Merge branch 'master' into staging

doc/build.scm

@@ -278,6 +278,7 @@ its <pre class=\"lisp\"> blocks (as produced by 'makeinfo --html')."
             (define entity->string
               (match-lambda
                 ("rArr"   "⇒")
+                ("rarr"   "→")
                 ("hellip" "…")
                 ("rsquo"  "’")
                 (e (pk 'unknown-entity e) (primitive-exit 2))))

doc/guix.texi

@@ -68,6 +68,7 @@ Copyright @copyright{} 2019 Ivan Petkov@*
 Copyright @copyright{} 2019 Jakob L. Kreuze@*
 Copyright @copyright{} 2019 Kyle Andrews@*
 Copyright @copyright{} 2019 Alex Griffin@*
+Copyright @copyright{} 2019 Guillaume Le Vaillant@*
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -305,6 +306,7 @@ Services
 * Virtualization Services::     Virtualization services.
 * Version Control Services::    Providing remote access to Git repositories.
 * Game Services::               Game servers.
+* PAM Mount Service::           Service to mount volumes when logging in.
 * Miscellaneous Services::      Other services.
 
 Defining Services
@@ -11931,6 +11933,7 @@ declaration.
 * Virtualization Services::     Virtualization services.
 * Version Control Services::    Providing remote access to Git repositories.
 * Game Services::               Game servers.
+* PAM Mount Service::           Service to mount volumes when logging in.
 * Guix Services::               Services relating specifically to Guix.
 * Miscellaneous Services::      Other services.
 @end menu
@@ -24656,6 +24659,89 @@ The port to bind the server to.
 @end deftp
 
 
+@node PAM Mount Service
+@subsection PAM Mount Service
+@cindex pam-mount
+
+The @code{(gnu services pam-mount)} module provides a service allowing
+users to mount volumes when they log in.  It should be able to mount any
+volume format supported by the system.
+
+@defvar {Scheme Variable} pam-mount-service-type
+Service type for PAM Mount support.
+@end defvar
+
+@deftp {Data Type} pam-mount-configuration
+Data type representing the configuration of PAM Mount.
+
+It takes the following parameters:
+
+@table @asis
+@item @code{rules}
+The configuration rules that will be used to generate
+@file{/etc/security/pam_mount.conf.xml}.
+
+The configuration rules are SXML elements (@pxref{SXML,,, guile, GNU
+Guile Reference Manual}), and the the default ones don't mount anything
+for anyone at login:
+
+@lisp
+`((debug (@@ (enable "0")))
+  (mntoptions (@@ (allow ,(string-join
+                          '("nosuid" "nodev" "loop"
+                            "encryption" "fsck" "nonempty"
+                            "allow_root" "allow_other")
+                          ","))))
+  (mntoptions (@@ (require "nosuid,nodev")))
+  (logout (@@ (wait "0")
+             (hup "0")
+             (term "no")
+             (kill "no")))
+  (mkmountpoint (@@ (enable "1")
+                   (remove "true"))))
+@end lisp
+
+Some @code{volume} elements must be added to automatically mount volumes
+at login.  Here's an example allowing the user @code{alice} to mount her
+encrypted @code{HOME} directory and allowing the user @code{bob} to mount
+the partition where he stores his data:
+
+@lisp
+(define pam-mount-rules
+`((debug (@@ (enable "0")))
+            (volume (@@ (user "alice")
+                       (fstype "crypt")
+                       (path "/dev/sda2")
+                       (mountpoint "/home/alice")))
+            (volume (@@ (user "bob")
+                       (fstype "auto")
+                       (path "/dev/sdb3")
+                       (mountpoint "/home/bob/data")
+                       (options "defaults,autodefrag,compress")))
+            (mntoptions (@@ (allow ,(string-join
+                                    '("nosuid" "nodev" "loop"
+                                      "encryption" "fsck" "nonempty"
+                                      "allow_root" "allow_other")
+                                    ","))))
+            (mntoptions (@@ (require "nosuid,nodev")))
+            (logout (@@ (wait "0")
+                       (hup "0")
+                       (term "no")
+                       (kill "no")))
+            (mkmountpoint (@@ (enable "1")
+                             (remove "true")))))
+
+(service pam-mount-service-type
+         (pam-mount-configuration
+           (rules pam-mount-rules)))
+@end lisp
+
+The complete list of possible options can be found in the man page for
+@uref{http://pam-mount.sourceforge.net/pam_mount.conf.5.html, pam_mount.conf}.
+@end table
+@end deftp
+
+
 @node Guix Services
 @subsection Guix Services
 

gnu/local.mk

@@ -551,6 +551,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/services/networking.scm			\
   %D%/services/nix.scm				\
   %D%/services/nfs.scm			\
+  %D%/services/pam-mount.scm			\
   %D%/services/security-token.scm		\
   %D%/services/shepherd.scm			\
   %D%/services/sound.scm			\

gnu/packages/cran.scm

@@ -5813,14 +5813,14 @@ clustering.")
 (define-public r-factominer
   (package
     (name "r-factominer")
-    (version "1.42")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "FactoMineR" version))
        (sha256
         (base32
-         "1yl16inb2m89l1czgaf0pgy9655dpr751hyx92yw6rqpd2ryznac"))))
+         "0qiw60ypf3bf5xsqz2b9l82i4jvprjm8lzpp12lhl8d9j5s8m0j8"))))
     (properties `((upstream-name . "FactoMineR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5828,6 +5828,8 @@ clustering.")
        ("r-cluster" ,r-cluster)
        ("r-ellipse" ,r-ellipse)
        ("r-flashclust" ,r-flashclust)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggrepel" ,r-ggrepel)
        ("r-lattice" ,r-lattice)
        ("r-leaps" ,r-leaps)
        ("r-mass" ,r-mass)
@@ -6419,14 +6421,14 @@ documents.")
 (define-public r-writexl
   (package
     (name "r-writexl")
-    (version "1.1")
+    (version "1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "writexl" version))
        (sha256
         (base32
-         "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46"))))
+         "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
     (home-page "https://github.com/ropensci/writexl")
@@ -8068,14 +8070,14 @@ Hothorn, Westfall, 2010, CRC Press).")
 (define-public r-emmeans
   (package
     (name "r-emmeans")
-    (version "1.4.2")
+    (version "1.4.3.01")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emmeans" version))
        (sha256
         (base32
-         "1sxwbh6sym2shrj7gva8q96ca2csqz3081q4d84avpxz15dfz1z1"))))
+         "16v5j31516nbqnj2zhgqvyp5yxd4zcs5zi0aspa5plr2qikvrkmg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-estimability" ,r-estimability)
@@ -10044,14 +10046,14 @@ Touzet and Varre (2007).")
 (define-public r-rnifti
   (package
     (name "r-rnifti")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RNifti" version))
        (sha256
         (base32
-         "0l61hjnzv043ibpkgrhc0yngaqmc58lkvii8j1dzh022z5wbqrj8"))))
+         "0hfid40pgfi1ykqka8y3v0m7h0iyd6fbvycvqlad3ibmbg621f0w"))))
     (properties `((upstream-name . "RNifti")))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -10157,14 +10159,14 @@ handling.")
 (define-public r-grimport
   (package
     (name "r-grimport")
-    (version "0.9-2")
+    (version "0.9-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "grImport" version))
        (sha256
         (base32
-         "0n3y6dzy8s0ifvyrgwbly6cl14lmgd54dyi74s5i984apszpsp16"))))
+         "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
     (properties `((upstream-name . "grImport")))
     (build-system r-build-system)
     (inputs
@@ -10181,14 +10183,14 @@ PostScript pictures in R plots.")
 (define-public r-grimport2
   (package
     (name "r-grimport2")
-    (version "0.1-5")
+    (version "0.2-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "grImport2" version))
        (sha256
         (base32
-         "0dyb3nrrvxnkk9q5b136bdivcz1jj3ajx1kscm3k0kkpqjif0pls"))))
+         "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
     (properties `((upstream-name . "grImport2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10212,18 +10214,17 @@ be imported and then exported via the @code{gridSVG} package.")
 (define-public r-kohonen
   (package
     (name "r-kohonen")
-    (version "3.0.8")
+    (version "3.0.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "kohonen" version))
        (sha256
         (base32
-         "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q"))))
+         "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-mass" ,r-mass)
+     `(("r-rcpp" ,r-rcpp)))
-       ("r-rcpp" ,r-rcpp)))
     (home-page "https://cran.r-project.org/web/packages/kohonen")
     (synopsis "Supervised and unsupervised self-organising maps")
     (description
@@ -15432,13 +15433,13 @@ function and interfaces to external frameworks.")
 (define-public r-covr
   (package
     (name "r-covr")
-    (version "3.3.2")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "covr" version))
        (sha256
-        (base32 "160w0m2d06kdd8dar57lpph39rxx55xwncbpl3b21l7j9drh1s5f"))))
+        (base32 "0p44kr6yz5sqza5zvq6divqglzkpv0if9pjpjmzhmdaaddjrqzg5"))))
     (properties `((upstream-name . "covr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15636,13 +15637,13 @@ effect size.")
 (define-public r-rgdal
   (package
     (name "r-rgdal")
-    (version "1.4-7")
+    (version "1.4-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rgdal" version))
        (sha256
-        (base32 "05rvqy8lr2c3phaylmc4g5761208b0xrmgwn9c4a60x7p251dzjs"))))
+        (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
     (properties `((upstream-name . "rgdal")))
     (build-system r-build-system)
     (inputs

gnu/packages/disk.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@gnu.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
@@ -364,10 +364,10 @@ and can dramatically shorten the lifespan of the drive if left unchecked.")
        ("glib" ,glib)
        ("gtkmm" ,gtkmm)
        ("libxml2" ,libxml2)
-       ("yelp-tools" ,yelp-tools)
+       ("yelp-tools" ,yelp-tools)))
-       ("itstool" ,itstool)))
     (native-inputs
      `(("intltool" ,intltool)
+       ("itstool" ,itstool)
        ("lvm2" ,lvm2) ; for tests
        ("pkg-config" ,pkg-config)))
     (home-page "https://gparted.org/")

gnu/packages/games.scm

@@ -27,7 +27,7 @@
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017, 2019 nee <nee-git@hidamari.blue>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
-;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2019 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
@@ -5139,7 +5139,7 @@ Crowther & Woods, its original authors, in 1995.  It has been known as
 (define-public tome4
   (package
     (name "tome4")
-    (version "1.6.1")
+    (version "1.6.4")
     (synopsis "Single-player, RPG roguelike game set in the world of Eyal")
     (source
      (origin
@@ -5148,7 +5148,7 @@ Crowther & Woods, its original authors, in 1995.  It has been known as
                            version ".tar.bz2"))
        (sha256
         (base32
-         "0c5a2bdyfccwkqnb6yqvzggyi2nk032v01kfc00zlgpdfzljcb9i"))
+         "1hrh79aqmvwwd7idlr3lzpdpc9dgm1k5p7w2462chcjvd8vhfhb7"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -6888,6 +6888,22 @@ a fortress beyond the forbidden swamp.")
                (("PATH_SUFFIXES \"src\" \"gtest\"")
                 "PATH_SUFFIXES \"src\""))
              #t))
+         (add-after 'unpack 'adjust-backward-cpp-includes
+           (lambda _
+             ;; XXX: The bundled backward-cpp exports a CMake "interface"
+             ;; that includes external libraries such as libdl from glibc.
+             ;; By default, CMake interface includes are treated as "system
+             ;; headers", and GCC behaves poorly when glibc is passed as a
+             ;; system header (causing #include_next failures).
+
+             ;; Here we prevent targets that consume the Backward::Backward
+             ;; interface from treating it as "system includes".
+             (substitute* "CMakeLists.txt"
+               (("target_link_libraries\\((.+) Backward::Backward\\)" all target)
+                (string-append "set_property(TARGET " target " PROPERTY "
+                               "NO_SYSTEM_FROM_IMPORTED true)\n"
+                               all)))
+             #t))
          (add-after 'unpack 'add-libiberty
            ;; Build fails upon linking executables without this.
            (lambda _
@@ -6939,7 +6955,7 @@ a fortress beyond the forbidden swamp.")
      "Multiplayer action game where you control small and nimble humanoids")
     (description "OpenClonk is a multiplayer action/tactics/skill game.  It is
 often referred to as a mixture of The Settlers and Worms.  In a simple 2D
-antfarm-style landscape, the player controls his crew of Clonks, small but
+antfarm-style landscape, the player controls a crew of Clonks, small but
 robust humanoid beings.  The game encourages free play but the normal goal is
 to either exploit valuable resources from the earth by building a mine or
 fight each other on an arena-like map.")

gnu/packages/gnome.scm

@@ -2431,6 +2431,7 @@ selection and URL hints.")))
               (patches (search-patches
                          "vte-CVE-2012-2738-pt1.patch"
                          "vte-CVE-2012-2738-pt2.patch"))))
+    (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--disable-python")))
     (native-inputs

gnu/packages/graph.scm

@@ -107,14 +107,14 @@ more.")
 (define-public r-igraph
   (package
     (name "r-igraph")
-    (version "1.2.4.1")
+    (version "1.2.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "igraph" version))
        (sha256
         (base32
-         "1074y8mvprrqlkb4vwa2qc9l03r8d7p5vaaqacj4ljjs7dvcq6l9"))))
+         "0scrbqb26pam8akblb4g9rkz888s0xffw3gcly78s4ijj67barxd"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))

gnu/packages/graphics.scm

@@ -71,6 +71,7 @@
   #:use-module (gnu packages readline)
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages swig)
+  #:use-module (gnu packages tbb)
   #:use-module (gnu packages video)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
@@ -87,14 +88,14 @@
 (define-public blender
   (package
     (name "blender")
-    (version "2.80")
+    (version "2.81")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.blender.org/source/"
-                                  "blender-" version ".tar.gz"))
+                                  "blender-" version ".tar.xz"))
               (sha256
                (base32
-                "1h550jisdbis50hxwk5kxrvrk1a6sh2fsri3yyj66vhzbi87x7fd"))))
+                "1prp0f2152f1sz23jlc86vndfvmplb7qhllikkirq7hgpykrshna"))))
     (build-system cmake-build-system)
     (arguments
       (let ((python-version (version-major+minor (package-version python))))
@@ -145,6 +146,8 @@
      `(("boost" ,boost)
        ("jemalloc" ,jemalloc)
        ("libx11" ,libx11)
+       ("libxi" ,libxi)
+       ("libxrender" ,libxrender)
        ("openimageio" ,openimageio)
        ("openexr" ,openexr)
        ("opensubdiv" ,opensubdiv)
@@ -162,6 +165,7 @@
        ("openal" ,openal)
        ("python" ,python)
        ("python-numpy" ,python-numpy)
+       ("tbb" ,tbb)
        ("zlib" ,zlib)))
     (home-page "https://blender.org/")
     (synopsis "3D graphics creation suite")

gnu/packages/kde.scm

@@ -517,8 +517,9 @@ cards.")
     (arguments
      `(#:tests? #f)) ; both tests fail, require display
     (inputs
+     `(("qtbase" ,qtbase)))
+    (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
-       ("qtbase" ,qtbase)
        ("qttools" ,qttools)))
     (home-page "https://techbase.kde.org/Projects/Snorenotify")
     (synopsis "Qt notification framework")

gnu/packages/lisp.scm

@@ -6,7 +6,7 @@
 ;;; Copyright © 2016, 2017 ng0 <ng0@n0.is>
 ;;; Copyright © 2016, 2017 Andy Patterson <ajpatter@uwaterloo.ca>
 ;;; Copyright © 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Benjamin Slade <slade@jnanam.net>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
@@ -1469,16 +1469,17 @@ JavaScript (ECMAScript 3).  It has basic support for ECMAScript 5.")
 (define-public sbcl-parse-number
   (package
     (name "sbcl-parse-number")
-    (version "1.5")
+    (version "1.7")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/sharplispers/parse-number/"
+       (uri (git-reference
-                           "archive/v" version ".tar.gz"))
+              (url "https://github.com/sharplispers/parse-number/")
-       (file-name (string-append name "-" version ".tar.gz"))
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1k6s4v65ksc1j5i0dprvzfvj213v6nah7i0rgd0726ngfjisj9ir"))))
+         "0sk06ib1bhqv9y39vwnnw44vmbc4b0kvqm37xxmkxd4dwchq82d7"))))
     (build-system asdf-build-system/sbcl)
     (home-page "http://www.cliki.net/PARSE-NUMBER")
     (synopsis "Parse numbers")
@@ -4140,11 +4141,13 @@ encoding table that uses only URI-compatible characters.")
     (version "1.1.7")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append
+       (uri (git-reference
-             "https://github.com/edicl/chunga/archive/v" version ".tar.gz"))
+              (url "https://github.com/edicl/chunga.git")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0ra17kyc9l7qbaw003ly111r1cbn4zixbfq1ydr9cxw10v30q1n7"))))
+        (base32 "0jzn3nyb3f22gm983rfk99smqs3mhb9ivjmasvhq9qla5cl9pyhd"))))
     (build-system asdf-build-system/sbcl)
     (inputs
      `(("sbcl-trivial-gray-streams" ,sbcl-trivial-gray-streams)))
@@ -4923,6 +4926,7 @@ reset to 0 and you're able to read it again.")
        (uri (git-reference
              (url "https://github.com/fukamachi/lack.git")
              (commit commit)))
+       (file-name (git-file-name "lack-request" version))
        (sha256
         (base32 "1avh4ygcj9xcx4m17nj0wnxxaisk26w4ljs2bibzxaln24x7pi85"))))
      (build-system asdf-build-system/sbcl)
@@ -5039,6 +5043,7 @@ performance and simplicity in mind.")
        (uri (git-reference
              (url "https://github.com/fukamachi/lack.git")
              (commit commit)))
+       (file-name (git-file-name "lack-component" version))
        (sha256
         (base32 "1avh4ygcj9xcx4m17nj0wnxxaisk26w4ljs2bibzxaln24x7pi85"))))
      (build-system asdf-build-system/sbcl)
@@ -5074,6 +5079,7 @@ performance and simplicity in mind.")
        (uri (git-reference
              (url "https://github.com/fukamachi/lack.git")
              (commit commit)))
+       (file-name (git-file-name "lack-util" version))
        (sha256
         (base32 "1avh4ygcj9xcx4m17nj0wnxxaisk26w4ljs2bibzxaln24x7pi85"))))
      (build-system asdf-build-system/sbcl)
@@ -5111,6 +5117,7 @@ performance and simplicity in mind.")
        (uri (git-reference
              (url "https://github.com/fukamachi/lack.git")
              (commit commit)))
+       (file-name (git-file-name "lack-middleware-backtrace" version))
        (sha256
         (base32 "1avh4ygcj9xcx4m17nj0wnxxaisk26w4ljs2bibzxaln24x7pi85"))))
      (build-system asdf-build-system/sbcl)
@@ -5193,6 +5200,7 @@ mime-type of a file.")
        (uri (git-reference
              (url "https://github.com/fukamachi/lack.git")
              (commit commit)))
+       (file-name (git-file-name "lack-middleware-static" version))
        (sha256
         (base32 "1avh4ygcj9xcx4m17nj0wnxxaisk26w4ljs2bibzxaln24x7pi85"))))
      (build-system asdf-build-system/sbcl)
@@ -5232,6 +5240,7 @@ performance and simplicity in mind.")
        (uri (git-reference
              (url "https://github.com/fukamachi/lack.git")
              (commit commit)))
+       (file-name (git-file-name "lack" version))
        (sha256
         (base32 "1avh4ygcj9xcx4m17nj0wnxxaisk26w4ljs2bibzxaln24x7pi85"))))
      (build-system asdf-build-system/sbcl)

gnu/packages/python-xyz.scm

@@ -4088,8 +4088,7 @@ convert between colorspaces like sRGB, XYZ, CIEL*a*b*, CIECAM02, CAM02-UCS, etc.
                        (assoc-ref inputs "jquery-ui")
                        "-d" dir))
              #t))
-         (delete 'check)
+         (replace 'check
-         (add-after 'install 'check
            (lambda* (#:key outputs inputs #:allow-other-keys)
              (add-installed-pythonpath inputs outputs)
              (invoke "python" "tests.py" "-v"
@@ -4147,6 +4146,7 @@ toolkits.")
                            (assoc-ref inputs "jquery-ui")
                            "-d" dir))
                  #t))
+             (delete 'fix-and-disable-failing-tests)
              (delete 'check))))) ; These tests weren't run the the past.
       ;; Make sure to use special packages for Python 2 instead
       ;; of those automatically rewritten by package-with-python2.

gnu/packages/statistics.scm

@@ -567,14 +567,14 @@ also flexible enough to handle most nonstandard requirements.")
 (define-public r-matrix
   (package
     (name "r-matrix")
-    (version "1.2-17")
+    (version "1.2-18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Matrix" version))
        (sha256
         (base32
-         "1k1zf92ycqr7fz44w7bp1p354ww7jg0wm23ybb8dzmbg37qfchyv"))))
+         "06b1rc1vq65b271f2wpzhqkvhng8hwwnvjflzxkng50i52603zzp"))))
     (properties `((upstream-name . "Matrix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2661,13 +2661,13 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "1.17")
+    (version "1.18")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
-          (base32 "18dj6nr1m79pv1pv9w2n0rhiidwqjb2w8w1rnpcwijwbz4i8d3k2"))))
+          (base32 "0fykzbb5kjsqc8v6gjcdma7rmq0gailp30qij6plgna4d8nhjw3w"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3332,14 +3332,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
 (define-public r-e1071
   (package
     (name "r-e1071")
-    (version "1.7-2")
+    (version "1.7-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "e1071" version))
        (sha256
         (base32
-         "0lipj692rjjw8rrhqh2k9i5dh8y2sjrw9q53rwm32irhx2f2j73j"))))
+         "0pf2pjb590z0jikgv1037xcp7dq06mg3dzmyffjw6gk7dd9blbdv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)))

gnu/packages/video.scm

@@ -1266,7 +1266,8 @@ streaming protocols.")
     (build-system gnu-build-system)
     ;; FIXME: Add additional inputs once available.
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("pkg-config" ,pkg-config)
+       ("yasm" ,yasm)))
     (inputs
      `(("alsa-lib" ,alsa-lib)
        ("cdparanoia" ,cdparanoia)
@@ -1297,7 +1298,6 @@ streaming protocols.")
        ("python" ,python-wrapper)
        ("sdl" ,sdl)
        ("speex" ,speex)
-       ("yasm" ,yasm)
        ("zlib" ,zlib)))
     (arguments
      `(#:tests? #f ; no test target
@@ -1943,7 +1943,11 @@ for use with HTML5 video.")
              (patches (search-patches "avidemux-install-to-lib.patch"))))
     (build-system cmake-build-system)
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("perl" ,perl)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python-wrapper)
+       ("qttools" ,qttools)
+       ("yasm" ,yasm)))
     ;; FIXME: Once packaged, add libraries not found during the build.
     (inputs
      `(("alsa-lib" ,alsa-lib)
@@ -1958,14 +1962,9 @@ for use with HTML5 video.")
        ("libvorbis" ,libvorbis)
        ("libvpx" ,libvpx)
        ("libxv" ,libxv)
-       ("perl" ,perl)
        ("pulseaudio" ,pulseaudio)
-       ("python" ,python-wrapper)
        ("qtbase" ,qtbase)
-       ("qttools" ,qttools)
-       ("sdl" ,sdl)
        ("sqlite" ,sqlite)
-       ("yasm" ,yasm)
        ("zlib" ,zlib)))
     (arguments
      `(#:tests? #f                      ; no check target
@@ -2002,7 +2001,6 @@ for use with HTML5 video.")
                (let* ((out (assoc-ref outputs "out"))
                       (lib (string-append out "/lib"))
                       (top (getcwd))
-                      (sdl (assoc-ref inputs "sdl"))
                       (build_component
                        (lambda* (component srcdir #:optional (args '()))
                          (let ((builddir (string-append "build_" component)))
@@ -2015,8 +2013,6 @@ for use with HTML5 video.")
                                     (string-append "-DCMAKE_SHARED_LINKER_FLAGS="
                                                    "\"-Wl,-rpath=" lib "\"")
                                     (string-append "-DAVIDEMUX_SOURCE_DIR=" top)
-                                    (string-append "-DSDL_INCLUDE_DIR="
-                                                   sdl "/include/SDL")
                                     (string-append "../" srcdir)
                                     "-DENABLE_QT5=True"
                                     args)

gnu/services/pam-mount.scm

@@ -0,0 +1,111 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu services pam-mount)
+  #:use-module (gnu packages admin)
+  #:use-module (gnu services)
+  #:use-module (gnu services configuration)
+  #:use-module (gnu system pam)
+  #:use-module (guix gexp)
+  #:use-module (guix records)
+  #:export (pam-mount-configuration
+            pam-mount-configuration?
+            pam-mount-service-type))
+
+(define %pam-mount-default-configuration
+  `((debug (@ (enable "0")))
+    (mntoptions (@ (allow ,(string-join
+                            '("nosuid" "nodev" "loop"
+                              "encryption" "fsck" "nonempty"
+                              "allow_root" "allow_other")
+                            ","))))
+    (mntoptions (@ (require "nosuid,nodev")))
+    (logout (@ (wait "0")
+               (hup "0")
+               (term "no")
+               (kill "no")))
+    (mkmountpoint (@ (enable "1")
+                     (remove "true")))))
+
+(define (make-pam-mount-configuration-file config)
+  (computed-file
+   "pam_mount.conf.xml"
+   #~(begin
+       (use-modules (sxml simple))
+       (call-with-output-file #$output
+         (lambda (port)
+           (sxml->xml
+            '(*TOP*
+              (*PI* xml "version='1.0' encoding='utf-8'")
+              (pam_mount
+               #$@(pam-mount-configuration-rules config)
+               (pmvarrun
+                #$(file-append pam-mount
+                               "/sbin/pmvarrun -u '%(USER)' -o '%(OPERATION)'"))
+               (cryptmount
+                #$(file-append pam-mount
+                               (string-append
+                                "/sbin/mount.crypt"
+                                " '%(if %(CIPHER),-ocipher=%(CIPHER))'"
+                                " '%(if %(FSKEYCIPHER),"
+                                "-ofsk_cipher=%(FSKEYCIPHER))'"
+                                " '%(if %(FSKEYHASH),-ofsk_hash=%(FSKEYHASH))'"
+                                " '%(if %(FSKEYPATH),-okeyfile=%(FSKEYPATH))'"
+                                " '%(if %(OPTIONS),-o%(OPTIONS))'"
+                                " '%(VOLUME)' '%(MNTPT)'")))
+               (cryptumount
+                #$(file-append pam-mount "/sbin/umount.crypt '%(MNTPT)'"))))
+            port))))))
+
+(define-record-type* <pam-mount-configuration>
+  pam-mount-configuration
+  make-pam-mount-configuration
+  pam-mount-configuration?
+  (rules pam-mount-configuration-rules
+         (default %pam-mount-default-configuration)))
+
+(define (pam-mount-etc-service config)
+  `(("security/pam_mount.conf.xml"
+     ,(make-pam-mount-configuration-file config))))
+
+(define (pam-mount-pam-service config)
+  (define optional-pam-mount
+    (pam-entry
+     (control "optional")
+     (module #~(string-append #$pam-mount "/lib/security/pam_mount.so"))))
+  (list (lambda (pam)
+          (if (member (pam-service-name pam)
+                      '("login" "su" "slim" "gdm-password"))
+              (pam-service
+               (inherit pam)
+               (auth (append (pam-service-auth pam)
+                             (list optional-pam-mount)))
+               (session (append (pam-service-session pam)
+                                (list optional-pam-mount))))
+              pam))))
+
+(define pam-mount-service-type
+  (service-type
+   (name 'pam-mount)
+   (extensions (list (service-extension etc-service-type
+                                        pam-mount-etc-service)
+                     (service-extension pam-root-service-type
+                                        pam-mount-pam-service)))
+   (default-value (pam-mount-configuration))
+   (description "Activate PAM-Mount support.  It allows mounting volumes for
+specific users when they log in.")))

gnu/services/web.scm

@@ -742,8 +742,8 @@ of index files."
                             (server-blocks
                               (append (nginx-configuration-server-blocks config)
                               servers)))))
-                (default-value
+                (default-value (nginx-configuration))
-                  (nginx-configuration))))
+                (description "Run the nginx Web server.")))
 
 (define-record-type* <fcgiwrap-configuration> fcgiwrap-configuration
   make-fcgiwrap-configuration

guix/lint.scm

@@ -292,6 +292,7 @@ of a package, and INPUT-NAMES, a list of package specifications such as
             "intltool"
             "itstool"
             "qttools"
+            "yasm" "nasm" "fasm"
             "python-coverage" "python2-coverage"
             "python-cython" "python2-cython"
             "python-docutils" "python2-docutils"

guix/scripts/substitute.scm

@@ -526,6 +526,9 @@ initial connection on which HTTP requests are sent."
   (let connect ((port     port)
                 (requests requests)
                 (result   seed))
+    (define batch
+      (at-most 1000 requests))
+
     ;; (format (current-error-port) "connecting (~a requests left)..."
     ;;         (length requests))
     (let ((p (or port (guix:open-connection-for-uri
@@ -536,7 +539,7 @@ initial connection on which HTTP requests are sent."
       (when (file-port? p)
         (setvbuf p 'block (expt 2 16)))
 
-      ;; Send REQUESTS, up to a certain number, in a row.
+      ;; Send BATCH in a row.
       ;; XXX: Do our own caching to work around inefficiencies when
       ;; communicating over TLS: <http://bugs.gnu.org/22966>.
       (let-values (((buffer get) (open-bytevector-output-port)))
@@ -544,16 +547,21 @@ initial connection on which HTTP requests are sent."
         (set-http-proxy-port?! buffer (http-proxy-port? p))
 
         (for-each (cut write-request <> buffer)
-                  (at-most 1000 requests))
+                  batch)
         (put-bytevector p (get))
         (force-output p))
 
       ;; Now start processing responses.
-      (let loop ((requests requests)
+      (let loop ((sent      batch)
-                 (result   result))
+                 (processed 0)
-        (match requests
+                 (result    result))
+        (match sent
           (()
-           (reverse result))
+           (match (drop requests processed)
+             (()
+              (reverse result))
+             (remainder
+              (connect port remainder result))))
           ((head tail ...)
            (let* ((resp   (read-response p))
                   (body   (response-body-port resp))
@@ -564,9 +572,11 @@ initial connection on which HTTP requests are sent."
              (match (assq 'connection (response-headers resp))
                (('connection 'close)
                 (close-connection p)
-                (connect #f tail result))         ;try again
+                (connect #f                       ;try again
+                         (append tail (drop requests processed))
+                         result))
                (_
-                (loop tail result))))))))))       ;keep going
+                (loop tail (+ 1 processed) result)))))))))) ;keep going
 
 (define (read-to-eof port)
   "Read from PORT until EOF is reached.  The data are discarded."

guix/ui.scm

@@ -111,6 +111,7 @@
             package-specification->name+version+output
 
             supports-hyperlinks?
+            file-hyperlink
             location->hyperlink
 
             relevance
@@ -1246,7 +1247,7 @@ documented at
   (string-append "\x1b]8;;" uri "\x1b\\"
                  text "\x1b]8;;\x1b\\"))
 
-(define (supports-hyperlinks? port)
+(define* (supports-hyperlinks? #:optional (port (current-output-port)))
   "Return true if PORT is a terminal that supports hyperlink escapes."
   ;; Note that terminals are supposed to ignore OSC escapes they don't
   ;; understand (this is the case of xterm as of version 349, for instance.)
@@ -1255,6 +1256,13 @@ documented at
   (and (isatty?* port)
        (not (getenv "INSIDE_EMACS"))))
 
+(define* (file-hyperlink file #:optional (text file))
+  "Return TEXT with escapes for a hyperlink to FILE."
+  (hyperlink (string-append "file://" (gethostname)
+                            (encode-and-join-uri-path
+                             (string-split file #\/)))
+             text))
+
 (define (location->hyperlink location)
   "Return a string corresponding to LOCATION, with escapes for a hyperlink."
   (let ((str  (location->string location))
@@ -1262,10 +1270,7 @@ documented at
                   (location-file location)
                   (search-path %load-path (location-file location)))))
     (if file
-        (hyperlink (string-append "file://" (gethostname)
+        (file-hyperlink file str)
-                                  (encode-and-join-uri-path
-                                   (string-split file #\/)))
-                   str)
         str)))
 
 (define* (package->recutils p port #:optional (width (%text-width))
@@ -1608,17 +1613,22 @@ DURATION-RELATION with the current time."
 (define (display-generation profile number)
   "Display a one-line summary of generation NUMBER of PROFILE."
   (unless (zero? number)
-    (let ((header (format #f (highlight (G_ "Generation ~a\t~a")) number
+    (let* ((file   (generation-file-name profile number))
-                          (date->string
+           (link   (if (supports-hyperlinks?)
-                           (time-utc->date
+                       (cut file-hyperlink file <>)
-                            (generation-time profile number))
+                       identity))
-                           ;; TRANSLATORS: This is a format-string for date->string.
+           (header (format #f (link (highlight (G_ "Generation ~a\t~a")))
-                           ;; Please choose a format that corresponds to the
+                           number
-                           ;; usual way of presenting dates in your locale.
+                           (date->string
-                           ;; See https://www.gnu.org/software/guile/manual/html_node/SRFI_002d19-Date-to-string.html
+                            (time-utc->date
-                           ;; for details.
+                             (generation-time profile number))
-                           (G_ "~b ~d ~Y ~T"))))
+                            ;; TRANSLATORS: This is a format-string for date->string.
-          (current (generation-number profile)))
+                            ;; Please choose a format that corresponds to the
+                            ;; usual way of presenting dates in your locale.
+                            ;; See https://www.gnu.org/software/guile/manual/html_node/SRFI_002d19-Date-to-string.html
+                            ;; for details.
+                            (G_ "~b ~d ~Y ~T"))))
+           (current (generation-number profile)))
       (if (= number current)
           ;; TRANSLATORS: The word "current" here is an adjective for
           ;; "Generation", as in "current generation".  Use the appropriate