Merge remote-tracking branch 'origin/master' into wip-texlive

author: Ricardo Wurmus <rekado@elephly.net> 2019-08-07 22:26:55 +0200
committer: Ricardo Wurmus <rekado@elephly.net> 2019-08-07 22:26:55 +0200
commit: 9bd1333e587c92fb3f0c12e080cb89e41713df01 (patch)
tree: f053e0174c052df046ef2ad320bcc5cdc8c76b01
parent: 378d94e51b00c30b19a39154278d01f1f3c4dbc1 (diff)
parent: 55e238f2ab24ce347047ebc7fd7c5eba62dac69d (diff)
download: guix-9bd1333e587c92fb3f0c12e080cb89e41713df01.tar.gz
24 files changed, 551 insertions, 334 deletions
diff --git a/doc/guix.texi b/doc/guix.texi
index cb60d5c7b7..734206a4b2 100644
--- a/doc/guix.texi
+++ b/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}
diff --git a/gnu/machine.scm b/gnu/machine.scm
index 0b79402b0a..30ae97f6ec 100644
--- a/gnu/machine.scm
+++ b/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>
-  (environment   machine-environment)  ; symbol
-  (configuration machine-configuration ; configuration object
-                 (default #f)))        ; specific to environment
+  (operating-system machine-operating-system) ; <operating-system>
+  (environment      machine-environment)      ; symbol
+  (configuration    machine-configuration     ; configuration object
+                    (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
diff --git a/gnu/machine/ssh.scm b/gnu/machine/ssh.scm
index 552eafa9de..274d56db26 100644
--- a/gnu/machine/ssh.scm
+++ b/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)
@@ -100,6 +104,145 @@ an environment type of 'managed-host."
 
 
 ;;;
+;;; 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)))
+
+
+;;;
 ;;; System deployment.
 ;;;
 
@@ -165,8 +308,9 @@ 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)))
-    (let* ((os (machine-system machine))
+  (mlet %store-monad ((_ (check-deployment-sanity 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))
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index c3b1e04901..393dcb21eb 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -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")
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index c6c42f66c6..fc0d6f80db 100644
--- a/gnu/packages/audio.scm
+++ b/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")))
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 74af02a47d..74620a2cbe 100644
--- a/gnu/packages/bioconductor.scm
+++ b/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)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bcec9cd279..956257d7bb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7458,13 +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
@@ -7525,13 +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")
@@ -7658,13 +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)
@@ -7819,13 +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)
@@ -7883,13 +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
@@ -7930,13 +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)
@@ -8354,13 +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
@@ -9418,14 +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
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3bd0d664da..4b998eb1fb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -78,14 +78,14 @@
 (define-public r-clipr
   (package
     (name "r-clipr")
-    (version "0.6.0")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "clipr" version))
        (sha256
         (base32
-         "0k9kimkmmj9k7290sxiqn4kd1vvm4w7q9a44wp0w30b7yjpavx2m"))))
+         "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
     (build-system r-build-system)
     (home-page "https://github.com/mdlincoln/clipr")
     (synopsis "Read and write from the system clipboard")
@@ -97,14 +97,14 @@ the system clipboards.")
 (define-public r-ellipsis
   (package
     (name "r-ellipsis")
-    (version "0.2.0")
+    (version "0.2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ellipsis" version))
        (sha256
         (base32
-         "0hdk79q4wn5nq52p8qd65kqz81l0b8gfzsbzyvmfais0p24qclib"))))
+         "0hx9l043433bwm1np9sypph77c7y9dddpz0wrhbkcv01x32jhr8f"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rlang" ,r-rlang)))
@@ -370,14 +370,14 @@ such as copy/paste from an R session.")
 (define-public r-callr
   (package
     (name "r-callr")
-    (version "3.2.0")
+    (version "3.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "callr" version))
        (sha256
         (base32
-         "1s5h2k7c1vgbry90xczin66q89cbkc6mvh4679l5rsz83087pd2b"))))
+         "0rvrlg86fxr5nadvqa0dr1iifqjs4d1rc32v76m3ccvx6m3xlq5z"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-r6" ,r-r6)
@@ -500,13 +500,13 @@ in systems and applications.")
 (define-public r-servr
   (package
     (name "r-servr")
-    (version "0.14")
+    (version "0.15")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "servr" version))
               (sha256
                (base32
-                "0zjjnfgas9d16fihksyk24kgkkqswb4sd0rz51id2ni1ymdyasjk"))))
+                "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-httpuv" ,r-httpuv)
@@ -614,13 +614,13 @@ LaTeX.")
 (define-public r-curl
   (package
     (name "r-curl")
-    (version "3.3")
+    (version "4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "curl" version))
               (sha256
                (base32
-                "1gd5i25anzi28lg1f8p7g63z9d46xi0qaw4lxpml5p0f52lvkc0c"))))
+                "0wb1j87fa2nd4a9x1w2nmc453nzvx6qiq8dviwc4jr36hsf9ra89"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -1205,14 +1205,14 @@ including functions for geolocation and routing.")
 (define-public r-haven
   (package
     (name "r-haven")
-    (version "2.1.0")
+    (version "2.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "haven" version))
        (sha256
         (base32
-         "0x5fwc4q2gdxwwp5sxdd6q17jhpisd769y9kv0xgnjcm0cdwz8f0"))))
+         "12h64r2v2451igyl7v4w2kg0hzw9rnanph0m7smffq29ybkv9g4h"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -1441,14 +1441,14 @@ processes.  Most of its code is based on the @code{psutil} Python package.")
 (define-public r-pkgbuild
   (package
     (name "r-pkgbuild")
-    (version "1.0.3")
+    (version "1.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgbuild" version))
        (sha256
         (base32
-         "0k8zwa66rm1ncx19ld5mbaxcjxkswiczpdqyssy44vl8k6scwfn9"))))
+         "0prvx91dha5pvd0k4jca2arkngvi6vnfs2indmiy3kwwzyjyyd19"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -1497,13 +1497,13 @@ you to rapidly iterate while developing a package.")
 (define-public r-rcpp
   (package
     (name "r-rcpp")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rcpp" version))
        (sha256
-        (base32 "015rmxns8mhmnd9wnz9bmma4iwx2sf4bcwkkp9hcgvdmblzf0vg7"))))
+        (base32 "170jlmjrs92z5qdv58badhxycjvfjpqwwpic7rm13pc9zkb3i4xd"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr))) ; for vignettes
@@ -2230,14 +2230,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).")
 (define-public r-lpsolve
   (package
     (name "r-lpsolve")
-    (version "5.6.13.1")
+    (version "5.6.13.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lpSolve" version))
        (sha256
         (base32
-         "1f10ywlaaldgjj84vs108ly0nsbkrdgbn5d6qj7nk93j1x1xrn3a"))))
+         "0fc5m259ayc880f5hvnq59ih6nb2rlp394n756n1khmxbjpw1w3m"))))
     (properties `((upstream-name . "lpSolve")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/lpSolve")
@@ -2315,14 +2315,14 @@ data).  Weighted versions of MLE, MME and QME are available.")
 (define-public r-energy
   (package
     (name "r-energy")
-    (version "1.7-5")
+    (version "1.7-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "energy" version))
        (sha256
         (base32
-         "15k9dg0a82cs9ypm0wpcsff3il1hzhnnv86dv5ngby1r144czhi4"))))
+         "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-boot" ,r-boot)
@@ -2450,14 +2450,14 @@ available in a vignette.")
 (define-public r-lava
   (package
     (name "r-lava")
-    (version "1.6.5")
+    (version "1.6.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lava" version))
        (sha256
         (base32
-         "13rlqdg42ylnz4hc932bl50xismrcr4d9ykcd9zs19cw5mckjx0f"))))
+         "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-numderiv" ,r-numderiv)
@@ -2640,20 +2640,41 @@ to access PostgreSQL database systems.")
     ;; under the PostgreSQL license.
     (license license:gpl2)))
 
+(define-public r-linprog
+  (package
+    (name "r-linprog")
+    (version "0.9-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "linprog" version))
+       (sha256
+        (base32
+         "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
+    (home-page "http://linprog.r-forge.r-project.org/")
+    (synopsis "Linear programming and optimization")
+    (description
+     "This package can be used to solve Linear Programming / Linear
+Optimization problems by using the simplex algorithm.")
+    (license license:gpl2+)))
+
 (define-public r-geometry
   (package
     (name "r-geometry")
-    (version "0.4.1")
+    (version "0.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "geometry" version))
        (sha256
         (base32
-         "0v3ivaw8vbjyxg08dd573qk3kqfyknj5hli9503dza6p6xz0dzmm"))))
+         "0vq334115qi039vy198ggv1dsp6n1s6jwcm9ivipf5r8lbm287zz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-magic" ,r-magic)
+       ("r-linprog" ,r-linprog)
        ("r-lpsolve" ,r-lpsolve)
        ("r-rcpp" ,r-rcpp)
        ("r-rcppprogress" ,r-rcppprogress)))
@@ -2871,14 +2892,14 @@ provides a one-row summary of model-level statistics.")
 (define-public r-recipes
   (package
     (name "r-recipes")
-    (version "0.1.5")
+    (version "0.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "recipes" version))
        (sha256
         (base32
-         "056zv4vhayyy8q9izcdknbb9hff2gxivg21g5mkssia78vw8g3mg"))))
+         "1ndz9h0zvdj141r63l8047wbhaj0x8fwzzyq7b8mh78pvrrdpq2i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -2890,7 +2911,6 @@ provides a one-row summary of model-level statistics.")
        ("r-magrittr" ,r-magrittr)
        ("r-matrix" ,r-matrix)
        ("r-purrr" ,r-purrr)
-       ("r-rcpproll" ,r-rcpproll)
        ("r-rlang" ,r-rlang)
        ("r-tibble" ,r-tibble)
        ("r-tidyr" ,r-tidyr)
@@ -3056,14 +3076,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.")
 (define-public r-jomo
   (package
     (name "r-jomo")
-    (version "2.6-8")
+    (version "2.6-9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "jomo" version))
        (sha256
         (base32
-         "097zfdcqc3a45ay8xxbraqh8xsfyivskkdmc2b4ca4n979lx8vyb"))))
+         "16ychdhhv8cii8zrdfdf5gzgnvmfaq573bmi00xqdf323q3lf3xr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lme4" ,r-lme4)
@@ -3129,14 +3149,14 @@ analysis of multiply imputed data sets.")
 (define-public r-mice
   (package
     (name "r-mice")
-    (version "3.5.0")
+    (version "3.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mice" version))
        (sha256
         (base32
-         "0icydc312sbvzbp0r0mhs2r77a2ly2xvz5w5amirz3wdkvgyrk2g"))))
+         "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
@@ -3212,14 +3232,14 @@ programming} (SQP) based solver).")
 (define-public r-hardyweinberg
   (package
     (name "r-hardyweinberg")
-    (version "1.6.2")
+    (version "1.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "HardyWeinberg" version))
        (sha256
         (base32
-         "15i7b444hikkfgqmx2ki827998xwra38k9v7a7kavwz6zmq5mmv9"))))
+         "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
     (properties `((upstream-name . "HardyWeinberg")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3289,14 +3309,14 @@ structure.")
 (define-public r-vioplot
   (package
     (name "r-vioplot")
-    (version "0.3.0")
+    (version "0.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vioplot" version))
        (sha256
         (base32
-         "1ddmmqq7qrnvr5q518afnysrl7ccr8am9njknv3dpwaqzcdr9akn"))))
+         "13kfjp747bnzksai8j39y2hyl3ljc6n53c2cfhaw78q3d63x0lbv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-sm" ,r-sm)
@@ -3631,14 +3651,14 @@ constants, and control debugging of packages via environment variables.")
 (define-public r-processx
   (package
     (name "r-processx")
-    (version "3.3.1")
+    (version "3.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "processx" version))
        (sha256
         (base32
-         "1bhbfacx2z2d97pz5bch45nvbvywhx2zp049czlfbdivkzgxn8v1"))))
+         "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ps" ,r-ps)
@@ -3839,18 +3859,19 @@ to variables on the left-hand side of the assignment.")
 (define-public r-vctrs
   (package
     (name "r-vctrs")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vctrs" version))
        (sha256
         (base32
-         "13w1r8zpalirpfaz5sykpn0mj4jmhxi2qkdcfq081ixlfjyzwa6c"))))
+         "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)
        ("r-digest" ,r-digest)
+       ("r-ellipsis" ,r-ellipsis)
        ("r-glue" ,r-glue)
        ("r-rlang" ,r-rlang)
        ("r-zeallot" ,r-zeallot)))
@@ -3877,14 +3898,14 @@ to variables on the left-hand side of the assignment.")
 (define-public r-pillar
   (package
     (name "r-pillar")
-    (version "1.4.1")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pillar" version))
        (sha256
         (base32
-         "0mcc09caxm69pghhz6b8vawj9ni63aijv5qba53pg4ph7rxclwgm"))))
+         "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -3923,14 +3944,14 @@ terminals.")
 (define-public r-tinytex
   (package
     (name "r-tinytex")
-    (version "0.14")
+    (version "0.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tinytex" version))
        (sha256
         (base32
-         "0aab7ybc6kkxxk3lzdmbla8zcpp6nmlahchc33miv28cmnqw363w"))))
+         "145dmgq7h55mmqqlnnj153j484x2a9s1fbvjbjkdyqzpnz9qh2ax"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-xfun" ,r-xfun)))
@@ -4628,14 +4649,14 @@ files.")
 (define-public r-shinyace
   (package
     (name "r-shinyace")
-    (version "0.3.3")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyAce" version))
        (sha256
         (base32
-         "02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j"))))
+         "0hvih5g0pswlnz5rf3blx5yqw11ssxvm8w4klxddp1ap20ncbgl1"))))
     (properties `((upstream-name . "shinyAce")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4678,14 +4699,14 @@ systems.")
 (define-public r-radiant-data
   (package
     (name "r-radiant-data")
-    (version "0.9.9")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "radiant.data" version))
        (sha256
         (base32
-         "17mgm0sggh4f7ihqmj9m3996p3pqc7h2cwx6ll1ha3kg5mx0znyn"))
+         "0b35jn4mcj10hqra18l8pi6s4pvj6fxipslbn6hkr4zza1z27gzw"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -5140,14 +5161,14 @@ misclassification probabilities of different models.")
 (define-public r-zip
   (package
     (name "r-zip")
-    (version "2.0.2")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "zip" version))
        (sha256
         (base32
-         "1xvgs7mhxi0sdp5ix4nisqm9lf8f75b7ip7b1hqpq9bzh0x6z8ix"))))
+         "0zii05jg9v9ljd0wd67g9x4bhlmpmsy5dzd093sbnc5n3vjbi32a"))))
     (build-system r-build-system)
     (home-page "https://github.com/gaborcsardi/zip")
     (synopsis "Cross-platform Zip compression")
@@ -5298,14 +5319,14 @@ promises, but with a syntax that is idiomatic R.")
 (define-public r-dosnow
   (package
     (name "r-dosnow")
-    (version "1.0.16")
+    (version "1.0.18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doSNOW" version))
        (sha256
         (base32
-         "13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n"))))
+         "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
     (properties `((upstream-name . "doSNOW")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5431,14 +5452,14 @@ obtain a better initial configuration in non-metric MDS.")
 (define-public r-reticulate
   (package
     (name "r-reticulate")
-    (version "1.12")
+    (version "1.13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reticulate" version))
        (sha256
         (base32
-         "0pqr1rcs8yg9nlh729mvlws93cqhpmv49j9bcgarh7vxzkwyv0kb"))))
+         "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
     (build-system r-build-system)
     (inputs `(("python" ,python)))
     (propagated-inputs
@@ -5548,14 +5569,14 @@ and adds the annotation to the plot.")
 (define-public r-ggpubr
   (package
     (name "r-ggpubr")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggpubr" version))
        (sha256
         (base32
-         "0a4dv6a752hwvc7l31xs7bgqhfzfdy94xp6wgwaxf5dxm46na7k1"))))
+         "0r5knv3707pmpngmj60zn761y3bh8lj89dhh1b80ss083xnxr4qw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cowplot" ,r-cowplot)
@@ -5569,6 +5590,7 @@ and adds the annotation to the plot.")
        ("r-magrittr" ,r-magrittr)
        ("r-polynom" ,r-polynom)
        ("r-purrr" ,r-purrr)
+       ("r-rlang" ,r-rlang)
        ("r-scales" ,r-scales)
        ("r-tidyr" ,r-tidyr)))
     (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
@@ -5628,14 +5650,14 @@ clustering.")
 (define-public r-factominer
   (package
     (name "r-factominer")
-    (version "1.41")
+    (version "1.42")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "FactoMineR" version))
        (sha256
         (base32
-         "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259"))))
+         "1yl16inb2m89l1czgaf0pgy9655dpr751hyx92yw6rqpd2ryznac"))))
     (properties `((upstream-name . "FactoMineR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5918,20 +5940,19 @@ to help insert or delete content at a specific location in the document.")
 (define-public r-abn
   (package
     (name "r-abn")
-    (version "1.3")
+    (version "2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abn" version))
        (sha256
         (base32
-         "1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm"))))
+         "08jlvb6i5f7ry2dwm0jgrnn2w95vr0l67dpx13n9878lz9ld131b"))))
     (build-system r-build-system)
     (inputs
      `(("gsl" ,gsl)))
     (propagated-inputs
-     `(("r-cairo" ,r-cairo)
-       ("r-lme4" ,r-lme4)
+     `(("r-lme4" ,r-lme4)
        ("r-mass" ,r-mass)
        ("r-nnet" ,r-nnet)
        ("r-rcpp" ,r-rcpp)
@@ -6070,14 +6091,14 @@ other add-on packages.")
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.3.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "1r288hc01cpyrk3nias30fw783z2vw20qr1k67vr65anh7mwm7vb"))))
+         "1lw1r3mb97z5p9z25jfzlhs0sbnwp6v8kzysf0am01x4m7l3iz82"))))
     (build-system r-build-system)
     (home-page "https://easystats.github.io/insight/")
     (synopsis "Easy access to model information for various model objects")
@@ -6527,14 +6548,14 @@ containing one or more SNPs that evolved under directional selection.")
 (define-public r-proc
   (package
     (name "r-proc")
-    (version "1.15.0")
+    (version "1.15.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pROC" version))
        (sha256
         (base32
-         "1dxxkwdhxfnj2znq4c5ggrr9m5klh5pmfxg17rz59vr2hfb73m24"))))
+         "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
     (properties `((upstream-name . "pROC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6900,14 +6921,14 @@ used to teach mathematics, statistics, computation and modeling.")
 (define-public r-raster
   (package
     (name "r-raster")
-    (version "2.9-5")
+    (version "2.9-23")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "raster" version))
        (sha256
         (base32
-         "0ljrymsp4zzaxdj1l0mw0a6hi88m5h0h920ixfzrg0szbyxqd0yk"))))
+         "1brqigic8ygr223bp2hgk5qjz3q03r4sfglrv4an0ghy7fgfralh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -7468,14 +7489,14 @@ multiple-imputation datasets.")
 (define-public r-magick
   (package
     (name "r-magick")
-    (version "2.0")
+    (version "2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "magick" version))
        (sha256
         (base32
-         "18y465325mhf48x2jn3jz9khwq1z2aj13wfbdkv8k3hln1sd572m"))))
+         "1pz71maz05gx4ds1wfw0alggc8nn2w75lj12dg1zr72s3kybhkzg"))))
     (build-system r-build-system)
     (inputs
      `(("imagemagick" ,imagemagick)
@@ -7857,14 +7878,14 @@ Hothorn, Westfall, 2010, CRC Press).")
 (define-public r-emmeans
   (package
     (name "r-emmeans")
-    (version "1.3.5.1")
+    (version "1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emmeans" version))
        (sha256
         (base32
-         "0rgzjvmp3yqhwgfg96v17wi8gbafzbrmz134shj2jsf5bsmw6vbj"))))
+         "1ynf9hhbch83k63lwps69ijfch30fk5v0sc418ck264c5vih26dh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-estimability" ,r-estimability)
@@ -8089,14 +8110,14 @@ differentiation.")
 (define-public r-bayestestr
   (package
     (name "r-bayestestr")
-    (version "0.2.2")
+    (version "0.2.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayestestR" version))
        (sha256
         (base32
-         "09r654lrhwwnshn5h2s2fbx3c8wigv3j4sva5hmfnkwjg8cclhd9"))))
+         "08d3bsb6li59n17bx1zrqnlnvniyb3vls9kl856km4chx3b2ff82"))))
     (properties `((upstream-name . "bayestestR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8114,14 +8135,14 @@ ROPE percentage and pd).")
 (define-public r-performance
   (package
     (name "r-performance")
-    (version "0.2.0")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "performance" version))
        (sha256
         (base32
-         "1pzd6z7i1jxr2xi1shg3d0bxlbpmjl7kpmwgjnfys6syv57znd1z"))))
+         "13j74ffhx950kacs86ixx84nviq9qlwzr7hjnhkmzw2hspjxq99w"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)
@@ -8141,14 +8162,14 @@ effects models and Bayesian models.")
 (define-public r-ggeffects
   (package
     (name "r-ggeffects")
-    (version "0.10.0")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggeffects" version))
        (sha256
         (base32
-         "0gmqzjk8k8q6j4q6asv9f3b1fv4qrw5w8xa48ha3y98shzm5np9k"))))
+         "1b0lxa8bljdh6h4lk7pql1lrhjlvh7p5c8qlgb8ac6ay8hb79vmi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -8175,14 +8196,14 @@ results using @code{ggplot2}.")
 (define-public r-sjplot
   (package
     (name "r-sjplot")
-    (version "2.6.3")
+    (version "2.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjPlot" version))
        (sha256
         (base32
-         "0h1mkmp5mrkbf7y3zh6m4cnm737cpg1m5si0lrmal7j2ixqicwjy"))))
+         "1m0gy991fmxvqry91kkzdkdapyalhrwql25d0hg2a2naxgfw4zpk"))))
     (properties `((upstream-name . "sjPlot")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8192,6 +8213,7 @@ results using @code{ggplot2}.")
        ("r-forcats" ,r-forcats)
        ("r-ggeffects" ,r-ggeffects)
        ("r-ggplot2" ,r-ggplot2)
+       ("r-ggrepel" ,r-ggrepel)
        ("r-glmmtmb" ,r-glmmtmb)
        ("r-insight" ,r-insight)
        ("r-knitr" ,r-knitr)
@@ -8311,14 +8333,14 @@ terminals that do not support Unicode.")
 (define-public r-usethis
   (package
     (name "r-usethis")
-    (version "1.5.0")
+    (version "1.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "usethis" version))
        (sha256
         (base32
-         "0pn6ka3726psaqlx573g6nxi90apf0rn5m4k2lz1jr66xdc19sag"))))
+         "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-clipr" ,r-clipr)
@@ -8674,14 +8696,14 @@ analysing multivariate abundance data in community ecology.")
 (define-public r-afex
   (package
     (name "r-afex")
-    (version "0.23-0")
+    (version "0.24-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "afex" version))
        (sha256
         (base32
-         "0yv4s7461swn0116y4wq9v139p1br5rr6hhnq1cmkbvybmwj2vp7"))))
+         "14w7kcwr5hxmjcjmdm5ia9ka3bw1nl18pxlm1vpw62nmvicn3455"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-car" ,r-car)
@@ -8908,14 +8930,14 @@ Bioconductor packages.")
 (define-public r-rgl
   (package
     (name "r-rgl")
-    (version "0.100.24")
+    (version "0.100.26")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rgl" version))
        (sha256
         (base32
-         "0nm3iyvhhmh0zlywkfmrq3vyh8z1l296xxfmcky0ifd2qnysfcqj"))))
+         "0h77akviwjd86j2qyx326xynbmwhypd6ydprzlwqnidd4ckrr271"))))
     (build-system r-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -9374,14 +9396,14 @@ maps.")
 (define-public r-tidytree
   (package
     (name "r-tidytree")
-    (version "0.2.4")
+    (version "0.2.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidytree" version))
        (sha256
         (base32
-         "04bznlfs617plv258nmsyq2pywnijcnzy2pbn5b2fgjk2xqkp29w"))))
+         "0vfjv33352dmk9cr2qn0knzg761068rdk6jg32csd9vpmcma8awp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ape" ,r-ape)
@@ -9442,14 +9464,14 @@ giving it a description in the specific format.")
 (define-public r-sparsesvd
   (package
     (name "r-sparsesvd")
-    (version "0.1-4")
+    (version "0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sparsesvd" version))
        (sha256
         (base32
-         "1yf373552wvdnd65r7hfcqa3v29dqn7jd4cn431mqd2acnqjrsam"))))
+         "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-matrix" ,r-matrix)))
     (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
@@ -9664,14 +9686,14 @@ diagnostics for controlling type-1 errors are also provided.")
 (define-public r-flare
   (package
     (name "r-flare")
-    (version "1.6.0")
+    (version "1.6.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "flare" version))
        (sha256
         (base32
-         "0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1"))))
+         "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-igraph" ,r-igraph)
@@ -9764,14 +9786,14 @@ Touzet and Varre (2007).")
 (define-public r-rnifti
   (package
     (name "r-rnifti")
-    (version "0.11.0")
+    (version "0.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RNifti" version))
        (sha256
         (base32
-         "0zs8ffa6gpi9cygxk7xjin6k3vpvfgb540a506zlk50bf6kc5nlf"))))
+         "0jcgdg5k2swmi57aqj347kfi1fc4nvag7pxdfz61kc0vqqamm0wg"))))
     (properties `((upstream-name . "RNifti")))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -9787,14 +9809,14 @@ used by other packages.")
 (define-public r-shades
   (package
     (name "r-shades")
-    (version "1.3.1")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shades" version))
        (sha256
         (base32
-         "0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv"))))
+         "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
     (build-system r-build-system)
     (home-page "https://github.com/jonclayden/shades")
     (synopsis "Simple color manipulation")
@@ -10143,23 +10165,51 @@ library.")
 and manipulating sets of ontological terms.")
     (license license:gpl2+)))
 
+(define-public r-gargle
+  (package
+    (name "r-gargle")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gargle" version))
+       (sha256
+        (base32
+         "0vqgp4w03sdyj0q96gxkybqflzzbaw84zifsbi7pxk5y08fimj2v"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-fs" ,r-fs)
+       ("r-glue" ,r-glue)
+       ("r-httr" ,r-httr)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-rlang" ,r-rlang)
+       ("r-withr" ,r-withr)))
+    (home-page "https://gargle.r-lib.org")
+    (synopsis "Utilities for working with Google APIs")
+    (description
+     "This package provides utilities for working with Google APIs.  This
+includes functions and classes for handling common credential types and for
+preparing, executing, and processing HTTP requests.")
+    (license license:expat)))
+
 (define-public r-bigrquery
   (package
     (name "r-bigrquery")
-    (version "1.1.1")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bigrquery" version))
        (sha256
         (base32
-         "1if39xkr231xmjq10fx2g7bgg4jgfd3wzx1p9g3pq4hbf2s6x0is"))))
+         "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
        ("r-bit64" ,r-bit64)
        ("r-curl" ,r-curl)
        ("r-dbi" ,r-dbi)
+       ("r-gargle" ,r-gargle)
        ("r-glue" ,r-glue)
        ("r-httr" ,r-httr)
        ("r-jsonlite" ,r-jsonlite)
@@ -10167,6 +10217,7 @@ and manipulating sets of ontological terms.")
        ("r-progress" ,r-progress)
        ("r-rapidjsonr" ,r-rapidjsonr)
        ("r-rcpp" ,r-rcpp)
+       ("r-rlang" ,r-rlang)
        ("r-tibble" ,r-tibble)))
     (home-page "https://github.com/rstats-db/bigrquery")
     (synopsis "R interface to Google's BigQuery API")
@@ -10724,14 +10775,14 @@ covariance functions for large data sets.")
 (define-public r-spatialextremes
   (package
     (name "r-spatialextremes")
-    (version "2.0-7")
+    (version "2.0-7.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "SpatialExtremes" version))
        (sha256
         (base32
-         "1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050"))))
+         "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
     (properties
      `((upstream-name . "SpatialExtremes")))
     (build-system r-build-system)
@@ -10994,14 +11045,14 @@ model with finite state space using the Aalen-Johansen estimator.")
 (define-public r-epi
   (package
     (name "r-epi")
-    (version "2.37")
+    (version "2.38")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Epi" version))
        (sha256
         (base32
-         "1lanr9x0c6w22406p56j7cwk6wck8njq6pscb4gzc613d68zj1lk"))))
+         "0ald9fjynrlyah8nzwfs49a08j4myd3c5bm56zn61gg5pyyhi8hd"))))
     (properties `((upstream-name . "Epi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11177,14 +11228,14 @@ them in distributed compute environments.")
 (define-public r-future
   (package
     (name "r-future")
-    (version "1.13.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future" version))
        (sha256
         (base32
-         "0h8ng2a6vg4axd5f75xcb3ip9d95zi22fa048dq2bzlnncwlznjz"))))
+         "1jyv2wlmpfqbk3hw269h4xg36na3wh1kd1lxmwdb40bsv4850lqa"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -11237,14 +11288,14 @@ machine or distributed on a compute cluster.")
 (define-public r-rsvd
   (package
     (name "r-rsvd")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rsvd" version))
        (sha256
         (base32
-         "1faskhf5j2bj9f971qljsmh182g3rnyilj1wwijz530a6skxidzz"))))
+         "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
@@ -11445,14 +11496,14 @@ identifying outliers.")
 (define-public r-bayesm
   (package
     (name "r-bayesm")
-    (version "3.1-1")
+    (version "3.1-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayesm" version))
        (sha256
         (base32
-         "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28"))))
+         "041ach2f2vrqzd5kz17v7wmkjz6z8cjjihpk4qvczm4cr9z85r2i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -11849,14 +11900,14 @@ probabilities from a standard bivariate normal CDF.")
 (define-public r-lavaan
   (package
     (name "r-lavaan")
-    (version "0.6-3")
+    (version "0.6-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lavaan" version))
        (sha256
         (base32
-         "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz"))))
+         "1zf0sxpms35rhq2syb7r3sshhc8kjvc3pv97dk9x0gf4xl7pck4g"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)
@@ -12073,14 +12124,14 @@ running IRkernel session.")
 (define-public r-irkernel
   (package
     (name "r-irkernel")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "IRkernel" version))
        (sha256
         (base32
-         "1gij59b068qp7sbn9d0b9ghmnhfks15a9anj7bp26acv0yvdsg3s"))))
+         "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp"))))
     (properties `((upstream-name . "IRkernel")))
     (build-system r-build-system)
     (arguments
@@ -12192,14 +12243,14 @@ R, enabling interactive analysis and visualization of genome-scale data.")
 (define-public r-rematch2
   (package
     (name "r-rematch2")
-    (version "2.0.1")
+    (version "2.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rematch2" version))
        (sha256
         (base32
-         "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6"))))
+         "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-tibble" ,r-tibble)))
@@ -12541,14 +12592,14 @@ classes.")
 (define-public r-classint
   (package
     (name "r-classint")
-    (version "0.3-3")
+    (version "0.4-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "classInt" version))
        (sha256
         (base32
-         "0c2z6shlxa928xa20yl956r06lx20mji3mwipdvmj3f4z5g6hgm9"))))
+         "00q1bpgblrldckn1rk166q1b0hgap2sjjyfmfcyh6ydk6y73ziir"))))
     (properties `((upstream-name . "classInt")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12616,14 +12667,14 @@ sampling.")
 (define-public r-deldir
   (package
     (name "r-deldir")
-    (version "0.1-21")
+    (version "0.1-23")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "deldir" version))
        (sha256
         (base32
-         "03392pl6j8rm3n32xrfkyfx866k1vm5sj87pva70yyiwh70vrnmr"))))
+         "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
     (home-page "https://cran.r-project.org/web/packages/deldir")
@@ -12640,14 +12691,14 @@ tessellation.")
 (define-public r-sf
   (package
     (name "r-sf")
-    (version "0.7-4")
+    (version "0.7-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sf" version))
        (sha256
         (base32
-         "0vnyr7xyfcl928kbrb1k8l4fkd0cjrfq486g6gxpvy5j0cc2h4i1"))))
+         "192hw52x1qlif8zyai1kff1wiyr3yl5f7jj1rk3k0nr8das0qy6i"))))
     (build-system r-build-system)
     (inputs
      `(("gdal" ,gdal)
@@ -13022,18 +13073,19 @@ inbred lines, F2 intercrosses, and association mapping populations.")
 (define-public r-ldheatmap
   (package
     (name "r-ldheatmap")
-    (version "0.99-5")
+    (version "0.99-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "LDheatmap" version))
        (sha256
         (base32
-         "0il3g3n3bzv74lz7dlhyiwc2x2417v6yhx2g47pahxdzqa09kf4s"))))
+         "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
     (properties `((upstream-name . "LDheatmap")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-genetics" ,r-genetics)
+       ("r-rcpp" ,r-rcpp)
        ("r-snpstats" ,r-snpstats)))
     (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
     (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
@@ -13112,13 +13164,13 @@ SELECT or UPDATE queries to an end-point.")
 (define-public r-bookdown
   (package
     (name "r-bookdown")
-    (version "0.11")
+    (version "0.12")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "bookdown" version))
               (sha256
                (base32
-                "0w4fkv5fqiaqgkx44p0s161imf29zir9742126xkz1pl1j25jn1r"))))
+                "1c2v0rpa1rrpbx8yb66sfvrf4gf57f6a8x7ydjqqbkbwhxdlrsrq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-htmltools" ,r-htmltools)
@@ -13585,14 +13637,14 @@ package.")
 (define-public r-ggplotify
   (package
     (name "r-ggplotify")
-    (version "0.0.3")
+    (version "0.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggplotify" version))
        (sha256
         (base32
-         "14hqlpvnaq5psz1ljcpw9isa06827rg3fm5c1dx159rsjfi56yby"))))
+         "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -14562,14 +14614,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "0.4")
+    (version "0.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "1mr8lqq8s4aacmh7xdhmkmv8vsjqjczlqlaw27xnsljgj2kgq87a"))))
+         "04i17ni8g595jj8dxdfwr9vsxmdn2kkam90ab68vlwws3ywqjl6r"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
     (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
@@ -14588,14 +14640,14 @@ and model output.")
 (define-public r-enrichr
   (package
     (name "r-enrichr")
-    (version "1.0")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "enrichR" version))
        (sha256
         (base32
-         "0lfdr45sdyqhvgz8q4qdbk12mpv86d6id665kq6aaslgr8jggfmn"))))
+         "056m6hksfss29fj7zvlk7pbh8g3gq84kjh3240isrsnhp9m1h9iz"))))
     (properties `((upstream-name . "enrichR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14698,18 +14750,17 @@ into R and converted to @code{BibEntry} objects.")
 (define-public r-citr
   (package
     (name "r-citr")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "citr" version))
        (sha256
         (base32
-         "0pik6s6xk5768s3kkppw2192dj455py53gsn6k2b7xgg96ircy0g"))))
+         "0p2sg0fl7cppxxmr20qyqzs2469kglmgpsvykynw4qx501as57rc"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
-       ("r-bibtex" ,r-bibtex)
        ("r-curl" ,r-curl)
        ("r-httr" ,r-httr)
        ("r-miniui" ,r-miniui)
@@ -14729,14 +14780,14 @@ the current document.")
 (define-public r-xgboost
   (package
     (name "r-xgboost")
-    (version "0.82.1")
+    (version "0.90.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xgboost" version))
        (sha256
         (base32
-         "0plhx63wcm4syslzmjfv6bdgaqn96fnav048hrj0vxk4dzgfp8sq"))))
+         "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-data-table" ,r-data-table)
diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index 8d0162a2d1..257591c8d3 100644
--- a/gnu/packages/emulators.scm
+++ b/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")
-        (revision "5"))
+  (let ((commit "24718c1a389e4f51db974575cd15c372485b92e2")
+        (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)))
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 8005c46129..edb3b49841 100644
--- a/gnu/packages/geo.scm
+++ b/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)))
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index d4273c6fa1..6928246509 100644
--- a/gnu/packages/image.scm
+++ b/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"
@@ -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
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 9f20d2bace..a5b9f6bfed 100644
--- a/gnu/packages/linux.scm
+++ b/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 "5.2.6")
+(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 "1whzgdz1wnjzkb78yqz4xs3mad02rv17ksmwaf4ykp4lfgxml45y")))
+        (hash (base32 "1aazhf0v8bv4py0wnqkdmiy80fchnix431l0hda2fkwsdf9njgnv")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.2)))
 
-(define-public linux-libre-4.19-version "4.19.64")
+(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 "1gasmcdsrsk81dscslmrsxqsvkfp5xxdx3ay95izggpk7piqnvvs")))
+        (hash (base32 "1pyyhr2airxzk4c6n7140yl723dc7yw7igy5i5i2ih0nd4c3k6g5")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
 
-(define-public linux-libre-4.14-version "4.14.136")
+(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 "0w6z5fhwqgpqnz2js8vj9j5dl6isx8n7rnzrm0vr9r8njaazz396")))
+        (hash (base32 "0a72pab0zxy28i02glnzj6avzcf0a4gxxnadbdd343rh549yky4k")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))
 
-(define-public linux-libre-4.9-version "4.9.187")
+(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 "1iyimwl4ysnk6m66m73sg0cnp4vac56d6yy174shfpnj5h2csjq1")))
+        (hash (base32 "08p2cfc9982b804vmkapfasgipf6969g625ih7z3062xn99rhlr7")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.9)))
 
-(define-public linux-libre-4.4-version "4.4.187")
+(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 "1dlzb5yzcsicd41myj3q4dq2ql8xcc49brs5f7xjmc5ynvvjjgnc")))
+        (hash (base32 "1llxamm62kgqd7dig98n8m16qas8dd8rrkmwpfcdgyf8rag216ff")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.4)))
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index dd5ee1e9ee..e48c91a2cf 100644
--- a/gnu/packages/machine-learning.scm
+++ b/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))
-           (add-after 'disable-broken-tests 'autogen
-             (lambda _
-               (invoke "bash" "autogen.sh"))))))
+               #t)))))
       (inputs
        `(("python" ,python-2) ; only Python 2 is supported
          ("libxml2" ,libxml2)))
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 40fe7d9450..b81b15d80c 100644
--- a/gnu/packages/mail.scm
+++ b/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"))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
+                                              "/lib/dovecot"))))
     (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"))
-         #:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'autogen
-             (lambda _
-               (invoke "sh" "autogen.sh"))))))
+                                                "/lib/dovecot"))))
       (home-page "https://github.com/LuckyFellow/dovecot-libsodium-plugin")
       (synopsis "Libsodium password hashing schemes plugin for Dovecot")
       (description
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index b204b314c6..e3c7d9ce91 100644
--- a/gnu/packages/maths.scm
+++ b/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
diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 2a40b2c736..5628a4b93f 100644
--- a/gnu/packages/perl.scm
+++ b/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")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6ed1e40108..f27f2229f7 100644
--- a/gnu/packages/statistics.scm
+++ b/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)
@@ -396,14 +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")
@@ -501,14 +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")
@@ -587,14 +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)))
@@ -803,13 +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.
@@ -1602,18 +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)
@@ -1695,13 +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)
@@ -1978,13 +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)))
@@ -2020,14 +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)
@@ -2135,14 +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)))
@@ -2332,14 +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)))
@@ -2365,13 +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)
@@ -2391,20 +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
-       ("openssl" ,openssl)
+     `(("libgit2" ,libgit2)
        ("zlib" ,zlib)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -2437,13 +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)
@@ -2456,9 +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")
@@ -2489,18 +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
@@ -2596,13 +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
@@ -2694,14 +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
@@ -2787,17 +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
@@ -2809,13 +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
@@ -3068,14 +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")
@@ -3088,14 +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)
@@ -3116,14 +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
@@ -3139,14 +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
@@ -3162,13 +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)
@@ -3176,6 +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")
@@ -3314,14 +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)
@@ -4565,19 +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")
@@ -4639,14 +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")
@@ -4748,14 +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)))
@@ -4918,14 +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)
@@ -5024,14 +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")
@@ -5137,14 +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)))
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index df8d1e4b79..9077d295db 100644
--- a/gnu/packages/terminals.scm
+++ b/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)
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 04715a5ce1..eda5b8fc39 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -792,17 +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)
@@ -901,6 +902,7 @@ operate properly.")
          "--enable-libbluray"
          "--enable-libcaca"
          "--enable-libcdio"
+         "--enable-libdav1d"
          "--enable-libfreetype"
          "--enable-libmp3lame"
          "--enable-libopus"
@@ -983,9 +985,10 @@ audio/video codec library.")
     (arguments
      (substitute-keyword-arguments (package-arguments ffmpeg)
        ((#:configure-flags flags)
-        `(delete "--enable-libaom" ,flags))))
-    (inputs (alist-delete "libaom"
-                          (package-inputs ffmpeg)))))
+        `(delete "--enable-libdav1d" (delete "--enable-libaom"
+                 ,flags)))))
+    (inputs (alist-delete "dav1d" (alist-delete "libaom"
+                          (package-inputs ffmpeg))))))
 
 (define-public ffmpeg-for-stepmania
   (hidden-package
@@ -2063,12 +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
@@ -2511,12 +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)))
@@ -2896,10 +2887,7 @@ practically any type of media.")
          (add-after 'unpack 'change-to-build-dir
            (lambda _
              (chdir "Project/GNU/Library")
-             #t))
-         (add-after 'change-to-build-dir 'autogen
-           (lambda _
-             (invoke "sh" "autogen.sh"))))))
+             #t)))))
     (home-page "https://mediaarea.net/en/MediaInfo")
     (synopsis "Library for retrieving media metadata")
     (description "MediaInfo is a library used for retrieving technical
diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index c7046b7f50..d1a7248536 100644
--- a/gnu/packages/vpn.scm
+++ b/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)))
diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index c56cf406ee..160c267882 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -290,8 +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"))
diff --git a/gnu/tests/reconfigure.scm b/gnu/tests/reconfigure.scm
index 3a2f0a2e53..fb11e6164e 100644
--- a/gnu/tests/reconfigure.scm
+++ b/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)))))
diff --git a/guix/scripts/deploy.scm b/guix/scripts/deploy.scm
index 52bba3f3bf..ebc99e52cc 100644
--- a/guix/scripts/deploy.scm
+++ b/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)
diff --git a/guix/scripts/system/reconfigure.scm b/guix/scripts/system/reconfigure.scm
index dee0c24bd2..579b7fffbe 100644
--- a/guix/scripts/system/reconfigure.scm
+++ b/guix/scripts/system/reconfigure.scm
@@ -195,21 +195,31 @@ BOOTLOADER-PACKAGE."
                         (srfi srfi-34)
                         (srfi srfi-35))
            (let* ((gc-root (string-append #$target %gc-roots-directory "/bootcfg"))
-                  (temp-gc-root (string-append gc-root ".new")))
-             (switch-symlinks temp-gc-root gc-root)
-             (install-boot-config #$bootcfg #$bootcfg-file #$target)
+                  (new-gc-root (string-append gc-root ".new")))
+             ;; #$bootcfg has dependencies.
+             ;; The bootloader magically loads the configuration from
+             ;; (string-append #$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
author	Ricardo Wurmus <rekado@elephly.net>	2019-08-07 22:26:55 +0200
committer	Ricardo Wurmus <rekado@elephly.net>	2019-08-07 22:26:55 +0200
commit	9bd1333e587c92fb3f0c12e080cb89e41713df01 (patch)
tree	f053e0174c052df046ef2ad320bcc5cdc8c76b01
parent	378d94e51b00c30b19a39154278d01f1f3c4dbc1 (diff)
parent	55e238f2ab24ce347047ebc7fd7c5eba62dac69d (diff)
download	guix-9bd1333e587c92fb3f0c12e080cb89e41713df01.tar.gz