LIB=.*")
-                  (string-append "HDF5_HL_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
-                 (("HDF5_HL_CXX_LIB=.*")
-                  (string-append "HDF5_HL_CXX_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
-                 ;; szip is non-free software
-                 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
-                 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
-             #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("hdf5" ,hdf5-1.10)))
-    (native-inputs
-     `(("hdf5-source" ,(package-source hdf5-1.10))
-       ("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/Rhdf5lib")
-    (synopsis "HDF5 library as an R package")
-    (description "This package provides C and C++ HDF5 libraries for use in R
-packages.")
-    (license license:artistic2.0)))
-
-(define-public r-beachmat
-  (package
-    (name "r-beachmat")
-    (version "2.4.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "beachmat" version))
-       (sha256
-        (base32
-         "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-matrix" ,r-matrix)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/beachmat")
-    (synopsis "Compiling Bioconductor to handle each matrix type")
-    (description "This package provides a consistent C++ class interface for a
-variety of commonly used matrix types, including sparse and HDF5-backed
-matrices.")
-    (license license:gpl3)))
-
-(define-public r-singlecellexperiment
-  (package
-    (name "r-singlecellexperiment")
-    (version "1.10.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "SingleCellExperiment" version))
-       (sha256
-        (base32
-         "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
-    (properties
-     `((upstream-name . "SingleCellExperiment")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/SingleCellExperiment")
-    (synopsis "S4 classes for single cell data")
-    (description "This package defines an S4 class for storing data from
-single-cell experiments.  This includes specialized methods to store and
-retrieve spike-in information, dimensionality reduction coordinates and size
-factors for each cell, along with the usual metadata for genes and
-libraries.")
-    (license license:gpl3)))
-
-(define-public r-scater
-  (package
-    (name "r-scater")
-    (version "1.16.2")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "scater" version))
-              (sha256
-               (base32
-                "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocneighbors" ,r-biocneighbors)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biocsingular" ,r-biocsingular)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-ggbeeswarm" ,r-ggbeeswarm)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rlang" ,r-rlang)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-viridis" ,r-viridis)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/davismcc/scater")
-    (synopsis "Single-cell analysis toolkit for gene expression data in R")
-    (description "This package provides a collection of tools for doing
-various analyses of single-cell RNA-seq gene expression data, with a focus on
-quality control.")
-    (license license:gpl2+)))
-
-(define-public r-scran
-  (package
-    (name "r-scran")
-    (version "1.16.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "scran" version))
-       (sha256
-        (base32
-         "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-beachmat" ,r-beachmat)
-       ("r-bh" ,r-bh)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocneighbors" ,r-biocneighbors)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biocsingular" ,r-biocsingular)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-delayedmatrixstats" ,r-delayedmatrixstats)
-       ("r-dqrng" ,r-dqrng)
-       ("r-edger" ,r-edger)
-       ("r-igraph" ,r-igraph)
-       ("r-iranges" ,r-iranges)
-       ("r-limma" ,r-limma)
-       ("r-matrix" ,r-matrix)
-       ("r-rcpp" ,r-rcpp)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scater" ,r-scater)
-       ("r-singlecellexperiment" ,r-singlecellexperiment)
-       ("r-statmod" ,r-statmod)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/scran")
-    (synopsis "Methods for single-cell RNA-Seq data analysis")
-    (description "This package implements a variety of low-level analyses of
-single-cell RNA-seq data.  Methods are provided for normalization of
-cell-specific biases, assignment of cell cycle phase, and detection of highly
-variable and significantly correlated genes.")
-    (license license:gpl3)))
-
-(define-public r-delayedmatrixstats
-  (package
-    (name "r-delayedmatrixstats")
-    (version "1.10.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "DelayedMatrixStats" version))
-       (sha256
-        (base32
-         "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
-    (properties
-     `((upstream-name . "DelayedMatrixStats")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-hdf5array" ,r-hdf5array)
-       ("r-iranges" ,r-iranges)
-       ("r-matrix" ,r-matrix)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-s4vectors" ,r-s4vectors)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
-    (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
-    (description
-     "This package provides a port of the @code{matrixStats} API for use with
-@code{DelayedMatrix} objects from the @code{DelayedArray} package.  It
-contains high-performing functions operating on rows and columns of
-@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
-@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}.  Functions
-are optimized per data type and for subsetted calculations such that both
-memory usage and processing time is minimized.")
-    (license license:expat)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
@@ -11484,7 +11154,6 @@ models.  TADbit is complemented by TADkit for visualizing 3D models.")
        ("tcsh" ,tcsh)
        ("perl" ,perl)
        ("libpng" ,libpng)
-       ("mariadb" ,mariadb "lib")
        ("mariadb-dev" ,mariadb "dev")
        ("openssl" ,openssl-1.0)))
     (home-page "https://genome.cse.ucsc.edu/index.html")
@@ -15881,7 +15550,7 @@ than is possible with plain-text methods alone.")
     (propagated-inputs
      `(("libxml2" ,libxml2)))
     (native-inputs
-     `(("check" ,check)
+     `(("check" ,check-0.14)
        ("swig" ,swig)))
     (home-page "http://sbml.org/Software/libSBML")
     (synopsis "Process SBML files and data streams")

gnu/packages/boost.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2015, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2015, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
@@ -41,6 +41,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages hurd)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
@@ -132,6 +133,15 @@
                                     ,(%current-target-system)))))
                      '())
 
+               ;; Change an #ifdef __MACH__ that really targets macOS.
+               ;; TODO: Inline this on the next rebuild cycle.
+               ,@(if (hurd-target?)
+                     '((substitute* "boost/test/utils/timer.hpp"
+                         (("defined\\(__MACH__\\)")
+                          "(defined __MACH__ && !defined __GNU__)"))
+                       #t)
+                     '())
+
                (invoke "./bootstrap.sh"
                        (string-append "--prefix=" out)
                        ;; Auto-detection looks for ICU only in traditional

gnu/packages/bootloaders.scm

@@ -465,7 +465,6 @@ tree binary files.  These are board description files used by Linux and BSD.")
        ("python" ,python)
        ("python-coverage" ,python-coverage)
        ("python-pytest" ,python-pytest)
-       ("sdl2" ,sdl2)
        ("swig" ,swig)))
     (build-system  gnu-build-system)
     (home-page "https://www.denx.de/wiki/U-Boot/")
@@ -478,6 +477,9 @@ also initializes the boards (RAM etc).")
   (package
     (inherit u-boot)
     (name "u-boot-tools")
+    (native-inputs
+     `(("sdl2" ,sdl2)
+       ,@(package-native-inputs u-boot)))
     (arguments
      `(#:make-flags '("HOSTCC=gcc")
        #:test-target "tests"

gnu/packages/build-tools.scm

@@ -111,8 +111,8 @@ generate such a compilation database.")
     (license license:gpl3+)))
 
 (define-public gn
-  (let ((commit "eb997b5ab9c3f1ba6a2c52072785884864a84eae")
+  (let ((commit "e327ffdc503815916db2543ec000226a8df45163")
-        (revision "1794"))            ;as returned by `git describe`, used below
+        (revision "1819"))            ;as returned by `git describe`, used below
     (package
       (name "gn")
       (version (git-version "0.0" revision commit))
@@ -122,7 +122,7 @@ generate such a compilation database.")
                 (uri (git-reference (url home-page) (commit commit)))
                 (sha256
                  (base32
-                  "1vfkcy34wqhg7wsk7jdzhgnnzwim10wgbxv5bnavxzjcs871i2xa"))
+                  "0kvlfj3www84zp1vmxh76x8fdjm9hyk8lkh2vdsidafpmm75fphr"))
                 (file-name (git-file-name name version))))
       (build-system gnu-build-system)
       (arguments

gnu/packages/c.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
-;;; Copyright @ 2020 Katherine Cox-Buday <cox.katherine.e@gmail.com>
+;;; Copyright © 2020 Katherine Cox-Buday <cox.katherine.e@gmail.com>
 ;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -40,6 +40,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages guile)
+  #:use-module (gnu packages lua)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages python)
@@ -257,6 +258,64 @@ string formatting and autoresizing, option and config file parsing, type
 checking casts and more.")
     (license license:lgpl2.1+)))
 
+(define-public libwuya
+  ;; This commit is the one before "wuy_pool.h" was removed from libwuya,
+  ;; which libleak currently requires.
+  (let ((revision "1")
+        (commit "883502041044f4616cfbf75c8f2bb60059f704a9"))
+    (package
+      (name "libwuya")
+      (version (git-version "0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/WuBingzheng/libwuya")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1xrsqbgr13g2v0ag165ryp7xrwzv41xfygzk2a3445ca98c1qpdc"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                    ;no test suite
+         #:phases (modify-phases %standard-phases
+                    (add-after 'unpack 'patch-lua-includes
+                      (lambda _
+                        (substitute* '("wuy_cflua.h" "wuy_cflua.c")
+                          (("<lua5\\.1/") "<"))
+                        #t))
+                    (add-after 'unpack 'add--fPIC-to-CFLAGS
+                      (lambda _
+                        (substitute* "Makefile"
+                          (("CFLAGS[^\n]*" all)
+                           (string-append all " -fPIC")))
+                        #t))
+                    (add-before 'build 'set-CC
+                      (lambda _
+                        (setenv "CC" "gcc")
+                        #t))
+                    (delete 'configure) ;no configure script
+                    (replace 'install
+                      (lambda* (#:key outputs #:allow-other-keys)
+                        (let* ((out (assoc-ref outputs "out"))
+                               (include-dir (string-append out "/include"))
+                               (headers (find-files "." "\\.h$")))
+                          (for-each (lambda (h)
+                                      (install-file h include-dir))
+                                    headers)
+                          (install-file "libwuya.a" (string-append out "/lib"))
+                          #t))))))
+      (inputs `(("lua" ,lua)))
+      (home-page "https://github.com/WuBingzheng/libwuya/")
+      (synopsis "C library implementing various data structures")
+      (description "The @code{libwuya} library implements data structures such
+as dictionaries, skip lists, and memory pools.")
+      ;; There is no clear information as to what license this is distributed
+      ;; under, but it is included (bundled) with libleak from the same author
+      ;; under the GNU GPL v2 or later license, so use this here until it is
+      ;; clarified (see: https://github.com/WuBingzheng/libwuya/issues/2).
+      (license license:gpl2+))))
+
 (define-public packcc
   (package
     (name "packcc")

gnu/packages/calendar.scm

@@ -9,6 +9,7 @@
 ;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com
 ;;; Copyright © 2020 Brendan Tildesley <mail@brendan.scot>
 ;;; Copyright © 2020 Tanguy Le Carrour <tanguy@bioneland.org>
+;;; Copyright © 2020 Peng Mei Yu <pengmeiyu@riseup.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -37,6 +38,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages check)
   #:use-module (gnu packages dav)
+  #:use-module (gnu packages docbook)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
@@ -124,12 +126,20 @@ the <tz.h> library for handling time zones and leap seconds.")
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; test suite appears broken
+       #:parallel-build? #f             ;may cause GIR generation failure
        #:configure-flags '("-DSHARED_ONLY=true"
                            ;; required by evolution-data-server
                            "-DGOBJECT_INTROSPECTION=true"
                            "-DICAL_GLIB_VAPI=true")
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'patch-docbook-reference
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "doc/reference/libical-glib/libical-glib-docs.sgml.in"
+               (("http://www.oasis-open.org/docbook/xml/4.3/")
+                (string-append (assoc-ref inputs "docbook-xml")
+                               "/xml/dtd/docbook/")))
+             #t))
          (add-before 'configure 'patch-paths
            (lambda* (#:key inputs #:allow-other-keys)
              ;; TODO: libical 3.1.0 supports using TZDIR instead of a hard-coded
@@ -144,7 +154,8 @@ the <tz.h> library for handling time zones and leap seconds.")
                  (("\\\"/usr/share/lib/zoneinfo\\\"") "")))
              #t)))))
     (native-inputs
-     `(("gobject-introspection" ,gobject-introspection)
+     `(("docbook-xml" ,docbook-xml-4.3)
+       ("gobject-introspection" ,gobject-introspection)
        ("gtk-doc" ,gtk-doc)
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
@@ -339,3 +350,45 @@ DebConf, FrOSCon, Grazer LinuxTage, and the CCC congresses.
 ConfClerk is targeted at mobile devices but works on any system running Qt.")
     (license (list license:gpl2+
                    license:lgpl3)))) ; or cc-by3.0 for src/icons/*
+
+(define-public ccal
+  (package
+    (name "ccal")
+    (version "2.5.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://ccal.chinesebay.com/ccal/ccal-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "15nza1d1lvk3dp0wcl53wsd32yhbgyzznha092mh5kh5z74vsk1x"))))
+    (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")))
+               (substitute* "Makefile"
+                 (("/usr/local/bin")
+                  (string-append out "/bin"))
+                 (("/usr/local/man")
+                  (string-append out "/share/man"))))
+             #t))
+         (add-after 'install 'install-manuals
+           (lambda _
+             (invoke "make" "install-man"))))
+       ;; no tests
+       #:tests? #f))
+    (home-page "http://ccal.chinesebay.com/ccal/ccal.htm")
+    (synopsis "Command line program for Chinese calendar")
+    (description "@command{ccal} is a command line program which writes a
+Gregorian calendar together with Chinese calendar to standard output.  Its
+usage is similar to the @command{cal} program.  In addition to console output,
+it can also generate Encapsulated Postscript and HTML table outputs for use in
+do-it-yourself calendars and web pages.  It supports both simplified and
+traditional Chinese characters.")
+    ;; Both licenses are in use in various source files.  Note that
+    ;; COPYING.LESSER specifies LGPL 3.0, but all source files say
+    ;; 'Lesser GPL version 2 or later'.
+    (license (list license:gpl2+ license:lgpl2.1+))))

gnu/packages/ccache.scm

@@ -30,14 +30,14 @@
 (define-public ccache
   (package
     (name "ccache")
-    (version "3.7.11")
+    (version "3.7.12")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/ccache/ccache/releases/download/v"
                            version "/ccache-" version ".tar.xz"))
        (sha256
-        (base32 "0s1g0ylrayzax68xlqnxx46f5bhvr2pcm1yzswmj0kcs14404icd"))))
+        (base32 "005liq8csgxdn7m9hj2ah07hishww855p8sc96y1hrnwc21lwbx0"))))
     (build-system gnu-build-system)
     (native-inputs `(("perl" ,perl)     ; for test/run
                      ("which" ,(@ (gnu packages base) which))))

gnu/packages/cdrom.scm

@@ -737,16 +737,15 @@ information is written to standard error.")
 (define-public asunder
   (package
     (name "asunder")
-    (version "2.9.6")
+    (version "2.9.7")
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              (uri
+       (method url-fetch)
-               (string-append "http://www.littlesvr.ca/asunder/releases/asunder-"
+       (uri
-                              version
+        (string-append "http://www.littlesvr.ca/asunder/releases/asunder-"
-                              ".tar.bz2"))
+                       version ".tar.bz2"))
-              (sha256
+       (sha256
-               (base32
+        (base32 "1x3l308ss0iqhz90qyjb94gyd8b4piyrm2nzjmg5kf049k9prjf1"))))
-                "1ycnd82lh7qy1pcbngd4b41s16j9hnm2kyfrncg4cwr3bfk7yg7a"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      '(#:out-of-source? #f

gnu/packages/certs.scm

@@ -76,7 +76,7 @@
 (define-public nss-certs
   (package
     (name "nss-certs")
-    (version "3.52.1")
+    (version "3.57")
     (source (origin
               (method url-fetch)
               (uri (let ((version-with-underscores
@@ -87,7 +87,7 @@
                       "nss-" version ".tar.gz")))
               (sha256
                (base32
-                "0y4jb9095f7bbgw7d7kvzm4c3g4p5i6y68fwhb8wlkpb7b1imj5w"))))
+                "10n3pncg6k81ikjz12la147rppwqn57bkrdl9gb820w6pq0nra2m"))))
     (build-system gnu-build-system)
     (outputs '("out"))
     (native-inputs

gnu/packages/check.scm

@@ -135,7 +135,7 @@ like Jasmine or Mocha.")
 (define-public check
   (package
     (name "check")
-    (version "0.14.0")
+    (version "0.15.2")
     (source
      (origin
       (method url-fetch)
@@ -143,7 +143,7 @@ like Jasmine or Mocha.")
                           version "/check-" version ".tar.gz"))
       (sha256
        (base32
-        "02zkfiyklckmivrfvdsrlzvzphkdsgjrz3igncw05dv5pshhq3xx"))))
+        "02m25y9m46pb6n46s51av62kpd936lkfv3b13kfpckgvmh5lxpm8"))))
     (build-system gnu-build-system)
     (home-page "https://libcheck.github.io/check/")
     (synopsis "Unit test framework for C")
@@ -156,7 +156,19 @@ faults or other signals.  The output from unit tests can be used within
 source code editors and IDEs.")
     (license license:lgpl2.1+)))
 
-;; Some packages require this older version.  Removed once no longer needed.
+;; Some packages require older versions.  Removed once no longer needed.
+(define-public check-0.14
+  (package
+    (inherit check)
+    (version "0.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/libcheck/check/releases"
+                                  "/download/" version "/check-" version ".tar.gz"))
+              (sha256
+               (base32
+                "02zkfiyklckmivrfvdsrlzvzphkdsgjrz3igncw05dv5pshhq3xx"))))))
+
 (define-public check-0.12
   (package
    (inherit check)
@@ -337,7 +349,7 @@ a multi-paradigm automated test framework for C++ and Objective-C.")
 (define-public catch-framework2
   (package
     (name "catch2")
-    (version "2.13.0")
+    (version "2.13.2")
     (home-page "https://github.com/catchorg/Catch2")
     (source (origin
               (method git-fetch)
@@ -347,7 +359,7 @@ a multi-paradigm automated test framework for C++ and Objective-C.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0i4w0c9280a5fyi00mvvf13wlnfzyifr487n1iyr30zvvj5s5f1h"))))
+                "100r0kmra8jmra2hv92lzvwcmphpaiccwvq3lpdsa5b7hailhach"))))
     (build-system cmake-build-system)
     (inputs
      `(("python" ,python-wrapper)))
@@ -924,13 +936,13 @@ and many external plugins.")
   (package
     (inherit (strip-python2-variant python-pytest))
     (name "python2-pytest")
-    (version "4.6.9")
+    (version "4.6.11")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pytest" version))
               (sha256
                (base32
-                "0fgkmpc31nzy97fxfrkqbzycigdwxwwmninx3qhkzp81migggs0r"))))
+                "0ls3pqr86xgif6bphsb6wrww9r2vc7p7a2naq8zcq8115wwq5yjh"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2
@@ -1562,14 +1574,14 @@ have failed since the last commit or what tests are currently failing.")))
 (define-public python-coverage
   (package
     (name "python-coverage")
-    (version "5.0.3")
+    (version "5.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "coverage" version))
        (sha256
         (base32
-         "1vrg8panqw79pswg52ygbrff3wdnxarrd9qz6c64ah0c4h2cmbvp"))))
+         "16z8i18msgs8k74n73dj9x49wzkl0vk4vq8k5pl1bsj70y7b4k53"))))
     (build-system python-build-system)
     (arguments
      ;; FIXME: 95 tests failed, 539 passed, 6 skipped, 2 errors.
@@ -2681,7 +2693,7 @@ provides a simple way to achieve this.")
 (define-public umockdev
   (package
     (name "umockdev")
-    (version "0.14.2")
+    (version "0.14.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/martinpitt/umockdev/"
@@ -2689,7 +2701,7 @@ provides a simple way to achieve this.")
                                   "umockdev-" version ".tar.xz"))
               (sha256
                (base32
-                "1nh6xsssmssmk0lxp9c9dmq3wzlpbpkg77nmmd09csbpybibgxfp"))))
+                "15smnxwplk48nas2c8ji6a5fqcsh770f1yl5nc2j5iprjspbm4mg"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/chicken.scm

@@ -59,7 +59,7 @@
 
        ;; Parallel builds are not supported, as noted in README.
        #:parallel-build? #f))
-    (propagated-inputs `(("gcc-toolchain", gcc-toolchain)))
+    (propagated-inputs `(("gcc-toolchain" ,gcc-toolchain)))
     (home-page "https://www.call-cc.org/")
     (synopsis "R5RS Scheme implementation that compiles native code via C")
     (description

gnu/packages/chromium.scm

@@ -83,6 +83,9 @@
     "base/third_party/symbolize" ;BSD-3
     "base/third_party/xdg_mime" ;LGPL2.0+ or Academic 2.0
     "base/third_party/xdg_user_dirs" ;Expat
+    ;; XXX: Chromium requires a newer C++ standard library.  Remove this when
+    ;; the default GCC is 9 or later.
+    "buildtools/third_party/libc++" ;ASL2.0, with LLVM exceptions
     "chrome/third_party/mozilla_security_manager" ;MPL-1.1/GPL2+/LGPL2.1+
     "courgette/third_party/bsdiff" ;BSD-2, BSD protection license
     "courgette/third_party/divsufsort" ;Expat
@@ -111,7 +114,6 @@
     "third_party/boringssl/src/third_party/fiat" ;Expat
     "third_party/breakpad" ;BSD-3
     "third_party/brotli" ;Expat
-    "third_party/cacheinvalidation" ;ASL2.0
     "third_party/catapult" ;BSD-3
     "third_party/catapult/common/py_vulcanize/third_party/rcssmin" ;ASL2.0
     "third_party/catapult/common/py_vulcanize/third_party/rjsmin" ;ASL2.0
@@ -139,9 +141,15 @@
     "third_party/depot_tools/owners.py" ;BSD-3
     "third_party/devtools-frontend" ;BSD-3
     "third_party/devtools-frontend/src/front_end/third_party/acorn" ;Expat
+    "third_party/devtools-frontend/src/front_end/third_party/chromium" ;BSD-3
     "third_party/devtools-frontend/src/front_end/third_party/codemirror" ;Expat
     "third_party/devtools-frontend/src/front_end/third_party/fabricjs" ;Expat
+    "third_party/devtools-frontend/src/front_end/third_party/i18n" ;ASL2.0
+    "third_party/devtools-frontend/src/front_end/third_party/intl-messageformat" ;BSD-3
     "third_party/devtools-frontend/src/front_end/third_party/lighthouse" ;ASL2.0
+    "third_party/devtools-frontend/src/front_end/third_party/lit-html" ;BSD-3
+    "third_party/devtools-frontend/src/front_end/third_party/lodash-isequal" ;Expat
+    "third_party/devtools-frontend/src/front_end/third_party/marked" ;Expat, BSD-3
     "third_party/devtools-frontend/src/front_end/third_party/wasmparser" ;ASL2.0
     "third_party/devtools-frontend/src/third_party/axe-core" ;MPL2.0
     "third_party/devtools-frontend/src/third_party/pyjson5" ;ASL2.0
@@ -159,6 +167,8 @@
     "third_party/iccjpeg" ;IJG
     "third_party/inspector_protocol" ;BSD-3
     "third_party/jinja2" ;BSD-3
+    ;; XXX: Unbundle this when switching back to libstdc++.
+    "third_party/jsoncpp" ;Public Domain or Expat
     "third_party/jstemplate" ;ASL2.0
     "third_party/khronos" ;Expat, SGI
     "third_party/leveldatabase" ;BSD-3
@@ -175,6 +185,11 @@
     "third_party/libsrtp" ;BSD-3
     "third_party/libsync" ;ASL2.0
     "third_party/libudev" ;LGPL2.1+
+
+    ;; FIXME: build/linux/unbundle/libvpx.gn does not work for all users.
+    "third_party/libvpx" ;BSD-3
+    "third_party/libvpx/source/libvpx/third_party/x86inc" ;Expat
+
     "third_party/libwebm" ;BSD-3
     "third_party/libxml/chromium" ;BSD-3
     "third_party/libyuv" ;BSD-3
@@ -186,6 +201,7 @@
     "third_party/metrics_proto" ;BSD-3
     "third_party/modp_b64" ;BSD-3
     "third_party/nasm" ;BSD-2
+    "third_party/nearby" ;ASL2.0
     "third_party/node" ;Expat
     "third_party/node/node_modules/polymer-bundler/lib/third_party/UglifyJS2" ;BSD-2
     "third_party/one_euro_filter" ;BSD-3
@@ -208,9 +224,13 @@
     "third_party/protobuf/third_party/six" ;Expat
     "third_party/pyjson5" ;ASL2.0
     "third_party/qcms" ;Expat
+    ;; XXX: System re2 cannot be used when Chromium uses libc++ because the re2
+    ;; ABI relies on libstdc++ internals.  See build/linux/unbundle/re2.gn.
+    "third_party/re2" ;BSD-3
     "third_party/rnnoise" ;BSD-3
     "third_party/s2cellid" ;ASL2.0
     "third_party/schema_org" ;CC-BY-SA3.0
+    "third_party/securemessage" ;ASL2.0
     "third_party/skia" ;BSD-3
     "third_party/skia/include/third_party/skcms" ;BSD-3
     "third_party/skia/third_party/skcms" ;BSD-3
@@ -222,12 +242,13 @@
     "third_party/sqlite" ;Public domain
     "third_party/swiftshader" ;ASL2.0
     "third_party/swiftshader/third_party/astc-encoder" ;ASL2.0
-    "third_party/swiftshader/third_party/llvm-7.0" ;NCSA
+    "third_party/swiftshader/third_party/llvm-10.0" ;ASL2.0, with LLVM exception
     "third_party/swiftshader/third_party/llvm-subzero" ;NCSA
     "third_party/swiftshader/third_party/marl" ;ASL2.0
     "third_party/swiftshader/third_party/subzero" ;NCSA
     "third_party/swiftshader/third_party/SPIRV-Headers" ;X11-style
     "third_party/tcmalloc/chromium" ;BSD-3
+    "third_party/ukey2" ;ASL2.0
     "third_party/usb_ids" ;BSD-3
     "third_party/usrsctp" ;BSD-2
     "third_party/vulkan_memory_allocator" ;Expat
@@ -246,8 +267,10 @@
     "third_party/widevine/cdm/widevine_cdm_version.h" ;BSD-3
     "third_party/widevine/cdm/widevine_cdm_common.h" ;BSD-3
     "third_party/woff2" ;ASL2.0
+    "third_party/xcbproto" ;X11
     "third_party/xdg-utils" ;Expat
     "third_party/zlib/google" ;BSD-3
+    "third_party/zxcvbn-cpp" ;Expat
     "url/third_party/mozilla" ;BSD-3, MPL1.1/GPL2+/LGPL2.1+
     "v8/src/third_party/siphash" ;Public domain
     "v8/src/third_party/utf8-decoder" ;Expat
@@ -258,27 +281,9 @@
 (define %blacklisted-files
   ;; 'third_party/blink/perf_tests/resources/svg/HarveyRayner.svg' carries a
   ;; nonfree license according to LICENSES in the same directory.  As we don't
-  ;; run the Blink performance tests, just remove everything to save ~24MiB.
+  ;; run the Blink performance tests, just remove everything to save ~70MiB.
   '("third_party/blink/perf_tests"))
 
-(define (gentoo-patch name revision hash)
-  (origin
-    (method url-fetch)
-    (uri (string-append "https://gitweb.gentoo.org/repo/gentoo.git/plain"
-                        "/www-client/chromium/files/" name "?id=" revision))
-    (file-name (string-append "ungoogled-" name))
-    (sha256 (base32 hash))))
-
-;; This repository contains libstdc++ compatibility patches for Chromium.
-(define (chromium-gcc-patchset commit hash)
-  (origin
-    (method git-fetch)
-    (uri (git-reference
-          (url "https://github.com/stha09/chromium-patches")
-          (commit commit)))
-    (file-name (git-file-name "chromium-gcc-patches" commit))
-    (sha256 (base32 hash))))
-
 (define (debian-patch name revision hash)
   (origin
     (method url-fetch)
@@ -289,38 +294,34 @@
                   (string-append "ungoogled-chromium-" category "-" name))))
     (sha256 (base32 hash))))
 
-(define %ungoogled-revision "57244cdfc21dc05910862152d91cc528103c988a")
+(define (arch-patch name revision hash)
-(define %debian-revision "debian/83.0.4103.116-3")
+  (origin
-(define %gentoo-revision "f3f649046d31ebdbc8c4a302b2384504eff78027")
+    (method url-fetch)
+    (uri (string-append "https://raw.githubusercontent.com/archlinux"
+                        "/svntogit-packages/" revision "/trunk/" name))
+    (sha256 (base32 hash))))
 
-(define %gentoo-patches
+(define %chromium-version "86.0.4240.75")
-  ;; This patch is necessary for compatibility with FFmpeg 4.3.
+(define %ungoogled-revision "c34a56db4c121238fface560e21531b6199ce5dd")
-  (list (gentoo-patch "chromium-84-mediaalloc.patch" %gentoo-revision
+(define %debian-revision "debian/84.0.4147.105-1")
-                      "0snxdc4nb8ykzncz62vpsl8hgxpy24m17mycx67i2gckmrpslzzv")))
+(define %arch-revision "2cbe439471932d30ff2c8ded6b3dfd51b312bbc9")
-
-(define %chromium-gcc-patches
-  (chromium-gcc-patchset
-   "chromium-84-patchset-3"
-   "0l05gx3pn703n47anjwsl5sjcqw8kaxmivf7llax97kj3k6d127v"))
 
 (define %debian-patches
   (list (debian-patch "system/zlib.patch" %debian-revision
-                      "0bp2vh1cgmwjrn1zkpphkd3bs662s23xwdhy3abm9cfjvwrj117n")
+                      "09vqgs37w9ycc7par14wa7rnvmg9bm0z9pqg6fyl3iqvpghyjyr4")
-        (debian-patch "system/jsoncpp.patch" %debian-revision
-                      "0d95brl4a5y5w142yd0rvf59z513h7chsz0vnm034d6lqf22ahwf")
         (debian-patch "system/openjpeg.patch" %debian-revision
                       "0zd6v5njx1pc7i0y6mslxvpx5j4cq01mmyx55qcqx8qzkm0gm48j")))
 
 (define %arch-patches
-  (list (origin
+  (list (arch-patch "check-for-enable-accelerated-video-decode-on-Linux.patch"
-          (method url-fetch)
+                    %arch-revision
-          (uri "https://git.archlinux.org/svntogit/packages.git/plain/trunk/\
+                    "12qj23dcp2g2ivyfyj13m4fzf68nllb9djwcxf1h195gn8wkml03")
-chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
+        (arch-patch "only-fall-back-to-the-i965-driver-if-we-re-on-iHD.patch"
-&id=93b5b90621b4827084288197c6e0e09b987b372a")
+                    %arch-revision
-          (file-name "ungoogled-chromium-fix-vaapi-on-intel.patch")
+                    "0073qjp0dp9kj2ix2j6cxrima01rpdpkcjj9crxlb9b43b4cc53m")
-          (sha256
+        (arch-patch "fix-invalid-end-iterator-usage-in-CookieMonster.patch"
-           (base32
+                    %arch-revision
-            "16jbjjf4d9jp52rdrrxx5vm69nx3w0qrijgjpwapnmcif13z55g4")))))
+                    "1p1wy3dfncw0hhz77a1km0xjhix69ksgbpa569qz86nv76jbgn39")))
 
 (define %ungoogled-origin
   (origin
@@ -331,7 +332,7 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
                               (string-take %ungoogled-revision 7)))
     (sha256
      (base32
-      "15a1xpmabdxr1mn61m0jm9a5l987rxdji8b1b6zy39mr636vcwfi"))))
+      "18p9a7qffmy8m03nqva7maalgil13lj2mn0s56v3crbs4wk4lalj"))))
 
 ;; This is a source 'snippet' that does the following:
 ;; *) Applies various patches for unbundling purposes and libstdc++ compatibility.
@@ -354,20 +355,18 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
           (for-each (lambda (patch)
                       (invoke "patch" "-p1" "--force" "--input"
                               patch "--no-backup-if-mismatch"))
-                    (append
+                    (append '#+%debian-patches '#+%arch-patches
-                     '#+%gentoo-patches '#+%debian-patches '#+%arch-patches
+                            '#+(list (local-file
-                     (find-files #$%chromium-gcc-patches "\\.patch$")
+                                      (search-patch
-                     '#+(list (local-file
+                                       "ungoogled-chromium-system-nspr.patch")))))
-                               (search-patch
-                                "ungoogled-chromium-system-nspr.patch")))))
 
           (with-directory-excursion #+%ungoogled-origin
             (format #t "Ungooglifying...~%")
             (force-output)
             (invoke "python" "utils/prune_binaries.py" chromium-dir
                     "pruning.list")
-            (invoke "python" "utils/patches.py" "apply"
+            (invoke "python" "utils/patches.py" "apply" chromium-dir
-                    chromium-dir "patches")
+                    "patches")
             (invoke "python" "utils/domain_substitution.py" "apply" "-r"
                     "domain_regex.list" "-f" "domain_substitution.list"
                     "-c" "/tmp/domainscache.tar.gz" chromium-dir))
@@ -396,8 +395,8 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
           (invoke "python" "build/linux/unbundle/replace_gn_files.py"
                   "--system-libraries" "ffmpeg" "flac" "fontconfig"
                   "freetype" "harfbuzz-ng" "icu" "libdrm" "libevent"
-                  "libjpeg" "libpng" "libvpx" "libwebp" "libxml"
+                  "libjpeg" "libpng" "libwebp" "libxml" "libxslt"
-                  "libxslt" "openh264" "opus" "re2" "snappy" "zlib")
+                  "openh264" "opus" "snappy" "zlib")
           #t))))
 
 (define opus+custom
@@ -412,16 +411,6 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
         `(cons "--enable-custom-modes"
                ,flags))))))
 
-;; Chromium still has Python2-only code, so we need this special Python 2
-;; variant of xcb-proto.
-(define xcb-proto/python2
-  (package/inherit
-   xcb-proto
-   (name "python2-xcb-proto")
-   (native-inputs
-    `(("pkg-config" ,pkg-config)
-      ("python" ,python-2)))))
-
 ;; 'make-ld-wrapper' can only work with an 'ld' executable, so we need
 ;; this trick to make it wrap 'lld'.
 (define (make-lld-wrapper lld)
@@ -450,7 +439,7 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
 (define-public ungoogled-chromium
   (package
     (name "ungoogled-chromium")
-    (version (string-append "84.0.4147.125-0."
+    (version (string-append %chromium-version "-0."
                             (string-take %ungoogled-revision 7)))
     (synopsis "Graphical web browser")
     (source (origin
@@ -460,7 +449,7 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
                                   (car (string-split version #\-)) ".tar.xz"))
               (sha256
                (base32
-                "1xdg9pnnvbzasmra09rl7wdrir61rfcqml46jj7kv39drwk9chwq"))
+                "1ddw4p9zfdzhi5hrd8x14k4w326znljzprnpfi2f917rlpnl2ynx"))
               (modules '((guix build utils)))
               (snippet (force ungoogled-chromium-snippet))))
     (build-system gnu-build-system)
@@ -470,8 +459,6 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
        #:validate-runpath? #f
        #:modules ((guix build gnu-build-system)
                   (guix build utils)
-                  (ice-9 ftw)
-                  (ice-9 regex)
                   (srfi srfi-26))
        #:configure-flags
        ;; See tools/gn/docs/cookbook.md and
@@ -486,7 +473,6 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
              (string-append "max_jobs_per_link="
                             (number->string (parallel-job-count)))
              "clang_use_chrome_plugins=false"
-             "use_custom_libcxx=false"
              "use_sysroot=false"
              "goma_dir=\"\""
              "enable_nacl=false"
@@ -505,16 +491,13 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
              "enable_vr=false"
              "enable_widevine=false"
              ;; Disable type-checking for the Web UI to avoid a Java dependency.
-             "closure_compile=false"
+             "enable_js_type_check=false"
 
              ;; Define a custom toolchain that simply looks up CC, AR and
              ;; friends from the environment.
              "custom_toolchain=\"//build/toolchain/linux/unbundle:default\""
              "host_toolchain=\"//build/toolchain/linux/unbundle:default\""
 
-             (string-append "xcbproto_path=\""
-                            (assoc-ref %build-inputs "xcb-proto") "/share/xcb\"")
-
              ;; Prefer system libraries.
              "use_system_freetype=true"
              "use_system_harfbuzz=true"
@@ -547,16 +530,13 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
              ;; WebRTC stuff.
              "rtc_use_h264=true"
              ;; Don't use bundled sources.
-             "rtc_build_json=false"
+             "rtc_build_json=true"      ;FIXME: libc++ std::string ABI difference
              "rtc_build_libevent=false"
              "rtc_build_libvpx=false"
              "rtc_build_opus=false"
              "rtc_build_ssl=false"
              "rtc_build_libsrtp=true"   ;FIXME: fails to find headers
              "rtc_build_usrsctp=true"   ;TODO: package this
-             (string-append "rtc_jsoncpp_root=\""
-                            (assoc-ref %build-inputs "jsoncpp")
-                            "/include/jsoncpp/json\"")
              (string-append "rtc_ssl_root=\""
                             (assoc-ref %build-inputs "openssl")
                             "/include/openssl\""))
@@ -564,12 +544,6 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-stuff
            (lambda _
-             ;; Fix build with newer re2.  Taken from:
-             ;; https://chromium-review.googlesource.com/c/chromium/src/+/2145261
-             (substitute* "components/autofill/core/browser/address_rewriter.cc"
-               (("options\\.set_utf8\\(true\\)")
-                "options.set_encoding(RE2::Options::EncodingUTF8)"))
-
              (substitute*
                  '("base/process/launch_posix.cc"
                    "base/third_party/dynamic_annotations/dynamic_annotations.c"
@@ -615,10 +589,8 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
 
              (substitute*
                  "third_party/breakpad/breakpad/src/common/linux/libcurl_wrapper.h"
-               (("include \"third_party/curl") "include \"curl"))
+               (("include \"third_party/curl")
-
+                "include \"curl"))
-             (substitute* "third_party/webrtc/rtc_base/strings/json.h"
-               (("#include \"third_party/jsoncpp/") "#include \"json/"))
 
              (substitute* '("components/viz/common/gpu/vulkan_context_provider.h"
                             "components/viz/common/resources/resource_format_utils.h"
@@ -628,17 +600,6 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
              (substitute* "third_party/skia/include/gpu/vk/GrVkVulkan.h"
                (("include/third_party/vulkan/") ""))
 
-             ;; Building chromedriver embeds some files using the ZIP
-             ;; format which doesn't support timestamps before
-             ;; 1980. Therefore, advance the timestamps of the files
-             ;; which are included so that building chromedriver
-             ;; works.
-             (let ((circa-1980 (* 10 366 24 60 60)))
-               (for-each (lambda (file)
-                           (utime file circa-1980 circa-1980))
-                         '("chrome/test/chromedriver/extension/background.js"
-                           "chrome/test/chromedriver/extension/manifest.json")))
-
              #t))
          (add-after 'patch-stuff 'add-absolute-references
            (lambda* (#:key inputs #:allow-other-keys)
@@ -660,10 +621,23 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
          (add-before 'configure 'prepare-build-environment
            (lambda* (#:key inputs #:allow-other-keys)
 
-             ;; Make sure the right build tools are used.
+             ;; Define the GN toolchain.
              (setenv "AR" "llvm-ar") (setenv "NM" "llvm-nm")
              (setenv "CC" "clang") (setenv "CXX" "clang++")
 
+             (let ((gcc (assoc-ref inputs  "gcc")))
+               ;; Remove the default compiler from CPLUS_INCLUDE_PATH to
+               ;; prevent header conflict with the bundled libcxx.
+               (setenv "CPLUS_INCLUDE_PATH"
+                       (string-join
+                        (delete (string-append gcc "/include/c++")
+                                (string-split (getenv "CPLUS_INCLUDE_PATH")
+                                              #\:))
+                        ":"))
+               (format #t
+                       "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+                       (getenv "CPLUS_INCLUDE_PATH")))
+
              (setenv "CXXFLAGS"
                      (string-join
                       '(;; Do not optimize away null pointer safety checks.
@@ -728,7 +702,10 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
                     (lib            (string-append out "/lib"))
                     (man            (string-append out "/share/man/man1"))
                     (applications   (string-append out "/share/applications"))
-                    (install-regexp (make-regexp "\\.(bin|pak|so)$"))
+                    (libs           '("chrome_100_percent.pak"
+                                      "chrome_200_percent.pak"
+                                      "resources.pak"
+                                      "v8_context_snapshot.bin"))
                     (locales        (string-append lib "/locales"))
                     (resources      (string-append lib "/resources"))
                     (preferences    (assoc-ref inputs "master-preferences"))
@@ -753,9 +730,7 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
                (copy-file preferences (string-append lib "/master_preferences"))
 
                (with-directory-excursion "out/Release"
-                 (for-each (lambda (file)
+                 (for-each (cut install-file <> lib) libs)
-                             (install-file file lib))
-                           (scandir "." (cut regexp-exec install-regexp <>)))
                  (copy-file "chrome" (string-append lib "/chromium"))
 
                  (copy-recursively "locales" locales)
@@ -785,7 +760,7 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
                #t))))))
     (native-inputs
      `(("bison" ,bison)
-       ("clang" ,clang-10)
+       ("clang" ,clang-11)
        ("gn" ,gn)
        ("gperf" ,gperf)
        ("ld-wrapper" ,(make-lld-wrapper lld))
@@ -817,7 +792,6 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
        ("gtk+" ,gtk+)
        ("harfbuzz" ,harfbuzz)
        ("icu4c" ,icu4c-67)
-       ("jsoncpp" ,jsoncpp)
        ("lcms" ,lcms)
        ("libevent" ,libevent)
        ("libffi" ,libffi)
@@ -851,13 +825,11 @@ chromium-fix-vaapi-on-intel.patch?h=packages/chromium\
        ("pango" ,pango)
        ("pciutils" ,pciutils)
        ("pulseaudio" ,pulseaudio)
-       ("re2" ,re2)
        ("snappy" ,snappy)
        ("speech-dispatcher" ,speech-dispatcher)
        ("udev" ,eudev)
        ("valgrind" ,valgrind)
-       ("vulkan-headers" ,vulkan-headers)
+       ("vulkan-headers" ,vulkan-headers)))
-       ("xcb-proto" ,xcb-proto/python2)))
 
     ;; Building Chromium takes ... a very long time.  On a single core, a busy
     ;; mid-end x86 system may need more than 24 hours to complete the build.

gnu/packages/ci.scm

@@ -39,6 +39,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages perl-compression)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages sqlite)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages version-control)
@@ -46,9 +47,29 @@
   #:use-module (gnu packages xml)
   #:use-module (guix build-system gnu))
 
+;; Guile-Sqlite3 package adding SQL query logging support.
+;; Remove it when next Guile-Sqlite3 release is out.
+(define-public guile-sqlite3-dev
+  (let ((commit "22ef45d268de7707cbbb943c404f9b0c1668e2e1")
+        (revision "1"))
+    (package
+      (inherit guile-sqlite3)
+      (name "guile-sqlite3")
+      (version (git-version "0.1.2" revision commit))
+      (home-page "https://notabug.org/mothacehe/guile-sqlite3.git")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url home-page)
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1q90f8zhw9n1c39szd2ba7aj5fi92m09pnlv0z7jbhnnjam5jwcd"))
+                (file-name (string-append name "-" version "-checkout")))))))
+
 (define-public cuirass
-  (let ((commit "cf11b73db00678b45b70108768138d0fb74d9506")
+  (let ((commit "df2d13621f4b2ace33a460746e704115b7b1541e")
-        (revision "45"))
+        (revision "53"))
     (package
       (name "cuirass")
       (version (git-version "0.0.1" revision commit))
@@ -60,7 +81,7 @@
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1f7jqnscy8vjqrpgl4cyynrvbx6zp3slsd82fykap6qvvwwn7xj8"))))
+                  "1vgb1wl1rkijm1vv5chqllf4i5w1j7g02xqlaf2xmqjh2phy5dxa"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)
@@ -122,11 +143,11 @@
                    `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,objs)))
                  #t))))))
       (inputs
-       `(("guile" ,@(assoc-ref (package-native-inputs guix) "guile"))
+       `(("guile" ,guile-3.0/libgc-7)
          ("guile-fibers" ,guile-fibers)
          ("guile-gcrypt" ,guile-gcrypt)
          ("guile-json" ,guile-json-4)
-         ("guile-sqlite3" ,guile-sqlite3)
+         ("guile-sqlite3" ,guile-sqlite3-dev)
          ("guile-git" ,guile-git)
          ("guile-zlib" ,guile-zlib)
          ;; FIXME: this is propagated by "guile-git", but it needs to be among

gnu/packages/cluster.scm

@@ -39,7 +39,7 @@
 (define-public drbd-utils
   (package
     (name "drbd-utils")
-    (version "9.13.1")
+    (version "9.15.0")
     (source (origin
               (method url-fetch)
               ;; Older releases are moved to /archive.  List it first because in
@@ -51,7 +51,7 @@
                                         "/utils/drbd-utils-" version ".tar.gz")))
               (sha256
                (base32
-                "0di55y0vzaw8jhcgz0fakww03h1gpg4a5q1zklxhjw3dwzjvysnk"))
+                "0jh7zdxpbjkq53pmrn0jfn33abi4vs8axp55h5256czwc2gfb6z8"))
               (modules '((guix build utils)))
               (snippet
                '(begin

gnu/packages/code.scm

@@ -233,7 +233,7 @@ COCOMO model or user-provided parameters.")
 (define-public cloc
   (package
     (name "cloc")
-    (version "1.86")
+    (version "1.88")
     (source
      (origin
        (method git-fetch)
@@ -242,7 +242,7 @@ COCOMO model or user-provided parameters.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "082gj2b3x11bilz8c572dd60vn6n0fhld5zhi7wk7g1wy9wlgm9w"))))
+        (base32 "1ixgswzbzv63bl50gb2kgaqr0jcicjz6w610hi9fal1i7744zraw"))))
     (build-system gnu-build-system)
     (inputs
      `(("coreutils" ,coreutils)
@@ -470,60 +470,53 @@ stack traces.")
     (license license:gpl3+)))
 
 (define-public lcov
-  ;; Use a recent commit from upstream since the latest official release
+  (package
-  ;; (1.14) doesn't support GCC 9 (see:
+    (name "lcov")
-  ;; https://github.com/linux-test-project/lcov/issues/58).
+    (version "1.15")
-  (let* ((commit "40580cd65909bc8324ae09b36bca2e178652ff3f")
+    (source
-         (revision "0")
+     (origin
-         (version (git-version "1.14" revision commit)))
+       (method url-fetch)
-    (package
+       (uri (string-append "https://github.com/linux-test-project/lcov"
-      (name "lcov")
+                           "/releases/download/v" version
-      (version "1.14")
+                           "/lcov-" version ".tar.gz"))
-      (source (origin
+       (sha256
-                (method git-fetch)
+        (base32 "0fh5z0q5wg2jxr2nn5w7321y0zg9rwk75j3k5hnamjdy6gxa5kf1"))))
-                (uri (git-reference
+    (build-system gnu-build-system)
-                      (url "https://github.com/linux-test-project/lcov")
+    (arguments
-                      (commit commit)))
+     '(#:test-target "test"
-                (file-name (git-file-name name version))
+       #:make-flags (list (string-append "PREFIX="
-                (sha256
+                                         (assoc-ref %outputs "out")))
-                 (base32
+       #:phases
-                  "0shgmh6fzhnj1qfdl90jgjmlbb1ih1qh879dca8hc58yggy3hqgb"))))
+       (modify-phases %standard-phases
-      (build-system gnu-build-system)
+         (add-after 'unpack 'patch-pwd
-      (arguments
+           ;; Lift the requirement of having a shell in PATH.
-       '(#:test-target "test"
+           (lambda _
-         #:make-flags (list (string-append "PREFIX="
+             (substitute* "bin/geninfo"
-                                           (assoc-ref %outputs "out")))
+               (("qw/abs_path/")
-         #:phases
+                "qw/abs_path getcwd/"))
-         (modify-phases %standard-phases
+             (substitute* '("bin/lcov" "bin/geninfo")
-           (add-after 'unpack 'patch-pwd
+               (("`pwd`")
-             ;; Lift the requirement of having a shell in PATH.
+                "getcwd()"))
-             (lambda _
+             #t))
-               (substitute* "bin/geninfo"
+         (delete 'configure)            ;no configure script
-                 (("qw/abs_path/")
+         (add-after 'install 'wrap
-                  "qw/abs_path getcwd/"))
+           (lambda* (#:key outputs #:allow-other-keys)
-               (substitute* '("bin/lcov" "bin/geninfo")
+             (let ((out (assoc-ref outputs "out")))
-                 (("`pwd`")
+               (wrap-program (string-append out "/bin/geninfo")
-                  "getcwd()"))
+                 `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))))
-               #t))
+             #t)))))
-           (delete 'configure)          ;no configure script
+    (inputs `(("perl" ,perl)
-           (add-after 'install 'wrap
+              ("perl-io-compress" ,perl-io-compress)
-             (lambda* (#:key outputs #:allow-other-keys)
+              ("perl-json" ,perl-json)))
-               (let ((out (assoc-ref outputs "out")))
+    (home-page "http://ltp.sourceforge.net/coverage/lcov.php")
-                 (wrap-program (string-append out "/bin/geninfo")
+    (synopsis "Code coverage tool that enhances GNU gcov")
-                   `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))))
+    (description "LCOV is an extension of @command{gcov}, a tool part of the
-               #t)))))
-      (inputs `(("perl" ,perl)
-                ("perl-json" ,perl-json)
-                ("perl-perlio-gzip" ,perl-perlio-gzip)))
-      (home-page "http://ltp.sourceforge.net/coverage/lcov.php")
-      (synopsis "Code coverage tool that enhances GNU gcov")
-      (description "LCOV is an extension of @command{gcov}, a tool part of the
 GNU@tie{}Binutils, which provides information about what parts of a program
 are actually executed (i.e., \"covered\") while running a particular test
 case.  The extension consists of a set of Perl scripts which build on the
 textual @command{gcov} output to implement the following enhanced
 functionality such as HTML output.")
-      (license license:gpl2+))))
+    (license license:gpl2+)))
 
 (define-public kcov
   (package

gnu/packages/commencement.scm

@@ -381,7 +381,7 @@ $MES -e '(mescc)' module/mescc.scm -- \"$@\"
     (inputs '())
     (propagated-inputs '())
     (native-inputs
-     `(("nyacc-source" ,(origin (inherit (package-source nyacc))
+     `(("nyacc-source" ,(origin (inherit (package-source nyacc-0.99))
                                 (snippet #f)))
        ("mes" ,%bootstrap-mes-rewired)
        ("mescc-tools" ,%bootstrap-mescc-tools)
@@ -477,7 +477,7 @@ $MES -e '(mescc)' module/mescc.scm -- \"$@\"
     (propagated-inputs '())
     (native-inputs
      `(("mes" ,mes-boot)
-       ("nyacc-source" ,(origin (inherit (package-source nyacc))
+       ("nyacc-source" ,(origin (inherit (package-source nyacc-0.99))
                                 (snippet #f)))
        ("mescc-tools" ,%bootstrap-mescc-tools)
        ,@(%boot-gash-inputs)))
@@ -3842,8 +3842,12 @@ COREUTILS-FINAL vs. COREUTILS, etc."
                                                      "libc-static")))
                        #t))))
 
-      (native-search-paths (package-native-search-paths gcc))
+      (native-search-paths
-      (search-paths (package-search-paths gcc))
+       (append (package-native-search-paths gcc)
+               (package-native-search-paths libc))) ;GUIX_LOCPATH
+      (search-paths
+       (append (package-search-paths gcc)
+               (package-search-paths libc)))
 
       (license (package-license gcc))
       (synopsis "Complete GCC tool chain for C/C++ development")

gnu/packages/compression.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2017, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2017, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
@@ -28,6 +28,7 @@
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2020 Lars-Dominik Braun <lars@6xq.net>
+;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -803,7 +804,7 @@ decompression of some loosely related file formats used by Microsoft.")
        ("valgrind" ,valgrind)))
     (arguments
      `(#:test-target "test"
-       #:make-flags (list "CC=gcc"
+       #:make-flags (list (string-append "CC=" ,(cc-for-target))
                           (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases (modify-phases %standard-phases
                   (delete 'configure)            ;no configure script
@@ -1769,7 +1770,8 @@ Clzip is intended to be fully compatible with the regular lzip package.")
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
-       (list "CC=gcc"
+       (list (string-append "CC=" ,(cc-for-target))
+             "--disable-static"
              "--enable-shared")))       ; only static (.a) is built by default
     (home-page "https://www.nongnu.org/lzip/lzlib.html")
     (synopsis "Lzip data compression C library")
@@ -2256,3 +2258,31 @@ computations.")
 with their error correction data losslessly rearranged for better compression,
 to their original, binary CD format.")
     (license license:gpl3+)))
+
+(define-public tarlz
+  (package
+    (name "tarlz")
+    (version "0.17")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://savannah/lzip/tarlz/"
+                           "tarlz-" version ".tar.lz"))
+       (sha256
+        (base32 "0gpdm6z9pdr5bn31kxg73wm686hhpb5pdf5782pbl5a4xqqhqj90"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("lzip" ,lzip)))
+    (inputs
+     `(("lzlib" ,lzlib)))
+    (home-page "https://www.nongnu.org/lzip/tarlz.html")
+    (synopsis "Combination of the tar archiver and the lzip compressor")
+    (description
+     "Tarlz is a massively parallel (multi-threaded) combined implementation of
+the tar archiver and the lzip compressor.  Tarlz creates, lists, and extracts
+archives in a simplified and safer variant of the POSIX pax format compressed
+with lzip, keeping the alignment between tar members and lzip members.  The
+resulting multimember tar.lz archive is fully backward compatible with standard
+tar tools like GNU tar, which treat it like any other tar.lz archive.  Tarlz
+can append files to the end of such compressed archives.")
+    (license license:gpl2+)))

gnu/packages/conky.scm

@@ -79,7 +79,7 @@
        ("libxext" ,libxext)
        ("libxft" ,libxft)
        ("libxinerama" ,libxinerama)
-       ("pulseaudio", pulseaudio)
+       ("pulseaudio" ,pulseaudio)
        ("lua" ,lua)
        ("ncurses" ,ncurses)
        ("curl" ,curl)))

gnu/packages/cpp.scm

@@ -14,6 +14,7 @@
 ;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2020 Alexandros Theodotou <alex@zrythm.org>
+;;; Copyright © 2020 Greg Hogan <code@greghogan.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -40,12 +41,22 @@
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages code)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages crypto)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages libevent)
+  #:use-module (gnu packages libunwind)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages llvm)
+  #:use-module (gnu packages logging)
+  #:use-module (gnu packages maths)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages popt)
+  #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web))
 
@@ -361,7 +372,7 @@ intuitive syntax and trivial integration.")
 (define-public xtl
   (package
     (name "xtl")
-    (version "0.6.18")
+    (version "0.6.19")
     (source (origin
               (method git-fetch)
               (uri
@@ -370,7 +381,7 @@ intuitive syntax and trivial integration.")
                 (commit version)))
               (sha256
                (base32
-                "0s9gnv1wq0cmpw878dmx0lnci86895hhdrwyc9x8lfbc1hr7ypnh"))
+                "1g98lfrp13fqfqrirg0rw90m7bajmjmy12yhrlj5jzwcby4dfs81"))
               (file-name (git-file-name name version))))
     (native-inputs
      `(("googletest" ,googletest)
@@ -647,3 +658,73 @@ Google's C++ code base.")
 a zero-dependency C++ header-only parser combinator library for creating
 parsers according to a Parsing Expression Grammar (PEG).")
     (license license:expat)))
+
+(define-public cxxopts
+  (package
+    (name "cxxopts")
+    (version "2.2.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/jarro2783/cxxopts")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0d3y747lsh1wkalc39nxd088rbypxigm991lk3j91zpn56whrpha"))))
+    (build-system cmake-build-system)
+    (synopsis "Lightweight C++ command line option parser")
+    (description
+     "A lightweight header-only C++ option parser library, supporting the
+standard GNU style syntax for options.")
+    (home-page "https://github.com/jarro2783/cxxopts/wiki")
+    (license license:expat)))
+
+(define-public folly
+  (package
+    (name "folly")
+    (version "2020.10.05.00")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/facebook/folly")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0q4w4cvjxffc462hvs8h4zryq4965j7015zvkwagcm6cj6wmz3cn"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(;; Tests must be explicitly enabled
+       ;;#:configure-flags '("-DBUILD_TESTS=ON")))
+       ;; Leave tests disabled; see https://github.com/facebook/folly/issues/1456
+       #:tests? #f))
+    (propagated-inputs
+     `(("boost" ,boost)
+       ("gflags" ,gflags)
+       ("glog" ,glog)
+       ("liburing" ,liburing)))
+    (inputs
+     `(("bzip2" ,bzip2)
+       ("double-conversion" ,double-conversion)
+       ("fmt" ,fmt)
+       ("libaio" ,libaio)
+       ("libevent" ,libevent)
+       ("libiberty" ,libiberty)
+       ("libsodium" ,libsodium)
+       ("libunwind" ,libunwind)
+       ("lz4" ,lz4)
+       ("openssl" ,openssl)
+       ("snappy" ,snappy)
+       ("zlib" ,zlib)
+       ("zstd" ,zstd "lib")))
+    (native-inputs
+     `(("googletest" ,googletest)))
+    (synopsis "Collection of C++ components complementing the standard library")
+    (description
+     "Folly (acronymed loosely after Facebook Open Source Library) is a library
+of C++14 components that complements @code{std} and Boost.")
+    (home-page "https://github.com/facebook/folly/wiki")
+    ;; 32-bit is not supported: https://github.com/facebook/folly/issues/103
+    (supported-systems '("aarch64-linux" "x86_64-linux"))
+    (license license:asl2.0)))

gnu/packages/crates-gtk.scm

@@ -0,0 +1,667 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages crates-gtk)
+  #:use-module (guix build-system cargo)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages crates-io)
+  #:use-module (gnu packages crates-graphics)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gtk))
+
+;;;
+;;; Please: Try to add new module packages in alphabetic order.
+;;;
+
+(define-public rust-cairo-rs-0.8
+  (package
+    (name "rust-cairo-rs")
+    (version "0.8.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cairo-rs" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "11303v1fv6hsc9n70ak380gknkf0098phpcxqdhkmahqjsx4jw0m"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-cairo-sys-rs" ,rust-cairo-sys-rs-0.9)
+        ("rust-glib" ,rust-glib-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2))
+       #:cargo-development-inputs
+       (("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("cairo" ,cairo)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "Rust bindings for the Cairo library")
+    (description
+     "Rust bindings for the Cairo library.")
+    (license license:expat)))
+
+(define-public rust-cairo-rs-0.7
+  (package
+    (inherit rust-cairo-rs-0.8)
+    (name "rust-cairo-rs")
+    (version "0.7.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cairo-rs" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "171m98g41avp5mmshqir4ka21napp7ma5fx45wi9mw5hwdyv8pg0"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-cairo-sys-rs" ,rust-cairo-sys-rs-0.9)
+        ("rust-glib" ,rust-glib-0.8)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-tempfile" ,rust-tempfile-3))))))
+
+(define-public rust-cairo-sys-rs-0.9
+  (package
+    (name "rust-cairo-sys-rs")
+    (version "0.9.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cairo-sys-rs" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0qsdy6s57yvscg2rfm7wdqrlhzbn1aq9lhk3dy1vw5f7r81blrgz"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-winapi" ,rust-winapi-0.3)
+        ("rust-x11" ,rust-x11-2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))))
+    (inputs
+     `(("cairo" ,cairo)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "FFI bindings to libcairo")
+    (description "This package provides FFI bindings to libcairo.")
+    (license license:expat)))
+
+(define-public rust-gdk-pixbuf-0.8
+  (package
+    (name "rust-gdk-pixbuf")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gdk-pixbuf" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1mxxca0fkcw2rsd3kl3nvlb8ys4cgxqx4n5isjbv0adk8q624j72"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-gdk-pixbuf-sys" ,rust-gdk-pixbuf-sys-0.9)
+        ("rust-gio" ,rust-gio-0.8)
+        ("rust-gio-sys" ,rust-gio-sys-0.9)
+        ("rust-glib" ,rust-glib-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))
+    (inputs
+     `(("gdk-pixbuf" ,gdk-pixbuf)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "Rust bindings for the GdkPixbuf library")
+    (description
+     "Rust bindings for the GdkPixbuf library.")
+    (license license:expat)))
+
+(define-public rust-gdk-pixbuf-0.7
+  (package
+    (inherit rust-gdk-pixbuf-0.8)
+    (name "rust-gdk-pixbuf")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gdk-pixbuf" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1k2g3w2p57m68bi5sldvkmgjgslgqswrjsijjhqaibdvw67409lp"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-fragile" ,rust-fragile-0.3)
+        ("rust-futures-preview" ,rust-futures-preview-0.3)
+        ("rust-gdk-pixbuf-sys" ,rust-gdk-pixbuf-sys-0.9)
+        ("rust-gio" ,rust-gio-0.7)
+        ("rust-gio-sys" ,rust-gio-sys-0.9)
+        ("rust-glib" ,rust-glib-0.8)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))))
+
+(define-public rust-gdk-pixbuf-sys-0.9
+  (package
+    (name "rust-gdk-pixbuf-sys")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gdk-pixbuf-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1c2andpjb10y7bahh6nxnksh9m3g5qh4mgq9znx634cy1831p6fq"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; tests not included in release
+       #:cargo-inputs
+       (("rust-gio-sys" ,rust-gio-sys-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("gdk-pixbuf" ,gdk-pixbuf)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "FFI bindings to libgdk_pixbuf-2.0")
+    (description "This package provides FFI bindings to @code{libgdk_pixbuf-2.0}.")
+    (license license:expat)))
+
+(define-public rust-gio-0.8
+  (package
+    (name "rust-gio")
+    (version "0.8.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gio" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "19cnla2ya0mi6wwaabd5mxbq2kzq46dg6jq2z19rpqyc2na0zl8c"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f  ; Not all files included in the tarball.
+       #:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-futures-channel" ,rust-futures-channel-0.3)
+        ("rust-futures-core" ,rust-futures-core-0.3)
+        ("rust-futures-io" ,rust-futures-io-0.3)
+        ("rust-futures-util" ,rust-futures-util-0.3)
+        ("rust-gio-sys" ,rust-gio-sys-0.9)
+        ("rust-glib" ,rust-glib-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1)
+        ("rust-serial-test" ,rust-serial-test-0.1)
+        ("rust-serial-test-derive" ,rust-serial-test-derive-0.1))))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "Rust bindings for the Gio library")
+    (description "Rust bindings for the Gio library.")
+    (license license:expat)))
+
+(define-public rust-gio-0.7
+  (package
+    (inherit rust-gio-0.8)
+    (name "rust-gio")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gio" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1qv0wc1hqyb81c03h81s3xrl9jslrw23fr4yhygxbhih9k9vaqb2"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-fragile" ,rust-fragile-0.3)
+        ("rust-futures-preview" ,rust-futures-preview-0.3)
+        ("rust-gio-sys" ,rust-gio-sys-0.9)
+        ("rust-glib" ,rust-glib-0.8)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))))
+
+(define-public rust-gio-sys-0.9
+  (package
+    (name "rust-gio-sys")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gio-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "049rafihxp3maxg3fwj6062ni9dcfilvhfq6ibnfgsmr89925bag"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Some test libraries not included in release.
+       #:cargo-inputs
+       (("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page "http://gtk-rs.org/")
+    (synopsis "FFI bindings to libgio-2.0")
+    (description "This package provides FFI bindings to libgio-2.0.")
+    (license license:expat)))
+
+(define-public rust-gir-format-check-0.1
+  (package
+    (name "rust-gir-format-check")
+    (version "0.1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gir-format-check" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0znl4qcgmg0656zk9vjkwdn9wj1zpkd0m0l5jnzmahd80ii7vf4b"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/gtk-rs/gir-format-check")
+    (synopsis "File format checker")
+    (description "File format checker in Rust.")
+    (license license:expat)))
+
+(define-public rust-glib-0.9
+  (package
+    (name "rust-glib")
+    (version "0.9.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "glib" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1h3100mf7kdfxibjz5na0sqzbd2mcsyd8pzivn3666w414x5gys0"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-futures-channel" ,rust-futures-channel-0.3)
+        ("rust-futures-core" ,rust-futures-core-0.3)
+        ("rust-futures-executor" ,rust-futures-executor-0.3)
+        ("rust-futures-preview" ,rust-futures-preview-0.3)
+        ("rust-futures-task" ,rust-futures-task-0.3)
+        ("rust-futures-util" ,rust-futures-util-0.3)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2))
+       #:cargo-development-inputs
+       (("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "Rust bindings for the GLib library")
+    (description
+     "Rust bindings for the GLib library.")
+    (license license:expat)))
+
+(define-public rust-glib-0.8
+  (package
+    (inherit rust-glib-0.9)
+    (name "rust-glib")
+    (version "0.8.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "glib" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0ysy87zrwyzhfpf3d8rkyyr3amwj85wky05fsl7kx95s84l269xy"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-futures-preview" ,rust-futures-preview-0.3)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2))
+       #:cargo-development-inputs
+       (("rust-tempfile" ,rust-tempfile-3))))))
+
+(define-public rust-glib-sys-0.9
+  (package
+    (name "rust-glib-sys")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "glib-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1qhnwfqqcp63mx4q9744rfkq78g6ky2j8ppsxxgw0ipl08w6z1cm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Some test libraries not included in release.
+       #:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page "http://gtk-rs.org/")
+    (synopsis "FFI bindings to libglib-2.0")
+    (description "This package provides FFI bindings to libglib-2.0.")
+    (license license:expat)))
+
+(define-public rust-gobject-sys-0.9
+  (package
+    (name "rust-gobject-sys")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gobject-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1nakflbp3gjaas4fw7sn3p1p32khyfpcq1h06z7yqd10yq2ail9i"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Some test libraries not included in release.
+       #:cargo-inputs
+       (("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page "http://gtk-rs.org/")
+    (synopsis "FFI bindings to libgobject-2.0")
+    (description "This package provides FFI bindings to libgobject-2.0.")
+    (license license:expat)))
+
+(define-public rust-gtk-rs-lgpl-docs-0.1
+  (package
+    (name "rust-gtk-rs-lgpl-docs")
+    (version "0.1.15")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gtk-rs-lgpl-docs" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "06b1j64zg0xmhwfkyhzh3y0apclg6qihn3f7s1bd7kgjmkia4jlr"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-rustdoc-stripper" ,rust-rustdoc-stripper-0.1))))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "LGPL-licensed docs for Gtk-rs crates")
+    (description
+     "LGPL-licensed docs for Gtk-rs crates.")
+    (license license:lgpl2.0)))
+
+(define-public rust-pango-0.8
+  (package
+    (name "rust-pango")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pango" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0xq50950il3228grzs4xvc5s6phxcl5l50grz6syvs0vixr6p70y"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-glib" ,rust-glib-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pango-sys" ,rust-pango-sys-0.9)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))
+    (inputs
+     `(("pango" ,pango)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "Rust bindings for the Pango library")
+    (description
+     "Rust bindings for the Pango library.")
+    (license license:expat)))
+
+(define-public rust-pango-0.7
+  (package
+    (inherit rust-pango-0.8)
+    (name "rust-pango")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pango" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "11np7nxb69g3kid2l78b7k519x1wk1c3f9yy7swgzy24n5qs0grr"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-glib" ,rust-glib-0.8)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pango-sys" ,rust-pango-sys-0.9)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))))
+
+(define-public rust-pango-sys-0.9
+  (package
+    (name "rust-pango-sys")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pango-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0zdynikh6jrfa31fpmbrwnz46a57idci73zzkf0z0g3vj223vfc6"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Some test files not included in release.
+       #:cargo-inputs
+       (("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("pango" ,pango)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "FFI bindings to libpango-1.0")
+    (description "This package provides FFI bindings to @code{libpango-1.0}.")
+    (license license:expat)))
+
+(define-public rust-pangocairo-0.9
+  (package
+    (name "rust-pangocairo")
+    (version "0.9.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pangocairo" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0bap3h78hdqdyln58349qjjbcv45m8a0a16c4n9fprdj1my0gldx"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-cairo-rs" ,rust-cairo-rs-0.8)
+        ("rust-cairo-sys-rs" ,rust-cairo-sys-rs-0.9)
+        ("rust-glib" ,rust-glib-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pango" ,rust-pango-0.8)
+        ("rust-pango-sys" ,rust-pango-sys-0.9)
+        ("rust-pangocairo-sys" ,rust-pangocairo-sys-0.10)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))
+    (inputs
+     `(("gtk+" ,gtk+)))
+    (home-page "http://gtk-rs.org/")
+    (synopsis "Rust bindings for the PangoCairo library")
+    (description
+     "Rust bindings for the PangoCairo library.")
+    (license license:expat)))
+
+(define-public rust-pangocairo-0.8
+  (package
+    (inherit rust-pangocairo-0.9)
+    (name "rust-pangocairo")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pangocairo" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0qjiwsp73x3w0493dzycyjzxnzwq7ixwmf1ccr5r41pjhxbnk1kl"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-cairo-rs" ,rust-cairo-rs-0.7)
+        ("rust-cairo-sys-rs" ,rust-cairo-sys-rs-0.9)
+        ("rust-glib" ,rust-glib-0.8)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-gobject-sys" ,rust-gobject-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pango" ,rust-pango-0.7)
+        ("rust-pango-sys" ,rust-pango-sys-0.9)
+        ("rust-pangocairo-sys" ,rust-pangocairo-sys-0.10)
+        ("rust-gtk-rs-lgpl-docs" ,rust-gtk-rs-lgpl-docs-0.1))
+       #:cargo-development-inputs
+       (("rust-gir-format-check" ,rust-gir-format-check-0.1))))))
+
+(define-public rust-pangocairo-sys-0.10
+  (package
+    (name "rust-pangocairo-sys")
+    (version "0.10.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pangocairo-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1zlyf5vajarnxg5034b8qa5w5zajv96lfvlgiki26svpmcqip4m3"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-cairo-sys-rs" ,rust-cairo-sys-rs-0.9)
+        ("rust-glib-sys" ,rust-glib-sys-0.9)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-pango-sys" ,rust-pango-sys-0.9)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))
+       #:cargo-development-inputs
+       (("rust-shell-words" ,rust-shell-words-0.1)
+        ("rust-tempfile" ,rust-tempfile-3))))
+    (inputs
+     `(("gtk+" ,gtk+)))
+    (home-page "https://gtk-rs.org/")
+    (synopsis "FFI bindings to libgtk-3")
+    (description "This package provides FFI bindings to libgtk-3.")
+    (license license:expat)))

gnu/packages/crypto.scm

@@ -143,7 +143,7 @@ communication, encryption, decryption, signatures, etc.")
 (define-public signify
   (package
     (name "signify")
-    (version "29")
+    (version "30")
     (home-page "https://github.com/aperezdc/signify")
     (source (origin
               (method url-fetch)
@@ -151,7 +151,7 @@ communication, encryption, decryption, signatures, etc.")
                                   "/download/v" version "/signify-" version ".tar.xz"))
               (sha256
                (base32
-                "1bzcax5kb4lr0rmpmrdpq5q0iq6b2dxzpl56li8aanbkck1c7hd9"))))
+                "11l67j04gyxnlw6zrzsygqs5cgsc1sww1rh0apl05yay131hd17n"))))
     (build-system gnu-build-system)
     ;; TODO Build with libwaive (described in README.md), to implement something
     ;; like OpenBSD's pledge().
@@ -359,10 +359,10 @@ secure operations. ")
           (base32
            "0lj38ldh8vzi11wp4ghw4k0fkwp0s04zv8k8d473p1snmbh7mx98"))))
       (inputs
-       `(("openssl" ,openssl))) ; It needs: openssl/{bn,pem,rsa,sha}.h
+       `(("openssl" ,openssl-1.0)))     ; for openssl/{bn,pem,rsa,sha}.h
       (build-system gnu-build-system)
       (arguments
-       `(#:make-flags (list "CC=gcc"
+       `(#:make-flags (list (string-append "CC=" ,(cc-for-target))
                             (string-append "PREFIX=" (assoc-ref %outputs "out"))
                             (string-append "INSTALL=" "install"))
          ;; XXX: make test would run a !VERY! long hashing of names with the use

gnu/packages/cryptsetup.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,7 +35,7 @@
 (define-public cryptsetup
   (package
    (name "cryptsetup")
-   (version "2.3.3")
+   (version "2.3.4")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://kernel.org/linux/utils/cryptsetup/v"
@@ -43,7 +43,7 @@
                                 "/cryptsetup-" version ".tar.xz"))
             (sha256
              (base32
-              "1pw2bq4nv2z3xyycckxkbp7dp9kkp2n6bspna3plryg277z4zjiv"))))
+              "0wrpz2fzbsszmsgxxbssxjgylpyiindh24z8g13m2fxmjsxyw5lx"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags

gnu/packages/cups.scm

@@ -418,16 +418,17 @@ should only be used as part of the Guix cups-pk-helper service.")
 (define-public hplip
   (package
     (name "hplip")
-    (version "3.20.6")
+    (version "3.20.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/hplip/hplip/" version
                                   "/hplip-" version ".tar.gz"))
               (sha256
                (base32
-                "083w58wpvvm6sir6rf5dwx3r0rman9sv1zpl26chl0a88crjsjy6"))
+                "1prdbp410405xrfggjc7y34nzljg7jnbgjzalgv4khwwma4i299n"))
               (modules '((guix build utils)))
-              (patches (search-patches "hplip-remove-imageprocessor.patch"))
+              (patches (search-patches "hplip-fix-bug-1898438.patch"
+                                       "hplip-remove-imageprocessor.patch"))
               (snippet
                '(begin
                   ;; Delete non-free blobs: .so files, pre-compiled
@@ -468,10 +469,7 @@ should only be used as part of the Guix cups-pk-helper service.")
                          (assoc-ref %outputs "out") "/lib")
          ;; Disable until mime.types merging works (FIXME).
          "--disable-fax-build"
-         "--enable-hpcups-install"
          "--enable-new-hpcups"
-         "--enable-cups_ppd_install"
-         "--enable-cups_drv_install"
          ;; TODO add foomatic drv install eventually.
          ;; TODO --enable-policykit eventually.
          ,(string-append "--with-cupsfilterdir="
@@ -752,20 +750,19 @@ HP@tie{}LaserJet, and possibly other printers.  See @file{README} for details.")
 (define-public escpr
   (package
     (name "escpr")
-    (version "1.6.30")
+    (version "1.7.7")
     ;; XXX: This currently works.  But it will break as soon as a newer
     ;; version is available since the URLs for older versions are not
     ;; preserved.  An alternative source will be added as soon as
     ;; available.
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              ;; The uri has to be chopped up in order to satisfy guix lint.
+       (method url-fetch)
-              (uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/08/18/20/"
+       (uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/10/49/18/"
-                                  "e94de600e28e510c1cfa158929d8b2c0aadc8aa0/"
+                           "f3016be6120a7271a6d9cb64872f817bce1920b8/"
-                                  "epson-inkjet-printer-escpr-1.6.30-1lsb3.2.tar.gz"))
+                           "epson-inkjet-printer-escpr-1.7.7-1lsb3.2.tar.gz"))
-              (sha256
+       (sha256
-               (base32
+        (base32 "0khdf2a9iwh9aplj2gzyzl53yyfnfv0kszk3p018jnirl5l475ld"))))
-                "0m8pyfkixisp0vclwxj340isn15zzisal0v2xvv66kxfd68dzf12"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -774,13 +771,30 @@ HP@tie{}LaserJet, and possibly other printers.  See @file{README} for details.")
          ,(string-append "--with-cupsfilterdir="
                          (assoc-ref %outputs "out") "/lib/cups/filter")
          ,(string-append "--with-cupsppddir="
-                         (assoc-ref %outputs "out") "/share/ppd"))))
+                         (assoc-ref %outputs "out") "/share/cups/model"))
-    (inputs `(("cups" ,cups-minimal)))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-autotools-version-requirement
+           (lambda _
+             (substitute* "aclocal.m4"
+               (("1\\.15")
+                ,(package-version automake)))
+             (substitute* "configure"
+               (("^(ACLOCAL=).*" _ match)
+                (string-append match "aclocal"))
+               (("^(AUTOMAKE=).*" _ match)
+                (string-append match "automake")))
+             #t)))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)))
+    (inputs
+     `(("cups" ,cups-minimal)))
     (synopsis "ESC/P-R printer driver")
     (description
-     "This package provides a filter for the Common UNIX Printing
+     "This package provides a filter for @acronym{CUPS, the Common UNIX Printing
-System (CUPS).  It offers high-quality printing with Seiko Epson color ink jet
+System} that offers high-quality printing with Seiko@tie{}Epson color ink jet
-printers.  It can only be used with printers that support the Epson ESC/P-R
+printers.  It can be used only with printers that support the Epson@tie{}ESC/P-R
 language.")
     (home-page "http://download.ebz.epson.net/dsc/search/01/search")
     (license license:gpl2+)))

gnu/packages/databases.scm

@@ -44,6 +44,7 @@
 ;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
 ;;; Copyright © 2020 Guy Fleury Iteriteka <gfleury@disroot.org>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
+;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -128,6 +129,7 @@
   #:use-module (guix download)
   #:use-module (guix bzr-download)
   #:use-module (guix git-download)
+  #:use-module (guix hg-download)
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
@@ -716,7 +718,7 @@ Language.")
 (define-public mariadb
   (package
     (name "mariadb")
-    (version "10.1.45")
+    (version "10.5.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://downloads.mariadb.com/MariaDB"
@@ -724,8 +726,7 @@ Language.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1mfs0x4c0z7d306n128dxdawk3llk25vxif5zwl20fv1z5qhz3wx"))
+                "1i257h0zdypdfj5wkg6ck9pxlkph0jvjs92k22pjr6gnx5lxs1gz"))
-              (patches (search-patches "mariadb-client-test-32bit.patch"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -743,8 +744,8 @@ Language.")
                   (for-each (lambda (file)
                               (unless (string-suffix? "CMakeLists.txt" file)
                                 (delete-file file)))
-                            (append (find-files "extra/yassl")
+                            (append (find-files "extra/wolfssl")
-                                    (find-files "pcre") (find-files "zlib")))
+                                    (find-files "zlib")))
                   #t))))
     (build-system cmake-build-system)
     (outputs '("out" "lib" "dev"))
@@ -798,29 +799,20 @@ Language.")
          "-DINSTALL_SHAREDIR=share")
        #:phases
        (modify-phases %standard-phases
-         ,@(if (string-prefix? "arm" (%current-system))
+         (add-after 'unpack 'adjust-output-references
-               ;; XXX: Because of the GCC 5 input, we need to hide GCC 7 from
-               ;; CPLUS_INCLUDE_PATH so that its headers do not shadow GCC 5.
-               '((add-after 'set-paths 'hide-default-gcc
-                   (lambda* (#:key inputs #:allow-other-keys)
-                     (let ((gcc (assoc-ref inputs "gcc")))
-                       (setenv "CPLUS_INCLUDE_PATH"
-                               (string-join
-                                (delete (string-append gcc "/include/c++")
-                                        (string-split (getenv "CPLUS_INCLUDE_PATH")
-                                                      #\:))
-                                ":"))
-                       #t))))
-               '())
-         (add-after 'unpack 'fix-pcre-detection
            (lambda _
-             ;; The bundled PCRE in MariaDB has a patch that was upstreamed
+             ;; The build system invariably prepends $CMAKE_INSTALL_PREFIX
-             ;; in version 8.34.  Unfortunately the upstream patch behaves
+             ;; to other variables such as $INSTALL_INCLUDEDIR, which does
-             ;; slightly differently and the build system fails to detect it.
+             ;; not work when the latter uses an absolute file name.
-             ;; See <https://bugs.exim.org/show_bug.cgi?id=2173>.
+             (substitute* "libmariadb/mariadb_config/mariadb_config.c.in"
-             ;; XXX: Consider patching PCRE instead.
+               (("@CMAKE_INSTALL_PREFIX@/@INSTALL_INCLUDEDIR@")
-             (substitute* "cmake/pcre.cmake"
+                "@INSTALL_INCLUDEDIR@"))
-               ((" OR NOT PCRE_STACK_SIZE_OK") ""))
+             (substitute* "libmariadb/mariadb_config/libmariadb.pc.in"
+               (("\\$\\{prefix\\}/@INSTALL_INCLUDEDIR@")
+                "@INSTALL_INCLUDEDIR@"))
+             (substitute* "include/CMakeLists.txt"
+               (("\\\\\\$\\{CMAKE_INSTALL_PREFIX\\}/\\$\\{INSTALL_INCLUDEDIR\\}")
+                "${INSTALL_INCLUDEDIR}"))
              #t))
          (add-after 'unpack 'adjust-tests
            (lambda _
@@ -828,6 +820,7 @@ Language.")
                     '(;; These fail because root@hostname == root@localhost in
                       ;; the build environment, causing a user count mismatch.
                       ;; See <https://jira.mariadb.org/browse/MDEV-7761>.
+                      "funcs_1.is_columns_mysql"
                       "main.join_cache"
                       "main.explain_non_select"
                       "main.stat_tables"
@@ -836,20 +829,7 @@ Language.")
 
                       ;; This file contains a time bomb which makes it fail after
                       ;; 2030-12-31.  See <https://bugs.gnu.org/34351> for details.
-                      "main.mysqldump"
+                      "main.mysqldump"))
-
-                      ;; FIXME: This test fails on i686:
-                      ;; -myisampack: Can't create/write to file (Errcode: 17 "File exists")
-                      ;; +myisampack: Can't create/write to file (Errcode: 17 "File exists)
-                      ;; When running "myisampack --join=foo/t3 foo/t1 foo/t2"
-                      ;; (all three tables must exist and be identical)
-                      ;; in a loop it produces the same error around 1/240 times.
-                      ;; montywi on #maria suggested removing the real_end check in
-                      ;; "strings/my_vsnprintf.c" on line 503, yet it still does not
-                      ;; reach the ending quote occasionally.  Disable it for now.
-                      "main.myisampack"
-                      ;; FIXME: This test fails on armhf-linux:
-                      "mroonga/storage.index_read_multiple_double"))
 
                    ;; This file contains a list of known-flaky tests for this
                    ;; release.  Append our own items.
@@ -860,9 +840,10 @@ Language.")
                          disabled-tests)
                (close-port unstable-tests)
 
-               ;; XXX: This test fails because it expects a latin1 charset and
+               ;; XXX: These fail because they expect a latin1 charset and
                ;; collation.  See <https://jira.mariadb.org/browse/MDEV-21264>.
-               (substitute* "mysql-test/r/gis_notembedded.result"
+               (substitute* '("mysql-test/main/gis_notembedded.result"
+                              "mysql-test/main/system_mysql_db.result")
                  (("latin1_swedish_ci") "utf8_general_ci")
                  (("\tlatin1") "\tutf8"))
 
@@ -895,6 +876,10 @@ Language.")
                            "--testcase-timeout=40"
                            "--suite-timeout=600"
                            "--parallel" (number->string (parallel-job-count))
+                           ;; Skip the replication tests: they are very I/O
+                           ;; intensive and frequently causes indeterministic
+                           ;; failures even on powerful hardware.
+                           "--skip-rpl"
                            "--skip-test-list=unstable-tests"))
                  (format #t "test suite not run~%"))
              #t))
@@ -905,56 +890,57 @@ Language.")
                    (dev     (assoc-ref outputs "dev"))
                    (lib     (assoc-ref outputs "lib"))
                    (openssl (assoc-ref inputs "openssl")))
-              (substitute* (string-append out "/bin/mysql_install_db")
+              (substitute* (list (string-append out "/bin/mariadb-install-db")
+                                 (string-append out "/bin/mysql_install_db"))
                 (("basedir=\"\"")
-                 (string-append "basedir=\"" out "\"")))
+                 (string-append "basedir=\"" out "\""))
+                (("\\$basedir/share/mysql")
+                 (string-append lib "/share/mysql")))
+
               ;; Remove unneeded files for testing.
               (with-directory-excursion lib
                 (for-each delete-file-recursively
-                          '("data" "mysql-test" "sql-bench"))
+                          '("mysql-test" "sql-bench"))
                 ;; And static libraries.
                 (for-each delete-file (find-files "lib" "\\.a$")))
               (with-directory-excursion out
                 (delete-file "share/man/man1/mysql-test-run.pl.1")
                 ;; Delete huge and unnecessary executables.
-                (for-each delete-file (find-files "bin" "(test|embedded)")))
+                (for-each delete-file (find-files "bin" "test$")))
               (mkdir-p (string-append dev "/share"))
               (mkdir-p (string-append dev "/bin"))
+              (rename-file (string-append lib "/bin/mariadbd")
+                           (string-append out "/bin/mariadbd"))
               (rename-file (string-append lib "/bin/mysqld")
                            (string-append out "/bin/mysqld"))
-              (rename-file (string-append lib "/share/pkgconfig")
+              (mkdir-p (string-append dev "/lib"))
-                           (string-append dev "/share/pkgconfig"))
+              (rename-file (string-append lib "/lib/pkgconfig")
+                           (string-append dev "/lib/pkgconfig"))
+              (rename-file (string-append lib "/bin/mariadb_config")
+                           (string-append dev "/bin/mariadb_config"))
               (rename-file (string-append out "/bin/mysql_config")
                            (string-append dev "/bin/mysql_config"))
 
-
-              (substitute*  (string-append out "/bin/mysql_install_db")
-                (("\\$basedir/share/mysql")
-                 (string-append lib "/share/mysql")))
-
               ;; Embed an absolute reference to OpenSSL in mysql_config
               ;; and the pkg-config file to avoid propagation.
+              ;; XXX: how to do this for mariadb_config.c.in?
               (substitute* (list (string-append dev "/bin/mysql_config")
-                                 (string-append dev "/share/pkgconfig/mariadb.pc"))
+                                 (string-append dev "/lib/pkgconfig/mariadb.pc"))
                 (("-lssl -lcrypto" all)
                  (string-append "-L" openssl "/lib " all)))
 
               #t))))))
     (native-inputs
      `(("bison" ,bison)
-       ;; XXX: On armhf, use GCC 5 to work around <https://bugs.gnu.org/37605>.
-       ,@(if (string-prefix? "armhf" (%current-system))
-             `(("gcc@5", gcc-5))
-             '())
        ("perl" ,perl)))
     (inputs
      `(("jemalloc" ,jemalloc)
        ("libaio" ,libaio)
        ("libxml2" ,libxml2)
        ("ncurses" ,ncurses)
-       ("openssl" ,openssl-1.0)
+       ("openssl" ,openssl)
        ("pam" ,linux-pam)
-       ("pcre" ,pcre)
+       ("pcre2" ,pcre2)
        ("xz" ,xz)
        ("zlib" ,zlib)))
     ;; The test suite is very resource intensive and can take more than three
@@ -970,7 +956,7 @@ as a drop-in replacement of MySQL.")
 (define-public mariadb-connector-c
   (package
     (name "mariadb-connector-c")
-    (version "3.1.9")
+    (version "3.1.10")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -979,7 +965,7 @@ as a drop-in replacement of MySQL.")
                     version "-src.tar.gz"))
               (sha256
                (base32
-                "1izjzf7yzjqzlk8dkp327fa9lawsv2hnnlnr7g5lshyx5azrk38h"))))
+                "13v5z4w1cl890lnr2fbwbziw638lqw2aga45vdq1z0cyrc9mcgmg"))))
     (inputs
      `(("openssl" ,openssl)))
     (build-system cmake-build-system)
@@ -1139,7 +1125,7 @@ organized in a hash table or B+ tree.")
 
     (native-inputs `(("bc" ,bc)
                      ("bash:include" ,bash "include")
-                     ("check" ,check)
+                     ("check" ,check-0.14)
                      ("libuuid" ,util-linux)
                      ("pkg-config" ,pkg-config)))
 
@@ -1343,7 +1329,7 @@ for example from a shell script.")
 (define-public sqitch
   (package
     (name "sqitch")
-    (version "1.0.0")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
@@ -1351,7 +1337,7 @@ for example from a shell script.")
              "mirror://cpan/authors/id/D/DW/DWHEELER/App-Sqitch-v"
              version ".tar.gz"))
        (sha256
-        (base32 "0p4wraqiscvwmmsvfqfy65blgsilwpvd9zj4d2zvm2xdx70ncr7l"))))
+        (base32 "1ayiwg9kh3w0nbacbcln7h944z94vq5vnnd5diz86033bpbnq57f"))))
     (build-system perl-build-system)
     (arguments
      '(#:phases
@@ -1383,6 +1369,7 @@ for example from a shell script.")
        ("perl-test-file" ,perl-test-file)
        ("perl-test-file-contents" ,perl-test-file-contents)
        ("perl-test-mockmodule" ,perl-test-mockmodule)
+       ("perl-test-mockobject" ,perl-test-mockobject)
        ("perl-test-nowarnings" ,perl-test-nowarnings)
        ("perl-test-warn" ,perl-test-warn)))
     (inputs
@@ -1391,7 +1378,9 @@ for example from a shell script.")
        ("perl-config-gitlike" ,perl-config-gitlike)
        ("perl-datetime" ,perl-datetime)
        ("perl-datetime-timezone" ,perl-datetime-timezone)
+       ("perl-dbd-mysql" ,perl-dbd-mysql)
        ("perl-dbd-pg" ,perl-dbd-pg)
+       ("perl-dbd-sqlite" ,perl-dbd-sqlite)
        ("perl-dbi" ,perl-dbi)
        ("perl-devel-stacktrace" ,perl-devel-stacktrace)
        ("perl-encode-locale" ,perl-encode-locale)
@@ -1738,7 +1727,7 @@ columns, primary keys, unique constraints and relationships.")
 (define-public perl-dbd-sqlite
   (package
     (name "perl-dbd-sqlite")
-    (version "1.64")
+    (version "1.66")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1746,7 +1735,7 @@ columns, primary keys, unique constraints and relationships.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "00gz5aw3xrr92lf9nfk0dhmy7a8jzmxhznddd9b0a8w4a1xqzbpl"))))
+                "1zljln5nh61gj3k22a1fv2vhx5l83waizmarwkh77hk6kzzmvrw9"))))
     (build-system perl-build-system)
     (inputs `(("sqlite" ,sqlite)))
     (propagated-inputs `(("perl-dbi" ,perl-dbi)))
@@ -1777,7 +1766,7 @@ module, and nothing else.")
     (synopsis "Parse and utilize MySQL's /etc/my.cnf and ~/.my.cnf files")
     (description
      "@code{MySQL::Config} emulates the @code{load_defaults} function from
-libmysqlclient.  It will fill an aray with long options, ready to be parsed by
+libmysqlclient.  It will fill an array with long options, ready to be parsed by
 @code{Getopt::Long}.")
     (license license:perl-license)))
 
@@ -1898,7 +1887,7 @@ valid SQL query.")
 (define-public unixodbc
   (package
    (name "unixodbc")
-   (version "2.3.7")
+   (version "2.3.9")
    (source (origin
             (method url-fetch)
             (uri
@@ -1906,7 +1895,7 @@ valid SQL query.")
               "ftp://ftp.unixodbc.org/pub/unixODBC/unixODBC-"
               version ".tar.gz"))
             (sha256
-             (base32 "0xry3sg497wly8f7715a7gwkn2k36bcap0mvzjw74jj53yx6kwa5"))))
+             (base32 "01xj65d02i3yjy7p9z08y9jakcs5szmz4rask868n7387nn3x0sj"))))
    (build-system gnu-build-system)
    (synopsis "Data source abstraction library")
    (description "Unixodbc is a library providing an API with which to access
@@ -2120,14 +2109,14 @@ database.")
 (define-public perl-db-file
  (package
   (name "perl-db-file")
-  (version "1.853")
+  (version "1.855")
   (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cpan/authors/id/P/PM/PMQS/DB_File-"
                           version ".tar.gz"))
       (sha256
-        (base32 "1y967si45vj0skip1hnhicbv9da29fv6qcfwnsbnvj06n36mkj6h"))))
+        (base32 "0q599h7g4jkzks5dxf1zifx9k7l9vif26r2dlgkzxkg6bfif5zyr"))))
   (build-system perl-build-system)
   (inputs `(("bdb" ,bdb)))
   (native-inputs `(("perl-test-pod" ,perl-test-pod)))
@@ -2140,8 +2129,7 @@ database.")
                        (("/usr/local/BerkeleyDB") (assoc-ref inputs "bdb")))
                      #t)))))
   (home-page "https://metacpan.org/release/DB_File")
-  (synopsis
+  (synopsis "Perl5 access to Berkeley DB version 1.x")
-    "Perl5 access to Berkeley DB version 1.x")
   (description
     "The DB::File module provides Perl bindings to the Berkeley DB version 1.x.")
   (license license:perl-license)))
@@ -2450,13 +2438,13 @@ etc., and an SQL engine for performing simple SQL queries.")
 (define-public python-lmdb
   (package
     (name "python-lmdb")
-    (version "0.99")
+    (version "1.0.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "lmdb" version))
               (sha256
                (base32
-                "12fwlzfd82471ss9xzbqwcqc6f5miy51y72y2yya9j5cm9589szr"))
+                "1di1gj2agbxwqqwrpk4w58dpfah0kl10ha20s63dlqdd1bgzydj1"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled lmdb source files.
@@ -2475,6 +2463,7 @@ etc., and an SQL engine for performing simple SQL queries.")
          (add-before 'build 'use-system-lmdb
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((lmdb (assoc-ref inputs "lmdb")))
+               (setenv "LMDB_PURE" "set") ; don't apply env-copy-txn.patch
                (setenv "LMDB_FORCE_SYSTEM" "set")
                (setenv "LMDB_INCLUDEDIR" (string-append lmdb "/include"))
                (setenv "LMDB_LIBDIR" (string-append lmdb "/lib"))
@@ -2632,13 +2621,13 @@ Database API 2.0T.")
 (define-public python-sqlalchemy
   (package
     (name "python-sqlalchemy")
-    (version "1.3.18")
+    (version "1.3.20")
     (source
      (origin
       (method url-fetch)
       (uri (pypi-uri "SQLAlchemy" version))
       (sha256
-       (base32 "1rwc6ss1cnz3kxx0p9p6xw0w79r8qw03lcc29k31yb3rcigvfbys"))))
+       (base32 "18b9am7bsqc4nj3d2h5r93i002apczxfvpfpcqbd6f0385zmrwnj"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-cython" ,python-cython) ; for C extensions
@@ -2712,16 +2701,57 @@ You might also want to install the following optional dependencies:
 (define-public python2-sqlalchemy-utils
   (package-with-python2 python-sqlalchemy-utils))
 
+(define-public python-alchemy-mock
+  (package
+    (name "python-alchemy-mock")
+    (version "0.4.3")
+    (home-page "https://github.com/miki725/alchemy-mock")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "alchemy-mock" version))
+              (sha256
+               (base32
+                "0ylxygl3bcdapzz529n8wgk7vx9gjwb3ism564ypkpd7dbsw653r"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda _
+                      ;; Create pytest.ini that adds doctest options to
+                      ;; prevent test failure.  Taken from tox.ini.
+                      (call-with-output-file "pytest.ini"
+                        (lambda (port)
+                          (format port "[pytest]
+doctest_optionflags=IGNORE_EXCEPTION_DETAIL
+")))
+                      (invoke "pytest" "-vv" "--doctest-modules"
+                              "alchemy_mock/"))))))
+    (native-inputs
+     `(("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)))
+    (propagated-inputs
+     `(("python-six" ,python-six)
+       ("python-sqlalchemy" ,python-sqlalchemy)))
+    (synopsis "Mock helpers for SQLAlchemy")
+    (description
+     "This package provides mock helpers for SQLAlchemy that makes it easy
+to mock an SQLAlchemy session while preserving the ability to do asserts.
+
+Normally Normally SQLAlchemy's expressions cannot be easily compared as
+comparison on binary expression produces yet another binary expression, but
+this library provides functions to facilitate such comparisons.")
+    (license license:expat)))
+
 (define-public python-alembic
   (package
     (name "python-alembic")
-    (version "1.4.2")
+    (version "1.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "alembic" version))
        (sha256
-        (base32 "1gsdrzx9h7wfva200qvvsc9sn4w79mk2vs0bbnzjhxi1jw2b0nh3"))))
+        (base32 "0if2dgb088clk738p26bwk50735h6jpd2kacdgc5capv2hiz6d2k"))))
     (build-system python-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
@@ -2897,13 +2927,13 @@ designed to be easy and intuitive to use.")
 (define-public python-psycopg2
   (package
     (name "python-psycopg2")
-    (version "2.8.5")
+    (version "2.8.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "psycopg2" version))
        (sha256
-        (base32 "06081jk9srkd4ra9j8b93x9ld3a2yxsbsf5bbbcivbm1yx065m7p"))))
+        (base32 "0hzmk6b1hb5riqkljr5xics6p4zbvmis6knbczb7zhq7273zc8zv"))))
     (build-system python-build-system)
     (arguments
      ;; Tests would require a postgresql database "psycopg2_test"
@@ -2948,27 +2978,51 @@ database).")
 (define-public python2-sadisplay
   (package-with-python2 python-sadisplay))
 
+(define-public yoyo-migrations
+  (package
+    (name "yoyo-migrations")
+    (version "7.2.0")
+    (source
+     (origin
+       ;; We use the upstream repository, as the tests are not included in the
+       ;; PyPI releases.
+       (method hg-fetch)
+       (uri (hg-reference
+             (url "https://hg.sr.ht/~olly/yoyo")
+             (changeset (string-append "v" version "-release"))))
+       (file-name (string-append name "-" version "-checkout"))
+       (sha256
+        (base32 "0q2z9bgdj3wyix7yvqsayfs21grp5av8ilh411lgmjhigszkvhcq"))))
+    (build-system python-build-system)
+    (arguments
+     ;; XXX: Tests require a connection to some pgsql database and psycopg
+     ;; fails to connect to it.
+     '(#:tests? #f))
+    (propagated-inputs
+     `(("python-sqlparse" ,python-sqlparse)
+       ("python-tabulate" ,python-tabulate)))
+    (home-page "https://ollycope.com/software/yoyo/latest/")
+    (synopsis "Database migrations with SQL")
+    (description
+     "Yoyo is a database schema migration tool.  Migrations are written as SQL
+files or Python scripts that define a list of migration steps.")
+    (license license:asl2.0)))
+
 (define-public python-mysqlclient
   (package
     (name "python-mysqlclient")
-    (version "1.3.13")
+    (version "2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "mysqlclient" version))
        (sha256
         (base32
-         "0kv4a1icwdav8jpl7qvnr931lw5h3v22ids6lwq6qpi1hjzf33pz"))))
+         "1rf5l8hazs3v18hmcrm90z3hi9wxv553ipwd5l6kj8j7l6p7abzv"))))
     (build-system python-build-system)
-    (native-inputs
+    (arguments '(#:tests? #f))          ;XXX: requires a live database
-     `(("nose" ,python-nose)
-       ("mock" ,python-mock)
-       ("py.test" ,python-pytest)))
     (inputs
-     `(("mysql" ,mariadb "lib")
+     `(("mysql-dev" ,mariadb "dev")))
-       ("mysql-dev" ,mariadb "dev")
-       ("libz" ,zlib)
-       ("openssl" ,openssl)))
     (home-page "https://github.com/PyMySQL/mysqlclient-python")
     (synopsis "MySQLdb is an interface to the popular MySQL database server for Python")
     (description "MySQLdb is an interface to the popular MySQL database server
@@ -2980,9 +3034,6 @@ for Python.  The design goals are:
 @end enumerate")
     (license license:gpl2)))
 
-(define-public python2-mysqlclient
-  (package-with-python2 python-mysqlclient))
-
 (define-public python-hiredis
   (package
     (name "python-hiredis")
@@ -3042,13 +3093,13 @@ reasonable substitute.")
 (define-public python-redis
   (package
     (name "python-redis")
-    (version "3.3.8")
+    (version "3.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "redis" version))
        (sha256
-        (base32 "0fyxzqax7lcwzwhvnz0i0q6v62hxyv1mv52ywx3bpff9a2vjz8lq"))))
+        (base32 "18h5b87g15x3j6pb1h2q27ri37p2qpvc9n2wgn5yl3b6m3y0qzhf"))))
     (build-system python-build-system)
     ;; Tests require a running Redis server.
     (arguments '(#:tests? #f))
@@ -3067,14 +3118,35 @@ reasonable substitute.")
 (define-public python-rq
   (package
     (name "python-rq")
-    (version "0.13.0")
+    (version "1.5.2")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "rq" version))
+       (uri (git-reference
+             (url "https://github.com/rq/rq")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0xvapd2bxnyq480i48bdkddzlqmv2axbsq85rlfy8k3al8zxxxrf"))))
+        (base32 "0ikqmpq0g1qiqwd7ar1286l4hqjb6aj2wr844gihhb8ijzwhp8va"))))
     (build-system python-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-before 'check 'start-redis
+                    (lambda _
+                      (invoke "redis-server" "--daemonize" "yes")))
+                  (replace 'check
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let ((out (assoc-ref outputs "out")))
+                        ;; Drop test that needs the SDK for Sentry.io.
+                        (delete-file "tests/test_sentry.py")
+                        ;; Ensure 'rq' and 'rqworker' ends up on PATH.
+                        (setenv "PATH" (string-append out "/bin:"
+                                                      (getenv "PATH")))
+                        (invoke "pytest" "-vv")))))))
+    (native-inputs
+     `(("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
+       ("redis" ,redis)))
     (propagated-inputs
      `(("python-click" ,python-click)
        ("python-redis" ,python-redis)))
@@ -3089,6 +3161,44 @@ is designed to have a low barrier to entry.")
 (define-public python2-rq
   (package-with-python2 python-rq))
 
+(define-public python-rq-scheduler
+  (package
+    (name "python-rq-scheduler")
+    (version "0.10.0")
+    (home-page "https://github.com/rq/rq-scheduler")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url home-page)
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0xg6yazqs5kbr2ayvhvljs1h5vgx5k5dds613fmhswln7gglf9hk"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-before 'check 'start-redis
+                    (lambda _
+                      (invoke "redis-server" "--daemonize" "yes")))
+                  (replace 'check
+                    (lambda _
+                      (substitute* "run_tests.py"
+                        (("/usr/bin/env")
+                         (which "env")))
+                      (invoke "./run_tests.py"))))))
+    (native-inputs
+     `(("redis" ,redis)
+       ("which" ,which)))
+    (propagated-inputs
+     `(("python-croniter" ,python-croniter)
+       ("python-rq" ,python-rq)))
+    (synopsis "Job scheduling capabilities for RQ (Redis Queue)")
+    (description
+     "This package provides job scheduling capabilities to @code{python-rq}
+(Redis Queue).")
+    (license license:expat)))
+
 (define-public python-trollius-redis
   (package
     (name "python-trollius-redis")
@@ -3593,8 +3703,7 @@ The drivers officially supported by @code{libdbi} are:
        ("sqlite" ,sqlite)
        ("odbc" ,unixodbc)
        ("boost" ,boost)
-       ("mariadb:dev" ,mariadb "dev")
+       ("mariadb:dev" ,mariadb "dev")))
-       ("mariadb:lib" ,mariadb "lib")))
     (arguments
      `(#:tests? #f ; Tests may require running database management systems.
        #:phases

gnu/packages/datastructures.scm

@@ -37,14 +37,16 @@
     (name "gdsl")
     (version "1.8")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "http://download.gna.org/gdsl/"
+              (uri (git-reference
-                                  "gdsl-" version ".tar.gz"))
+                    (url "https://example.org") ;only hosted on Software Heritage
+                    (commit "6adb53be8b8f9f2e4bbfc92d357eedeefb4c7430")))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1v64jvlnj8jfpphphgjgb36p0kv50kwfyqncf0y12f16v8ydyiaw"))))
+                "0a52g12d9sf9hhcyvwfd7xdazj2a9i9jh97cnlqf2ymvwnvjk1g0"))))
     (build-system gnu-build-system)
-    (home-page "http://home.gna.org/gdsl/")
+    (home-page "https://web.archive.org/web/20170502005430/http://home.gna.org/gdsl/")
     (synopsis "Generic data structures library")
     (description "The Generic Data Structures Library (GDSL) is a collection
 of routines for generic data structures manipulation.  It is a re-entrant

gnu/packages/debug.scm

@@ -6,6 +6,7 @@
 ;;; Copyright © 2019 Pkill -9 <pkill9@runbox.com>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2020 Morgan Smith <Morgan.J.Smith@outlook.com>
+;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -36,6 +37,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
+  #:use-module (gnu packages c)
   #:use-module (gnu packages code)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages flex)
@@ -624,6 +626,78 @@ GDB/x86 features like hardware data watchpoints, makes debugging much more
 fun.")
     (license license:expat)))
 
+(define-public libbacktrace
+  ;; There are no releases nor tags.
+  (let ((revision "1")
+        (commit "5009c113981431ae1843ebd29d6ad24eb32fc1b2"))
+    (package
+      (name "libbacktrace")
+      (version (git-version "1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ianlancetaylor/libbacktrace")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0663zjpfpnsyv9h3pbp7cgmg9gz79n68bqpdl97y6i0jsx93v1zg"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:make-flags '("CFLAGS=-fPIC")))
+      (home-page "https://github.com/ianlancetaylor/libbacktrace")
+      (synopsis "C library for producing symbolic backtraces")
+      (description "The @code{libbacktrace} library can be linked into a C/C++
+program to produce symbolic backtraces.")
+      (license license:bsd-3))))
+
+(define-public libleak
+  (package
+    (name "libleak")
+    (version "0.3.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/WuBingzheng/libleak")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1p8mb0hcfp8hdv1klv6rrpkn2zlhjxgkxbbjsk8kszxv7ijln87d"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ;no test suite
+       #:parallel-build? #f             ;jobserver unavailable
+       #:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'unbundle-libwuya
+                    (lambda _
+                      (substitute* "Makefile"
+                        ((".*make -C libwuya.*") ""))
+                      #t))
+                  (add-before 'build 'set-CC
+                    (lambda _
+                      (setenv "CC" "gcc")
+                      #t))
+                  (delete 'configure)   ;no configure script
+                  (replace 'install
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let* ((out (assoc-ref outputs "out")))
+                        (install-file "libleak.so" (string-append out "/lib"))
+                        #t))))))
+    (inputs `(("libbacktrace" ,libbacktrace)
+              ("libwuya" ,libwuya)))
+    (home-page "https://github.com/WuBingzheng/libleak")
+    (synopsis "Memory leaks detection tool")
+    (description "The libleak tool detects memory leaks by hooking memory
+functions such as @code{malloc}.  It comes as a shared object to be pre-loaded
+via @code{LD_PRELOAD} when launching the application.  It prints the full call
+stack at suspicious memory leak points.  Modifying or recompiling the target
+program is not required, and the detection can be enabled or disabled while
+the target application is running.  The overhead incurred by libleak is
+smaller than that of other tools such as Valgrind, and it aims to be easier to
+use than similar tools like @command{mtrace}.")
+    (license license:gpl2+)))
+
 (define-public mspdebug
   (package
     (name "mspdebug")

gnu/packages/dico.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -39,14 +39,14 @@
 (define-public dico
   (package
     (name "dico")
-    (version "2.9")
+    (version "2.10")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/dico/dico-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0i9xqhy3h5nlizcmav4mv5ay8ivdgn4l4k0k7fxix3fsc87nijyr"))))
+               "0qag47mzs00d53hnrmh381r0jay42766vp5xrffmzmsn2307x8vl"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags (list (string-append "--with-guile-site-dir=" %output

gnu/packages/dictionaries.scm

@@ -205,14 +205,14 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
 (define-public grammalecte
   (package
     (name "grammalecte")
-    (version "1.12.0")
+    (version "1.12.2")
     (source
      (origin
        (method url-fetch/zipbomb)
        (uri (string-append "https://grammalecte.net/grammalecte/zip/"
                            "Grammalecte-fr-v" version ".zip"))
        (sha256
-        (base32 "1aifa7rj8zyxgk5cgmlgcws2hip7a7y6sr7kddjdnpfgdgy4jjgh"))))
+        (base32 "1qny2l5dr08pfj2dnzmvm5gmwqz8m879ryxfaw4k8dhaacrrrf62"))))
     (build-system python-build-system)
     (home-page "https://grammalecte.net")
     (synopsis "French spelling and grammar checker")

gnu/packages/diffoscope.scm

@@ -254,7 +254,7 @@ install.")
     (inputs
      `(("python-debian" ,python-debian)
        ("python-distro" ,python-distro)
-       ("python-libarchive-c", python-libarchive-c)
+       ("python-libarchive-c" ,python-libarchive-c)
        ("python-rstr" ,python-rstr)))
     (native-inputs
      `(("diffoscope" ,diffoscope)

gnu/packages/disk.scm

@@ -689,7 +689,7 @@ passphrases.")
 (define-public ndctl
   (package
     (name "ndctl")
-    (version "69")
+    (version "70.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -698,7 +698,7 @@ passphrases.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1l7p0ycj27d4z07gf9qp796xpg16kfsg3rwx6plhilbhip1as4w7"))))
+                "09ymdibcr18vpmyf2n0xrnzgccfvr7iy3p2l5lbh7cgz7djyl5wq"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("asciidoc" ,asciidoc)
@@ -1038,6 +1038,50 @@ of choice for all light thinking Unix addicts!")
     (home-page "https://savannah.nongnu.org/projects/hddtemp/")
     (synopsis "Report the temperature of hard drives from S.M.A.R.T. information")
     (description "@command{hddtemp} is a small utility that gives you the
-temperature of your hard drive by reading S.M.A.R.T. informations (for drives
+temperature of your hard drive by reading S.M.A.R.T. information (for drives
 that support this feature).")
     (license license:gpl2+)))
+
+(define-public memkind
+  (package
+    (name "memkind")
+    (version "1.10.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/memkind/memkind.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "11iz887f3cp5pzf1bzm644wzab8gkbhz3b7x1w6pcps71yd94ylj"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(;; memkind patched jemalloc to add je_arenalookupx,
+       ;; je_check_reallocatex--i.e. they forked jemalloc.
+       ;("jemalloc" ,jemalloc)
+       ("ndctl" ,ndctl)
+       ("numactl" ,numactl)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (arguments
+     `(#:tests? #f ; Tests require a NUMA-enabled system.
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'autogen-jemalloc
+           (lambda _
+             (with-directory-excursion "jemalloc"
+               (substitute* "Makefile.in"
+                (("/bin/sh") (which "sh")))
+               (invoke "autoconf")
+               (substitute* "configure"
+                (("/bin/sh") (which "sh"))))
+             #t)))))
+    (home-page "https://github.com/memkind/memkind")
+    (synopsis "Heap manager with memory kinds (for NUMA)")
+    (description "This package provides a user-extensible heap manager
+built on top of jemalloc which enables control of memory characteristics
+and a partitioning of the heap between kinds of memory (for NUMA).")
+    (license license:bsd-3)))

gnu/packages/dns.scm

@@ -17,6 +17,7 @@
 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2020 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
+;;; Copyright © 2020 Simon South <simon@simonsouth.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -45,6 +46,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages datastructures)
+  #:use-module (gnu packages elf)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gcc)
@@ -65,9 +67,11 @@
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages ragel)
   #:use-module (gnu packages shells)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages swig)
+  #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
@@ -313,7 +317,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
   (package
     (name "bind")
     ;; When updating, check whether isc-dhcp's bundled copy should be as well.
-    (version "9.16.6")
+    (version "9.16.7")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -321,7 +325,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
                     "/bind-" version ".tar.xz"))
               (sha256
                (base32
-                "1jvi6ms51vyrhpflx05xlb7gblyd59zsyj28b8s3pl3xnkrv0rxm"))))
+                "1l8lhgnkj3fnl1101bs3pzj5gv2x5m9ahvrbyscsc9mxxc91hzcz"))))
     (build-system gnu-build-system)
     (outputs `("out" "utils"))
     (inputs
@@ -529,14 +533,14 @@ asynchronous fashion.")
 (define-public nsd
   (package
     (name "nsd")
-    (version "4.3.2")
+    (version "4.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.nlnetlabs.nl/downloads/nsd/nsd-"
                            version ".tar.gz"))
        (sha256
-        (base32 "0ac3mbn5z4nc18782m9aswdpi2m9f4665vidw0ciyigdh0pywp2v"))))
+        (base32 "0lgdiqnkfvy245h6kkiqic586qjwmg51lsfs86vlc0kwjwddiijz"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -756,16 +760,16 @@ served by AS112.  Stub and forward zones are supported.")
 (define-public yadifa
   (package
     (name "yadifa")
-    (version "2.3.9")
+    (version "2.3.10")
     (source
-     (let ((build "8497"))
+     (let ((build "9729"))
        (origin
          (method url-fetch)
          (uri
           (string-append "http://cdn.yadifa.eu/sites/default/files/releases/"
                          "yadifa-" version "-" build ".tar.gz"))
          (sha256
-          (base32 "0xvyr91sfgzkpw6g3h893ldbwnki3w2472n56rr18w67qghs1sa5")))))
+          (base32 "0azaignqmylfdzr4x02s8y3pkn4f0xkpz3d1pkiiz8mwk92zgybn")))))
     (build-system gnu-build-system)
     (native-inputs
      `(("which" ,which)))
@@ -803,44 +807,63 @@ Extensions} (DNSSEC).")
 (define-public knot
   (package
     (name "knot")
-    (version "2.9.6")
+    (version "3.0.1")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://secure.nic.cz/files/knot-dns/"
+       (uri (git-reference
-                           "knot-" version ".tar.xz"))
+             (url "https://gitlab.nic.cz/knot/knot-dns")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1rxjjisr6rz1wa4279ghvj5zzhgyjhncmb9dkzqm8nw2qs1jhx5z"))
+        (base32 "10mlzldxqvbaw78nghkr0s73rlbpz9wg16z14321xw2l9xfibkad"))
        (modules '((guix build utils)))
        (snippet
         '(begin
-           ;; Delete bundled libraries.
+           ;; Remove Ragel-generated C files.  We'll recreate them below.
-           (with-directory-excursion "src/contrib"
+           (for-each delete-file (find-files "." "\\.c\\.[gt]."))
-             (delete-file-recursively "lmdb"))
+           (delete-file "src/libknot/yparser/ypbody.c")
+           ;; Remove bundled library to ensure we always use the system's.
+           (delete-file-recursively "src/contrib/libbpf")
            #t))))
     (build-system gnu-build-system)
-    (native-inputs
+    (outputs (list "out" "doc" "lib" "tools"))
-     `(("pkg-config" ,pkg-config)))
-    (inputs
-     `(("fstrm" ,fstrm)
-       ("gnutls" ,gnutls)
-       ("jansson" ,jansson)
-       ("libcap-ng" ,libcap-ng)
-       ("libedit" ,libedit)
-       ("libidn" ,libidn)
-       ("liburcu" ,liburcu)
-       ("lmdb" ,lmdb)
-       ("ncurses" ,ncurses)
-       ("protobuf-c" ,protobuf-c)))
     (arguments
-     `(#:phases
+     `(#:configure-flags
+       (list (string-append "--docdir=" (assoc-ref %outputs "doc")
+                            "/share/" ,name "-" ,version)
+             (string-append "--infodir=" (assoc-ref %outputs "doc")
+                            "/share/info")
+             (string-append "--libdir=" (assoc-ref %outputs "lib") "/lib")
+             "--sysconfdir=/etc"
+             "--localstatedir=/var"
+             "--enable-dnstap"          ; let tools read/write capture files
+             "--enable-fastparser"      ; disabled by default when .git/ exists
+             "--enable-xdp=auto"        ; XXX [=yes] currently means =embedded
+             "--with-module-dnstap=yes") ; detailed query capturing & logging
+       #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'link-missing-libbpf-dependency
+           ;; Linking against -lbpf later would fail to find -lz: libbpf.pc has
+           ;; zlib in its Requires.private (not Requires) field.  Add it here.
+           (lambda _
+             (substitute* "configure.ac"
+               (("enable_xdp=yes" match)
+                (string-append match "\nlibbpf_LIBS=\"$libbpf_LIBS -lz\"")))
+             #true))
+         (add-before 'bootstrap 'update-parser
+           (lambda _
+             (with-directory-excursion "src"
+               (invoke "sh" "../scripts/update-parser.sh"))))
          (add-before 'configure 'disable-directory-pre-creation
            (lambda _
              ;; Don't install empty directories like ‘/etc’ outside the store.
              ;; This is needed even when using ‘make config_dir=... install’.
              (substitute* "src/Makefile.in" (("\\$\\(INSTALL\\) -d") "true"))
              #t))
+         (add-after 'build 'build-info
+           (lambda _
+             (invoke "make" "info")))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -848,15 +871,51 @@ Extensions} (DNSSEC).")
                     (etc (string-append doc "/examples/etc")))
                (invoke "make"
                        (string-append "config_dir=" etc)
-                       "install")))))
+                       "install"))))
-       #:configure-flags
+         (add-after 'install 'install-info
-       (list "--sysconfdir=/etc"
+           (lambda _
-             "--localstatedir=/var"
+             (invoke "make" "install-info")))
-             "--enable-dnstap"          ; let tools read/write capture files
+         (add-after 'install 'break-circular-:lib->:out-reference
-             "--with-module-dnstap=yes" ; detailed query capturing & logging
+           (lambda* (#:key outputs #:allow-other-keys)
-             (string-append "--with-bash-completions="
+             (let ((lib (assoc-ref outputs "lib")))
-                            (assoc-ref %outputs "out")
+               (for-each (lambda (file)
-                            "/etc/bash_completion.d"))))
+                           (substitute* file
+                             (("(prefix=).*" _ assign)
+                              (string-append assign lib "\n"))))
+                         (find-files lib "\\.pc$"))
+               #true)))
+         (add-after 'install 'split-:tools
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out   (assoc-ref outputs "out"))
+                    (tools (assoc-ref outputs "tools")))
+               (mkdir-p (string-append tools "/share/man"))
+               (rename-file (string-append out   "/bin")
+                            (string-append tools "/bin"))
+               (rename-file (string-append out   "/share/man/man1")
+                            (string-append tools "/share/man/man1"))
+               #true))))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)
+       ("python-sphinx" ,python-sphinx)
+       ("ragel" ,ragel)
+       ("texinfo" ,texinfo)))
+    (inputs
+     `(("fstrm" ,fstrm)
+       ("gnutls" ,gnutls)
+       ("jansson" ,jansson)
+       ("libbpf" ,libbpf)
+       ("libcap-ng" ,libcap-ng)
+       ("libedit" ,libedit)
+       ("libelf" ,libelf)
+       ("libidn" ,libidn)
+       ("libnghttp2" ,nghttp2 "lib")
+       ("liburcu" ,liburcu)
+       ("lmdb" ,lmdb)
+       ("ncurses" ,ncurses)
+       ("protobuf-c" ,protobuf-c)))
     (home-page "https://www.knot-dns.cz/")
     (synopsis "Authoritative DNS name server")
     (description "Knot DNS is an authoritative name server for the @dfn{Domain
@@ -878,14 +937,14 @@ synthesis, and on-the-fly re-configuration.")
 (define-public knot-resolver
   (package
     (name "knot-resolver")
-    (version "4.3.0")
+    (version "5.1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://secure.nic.cz/files/knot-resolver/"
                                   "knot-resolver-" version ".tar.xz"))
               (sha256
                (base32
-                "09ffmqx79lv5psr433x4n946njgsn071b9b7161pcb9bmrqz380c"))))
+                "12s5070nqqf599s1mb6rjas2as481rjf751qk5yrz6p34y885k90"))))
     (build-system meson-build-system)
     (arguments
      '(#:configure-flags '("-Ddoc=enabled")
@@ -927,16 +986,12 @@ synthesis, and on-the-fly re-configuration.")
     (inputs
      `(("fstrm" ,fstrm)
        ("gnutls" ,gnutls)
-       ("knot" ,knot)
+       ("knot:lib" ,knot "lib")
        ("libuv" ,libuv)
        ("lmdb" ,lmdb)
        ("luajit" ,luajit)
        ;; TODO: Add optional lua modules: basexx and psl.
-       ("lua-bitop" ,lua5.1-bitop)
+       ("lua-bitop" ,lua5.1-bitop)))
-       ("lua-cqueues" ,lua5.1-cqueues)
-       ("lua-filesystem" ,lua5.1-filesystem)
-       ("lua-sec" ,lua5.1-sec)
-       ("lua-socket" ,lua5.1-socket)))
     (home-page "https://www.knot-resolver.cz/")
     (synopsis "Caching validating DNS resolver")
     (description