Merge branch 'master' into staging
authorMarius Bakke <mbakke@fastmail.com>
Wed, 22 Aug 2018 16:14:04 +0000 (18:14 +0200)
committerMarius Bakke <mbakke@fastmail.com>
Wed, 22 Aug 2018 16:14:04 +0000 (18:14 +0200)
1  2 
gnu/packages/algebra.scm
gnu/packages/databases.scm
gnu/packages/gnome.scm
gnu/packages/gtk.scm
gnu/packages/statistics.scm
gnu/packages/xdisorg.scm

diff --combined gnu/packages/algebra.scm
@@@ -399,15 -399,21 +399,21 @@@ matrices, and polynomials over the inte
  (define-public singular
    (package
     (name "singular")
-    (version "4.0.3")
-    (source (origin
-             (method url-fetch)
-             (uri (string-append "http://www.mathematik.uni-kl.de/ftp/pub/"
-                                 "Math/Singular/SOURCES/"
-                                 (string-join (string-split version #\.) "-")
-                                 "/singular-" version ".tar.gz"))
-             (sha256 (base32
-                      "0viidy2fz62rln9p0s9qfs7fnm55c6fw1agydd1py26gxylp1ksc"))))
+    (version "4.1.1p3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
+                       "Singular/SOURCES/"
+                       (string-join
+                        (string-split
+                         (string-trim-right version #\p
+                                            0 (1- (string-length version)))
+                         #\.) "-")
+                       "/singular-" version ".tar.gz"))
+              (sha256 (base32
+                       "1qqj9bm9pkzm0iyycpvm8x6s79wws3nq60lz25h8x1q61h3426sm"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
@@@ -522,14 -528,14 +528,14 @@@ a C program."
  (define-public fftw
    (package
      (name "fftw")
 -    (version "3.3.7")
 +    (version "3.3.8")
      (source (origin
               (method url-fetch)
               (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
                                   version".tar.gz"))
               (sha256
                (base32
 -               "0wsms8narnbhfsa8chdflv2j9hzspvflblnqdn7hw8x5xdzrnq1v"))))
 +               "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
      (build-system gnu-build-system)
      (arguments
       `(#:configure-flags
@@@ -697,16 -703,15 +703,15 @@@ Sine Transform} (DST) and @dfn{Discret
  (define-public eigen
    (package
      (name "eigen")
-     (version "3.3.4")
+     (version "3.3.5")
      (source (origin
                (method url-fetch)
                (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
                                    version ".tar.bz2"))
                (sha256
                 (base32
-                 "19m4406jvqnwh7kpcvx1lfx2vdc5zwia5q9ayv89bimg1gmln9fx"))
+                 "1qh3yrwn78ms5yhwbpl5wvblk4gbz02cacdygxylr7i9xbrvylkk"))
                (file-name (string-append name "-" version ".tar.bz2"))
-             (patches (search-patches "eigen-arm-neon-fixes.patch"))
                (modules '((guix build utils)))
                (snippet
                 ;; There are 3 test failures in the "unsupported" directory,
                    (substitute* "unsupported/CMakeLists.txt"
                      (("add_subdirectory\\(test.*")
                       "# Do not build the tests for unsupported features.\n"))
-                 (substitute* "CMakeLists.txt"
-                     ;; Work around
-                     ;; <http://eigen.tuxfamily.org/bz/show_bug.cgi?id=1114>.
-                     (("\"include/eigen3\"")
-                      "\"${CMAKE_INSTALL_PREFIX}/include/eigen3\""))
-                 (substitute* "test/bdcsvd.cpp"
-                     ;; See
-                     ;; https://bitbucket.org/eigen/eigen/commits/ea8c22ce6920e982d15245ee41d0531a46a28e5d
-                     ((".*svd_preallocate[^\n]*" &)
-                      (string-append "//" & " // Not supported by BDCSVD")))
                    #t))))
      (build-system cmake-build-system)
      (arguments
                        (setenv "EIGEN_SEED" "1") ;for reproducibility
                          ;; First build the tests, in parallel.  See
                          ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
-                         (and (zero? (system* "make" "buildtests" dash-j))
+                         (invoke "make" "buildtests" dash-j)
  
-                              ;; Then run 'CTest' with -V so we get more
-                              ;; details upon failure.
-                              (zero? (system* "ctest" "-V" dash-j)))))))))
+                         ;; Then run 'CTest' with -V so we get more
+                         ;; details upon failure.
+                         (invoke "ctest" "-V" dash-j)))))))
      (home-page "https://eigen.tuxfamily.org")
      (synopsis "C++ template library for linear algebra")
      (description
@@@ -761,16 -756,16 +756,16 @@@ features, and more."
  (define-public xtensor
    (package
      (name "xtensor")
-     (version "0.15.9")
+     (version "0.17.1")
      (source (origin
-               (method url-fetch)
-               (uri (string-append
-                     "https://github.com/QuantStack/xtensor/archive/"
-                     version ".tar.gz"))
+               (method git-fetch)
+               (uri (git-reference
+                     (url "https://github.com/QuantStack/xtensor.git")
+                     (commit version)))
                (sha256
                 (base32
-                 "0mlsw4p1w5mh7pscddfdamz27zq3wml5qla3vbzgvif34vsqc8ra"))
-               (file-name (string-append name "-" version ".tar.gz"))))
+                 "0w40v5lp0hp8ihf8nnvak373sb5xx0768pxgiqh3nzn57wf8px4r"))
+               (file-name (git-file-name name version))))
      (build-system cmake-build-system)
      (native-inputs
       `(("googletest" ,googletest)
@@@ -84,6 -84,7 +84,7 @@@
    #:use-module (gnu packages pkg-config)
    #:use-module (gnu packages popt)
    #:use-module (gnu packages python)
+   #:use-module (gnu packages python-crypto)
    #:use-module (gnu packages rdf)
    #:use-module (gnu packages readline)
    #:use-module (gnu packages ruby)
@@@ -548,10 -549,26 +549,26 @@@ RDBMS systems (which are deep in functi
                     ;; Some parts are licensed under the Apache License
                     license:asl2.0))))
  
+ (define boost-for-mysql
+   (package
+     (inherit boost)
+     (version "1.59.0")
+     (source (origin
+               (method url-fetch)
+               (uri (string-append
+                     "mirror://sourceforge/boost/boost/" version "/boost_"
+                     (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version)
+                     ".tar.bz2"))
+               (sha256
+                (base32
+                 "1jj1aai5rdmd72g90a3pd8sw9vi32zad46xv5av8fhnr48ir6ykj"))))))
+ ;; XXX When updating, check whether boost-for-mysql is still needed.
+ ;; It might suffice to patch ‘cmake/boost.cmake’ as done in the past.
  (define-public mysql
    (package
      (name "mysql")
-     (version "5.7.21")
+     (version "5.7.23")
      (source (origin
               (method url-fetch)
               (uri (list (string-append
                            name "-" version ".tar.gz")))
               (sha256
                (base32
-                "1dq9bgnajf7cq3mrjkwv6w5nwslhs26lkrw56i7w4fbsq9wm087s"))))
+                "0rbc3xsc11lq2dm0ip6gxa16c06hi74scb97x5cw7yhbabaz4c07"))))
      (build-system cmake-build-system)
      (arguments
       `(#:configure-flags
           "-DINSTALL_MYSQLTESTDIR="
           "-DINSTALL_SQLBENCHDIR=")
         #:phases (modify-phases %standard-phases
-                   (add-after
-                    'unpack 'patch-boost-version
-                    (lambda _
-                      ;; Mysql wants boost-1.59.0 specifically
-                      (substitute* "cmake/boost.cmake"
-                        (("59")
-                         ,(match (string-split (package-version boost) #\.)
-                            ((_ minor . _) minor))))
-                      #t))
                    (add-after
                     'install 'remove-extra-binaries
                     (lambda* (#:key outputs #:allow-other-keys)
       `(("bison" ,bison)
         ("perl" ,perl)))
      (inputs
-      `(("boost" ,boost)
+      `(("boost" ,boost-for-mysql)
         ("libaio" ,libaio)
         ("ncurses" ,ncurses)
         ("openssl" ,openssl)
@@@ -779,8 -787,8 +787,8 @@@ Language."
                  (for-each delete-file-recursively
                            '("data" "mysql-test" "sql-bench"
                              "share/man/man1/mysql-test-run.pl.1"))
 -                ;; Delete huge mysqltest executables.
 -                (for-each delete-file (find-files "bin" "test"))
 +                ;; Delete huge and unnecessary executables.
 +                (for-each delete-file (find-files "bin" "(test|embedded)"))
                  ;; And static libraries.
                  (for-each delete-file (find-files "lib" "\\.a$")))
                #t))))))
         ("libaio" ,libaio)
         ("libxml2" ,libxml2)
         ("ncurses" ,ncurses)
 -       ("openssl" ,openssl)
         ("pcre" ,pcre)
         ("snappy" ,snappy)
         ("xz" ,xz)
         ("zlib" ,zlib)))
 +    (propagated-inputs
 +     ;; mariadb.pc says -lssl -lcrypto, so propagate it.
 +     `(("openssl" ,openssl)))
      ;; The test suite is very resource intensive and can take more than three
      ;; hours on a x86_64 system.  Give slow and busy machines some leeway.
      (properties '((timeout . 64800)))        ;18 hours
@@@ -867,6 -873,34 +875,34 @@@ pictures, sounds, or video."
                 (base32
                  "0biy8j69dbvdmrag55pdszpc0702agzqhhcwdx21xp02mzim4ydr"))))))
  
+ (define-public python-pymysql
+   (package
+     (name "python-pymysql")
+     (version "0.9.2")
+     (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "PyMySQL" version))
+        (sha256
+         (base32
+          "0gvi63f1zq1bbd30x28kqyx351hal1yc323ckp0mihainb5n1iwy"))))
+     (build-system python-build-system)
+     (native-inputs
+      `(("python-unittest2" ,python-unittest2)))
+     (inputs
+      `(("python-cryptography" ,python-cryptography)))
+     (arguments
+      `(#:tests? #f))                    ; tests expect a running MySQL
+     (home-page "https://github.com/PyMySQL/PyMySQL/")
+     (synopsis "Pure-Python MySQL driver")
+     (description
+      "PyMySQL is a pure-Python MySQL client library, based on PEP 249.
+ Most public APIs are compatible with @command{mysqlclient} and MySQLdb.")
+     (license license:expat)))
+ (define-public python2-pymysql
+   (package-with-python2 python-pymysql))
  (define-public qdbm
    (package
      (name "qdbm")
@@@ -1113,6 -1147,37 +1149,37 @@@ for example from a shell script."
      ;; others (like sparql-query.c) contain a GPLv2+ license header.
      (license (list license:gpl3+))))
  
+ (define-public sqlcrush
+   ;; Unfortunately, there is no proper upstream release and may never be.
+   (let ((commit "b5f6868f189566a26eecc78d0f0659813c1aa98a")
+         (revision "1"))
+     (package
+       (name "sqlcrush")
+       (version (git-version "0.1.5" revision commit))
+       (source (origin
+                 (method git-fetch)
+                 (uri (git-reference
+                       (url "https://github.com/coffeeandscripts/sqlcrush.git")
+                       (commit commit)))
+                 (file-name (git-file-name name version))
+                 (sha256
+                  (base32
+                   "0x3wy40r93p0jv3nbwj9a77wa4ff697d13r0wffmm7q9h3mzsww8"))))
+       (build-system python-build-system)
+       (inputs
+        `(("python-cryptography" ,python-cryptography)
+          ("python-psycopg2" ,python-psycopg2)
+          ("python-pymysql" ,python-pymysql)
+          ("python-sqlalchemy" ,python-sqlalchemy)))
+       (home-page "https://github.com/coffeeandscripts/sqlcrush")
+       (synopsis "Text console-based database viewer and editor")
+       (description
+        "SQLcrush lets you view and edit a database directly from the text
+ console through an ncurses interface.  You can explore each table's structure,
+ browse and edit the contents, add and delete entries, all while tracking your
+ changes.")
+       (license license:gpl3+)))) ; no headers, see README.md
  (define-public sqlite
    (package
     (name "sqlite")
@@@ -1432,7 -1497,7 +1499,7 @@@ columns, primary keys, unique constrain
  (define-public perl-dbd-sqlite
    (package
      (name "perl-dbd-sqlite")
-     (version "1.54")
+     (version "1.58")
      (source (origin
                (method url-fetch)
                (uri (string-append
                      version ".tar.gz"))
                (sha256
                 (base32
-                 "0sbj9lx9syzpknvjv8cz9jndg32qz775vy2prgq305npv3dsca9r"))))
+                 "0fqx386jgs9mmrknr7smmzapf07izgivza7x08lfm39ks2cxs83i"))))
      (build-system perl-build-system)
      (inputs `(("sqlite" ,sqlite)))
      (propagated-inputs `(("perl-dbi" ,perl-dbi)))
@@@ -1534,7 -1599,7 +1601,7 @@@ valid SQL query."
  (define-public unixodbc
    (package
     (name "unixodbc")
 -   (version "2.3.6")
 +   (version "2.3.7")
     (source (origin
              (method url-fetch)
              (uri
                "ftp://ftp.unixodbc.org/pub/unixODBC/unixODBC-"
                version ".tar.gz"))
              (sha256
 -             (base32 "0sads5b8cmmj526gyjba7ccknl1vbhkslfqshv1yqln08zv3gdl8"))))
 +             (base32 "0xry3sg497wly8f7715a7gwkn2k36bcap0mvzjw74jj53yx6kwa5"))))
     (build-system gnu-build-system)
     (synopsis "Data source abstraction library")
     (description "Unixodbc is a library providing an API with which to access
@@@ -1955,14 -2020,14 +2022,14 @@@ for ODBC."
  (define-public python-pyodbc
    (package
      (name "python-pyodbc")
-     (version "4.0.21")
+     (version "4.0.24")
      (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pyodbc" version))
         (sha256
          (base32
-          "0a83zwz3h1agshnsc6r7al6q83222w8601gpzzzjvjz5m56ghmcn"))
+          "1m311vi7vpay1j7rkq71fpsk0gb7454k4lldk5b63hyy6yvsn9j3"))
         (file-name (string-append name "-" version ".tar.gz"))))
      (build-system python-build-system)
      (inputs
@@@ -2122,7 -2187,7 +2189,7 @@@ implementation for Python."
  (define-public virtuoso-ose
    (package
      (name "virtuoso-ose")
-     (version "7.2.4.2")
+     (version "7.2.5")
      (source
       (origin
         (method url-fetch)
               "https://github.com/openlink/virtuoso-opensource/releases/"
               "download/v" version "/virtuoso-opensource-" version ".tar.gz"))
         (sha256
-         (base32 "12dqam1gc1v93l0bj0vlpvjqppki6y1hqrlznywxnw0rrz9pb002"))))
+         (base32 "0r1xakclkfi69pzh8z2k16z3x0m49pxp764icj0ad4w4bb97fr42"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f ; Tests require a network connection.
@@@ -2169,6 -2234,9 +2236,6 @@@ and web services platform functionality
       `(("pkg-config" ,pkg-config)))
      (inputs
       `(("mariadb" ,mariadb)
 -       ;; FIXME: This should be propagated from MariaDB, but add it here
 -       ;; for now to prevent a large rebuild.
 -       ("openssl" ,openssl)
         ("zlib" ,zlib)))
      (propagated-inputs
       `(("r-dbi" ,r-dbi)))
@@@ -2533,14 -2601,14 +2600,14 @@@ database)."
  (define-public python-mysqlclient
    (package
      (name "python-mysqlclient")
-     (version "1.3.10")
+     (version "1.3.13")
      (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "mysqlclient" version))
         (sha256
          (base32
-          "0qkj570x4rbsblji6frvsvp2v1ap32dqzj1lq62zp9515ffsyaj5"))))
+          "0kv4a1icwdav8jpl7qvnr931lw5h3v22ids6lwq6qpi1hjzf33pz"))))
      (build-system python-build-system)
      (native-inputs
       `(("mariadb" ,mariadb)
diff --combined gnu/packages/gnome.scm
@@@ -1176,7 -1176,7 +1176,7 @@@ XML/CSS rendering engine."
  (define-public libgsf
    (package
      (name "libgsf")
 -    (version "1.14.43")
 +    (version "1.14.44")
      (source (origin
                (method url-fetch)
                (uri (string-append "mirror://gnome/sources/" name "/"
                                    name "-" version ".tar.xz"))
                (sha256
                 (base32
 -                "05pf3h0dha3s20ddsrljbx7m94qyiqs5igwxx1ql0vlsdlylx50j"))))
 +                "1ppzfk3zmmgrg9jh8vc4dacddbfngjslq2wpj94pcr3i0c8dxgk8"))))
      (build-system gnu-build-system)
      (native-inputs
       `(("intltool" ,intltool)
@@@ -2444,7 -2444,7 +2444,7 @@@ library."
       `(("glib"    ,glib)
         ("libsoup" ,libsoup)
         ("libxml2" ,libxml2)))
-     (home-page "http://www.gtk.org/")
+     (home-page "https://www.gtk.org/")
      (synopsis "RESTful web api query library")
      (description
       "This library was designed to make it easier to access web services that
@@@ -6708,7 -6708,7 +6708,7 @@@ is suitable as a default application i
  (define-public xpad
    (package
      (name "xpad")
-     (version "5.0.0")
+     (version "5.1.0")
      (source
       (origin
         (method url-fetch)
                             name "-" version ".tar.bz2"))
         (sha256
          (base32
-          "02yikxg6z9bwla09ka001ppjlpbv5kbza3za9asazm5aiz376mkb"))))
+          "0l0g5x8g6dwhf5ksnqqrjjsycy57kcvdslkmsr6bl3vrsjd7qml3"))))
      (build-system gnu-build-system)
-     (arguments
-      `(#:phases
-        (modify-phases %standard-phases
-          (add-after 'unpack 'run-autogen
-            (lambda _
-              (system* "sh" "autogen.sh"))))))
      (native-inputs
       `(("autoconf" ,autoconf)
         ("automake" ,automake)
@@@ -7038,16 -7032,16 +7032,16 @@@ views can be printed as PDF or PostScri
  (define-public lollypop
    (package
      (name "lollypop")
-     (version "0.9.306")
+     (version "0.9.521")
      (source
       (origin
         (method url-fetch)
-        (uri (string-append "https://gitlab.gnome.org/gnumdk/lollypop/uploads/"
-                            "b769805b7063ef9807e4e832e7e87ad2/"
+        (uri (string-append "https://gitlab.gnome.org/World/lollypop/uploads/"
+                            "e4df2ed75c5ed71d64afcc668e579b2a/"
                             name "-" version ".tar.xz"))
         (sha256
          (base32
-          "0c49v6793bywvh295xbii9yq21hh3qpmxwbgp9i71kj6r9grvhan"))))
+          "0knsqh24siyw98vmiq6b1hzq4y4cazs9f1hq1js9c96hqqj9rvdx"))))
      (build-system meson-build-system)
      (arguments
       `(#:imported-modules ((guix build python-build-system)
         ;; the others are required to play streaming.
         ("gst-plugins-good" ,gst-plugins-good)
         ("gst-plugins-ugly" ,gst-plugins-ugly)))
-     (home-page "https://gnumdk.github.io/lollypop-web")
+     (home-page "https://wiki.gnome.org/Apps/Lollypop")
      (synopsis "GNOME music playing application")
      (description
       "Lollypop is a music player designed to play well with GNOME desktop.
diff --combined gnu/packages/gtk.scm
@@@ -570,7 -570,7 +570,7 @@@ is part of the GNOME accessibility proj
  (define-public at-spi2-atk
    (package
     (name "at-spi2-atk")
 -   (version "2.26.1")
 +   (version "2.26.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnome/sources/" name "/"
                                  name "-" version ".tar.xz"))
              (sha256
               (base32
 -              "0x9vc99ni46fg5dzlx67vbw0zqffr24gz8jvbdxbmzyvc5xw5w5l"))))
 +              "0vkan52ab9vrkknnv8y4f1cspk8x7xd10qx92xk9ys71p851z2b1"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@@ -664,7 -664,7 +664,7 @@@ graphical user interfaces.  Offering a 
  suitable for projects ranging from small one-off tools to complete
  application suites.")
     (license license:lgpl2.0+)
-    (home-page "http://www.gtk.org/")))
+    (home-page "https://www.gtk.org/")))
  
  (define-public gtk+
    (package (inherit gtk+-2)
@@@ -1492,7 -1492,7 +1492,7 @@@ information."
         ("source-highlight" ,source-highlight)
         ("glib" ,glib)
         ("python-six" ,python-six)))
-     (home-page "http://www.gtk.org/gtk-doc/")
+     (home-page "https://www.gtk.org/gtk-doc/")
      (synopsis "Documentation generator from C source code")
      (description
       "GTK-Doc generates API documentation from comments added to C code.  It is
@@@ -213,9 -213,9 +213,9 @@@ as.POSIXct(if (\"\" != Sys.getenv(\"SOU
                                      "/share/zoneinfo"))
               #t))
           (add-after 'build 'make-info
 -          (lambda _ (zero? (system* "make" "info"))))
 +          (lambda _ (invoke "make" "info")))
           (add-after 'build 'install-info
 -          (lambda _ (zero? (system* "make" "install-info")))))
 +          (lambda _ (invoke "make" "install-info"))))
         #:configure-flags
         `(;; We build the recommended packages here, because they are needed in
           ;; order to run the test suite.  We disable them in the r-minimal
@@@ -423,14 -423,14 +423,14 @@@ code for possible problems."
  (define-public r-foreign
    (package
      (name "r-foreign")
-     (version "0.8-70")
+     (version "0.8-71")
      (source
       (origin
         (method url-fetch)
         (uri (cran-uri "foreign" version))
         (sha256
          (base32
-          "11mql8q3i1q593dvd351fhvkvfab25li80d1ahl4xjjzy52qdkc6"))))
+          "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
      (build-system r-build-system)
      (home-page "https://cran.r-project.org/web/packages/foreign")
      (synopsis "Read data stored by other statistics software")
@@@ -614,14 -614,14 +614,14 @@@ analysis."
  (define-public r-survival
    (package
      (name "r-survival")
-     (version "2.42-3")
+     (version "2.42-6")
      (source
       (origin
         (method url-fetch)
         (uri (cran-uri "survival" version))
         (sha256
          (base32
-          "15pasbfzmg2r5bfpsadp9ia4cpybqz6n1kwm7ma02ykzf7bk4xx0"))))
+          "1bsxc2fir9pbvdzy9n474fkl7har606h9zhspp0z67wnjpp48g73"))))
      (build-system r-build-system)
      (propagated-inputs
       `(("r-matrix" ,r-matrix)))
@@@ -1577,13 -1577,13 +1577,13 @@@ defined in different packages."
  (define-public r-rlang
    (package
      (name "r-rlang")
-     (version "0.2.1")
+     (version "0.2.2")
      (source (origin
                (method url-fetch)
                (uri (cran-uri "rlang" version))
                (sha256
                 (base32
-                 "0ghg66vyri8nck4p6kl1nh47qdppbmxvjiyms69nhvipphk4ifpj"))))
+                 "0cqd894wzi53rs53prg0j7i75h0yzgi0127fzjqbdbhczwh984f9"))))
      (build-system r-build-system)
      (home-page "http://rlang.tidyverse.org")
      (synopsis "Functions for base types, core R and Tidyverse features")
@@@ -2265,14 -2265,14 +2265,14 @@@ collation, and NAMESPACE files."
  (define-public r-openssl
    (package
      (name "r-openssl")
-     (version "1.0.1")
+     (version "1.0.2")
      (source
       (origin
         (method url-fetch)
         (uri (cran-uri "openssl" version))
         (sha256
          (base32
-          "1qyql5gpwf88bkm1qarjhbqbq4hn6w0d8j4pxb5x7i96is30ap30"))))
+          "1djfpnphkcxx8idk5rjfzg8r8dnqsgc0shh2pw8lns5hap2wc5rc"))))
      (build-system r-build-system)
      (inputs
       `(("libressl" ,libressl)))
@@@ -2687,13 -2687,13 +2687,13 @@@ and draw tables."
  (define-public r-pkgconfig
    (package
      (name "r-pkgconfig")
-     (version "2.0.1")
+     (version "2.0.2")
      (source (origin
                (method url-fetch)
                (uri (cran-uri "pkgconfig" version))
                (sha256
                 (base32
-                 "0h2sp93fqqjbfqgq82a3i94ybnndx6ghaal8pbf99firnsjb40mb"))))
+                 "1jk9ip549xphb3anfixqv1yx5kidnndqgy9v3qjpmgmds5a7g695"))))
      (build-system r-build-system)
      (home-page "https://github.com/gaborcsardi/pkgconfig")
      (synopsis "Private configuration for R packages")
@@@ -2986,14 -2986,14 +2986,14 @@@ standard R subsetting and Kronecker pro
  (define-public r-iterators
    (package
      (name "r-iterators")
-     (version "1.0.9")
+     (version "1.0.10")
      (source
       (origin
         (method url-fetch)
         (uri (cran-uri "iterators" version))
         (sha256
          (base32
-          "16sycjq912ix52fjxjhcwiaqr0yj1v5iqmrvjljd3z857031w06y"))))
+          "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
      (build-system r-build-system)
      (home-page "https://cran.r-project.org/web/packages/iterators")
      (synopsis "Iterator construct for R")
@@@ -4607,14 -4607,14 +4607,14 @@@ original public code has been corrected
  (define-public r-modeltools
    (package
      (name "r-modeltools")
-     (version "0.2-21")
+     (version "0.2-22")
      (source
       (origin
         (method url-fetch)
         (uri (cran-uri "modeltools" version))
         (sha256
          (base32
-          "0ynds453xprxv0jqqzi3blnv5w6vrdww9pvd1sq4lrr5ar3k3cq7"))))
+          "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5"))))
      (build-system r-build-system)
      (home-page "https://cran.r-project.org/web/packages/modeltools")
      (synopsis "Tools and classes for statistical models")
@@@ -4653,14 -4653,14 +4653,14 @@@ models, generalized linear models and m
  (define-public r-mclust
    (package
      (name "r-mclust")
-     (version "5.4")
+     (version "5.4.1")
      (source
       (origin
         (method url-fetch)
         (uri (cran-uri "mclust" version))
         (sha256
          (base32
-          "1i3v1q8qq0al3ifvjhcvxfsg68cx9mq8jz67jwmiqai78mw0aqvk"))))
+          "1vcl4nl8by2vj2k9k84imy5m850khkgd8q02a8ica1h8vz9ijgn4"))))
      (build-system r-build-system)
      (native-inputs
       `(("gfortran" ,gfortran)))
@@@ -4872,14 -4872,14 +4872,14 @@@ of the points."
  (define-public r-fpc
    (package
      (name "r-fpc")
-     (version "2.1-11")
+     (version "2.1-11.1")
      (source
       (origin
         (method url-fetch)
         (uri (cran-uri "fpc" version))
         (sha256
          (base32
-          "04alsqb5gbhsjg1000d8w52pmpnlwca29r0s12f7n7mdccdv6xar"))))
+          "1ari57hkgqsxh6khr6j52cfrzc0096cnn1q7ghxk2z4brdd4rznc"))))
      (build-system r-build-system)
      (propagated-inputs
       `(("r-class" ,r-class)
@@@ -4906,14 -4906,14 +4906,14 @@@ groupings."
  (define-public r-vgam
    (package
      (name "r-vgam")
-     (version "1.0-5")
+     (version "1.0-6")
      (source
       (origin
         (method url-fetch)
         (uri (cran-uri "VGAM" version))
         (sha256
          (base32
-          "0ik3wyv6jj54bg34z0fzzk4xg0h6x98jqx4q2r7g1f0in0qgbb01"))))
+          "1fg31xz86jblqraifiy3q36d0hjqnll01jxx85xq87j1cyhj060j"))))
      (properties `((upstream-name . "VGAM")))
      (build-system r-build-system)
      (inputs
@@@ -5097,14 -5097,14 +5097,14 @@@ algorithms."
  (define-public r-lme4
    (package
      (name "r-lme4")
-     (version "1.1-17")
+     (version "1.1-18-1")
      (source
       (origin
         (method url-fetch)
         (uri (cran-uri "lme4" version))
         (sha256
          (base32
-          "0czwdy1s8h3slaw73pz0h8qmqczf5135fz6i46i2dv1ql2pbq49x"))))
+          "01ar4fak8zj7c1vmh9m576wchxj5qzpfqn637s7fh3fl6cpz0alq"))))
      (build-system r-build-system)
      (native-inputs
       `(("r-rcpp" ,r-rcpp)
diff --combined gnu/packages/xdisorg.scm
@@@ -157,14 -157,14 +157,14 @@@ avoiding password prompts when X11 forw
  (define-public libxkbcommon
    (package
      (name "libxkbcommon")
 -    (version "0.8.0")
 +    (version "0.8.2")
      (source (origin
               (method url-fetch)
               (uri (string-append "https://xkbcommon.org/download/" name "-"
                                   version ".tar.xz"))
               (sha256
                (base32
 -               "0vgy84vfbig5bqznr137h5arjidnfwrxrdli0pxyn2jfn1fjcag8"))))
 +               "136mdq11lrwg6rjmm44lmysxxgb9c35p4sq6k0cd129x82rw9f3s"))))
      (build-system gnu-build-system)
      (inputs
       `(("libx11" ,libx11)
@@@ -987,7 -987,7 +987,7 @@@ color temperature should be set to matc
  (define-public xscreensaver
    (package
      (name "xscreensaver")
-     (version "5.39")
+     (version "5.40")
      (source
       (origin
         (method url-fetch)
                         version ".tar.gz"))
         (sha256
          (base32
-          "09i47h4hdgwxyqgrsnshl4l5dv5mrsp37h705cc22lwby601ikj8"))))
+          "1q2sr7h6ps6d3hk8895g12rrcqiihjl7py1ly077ikv4866r181h"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f  ; no check target