Merge branch 'master' into staging

doc/guix.texi

@@ -25510,7 +25510,7 @@ evaluates to.  As an example, @var{file} might contain a definition like this:
             %base-services))))
 
 (list (machine
-       (system %system)
+       (operating-system %system)
        (environment managed-host-environment-type)
        (configuration (machine-ssh-configuration
                        (host-name "localhost")
@@ -25530,12 +25530,28 @@ complex deployment may involve, for example, starting virtual machines through
 a Virtual Private Server (VPS) provider.  In such a case, a different
 @var{environment} type would be used.
 
+Do note that you first need to generate a key pair on the coordinator machine
+to allow the daemon to export signed archives of files from the store
+(@pxref{Invoking guix archive}).
+
+@example
+# guix archive --generate-key
+@end example
+
+@noindent
+Each target machine must authorize the key of the master machine so that it
+accepts store items it receives from the coordinator:
+
+@example
+# guix archive --authorize < coordinator-public-key.txt
+@end example
+
 @deftp {Data Type} machine
 This is the data type representing a single machine in a heterogeneous Guix
 deployment.
 
 @table @asis
-@item @code{system}
+@item @code{operating-system}
 The object of the operating system configuration to deploy.
 
 @item @code{environment}

gnu/local.mk

@@ -772,6 +772,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/elfutils-tests-ptrace.patch		\
   %D%/packages/patches/elixir-path-length.patch			\
   %D%/packages/patches/einstein-build.patch			\
+  %D%/packages/patches/emacs-dired-toggle-sudo-emacs-26.patch   \
   %D%/packages/patches/emacs-exec-path.patch			\
   %D%/packages/patches/emacs-fix-scheme-indent-function.patch	\
   %D%/packages/patches/emacs-json-reformat-fix-tests.patch	\
@@ -1022,7 +1023,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/libotr-test-auth-fix.patch		\
   %D%/packages/patches/libmad-armv7-thumb-pt1.patch		\
   %D%/packages/patches/libmad-armv7-thumb-pt2.patch		\
-  %D%/packages/patches/libmad-frame-length.patch		\
+  %D%/packages/patches/libmad-length-check.patch		\
+  %D%/packages/patches/libmad-md_size.patch			\
   %D%/packages/patches/libmad-mips-newgcc.patch			\
   %D%/packages/patches/libmygpo-qt-fix-qt-5.11.patch		\
   %D%/packages/patches/libmygpo-qt-missing-qt5-modules.patch	\
@@ -1043,7 +1045,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/libutils-add-includes.patch		\
   %D%/packages/patches/libutils-remove-damaging-includes.patch	\
   %D%/packages/patches/libvdpau-va-gl-unbundle.patch		\
-  %D%/packages/patches/libvirt-remove-ATTRIBUTE_UNUSED.patch	\
   %D%/packages/patches/libvpx-CVE-2016-2818.patch		\
   %D%/packages/patches/libvpx-use-after-free-in-postproc.patch	\
   %D%/packages/patches/libxslt-generated-ids.patch		\
@@ -1305,6 +1306,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/soundconverter-remove-gconf-dependency.patch	\
   %D%/packages/patches/sssd-curl-compat.patch			\
   %D%/packages/patches/steghide-fixes.patch			\
+  %D%/packages/patches/strace-ipc-tests.patch			\
   %D%/packages/patches/streamlink-update-test.patch		\
   %D%/packages/patches/stumpwm-fix-broken-read-one-line.patch	\
   %D%/packages/patches/superlu-dist-awpm-grid.patch		\

gnu/machine.scm

@@ -34,7 +34,7 @@
             machine?
             this-machine
 
-            machine-system
+            machine-operating-system
             machine-environment
             machine-configuration
             machine-display-name
@@ -85,14 +85,14 @@
   make-machine
   machine?
   this-machine
-  (system        machine-system)       ; <operating-system>
+  (operating-system machine-operating-system) ; <operating-system>
-  (environment   machine-environment)  ; symbol
+  (environment      machine-environment)      ; symbol
-  (configuration machine-configuration ; configuration object
+  (configuration    machine-configuration     ; configuration object
-                 (default #f)))        ; specific to environment
+                    (default #f)))            ; specific to environment
 
 (define (machine-display-name machine)
   "Return the host-name identifying MACHINE."
-  (operating-system-host-name (machine-system machine)))
+  (operating-system-host-name (machine-operating-system machine)))
 
 (define (machine-remote-eval machine exp)
   "Evaluate EXP, a gexp, on MACHINE. Ensure that all the elements EXP refers to

gnu/machine/ssh.scm

@@ -20,6 +20,9 @@
   #:use-module (gnu machine)
   #:autoload   (gnu packages gnupg) (guile-gcrypt)
   #:use-module (gnu system)
+  #:use-module (gnu system file-systems)
+  #:use-module (gnu system uuid)
+  #:use-module (guix diagnostics)
   #:use-module (guix gexp)
   #:use-module (guix i18n)
   #:use-module (guix modules)
@@ -29,6 +32,7 @@
   #:use-module (guix scripts system reconfigure)
   #:use-module (guix ssh)
   #:use-module (guix store)
+  #:use-module (guix utils)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-19)
   #:use-module (srfi srfi-26)
@@ -40,6 +44,7 @@
             machine-ssh-configuration
 
             machine-ssh-configuration-host-name
+            machine-ssh-configuration-build-locally?
             machine-ssh-configuration-port
             machine-ssh-configuration-user
             machine-ssh-configuration-session))
@@ -62,15 +67,17 @@
   make-machine-ssh-configuration
   machine-ssh-configuration?
   this-machine-ssh-configuration
-  (host-name machine-ssh-configuration-host-name) ; string
+  (host-name      machine-ssh-configuration-host-name) ; string
-  (port      machine-ssh-configuration-port       ; integer
+  (build-locally? machine-ssh-configuration-build-locally?
-             (default 22))
+                  (default #t))
-  (user      machine-ssh-configuration-user       ; string
+  (port           machine-ssh-configuration-port       ; integer
-             (default "root"))
+                  (default 22))
-  (identity  machine-ssh-configuration-identity   ; path to a private key
+  (user           machine-ssh-configuration-user       ; string
-             (default #f))
+                  (default "root"))
-  (session   machine-ssh-configuration-session    ; session
+  (identity       machine-ssh-configuration-identity   ; path to a private key
-             (default #f)))
+                  (default #f))
+  (session        machine-ssh-configuration-session    ; session
+                  (default #f)))
 
 (define (machine-ssh-session machine)
   "Return the SSH session that was given in MACHINE's configuration, or create
@@ -96,7 +103,149 @@ one from the configuration's parameters if one was not provided."
   "Internal implementation of 'machine-remote-eval' for MACHINE instances with
 an environment type of 'managed-host."
   (maybe-raise-unsupported-configuration-error machine)
-  (remote-eval exp (machine-ssh-session machine)))
+  (remote-eval exp (machine-ssh-session machine)
+               #:build-locally?
+               (machine-ssh-configuration-build-locally?
+                (machine-configuration machine))))
+
+
+;;;
+;;; Safety checks.
+;;;
+
+(define (machine-check-file-system-availability machine)
+  "Raise a '&message' error condition if any of the file-systems specified in
+MACHINE's 'system' declaration do not exist on the machine."
+  (define file-systems
+    (filter (lambda (fs)
+              (and (file-system-mount? fs)
+                   (not (member (file-system-type fs)
+                                %pseudo-file-system-types))
+                   (not (memq 'bind-mount (file-system-flags fs)))))
+            (operating-system-file-systems (machine-operating-system machine))))
+
+  (define (check-literal-file-system fs)
+    (define remote-exp
+      #~(catch 'system-error
+          (lambda ()
+            (stat #$(file-system-device fs))
+            #t)
+          (lambda args
+            (system-error-errno args))))
+
+    (mlet %store-monad ((errno (machine-remote-eval machine remote-exp)))
+      (when (number? errno)
+        (raise (condition
+                (&message
+                 (message (format #f (G_ "device '~a' not found: ~a")
+                                  (file-system-device fs)
+                                  (strerror errno)))))))
+      (return #t)))
+
+  (define (check-labeled-file-system fs)
+    (define remote-exp
+      (with-imported-modules '((gnu build file-systems))
+        #~(begin
+            (use-modules (gnu build file-systems))
+            (find-partition-by-label #$(file-system-label->string
+                                        (file-system-device fs))))))
+
+    (mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
+      (unless result
+        (raise (condition
+                (&message
+                 (message (format #f (G_ "no file system with label '~a'")
+                                  (file-system-label->string
+                                   (file-system-device fs))))))))
+      (return #t)))
+
+  (define (check-uuid-file-system fs)
+    (define remote-exp
+      (with-imported-modules (source-module-closure
+                              '((gnu build file-systems)
+                                (gnu system uuid)))
+        #~(begin
+            (use-modules (gnu build file-systems)
+                         (gnu system uuid))
+
+            (define uuid
+              (string->uuid #$(uuid->string (file-system-device fs))))
+
+            (find-partition-by-uuid uuid))))
+
+    (mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
+      (unless result
+        (raise (condition
+                (&message
+                 (message (format #f (G_ "no file system with UUID '~a'")
+                                  (uuid->string (file-system-device fs))))))))
+      (return #t)))
+
+  (mbegin %store-monad
+    (mapm %store-monad check-literal-file-system
+          (filter (lambda (fs)
+                    (string? (file-system-device fs)))
+                  file-systems))
+    (mapm %store-monad check-labeled-file-system
+          (filter (lambda (fs)
+                    (file-system-label? (file-system-device fs)))
+                  file-systems))
+    (mapm %store-monad check-uuid-file-system
+          (filter (lambda (fs)
+              (uuid? (file-system-device fs)))
+                  file-systems))))
+
+(define (machine-check-initrd-modules machine)
+  "Raise a '&message' error condition if any of the modules needed by
+'needed-for-boot' file systems in MACHINE are not available in the initrd."
+  (define file-systems
+    (filter file-system-needed-for-boot?
+            (operating-system-file-systems (machine-operating-system machine))))
+
+  (define (missing-modules fs)
+    (define remote-exp
+      (let ((device (file-system-device fs)))
+        (with-imported-modules (source-module-closure
+                                '((gnu build file-systems)
+                                  (gnu build linux-modules)
+                                  (gnu system uuid)))
+          #~(begin
+              (use-modules (gnu build file-systems)
+                           (gnu build linux-modules)
+                           (gnu system uuid))
+
+              (define dev
+                #$(cond ((string? device) device)
+                        ((uuid? device) #~(find-partition-by-uuid
+                                           (string->uuid
+                                            #$(uuid->string device))))
+                        ((file-system-label? device)
+                         #~(find-partition-by-label
+                            (file-system-label->string #$device)))))
+
+              (missing-modules dev '#$(operating-system-initrd-modules
+                                       (machine-operating-system machine)))))))
+    (mlet %store-monad ((missing (machine-remote-eval machine remote-exp)))
+      (return (list fs missing))))
+
+  (mlet %store-monad ((device (mapm %store-monad missing-modules file-systems)))
+    (for-each (match-lambda
+                ((fs missing)
+                 (unless (null? missing)
+                   (raise (condition
+                           (&message
+                            (message (format #f (G_ "~a missing modules ~{ ~a~}~%")
+                                             (file-system-device fs)
+                                             missing))))))))
+              device)
+    (return #t)))
+
+(define (check-deployment-sanity machine)
+  "Raise a '&message' error condition if it is clear that deploying MACHINE's
+'system' declaration would fail."
+  (mbegin %store-monad
+    (machine-check-file-system-availability machine)
+    (machine-check-initrd-modules machine)))
 
 
 ;;;
@@ -165,8 +314,9 @@ of MACHINE's system profile, ordered from most recent to oldest."
   "Internal implementation of 'deploy-machine' for MACHINE instances with an
 environment type of 'managed-host."
   (maybe-raise-unsupported-configuration-error machine)
-  (mlet %store-monad ((boot-parameters (machine-boot-parameters machine)))
+  (mlet %store-monad ((_ (check-deployment-sanity machine))
-    (let* ((os (machine-system machine))
+                      (boot-parameters (machine-boot-parameters machine)))
+    (let* ((os (machine-operating-system machine))
            (eval (cut machine-remote-eval machine <>))
            (menu-entries (map boot-parameters->menu-entry boot-parameters))
            (bootloader-configuration (operating-system-bootloader os))

gnu/packages/admin.scm

@@ -1181,7 +1181,7 @@ commands and their arguments.")
 (define-public wpa-supplicant-minimal
   (package
     (name "wpa-supplicant-minimal")
-    (version "2.8")
+    (version "2.9")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1189,7 +1189,7 @@ commands and their arguments.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "15ixzm347n8w6gdvi3j3yks3i15qmp6by9ayvswm34d929m372d6"))
+                "05qzak1mssnxcgdrafifxh9w86a4ha69qabkg4bsigk499xyxggw"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -2606,7 +2606,7 @@ buffers.")
      `(#:tests? #f              ; many of the tests try to load kernel modules
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
+         (replace 'bootstrap
            (lambda _
              ;; Don't run configure in this phase.
              (setenv "NOCONFIGURE" "1")

gnu/packages/algebra.scm

@@ -236,8 +236,7 @@ the real span of the lattice.")
     (build-system gnu-build-system)
     (native-inputs
      `(("texlive" ,(texlive-union
-                    (list texlive-fonts-amsfonts
+                    (list texlive-amsfonts)))))
-                          texlive-latex-amsfonts)))))
     (inputs `(("gmp" ,gmp)
               ("libx11" ,libx11)
               ("perl" ,perl)

gnu/packages/audio.scm

@@ -3700,7 +3700,7 @@ library.")
 (define-public faudio
   (package
     (name "faudio")
-    (version "19.07")
+    (version "19.08")
     (source
      (origin
        (method git-fetch)
@@ -3709,7 +3709,7 @@ library.")
              (commit version)))
        (file-name (string-append name "-" version "-checkout"))
        (sha256
-        (base32 "1wf6skc5agaikc9qgwk8bx56sad31fafs53lqqn4jmx8i76pl0lw"))))
+        (base32 "1v13kfhyr46241vb6a4dcb4gw5f149525sprwa9cj4rv6wlcqgm5"))))
     (arguments
      '(#:tests? #f                      ; No tests.
        #:configure-flags '("-DFFMPEG=ON")))

gnu/packages/bioconductor.scm

@@ -1212,14 +1212,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.18.1")
+    (version "3.18.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji"))))
+         "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1521,14 +1521,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
+         "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -3529,14 +3529,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.8.1")
+    (version "1.8.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69"))))
+         "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3621,14 +3621,14 @@ annotations and ontologies.")
 (define-public r-abaenrichment
   (package
     (name "r-abaenrichment")
-    (version "1.14.0")
+    (version "1.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ABAEnrichment" version))
        (sha256
         (base32
-         "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
+         "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
     (properties `((upstream-name . "ABAEnrichment")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4841,14 +4841,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "1.34.4")
+    (version "1.34.6")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "1230p8nsakifmpsqfiaj8rpm7npa8ab903mfjmayfa71n6yzvcbs"))))
+         "0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))

gnu/packages/bioinformatics.scm

@@ -13,6 +13,7 @@
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -4206,8 +4207,15 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
        (modify-phases %standard-phases
          (add-after 'unpack 'set-cc
            (lambda _ (setenv "CC" "gcc") #t))
-         ;; FIXME: This fails with "permission denied".
+
-         (delete 'reset-gzip-timestamps))))
+         (add-before 'reset-gzip-timestamps 'make-files-writable
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Make sure .gz files are writable so that the
+             ;; 'reset-gzip-timestamps' phase can do its work.
+             (let ((out (assoc-ref outputs "out")))
+               (for-each make-file-writable
+                         (find-files out "\\.gz$"))
+               #t))))))
     (native-inputs
      `(("python-cython" ,python-cython)
        ("python-pytest" ,python-pytest)
@@ -7450,13 +7458,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.26.5")
+    (version "3.26.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "0iba4krz30dx5b0s89n5cfkwn64867s7vmvvfqms9lbcr4kj439m"))))
+                "17vadhamjv4x0l4qqq2p2fi6j2bkllz5zd8dq761vgd5ic23zizm"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7517,13 +7525,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.40.2")
+    (version "3.40.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1d4ig2b7fa9mwja52isxrwmprfdjdk1mlcf2skhdp51l24z6wbk7"))))
+                "166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7650,13 +7658,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.40.1")
+    (version "2.40.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "1abl0c4qbhfqf9ixdp74183phm7s8rszrr5ldczm59b8vyng8rhx"))))
+                "022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -7811,13 +7819,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.14.0")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci"))))
+                "0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -7875,13 +7883,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.44.0")
+    (version "1.44.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "161gcks9b12993g9k27gf7wfh8lgd8m8rr7x2slgfqqssk0yrmpd"))))
+                "03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -7922,13 +7930,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.36.3")
+    (version "1.36.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0zkd57i5qjxsravv0gbyckc0wrnqzgxd61ibh3jmhmrccrr9ihn3"))))
+                "0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -8346,13 +8354,13 @@ paired-end data.")
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.10.0")
+    (version "1.10.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "1h4vf5gzilqbdrd8m9l3zc2m4sca8cir8366a7njgd558k7ld5kl"))))
+                "06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz"))))
     (properties `((upstream-name . "RCAS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9410,14 +9418,14 @@ of mass spectrometry based proteomics data.")
 (define-public r-msnid
   (package
     (name "r-msnid")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnID" version))
        (sha256
         (base32
-         "18mp8zacawhfapfwpq8czbswxix2ykvqhwjga54v0a99zg3k87h3"))))
+         "1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb"))))
     (properties `((upstream-name . "MSnID")))
     (build-system r-build-system)
     (propagated-inputs

gnu/packages/docbook.scm

@@ -195,7 +195,7 @@ by no means limited to these applications.)  This package provides XML DTDs.")
     (build-system python-build-system)
     ;; TODO: Add xfig/transfig for fig2dev utility
     (inputs
-     `(("texlive" ,(texlive-union (list texlive-latex-amsfonts
+     `(("texlive" ,(texlive-union (list texlive-amsfonts
                                         texlive-latex-anysize
                                         texlive-latex-appendix
                                         texlive-latex-changebar
@@ -219,7 +219,6 @@ by no means limited to these applications.)  This package provides XML DTDs.")
                                         texlive-latex-url
                                         texlive-latex-wasysym
 
-                                        texlive-fonts-amsfonts
                                         texlive-fonts-ec
                                         texlive-fonts-rsfs
                                         texlive-fonts-stmaryrd

gnu/packages/docker.scm

@@ -63,12 +63,13 @@
     (arguments '(#:tests? #f))
     (inputs
      `(("python-requests" ,python-requests-2.20)
-       ("python-docker-pycreds" ,python-docker-pycreds)
        ("python-ipaddress" ,python-ipaddress)
-       ("python-paramiko" ,python-paramiko)
        ("python-six" ,python-six)
        ("python-urllib3" ,python-urllib3-1.24)
        ("python-websocket-client" ,python-websocket-client)))
+    (propagated-inputs
+     `(("python-docker-pycreds" ,python-docker-pycreds)
+       ("python-paramiko" ,python-paramiko))) ; adds SSH support
     (home-page "https://github.com/docker/docker-py/")
     (synopsis "Python client for Docker")
     (description "Docker-Py is a Python client for the Docker container
@@ -113,17 +114,11 @@ client.")
     ;; TODO: Tests require running Docker daemon.
     (arguments '(#:tests? #f))
     (inputs
-     `(("python2-backport-ssl-match-hostname"
+     `(("python-cached-property"
-        ,python2-backport-ssl-match-hostname)
-       ("python-cached-property"
         ,python-cached-property)
-       ("python-colorama" ,python-colorama)
        ("python-docker-py" ,python-docker-py)
-       ("python-docker-pycreds" ,python-docker-pycreds)
        ("python-dockerpty" ,python-dockerpty)
        ("python-docopt" ,python-docopt)
-       ("python-ipaddress" ,python-ipaddress)
-       ("python-paramiko" ,python-paramiko)
        ("python-jsonschema" ,python-jsonschema-2.6)
        ("python-pyyaml" ,python-pyyaml)
        ("python-requests" ,python-requests-2.20)

gnu/packages/emacs-xyz.scm

@@ -3389,6 +3389,76 @@ for the current function or variable in the minibuffer.")
 completion candidate when using the Company text completion framework.")
     (license license:gpl3+)))
 
+(define-public emacs-math-symbol-lists
+  (let ((commit "dc7531cff0c845d5470a50c24d5d7309b2ced7eb")
+        (revision "1"))
+    (package
+      (name "emacs-math-symbol-lists")
+      (version (git-version "1.2.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/vspinu/math-symbol-lists.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "094m21i9rns6m59cmhxcivxxafbg52w8f8na4y3v47aq67zmhhqm"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/vspinu/math-symbol-lists")
+      (synopsis "Lists of Unicode math symbols and @code{LaTeX} commands")
+      (description "This is a storage package used by completion engines like
+@code{company-math}.")
+      (license license:gpl3+))))
+
+(define-public emacs-company-math
+  (let ((commit "600e49449644f6835f9dc3501bc58461999e8ab9")
+        (revision "1"))
+    (package
+      (name "emacs-company-math")
+      (version (git-version "1.3" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/vspinu/company-math.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1ps2lpkzn8mjbpcbvvy1qz3xbgrh6951x8y9bsd1fm32drdph9lh"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-math-symbol-lists" ,emacs-math-symbol-lists)
+         ("emacs-company" ,emacs-company)))
+      (home-page "https://github.com/vspinu/company-math")
+      (synopsis "Completion backends for Unicode math symbols and @code{LaTeX} tags")
+      (description "This package provides a backend for use with
+@code{company-mode} allowing for completion of common math symbols.")
+      (license license:gpl3+))))
+
+(define-public emacs-nswbuff
+  (let ((commit "362da7f3687e2eb5bb11667347de85f4a9d002bc")
+        (revision "1"))
+    (package
+      (name "emacs-nswbuff")
+      (version (git-version "1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/joostkremers/nswbuff.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0l2xfz8z5qd4hz3kv6zn7h6qq3narkilri8a071y1n8j31jps4ma"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/joostkremers/nswbuff")
+      (synopsis "Quickly switch between buffers")
+      (description "This package allows for navigating between buffers within
+a customizable list.")
+      (license license:gpl3+))))
+
 (define-public emacs-multiple-cursors
   (package
     (name "emacs-multiple-cursors")
@@ -3410,6 +3480,32 @@ completion candidate when using the Company text completion framework.")
 simultaneous cursors.")
     (license license:gpl3+)))
 
+(define-public emacs-mc-extras
+  (let ((commit "053abc52181b8718559d7361a587bbb795faf164")
+        (revision "1"))
+    (package
+      (name "emacs-mc-extras")
+      (version (git-version "1.2.4" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/knu/mc-extras.el.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "16y48qrd20m20vypvys5jp4v4gc1qrqlkm75s1pk1r68i9zrw481"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-multiple-cursors" ,emacs-multiple-cursors)))
+      (home-page "https://github.com/knu/mc-extras.el")
+      (synopsis "Extra functions for manipulating multiple cursors")
+      (description
+       "This package provides additional functions for
+@code{multiple-cursors}, including functions for marking s-expressions,
+comparing characters, removing cursors, and more.")
+      (license license:bsd-2))))
+
 (define-public emacs-typo
   (package
     (name "emacs-typo")
@@ -4011,6 +4107,38 @@ minutes is started automatically.  Every 4 breaks a long break is
 started with 20 minutes.  All values are customizable.")
     (license license:gpl3+)))
 
+(define-public emacs-org-sidebar
+  (let ((commit "74ca98b9920f3de3f13d49866581435e1ec63ec5")
+        (revision "1"))
+    (package
+      (name "emacs-org-sidebar")
+      (version (git-version "0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/alphapapa/org-sidebar.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "03p1ndyw2qp2skib5hszc4xyh84w7p2mhkd4a9dy6qv8q47xpsqn"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-dash" ,emacs-dash)
+         ("emacs-org-super-agenda" ,emacs-org-super-agenda)
+         ("emacs-org" ,emacs-org)
+         ("emacs-org-ql" ,emacs-org-ql)
+         ("emacs-s" ,emacs-s)))
+      (home-page "https://github.com/alphapapa/org-sidebar")
+      (synopsis "Helpful sidebar for Org buffers")
+      (description "This package provides a sidebar for Org buffers.  At the
+top is a chronological list of scheduled and deadlined tasks in the current
+buffer (similar to the Org agenda ,but without all its features), and below
+that is a list of all other non-done to-do items.  If the buffer is narrowed,
+the sidebar only shows items in the narrowed portion; this allows seeing an
+overview of tasks in a subtree.")
+      (license license:gpl3+))))
+
 (define-public emacs-org-trello
   (package
     (name "emacs-org-trello")
@@ -4604,45 +4732,50 @@ automatically.")
     (license license:gpl3+)))
 
 (define-public emacs-ivy
-  (package
+  ;; The latest release version introduced a new feature, swiper-isearch, that
-    (name "emacs-ivy")
+  ;; generally works well but had some noticeable bugs; this later commit
-    (version "0.12.0")
+  ;; includes fixes for several of them.
-    (source
+  (let ((commit "d3e4514fd72f217c704ae18afdf711bb9036a04d")
-     (origin
+        (revision "1"))
-       (method git-fetch)
+    (package
-       (uri (git-reference
+      (name "emacs-ivy")
-             (url "https://github.com/abo-abo/swiper.git")
+      (version (git-version "0.12.0" revision commit))
-             (commit version)))
+      (source
-       (file-name (git-file-name name version))
+       (origin
-       (sha256
+         (method git-fetch)
-        (base32
+         (uri (git-reference
-         "0xgngn3jhmyn6mlkk9kmgfgh0w5i50b27syr4cgfgarg6p77j05w"))))
+               (url "https://github.com/abo-abo/swiper.git")
-    (build-system emacs-build-system)
+               (commit commit)))
-    (arguments
+         (file-name (git-file-name name version))
-     `(#:phases
+         (sha256
-       (modify-phases %standard-phases
+          (base32
-         (add-after 'install 'install-doc
+           "142axxc6vsl14cfyvzj9csiykxdn7vhw88fy955hzx7av4qfqg4x"))))
-           (lambda* (#:key outputs #:allow-other-keys)
+      (build-system emacs-build-system)
-             (let* ((out (assoc-ref outputs "out"))
+      (arguments
-                    (info (string-append out "/share/info")))
+       `(#:phases
-               (with-directory-excursion "doc"
+         (modify-phases %standard-phases
-                 (invoke "makeinfo" "ivy.texi")
+           (add-after 'install 'install-doc
-                 (install-file "ivy.info" info)
+             (lambda* (#:key outputs #:allow-other-keys)
-                 #t)))))))
+               (let* ((out (assoc-ref outputs "out"))
-    (propagated-inputs
+                      (info (string-append out "/share/info")))
-     `(("emacs-hydra" ,emacs-hydra)))
+                 (with-directory-excursion "doc"
-    (native-inputs
+                   (invoke "makeinfo" "ivy.texi")
-     `(("texinfo" ,texinfo)))
+                   (install-file "ivy.info" info)
-    (home-page "http://oremacs.com/swiper/")
+                   #t)))))))
-    (synopsis "Incremental vertical completion for Emacs")
+      (propagated-inputs
-    (description
+       `(("emacs-hydra" ,emacs-hydra)))
-     "This package provides @code{ivy-read} as an alternative to
+      (native-inputs
+       `(("texinfo" ,texinfo)))
+      (home-page "http://oremacs.com/swiper/")
+      (synopsis "Incremental vertical completion for Emacs")
+      (description
+       "This package provides @code{ivy-read} as an alternative to
 @code{completing-read} and similar functions.  No attempt is made to determine
 the best candidate.  Instead, the user can navigate candidates with
 @code{ivy-next-line} and @code{ivy-previous-line}.  The matching is done by
 splitting the input text by spaces and re-building it into a regular
 expression.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-ivy-pass
   (let ((commit "5b523de1151f2109fdd6a8114d0af12eef83d3c5")
@@ -5228,7 +5361,7 @@ strings, and code folding.")
 (define-public emacs-nodejs-repl
   (package
     (name "emacs-nodejs-repl")
-    (version "0.2.1")
+    (version "0.2.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5237,7 +5370,7 @@ strings, and code folding.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "05ccv87rnw7fss3lib8m9sywjrj6n92fnd7mmhmjh27g2klqc83z"))))
+                "1kkj888k9x5n0i7xkia177gzsa84my3g8n0n7v65281cc4f1yhk5"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/abicky/nodejs-repl.el")
     (synopsis "Node.js REPL inside Emacs")
@@ -5580,28 +5713,35 @@ environments (virtualenv) inside Emacs.")
     (license license:gpl3+)))
 
 (define-public emacs-highlight-indentation
-  (package
+  ;; Last release version is from 2015.
-    (name "emacs-highlight-indentation")
+  (let ((commit "d03803f2c06749c430443a3d24e039cbafc9c58f")
-    (version "0.7.0")
+        (revision "1"))
-    (source (origin
+    (package
-              (method git-fetch)
+      (name "emacs-highlight-indentation")
-              (uri (git-reference
+      (version (git-version "0.7.0" revision commit))
-                    (url "https://github.com/antonj/Highlight-Indentation-for-Emacs.git")
+      (source
-                    (commit (string-append "v" version))))
+       (origin
-              (file-name (git-file-name name version))
+         (method git-fetch)
-              (sha256
+         (uri (git-reference
-               (base32
+               (url "https://github.com/antonj/Highlight-Indentation-for-Emacs.git")
-                "00l54k75qk24a0znzl4ij3s3nrnr2wy9ha3za8apphzlm98m907k"))))
+               (commit commit)))
-    (build-system emacs-build-system)
+         (file-name (git-file-name name version))
-    (home-page "https://github.com/antonj/Highlight-Indentation-for-Emacs/")
+         (sha256
-    (synopsis "Highlighting indentation for Emacs")
+          (base32
-    (description "Provides two minor modes to highlight indentation guides in Emacs:
+           "1jq0gf4kcx9hvrw40rnw5c2qynjpjw1vsjbi2i4lqjbsnfnxn4wz"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/antonj/Highlight-Indentation-for-Emacs/")
+      (synopsis "Highlighting indentation for Emacs")
+      (description "This package provides two minor modes to highlight
+indentation guides in Emacs:
+
 @enumerate
 @item @code{highlight-indentation-mode}, which displays guidelines
-indentation (space indentation only).
+  indentation (space indentation only).
-@item @code{highlight-indentation-current-column-mode}, which displays guidelines for the current-point indentation (space indentation only).
+@item @code{highlight-indentation-current-column-mode}, which displays
+  guidelines for the current-point indentation (space indentation only).
 @end enumerate")
-    (license license:gpl2+)))
+      (license license:gpl2+))))
 
 (define-public emacs-elpy
   (package
@@ -5931,7 +6071,7 @@ ack, ag, helm and pt.")
 (define-public emacs-helm
   (package
     (name "emacs-helm")
-    (version "3.2")
+    (version "3.3")
     (source
      (origin
        (method git-fetch)
@@ -5940,7 +6080,7 @@ ack, ag, helm and pt.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12yyprpgh2by2pd41i4z9gz55fxg0f90x03bfrsf791xwbhf6931"))))
+        (base32 "0fqhw7r9fcsja5d3pgbipw7pkw9nj534faav6hi45413hc3gyv92"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-async" ,emacs-async)
@@ -6119,21 +6259,21 @@ xref, etc...) are still available, but with better integration.")
       (license license:gpl3+))))
 
 (define-public emacs-lua-mode
-  (let ((commit "652e299cb967fccca827dda381d61a9c144d97de")
+  (let ((commit "95c64bb5634035630e8c59d10d4a1d1003265743")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "emacs-lua-mode")
-      (version (string-append "20151025." revision "-" (string-take commit 9)))
+      (version (git-version "20151025" revision commit))
       (home-page "https://github.com/immerrr/lua-mode/")
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
                       (url home-page)
                       (commit commit)))
-                (file-name (string-append name "-" version ".checkout"))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "053025k930wh0lak6rc1973ynfrmm8zsyzfqhhd39x7abkl41hc9"))))
+                  "1mra4db25ds64526dsj8m5yv0kfq3lgggjh1x6xmqypdaryddbcp"))))
       (build-system emacs-build-system)
       (synopsis "Major mode for lua")
       (description
@@ -6399,12 +6539,11 @@ aligning text objects based on separators.")
       (license license:gpl3+))))
 
 (define-public emacs-evil-expat
-  (let ((commit "4c344ea19b789002d759a202ffbf594730d2c59a")
+  (let ((commit "f4fcd0aa3edc359adb5c986b5dd9188d220d84e2")
-        (version "0.0.1")
         (revision "1"))
     (package
       (name "emacs-evil-expat")
-      (version (git-version version revision commit))
+      (version (git-version "0.0.1" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -6414,7 +6553,7 @@ aligning text objects based on separators.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "16v7fnldxag6l1lsnrnhdjkga9qi78lbdfbb82k6pmv04991mbkr"))))
+           "0872ix682hkdz0k8pn6sb54rqkx00rz5fxpd5j2snx406yagpaxz"))))
       (build-system emacs-build-system)
       (propagated-inputs `(("emacs-evil" ,emacs-evil)))
       (home-page "https://github.com/edkolev/evil-expat")
@@ -6587,14 +6726,14 @@ passive voice.")
     (name "emacs-org")
     ;; emacs-org-contrib inherits from this package.  Please update its sha256
     ;; checksum as well.
-    (version "9.2.3")
+    (version "9.2.5")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://elpa.gnu.org/packages/org-"
+              (uri (string-append "https://elpa.gnu.org/packages/org-"
                                   version ".tar"))
               (sha256
                (base32
-                "0hqy4lns9q5p0l1ylgmlckqprn9sbasszhznanmv0rsh0gzhsbyw"))))
+                "1pid1sykgz83i4ry5n8f270finag6sm7ckqxn5lkikyya43wlzx1"))))
     (build-system emacs-build-system)
     (home-page "https://orgmode.org/")
     (synopsis "Outline-based notes management and organizer")
@@ -6608,14 +6747,14 @@ programming and reproducible research.")
   (package
     (inherit emacs-org)
     (name "emacs-org-contrib")
-    (version "20190715")
+    (version "20190805")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://orgmode.org/elpa/org-plus-contrib-"
                                   version ".tar"))
               (sha256
                (base32
-                "0yxxkcaxhp5bmjsfdd9pz79rj9s7nb4gj5ci51sh4pf8mimk9542"))))
+                "1mw91hwbqyjq5pyz9hzdhvjlc2bphqpi23yqd3sdk1crpc87s40c"))))
     (arguments
      `(#:modules ((guix build emacs-build-system)
                   (guix build utils)
@@ -7159,6 +7298,56 @@ find files owned by packages...  And much more, including performing all the
 above over the network.")
       (license license:gpl3+))))
 
+(define-public emacs-helm-org-rifle
+  (package
+    (name "emacs-helm-org-rifle")
+    (version "1.6.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/alphapapa/helm-org-rifle")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1r38xhwvgbv6kn5x159phz3xgss7f1rc7icq27rnr4d8aj91wm6k"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-dash" ,emacs-dash)
+       ("emacs-f" ,emacs-f)
+       ("emacs-helm" ,emacs-helm)
+       ("emacs-s" ,emacs-s)))
+    (home-page "https://github.com/alphapapa/helm-org-rifle")
+    (synopsis "Rifle through Org files")
+    (description "This package searches both headings and contents of entries
+in Org buffers and displays matching entries.")
+    (license license:gpl3+)))
+
+(define-public emacs-dired-toggle-sudo
+  (package
+    (name "emacs-dired-toggle-sudo")
+    (version "1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/renard/dired-toggle-sudo")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0ajj8d6k5in2hclcrqckinfh80ylddplva0ryfbkzsjkfq167cv2"))
+       (patches
+        (search-patches
+         "emacs-dired-toggle-sudo-emacs-26.patch"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/renard/dired-toggle-sudo")
+    (synopsis "Browse directory with @code{sudo} privileges")
+    (description "This package allows for the use of @code{dired} with
+@code{sudo} privileges.")
+    (license license:wtfpl2)))
+
 (define-public emacs-memoize
   (package
     (name "emacs-memoize")
@@ -8528,12 +8717,11 @@ the actual transformations.")
       (license license:gpl2+))))
 
 (define-public emacs-dired-hacks
-  (let ((commit "2c1234592aee91dcd9401bcd67213e6a4a464fd9")
+  (let ((commit "886befe113fae397407c804f72c45613d1d43535")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "emacs-dired-hacks")
-      (version (string-append "0.0.1-" revision "."
+      (version (git-version "0.0.1" revision commit))
-                              (string-take commit 7)))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -8542,7 +8730,7 @@ the actual transformations.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1g7mky41cahpryzj6frdgzdymknpqq7pidzfjj9304887kijmhj3"))))
+                  "1cvibg90ggyrivpjmcfprpi2fx7dpa68f8kzg08s88gw5ib75djl"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-dash" ,emacs-dash)
@@ -8553,7 +8741,9 @@ the actual transformations.")
       (synopsis
        "Collection of useful dired additions")
       (description
-       "Collection of Emacs dired mode additions:
+       "This package provides the following collection of Emacs dired mode
+additions:
+
 @itemize
 @item dired-avfs
 @item dired-columns
@@ -8623,6 +8813,32 @@ available key bindings that follow C-x (or as many as space allows given your
 settings).")
     (license license:gpl3+)))
 
+(define-public emacs-hercules
+  (let ((commit "3345904a0dab4c7a4d4478f0766f1d9f5d1bb501")
+        (revision "1"))
+    (package
+      (name "emacs-hercules")
+      (version (git-version "0.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.com/jjzmajic/hercules.el.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0cpq8h6l47nqhzch6snax5yrhxl8p4wn35q13ci35lj3iq8kmlk8"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-which-key" ,emacs-which-key)))
+      (home-page "https://gitlab.com/jjzmajic/hercules.el")
+      (synopsis "Call a chain of related commands without repeated prefix keys")
+      (description
+       "This package provides sticky-key-like functionality to obviate the
+need for repeated prefix-key sequences, and can reuse existing keymaps. The
+list of commands is displayed in a handy popup.")
+      (license license:gpl3+))))
+
 (define-public emacs-ws-butler
   (package
     (name "emacs-ws-butler")
@@ -10433,29 +10649,32 @@ as well as functions for navigating between these headings.")
     (license license:gpl3+)))
 
 (define-public emacs-org-super-agenda
-  (package
+  ;; emacs-org-sidebar depends on a newer commit than the latest release version.
-   (name "emacs-org-super-agenda")
+  (let ((commit "375bde4ca72494ac88a2a9738754f047fe45cc4e")
-   (version "1.1")
+        (revision "1"))
-   (source (origin
+    (package
-            (method git-fetch)
+      (name "emacs-org-super-agenda")
-            (uri (git-reference
+      (version (git-version "1.1.1" revision commit))
-                  (url "https://github.com/alphapapa/org-super-agenda")
+      (source (origin
-                  (commit version)))
+                (method git-fetch)
-            (file-name (git-file-name name version))
+                (uri (git-reference
-            (sha256
+                      (url "https://github.com/alphapapa/org-super-agenda")
-             (base32
+                      (commit commit)))
-              "0vzf91lsxnhwf52kvm8ycpf0wb9c8l91689vyhwgv4wz8q6cvjwp"))))
+                (file-name (git-file-name name version))
-   (build-system emacs-build-system)
+                (sha256
-   (propagated-inputs
+                 (base32
-    `(("emacs-org" ,emacs-org)
+                  "0hrwf02fqjm0d9gj146ax67ib76093qpqh7066dcxj2gy20625yj"))))
-      ("emacs-dash" ,emacs-dash)
+      (build-system emacs-build-system)
-      ("emacs-ht" ,emacs-ht)
+      (propagated-inputs
-      ("emacs-s" ,emacs-s)))
+       `(("emacs-org" ,emacs-org)
-   (home-page "https://github.com/alphapapa/org-super-agenda")
+         ("emacs-dash" ,emacs-dash)
-   (synopsis "Supercharged Org agenda")
+         ("emacs-ht" ,emacs-ht)
-   (description "This package allows items in the Org agenda to be grouped
+         ("emacs-s" ,emacs-s)))
+      (home-page "https://github.com/alphapapa/org-super-agenda")
+      (synopsis "Supercharged Org agenda")
+      (description "This package allows items in the Org agenda to be grouped
 into sections while preserving the structure imposed by any timestamps.")
-   (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-org-make-toc
   (package
@@ -12676,6 +12895,29 @@ When @code{gac-automatically-push-p} is non-nil, it also tries to push to
 the current upstream.")
     (license license:gpl3+)))
 
+(define-public emacs-scroll-on-drag
+  (let ((commit "888abd04c34753b1fc4b2fe541bc004ebec5c996")
+        (revision "1"))
+    (package
+      (name "emacs-scroll-on-drag")
+      (version (git-version "0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.com/ideasman42/emacs-scroll-on-drag.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1si4hdqa3jw1inbyh3wb3i5i9grbms1nwky3vyk9zg7iznwm8a9p"))))
+      (build-system emacs-build-system)
+      (home-page "https://gitlab.com/ideasman42/emacs-scroll-on-drag")
+      (synopsis "Interactive scrolling")
+      (description "This package permits scrolling at increasing speeds based
+on drag distance.")
+      (license license:gpl3+))))
+
 (define-public emacs-company-restclient
   (package
     (name "emacs-company-restclient")
@@ -13692,12 +13934,11 @@ server with @code{M-x pinentry-start}.")
       (license license:gpl3+))))
 
 (define-public emacs-so-long
-  (let ((commit "3ebe97decdb5cbbfba82ca686e0ad2c7d2722b4a")
+  (let ((commit "cfae473b1bf65f78ddb015159e667ec0103d881c")
-        (version "1.0")
+        (revision "2"))
-        (revision "1"))
     (package
       (name "emacs-so-long")
-      (version (git-version version revision commit))
+      (version (git-version "1.0" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -13707,7 +13948,7 @@ server with @code{M-x pinentry-start}.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0fi71g5rsdsi978jz8406k8hvzgnssm9wxar8yqfhs97178r9s5m"))))
+           "0g943n5cl9lz5s7hszg6yvp10xd1xvd8mfgxyg0yckmp8fqkswin"))))
       (build-system emacs-build-system)
       (home-page "https://www.emacswiki.org/emacs/SoLong")
       (synopsis "Improve performance in files with long lines")
@@ -14142,7 +14383,7 @@ buffers – other modes on the TODO list).
 (define-public emacs-magit-todos
   (package
     (name "emacs-magit-todos")
-    (version "1.2")
+    (version "1.3")
     (source
      (origin
        (method git-fetch)
@@ -14152,7 +14393,7 @@ buffers – other modes on the TODO list).
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "17a18gszbypz82bj36xbfyykc4s9rz83vwmpxvlf65svhd51c0nh"))))
+         "0gfm6wn2a4v5i9lfsvvin0kwpr9n96ddm3z4yf50jd3kg2igzry1"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-async" ,emacs-async)
@@ -16189,7 +16430,7 @@ previewed by scrolling up and down within a @code{dired} buffer.")
 (define-public emacs-counsel-etags
   (package
     (name "emacs-counsel-etags")
-    (version "1.8.4")
+    (version "1.8.7")
     (source
      (origin
        (method git-fetch)
@@ -16199,7 +16440,7 @@ previewed by scrolling up and down within a @code{dired} buffer.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "14my9jvxl26a5yn381h5pi5481y9d9gyk7wnxxd0s4sjc964c5h5"))))
+         "0vjcjspfrz1csnmfi6r7p7f070a496adxkqnsxwx1gx8cpylwp1g"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-ivy" ,emacs-ivy)))
@@ -16632,6 +16873,30 @@ provided.  Those alternative commands are and bound by default to their
 corresponding Evil keys.")
       (license license:expat))))
 
+(define-public emacs-evil-traces
+  (let ((commit "b41b7432b8110378c199a3d25af464083777f453")
+        (revision "1"))
+    (package
+      (name "emacs-evil-traces")
+      (version (git-version "0.0.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mamapanda/evil-traces.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0a15f2saynz9fws1h5s7py3cshsk4xs1kwgwj1m5rsin36g0j6hc"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-evil" ,emacs-evil)))
+      (home-page "https://github.com/mamapanda/evil-traces")
+      (synopsis "Visual hints for @code{evil-ex}")
+      (description "This package adds visual hints to certain @code{ex}
+commands in @code{evil-mode}.")
+      (license license:gpl3+))))
+
 (define-public emacs-xterm-color
   (let ((commit "a452ab38a7cfae97078062ff8885b5d74fd1e5a6")
         (version "1.8")

gnu/packages/emulators.scm

@@ -119,8 +119,8 @@
 
 ;; Building from recent Git because the official 5.0 release no longer builds.
 (define-public dolphin-emu
-  (let ((commit "2c57e709d0f9e4010a4415de4192de887e37f187")
+  (let ((commit "24718c1a389e4f51db974575cd15c372485b92e2")
-        (revision "5"))
+        (revision "6"))
     (package
       (name "dolphin-emu")
       (version (git-version "5.0" revision commit))
@@ -146,7 +146,7 @@
              #t))
          (sha256
           (base32
-           "0aszfdfvs7yg4bmrd3qxwsiz7hx3mrj29f4aw86bz7h9j7hkh57f"))))
+           "1d92rhnw307j3m6swk6bycb8fyc7vw2hfgakd5hpsc4qw65vxfq8"))))
       (build-system cmake-build-system)
       (arguments
        '(#:tests? #f
@@ -250,12 +250,6 @@ turbo speed, networked multiplayer, and graphical enhancements.")
                (base32
                 "02i648i50dwicv1vaql15rccv4g8h5blf5g6inv67lrfxpbkvlf0"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (add-after
-                   'unpack 'autogen.sh
-                   (lambda _
-                     (invoke "sh" "autogen.sh"))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)))

gnu/packages/enchant.scm

@@ -33,7 +33,7 @@
 (define-public enchant
   (package
     (name "enchant")
-    (version "2.2.4")
+    (version "2.2.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/AbiWord/enchant/releases"
@@ -41,7 +41,7 @@
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1p6a3qmrh8bjzds6x7rg9da0ir44gg804jzkf634h39wsa4vdmpm"))))
+                "0iqwzs11i9fvqdxv5kn0svcn2mzymn657qf3j66lg8dx1nh4xkpz"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--disable-static"

gnu/packages/geo.scm

@@ -131,7 +131,12 @@ topology functions.")
                    (gi-typelib-path (getenv "GI_TYPELIB_PATH"))
                    (goa-path (string-append
                               (assoc-ref inputs "gnome-online-accounts")
+                              "/lib:"
+                              (assoc-ref inputs "gnome-online-accounts:lib")
                               "/lib"))
+                   (geocode-glib-path (string-append
+                                       (assoc-ref inputs "geocode-glib")
+                                       "/lib"))
                    (webkitgtk-path (string-append
                                     (assoc-ref inputs "webkitgtk")
                                     "/lib")))
@@ -141,7 +146,8 @@ topology functions.")
                  ;; There seems to be no way to embed the path of
                  ;; libgoa-1.0.so.0, libwebkit2gtk-4.0.so.37 and
                  ;; libjavascriptcoregtk-4.0.so.18.
-                 `("LD_LIBRARY_PATH" ":" prefix (,goa-path ,webkitgtk-path)))
+                 `("LD_LIBRARY_PATH" ":" prefix
+                   (,goa-path ,webkitgtk-path ,geocode-glib-path)))
                #t))))))
     (native-inputs
      `(("gobject-introspection" ,gobject-introspection)
@@ -163,6 +169,7 @@ topology functions.")
        ("gjs" ,gjs)
        ("glib" ,glib)
        ("gnome-online-accounts" ,gnome-online-accounts)
+       ("gnome-online-accounts:lib" ,gnome-online-accounts "lib")
        ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
        ("rest" ,rest)
        ("webkitgtk" ,webkitgtk)))

gnu/packages/gnome.scm

@@ -38,6 +38,7 @@
 ;;; Copyright © 2019 Florian Pelz <pelzflorian@pelzflorian.de>
 ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2019 Jelle Licht <jlicht@fsfe.org>
+;;; Copyright © 2019 Jonathan Frederickson <jonathan@terracrypt.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -8152,15 +8153,18 @@ advanced image management tool")
     (inputs
      `(("cairo" ,cairo)
        ("gobject-introspection" ,gobject-introspection)
+       ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
        ("python2-pycairo" ,python2-pycairo)
        ("python2-pygobject" ,python2-pygobject)
        ("python2-psutil" ,python2-psutil)
        ("vte" ,vte)))
-    (propagated-inputs
-     ;; Terminator refuses to start when these are not present.
-     `(("gsettings-desktop-schemas" ,gsettings-desktop-schemas)))
     (arguments
-     `(#:python ,python-2                          ;Python 3 not supported
+     `(#:python ,python-2                          ; Python 3 isn't supported
+       #:imported-modules ((guix build glib-or-gtk-build-system)
+                           ,@%python-build-system-modules)
+       #:modules ((guix build python-build-system)
+                  ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
+                  (guix build utils))
        #:phases
        (modify-phases %standard-phases
          (add-after
@@ -8171,10 +8175,60 @@ advanced image management tool")
               (wrap-program prog
                 `("PYTHONPATH" = (,(getenv "PYTHONPATH")))
                 `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH"))))
-              #t))))))
+              #t)))
+         (add-after 'wrap-program 'glib-or-gtk-wrap
+           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
     (home-page "https://gnometerminator.blogspot.com/")
     (synopsis "Store and run multiple GNOME terminals in one window")
     (description
      "Terminator allows you to run multiple GNOME terminals in a grid and
 +tabs, and it supports drag and drop re-ordering of terminals.")
     (license license:gpl2)))
+
+(define-public libhandy
+  (package
+    (name "libhandy")
+    (version "0.0.10")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://source.puri.sm/Librem5/libhandy")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1702hbdqhfpgw0c4vj2ag08vgl83byiryrbngbq11b9azmj3jhzs"))))
+    (build-system meson-build-system)
+    (arguments
+     `(#:configure-flags
+       '("-Dglade_catalog=disabled"
+         "-Dgtk_doc=true")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-broken-test
+           (lambda _
+             ;; This test fails for unknown reasons
+             (substitute* "tests/meson.build"
+               (("'test-dialog',") ""))
+             #t))
+         (add-before 'check 'pre-check
+           (lambda _
+             ;; Tests require a running X server.
+             (system "Xvfb :1 &")
+             (setenv "DISPLAY" ":1")
+             #t)))))
+    (inputs
+     `(("gtk+" ,gtk+)))
+    (native-inputs
+     `(("glib:bin" ,glib "bin")
+       ("gobject-introspection" ,gobject-introspection) ; for g-ir-scanner
+       ("vala" ,vala)
+       ("gtk-doc" ,gtk-doc)
+       ("pkg-config" ,pkg-config)
+       ("gettext" ,gettext-minimal)
+       ("xorg-server" ,xorg-server)))
+    (home-page "https://source.puri.sm/Librem5/libhandy")
+    (synopsis "Library full of GTK+ widgets for mobile phones")
+    (description "The aim of the handy library is to help with developing user
+intefaces for mobile devices using GTK+.")
+    (license license:lgpl2.1+)))

gnu/packages/image.scm

@@ -595,9 +595,6 @@ collection of tools for doing simple manipulations of TIFF images.")
     (arguments
      '(#:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _
-             (invoke "sh" "autobuild")))
          (add-after 'unpack 'patch-reg-wrapper
            (lambda _
              (substitute* "prog/reg_wrapper.sh"
@@ -1108,14 +1105,14 @@ channels.")
 (define-public exiv2
   (package
     (name "exiv2")
-    (version "0.27.1")
+    (version "0.27.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.exiv2.org/builds/exiv2-" version
                            "-Source.tar.gz"))
        (sha256
-        (base32 "109hbfk63dh14fz20ivq20gcclb9jj9jmh48w4lcn6zxh1ljh9gi"))))
+        (base32 "0gqminvj14xm3rgbnydbywf22608js80rp7nmxxk4497j5mzali6"))))
     (build-system cmake-build-system)
     (arguments '(#:tests? #f))          ; no test suite
     (propagated-inputs
@@ -1240,12 +1237,6 @@ ISO/IEC 15444-1).")
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
        ("libtool" ,libtool)))
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     (synopsis "Scaling, colorspace conversion, and dithering library")
     (description "Zimg implements the commonly required image processing basics
 of scaling, colorspace conversion, and depth conversion.  A simple API enables

gnu/packages/libevent.scm

@@ -41,7 +41,7 @@
 (define-public libevent
   (package
     (name "libevent")
-    (version "2.1.10")
+    (version "2.1.11")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -49,7 +49,7 @@
                    version "-stable/libevent-" version "-stable.tar.gz"))
              (sha256
               (base32
-               "1c25928gdv495clxk2v1d4gkr5py7ack4gx2n7d13frnld0syr78"))))
+               "0g988zqm45sj1hlhhz4il5z4dpi5dl74hzjwzl4md37a09iaqnx6"))))
     (build-system gnu-build-system)
     (arguments
       ;; This skips some of the tests which fail on armhf and aarch64.

gnu/packages/linux.scm

@@ -350,42 +350,42 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                         "linux-" version ".tar.xz"))
     (sha256 hash)))
 
-(define-public linux-libre-5.2-version "5.2.5")
+(define-public linux-libre-5.2-version "5.2.7")
 (define-public linux-libre-5.2-pristine-source
   (let ((version linux-libre-5.2-version)
-        (hash (base32 "15ndscsp3yqgas901g6inpmyvinz4cwr5y3md516j2pr8cl40if6")))
+        (hash (base32 "1aazhf0v8bv4py0wnqkdmiy80fchnix431l0hda2fkwsdf9njgnv")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.2)))
 
-(define-public linux-libre-4.19-version "4.19.63")
+(define-public linux-libre-4.19-version "4.19.65")
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "0pfjwpa6szvdr941y13806hlsgsbslfsvkrd5534p1iip5h8g63m")))
+        (hash (base32 "1pyyhr2airxzk4c6n7140yl723dc7yw7igy5i5i2ih0nd4c3k6g5")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
 
-(define-public linux-libre-4.14-version "4.14.135")
+(define-public linux-libre-4.14-version "4.14.137")
 (define-public linux-libre-4.14-pristine-source
   (let ((version linux-libre-4.14-version)
-        (hash (base32 "0x2v0pj4hjb71qkxbqn4ymg6zmyabp91kylyzd270nbig7i234a2")))
+        (hash (base32 "0a72pab0zxy28i02glnzj6avzcf0a4gxxnadbdd343rh549yky4k")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))
 
-(define-public linux-libre-4.9-version "4.9.186")
+(define-public linux-libre-4.9-version "4.9.188")
 (define-public linux-libre-4.9-pristine-source
   (let ((version linux-libre-4.9-version)
-        (hash (base32 "0sjbp7m6d625rw06wv34a0805d1lgldii4pxiqfpja871m1q8914")))
+        (hash (base32 "08p2cfc9982b804vmkapfasgipf6969g625ih7z3062xn99rhlr7")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.9)))
 
-(define-public linux-libre-4.4-version "4.4.186")
+(define-public linux-libre-4.4-version "4.4.188")
 (define-public linux-libre-4.4-pristine-source
   (let ((version linux-libre-4.4-version)
-        (hash (base32 "113rjf8842glzi23y1g1yrwncihv2saah6wz0r726r06bk9p64hb")))
+        (hash (base32 "1llxamm62kgqd7dig98n8m16qas8dd8rrkmwpfcdgyf8rag216ff")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.4)))
@@ -1402,15 +1402,18 @@ Zerofree requires the file system to be unmounted or mounted read-only.")
 (define-public strace
   (package
     (name "strace")
-    (version "5.1")
+    (version "5.2")
     (home-page "https://strace.io")
     (source (origin
              (method url-fetch)
              (uri (string-append home-page "/files/" version
                                  "/strace-" version ".tar.xz"))
+             ;; XXX Remove the 'regenerate-tests' phase below when
+             ;; "strace-ipc-tests.patch" is no longer applied.
+             (patches (search-patches "strace-ipc-tests.patch"))
              (sha256
               (base32
-               "12wsga1v3rab24gr0mpfip7j7gwr90m8f9h6fviqxa3xgnwl38zm"))))
+               "1li49i75wrdw91hchyyd8spnzfcmxcfyfb5g9zbaza89aq4bq4ym"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -1419,7 +1422,14 @@ Zerofree requires the file system to be unmounted or mounted read-only.")
            (lambda _
              (substitute* "strace.c"
                (("/bin/sh") (which "sh")))
-             #t)))
+             #t))
+         (add-before 'configure 'regenerate-tests
+           ;; XXX Remove this phase when "strace-ipc-tests.patch" is no longer
+           ;; applied in the 'source' field above.  This phase is needed to
+           ;; regenerate many other files from tests/gen_tests.in, which is
+           ;; modified by the aforementioned patch.
+           (lambda _
+             (invoke "tests/gen_tests.sh"))))
        ;; Don't fail if the architecture doesn't support different personalities.
        #:configure-flags '("--enable-mpers=check")
        ;; See <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=32459>.

gnu/packages/machine-learning.scm

@@ -193,7 +193,7 @@ classification.")
                 (uri (svn-reference
                       (url "http://svn.code.sf.net/p/ghmm/code/trunk")
                       (revision svn-revision)))
-                (file-name (string-append name "-" version))
+                (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
                   "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
@@ -251,10 +251,7 @@ classification.")
                   (string-append indent
                                  "@unittest.skip(\"Disabled by Guix\")\n"
                                  line)))
-               #t))
+               #t)))))
-           (add-after 'disable-broken-tests 'autogen
-             (lambda _
-               (invoke "bash" "autogen.sh"))))))
       (inputs
        `(("python" ,python-2) ; only Python 2 is supported
          ("libxml2" ,libxml2)))
@@ -821,8 +818,14 @@ computing environments.")
              (setenv "HOME" "/tmp")
 
              (invoke "pytest" "sklearn" "-m" "not network")))
-         ;; FIXME: This fails with permission denied
+         (add-before 'reset-gzip-timestamps 'make-files-writable
-         (delete 'reset-gzip-timestamps))))
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Make sure .gz files are writable so that the
+             ;; 'reset-gzip-timestamps' phase can do its work.
+             (let ((out (assoc-ref outputs "out")))
+               (for-each make-file-writable
+                         (find-files out "\\.gz$"))
+               #t))))))
     (inputs
      `(("openblas" ,openblas)))
     (native-inputs

gnu/packages/mail.scm

@@ -1051,7 +1051,7 @@ useful features.")
     (arguments
       '(#:phases
         (modify-phases %standard-phases
-          (add-after 'unpack 'autogen
+          (replace 'bootstrap
             (lambda _
               (setenv "NOCONFIGURE" "true")
               (invoke "sh" "autogen.sh"))))
@@ -1365,12 +1365,7 @@ It supports mbox/Maildir and its own dbox/mdbox formats.")
      `(#:tests? #f ;No tests exist.
        #:configure-flags (list (string-append "--with-dovecot="
                                               (assoc-ref %build-inputs "dovecot")
-                                              "/lib/dovecot"))
+                                              "/lib/dovecot"))))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     (home-page "https://0xacab.org/riseuplabs/trees")
     (synopsis "NaCL-based Dovecot email storage encryption plugin")
     (description
@@ -1421,12 +1416,7 @@ using libsodium sealed boxes.
        `(#:tests? #f ;No tests exist.
          #:configure-flags (list (string-append "--with-dovecot="
                                                 (assoc-ref %build-inputs "dovecot")
-                                                "/lib/dovecot"))
+                                                "/lib/dovecot"))))
-         #:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'autogen
-             (lambda _
-               (invoke "sh" "autogen.sh"))))))
       (home-page "https://github.com/LuckyFellow/dovecot-libsodium-plugin")
       (synopsis "Libsodium password hashing schemes plugin for Dovecot")
       (description

gnu/packages/maths.scm

@@ -4333,14 +4333,14 @@ are noisy or are discontinuous at the solution.")
 (define-public r-desolve
   (package
     (name "r-desolve")
-    (version "1.21")
+    (version "1.24")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "deSolve" version))
         (sha256
          (base32
-          "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
+          "0hkvspq0fp8j64l9zayab2l2nazazhwfgfym0jllh0xv5a12r99s"))))
     (properties `((upstream-name . "deSolve")))
     (build-system r-build-system)
     (native-inputs

gnu/packages/mp3.scm

@@ -65,7 +65,8 @@
               "14460zhacxhswnzb36qfpd1f2wbk10qvksvm6wyq5hpvdgnw7ymv"))
             (patches (search-patches "libmad-armv7-thumb-pt1.patch"
                                      "libmad-armv7-thumb-pt2.patch"
-                                     "libmad-frame-length.patch"
+                                     "libmad-md_size.patch"
+                                     "libmad-length-check.patch"
                                      "libmad-mips-newgcc.patch"))))
    (build-system gnu-build-system)
    (arguments

gnu/packages/package-management.scm

@@ -1027,7 +1027,7 @@ the boot loader configuration.")
 (define-public flatpak
   (package
    (name "flatpak")
-   (version "1.2.4")
+   (version "1.4.2")
    (source
     (origin
      (method url-fetch)
@@ -1035,7 +1035,7 @@ the boot loader configuration.")
                          version "/flatpak-" version ".tar.xz"))
      (sha256
       (base32
-       "1qf3ys84fzv11z6f6li59rxjdjbyrv7cyi9539k73r9i9pckjr8v"))))
+       "08nmpp26mgv0vp3mlwk97rnp0j7i108h4hr9nllja19sjxnrlygj"))))
 
    ;; Wrap 'flatpak' so that GIO_EXTRA_MODULES is set, thereby allowing GIO to
    ;; find the TLS backend in glib-networking.
@@ -1063,6 +1063,7 @@ the boot loader configuration.")
    (inputs `(("appstream-glib" ,appstream-glib)
              ("bubblewrap" ,bubblewrap)
              ("dconf" ,dconf)
+             ("fuse" ,fuse)
              ("gdk-pixbuf" ,gdk-pixbuf)
              ("gpgme" ,gpgme)
              ("json-glib" ,json-glib)

gnu/packages/patches/emacs-dired-toggle-sudo-emacs-26.patch

@@ -0,0 +1,49 @@
+From 3c0f4b27a079b90dc632f5061a81ce28cef24801 Mon Sep 17 00:00:00 2001
+From: eryx67 <eryx67@gmail.com>
+Date: Thu, 29 Nov 2018 10:30:20 +0500
+Subject: [PATCH] fix for latest emacs
+
+---
+ dired-toggle-sudo.el | 11 +++++++----
+ 1 file changed, 7 insertions(+), 4 deletions(-)
+
+diff --git a/dired-toggle-sudo.el b/dired-toggle-sudo.el
+index 386921b..fe5898e 100644
+--- a/dired-toggle-sudo.el
++++ b/dired-toggle-sudo.el
+@@ -37,17 +37,20 @@
+ unless SUDO-USER is provided."
+   (let* (;; Handle the case of local files. `tramp-dissect-file-name' does
+ 	 ;; not raise an error anymore.
+-	 (path (if (tramp-tramp-file-p path) path (concat "/:" path)))
++	 ;;(path (if (tramp-tramp-file-p path) path (concat "/-::" path)))
+ 	 (file-vec (or (ignore-errors (tramp-dissect-file-name
+ 				       path))
+ 		       (tramp-dissect-file-name
+-			(concat "/:" path) 1)))
++			(concat "/-::" path) 1)))
+ 	 (method  (tramp-file-name-method file-vec))
+ 	 (user (tramp-file-name-user file-vec))
+ 	 (host  (tramp-file-name-host file-vec))
++         (domain  (tramp-file-name-domain file-vec))
++         (port  (tramp-file-name-port file-vec))
+ 	 (localname (expand-file-name
+ 		     (tramp-file-name-localname file-vec))))
+-    (when (string= system-name host)
++    (when (or (string= (system-name) host)
++              (string= "-" host))
+       (setq host nil))
+     (cond
+      ;; remote directory -> sudo
+@@ -67,7 +70,7 @@ unless SUDO-USER is provided."
+       (setq method "sudo" user sudo-user)))
+     (replace-regexp-in-string
+      "^/:/" "/"
+-     (tramp-make-tramp-file-name method user host localname))))
++     (tramp-make-tramp-file-name method domain user host port localname))))
+ 
+ (defun dired-toggle-sudo-find (fname)
+   "Create a new buffer for file name FNAME."
+-- 
+2.22.0
+

gnu/packages/patches/libmad-frame-length.patch

@@ -1,199 +0,0 @@
-Copied from Debian.
-
-; You can calculate where the next frame will start depending on things
-; like the bitrate. See mad_header_decode().  It seems that when decoding
-; the frame you can go past that boundary.  This attempts to catch those cases,
-; but might not catch all of them.
-; For more info see http://bugs.debian.org/508133
-Index: libmad-0.15.1b/layer12.c
-===================================================================
---- libmad-0.15.1b.orig/layer12.c	2008-12-23 21:38:07.000000000 +0100
-+++ libmad-0.15.1b/layer12.c	2008-12-23 21:38:12.000000000 +0100
-@@ -134,6 +134,12 @@
-   for (sb = 0; sb < bound; ++sb) {
-     for (ch = 0; ch < nch; ++ch) {
-       nb = mad_bit_read(&stream->ptr, 4);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
-       if (nb == 15) {
- 	stream->error = MAD_ERROR_BADBITALLOC;
-@@ -146,6 +152,12 @@
- 
-   for (sb = bound; sb < 32; ++sb) {
-     nb = mad_bit_read(&stream->ptr, 4);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
-     if (nb == 15) {
-       stream->error = MAD_ERROR_BADBITALLOC;
-@@ -162,6 +174,12 @@
-     for (ch = 0; ch < nch; ++ch) {
-       if (allocation[ch][sb]) {
- 	scalefactor[ch][sb] = mad_bit_read(&stream->ptr, 6);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
- # if defined(OPT_STRICT)
- 	/*
-@@ -187,6 +205,12 @@
- 	frame->sbsample[ch][s][sb] = nb ?
- 	  mad_f_mul(I_sample(&stream->ptr, nb),
- 		    sf_table[scalefactor[ch][sb]]) : 0;
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
-       }
-     }
- 
-@@ -195,6 +219,12 @@
- 	mad_fixed_t sample;
- 
- 	sample = I_sample(&stream->ptr, nb);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
- 	for (ch = 0; ch < nch; ++ch) {
- 	  frame->sbsample[ch][s][sb] =
-@@ -403,7 +433,15 @@
-     nbal = bitalloc_table[offsets[sb]].nbal;
- 
-     for (ch = 0; ch < nch; ++ch)
-+    {
-       allocation[ch][sb] = mad_bit_read(&stream->ptr, nbal);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
-+    }
-   }
- 
-   for (sb = bound; sb < sblimit; ++sb) {
-@@ -411,6 +449,13 @@
- 
-     allocation[0][sb] =
-     allocation[1][sb] = mad_bit_read(&stream->ptr, nbal);
-+
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
-   }
- 
-   /* decode scalefactor selection info */
-@@ -419,6 +464,12 @@
-     for (ch = 0; ch < nch; ++ch) {
-       if (allocation[ch][sb])
- 	scfsi[ch][sb] = mad_bit_read(&stream->ptr, 2);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
-     }
-   }
- 
-@@ -442,6 +493,12 @@
-     for (ch = 0; ch < nch; ++ch) {
-       if (allocation[ch][sb]) {
- 	scalefactor[ch][sb][0] = mad_bit_read(&stream->ptr, 6);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
- 	switch (scfsi[ch][sb]) {
- 	case 2:
-@@ -452,11 +509,23 @@
- 
- 	case 0:
- 	  scalefactor[ch][sb][1] = mad_bit_read(&stream->ptr, 6);
-+		if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+		{
-+			stream->error = MAD_ERROR_LOSTSYNC;
-+			stream->sync = 0;
-+			return -1;
-+		}
- 	  /* fall through */
- 
- 	case 1:
- 	case 3:
- 	  scalefactor[ch][sb][2] = mad_bit_read(&stream->ptr, 6);
-+		if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+		{
-+			stream->error = MAD_ERROR_LOSTSYNC;
-+			stream->sync = 0;
-+			return -1;
-+		}
- 	}
- 
- 	if (scfsi[ch][sb] & 1)
-@@ -488,6 +557,12 @@
- 	  index = offset_table[bitalloc_table[offsets[sb]].offset][index - 1];
- 
- 	  II_samples(&stream->ptr, &qc_table[index], samples);
-+		if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+		{
-+			stream->error = MAD_ERROR_LOSTSYNC;
-+			stream->sync = 0;
-+			return -1;
-+		}
- 
- 	  for (s = 0; s < 3; ++s) {
- 	    frame->sbsample[ch][3 * gr + s][sb] =
-@@ -506,6 +581,12 @@
- 	index = offset_table[bitalloc_table[offsets[sb]].offset][index - 1];
- 
- 	II_samples(&stream->ptr, &qc_table[index], samples);
-+	if (mad_bit_nextbyte(&stream->ptr) > stream->next_frame)
-+	{
-+		stream->error = MAD_ERROR_LOSTSYNC;
-+		stream->sync = 0;
-+		return -1;
-+	}
- 
- 	for (ch = 0; ch < nch; ++ch) {
- 	  for (s = 0; s < 3; ++s) {
-Index: libmad-0.15.1b/layer3.c
-===================================================================
---- libmad-0.15.1b.orig/layer3.c	2008-12-23 21:38:07.000000000 +0100
-+++ libmad-0.15.1b/layer3.c	2008-12-23 21:38:12.000000000 +0100
-@@ -2608,6 +2608,12 @@
-     next_md_begin = 0;
- 
-   md_len = si.main_data_begin + frame_space - next_md_begin;
-+  if (md_len + MAD_BUFFER_GUARD > MAD_BUFFER_MDLEN)
-+  {
-+	stream->error = MAD_ERROR_LOSTSYNC;
-+	stream->sync = 0;
-+	return -1;
-+  }
- 
-   frame_used = 0;
- 

gnu/packages/patches/libmad-length-check.patch

@@ -0,0 +1,819 @@
+Copied from Debian.
+
+From: Kurt Roeckx <kurt@roeckx.be>
+Date: Sun, 28 Jan 2018 19:26:36 +0100
+Subject: Check the size before reading with mad_bit_read
+
+There are various cases where it attemps to read past the end of the buffer
+using mad_bit_read(). Most functions didn't even know the size of the buffer
+they were reading from.
+
+Index: libmad-0.15.1b/bit.c
+===================================================================
+--- libmad-0.15.1b.orig/bit.c
++++ libmad-0.15.1b/bit.c
+@@ -138,6 +138,9 @@ unsigned long mad_bit_read(struct mad_bi
+ {
+   register unsigned long value;
+ 
++  if (len == 0)
++    return 0;
++
+   if (bitptr->left == CHAR_BIT)
+     bitptr->cache = *bitptr->byte;
+ 
+Index: libmad-0.15.1b/frame.c
+===================================================================
+--- libmad-0.15.1b.orig/frame.c
++++ libmad-0.15.1b/frame.c
+@@ -120,11 +120,18 @@ static
+ int decode_header(struct mad_header *header, struct mad_stream *stream)
+ {
+   unsigned int index;
++  struct mad_bitptr bufend_ptr;
+ 
+   header->flags        = 0;
+   header->private_bits = 0;
+ 
++  mad_bit_init(&bufend_ptr, stream->bufend);
++
+   /* header() */
++  if (mad_bit_length(&stream->ptr, &bufend_ptr) < 32) {
++    stream->error = MAD_ERROR_BUFLEN;
++    return -1;
++  }
+ 
+   /* syncword */
+   mad_bit_skip(&stream->ptr, 11);
+@@ -225,8 +232,13 @@ int decode_header(struct mad_header *hea
+   /* error_check() */
+ 
+   /* crc_check */
+-  if (header->flags & MAD_FLAG_PROTECTION)
++  if (header->flags & MAD_FLAG_PROTECTION) {
++    if (mad_bit_length(&stream->ptr, &bufend_ptr) < 16) {
++      stream->error = MAD_ERROR_BUFLEN;
++      return -1;
++    }
+     header->crc_target = mad_bit_read(&stream->ptr, 16);
++  }
+ 
+   return 0;
+ }
+@@ -338,7 +350,7 @@ int mad_header_decode(struct mad_header
+       stream->error = MAD_ERROR_BUFLEN;
+       goto fail;
+     }
+-    else if (!(ptr[0] == 0xff && (ptr[1] & 0xe0) == 0xe0)) {
++    else if ((end - ptr >= 2) && !(ptr[0] == 0xff && (ptr[1] & 0xe0) == 0xe0)) {
+       /* mark point where frame sync word was expected */
+       stream->this_frame = ptr;
+       stream->next_frame = ptr + 1;
+@@ -361,6 +373,8 @@ int mad_header_decode(struct mad_header
+     ptr = mad_bit_nextbyte(&stream->ptr);
+   }
+ 
++  stream->error = MAD_ERROR_NONE;
++
+   /* begin processing */
+   stream->this_frame = ptr;
+   stream->next_frame = ptr + 1;  /* possibly bogus sync word */
+@@ -413,7 +427,7 @@ int mad_header_decode(struct mad_header
+     /* check that a valid frame header follows this frame */
+ 
+     ptr = stream->next_frame;
+-    if (!(ptr[0] == 0xff && (ptr[1] & 0xe0) == 0xe0)) {
++    if ((end - ptr >= 2) && !(ptr[0] == 0xff && (ptr[1] & 0xe0) == 0xe0)) {
+       ptr = stream->next_frame = stream->this_frame + 1;
+       goto sync;
+     }
+Index: libmad-0.15.1b/layer12.c
+===================================================================
+--- libmad-0.15.1b.orig/layer12.c
++++ libmad-0.15.1b/layer12.c
+@@ -72,10 +72,18 @@ mad_fixed_t const linear_table[14] = {
+  * DESCRIPTION:	decode one requantized Layer I sample from a bitstream
+  */
+ static
+-mad_fixed_t I_sample(struct mad_bitptr *ptr, unsigned int nb)
++mad_fixed_t I_sample(struct mad_bitptr *ptr, unsigned int nb, struct mad_stream *stream)
+ {
+   mad_fixed_t sample;
++  struct mad_bitptr frameend_ptr;
+ 
++  mad_bit_init(&frameend_ptr, stream->next_frame);
++
++  if (mad_bit_length(ptr, &frameend_ptr) < nb) {
++    stream->error = MAD_ERROR_LOSTSYNC;
++    stream->sync = 0;
++    return 0;
++  }
+   sample = mad_bit_read(ptr, nb);
+ 
+   /* invert most significant bit, extend sign, then scale to fixed format */
+@@ -106,6 +114,10 @@ int mad_layer_I(struct mad_stream *strea
+   struct mad_header *header = &frame->header;
+   unsigned int nch, bound, ch, s, sb, nb;
+   unsigned char allocation[2][32], scalefactor[2][32];
++  struct mad_bitptr bufend_ptr, frameend_ptr;
++
++  mad_bit_init(&bufend_ptr, stream->bufend);
++  mad_bit_init(&frameend_ptr, stream->next_frame);
+ 
+   nch = MAD_NCHANNELS(header);
+ 
+@@ -118,6 +130,11 @@ int mad_layer_I(struct mad_stream *strea
+   /* check CRC word */
+ 
+   if (header->flags & MAD_FLAG_PROTECTION) {
++    if (mad_bit_length(&stream->ptr, &bufend_ptr)
++		< 4 * (bound * nch + (32 - bound))) {
++      stream->error = MAD_ERROR_BADCRC;
++      return -1;
++    }
+     header->crc_check =
+       mad_bit_crc(stream->ptr, 4 * (bound * nch + (32 - bound)),
+ 		  header->crc_check);
+@@ -133,6 +150,11 @@ int mad_layer_I(struct mad_stream *strea
+ 
+   for (sb = 0; sb < bound; ++sb) {
+     for (ch = 0; ch < nch; ++ch) {
++      if (mad_bit_length(&stream->ptr, &frameend_ptr) < 4) {
++	stream->error = MAD_ERROR_LOSTSYNC;
++	stream->sync = 0;
++	return -1;
++      }
+       nb = mad_bit_read(&stream->ptr, 4);
+ 
+       if (nb == 15) {
+@@ -145,6 +167,11 @@ int mad_layer_I(struct mad_stream *strea
+   }
+ 
+   for (sb = bound; sb < 32; ++sb) {
++    if (mad_bit_length(&stream->ptr, &frameend_ptr) < 4) {
++      stream->error = MAD_ERROR_LOSTSYNC;
++      stream->sync = 0;
++      return -1;
++    }
+     nb = mad_bit_read(&stream->ptr, 4);
+ 
+     if (nb == 15) {
+@@ -161,6 +188,11 @@ int mad_layer_I(struct mad_stream *strea
+   for (sb = 0; sb < 32; ++sb) {
+     for (ch = 0; ch < nch; ++ch) {
+       if (allocation[ch][sb]) {
++        if (mad_bit_length(&stream->ptr, &frameend_ptr) < 6) {
++	  stream->error = MAD_ERROR_LOSTSYNC;
++	  stream->sync = 0;
++	  return -1;
++	}
+ 	scalefactor[ch][sb] = mad_bit_read(&stream->ptr, 6);
+ 
+ # if defined(OPT_STRICT)
+@@ -185,8 +217,10 @@ int mad_layer_I(struct mad_stream *strea
+       for (ch = 0; ch < nch; ++ch) {
+ 	nb = allocation[ch][sb];
+ 	frame->sbsample[ch][s][sb] = nb ?
+-	  mad_f_mul(I_sample(&stream->ptr, nb),
++	  mad_f_mul(I_sample(&stream->ptr, nb, stream),
+ 		    sf_table[scalefactor[ch][sb]]) : 0;
++	if (stream->error != 0)
++	  return -1;
+       }
+     }
+ 
+@@ -194,7 +228,14 @@ int mad_layer_I(struct mad_stream *strea
+       if ((nb = allocation[0][sb])) {
+ 	mad_fixed_t sample;
+ 
+-	sample = I_sample(&stream->ptr, nb);
++	if (mad_bit_length(&stream->ptr, &frameend_ptr) < nb) {
++	  stream->error = MAD_ERROR_LOSTSYNC;
++	  stream->sync = 0;
++          return -1;
++	}
++	sample = I_sample(&stream->ptr, nb, stream);
++        if (stream->error != 0)
++	  return -1;
+ 
+ 	for (ch = 0; ch < nch; ++ch) {
+ 	  frame->sbsample[ch][s][sb] =
+@@ -280,13 +321,21 @@ struct quantclass {
+ static
+ void II_samples(struct mad_bitptr *ptr,
+ 		struct quantclass const *quantclass,
+-		mad_fixed_t output[3])
++		mad_fixed_t output[3], struct mad_stream *stream)
+ {
+   unsigned int nb, s, sample[3];
++  struct mad_bitptr frameend_ptr;
++
++  mad_bit_init(&frameend_ptr, stream->next_frame);
+ 
+   if ((nb = quantclass->group)) {
+     unsigned int c, nlevels;
+ 
++    if (mad_bit_length(ptr, &frameend_ptr) < quantclass->bits) {
++      stream->error = MAD_ERROR_LOSTSYNC;
++      stream->sync = 0;
++      return;
++    }
+     /* degrouping */
+     c = mad_bit_read(ptr, quantclass->bits);
+     nlevels = quantclass->nlevels;
+@@ -299,8 +348,14 @@ void II_samples(struct mad_bitptr *ptr,
+   else {
+     nb = quantclass->bits;
+ 
+-    for (s = 0; s < 3; ++s)
++    for (s = 0; s < 3; ++s) {
++      if (mad_bit_length(ptr, &frameend_ptr) < nb) {
++	stream->error = MAD_ERROR_LOSTSYNC;
++	stream->sync = 0;
++	return;
++      }
+       sample[s] = mad_bit_read(ptr, nb);
++    }
+   }
+ 
+   for (s = 0; s < 3; ++s) {
+@@ -336,6 +391,9 @@ int mad_layer_II(struct mad_stream *stre
+   unsigned char const *offsets;
+   unsigned char allocation[2][32], scfsi[2][32], scalefactor[2][32][3];
+   mad_fixed_t samples[3];
++  struct mad_bitptr frameend_ptr;
++
++  mad_bit_init(&frameend_ptr, stream->next_frame);
+ 
+   nch = MAD_NCHANNELS(header);
+ 
+@@ -402,13 +460,24 @@ int mad_layer_II(struct mad_stream *stre
+   for (sb = 0; sb < bound; ++sb) {
+     nbal = bitalloc_table[offsets[sb]].nbal;
+ 
+-    for (ch = 0; ch < nch; ++ch)
++    for (ch = 0; ch < nch; ++ch) {
++      if (mad_bit_length(&stream->ptr, &frameend_ptr) < nbal) {
++	stream->error = MAD_ERROR_LOSTSYNC;
++	stream->sync = 0;
++	return -1;
++      }
+       allocation[ch][sb] = mad_bit_read(&stream->ptr, nbal);
++    }
+   }
+ 
+   for (sb = bound; sb < sblimit; ++sb) {
+     nbal = bitalloc_table[offsets[sb]].nbal;
+ 
++    if (mad_bit_length(&stream->ptr, &frameend_ptr) < nbal) {
++      stream->error = MAD_ERROR_LOSTSYNC;
++      stream->sync = 0;
++      return -1;
++    }
+     allocation[0][sb] =
+     allocation[1][sb] = mad_bit_read(&stream->ptr, nbal);
+   }
+@@ -417,8 +486,14 @@ int mad_layer_II(struct mad_stream *stre
+ 
+   for (sb = 0; sb < sblimit; ++sb) {
+     for (ch = 0; ch < nch; ++ch) {
+-      if (allocation[ch][sb])
++      if (allocation[ch][sb]) {
++	if (mad_bit_length(&stream->ptr, &frameend_ptr) < 2) {
++	  stream->error = MAD_ERROR_LOSTSYNC;
++	  stream->sync = 0;
++	  return -1;
++	}
+ 	scfsi[ch][sb] = mad_bit_read(&stream->ptr, 2);
++      }
+     }
+   }
+ 
+@@ -441,6 +516,11 @@ int mad_layer_II(struct mad_stream *stre
+   for (sb = 0; sb < sblimit; ++sb) {
+     for (ch = 0; ch < nch; ++ch) {
+       if (allocation[ch][sb]) {
++	if (mad_bit_length(&stream->ptr, &frameend_ptr) < 6) {
++	  stream->error = MAD_ERROR_LOSTSYNC;
++	  stream->sync = 0;
++	  return -1;
++	}
+ 	scalefactor[ch][sb][0] = mad_bit_read(&stream->ptr, 6);
+ 
+ 	switch (scfsi[ch][sb]) {
+@@ -451,11 +531,21 @@ int mad_layer_II(struct mad_stream *stre
+ 	  break;
+ 
+ 	case 0:
++	  if (mad_bit_length(&stream->ptr, &frameend_ptr) < 6) {
++	    stream->error = MAD_ERROR_LOSTSYNC;
++	    stream->sync = 0;
++	    return -1;
++	  }
+ 	  scalefactor[ch][sb][1] = mad_bit_read(&stream->ptr, 6);
+ 	  /* fall through */
+ 
+ 	case 1:
+ 	case 3:
++	  if (mad_bit_length(&stream->ptr, &frameend_ptr) < 6) {
++	    stream->error = MAD_ERROR_LOSTSYNC;
++	    stream->sync = 0;
++	    return -1;
++	  }
+ 	  scalefactor[ch][sb][2] = mad_bit_read(&stream->ptr, 6);
+ 	}
+ 
+@@ -487,7 +577,9 @@ int mad_layer_II(struct mad_stream *stre
+ 	if ((index = allocation[ch][sb])) {
+ 	  index = offset_table[bitalloc_table[offsets[sb]].offset][index - 1];
+ 
+-	  II_samples(&stream->ptr, &qc_table[index], samples);
++	  II_samples(&stream->ptr, &qc_table[index], samples, stream);
++	  if (stream->error != 0)
++            return -1;
+ 
+ 	  for (s = 0; s < 3; ++s) {
+ 	    frame->sbsample[ch][3 * gr + s][sb] =
+@@ -505,7 +597,9 @@ int mad_layer_II(struct mad_stream *stre
+       if ((index = allocation[0][sb])) {
+ 	index = offset_table[bitalloc_table[offsets[sb]].offset][index - 1];
+ 
+-	II_samples(&stream->ptr, &qc_table[index], samples);
++	II_samples(&stream->ptr, &qc_table[index], samples, stream);
++	if (stream->error != 0)
++          return -1;
+ 
+ 	for (ch = 0; ch < nch; ++ch) {
+ 	  for (s = 0; s < 3; ++s) {
+Index: libmad-0.15.1b/layer3.c
+===================================================================
+--- libmad-0.15.1b.orig/layer3.c
++++ libmad-0.15.1b/layer3.c
+@@ -598,7 +598,8 @@ enum mad_error III_sideinfo(struct mad_b
+ static
+ unsigned int III_scalefactors_lsf(struct mad_bitptr *ptr,
+ 				  struct channel *channel,
+-				  struct channel *gr1ch, int mode_extension)
++				  struct channel *gr1ch, int mode_extension,
++				  unsigned int bits_left, unsigned int *part2_length)
+ {
+   struct mad_bitptr start;
+   unsigned int scalefac_compress, index, slen[4], part, n, i;
+@@ -644,8 +645,12 @@ unsigned int III_scalefactors_lsf(struct
+ 
+     n = 0;
+     for (part = 0; part < 4; ++part) {
+-      for (i = 0; i < nsfb[part]; ++i)
++      for (i = 0; i < nsfb[part]; ++i) {
++	if (bits_left < slen[part])
++	  return MAD_ERROR_BADSCFSI;
+ 	channel->scalefac[n++] = mad_bit_read(ptr, slen[part]);
++	bits_left -= slen[part];
++      }
+     }
+ 
+     while (n < 39)
+@@ -690,7 +695,10 @@ unsigned int III_scalefactors_lsf(struct
+       max = (1 << slen[part]) - 1;
+ 
+       for (i = 0; i < nsfb[part]; ++i) {
++	if (bits_left < slen[part])
++	  return MAD_ERROR_BADSCFSI;
+ 	is_pos = mad_bit_read(ptr, slen[part]);
++	bits_left -= slen[part];
+ 
+ 	channel->scalefac[n] = is_pos;
+ 	gr1ch->scalefac[n++] = (is_pos == max);
+@@ -703,7 +711,8 @@ unsigned int III_scalefactors_lsf(struct
+     }
+   }
+ 
+-  return mad_bit_length(&start, ptr);
++  *part2_length = mad_bit_length(&start, ptr);
++  return MAD_ERROR_NONE;
+ }
+ 
+ /*
+@@ -712,7 +721,8 @@ unsigned int III_scalefactors_lsf(struct
+  */
+ static
+ unsigned int III_scalefactors(struct mad_bitptr *ptr, struct channel *channel,
+-			      struct channel const *gr0ch, unsigned int scfsi)
++			      struct channel const *gr0ch, unsigned int scfsi,
++			      unsigned int bits_left, unsigned int *part2_length)
+ {
+   struct mad_bitptr start;
+   unsigned int slen1, slen2, sfbi;
+@@ -728,12 +738,20 @@ unsigned int III_scalefactors(struct mad
+     sfbi = 0;
+ 
+     nsfb = (channel->flags & mixed_block_flag) ? 8 + 3 * 3 : 6 * 3;
+-    while (nsfb--)
++    while (nsfb--) {
++      if (bits_left < slen1)
++	return MAD_ERROR_BADSCFSI;
+       channel->scalefac[sfbi++] = mad_bit_read(ptr, slen1);
++      bits_left -= slen1;
++    }
+ 
+     nsfb = 6 * 3;
+-    while (nsfb--)
++    while (nsfb--) {
++      if (bits_left < slen2)
++	return MAD_ERROR_BADSCFSI;
+       channel->scalefac[sfbi++] = mad_bit_read(ptr, slen2);
++      bits_left -= slen2;
++    }
+ 
+     nsfb = 1 * 3;
+     while (nsfb--)
+@@ -745,8 +763,12 @@ unsigned int III_scalefactors(struct mad
+ 	channel->scalefac[sfbi] = gr0ch->scalefac[sfbi];
+     }
+     else {
+-      for (sfbi = 0; sfbi < 6; ++sfbi)
++      for (sfbi = 0; sfbi < 6; ++sfbi) {
++	if (bits_left < slen1)
++	  return MAD_ERROR_BADSCFSI;
+ 	channel->scalefac[sfbi] = mad_bit_read(ptr, slen1);
++	bits_left -= slen1;
++      }
+     }
+ 
+     if (scfsi & 0x4) {
+@@ -754,8 +776,12 @@ unsigned int III_scalefactors(struct mad
+ 	channel->scalefac[sfbi] = gr0ch->scalefac[sfbi];
+     }
+     else {
+-      for (sfbi = 6; sfbi < 11; ++sfbi)
++      for (sfbi = 6; sfbi < 11; ++sfbi) {
++	if (bits_left < slen1)
++	  return MAD_ERROR_BADSCFSI;
+ 	channel->scalefac[sfbi] = mad_bit_read(ptr, slen1);
++	bits_left -= slen1;
++      }
+     }
+ 
+     if (scfsi & 0x2) {
+@@ -763,8 +789,12 @@ unsigned int III_scalefactors(struct mad
+ 	channel->scalefac[sfbi] = gr0ch->scalefac[sfbi];
+     }
+     else {
+-      for (sfbi = 11; sfbi < 16; ++sfbi)
++      for (sfbi = 11; sfbi < 16; ++sfbi) {
++	if (bits_left < slen2)
++	  return MAD_ERROR_BADSCFSI;
+ 	channel->scalefac[sfbi] = mad_bit_read(ptr, slen2);
++	bits_left -= slen2;
++      }
+     }
+ 
+     if (scfsi & 0x1) {
+@@ -772,14 +802,19 @@ unsigned int III_scalefactors(struct mad
+ 	channel->scalefac[sfbi] = gr0ch->scalefac[sfbi];
+     }
+     else {
+-      for (sfbi = 16; sfbi < 21; ++sfbi)
++      for (sfbi = 16; sfbi < 21; ++sfbi) {
++	if (bits_left < slen2)
++	  return MAD_ERROR_BADSCFSI;
+ 	channel->scalefac[sfbi] = mad_bit_read(ptr, slen2);
++	bits_left -= slen2;
++      }
+     }
+ 
+     channel->scalefac[21] = 0;
+   }
+ 
+-  return mad_bit_length(&start, ptr);
++  *part2_length = mad_bit_length(&start, ptr);
++  return MAD_ERROR_NONE;
+ }
+ 
+ /*
+@@ -933,19 +968,17 @@ static
+ enum mad_error III_huffdecode(struct mad_bitptr *ptr, mad_fixed_t xr[576],
+ 			      struct channel *channel,
+ 			      unsigned char const *sfbwidth,
+-			      unsigned int part2_length)
++			      signed int part3_length)
+ {
+   signed int exponents[39], exp;
+   signed int const *expptr;
+   struct mad_bitptr peek;
+-  signed int bits_left, cachesz;
++  signed int bits_left, cachesz, fakebits;
+   register mad_fixed_t *xrptr;
+   mad_fixed_t const *sfbound;
+   register unsigned long bitcache;
+ 
+-  bits_left = (signed) channel->part2_3_length - (signed) part2_length;
+-  if (bits_left < 0)
+-    return MAD_ERROR_BADPART3LEN;
++  bits_left = part3_length;
+ 
+   III_exponents(channel, sfbwidth, exponents);
+ 
+@@ -956,8 +989,12 @@ enum mad_error III_huffdecode(struct mad
+   cachesz  = mad_bit_bitsleft(&peek);
+   cachesz += ((32 - 1 - 24) + (24 - cachesz)) & ~7;
+ 
++  if (bits_left < cachesz) {
++    cachesz = bits_left;
++  }
+   bitcache   = mad_bit_read(&peek, cachesz);
+   bits_left -= cachesz;
++  fakebits = 0;
+ 
+   xrptr = &xr[0];
+ 
+@@ -986,7 +1023,7 @@ enum mad_error III_huffdecode(struct mad
+ 
+     big_values = channel->big_values;
+ 
+-    while (big_values-- && cachesz + bits_left > 0) {
++    while (big_values-- && cachesz + bits_left - fakebits > 0) {
+       union huffpair const *pair;
+       unsigned int clumpsz, value;
+       register mad_fixed_t requantized;
+@@ -1023,10 +1060,19 @@ enum mad_error III_huffdecode(struct mad
+ 	unsigned int bits;
+ 
+ 	bits       = ((32 - 1 - 21) + (21 - cachesz)) & ~7;
++	if (bits_left < bits) {
++	  bits = bits_left;
++	}
+ 	bitcache   = (bitcache << bits) | mad_bit_read(&peek, bits);
+ 	cachesz   += bits;
+ 	bits_left -= bits;
+       }
++      if (cachesz < 21) {
++	unsigned int bits = 21 - cachesz;
++	bitcache <<= bits;
++	cachesz += bits;
++	fakebits += bits;
++      }
+ 
+       /* hcod (0..19) */
+ 
+@@ -1041,6 +1087,8 @@ enum mad_error III_huffdecode(struct mad
+       }
+ 
+       cachesz -= pair->value.hlen;
++      if (cachesz < fakebits)
++	return MAD_ERROR_BADHUFFDATA;
+ 
+       if (linbits) {
+ 	/* x (0..14) */
+@@ -1054,10 +1102,15 @@ enum mad_error III_huffdecode(struct mad
+ 
+ 	case 15:
+ 	  if (cachesz < linbits + 2) {
+-	    bitcache   = (bitcache << 16) | mad_bit_read(&peek, 16);
+-	    cachesz   += 16;
+-	    bits_left -= 16;
++	    unsigned int bits = 16;
++	    if (bits_left < 16)
++	      bits = bits_left;
++	    bitcache   = (bitcache << bits) | mad_bit_read(&peek, bits);
++	    cachesz   += bits;
++	    bits_left -= bits;
+ 	  }
++	  if (cachesz - fakebits < linbits)
++	    return MAD_ERROR_BADHUFFDATA;
+ 
+ 	  value += MASK(bitcache, cachesz, linbits);
+ 	  cachesz -= linbits;
+@@ -1074,6 +1127,8 @@ enum mad_error III_huffdecode(struct mad
+ 	  }
+ 
+ 	x_final:
++	  if (cachesz - fakebits < 1)
++	    return MAD_ERROR_BADHUFFDATA;
+ 	  xrptr[0] = MASK1BIT(bitcache, cachesz--) ?
+ 	    -requantized : requantized;
+ 	}
+@@ -1089,10 +1144,15 @@ enum mad_error III_huffdecode(struct mad
+ 
+ 	case 15:
+ 	  if (cachesz < linbits + 1) {
+-	    bitcache   = (bitcache << 16) | mad_bit_read(&peek, 16);
+-	    cachesz   += 16;
+-	    bits_left -= 16;
++	    unsigned int bits = 16;
++	    if (bits_left < 16)
++	      bits = bits_left;
++	    bitcache   = (bitcache << bits) | mad_bit_read(&peek, bits);
++	    cachesz   += bits;
++	    bits_left -= bits;
+ 	  }
++	  if (cachesz - fakebits < linbits)
++	    return MAD_ERROR_BADHUFFDATA;
+ 
+ 	  value += MASK(bitcache, cachesz, linbits);
+ 	  cachesz -= linbits;
+@@ -1109,6 +1169,8 @@ enum mad_error III_huffdecode(struct mad
+ 	  }
+ 
+ 	y_final:
++	  if (cachesz - fakebits < 1)
++	    return MAD_ERROR_BADHUFFDATA;
+ 	  xrptr[1] = MASK1BIT(bitcache, cachesz--) ?
+ 	    -requantized : requantized;
+ 	}
+@@ -1128,6 +1190,8 @@ enum mad_error III_huffdecode(struct mad
+ 	    requantized = reqcache[value] = III_requantize(value, exp);
+ 	  }
+ 
++	  if (cachesz - fakebits < 1)
++	    return MAD_ERROR_BADHUFFDATA;
+ 	  xrptr[0] = MASK1BIT(bitcache, cachesz--) ?
+ 	    -requantized : requantized;
+ 	}
+@@ -1146,6 +1210,8 @@ enum mad_error III_huffdecode(struct mad
+ 	    requantized = reqcache[value] = III_requantize(value, exp);
+ 	  }
+ 
++	  if (cachesz - fakebits < 1)
++	    return MAD_ERROR_BADHUFFDATA;
+ 	  xrptr[1] = MASK1BIT(bitcache, cachesz--) ?
+ 	    -requantized : requantized;
+ 	}
+@@ -1155,9 +1221,6 @@ enum mad_error III_huffdecode(struct mad
+     }
+   }
+ 
+-  if (cachesz + bits_left < 0)
+-    return MAD_ERROR_BADHUFFDATA;  /* big_values overrun */
+-
+   /* count1 */
+   {
+     union huffquad const *table;
+@@ -1167,15 +1230,24 @@ enum mad_error III_huffdecode(struct mad
+ 
+     requantized = III_requantize(1, exp);
+ 
+-    while (cachesz + bits_left > 0 && xrptr <= &xr[572]) {
++    while (cachesz + bits_left - fakebits > 0 && xrptr <= &xr[572]) {
+       union huffquad const *quad;
+ 
+       /* hcod (1..6) */
+ 
+       if (cachesz < 10) {
+-	bitcache   = (bitcache << 16) | mad_bit_read(&peek, 16);
+-	cachesz   += 16;
+-	bits_left -= 16;
++	unsigned int bits = 16;
++	if (bits_left < 16)
++	  bits = bits_left;
++	bitcache   = (bitcache << bits) | mad_bit_read(&peek, bits);
++	cachesz   += bits;
++	bits_left -= bits;
++      }
++      if (cachesz < 10) {
++	unsigned int bits = 10 - cachesz;
++	bitcache <<= bits;
++	cachesz += bits;
++	fakebits += bits;
+       }
+ 
+       quad = &table[MASK(bitcache, cachesz, 4)];
+@@ -1188,6 +1260,11 @@ enum mad_error III_huffdecode(struct mad
+ 		      MASK(bitcache, cachesz, quad->ptr.bits)];
+       }
+ 
++      if (cachesz - fakebits < quad->value.hlen + quad->value.v
++        + quad->value.w + quad->value.x + quad->value.y)
++	/* We don't have enough bits to read one more entry, consider them
++	 * stuffing bits. */
++	break;
+       cachesz -= quad->value.hlen;
+ 
+       if (xrptr == sfbound) {
+@@ -1236,22 +1313,8 @@ enum mad_error III_huffdecode(struct mad
+ 
+       xrptr += 2;
+     }
+-
+-    if (cachesz + bits_left < 0) {
+-# if 0 && defined(DEBUG)
+-      fprintf(stderr, "huffman count1 overrun (%d bits)\n",
+-	      -(cachesz + bits_left));
+-# endif
+-
+-      /* technically the bitstream is misformatted, but apparently
+-	 some encoders are just a bit sloppy with stuffing bits */
+-
+-      xrptr -= 4;
+-    }
+   }
+ 
+-  assert(-bits_left <= MAD_BUFFER_GUARD * CHAR_BIT);
+-
+ # if 0 && defined(DEBUG)
+   if (bits_left < 0)
+     fprintf(stderr, "read %d bits too many\n", -bits_left);
+@@ -2348,10 +2411,11 @@ void III_freqinver(mad_fixed_t sample[18
+  */
+ static
+ enum mad_error III_decode(struct mad_bitptr *ptr, struct mad_frame *frame,
+-			  struct sideinfo *si, unsigned int nch)
++			  struct sideinfo *si, unsigned int nch, unsigned int md_len)
+ {
+   struct mad_header *header = &frame->header;
+   unsigned int sfreqi, ngr, gr;
++  int bits_left = md_len * CHAR_BIT;
+ 
+   {
+     unsigned int sfreq;
+@@ -2383,6 +2447,7 @@ enum mad_error III_decode(struct mad_bit
+     for (ch = 0; ch < nch; ++ch) {
+       struct channel *channel = &granule->ch[ch];
+       unsigned int part2_length;
++      unsigned int part3_length;
+ 
+       sfbwidth[ch] = sfbwidth_table[sfreqi].l;
+       if (channel->block_type == 2) {
+@@ -2391,18 +2456,30 @@ enum mad_error III_decode(struct mad_bit
+       }
+ 
+       if (header->flags & MAD_FLAG_LSF_EXT) {
+-	part2_length = III_scalefactors_lsf(ptr, channel,
++	error = III_scalefactors_lsf(ptr, channel,
+ 					    ch == 0 ? 0 : &si->gr[1].ch[1],
+-					    header->mode_extension);
++					    header->mode_extension, bits_left, &part2_length);
+       }
+       else {
+-	part2_length = III_scalefactors(ptr, channel, &si->gr[0].ch[ch],
+-					gr == 0 ? 0 : si->scfsi[ch]);
++	error = III_scalefactors(ptr, channel, &si->gr[0].ch[ch],
++					gr == 0 ? 0 : si->scfsi[ch], bits_left, &part2_length);
+       }
++      if (error)
++        return error;
++
++      bits_left -= part2_length;
+ 
+-      error = III_huffdecode(ptr, xr[ch], channel, sfbwidth[ch], part2_length);
++      if (part2_length > channel->part2_3_length)
++        return MAD_ERROR_BADPART3LEN;
++
++      part3_length = channel->part2_3_length - part2_length;
++      if (part3_length > bits_left)
++        return MAD_ERROR_BADPART3LEN;
++
++      error = III_huffdecode(ptr, xr[ch], channel, sfbwidth[ch], part3_length);
+       if (error)
+ 	return error;
++      bits_left -= part3_length;
+     }
+ 
+     /* joint stereo processing */
+@@ -2519,11 +2596,13 @@ int mad_layer_III(struct mad_stream *str
+   unsigned int nch, priv_bitlen, next_md_begin = 0;
+   unsigned int si_len, data_bitlen, md_len;
+   unsigned int frame_space, frame_used, frame_free;
+-  struct mad_bitptr ptr;
++  struct mad_bitptr ptr, bufend_ptr;
+   struct sideinfo si;
+   enum mad_error error;
+   int result = 0;
+ 
++  mad_bit_init(&bufend_ptr, stream->bufend);
++
+   /* allocate Layer III dynamic structures */
+ 
+   if (stream->main_data == 0) {
+@@ -2587,14 +2666,15 @@ int mad_layer_III(struct mad_stream *str
+     unsigned long header;
+ 
+     mad_bit_init(&peek, stream->next_frame);
++    if (mad_bit_length(&peek, &bufend_ptr) >= 57) {
++      header = mad_bit_read(&peek, 32);
++      if ((header & 0xffe60000L) /* syncword | layer */ == 0xffe20000L) {
++        if (!(header & 0x00010000L))  /* protection_bit */
++	  mad_bit_skip(&peek, 16);  /* crc_check */
+ 
+-    header = mad_bit_read(&peek, 32);
+-    if ((header & 0xffe60000L) /* syncword | layer */ == 0xffe20000L) {
+-      if (!(header & 0x00010000L))  /* protection_bit */
+-	mad_bit_skip(&peek, 16);  /* crc_check */
+-
+-      next_md_begin =
+-	mad_bit_read(&peek, (header & 0x00080000L) /* ID */ ? 9 : 8);
++        next_md_begin =
++	  mad_bit_read(&peek, (header & 0x00080000L) /* ID */ ? 9 : 8);
++      }
+     }
+ 
+     mad_bit_finish(&peek);
+@@ -2653,7 +2733,7 @@ int mad_layer_III(struct mad_stream *str
+   /* decode main_data */
+ 
+   if (result == 0) {
+-    error = III_decode(&ptr, frame, &si, nch);
++    error = III_decode(&ptr, frame, &si, nch, md_len);
+     if (error) {
+       stream->error = error;
+       result = -1;

gnu/packages/patches/libmad-md_size.patch

@@ -0,0 +1,60 @@
+Copied from Debian.
+
+From: Kurt Roeckx <kurt@roeckx.be>
+Date: Sun, 28 Jan 2018 15:44:08 +0100
+Subject: Check the size of the main data
+
+The main data to decode a frame can come from the current frame and part of the
+previous frame, the so called bit reservoir. si.main_data_begin is the part of
+the previous frame we need for this frame. frame_space is the amount of main
+data that can be in this frame, and next_md_begin is the part of this frame that
+is going to be used for the next frame.
+
+The maximum amount of data from a previous frame that the format allows is 511
+bytes. The maximum frame size for the defined bitrates is at MPEG 2.5 layer 2
+at 320 kbit/s and 8 kHz sample rate which gives 72 * (320000 / 8000) + 1 = 2881.
+So those defines are not large enough:
+ # define MAD_BUFFER_GUARD      8
+ # define MAD_BUFFER_MDLEN      (511 + 2048 + MAD_BUFFER_GUARD)
+
+There is also support for a "free" bitrate which allows you to create any frame
+size, which can be larger than the buffer.
+
+Changing the defines is not an option since it's part of the ABI, so we check
+that the main data fits in the bufer.
+
+The previous frame data is stored in *stream->main_data and contains
+stream->md_len bytes. If stream->md_len is larger than the data we
+need from the previous frame (si.main_data_begin) it still wouldn't fit
+in the buffer, so just keep the data that we need.
+
+Index: libmad-0.15.1b/layer3.c
+===================================================================
+--- libmad-0.15.1b.orig/layer3.c
++++ libmad-0.15.1b/layer3.c
+@@ -2608,6 +2608,11 @@ int mad_layer_III(struct mad_stream *str
+     next_md_begin = 0;
+ 
+   md_len = si.main_data_begin + frame_space - next_md_begin;
++  if (md_len + MAD_BUFFER_GUARD > MAD_BUFFER_MDLEN) {
++    stream->error = MAD_ERROR_LOSTSYNC;
++    stream->sync = 0;
++    return -1;
++  }
+ 
+   frame_used = 0;
+ 
+@@ -2625,8 +2630,11 @@ int mad_layer_III(struct mad_stream *str
+       }
+     }
+     else {
+-      mad_bit_init(&ptr,
+-		   *stream->main_data + stream->md_len - si.main_data_begin);
++      memmove(stream->main_data,
++	*stream->main_data + stream->md_len - si.main_data_begin,
++	si.main_data_begin);
++      stream->md_len = si.main_data_begin;
++      mad_bit_init(&ptr, *stream->main_data);
+ 
+       if (md_len > si.main_data_begin) {
+ 	assert(stream->md_len + md_len -

gnu/packages/patches/libvirt-remove-ATTRIBUTE_UNUSED.patch

@@ -1,34 +0,0 @@
-From: Tobias Geerinckx-Rice <me@tobias.gr>
-Date: Thu, 25 Jul 2019 21:48:25 +0200
-Subject: [PATCH]: libvirt: remove ATTRIBUTE_UNUSED
-
-This should fix the error reported here[0].  Patch taken verbatim from
-upstream[1].
-
-[0]: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36634#28
-[1]: https://github.com/libvirt/libvirt/commit/759bf903a6c24a8efa25c7cf4b099d952eda9bd3
-
-From 759bf903a6c24a8efa25c7cf4b099d952eda9bd3 Mon Sep 17 00:00:00 2001
-From: Pavel Hrdina <phrdina@redhat.com>
-Date: Mon, 22 Jul 2019 14:46:34 +0200
-Subject: [PATCH] vircgroupv2: remove ATTRIBUTE_UNUSED for used attribute
-
-Signed-off-by: Pavel Hrdina <phrdina@redhat.com>
-Acked-by: Peter Krempa <pkrempa@redhat.com>
----
- src/util/vircgroupv2.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/util/vircgroupv2.c b/src/util/vircgroupv2.c
-index af3192c99c..e36c36685b 100644
---- a/src/util/vircgroupv2.c
-+++ b/src/util/vircgroupv2.c
-@@ -399,7 +399,7 @@ virCgroupV2EnableController(virCgroupPtr group,
- 
- 
- static int
--virCgroupV2MakeGroup(virCgroupPtr parent ATTRIBUTE_UNUSED,
-+virCgroupV2MakeGroup(virCgroupPtr parent,
-                      virCgroupPtr group,
-                      bool create,
-                      unsigned int flags)

gnu/packages/patches/strace-ipc-tests.patch

@@ -0,0 +1,30 @@
+Fix a test failure on some systems.
+
+Taken from upstream:
+https://github.com/strace/strace/commit/4377e3a1535a0ec3a42da8a1366ad6943f4efa0e
+
+diff --git a/tests/gen_tests.in b/tests/gen_tests.in
+index 4a506b94c..4fdf4722c 100644
+--- a/tests/gen_tests.in
++++ b/tests/gen_tests.in
+@@ -168,16 +168,16 @@ ipc_msg-Xabbrev	+ipc.sh -Xabbrev -a26
+ ipc_msg-Xraw	+ipc.sh -Xraw -a16
+ ipc_msg-Xverbose	+ipc.sh -Xverbose -a34
+ ipc_msgbuf-Xabbrev	+ipc_msgbuf.test -Xabbrev
+-ipc_msgbuf-Xraw	+ipc_msgbuf.test -Xraw -a22
++ipc_msgbuf-Xraw	+ipc_msgbuf.test -Xraw -a20
+ ipc_msgbuf-Xverbose	+ipc_msgbuf.test -Xverbose
+ ipc_sem	+ipc.sh -a29
+ ipc_sem-Xabbrev	+ipc.sh -Xabbrev -a29
+ ipc_sem-Xraw	+ipc.sh -Xraw -a19
+ ipc_sem-Xverbose	+ipc.sh -Xverbose -a36
+-ipc_shm	+ipc.sh -a29
+-ipc_shm-Xabbrev	+ipc.sh -Xabbrev -a29
++ipc_shm	+ipc.sh -a26
++ipc_shm-Xabbrev	+ipc.sh -Xabbrev -a26
+ ipc_shm-Xraw	+ipc.sh -Xraw -a19
+-ipc_shm-Xverbose	+ipc.sh -Xverbose -a36
++ipc_shm-Xverbose	+ipc.sh -Xverbose -a34
+ kcmp	-a22
+ kcmp-y	-a22 -y -e trace=kcmp
+ kern_features -a16

gnu/packages/perl.scm

@@ -4082,7 +4082,7 @@ relic support.")
         (base32
          "0h3wfnpv5d4d3f9xzmwkchay6251nhzngdv3f6xia56mj4hxabs0"))))
     (build-system perl-build-system)
-    (inputs
+    (propagated-inputs
      `(("perl-clone-choose" ,perl-clone-choose)))
     (home-page "https://metacpan.org/release/Hash-Merge")
     (synopsis "Merge arbitrarily deep hashes into a single hash")

gnu/packages/plotutils.scm

@@ -198,8 +198,7 @@ colors, styles, options and details.")
        ("perl" ,perl)
        ("texinfo" ,texinfo)           ;For generating documentation
        ;; For the manual and the tests.
-       ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
+       ("texlive" ,(texlive-union (list texlive-amsfonts
-                                        texlive-latex-amsfonts
                                         texlive-latex-geometry
                                         texlive-latex-graphics
                                         texlive-latex-oberdiek ; for ifluatex

gnu/packages/python-xyz.scm

@@ -3500,12 +3500,11 @@ color scales, and color space conversion easy.  It has support for:
        ("pkg-config" ,pkg-config)
        ("python-sphinx" ,python-sphinx)
        ("python-numpydoc" ,python-numpydoc)
-       ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
+       ("texlive" ,(texlive-union (list texlive-fonts-cm-super
-                                        texlive-fonts-cm-super
                                         texlive-fonts-ec
                                         texlive-generic-ifxetex
                                         texlive-generic-pdftex
-                                        texlive-latex-amsfonts
+                                        texlive-amsfonts
                                         texlive-latex-capt-of
                                         texlive-latex-cmap
                                         texlive-latex-environ
@@ -3904,7 +3903,7 @@ toolkits.")
        ("python-ipykernel" ,python-ipykernel)
        ("python-mock" ,python-mock)
        ("graphviz" ,graphviz)
-       ("texlive" ,(texlive-union (list texlive-latex-amsfonts
+       ("texlive" ,(texlive-union (list texlive-amsfonts
                                         texlive-latex-amsmath
                                         texlive-latex-enumitem
                                         texlive-latex-expdlist
@@ -3915,7 +3914,6 @@ toolkits.")
 
                                         texlive-generic-pdftex
 
-                                        texlive-fonts-amsfonts
                                         texlive-fonts-ec
                                         texlive-fonts-adobe-times
                                         texlive-fonts-txfonts)))
@@ -5472,11 +5470,10 @@ computing.")
      `(("python-sphinx" ,python-sphinx)
        ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme)
        ;; FIXME: It's possible that a smaller union would work just as well.
-       ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
+       ("texlive" ,(texlive-union (list texlive-amsfonts
                                         texlive-fonts-ec
                                         texlive-generic-ifxetex
                                         texlive-generic-pdftex
-                                        texlive-latex-amsfonts
                                         texlive-latex-capt-of
                                         texlive-latex-cmap
                                         texlive-latex-environ

gnu/packages/samba.scm

@@ -153,14 +153,14 @@ anywhere.")
 (define-public samba
   (package
     (name "samba")
-    (version "4.10.5")
+    (version "4.10.6")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://download.samba.org/pub/samba/stable/"
                                  "samba-" version ".tar.gz"))
              (sha256
               (base32
-               "0xb3mz38hcayqxchk0ws9mxn10vswsn97jbxl4gcwi4cbrnjc43c"))))
+               "0hpgdqlyczj98pkh2ldglvvnkrb1q541r3qikdvxq0qjvd9fpywy"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/statistics.scm

@@ -75,6 +75,7 @@
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
@@ -319,9 +320,8 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("texinfo" ,texinfo) ; for building HTML manuals
-       ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
+       ("texlive" ,(texlive-union (list texlive-fonts-ec
-                                        texlive-fonts-ec
+                                        texlive-amsfonts
-                                        texlive-latex-amsfonts
                                         texlive-latex-base
                                         texlive-latex-fancyvrb
                                         texlive-latex-graphics
@@ -397,14 +397,14 @@ available, greatly increasing its breadth and scope.")
 (define-public r-boot
   (package
     (name "r-boot")
-    (version "1.3-22")
+    (version "1.3-23")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "boot" version))
        (sha256
         (base32
-         "1z2dig1mi76b3b9ck6qlkh07l3hs478gaf70db5nv8x7w2qhq7yg"))))
+         "0bx07zbb5nfz2xfgnzbspg7r5vxz4bjdz1ry4d1vk434vlcrxj1h"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/boot")
     (synopsis "Bootstrap functions for R")
@@ -502,14 +502,14 @@ code for possible problems.")
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-71")
+    (version "0.8-72")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
+         "124c9229is44p2rv7xyh2q86nsfi7vzyyh5n3c5ihziqrp4ig723"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")
@@ -588,14 +588,14 @@ and operations on them using LAPACK and SuiteSparse.")
 (define-public r-nlme
   (package
     (name "r-nlme")
-    (version "3.1-140")
+    (version "3.1-141")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nlme" version))
        (sha256
         (base32
-         "0k9x5j34fx093a023da9ny3b3101lbwpmfm27mkvfj950l22z88x"))))
+         "0ml00g79bimjcl0sgn6h55l5b4gfmnsnc1vvmivggn0318k4c04i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -804,13 +804,13 @@ effects of different types of color-blindness.")
 (define-public r-digest
   (package
     (name "r-digest")
-    (version "0.6.19")
+    (version "0.6.20")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "digest" version))
        (sha256
-        (base32 "1x6cbj9qvkk7pxv9xdqibazw3x8psjp6x0m0ildx1jwyb2ymkl98"))))
+        (base32 "1irhk2jaj9cg57cxprgyn1if06x121xwcxh1fzzn3148bl5lnrq5"))))
     (build-system r-build-system)
     ;; Vignettes require r-knitr, which requires r-digest, so we have to
     ;; disable them and the tests.
@@ -1603,18 +1603,19 @@ R packages that praise their users.")
 (define-public r-testthat
   (package
     (name "r-testthat")
-    (version "2.1.1")
+    (version "2.2.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "testthat" version))
               (sha256
                (base32
-                "03jgr0hlr77yp0aib4v30yjyjrjsa8dczr02yk21m93vl25vqvkp"))))
+                "0y0bvggm4pzkzp6xn7b8cf3ybqp9ijxkhhyp3z49a9iipc90bvk7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
        ("r-crayon" ,r-crayon)
        ("r-digest" ,r-digest)
+       ("r-evaluate" ,r-evaluate)
        ("r-magrittr" ,r-magrittr)
        ("r-praise" ,r-praise)
        ("r-r6" ,r-r6)
@@ -1696,13 +1697,13 @@ and printing capabilities than traditional data frames.")
 (define-public r-dplyr
   (package
     (name "r-dplyr")
-    (version "0.8.1")
+    (version "0.8.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "dplyr" version))
               (sha256
                (base32
-                "1nw12hzk1jcac5879nfmf1yp98jpb3i59qkb8sfpk2cd6zqgfgjz"))))
+                "032c89wa04g9rih9shyvwl3il0bsrv3xk489x6867sk9bb3amd38"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -1979,13 +1980,13 @@ inference for statistical models.")
 (define-public r-coda
   (package
     (name "r-coda")
-    (version "0.19-2")
+    (version "0.19-3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "coda" version))
               (sha256
                (base32
-                "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7"))))
+                "1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -2021,14 +2022,14 @@ and environmental data in the framework of Euclidean exploratory methods.")
 (define-public r-xml2
   (package
     (name "r-xml2")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xml2" version))
        (sha256
         (base32
-         "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
+         "0186d7r36xw1z9f8ajz35a0dz4ch6hmrjl9536yc7vq78v4vn5an"))))
     (build-system r-build-system)
     (inputs
      `(("libxml2" ,libxml2)
@@ -2136,14 +2137,14 @@ R version.")
 (define-public r-checkmate
   (package
     (name "r-checkmate")
-    (version "1.9.3")
+    (version "1.9.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "checkmate" version))
        (sha256
         (base32
-         "15ccwvmw73c2zz1k10k5zdn8px0rrbnvs1b4nzvlb0iwj7cimhp4"))))
+         "08ddpgs4mv5d5y4j054pm8drmxkn7yvhfpbghwxlizjpnxa5g8ps"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)))
@@ -2333,14 +2334,14 @@ collation, and NAMESPACE files.")
 (define-public r-openssl
   (package
     (name "r-openssl")
-    (version "1.4")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openssl" version))
        (sha256
         (base32
-         "0mh4xwb9wnn5j2n1zzmjldqjqv2nn4wdidiixxciaqrqsi0l9834"))))
+         "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
     (build-system r-build-system)
     (inputs
      `(("libressl" ,libressl)))
@@ -2366,13 +2367,13 @@ integers.")
 (define-public r-httr
   (package
     (name "r-httr")
-    (version "1.4.0")
+    (version "1.4.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httr" version))
               (sha256
                (base32
-                "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn"))))
+                "0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-curl" ,r-curl)
@@ -2392,20 +2393,16 @@ functions make it easy to control additional request components.")
 (define-public r-git2r
   (package
     (name "r-git2r")
-    (version "0.25.2")
+    (version "0.26.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "git2r" version))
               (sha256
                (base32
-                "15kpvz6ry2r8ii5hzinjwkggc5kgmkbcpsdwzahsf8gha52w80p0"))))
+                "0dbl845sahv2i641ncaf06w06djravwc5wknp9syzx0ad8l0kmhk"))))
     (build-system r-build-system)
-    ;; This R package contains modified sources of libgit2.  This modified
-    ;; version of libgit2 is built as the package is built.  Hence libgit2 is
-    ;; not among the inputs of this package.
     (inputs
-     `(("libssh2" ,libssh2) ; for SSH transport
+     `(("libgit2" ,libgit2)
-       ("openssl" ,openssl)
        ("zlib" ,zlib)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -2438,13 +2435,13 @@ informative error messages when it's not available.")
 (define-public r-devtools
   (package
     (name "r-devtools")
-    (version "2.0.2")
+    (version "2.1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "devtools" version))
               (sha256
                (base32
-                "028pppj39ng7q17k27531s8k00lmw982vz5krn74n9b8f2azm8lr"))))
+                "0393v7nr22gr5g9afgrhq4ab3lwbqy6fd3shnmlhdpqam5357xy1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -2457,9 +2454,11 @@ informative error messages when it's not available.")
        ("r-pkgbuild" ,r-pkgbuild)
        ("r-pkgload" ,r-pkgload)
        ("r-rcmdcheck" ,r-rcmdcheck)
+       ("r-roxygen2" ,r-roxygen2)
        ("r-remotes" ,r-remotes)
        ("r-rstudioapi" ,r-rstudioapi)
        ("r-sessioninfo" ,r-sessioninfo)
+       ("r-testthat" ,r-testthat)
        ("r-usethis" ,r-usethis)
        ("r-withr" ,r-withr)))
     (home-page "https://github.com/hadley/devtools")
@@ -2490,18 +2489,19 @@ were originally a part of the r-devtools package.")
 (define-public r-hms
   (package
     (name "r-hms")
-    (version "0.4.2")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hms" version))
        (sha256
         (base32
-         "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
+         "06snfqdczr0x0nbp7qnvwhlp2pw0wx9c2y3xb4gr1wrvbik74y58"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rlang" ,r-rlang)
-       ("r-pkgconfig" ,r-pkgconfig)))
+       ("r-pkgconfig" ,r-pkgconfig)
+       ("r-vctrs" ,r-vctrs)))
     (home-page "https://github.com/rstats-db/hms")
     (synopsis "Pretty time of day")
     (description
@@ -2597,13 +2597,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.500.2.0")
+    (version "0.9.600.4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1lyvpb7n54ijlqns29qiixqr39334knf67cnixvlic58945glrhv"))))
+                "07jg2667xyhmp1fbcdi5nnhmkk81da76s9rlswfq4k2sjsmbfmr0"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     ;; All needed for vignettes
@@ -2695,14 +2695,14 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "1.13")
+    (version "1.14")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
           (base32
-            "1vv3b8nlw8ra19492rjg3na42lwh3xr5a2jy2ia81fvvs846pywn"))))
+            "0qfw5rkvwqpgix32g6qy9xrr50awmm146aqbm836xravih2b2dpn"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2788,17 +2788,18 @@ that package, other packages are unaffected.")
 (define-public r-blob
   (package
     (name "r-blob")
-    (version "1.1.1")
+    (version "1.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "blob" version))
               (sha256
                (base32
-                "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
+                "08z071jzac4gasgfgab0y5g3ilfmlw08ln813wphxg07hsiczw8s"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-prettyunits" ,r-prettyunits)
-       ("r-tibble" ,r-tibble)))
+       ("r-rlang" ,r-rlang)
+       ("r-vctrs" ,r-vctrs)))
     (home-page "https://github.com/hadley/blob")
     (synopsis "Simple S3 Class for representing vectors of binary data")
     (description "Raw vectors in R are useful for storing a single binary
@@ -2810,13 +2811,13 @@ a column in data frame.")
 (define-public r-rsqlite
   (package
     (name "r-rsqlite")
-    (version "2.1.1")
+    (version "2.1.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RSQLite" version))
               (sha256
                (base32
-                "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
+                "1inrhap5cs0wry2jbw42fx9wwxb3qdzlpy0ba4f6a29bs8jx9nk6"))))
     (properties `((upstream-name . "RSQLite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3069,14 +3070,14 @@ standard R subsetting and Kronecker products.")
 (define-public r-iterators
   (package
     (name "r-iterators")
-    (version "1.0.10")
+    (version "1.0.12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "iterators" version))
        (sha256
         (base32
-         "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
+         "0jwzxaa3jm1xzgfv5pn0xqkk7rhm0xwvgn85w7xaw8xx1vb33gwn"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/iterators")
     (synopsis "Iterator construct for R")
@@ -3089,14 +3090,14 @@ data.")
 (define-public r-foreach
   (package
     (name "r-foreach")
-    (version "1.4.4")
+    (version "1.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreach" version))
        (sha256
         (base32
-         "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
+         "0q7iyniw5iri4hl57bhil3r69s5wnaijzn0q0x4h3z42245jqqwm"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-codetools" ,r-codetools)
@@ -3117,14 +3118,14 @@ parallel.")
 (define-public r-doparallel
   (package
     (name "r-doparallel")
-    (version "1.0.14")
+    (version "1.0.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doParallel" version))
        (sha256
         (base32
-         "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb"))))
+         "0vnqbha3gig3awbfvsfx3ni5jir398md1n7xmsb8jihnjsk7xbbi"))))
     (properties `((upstream-name . "doParallel")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3140,14 +3141,14 @@ using the parallel package.")
 (define-public r-domc
   (package
     (name "r-domc")
-    (version "1.3.5")
+    (version "1.3.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doMC" version))
        (sha256
         (base32
-         "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
+         "1cn9gxavhvjswip8pwvkpi7q6wpzdllcsdjabga8akf55nggqxr9"))))
     (properties `((upstream-name . "doMC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3163,13 +3164,13 @@ using the multicore functionality of the parallel package.")
 (define-public r-dt
   (package
     (name "r-dt")
-    (version "0.7")
+    (version "0.8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DT" version))
               (sha256
                (base32
-                "0b6ywgzk9b35y5f69zwfz3vv7qwqqj3xsmy0xymf7nfcvrqg3qqx"))))
+                "08cfmv3d5awvd9h8648bvidcg2ak5pvl2p6vqwqwy1l82ia506ch"))))
     (properties
      `((upstream-name . "DT")))
     (build-system r-build-system)
@@ -3177,6 +3178,7 @@ using the multicore functionality of the parallel package.")
      `(("r-crosstalk" ,r-crosstalk)
        ("r-htmltools" ,r-htmltools)
        ("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-jsonlite" ,r-jsonlite)
        ("r-magrittr" ,r-magrittr)
        ("r-promises" ,r-promises)))
     (home-page "http://rstudio.github.io/DT")
@@ -3315,14 +3317,14 @@ package registries.")
 (define-public r-rngtools
   (package
     (name "r-rngtools")
-    (version "1.3.1.1")
+    (version "1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rngtools" version))
        (sha256
         (base32
-         "0k1nlcxggflq0043m15dfclnqnzchkpw2ik7jk82h4dqwvysiqcr"))))
+         "1kivj594bn774lbn29ws2rmzy2km99sza0j3jqvhal6hwmk27a9s"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -4566,19 +4568,19 @@ Farebrother's algorithm or Liu et al.'s algorithm.")
 (define-public r-cowplot
   (package
     (name "r-cowplot")
-    (version "0.9.4")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cowplot" version))
        (sha256
         (base32
-         "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv"))))
+         "19cqdhgfyr1wj0fz0c5ly8f0aiy9sfgzq6lzb78hkx0hdp2agybh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
        ("r-gtable" ,r-gtable)
-       ("r-plyr" ,r-plyr)
+       ("r-rlang" ,r-rlang)
        ("r-scales" ,r-scales)))
     (home-page "https://github.com/wilkelab/cowplot")
     (synopsis "Streamlined plot theme and plot annotations for ggplot2")
@@ -4640,14 +4642,14 @@ regression.")
 (define-public r-fastica
   (package
     (name "r-fastica")
-    (version "1.2-1")
+    (version "1.2-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fastICA" version))
        (sha256
         (base32
-         "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
+         "1zpijqcipm0aa3rxj0mys06lskqy4dbppjpxr1aby0j16y9ka8ij"))))
     (properties `((upstream-name . "fastICA")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/fastICA")
@@ -4749,14 +4751,14 @@ models, generalized linear models and model-based clustering.")
 (define-public r-mclust
   (package
     (name "r-mclust")
-    (version "5.4.4")
+    (version "5.4.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mclust" version))
        (sha256
         (base32
-         "039ymr57bq5327gypizw0v2qb81j6bkqhjdh8yj23qa5sh51phyc"))))
+         "0whandnda1fnjn5k3hgxdbp3b0xr7nlzy1j37saqb536h8q9dwkm"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -4919,14 +4921,14 @@ generally.")
 (define-public r-robust
   (package
     (name "r-robust")
-    (version "0.4-18")
+    (version "0.4-18.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "robust" version))
        (sha256
         (base32
-         "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
+         "0xs098pfw5zdcdk3rsxkylfl6d2pyp566s5v92bzhgl7h8c90cfy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-fit-models" ,r-fit-models)
@@ -5025,14 +5027,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.")
 (define-public r-pbapply
   (package
     (name "r-pbapply")
-    (version "1.4-0")
+    (version "1.4-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pbapply" version))
        (sha256
         (base32
-         "0bn7a9ni36xy5acnrl9ky3gd1k8jr5kxgazzh3pzd1q6bri1nx7k"))))
+         "1bbws9n90cqnnp5k58hp852jwmm6513jnhn4vzhl9f8x314k6qxk"))))
     (build-system r-build-system)
     (home-page "https://github.com/psolymos/pbapply")
     (synopsis "Adding progress bar to apply functions")
@@ -5138,14 +5140,14 @@ using modular prediction and response module classes.")
 (define-public r-quantreg
   (package
     (name "r-quantreg")
-    (version "5.41")
+    (version "5.42.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "quantreg" version))
        (sha256
         (base32
-         "110ax3ngn6i94h7iw7ha67kfsmj94hycp7lk62nmyvkp34vpfykh"))))
+         "1aycnghci329yqw63kybv7sfjjx5whq3xs7xzic4wsaj7j4b1hjc"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))

gnu/packages/terminals.scm

@@ -57,6 +57,7 @@
   #:use-module (gnu packages golang)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages libcanberra)
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages ncurses)
@@ -954,7 +955,7 @@ tmux.")
 (define-public kitty
   (package
     (name "kitty")
-    (version "0.14.2")
+    (version "0.14.3")
     (home-page "https://sw.kovidgoyal.net/kitty/")
     (source
      (origin
@@ -965,7 +966,7 @@ tmux.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "15iv3k7iryf10n8n67d37x24pzcarq97a3dr42lbld00k1lx19az"))
+         "0wi6b6b1nyp16rcpcghk6by62wy6qsamv1xdymyn0zbqgd8h9n6b"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -984,6 +985,7 @@ tmux.")
      `(("python" ,python)
        ("harfbuzz" ,harfbuzz)
        ("zlib" ,zlib)
+       ("libcanberra" ,libcanberra)
        ("libpng" ,libpng)
        ("freetype" ,freetype)
        ("fontconfig" ,fontconfig)

gnu/packages/video.scm

@@ -473,16 +473,18 @@ and creating Matroska files from other media files (@code{mkvmerge}).")
 (define-public x265
   (package
     (name "x265")
-    (version "3.1.1")
+    (version "3.1.2")
     (outputs '("out" "static"))
     (source
       (origin
         (method url-fetch)
-        (uri (string-append "https://download.videolan.org/videolan/x265/"
+        (uri (list (string-append "https://bitbucket.org/multicoreware/x265"
-                            "x265_" version ".tar.gz"))
+                                  "/downloads/x265_" version ".tar.gz")
+                   (string-append "https://download.videolan.org/videolan/x265/"
+                                  "x265_" version ".tar.gz")))
         (sha256
          (base32
-          "1l68lgdbsi4wjz5vad98ggx7mf92rnvzlq34m6w0a08ark3h0yc2"))
+          "1ajr59gjj47gnczfb2qhmzclj746pdiq9a1d81b0mq22k8f5yy3g"))
         (patches (search-patches "x265-arm-flags.patch"))
         (modules '((guix build utils)))
         (snippet '(begin
@@ -790,17 +792,18 @@ operate properly.")
 (define-public ffmpeg
   (package
     (name "ffmpeg")
-    (version "4.1.4")
+    (version "4.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "1qd7a10gs12ifcp31gramcgqjl77swskjfp7cijibgyg5yl4kw7i"))))
+               "1mgcxm7sqkajx35px05szsmn9mawwm03cfpmk3br7bcp3a1i0gq2"))))
     (build-system gnu-build-system)
     (inputs
-     `(("fontconfig" ,fontconfig)
+     `(("dav1d" ,dav1d)
+       ("fontconfig" ,fontconfig)
        ("freetype" ,freetype)
        ("frei0r-plugins" ,frei0r-plugins)
        ("gnutls" ,gnutls)
@@ -899,6 +902,7 @@ operate properly.")
          "--enable-libbluray"
          "--enable-libcaca"
          "--enable-libcdio"
+         "--enable-libdav1d"
          "--enable-libfreetype"
          "--enable-libmp3lame"
          "--enable-libopus"
@@ -981,9 +985,10 @@ audio/video codec library.")
     (arguments
      (substitute-keyword-arguments (package-arguments ffmpeg)
        ((#:configure-flags flags)
-        `(delete "--enable-libaom" ,flags))))
+        `(delete "--enable-libdav1d" (delete "--enable-libaom"
-    (inputs (alist-delete "libaom"
+                 ,flags)))))
-                          (package-inputs ffmpeg)))))
+    (inputs (alist-delete "dav1d" (alist-delete "libaom"
+                          (package-inputs ffmpeg))))))
 
 (define-public ffmpeg-for-stepmania
   (hidden-package
@@ -2061,12 +2066,6 @@ capabilities.")
        ("libass" ,libass)
        ("tesseract-ocr" ,tesseract-ocr)
        ("zimg" ,zimg)))
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     (home-page "http://www.vapoursynth.com/")
     (synopsis "Video processing framework")
     (description "VapourSynth is a C++ library and Python module for video
@@ -2509,12 +2508,6 @@ Other features include a live preview and live streaming.")
                (base32
                 "18yfkr70lr1x1hc8snn2ldnbzdcc7b64xmkqrfk8w59gpg7sl1xn"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen.sh
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)))
@@ -2894,10 +2887,7 @@ practically any type of media.")
          (add-after 'unpack 'change-to-build-dir
            (lambda _
              (chdir "Project/GNU/Library")
-             #t))
+             #t)))))
-         (add-after 'change-to-build-dir 'autogen
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
     (home-page "https://mediaarea.net/en/MediaInfo")
     (synopsis "Library for retrieving media metadata")
     (description "MediaInfo is a library used for retrieving technical

gnu/packages/virtualization.scm

@@ -390,16 +390,14 @@ manage system or application containers.")
 (define-public libvirt
   (package
     (name "libvirt")
-    (version "5.5.0")
+    (version "5.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://libvirt.org/sources/libvirt-"
                            version ".tar.xz"))
        (sha256
-        (base32 "1s1mzw4cmkcfivs1kphpgy4lpddx0w1qnjysr4ggk5558w4yy1i3"))
+        (base32 "1d5rmcx5fgb024hw8chbiv886n3jal5wp2yajjk5l4qh9s9gkx35"))))
-       (patches
-        (search-patches "libvirt-remove-ATTRIBUTE_UNUSED.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -523,15 +521,15 @@ three libraries:
 (define-public python-libvirt
   (package
     (name "python-libvirt")
-    (version "5.5.0")
+    (version "5.6.0")
     (source
      (origin
        (method url-fetch)
-       ;; The latest version hosted on PyPI at 5.5.0 release time was 5.3.0.
+       ;; The latest version hosted on PyPI at 5.6.0 release time was 5.5.0.
        (uri (string-append "https://libvirt.org/sources/python/libvirt-python-"
                            version ".tar.gz"))
        (sha256
-        (base32 "00x6idyw9xrrr21vrnsyw37q2sd8yh4n6pwh0l28hh9yp3nsy72n"))))
+        (base32 "11i440aibykxw22fzyavmrvn67s8rmnijw5bag0yx9r8jpnkzwad"))))
     (build-system python-build-system)
     (arguments
      `(#:phases

gnu/packages/vpn.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2013, 2016, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
@@ -227,11 +227,6 @@ the entire VPN in a network namespace accessible only through SSH.")
        ("automake" ,automake)))
     (inputs
      `(("libevent" ,libevent)))
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _ (invoke "sh" "autogen.sh"))))))
     (home-page "https://github.com/cernekee/ocproxy")
     (synopsis "OpenConnect proxy")
     (description
@@ -252,11 +247,12 @@ the user specifically asks to proxy, so the @dfn{VPN} interface no longer
             (sha256 (base32
                      "1wlypi68kqqg2mdck8wvf6aanhrmf9i7z6lngyxvcrp23jdzz34h"))))
    (build-system gnu-build-system)
-   (inputs
+   (propagated-inputs
     `(("libxml2" ,libxml2)
       ("gnutls" ,gnutls)
-      ("vpnc-scripts" ,vpnc-scripts)
       ("zlib" ,zlib)))
+   (inputs
+    `(("vpnc-scripts" ,vpnc-scripts)))
    (native-inputs
     `(("gettext" ,gettext-minimal)
       ("pkg-config" ,pkg-config)))

gnu/packages/wm.scm

@@ -131,20 +131,19 @@ the leaves of a full binary tree.")
 (define-public i3status
   (package
     (name "i3status")
-    (version "2.12")
+    (version "2.13")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://i3wm.org/i3status/i3status-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "06krpbijv4yi33nypg6qcn4hilcrdyarsdpd9fmr2cq46qaqiikg"))))
+                "0rhlzb96mw64z2jnhwz9nibc7pxg549626lz5642xxk5hpzwk2ff"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:make-flags (list "CC=gcc" (string-append "PREFIX=" %output))
+     `(;; XXX: Do an "out of source" build to work around
-       #:phases
+       ;; <https://github.com/i3/i3status/issues/339>.
-       (modify-phases %standard-phases
+       #:out-of-source? #t
-         (delete 'configure))
        #:tests? #f)) ; no test suite
     (inputs
      `(("openlibm" ,openlibm)
@@ -156,7 +155,10 @@ the leaves of a full binary tree.")
        ("libcap" ,libcap)
        ("asciidoc" ,asciidoc)))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("pkg-config" ,pkg-config)
+       ("docbook-xsl" ,docbook-xsl)
+       ("libxml2" ,libxml2)             ;for XML_CATALOG_FILES
+       ("xmlto" ,xmlto)))
     (home-page "https://i3wm.org/i3status/")
     (synopsis "Status bar for i3bar, dzen2, xmobar or similar programs")
     (description "i3status is a small program for generating a status bar for
@@ -171,14 +173,14 @@ commands would.")
 (define-public i3-wm
   (package
     (name "i3-wm")
-    (version "4.16.1")
+    (version "4.17")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://i3wm.org/downloads/i3-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "0xl56y196vxv001gvx35xwfr25zah8m3xwizp9ycdgdc0rfc4rdb"))))
+                "1z8qmkkq9dhqmqy8sjw3rnpnmnb8v7lr456bs0qzp23bgpj17gjf"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -288,8 +290,6 @@ Despite the name it should work with any X11 window manager.")
       (arguments
        `(#:make-flags (list "CC=gcc" (string-append "PREFIX=" %output))
          #:phases (modify-phases %standard-phases
-                    (add-after 'unpack 'autogen
-                      (lambda _ (invoke "sh" "autogen.sh")))
                     (add-after 'install 'install-doc
                       (lambda* (#:key outputs #:allow-other-keys)
                         (let* ((out (assoc-ref outputs "out"))

gnu/packages/xorg.scm

@@ -2909,8 +2909,8 @@ X server.")
 
 
 (define-public xf86-video-intel
-  (let ((commit "6afed33b2d673d88674f0c76efe500ae414e8e1b")
+  (let ((commit "6f4972d5c368c30e971a23c1dc370d3e43761282")
-        (revision "13"))
+        (revision "14"))
     (package
       (name "xf86-video-intel")
       (version (git-version "2.99.917" revision commit))
@@ -2923,7 +2923,7 @@ X server.")
                (commit commit)))
          (sha256
           (base32
-           "1s3fqlqzmql7s15m7qy21vai93n6q9f0ccpv0p353rwfx16mmf35"))
+           "0bc46qqglzfm4g9q4c2vgynvps2ng0xvlxnjpm9d6z4q6scdhz59"))
          (file-name (git-file-name name version))))
       (build-system gnu-build-system)
       (inputs `(("mesa" ,mesa)

gnu/tests/reconfigure.scm

@@ -19,8 +19,10 @@
 (define-module (gnu tests reconfigure)
   #:use-module (gnu bootloader)
   #:use-module (gnu services shepherd)
-  #:use-module (gnu system vm)
   #:use-module (gnu system)
+  #:use-module (gnu system accounts)
+  #:use-module (gnu system shadow)
+  #:use-module (gnu system vm)
   #:use-module (gnu tests)
   #:use-module (guix derivations)
   #:use-module (guix gexp)
@@ -43,7 +45,13 @@
 generation of the system profile."
   (define os
     (marionette-operating-system
-     (simple-operating-system)
+     (operating-system
+       (inherit (simple-operating-system))
+       (users (cons (user-account
+                     (name "jakob")
+                     (group "users")
+                     (home-directory "/home/jakob"))
+                    %base-user-accounts)))
      #:imported-modules '((gnu services herd)
                           (guix combinators))))
 
@@ -84,7 +92,25 @@ generation of the system profile."
 
             (test-equal "script created new generation"
               (length (system-generations marionette))
-              (1+ (length generations-prior))))
+              (1+ (length generations-prior)))
+
+            (test-assert "script activated the new generation"
+              (and (eqv? 'symlink
+                         (marionette-eval
+                          '(stat:type (lstat "/run/current-system"))
+                          marionette))
+                   (string= #$os
+                            (marionette-eval
+                             '(readlink "/run/current-system")
+                             marionette))))
+
+            (test-assert "script activated user accounts"
+              (marionette-eval
+               '(string-contains (call-with-input-file "/etc/passwd"
+                                   (lambda (port)
+                                     (get-string-all port)))
+                                 "jakob")
+               marionette)))
 
           (test-end)
           (exit (= (test-runner-fail-count (test-runner-current)) 0)))))

guix/build-system/texlive.scm

@@ -30,6 +30,7 @@
             texlive-build
             texlive-build-system
             texlive-ref
+            texlive-origin
             %texlive-tag
             %texlive-revision))
 
@@ -44,6 +45,20 @@
 (define %texlive-tag "texlive-2018.2")
 (define %texlive-revision 49435)
 
+(define (texlive-origin name version locations hash)
+  "Return an <origin> object for a TeX Live package consisting of multiple
+LOCATIONS with a provided HASH.  Use NAME and VERSION to compute a prettier
+name for the checkout directory."
+  (origin
+    (method svn-multi-fetch)
+    (uri (svn-multi-reference
+          (url (string-append "svn://www.tug.org/texlive/tags/"
+                              %texlive-tag "/Master/texmf-dist/"))
+          (locations locations)
+          (revision %texlive-revision)))
+    (file-name (string-append name "-" version "-checkout"))
+    (sha256 hash)))
+
 (define (texlive-ref component id)
   "Return a <svn-reference> object for the package ID, which is part of the
 given Texlive COMPONENT."

guix/build/svn.scm

@@ -36,7 +36,7 @@
   "Fetch REVISION from URL into DIRECTORY.  REVISION must be an integer, and a
 valid Subversion revision.  Return #t on success, #f otherwise."
   (apply invoke svn-command
-         "checkout" "--non-interactive"
+         "export" "--non-interactive"
          ;; Trust the server certificate.  This is OK as we
          ;; verify the checksum later.  This can be removed when
          ;; ca-certificates package is added.
@@ -46,13 +46,6 @@ valid Subversion revision.  Return #t on success, #f otherwise."
                        (string-append "--password=" password))
                  '())
            ,url ,directory))
-
-  ;; The contents of '.svn' vary as a function of the current status
-  ;; of the repo.  Since we want a fixed output, this directory needs
-  ;; to be taken out.
-  (with-directory-excursion directory
-    (for-each delete-file-recursively (find-files "." "^\\.svn$" #:directories? #t)))
-
   #t)
 
 ;;; svn.scm ends here

guix/scripts/deploy.scm

@@ -19,6 +19,7 @@
 
 (define-module (guix scripts deploy)
   #:use-module (gnu machine)
+  #:use-module (guix discovery)
   #:use-module (guix scripts)
   #:use-module (guix scripts build)
   #:use-module (guix store)
@@ -74,7 +75,10 @@ Perform the deployment specified by FILE.\n"))
 
 (define (load-source-file file)
   "Load FILE as a user module."
-  (let ((module (make-user-module '((gnu) (gnu machine) (gnu machine ssh)))))
+  (let* ((guix-path (dirname (search-path %load-path "guix.scm")))
+         (environment-modules (scheme-modules* guix-path "gnu/machine"))
+         (module (make-user-module (append '((gnu) (gnu machine))
+                                           environment-modules))))
     (load* file module)))
 
 (define (guix-deploy . args)

guix/scripts/system/reconfigure.scm

@@ -195,21 +195,31 @@ BOOTLOADER-PACKAGE."
                         (srfi srfi-34)
                         (srfi srfi-35))
            (let* ((gc-root (string-append #$target %gc-roots-directory "/bootcfg"))
-                  (temp-gc-root (string-append gc-root ".new")))
+                  (new-gc-root (string-append gc-root ".new")))
-             (switch-symlinks temp-gc-root gc-root)
+             ;; #$bootcfg has dependencies.
-             (install-boot-config #$bootcfg #$bootcfg-file #$target)
+             ;; The bootloader magically loads the configuration from
+             ;; (string-append #$target #$bootcfg-file) (for example
+             ;; "/boot/grub/grub.cfg").
+             ;; If we didn't do something special, the garbage collector
+             ;; would remove the dependencies of #$bootcfg.
+             ;; Register #$bootcfg as a GC root.
              ;; Preserve the previous activation's garbage collector root
              ;; until the bootloader installer has run, so that a failure in
              ;; the bootloader's installer script doesn't leave the user with
              ;; a broken installation.
+             (switch-symlinks new-gc-root #$bootcfg)
+             (install-boot-config #$bootcfg #$bootcfg-file #$target)
              (when #$installer
                (catch #t
                  (lambda ()
                    (#$installer #$bootloader-package #$device #$target))
                  (lambda args
-                   (delete-file temp-gc-root)
+                   (delete-file new-gc-root)
                    (apply throw args))))
-             (rename-file temp-gc-root gc-root)))))))
+             ;; We are sure that the installation of the bootloader
+             ;; succeeded, so we can replace the old GC root by the new
+             ;; GC root now.
+             (rename-file new-gc-root gc-root)))))))
 
 (define* (install-bootloader eval configuration bootcfg
                              #:key

guix/svn-download.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Sree Harsha Totakura <sreeharsha@totakura.in>
-;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,7 +32,14 @@
             svn-reference-url
             svn-reference-revision
             svn-fetch
-            download-svn-to-store))
+            download-svn-to-store
+
+            svn-multi-reference
+            svn-multi-reference?
+            svn-multi-reference-url
+            svn-multi-reference-revision
+            svn-multi-reference-locations
+            svn-multi-fetch))
 
 ;;; Commentary:
 ;;;
@@ -83,6 +90,54 @@ HASH-ALGO (a symbol).  Use NAME as the file name, or a generic name if #f."
                       #:guile-for-build guile
                       #:local-build? #t)))
 
+(define-record-type* <svn-multi-reference>
+  svn-multi-reference make-svn-multi-reference
+  svn-multi-reference?
+  (url        svn-multi-reference-url)                 ; string
+  (revision   svn-multi-reference-revision)            ; number
+  (locations  svn-multi-reference-locations)           ; list of strings
+  (user-name  svn-multi-reference-user-name (default #f))
+  (password   svn-multi-reference-password (default #f)))
+
+(define* (svn-multi-fetch ref hash-algo hash
+                          #:optional name
+                          #:key (system (%current-system)) (guile (default-guile))
+                          (svn (subversion-package)))
+  "Return a fixed-output derivation that fetches REF, a <svn-multi-reference>
+object.  The output is expected to have recursive hash HASH of type
+HASH-ALGO (a symbol).  Use NAME as the file name, or a generic name if #f."
+  (define build
+    (with-imported-modules '((guix build svn)
+                             (guix build utils))
+      #~(begin
+          (use-modules (guix build svn)
+                       (guix build utils)
+                       (srfi srfi-1))
+          (every (lambda (location)
+                   ;; The directory must exist if we are to fetch only a
+                   ;; single file.
+                   (unless (string-suffix? "/" location)
+                     (mkdir-p (string-append #$output "/" (dirname location))))
+                   (svn-fetch (string-append '#$(svn-multi-reference-url ref)
+                                             "/" location)
+                              '#$(svn-multi-reference-revision ref)
+                              (if (string-suffix? "/" location)
+                                  (string-append #$output "/" location)
+                                  (string-append #$output "/" (dirname location)))
+                              #:svn-command (string-append #+svn "/bin/svn")
+                              #:user-name #$(svn-multi-reference-user-name ref)
+                              #:password #$(svn-multi-reference-password ref)))
+                 '#$(svn-multi-reference-locations ref)))))
+
+  (mlet %store-monad ((guile (package->derivation guile system)))
+    (gexp->derivation (or name "svn-checkout") build
+                      #:system system
+                      #:hash-algo hash-algo
+                      #:hash hash
+                      #:recursive? #t
+                      #:guile-for-build guile
+                      #:local-build? #t)))
+
 (define* (download-svn-to-store store ref
                                 #:optional (name (basename (svn-reference-url ref)))
                                 #:key (log (current-error-port)))