Merge branch 'master' into core-updates

.dir-locals.el

@@ -35,6 +35,8 @@
    (eval . (put 'modify-services 'scheme-indent-function 1))
    (eval . (put 'with-directory-excursion 'scheme-indent-function 1))
    (eval . (put 'with-file-lock 'scheme-indent-function 1))
+   (eval . (put 'with-file-lock/no-wait 'scheme-indent-function 1))
+   (eval . (put 'with-profile-lock 'scheme-indent-function 1))
 
    (eval . (put 'package 'scheme-indent-function 0))
    (eval . (put 'origin 'scheme-indent-function 0))

Makefile.am

@@ -132,6 +132,7 @@ MODULES =					\
   guix/build-system/perl.scm			\
   guix/build-system/python.scm			\
   guix/build-system/ocaml.scm			\
+  guix/build-system/qt.scm			\
   guix/build-system/waf.scm			\
   guix/build-system/r.scm			\
   guix/build-system/rakudo.scm			\
@@ -178,6 +179,7 @@ MODULES =					\
   guix/build/perl-build-system.scm		\
   guix/build/python-build-system.scm		\
   guix/build/ocaml-build-system.scm		\
+  guix/build/qt-build-system.scm		\
   guix/build/r-build-system.scm			\
   guix/build/rakudo-build-system.scm		\
   guix/build/ruby-build-system.scm		\

build-aux/hydra/gnu-system.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
-;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018, 2019 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -34,16 +34,22 @@
 (setvbuf (current-error-port) _IOLBF)
 (set-current-output-port (current-error-port))
 
+(define (find-current-checkout arguments)
+  "Find the first checkout of ARGUMENTS that provided the current file.
+Return #f if no such checkout is found."
+  (let ((current-root
+         (canonicalize-path
+          (string-append (dirname (current-filename)) "/../.."))))
+    (find (lambda (argument)
+            (and=> (assq-ref argument 'file-name)
+                   (lambda (name)
+                     (string=? name current-root)))) arguments)))
+
 (define (hydra-jobs store arguments)
   "Return a list of jobs where each job is a NAME/THUNK pair."
+
   (define checkout
-    ;; Extract metadata about the 'guix' checkout.  Its key in ARGUMENTS may
+    (find-current-checkout arguments))
-    ;; vary, so pick up the first one that's neither 'subset' nor 'systems'.
-    (any (match-lambda
-           ((key . value)
-            (and (not (memq key '(systems subset)))
-                 value)))
-         arguments))
 
   (define commit
     (assq-ref checkout 'revision))
@@ -70,9 +76,11 @@
            ((name . fields)
             ;; Hydra expects a thunk, so here it is.
             (cons name (lambda () fields))))
-         (inferior-eval-with-store inferior store
+         (inferior-eval-with-store
-                                   `(lambda (store)
+          inferior store
-                                      (map (match-lambda
+          `(lambda (store)
-                                             ((name . thunk)
+             (map (match-lambda
-                                              (cons name (thunk))))
+                    ((name . thunk)
-                                           (hydra-jobs store ',arguments)))))))
+                     (cons name (thunk))))
+                  (hydra-jobs store '((superior-guix-checkout . ,checkout)
+                                      ,@arguments))))))))

config-daemon.ac

@@ -91,8 +91,9 @@ if test "x$guix_build_daemon" = "xyes"; then
   dnl sched_setaffinity: to improve RPC locality.
   dnl statvfs: to detect disk-full conditions.
   dnl strsignal: for error reporting.
+  dnl statx: fine-grain 'stat' call, new in glibc 2.28.
   AC_CHECK_FUNCS([lutimes lchown posix_fallocate sched_setaffinity \
-     statvfs nanosleep strsignal])
+     statvfs nanosleep strsignal statx])
 
   dnl Check whether the store optimiser can optimise symlinks.
   AC_MSG_CHECKING([whether it is possible to create a link to a symlink])

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-cookbook.texi

@@ -111,9 +111,10 @@ REPL} by running @code{guile} from the command line.
 Alternatively you can also run @code{guix environment --ad-hoc guile -- guile}
 if you'd rather not have Guile installed in your user profile.
 
-In the following examples we use the @code{>} symbol to denote the REPL
+In the following examples, lines show what you would type at the REPL;
-prompt, that is, the line reserved for user input.  @xref{Using Guile
+lines starting with ``@result{}'' show evaluation results, while lines
-Interactively,,, guile, GNU Guile Reference Manual}) for more details on the
+starting with ``@print{}'' show things that get printed.  @xref{Using Guile
+Interactively,,, guile, GNU Guile Reference Manual}), for more details on the
 REPL.
 
 @itemize
@@ -121,17 +122,20 @@ REPL.
 Scheme syntax boils down to a tree of expressions (or @emph{s-expression} in
 Lisp lingo).  An expression can be a literal such as numbers and strings, or a
 compound which is a parenthesized list of compounds and literals.  @code{#t}
-and @code{#f} stand for the booleans "true" and "false", respectively.
+and @code{#f} stand for the Booleans ``true'' and ``false'', respectively.
 
 Examples of valid expressions:
 
 @lisp
-> "Hello World!"
 "Hello World!"
-> 17
+@result{} "Hello World!"
+
 17
-> (display (string-append "Hello " "Guix" "\n"))
+@result{} 17
-"Hello Guix!"
+
+(display (string-append "Hello " "Guix" "\n"))
+@print{} Hello Guix!
+@result{} #<unspecified>
 @end lisp
 
 @item
@@ -144,8 +148,8 @@ last evaluated expression as its return value.
 Anonymous functions are declared with the @code{lambda} term:
 
 @lisp
-> (lambda (x) (* x x))
+(lambda (x) (* x x))
-#<procedure 120e348 at <unknown port>:24:0 (x)>
+@result{} #<procedure 120e348 at <unknown port>:24:0 (x)>
 @end lisp
 
 The above procedure returns the square of its argument.  Since everything is
@@ -153,18 +157,18 @@ an expression, the @code{lambda} expression returns an anonymous procedure,
 which can in turn be applied to an argument:
 
 @lisp
-> ((lambda (x) (* x x)) 3)
+((lambda (x) (* x x)) 3)
-9
+@result{} 9
 @end lisp
 
 @item
 Anything can be assigned a global name with @code{define}:
 
 @lisp
-> (define a 3)
+(define a 3)
-> (define square (lambda (x) (* x x)))
+(define square (lambda (x) (* x x)))
-> (square a)
+(square a)
-9
+@result{} 9
 @end lisp
 
 @item
@@ -178,58 +182,63 @@ Procedures can be defined more concisely with the following syntax:
 A list structure can be created with the @code{list} procedure:
 
 @lisp
-> (list 2 a 5 7)
+(list 2 a 5 7)
-(2 3 5 7)
+@result{} (2 3 5 7)
 @end lisp
 
 @item
-The @emph{quote} disables evaluation of a parenthesized expression: the first
+The @dfn{quote} disables evaluation of a parenthesized expression: the
-term is not called over the other terms.  Thus it effectively returns a list
+first term is not called over the other terms (@pxref{Expression Syntax,
-of terms.
+quote,, guile, GNU Guile Reference Manual}).  Thus it effectively
+returns a list of terms.
 
 @lisp
-> '(display (string-append "Hello " "Guix" "\n"))
+'(display (string-append "Hello " "Guix" "\n"))
-(display (string-append "Hello " "Guix" "\n"))
+@result{} (display (string-append "Hello " "Guix" "\n"))
-> '(2 a 5 7)
+
-(2 a 5 7)
+'(2 a 5 7)
+@result{} (2 a 5 7)
 @end lisp
 
 @item
-The @emph{quasiquote} disables evaluation of a parenthesized expression until
+The @dfn{quasiquote} disables evaluation of a parenthesized expression
-a comma re-enables it.  Thus it provides us with fine-grained control over
+until @dfn{unquote} (a comma) re-enables it.  Thus it provides us with
-what is evaluated and what is not.
+fine-grained control over what is evaluated and what is not.
 
 @lisp
-> `(2 a 5 7 (2 ,a 5 ,(+ a 4)))
+`(2 a 5 7 (2 ,a 5 ,(+ a 4)))
-(2 a 5 7 (2 3 5 7))
+@result{} (2 a 5 7 (2 3 5 7))
 @end lisp
 
 Note that the above result is a list of mixed elements: numbers, symbols (here
 @code{a}) and the last element is a list itself.
 
 @item
-Multiple variables can be named locally with @code{let}:
+Multiple variables can be named locally with @code{let} (@pxref{Local
+Bindings,,, guile, GNU Guile Reference Manual}):
 
 @lisp
-> (define x 10)
+(define x 10)
-> (let ((x 2)
+(let ((x 2)
-        (y 3))
+      (y 3))
-    (list x y))
+  (list x y))
-(2 3)
+@result{} (2 3)
-> x
+
-10
+x
-> y
+@result{} 10
-ERROR: In procedure module-lookup: Unbound variable: y
+
+y
+@error{} In procedure module-lookup: Unbound variable: y
 @end lisp
 
 Use @code{let*} to allow later variable declarations to refer to earlier
 definitions.
 
 @lisp
-> (let* ((x 2)
+(let* ((x 2)
-         (y (* x 3)))
+       (y (* x 3)))
-    (list x y))
+  (list x y))
-(2 6)
+@result{} (2 6)
 @end lisp
 
 @item
@@ -242,7 +251,8 @@ the build stage.  Note that it is merely a convention, like @code{_} in C.
 Scheme treats @code{%} exactly the same as any other letter.
 
 @item
-Modules are created with @code{define-module}.  For instance
+Modules are created with @code{define-module} (@pxref{Creating Guile
+Modules,,, guile, GNU Guile Reference Manual}).  For instance
 
 @lisp
 (define-module (guix build-system ruby)
@@ -331,14 +341,14 @@ It does not assume much knowledge of the Guix system nor of the Lisp language.
 The reader is only expected to be familiar with the command line and to have some
 basic programming knowledge.
 
-@node A "Hello World" package
+@node A ``Hello World'' package
-@subsection A "Hello World" package
+@subsection A ``Hello World'' package
 
-The “Defining Packages” section of the manual introduces the basics of Guix
+The ``Defining Packages'' section of the manual introduces the basics of Guix
 packaging (@pxref{Defining Packages,,, guix, GNU Guix Reference Manual}).  In
 the following section, we will partly go over those basics again.
 
-``GNU hello'' is a dummy project that serves as an idiomatic example for
+GNU@tie{}Hello is a dummy project that serves as an idiomatic example for
 packaging.  It uses the GNU build system (@code{./configure && make && make
 install}).  Guix already provides a package definition which is a perfect
 example to start with.  You can look up its declaration with @code{guix edit
@@ -416,10 +426,10 @@ available licenses.
 @end table
 
 Time to build our first package!  Nothing fancy here for now: we will stick to a
-dummy "my-hello", a copy of the above declaration.
+dummy @code{my-hello}, a copy of the above declaration.
 
-As with the ritualistic "Hello World" taught with most programming languages,
+As with the ritualistic ``Hello World'' taught with most programming languages,
-this will possibly be the most "manual" approach.  We will work out an ideal
+this will possibly be the most ``manual'' approach.  We will work out an ideal
 setup later; for now we will go the simplest route.
 
 Save the following to a file @file{my-hello.scm}.
@@ -554,20 +564,20 @@ earlier example.
 
 The @code{use-modules} expression tells which of the modules we need in the file.
 Modules are a collection of values and procedures.  They are commonly called
-"libraries" or "packages" in other programming languages.
+``libraries'' or ``packages'' in other programming languages.
 
 @node @samp{GUIX_PACKAGE_PATH}
 @subsubsection @samp{GUIX_PACKAGE_PATH}
 
-@emph{Note: Starting from Guix 0.16, the more flexible Guix "channels" are the
+@emph{Note: Starting from Guix 0.16, the more flexible Guix @dfn{channels} are the
 preferred way and supersede @samp{GUIX_PACKAGE_PATH}.  See next section.}
 
 It can be tedious to specify the file from the command line instead of simply
 calling @code{guix package --install my-hello} as you would do with the official
 packages.
 
-Guix makes it possible to streamline the process by adding as many "package
+Guix makes it possible to streamline the process by adding as many ``package
-declaration paths" as you want.
+declaration directories'' as you want.
 
 Create a directory, say @samp{~./guix-packages} and add it to the @samp{GUIX_PACKAGE_PATH}
 environment variable:
@@ -581,7 +591,7 @@ To add several directories, separate them with a colon (@code{:}).
 
 Our previous @samp{my-hello} needs some adjustments though:
 
-@example
+@lisp
 (define-module (my-hello)
   #:use-module (guix licenses)
   #:use-module (guix packages)
@@ -607,7 +617,7 @@ serves as an example of standard GNU coding practices.  As such, it supports
 command-line arguments, multiple languages, and so on.")
     (home-page "https://www.gnu.org/software/hello/")
     (license gpl3+)))
-@end example
+@end lisp
 
 Note that we have assigned the package value to an exported variable name with
 @code{define-public}.  This is effectively assigning the package to the @code{my-hello}
@@ -619,14 +629,14 @@ will fail because the last expression, @code{define-public}, does not return a
 package.  If you want to use @code{define-public} in this use-case nonetheless, make
 sure the file ends with an evaluation of @code{my-hello}:
 
-@example
+@lisp
 ; ...
 (define-public my-hello
   ; ...
   )
 
 my-hello
-@end example
+@end lisp
 
 This last example is not very typical.
 
@@ -670,7 +680,7 @@ In the rest of this article, we use @samp{$GUIX_CHECKOUT} to refer to the locati
 the checkout.
 
 
-Follow the instruction in the manual (@pxref{Contributing,,, guix, GNU Guix
+Follow the instructions in the manual (@pxref{Contributing,,, guix, GNU Guix
 Reference Manual}) to set up the repository environment.
 
 Once ready, you should be able to use the package definitions from the
@@ -679,7 +689,8 @@ repository environment.
 Feel free to edit package definitions found in @samp{$GUIX_CHECKOUT/gnu/packages}.
 
 The @samp{$GUIX_CHECKOUT/pre-inst-env} script lets you use @samp{guix} over the package
-collection of the repository.
+collection of the repository (@pxref{Running Guix Before It Is
+Installed,,, guix, GNU Guix Reference Manual}).
 
 @itemize
 @item
@@ -735,11 +746,11 @@ It's a community effort so the more join in, the better Guix becomes!
 @node Extended example
 @subsection Extended example
 
-The above "Hello World" example is as simple as it goes.  Packages can be more
+The above ``Hello World'' example is as simple as it goes.  Packages can be more
 complex than that and Guix can handle more advanced scenarios.  Let's look at
 another, more sophisticated package (slightly modified from the source):
 
-@example
+@lisp
 (define-module (gnu packages version-control)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix utils)
@@ -812,7 +823,7 @@ provided as a re-entrant linkable library with a solid API, allowing you to
 write native speed custom Git applications in any language with bindings.")
       ;; GPLv2 with linking exception
       (license license:gpl2))))
-@end example
+@end lisp
 
 (In those cases were you only want to tweak a few fields from a package
 definition, you should rely on inheritance instead of copy-pasting everything.
@@ -840,9 +851,7 @@ version when packaging programs for a specific commit.
 Snippets are quoted (i.e. non-evaluated) Scheme code that are a means of patching
 the source.  They are a Guix-y alternative to the traditional @samp{.patch} files.
 Because of the quote, the code in only evaluated when passed to the Guix daemon
-for building.
+for building.  There can be as many snippets as needed.
-
-There can be as many snippet as needed.
 
 Snippets might need additional Guile modules which can be imported from the
 @code{modules} field.
@@ -851,17 +860,17 @@ Snippets might need additional Guile modules which can be imported from the
 
 First, a syntactic comment: See the quasi-quote / comma syntax?
 
-@example
+@lisp
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-@end example
+@end lisp
 
 is equivalent to
 
-@example
+@lisp
     (native-inputs
      (list (list "pkg-config" pkg-config)))
-@end example
+@end lisp
 
 You'll mostly see the former because it's shorter.
 
@@ -883,7 +892,7 @@ being present at build time.
 
 The distinction between the various inputs is important: if a dependency can be
 handled as an @emph{input} instead of a @emph{propagated input}, it should be done so, or
-else it "pollutes" the user profile for no good reason.
+else it ``pollutes'' the user profile for no good reason.
 
 For instance, a user installing a graphical program that depends on a
 command line tool might only be interested in the graphical part, so there is no
@@ -930,10 +939,10 @@ Another  common argument is @code{:make-flags}, which specifies a list of flags
 append when running make, as you would from the command line.  For instance, the
 following flags
 
-@example
+@lisp
 #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))
                    "CC=gcc")
-@end example
+@end lisp
 
 translate into
 
@@ -946,11 +955,11 @@ directory in Make parlance) to @code{(assoc-ref %outputs "out")}, which is a bui
 global variable pointing to the destination directory in the store (something like
 @samp{/gnu/store/...-my-libgit2-20180408}).
 
-Similarly, it's possible to set the "configure" flags.
+Similarly, it's possible to set the configure flags:
 
-@example
+@lisp
 #:configure-flags '("-DUSE_SHA1DC=ON")
-@end example
+@end lisp
 
 The @code{%build-inputs} variable is also generated in scope.  It's an association
 table that maps the input names to their store directories.
@@ -960,7 +969,7 @@ phases include @code{unpack}, @code{configure}, @code{build}, @code{install} and
 more about those phases, you need to work out the appropriate build system
 definition in @samp{$GUIX_CHECKOUT/guix/build/gnu-build-system.scm}:
 
-@example
+@lisp
 (define %standard-phases
   ;; Standard build phases, as a list of symbol/procedure pairs.
   (let-syntax ((phases (syntax-rules ()
@@ -978,16 +987,16 @@ definition in @samp{$GUIX_CHECKOUT/guix/build/gnu-build-system.scm}:
             install-license-files
             reset-gzip-timestamps
             compress-documentation)))
-@end example
+@end lisp
 
 Or from the REPL:
 
-@example
+@lisp
-> (add-to-load-path "/path/to/guix/checkout")
+(add-to-load-path "/path/to/guix/checkout")
-> ,module (guix build gnu-build-system)
+,use (guix build gnu-build-system)
-> (map first %standard-phases)
+(map first %standard-phases)
-(set-SOURCE-DATE-EPOCH set-paths install-locale unpack bootstrap patch-usr-bin-file patch-source-shebangs configure patch-generated-file-shebangs build check install patch-shebangs strip validate-runpath validate-documentation-location delete-info-dir-file patch-dot-desktop-files install-license-files reset-gzip-timestamps compress-documentation)
+@result{} (set-SOURCE-DATE-EPOCH set-paths install-locale unpack bootstrap patch-usr-bin-file patch-source-shebangs configure patch-generated-file-shebangs build check install patch-shebangs strip validate-runpath validate-documentation-location delete-info-dir-file patch-dot-desktop-files install-license-files reset-gzip-timestamps compress-documentation)
-@end example
+@end lisp
 
 If you want to know more about what happens during those phases, consult the
 associated procedures.
@@ -995,7 +1004,7 @@ associated procedures.
 For instance, as of this writing the definition of @code{unpack} for the GNU build
 system is
 
-@example
+@lisp
 (define* (unpack #:key source #:allow-other-keys)
   "Unpack SOURCE in the working directory, and change directory within the
 source.  When SOURCE is a directory, copy it in a sub-directory of the current
@@ -1015,7 +1024,7 @@ working directory."
             (invoke "tar" "xvf" source))
         (chdir (first-subdirectory "."))))
   #t)
-@end example
+@end lisp
 
 Note the @code{chdir} call: it changes the working directory to where the source was
 unpacked.
@@ -1045,14 +1054,14 @@ by their name in those variables.  Thus @code{(assoc-ref outputs "out")} is the
 directory of the main output of the package.  A phase procedure may look like
 this:
 
-@example
+@lisp
 (lambda* (#:key inputs outputs #:allow-other-keys)
   (let (((bash-directory (assoc-ref inputs "bash"))
          (output-directory (assoc-ref outputs "out"))
          (doc-directory (assoc-ref outputs "doc"))
   ; ...
   #t)
-@end example
+@end lisp
 
 The procedure must return @code{#t} on success.  It's brittle to rely on the return
 value of the last expression used to tweak the phase because there is no
@@ -1066,11 +1075,11 @@ argument field.  Indeed, the build code in the package declaration should not be
 evaluated on the client side, but only when passed to the Guix daemon.  This
 mechanism of passing code around two running processes is called @uref{https://arxiv.org/abs/1709.00833, code staging}.
 
-@subsubsection "Utils" functions
+@subsubsection Utility functions
 
 When customizing @code{phases}, we often need to write code that mimics the
 equivalent system invocations (@code{make}, @code{mkdir}, @code{cp}, etc.) commonly used during
-regular "Unix-style" installations.
+regular ``Unix-style'' installations.
 
 Some like @code{chmod} are native to Guile.
 @xref{,,, guile, Guile reference manual} for a complete list.
@@ -1103,7 +1112,7 @@ Run an executable.  This should be used instead of @code{system*}.
 Run the body in a different working directory,
 then restore the previous working directory.
 @item substitute*
-A "sed-like" function.
+A ``@command{sed}-like'' function.
 @end table
 
 @subsubsection Module prefix
@@ -1233,7 +1242,7 @@ $ guix refresh hello --update
 If you've started browsing the existing package definitions, you might have
 noticed that a significant number of them have a @code{inherit} field:
 
-@example
+@lisp
 (define-public adwaita-icon-theme
   (package (inherit gnome-icon-theme)
     (name "adwaita-icon-theme")
@@ -1248,7 +1257,7 @@ noticed that a significant number of them have a @code{inherit} field:
                 "17fpahgh5dyckgz7rwqvzgnhx53cx9kr2xw0szprc6bnqy977fi8"))))
     (native-inputs
      `(("gtk-encode-symbolic-svg" ,gtk+ "bin")))))
-@end example
+@end lisp
 
 All unspecified fields are inherited from the parent package.  This is very
 convenient to create alternative packages, for instance with different source,
@@ -1299,7 +1308,7 @@ The @uref{https://www.gnu.org/software/guix/manual/en/html_node/Defining-Package
 @uref{https://gitlab.com/pjotrp/guix-notes/blob/master/HACKING.org, Pjotr’s hacking guide to GNU Guix}
 
 @item
-@uref{https://www.gnu.org/software/guix/guix-ghm-andreas-20130823.pdf, "GNU Guix: Package without a scheme!"}, by Andreas Enge
+@uref{https://www.gnu.org/software/guix/guix-ghm-andreas-20130823.pdf, ``GNU Guix: Package without a scheme!''}, by Andreas Enge
 @end itemize
 
 @c *********************************************************************
@@ -1533,7 +1542,7 @@ CONFIG_VIRTIO=m
 @end example
 
 After copying all the configuration options, run @code{make localmodconfig}
-again to make sure that you don't have any output starting with "module".
+again to make sure that you don't have any output starting with ``module''.
 After all of these machine specific modules there are a couple more left that
 are also needed.  @code{CONFIG_MODULES} is necessary so that you can build and
 load modules separately and not have everything built into the kernel.

doc/guix.texi

@@ -47,7 +47,7 @@ Copyright @copyright{} 2017 Thomas Danckaert@*
 Copyright @copyright{} 2017 humanitiesNerd@*
 Copyright @copyright{} 2017 Christopher Allan Webber@*
 Copyright @copyright{} 2017, 2018 Marius Bakke@*
-Copyright @copyright{} 2017 Hartmut Goebel@*
+Copyright @copyright{} 2017, 2019 Hartmut Goebel@*
 Copyright @copyright{} 2017, 2019 Maxim Cournoyer@*
 Copyright @copyright{} 2017, 2018, 2019 Tobias Geerinckx-Rice@*
 Copyright @copyright{} 2017 George Clemmer@*
@@ -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
@@ -1368,13 +1370,11 @@ source URLs.  When this option is omitted,
 This means that substitutes may be downloaded from @var{urls}, as long
 as they are signed by a trusted signature (@pxref{Substitutes}).
 
-@cindex build hook
+@cindex offloading
-@item --no-build-hook
+@item --no-offload
-Do not use the @dfn{build hook}.
+Do not use offload builds to other machines (@pxref{Daemon Offload
-
+Setup}).  That is, always build things locally instead of offloading
-The build hook is a helper program that the daemon can start and to
+builds to remote machines.
-which it submits build requests.  This mechanism is used to offload
-builds to other machines (@pxref{Daemon Offload Setup}).
 
 @item --cache-failures
 Cache build failures.  By default, only successful builds are cached.
@@ -2830,7 +2830,8 @@ $ guix package --upgrade . --do-not-upgrade emacs
 @cindex profile declaration
 @cindex profile manifest
 Create a new generation of the profile from the manifest object
-returned by the Scheme code in @var{file}.
+returned by the Scheme code in @var{file}.  This option can be repeated
+several times, in which case the manifests are concatenated.
 
 This allows you to @emph{declare} the profile's contents rather than
 constructing it through a sequence of @code{--install} and similar
@@ -4802,7 +4803,8 @@ As an example, @var{file} might contain a definition like this
 @item --manifest=@var{file}
 @itemx -m @var{file}
 Create an environment for the packages contained in the manifest object
-returned by the Scheme code in @var{file}.
+returned by the Scheme code in @var{file}.  This option can be repeated
+several times, in which case the manifests are concatenated.
 
 This is similar to the same-named option in @command{guix package}
 (@pxref{profile-manifest, @option{--manifest}}) and uses the same
@@ -5176,7 +5178,8 @@ build} (@pxref{Additional Build Options, @code{--expression} in
 @item --manifest=@var{file}
 @itemx -m @var{file}
 Use the packages contained in the manifest object returned by the Scheme
-code in @var{file}.
+code in @var{file}.  This option can be repeated several times, in which
+case the manifests are concatenated.
 
 This has a similar purpose as the same-named option in @command{guix
 package} (@pxref{profile-manifest, @option{--manifest}}) and uses the
@@ -5253,6 +5256,10 @@ added to it or removed from it after extraction of the pack.
 One use case for this is the Guix self-contained binary tarball
 (@pxref{Binary Installation}).
 
+@item --derivation
+@itemx -d
+Print the name of the derivation that builds the pack.
+
 @item --bootstrap
 Use the bootstrap binaries to build the pack.  This option is only
 useful to Guix developers.
@@ -6403,6 +6410,25 @@ passes flags specified by the @code{#:make-maker-flags} or
 Which Perl package is used can be specified with @code{#:perl}.
 @end defvr
 
+@defvr {Scheme Variable} qt-build-system
+This variable is exported by @code{(guix build-system qt)}.  It
+is intended for use with applications using Qt or KDE.
+
+This build system adds the phase @code{qt-wrap} to the ones defined by
+@var{cmake-build-system}, after the @code{install} phase.
+
+This phase searches for Qt5 plugin paths, QML paths and some XDG in the inputs
+and output.  In case some path is found, all programs in the output's
+@file{bin/}, @file{sbin/}, @file{libexec/} and @file{lib/libexec/} directories
+are wrapped in scripts defining the necessary environment variables.
+
+It is possible to exclude specific package outputs from that wrapping process
+by listing their names in the @code{#:qt-wrap-excluded-outputs} parameter.
+This is useful when an output is known not to contain any Qt binaries, and
+where wrapping would gratuitously add a dependency of that output on Qt, KDE,
+or such.
+@end defvr
+
 @defvr {Scheme Variable} r-build-system
 This variable is exported by @code{(guix build-system r)}.  It
 implements the build procedure used by @uref{https://r-project.org, R}
@@ -7677,10 +7703,13 @@ content is directly passed as a string.
 
 @deffn {Scheme Procedure} local-file @var{file} [@var{name}] @
    [#:recursive? #f] [#:select? (const #t)]
-Return an object representing local file @var{file} to add to the store; this
+Return an object representing local file @var{file} to add to the store;
-object can be used in a gexp.  If @var{file} is a relative file name, it is looked
+this object can be used in a gexp.  If @var{file} is a literal string
-up relative to the source file where this form appears.  @var{file} will be added to
+denoting a relative file name, it is looked up relative to the source
-the store under @var{name}--by default the base name of @var{file}.
+file where it appears; if @var{file} is not a literal string, it is
+looked up relative to the current working directory at run time.
+@var{file} will be added to the store under @var{name}--by default the
+base name of @var{file}.
 
 When @var{recursive?} is true, the contents of @var{file} are added recursively; if @var{file}
 designates a flat file and @var{recursive?} is true, its contents are added, and its
@@ -8046,9 +8075,9 @@ the end of the build log.  This is useful when debugging build issues.
 @xref{Debugging Build Failures}, for tips and tricks on how to debug
 build issues.
 
-This option has no effect when connecting to a remote daemon with a
+This option implies @option{--no-offload}, and it has no effect when
-@code{guix://} URI (@pxref{The Store, the @code{GUIX_DAEMON_SOCKET}
+connecting to a remote daemon with a @code{guix://} URI (@pxref{The
-variable}).
+Store, the @code{GUIX_DAEMON_SOCKET} variable}).
 
 @item --keep-going
 @itemx -k
@@ -8105,10 +8134,10 @@ stashing one of the build results with @code{guix archive --export}
 (@pxref{Invoking guix archive}), then rebuilding, and finally comparing
 the two results.
 
-@item --no-build-hook
+@item --no-offload
-Do not attempt to offload builds @i{via} the ``build hook'' of the daemon
+Do not use offload builds to other machines (@pxref{Daemon Offload
-(@pxref{Daemon Offload Setup}).  That is, always build things locally
+Setup}).  That is, always build things locally instead of offloading
-instead of offloading builds to remote machines.
+builds to remote machines.
 
 @item --max-silent-time=@var{seconds}
 When the build or substitution process remains silent for more than
@@ -11926,6 +11955,7 @@ 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
@@ -15580,6 +15610,13 @@ capabilities to ordinary users.  For example, an ordinary user can be granted
 the capability to suspend the system if the user is logged in locally.
 @end deffn
 
+@defvr {Scheme Variable} polkit-wheel-service
+Service that adds the @code{wheel} group as admins to the Polkit
+service.  This makes it so that users in the @code{wheel} group are queried
+for their own passwords when performing administrative actions instead of
+@code{root}'s, similar to the behaviour used by @code{sudo}.
+@end defvr
+
 @defvr {Scheme Variable} upower-service-type
 Service that runs @uref{https://upower.freedesktop.org/, @command{upowerd}}, a
 system-wide monitor for power consumption and battery levels, with the given
@@ -15716,6 +15753,41 @@ bluetooth keyboard or mouse.
 Users need to be in the @code{lp} group to access the D-Bus service.
 @end deffn
 
+@defvr {Scheme Variable} gnome-keyring-service-type
+This is the type of the service that adds the
+@uref{https://wiki.gnome.org/Projects/GnomeKeyring, GNOME Keyring}.  Its
+value is a @code{gnome-keyring-configuration} object (see below.)
+
+This service adds the @code{gnome-keyring} package to the system profile
+and extends PAM with entries using @code{pam_gnome_keyring.so}, unlocking
+a user's login keyring when they log in or setting its password with passwd.
+@end defvr
+
+@deftp {Data Type} gnome-keyring-configuration
+Configuration record for the GNOME Keyring service.
+
+@table @asis
+@item @code{keyring} (default: @code{gnome-keyring})
+The GNOME keyring package to use.
+
+@item @code{pam-services}
+A list of @code{(@var{service} . @var{kind})} pairs denoting PAM
+services to extend, where @var{service} is the name of an existing
+service to extend and @var{kind} is one of @code{login} or
+@code{passwd}.
+
+If @code{login} is given, it adds an optional
+@code{pam_gnome_keyring.so} to the auth block without arguments and to
+the session block with @code{auto_start}.  If @code{passwd} is given, it
+adds an optional @code{pam_gnome_keyring.so} to the password block
+without arguments.
+
+By default, this field contains ``gdm-password'' with the value @code{login}
+and ``passwd'' is with the value @code{passwd}.
+@end table
+@end deftp
+
+
 @node Sound Services
 @subsection Sound Services
 
@@ -20302,7 +20374,7 @@ the corresponding user and/or group is present on the system.
 It is possible to configure a FastCGI-backed web service to pass HTTP
 authentication information from the front-end to the back-end, and to
 allow @code{fcgiwrap} to run the back-end process as a corresponding
-local user.  To enable this capability on the back-end., run
+local user.  To enable this capability on the back-end, run
 @code{fcgiwrap} as the @code{root} user and group.  Note that this
 capability also has to be configured on the front-end as well.
 @end table
@@ -20355,7 +20427,7 @@ User who will own the php worker processes.
 Group of the worker processes.
 @item @code{socket-user} (default: @code{php-fpm})
 User who can speak to the php-fpm socket.
-@item @code{socket-group} (default: @code{php-fpm})
+@item @code{socket-group} (default: @code{nginx})
 Group that can speak to the php-fpm socket.
 @item @code{pid-file} (default: @code{(string-append "/var/run/php" (version-major (package-version php)) "-fpm.pid")})
 The process id of the php-fpm process is written to this file
@@ -20364,7 +20436,7 @@ once the service has started.
 Log for the php-fpm master process.
 @item @code{process-manager} (default: @code{(php-fpm-dynamic-process-manager-configuration)})
 Detailed settings for the php-fpm process manager.
-Must be either:
+Must be one of:
 @table @asis
 @item @code{<php-fpm-dynamic-process-manager-configuration>}
 @item @code{<php-fpm-static-process-manager-configuration>}
@@ -24651,6 +24723,89 @@ 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
 
@@ -26282,8 +26437,8 @@ with an @code{environment} of @code{managed-host-environment-type}.
 @item @code{build-locally?} (default: @code{#t})
 If false, system derivations will be built on the machine being deployed to.
 @item @code{system}
-The Nix system type describing the architecture of the machine being deployed
+The system type describing the architecture of the machine being deployed
-to. This should look something like ``x86_64-linux''.
+to---e.g., @code{"x86_64-linux"}.
 @item @code{authorize?} (default: @code{#t})
 If true, the coordinator's signing key will be added to the remote's ACL
 keyring.
@@ -26292,6 +26447,18 @@ keyring.
 @item @code{identity} (default: @code{#f})
 If specified, the path to the SSH private key to use to authenticate with the
 remote host.
+
+@item @code{host-key} (default: @code{#f})
+This should be the SSH host key of the machine, which looks like this:
+
+@example
+ssh-ed25519 AAAAC3Nz@dots{} root@@example.org
+@end example
+
+When @code{host-key} is @code{#f}, the server is authenticated against
+the @file{~/.ssh/known_hosts} file, just like the OpenSSH @command{ssh}
+client does.
+
 @end table
 @end deftp
 

etc/completion/fish/guix.fish

@@ -133,7 +133,7 @@ complete -f -c guix -n '__fish_guix_using_command pull' -l url -d 'download the
 complete -f -c guix -n '__fish_guix_using_command pull' -l bootstrap -d 'use the bootstrap Guile to build the new Guix'
 
 #### system
-set -l remotecommands reconfigure roll-back switch-generation list-generations build container vm vm-image disk-image init extension-graph shepherd-graph load-path keep-failed keep-going dry-run fallback no-substitutes substitutes-urls no-grafts no-build-hook max-silent-time timeout verbosity rounds cores max-jobs derivation on-error image-size no-grub share expose full-boot
+set -l remotecommands reconfigure roll-back switch-generation list-generations build container vm vm-image disk-image init extension-graph shepherd-graph load-path keep-failed keep-going dry-run fallback no-substitutes substitutes-urls no-grafts no-offload max-silent-time timeout verbosity rounds cores max-jobs derivation on-error image-size no-grub share expose full-boot
 complete -f -c guix -n '__fish_guix_needs_command' -a system -d 'Build the operating system declared in FILE according to ACTION.'
 complete -f -c guix -n '__fish_guix_using_command system' -l reconfigure -d 'switch to a new operating system configuration'
 complete -f -c guix -n '__fish_guix_using_command system' -l roll-back -d 'switch to the previous operating system configuration'
@@ -156,7 +156,7 @@ complete -f -c guix -n '__fish_guix_using_command system' -l fallback -d 'fall b
 complete -f -c guix -n '__fish_guix_using_command system' -l no-substitutes -d 'build instead of resorting to pre-built substitutes'
 complete -f -c guix -n '__fish_guix_using_command system' -a "--substitute-urls=" -d 'fetch substitute from URLS if they are authorized'
 complete -f -c guix -n '__fish_guix_using_command system' -l no-grafts -d 'do not graft packages'
-complete -f -c guix -n '__fish_guix_using_command system' -l no-build-hook -d 'do not attempt to offload builds via the build hook'
+complete -f -c guix -n '__fish_guix_using_command system' -l no-offload -d 'do not attempt to offload builds'
 complete -f -c guix -n '__fish_guix_using_command system' -a "--max-silent-time=" -d 'mark the build as failed after SECONDS of silence'
 complete -f -c guix -n '__fish_guix_using_command system' -a "--timeout=" -d 'mark the build as failed after SECONDS of activity'
 complete -f -c guix -n '__fish_guix_using_command system' -a "--verbosity=" -d 'use the given verbosity LEVEL'
@@ -174,7 +174,7 @@ complete -f -c guix -n '__fish_guix_using_command system' -a "--expose=" -d 'for
 complete -f -c guix -n '__fish_guix_using_command system' -l full-boot -d 'for \'vm\', make a full boot sequence'
 
 #### build
-set -l remotecommands expression file source sources system target derivations check repair root quiet log-file load-path keep-failed keep-going dry-run fallback no-substitutes substitute-urls no-grafts no-build-hook max-silent-time timeout verbosity rounds cores max-jobs with-source with-input with-graft
+set -l remotecommands expression file source sources system target derivations check repair root quiet log-file load-path keep-failed keep-going dry-run fallback no-substitutes substitute-urls no-grafts no-offload max-silent-time timeout verbosity rounds cores max-jobs with-source with-input with-graft
 complete -f -c guix -n '__fish_guix_needs_command' -a build -d 'Build the given PACKAGE-OR-DERIVATION and return their output paths.'
 complete -f -c guix -n '__fish_guix_using_command build' -a "--expression=" -d 'build the package or derivation EXPR evaluates to'
 complete -f -c guix -n '__fish_guix_using_command build' -s f -d 'build the package or derivation that the code within FILE evaluates to' --exclusive --arguments "(ls -ap)"
@@ -201,7 +201,7 @@ complete -f -c guix -n '__fish_guix_using_command build' -l fallback -d 'fall ba
 complete -f -c guix -n '__fish_guix_using_command build' -l no-substitutes -d 'build instead of resorting to pre-built substitutes'
 complete -f -c guix -n '__fish_guix_using_command build' -a "--substitute-urls=" -d 'fetch substitute from URLS if they are authorized'
 complete -f -c guix -n '__fish_guix_using_command build' -l no-grafts -d 'do not graft packages'
-complete -f -c guix -n '__fish_guix_using_command build' -l no-build-hook -d 'do not attempt to offload builds via the build hook'
+complete -f -c guix -n '__fish_guix_using_command build' -l no-offload -d 'do not attempt to offload builds'
 complete -f -c guix -n '__fish_guix_using_command build' -a "--max-silent-time=" -d 'mark the build as failed after SECONDS of silence'
 complete -f -c guix -n '__fish_guix_using_command build' -a "--timeout=" -d 'mark the build as failed after SECONDS of activity'
 complete -f -c guix -n '__fish_guix_using_command build' -a "--verbosity=" -d 'use the given verbosity LEVEL'
@@ -215,7 +215,7 @@ complete -f -c guix -n '__fish_guix_using_command build' -a "--with-input=" -d '
 complete -f -c guix -n '__fish_guix_using_command build' -a "--with-graft=" -d 'PACKAGE=REPLACEMENT .. graft REPLACEMENT on packages that refer to PACKAGE'
 
 #### package
-set -l remotecommands install install-from-expression install-from-file remove upgrade manifest do-no-upgrade roll-back search-paths list-generations delete-generations switch-generation profile bootstrap verbose search list-installed list-available show load-path keep-failed keep-going dry-run fallback no.substitutes substitute-urls no-grafts no-build-hook max-silent-time timenout verbosity rounds cores max-jobs with-source with-input with-graft
+set -l remotecommands install install-from-expression install-from-file remove upgrade manifest do-no-upgrade roll-back search-paths list-generations delete-generations switch-generation profile bootstrap verbose search list-installed list-available show load-path keep-failed keep-going dry-run fallback no.substitutes substitute-urls no-grafts no-offload max-silent-time timenout verbosity rounds cores max-jobs with-source with-input with-graft
 complete -f -c guix -n '__fish_guix_needs_command' -a package -d 'Install, remove, or upgrade packages in a single transaction.'
 complete -f -c guix -n '__fish_guix_using_command package' -s i -l install -d 'install PACKAGEs'
 complete -f -c guix -n '__fish_guix_using_command package' -s e -d 'install the package EXP evaluates to'
@@ -252,7 +252,7 @@ complete -f -c guix -n '__fish_guix_using_command package' -l fallback -d 'fall
 complete -f -c guix -n '__fish_guix_using_command package' -l no-substitutes -d 'build instead of resorting to pre-built substitutes'
 complete -f -c guix -n '__fish_guix_using_command package' -a "--substitute-urls=" -d 'URLS fetch substitute from URLS if they are authorized'
 complete -f -c guix -n '__fish_guix_using_command package' -l no-grafts -d 'do not graft packages'
-complete -f -c guix -n '__fish_guix_using_command package' -l no-build-hook -d 'do not attempt to offload builds via the build hook'
+complete -f -c guix -n '__fish_guix_using_command package' -l no-offload -d 'do not attempt to offload builds'
 complete -f -c guix -n '__fish_guix_using_command package' -a "--max-silent-time=" -d 'SECONDS mark the build as failed after SECONDS of silence'
 complete -f -c guix -n '__fish_guix_using_command package' -a "--timeout=" -d 'SECONDS mark the build as failed after SECONDS of activity'
 complete -f -c guix -n '__fish_guix_using_command package' -a "--verbosity=" -d 'LEVEL use the given verbosity LEVEL'
@@ -391,7 +391,7 @@ complete -f -c guix -n '__fish_guix_using_command gc' -l list-failures -d 'list
 complete -f -c guix -n '__fish_guix_using_command gc' -l clear-failures -d 'remove PATHS from the set of cached failures'
 
 #### environment
-set -l remotecommands expression load ad-hoc pure search-paths system root container network share expose bootstrap load-path keep-failed keep-going dry-run fallback no-substitutes substitute-urls no-grafts no-build-hook max-silent-time timeout verbosity rounds cores max-jobs
+set -l remotecommands expression load ad-hoc pure search-paths system root container network share expose bootstrap load-path keep-failed keep-going dry-run fallback no-substitutes substitute-urls no-grafts no-offload max-silent-time timeout verbosity rounds cores max-jobs
 complete -f -c guix -n '__fish_guix_needs_command' -a environment -d 'Build an environment that includes the dependencies of PACKAGE and execute COMMAND or an interactive shell in that environment.'
 complete -f -c guix -n '__fish_guix_using_command environment' -s e -d 'Create environment for the package that EXPR evaluates to'
 complete -f -c guix -n '__fish_guix_using_command environment' -a "--expression=" -d 'Create environment for the package that EXPR evaluates to'
@@ -418,7 +418,7 @@ complete -f -c guix -n '__fish_guix_using_command environment' -l fallback -d 'f
 complete -f -c guix -n '__fish_guix_using_command environment' -l no-substitutes -d 'build instead of resorting to pre-built substitutes'
 complete -f -c guix -n '__fish_guix_using_command environment' -a "--substitute-urls=" -d 'fetch substitute from URLS if they are authorized'
 complete -f -c guix -n '__fish_guix_using_command environment' -l no-grafts -d 'do not graft packages'
-complete -f -c guix -n '__fish_guix_using_command environment' -l no-build-hook -d 'do not attempt to offload builds via the build hook'
+complete -f -c guix -n '__fish_guix_using_command environment' -l no-offload -d 'do not attempt to offload builds'
 complete -f -c guix -n '__fish_guix_using_command environment' -a "--max-silent-time=" -d 'mark the build as failed after SECONDS of silence'
 complete -f -c guix -n '__fish_guix_using_command environment' -a "--timeout=" -d 'mark the build as failed after SECONDS of activity'
 complete -f -c guix -n '__fish_guix_using_command environment' -a "--verbosity=" -d 'use the given verbosity LEVEL'
@@ -432,7 +432,7 @@ complete -f -c guix -n '__fish_guix_using_command environment' -a "--max-jobs="
 complete -f -c guix -n '__fish_guix_needs_command' -a edit -d 'Start $VISUAL or $EDITOR to edit the definitions of PACKAGE.'
 
 #### copy
-set -l remotecommands to= from= load-path= keep-failed keep-going dry-run fallback no-substitutes substitute-urls= no-grafts no-build-hook max-silent-time= timeout= verbosity= rounds= cores= max-jobs=
+set -l remotecommands to= from= load-path= keep-failed keep-going dry-run fallback no-substitutes substitute-urls= no-grafts no-offload max-silent-time= timeout= verbosity= rounds= cores= max-jobs=
 complete -f -c guix -n '__fish_guix_needs_command' -a copy -d 'Copy ITEMS to or from the specified host over SSH.'
 complete -f -c guix -n '__fish_guix_using_command copy' -a "--to=" -d 'send ITEMS to HOST'
 complete -f -c guix -n '__fish_guix_using_command copy' -a "--from=" -d 'receive ITEMS from HOST'
@@ -445,7 +445,7 @@ complete -f -c guix -n '__fish_guix_using_command copy' -l fallback -d 'fall bac
 complete -f -c guix -n '__fish_guix_using_command copy' -l no-substitutes -d 'build instead of resorting to pre-built substitutes'
 complete -f -c guix -n '__fish_guix_using_command copy' -a "--substitute-urls=" -d 'fetch substitute from URLS if they are authorized'
 complete -f -c guix -n '__fish_guix_using_command copy' -l no-grafts -d 'do not graft packages'
-complete -f -c guix -n '__fish_guix_using_command copy' -l no-build-hook -d 'do not attempt to offload builds via the build hook'
+complete -f -c guix -n '__fish_guix_using_command copy' -l no-offload -d 'do not attempt to offload builds'
 complete -f -c guix -n '__fish_guix_using_command copy' -a "--max-silent-time=" -d 'mark the build as failed after SECONDS of silence'
 complete -f -c guix -n '__fish_guix_using_command copy' -a "--timeout=" -d 'mark the build as failed after SECONDS of activity'
 complete -f -c guix -n '__fish_guix_using_command copy' -a "--verbosity=" -d 'use the given verbosity LEVEL'
@@ -467,7 +467,7 @@ complete -f -c guix -n '__fish_guix_using_command challenge' -a "--substitute-ur
 complete -f -c guix -n '__fish_guix_using_command challenge' -s v -l verbose -d 'show details about successful comparisons'
 
 #### archive
-set -l remotecommands export format= recursive import missing extract= generate-key authorize expression= source system= target= load-path= keep-failed keep-going dry-run fallback no-substitutes substitute-urls= no-grafts no-build-hook max-silent-time= timeout= verbosity= rounds= cores= max-jobs=
+set -l remotecommands export format= recursive import missing extract= generate-key authorize expression= source system= target= load-path= keep-failed keep-going dry-run fallback no-substitutes substitute-urls= no-grafts no-offload max-silent-time= timeout= verbosity= rounds= cores= max-jobs=
 complete -f -c guix -n '__fish_guix_needs_command' -a archive -d 'Export/import one or more packages from/to the store.'
 complete -f -c guix -n '__fish_guix_using_command archive' -l export -d 'export the specified files/packages to stdout'
 complete -f -c guix -n '__fish_guix_using_command archive' -a "--format=" -d 'export files/packages in the specified format FMT'
@@ -489,7 +489,7 @@ complete -f -c guix -n '__fish_guix_using_command archive' -l fallback -d 'fall
 complete -f -c guix -n '__fish_guix_using_command archive' -l no-substitutes -d 'build instead of resorting to pre-built substitutes'
 complete -f -c guix -n '__fish_guix_using_command archive' -a "--substitute-urls=" -d 'fetch substitute from URLS if they are authorized'
 complete -f -c guix -n '__fish_guix_using_command archive' -l no-grafts -d 'do not graft packages'
-complete -f -c guix -n '__fish_guix_using_command archive' -l no-build-hook -d 'do not attempt to offload builds via the build hook'
+complete -f -c guix -n '__fish_guix_using_command archive' -l no-offload -d 'do not attempt to offload builds'
 complete -f -c guix -n '__fish_guix_using_command archive' -a "--max-silent-time=" -d 'mark the build as failed after SECONDS of silence'
 complete -f -c guix -n '__fish_guix_using_command archive' -a "--timeout=" -f -d 'mark the build as failed after SECONDS of activity'
 complete -f -c guix -n '__fish_guix_using_command archive' -a "--verbosity=" -d 'use the given verbosity LEVEL'
@@ -498,7 +498,7 @@ complete -f -c guix -n '__fish_guix_using_command archive' -a "--cores=" -d 'all
 complete -f -c guix -n '__fish_guix_using_command archive' -a "--max-jobs=" -d 'allow at most N build jobs'
 
 #### pack
-set -l remotecommands --load-path= --keep-failed --keep-going --dry-run --fallback --no-substitutes --substitute-urls= --no-grafts --no-build-hook --max-silent-time= --timeout= --verbosity= --rounds= --cores= --max-jobs= --with-source= --with-input= --with-graft= --format= --expression= --system= --target= --compression= --symlink= --localstatedir --help --version
+set -l remotecommands --load-path= --keep-failed --keep-going --dry-run --fallback --no-substitutes --substitute-urls= --no-grafts --no-offload --max-silent-time= --timeout= --verbosity= --rounds= --cores= --max-jobs= --with-source= --with-input= --with-graft= --format= --expression= --system= --target= --compression= --symlink= --localstatedir --help --version
 complete -f -c guix -n '__fish_guix_needs_command' -a pack -d 'Create a bundle of PACKAGE.'
 complete -f -c guix -n '__fish_guix_using_command pack' -a "--load-path=" -d 'prepend DIR to the package module search path'
 complete -f -c guix -n '__fish_guix_using_command pack' -s L -d 'prepend DIR to the package module search path'
@@ -512,7 +512,7 @@ complete -f -c guix -n '__fish_guix_using_command pack' -a "--fallback" -d 'fall
 complete -f -c guix -n '__fish_guix_using_command pack' -a "--no-substitutes" -d 'build instead of resorting to pre-built substitutes'
 complete -f -c guix -n '__fish_guix_using_command pack' -a "--substitute-urls=" -d 'fetch substitute from URLS if they are authorized'
 complete -f -c guix -n '__fish_guix_using_command pack' -a "--no-grafts" -d 'do not graft packages'
-complete -f -c guix -n '__fish_guix_using_command pack' -a "--no-build-hook" -d 'do not attempt to offload builds via the build hook'
+complete -f -c guix -n '__fish_guix_using_command pack' -a "--no-offload" -d 'do not attempt to offload builds via the build hook'
 complete -f -c guix -n '__fish_guix_using_command pack' -a "--max-silent-time=" -d 'mark the build as failed after SECONDS of silence'
 complete -f -c guix -n '__fish_guix_using_command pack' -a "--timeout=" -d 'mark the build as failed after SECONDS of activity'
 complete -f -c guix -n '__fish_guix_using_command pack' -a "--verbosity=" -d 'use the given verbosity LEVEL'

etc/completion/zsh/_guix

@@ -87,7 +87,7 @@ _guix_list_installed_packages()
         '--no-substitutes[build instead of resorting to pre-built substitutes]' \
         '--substitute-urls=[fetch substitute from URLS if they are authorized]:URLS:_urls' \
         '--no-grafts[do not graft packages]' \
-        '--no-build-hook[do not attempt to offload builds via the build hook]' \
+        '--no-offload[do not attempt to offload builds]' \
         '--max-silent-time=[mark the build as failed after SECONDS of silence]:SECONDS' \
         '--timeout=[mark the build as failed after SECONDS of activity]:SECONDS' \
         '--verbosity=[use the given verbosity LEVEL]:LEVEL' \
@@ -158,7 +158,7 @@ _guix_list_installed_packages()
         '--no-substitutes[build instead of resorting to pre-built substitutes]' \
         '--substitute-urls=[fetch substitute from URLS if they are authorized]:URLS:_urls' \
         '--no-grafts[do not graft packages]' \
-        '--no-build-hook[do not attempt to offload builds via the build hook]' \
+        '--no-offload[do not attempt to offload builds]' \
         '--max-silent-time=[mark the build as failed after SECONDS of silence]:SECONDS' \
         '--timeout=[mark the build as failed after SECONDS of activity]:SECONDS' \
         '--verbosity=[use the given verbosity LEVEL]:LEVEL' \
@@ -282,7 +282,7 @@ _guix_list_installed_packages()
         '--no-substitutes[build instead of resorting to pre-built substitutes]' \
         '--substitute-urls=[fetch substitute from URLS if they are authorized]:URLS:_urls' \
         '--no-grafts[do not graft packages]' \
-        '--no-build-hook[do not attempt to offload builds via the build hook]' \
+        '--no-offload[do not attempt to offload builds]' \
         '--max-silent-time=[mark the build as failed after SECONDS of silence]:SECONDS' \
         '--timeout=[mark the build as failed after SECONDS of activity]:SECONDS' \
         '--verbosity=[use the given verbosity LEVEL]:LEVEL' \
@@ -374,7 +374,7 @@ _guix_list_installed_packages()
         '--no-substitutes[build instead of resorting to pre-built substitutes]' \
         '--substitute-urls=[fetch substitute from URLS if they are authorized]:URL:_urls' \
         '--no-grafts[do not graft packages]' \
-        '--no-build-hook[do not attempt to offload builds via the build hook]' \
+        '--no-offload[do not attempt to offload builds]' \
         '--max-silent-time=[mark the build as failed after SECONDS of silence]:SECONDS' \
         '--timeout=[mark the build as failed after SECONDS of activity]:SECONDS' \
         '--verbosity=[use the given verbosity LEVEL]:LEVEL' \

etc/guix-install.sh

@@ -439,6 +439,7 @@ main()
 
     _msg "${INF}system is ${ARCH_OS}"
 
+    umask 0022
     tmp_path="$(mktemp -t -d guix.XXX)"
 
     guix_get_bin_list "${GNU_URL}"

etc/news.scm

@@ -19,9 +19,9 @@ It can be used to install different versions of packages, and to
 re-create computational environments exactly as used in the past.")
               (de "Der neue Befehl @command{guix time-machine} vereinfacht
 den Zugriff auf ältere oder neuere Guix-Versionen als die installierte.
-Er kann zur Installation bestimmer Paketversionen verwendet werden, aber
+Er kann zur Installation bestimmter Paketversionen verwendet werden, aber
 auch zur Wiederherstellung von Entwicklungsumgebungen, wie sie in der
-Vergagngenheit verwendet wurden.")
+Vergangenheit verwendet wurden.")
               (fr "La nouvelle commande @command{guix time-machine}
 facilite l'accès à des versions antérieures ou postérieures par rapport
 à la version installée.  Elle sert à installer des versions spécifiques

gnu/build/file-systems.scm

@@ -581,11 +581,7 @@ corresponds to the symbols listed in FLAGS."
        0))))
 
 (define* (mount-file-system fs #:key (root "/root"))
-  "Mount the file system described by FS, a <file-system> object, under ROOT.
+  "Mount the file system described by FS, a <file-system> object, under ROOT."
-
-DEVICE, MOUNT-POINT, and TYPE must be strings; OPTIONS can be a string or #f;
-FLAGS must be a list of symbols.  CHECK? is a Boolean indicating whether to
-run a file system check."
 
   (define (mount-nfs source mount-point type flags options)
     (let* ((idx (string-rindex source #\:))

gnu/build/linux-boot.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
+;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -357,15 +358,16 @@ the last argument of `mknod'."
           (filter-map string->number (scandir "/proc")))))
 
 (define* (mount-root-file-system root type
-                                 #:key volatile-root?)
+                                 #:key volatile-root? options)
   "Mount the root file system of type TYPE at device ROOT.  If VOLATILE-ROOT?
 is true, mount ROOT read-only and make it an overlay with a writable tmpfs
-using the kernel built-in overlayfs."
+using the kernel built-in overlayfs.  OPTIONS indicates the options to use
+to mount ROOT."
 
   (if volatile-root?
       (begin
         (mkdir-p "/real-root")
-        (mount root "/real-root" type MS_RDONLY)
+        (mount root "/real-root" type MS_RDONLY options)
         (mkdir-p "/rw-root")
         (mount "none" "/rw-root" "tmpfs")
 
@@ -382,7 +384,7 @@ using the kernel built-in overlayfs."
                "lowerdir=/real-root,upperdir=/rw-root/upper,workdir=/rw-root/work"))
       (begin
         (check-file-system root type)
-        (mount root "/root" type)))
+        (mount root "/root" type 0 options)))
 
   ;; Make sure /root/etc/mtab is a symlink to /proc/self/mounts.
   (false-if-exception
@@ -472,83 +474,90 @@ upon error."
              mounts)
         "ext4"))
 
+  (define root-fs-options
+    (any (lambda (fs)
+           (and (root-mount-point? fs)
+                (file-system-options fs)))
+         mounts))
+
   (display "Welcome, this is GNU's early boot Guile.\n")
   (display "Use '--repl' for an initrd REPL.\n\n")
 
   (call-with-error-handling
-   (lambda ()
+    (lambda ()
-     (mount-essential-file-systems)
+      (mount-essential-file-systems)
-     (let* ((args    (linux-command-line))
+      (let* ((args    (linux-command-line))
-            (to-load (find-long-option "--load" args))
+             (to-load (find-long-option "--load" args))
-            (root    (find-long-option "--root" args)))
+             (root    (find-long-option "--root" args)))
 
-       (when (member "--repl" args)
+        (when (member "--repl" args)
-         (start-repl))
+          (start-repl))
 
-       (display "loading kernel modules...\n")
+        (display "loading kernel modules...\n")
-       (load-linux-modules-from-directory linux-modules
+        (load-linux-modules-from-directory linux-modules
-                                          linux-module-directory)
+                                           linux-module-directory)
 
-       (when keymap-file
+        (when keymap-file
-         (let ((status (system* "loadkeys" keymap-file)))
+          (let ((status (system* "loadkeys" keymap-file)))
-           (unless (zero? status)
+            (unless (zero? status)
-             ;; Emit a warning rather than abort when we cannot load
+              ;; Emit a warning rather than abort when we cannot load
-             ;; KEYMAP-FILE.
+              ;; KEYMAP-FILE.
-             (format (current-error-port)
+              (format (current-error-port)
-                     "warning: 'loadkeys' exited with status ~a~%"
+                      "warning: 'loadkeys' exited with status ~a~%"
-                     status))))
+                      status))))
 
-       (when qemu-guest-networking?
+        (when qemu-guest-networking?
-         (unless (configure-qemu-networking)
+          (unless (configure-qemu-networking)
-           (display "network interface is DOWN\n")))
+            (display "network interface is DOWN\n")))
 
-       ;; Prepare the real root file system under /root.
+        ;; Prepare the real root file system under /root.
-       (unless (file-exists? "/root")
+        (unless (file-exists? "/root")
-         (mkdir "/root"))
+          (mkdir "/root"))
 
-       (when (procedure? pre-mount)
+        (when (procedure? pre-mount)
-         ;; Do whatever actions are needed before mounting the root file
+          ;; Do whatever actions are needed before mounting the root file
-         ;; system--e.g., installing device mappings.  Error out when the
+          ;; system--e.g., installing device mappings.  Error out when the
-         ;; return value is false.
+          ;; return value is false.
-         (unless (pre-mount)
+          (unless (pre-mount)
-           (error "pre-mount actions failed")))
+            (error "pre-mount actions failed")))
 
-       (setenv "EXT2FS_NO_MTAB_OK" "1")
+        (setenv "EXT2FS_NO_MTAB_OK" "1")
 
-       (if root
+        (if root
-           ;; The "--root=SPEC" kernel command-line option always provides a
+            ;; The "--root=SPEC" kernel command-line option always provides a
-           ;; string, but the string can represent a device, a UUID, or a
+            ;; string, but the string can represent a device, a UUID, or a
-           ;; label.  So check for all three.
+            ;; label.  So check for all three.
-           (let ((root (cond ((string-prefix? "/" root) root)
+            (let ((root (cond ((string-prefix? "/" root) root)
-                             ((uuid root) => identity)
+                              ((uuid root) => identity)
-                             (else (file-system-label root)))))
+                              (else (file-system-label root)))))
-             (mount-root-file-system (canonicalize-device-spec root)
+              (mount-root-file-system (canonicalize-device-spec root)
-                                     root-fs-type
+                                      root-fs-type
-                                     #:volatile-root? volatile-root?))
+                                      #:volatile-root? volatile-root?
-           (mount "none" "/root" "tmpfs"))
+                                      #:options root-fs-options))
+            (mount "none" "/root" "tmpfs"))
 
-       ;; Mount the specified file systems.
+        ;; Mount the specified file systems.
-       (for-each mount-file-system
+        (for-each mount-file-system
-                 (remove root-mount-point? mounts))
+                  (remove root-mount-point? mounts))
 
-       (setenv "EXT2FS_NO_MTAB_OK" #f)
+        (setenv "EXT2FS_NO_MTAB_OK" #f)
 
-       (if to-load
+        (if to-load
-           (begin
+            (begin
-             (switch-root "/root")
+              (switch-root "/root")
-             (format #t "loading '~a'...\n" to-load)
+              (format #t "loading '~a'...\n" to-load)
 
-             (primitive-load to-load)
+              (primitive-load to-load)
 
-             (format (current-error-port)
+              (format (current-error-port)
-                     "boot program '~a' terminated, rebooting~%"
+                      "boot program '~a' terminated, rebooting~%"
-                     to-load)
+                      to-load)
-             (sleep 2)
+              (sleep 2)
-             (reboot))
+              (reboot))
-           (begin
+            (begin
-             (display "no boot file passed via '--load'\n")
+              (display "no boot file passed via '--load'\n")
-             (display "entering a warm and cozy REPL\n")
+              (display "entering a warm and cozy REPL\n")
-             (start-repl)))))
+              (start-repl)))))
-   #:on-error on-error))
+    #:on-error on-error))
 
 ;;; linux-initrd.scm ends here

gnu/build/vm.scm

@@ -70,9 +70,10 @@
   (let ((cpu (substring system 0
                         (string-index system #\-))))
     (string-append "qemu-system-"
-                   (if (string-match "^i[3456]86$" cpu)
+                   (cond
-                       "i386"
+                    ((string-match "^i[3456]86$" cpu) "i386")
-                       cpu))))
+                    ((string-match "armhf" cpu) "arm")
+                    (else cpu)))))
 
 (define* (load-in-linux-vm builder
                            #:key

gnu/ci.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
-;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018, 2019 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -374,6 +374,17 @@ valid."
                              load-manifest)
                     manifests))))
 
+(define (find-current-checkout arguments)
+  "Find the first checkout of ARGUMENTS that provided the current file.
+Return #f if no such checkout is found."
+  (let ((current-root
+         (canonicalize-path
+          (string-append (dirname (current-filename)) "/.."))))
+    (find (lambda (argument)
+            (and=> (assq-ref argument 'file-name)
+                   (lambda (name)
+                     (string=? name current-root)))) arguments)))
+
 
 ;;;
 ;;; Hydra entry point.
@@ -396,13 +407,8 @@ valid."
       ((? string? str) (call-with-input-string str read))))
 
   (define checkout
-    ;; Extract metadata about the 'guix' checkout.  Its key in ARGUMENTS may
+    (or (find-current-checkout arguments)
-    ;; vary, so pick up the first one that's neither 'subset' nor 'systems'.
+        (assq-ref arguments 'superior-guix-checkout)))
-    (any (match-lambda
-           ((key . value)
-            (and (not (memq key '(systems subset)))
-                 value)))
-         arguments))
 
   (define commit
     (assq-ref checkout 'revision))

gnu/local.mk

@@ -308,6 +308,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/linux.scm			\
   %D%/packages/lirc.scm				\
   %D%/packages/lisp.scm				\
+  %D%/packages/lisp-xyz.scm			\
   %D%/packages/llvm.scm				\
   %D%/packages/lout.scm				\
   %D%/packages/logging.scm			\
@@ -407,6 +408,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/python-check.scm			\
   %D%/packages/python-compression.scm		\
   %D%/packages/python-crypto.scm		\
+  %D%/packages/python-science.scm		\
   %D%/packages/python-web.scm			\
   %D%/packages/python-xyz.scm			\
   %D%/packages/toys.scm				\
@@ -551,6 +553,7 @@ 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			\
@@ -799,7 +802,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/elixir-path-length.patch			\
   %D%/packages/patches/elm-compiler-disable-reactor.patch	\
   %D%/packages/patches/elm-compiler-fix-map-key.patch		\
-  %D%/packages/patches/elm-compiler-relax-glsl-bound.patch	\
   %D%/packages/patches/emacs-dired-toggle-sudo-emacs-26.patch   \
   %D%/packages/patches/emacs-exec-path.patch			\
   %D%/packages/patches/emacs-fix-scheme-indent-function.patch	\
@@ -828,8 +830,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/fasthenry-spSolve.patch			\
   %D%/packages/patches/fasthenry-spFactor.patch			\
   %D%/packages/patches/fbreader-curl-7.62.patch		\
-  %D%/packages/patches/fcgi-2.4.0-gcc44-fixes.patch		\
-  %D%/packages/patches/fcgi-2.4.0-poll.patch			\
   %D%/packages/patches/fifo-map-fix-flags-for-gcc.patch		\
   %D%/packages/patches/fifo-map-remove-catch.hpp.patch		\
   %D%/packages/patches/file-CVE-2019-18218.patch		\
@@ -881,8 +881,14 @@ dist_patch_DATA =						\
   %D%/packages/patches/gd-freetype-test-failure.patch		\
   %D%/packages/patches/geoclue-config.patch			\
   %D%/packages/patches/ghc-8.0-fall-back-to-madv_dontneed.patch \
+  %D%/packages/patches/ghc-diff-swap-cover-args.patch           \
   %D%/packages/patches/ghc-dont-pass-linker-flags-via-response-files.patch	\
-  %D%/packages/patches/ghc-haddock-library-unbundle.patch		\
+  %D%/packages/patches/ghc-haddock-api-fix-haddock.patch	\
+  %D%/packages/patches/ghc-hpack-fix-tests.patch		\
+  %D%/packages/patches/ghc-microlens-aeson-fix-tests.patch	\
+  %D%/packages/patches/ghc-monad-par-fix-tests.patch		\
+  %D%/packages/patches/ghc-pandoc-fix-html-tests.patch		\
+  %D%/packages/patches/ghc-pandoc-fix-latex-test.patch		\
   %D%/packages/patches/ghostscript-no-header-id.patch		\
   %D%/packages/patches/ghostscript-no-header-uuid.patch		\
   %D%/packages/patches/ghostscript-no-header-creationdate.patch \
@@ -950,7 +956,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/guile-rsvg-pkgconfig.patch		\
   %D%/packages/patches/guile-emacs-fix-configure.patch		\
   %D%/packages/patches/guile-sqlite3-fix-cross-compilation.patch \
-  %D%/packages/patches/gstreamer-buffer-reset-offset.patch	\
   %D%/packages/patches/gtk2-respect-GUIX_GTK2_PATH.patch	\
   %D%/packages/patches/gtk2-respect-GUIX_GTK2_IM_MODULE_FILE.patch \
   %D%/packages/patches/gtk2-theme-paths.patch			\
@@ -959,7 +964,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/gtkglext-disable-disable-deprecated.patch \
   %D%/packages/patches/gtksourceview-2-add-default-directory.patch \
   %D%/packages/patches/gzdoom-search-in-installed-share.patch	\
-  %D%/packages/patches/handbrake-opt-in-nvenc.patch		\
   %D%/packages/patches/haskell-mode-unused-variables.patch	\
   %D%/packages/patches/haskell-mode-make-check.patch		\
   %D%/packages/patches/hdf4-architectures.patch 		\
@@ -976,12 +980,12 @@ dist_patch_DATA =						\
   %D%/packages/patches/hdf-eos5-remove-gctp.patch		\
   %D%/packages/patches/hdf-eos5-fix-szip.patch			\
   %D%/packages/patches/hdf-eos5-fortrantests.patch		\
+  %D%/packages/patches/hexchat-crash-exit.patch			\
   %D%/packages/patches/higan-remove-march-native-flag.patch	\
   %D%/packages/patches/hubbub-sort-entities.patch		\
   %D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch        \
   %D%/packages/patches/hplip-remove-imageprocessor.patch	\
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
-  %D%/packages/patches/icecat-gnuzilla-fixes.patch			\
   %D%/packages/patches/icecat-makeicecat.patch			\
   %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
   %D%/packages/patches/icecat-use-system-graphite2+harfbuzz.patch	\
@@ -1023,6 +1027,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/kmod-module-directory.patch		\
   %D%/packages/patches/kmscon-runtime-keymap-switch.patch	\
   %D%/packages/patches/kpackage-allow-external-paths.patch	\
+  %D%/packages/patches/kpmcore-fix-tests.patch			\
+  %D%/packages/patches/kpmcore-remove-broken-test.patch		\
   %D%/packages/patches/kobodeluxe-paths.patch			\
   %D%/packages/patches/kobodeluxe-enemies-pipe-decl.patch	\
   %D%/packages/patches/kobodeluxe-const-charp-conversion.patch	\
@@ -1060,6 +1066,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libgnomeui-utf8.patch			\
   %D%/packages/patches/libgpg-error-gawk-compat.patch		\
   %D%/packages/patches/libffi-3.2.1-complex-alpha.patch		\
+  %D%/packages/patches/libjpeg-turbo-CVE-2019-2201.patch	\
   %D%/packages/patches/libjxr-fix-function-signature.patch	\
   %D%/packages/patches/libjxr-fix-typos.patch			\
   %D%/packages/patches/libotr-test-auth-fix.patch		\
@@ -1075,6 +1082,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libmygpo-qt-missing-qt5-modules.patch	\
   %D%/packages/patches/libreoffice-icu.patch			\
   %D%/packages/patches/libreoffice-glm.patch			\
+  %D%/packages/patches/libseccomp-open-aarch64.patch		\
   %D%/packages/patches/libsndfile-armhf-type-checks.patch	\
   %D%/packages/patches/libsndfile-CVE-2017-8361-8363-8365.patch	\
   %D%/packages/patches/libsndfile-CVE-2017-8362.patch		\
@@ -1129,11 +1137,14 @@ dist_patch_DATA =						\
   %D%/packages/patches/mcrypt-CVE-2012-4426.patch			\
   %D%/packages/patches/mcrypt-CVE-2012-4527.patch			\
   %D%/packages/patches/mesa-skip-disk-cache-test.patch		\
+  %D%/packages/patches/mesa-timespec-test-32bit.patch		\
   %D%/packages/patches/mescc-tools-boot.patch			\
   %D%/packages/patches/meson-for-build-rpath.patch		\
   %D%/packages/patches/metabat-fix-compilation.patch		\
   %D%/packages/patches/mhash-keygen-test-segfault.patch		\
   %D%/packages/patches/mingw-w64-6.0.0-gcc.patch		\
+  %D%/packages/patches/minisat-friend-declaration.patch		\
+  %D%/packages/patches/minisat-install.patch			\
   %D%/packages/patches/mpc123-initialize-ao.patch		\
   %D%/packages/patches/module-init-tools-moduledir.patch	\
   %D%/packages/patches/monero-use-system-miniupnpc.patch			\
@@ -1187,7 +1198,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/ocaml-dose3-Fix-for-ocaml-4.06.patch	\
   %D%/packages/patches/ocaml-dose3-dont-make-printconf.patch	\
   %D%/packages/patches/ocaml-dose3-Install-mli-cmx-etc.patch	\
-  %D%/packages/patches/ocaml-piqilib-Update-base64.patch	\
   %D%/packages/patches/omake-fix-non-determinism.patch	\
   %D%/packages/patches/ola-readdir-r.patch			\
   %D%/packages/patches/openbabel-fix-crash-on-nwchem-output.patch	\
@@ -1195,7 +1205,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/opencv-rgbd-aarch64-test-fix.patch	\
   %D%/packages/patches/openfoam-4.1-cleanup.patch			\
   %D%/packages/patches/openjdk-10-idlj-reproducibility.patch	\
-  %D%/packages/patches/openmpi-psm2-priority.patch		\
+  %D%/packages/patches/openmpi-mtl-priorities.patch		\
   %D%/packages/patches/openocd-nrf52.patch			\
   %D%/packages/patches/opensmtpd-fix-crash.patch		\
   %D%/packages/patches/openssl-runpath.patch			\
@@ -1203,6 +1213,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/openssl-c-rehash-in.patch		\
   %D%/packages/patches/openssl-CVE-2019-1559.patch		\
   %D%/packages/patches/open-zwave-hidapi.patch			\
+  %D%/packages/patches/orc-typedef-enum.patch			\
   %D%/packages/patches/orpheus-cast-errors-and-includes.patch	\
   %D%/packages/patches/osip-CVE-2017-7853.patch			\
   %D%/packages/patches/ots-no-include-missing-file.patch	\
@@ -1210,6 +1221,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/p7zip-CVE-2016-9296.patch		\
   %D%/packages/patches/p7zip-CVE-2017-17969.patch		\
   %D%/packages/patches/p7zip-remove-unused-code.patch		\
+  %D%/packages/patches/pam-mount-luks2-support.patch		\
   %D%/packages/patches/patchutils-test-perms.patch		\
   %D%/packages/patches/patch-hurd-path-max.patch		\
   %D%/packages/patches/pcre2-fix-jit_match-crash.patch		\
@@ -1250,9 +1262,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/procmail-CVE-2017-16844.patch		\
   %D%/packages/patches/proot-test-fhs.patch			\
   %D%/packages/patches/psm-arch.patch				\
+  %D%/packages/patches/psm-disable-memory-stats.patch		\
   %D%/packages/patches/psm-ldflags.patch			\
   %D%/packages/patches/psm-repro.patch				\
-  %D%/packages/patches/pugixml-versioned-libdir.patch		\
   %D%/packages/patches/pulseaudio-fix-mult-test.patch		\
   %D%/packages/patches/pulseaudio-longer-test-timeout.patch	\
   %D%/packages/patches/pybugz-encode-error.patch		\
@@ -1260,6 +1272,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/pygpgme-disable-problematic-tests.patch  \
   %D%/packages/patches/pyqt-configure.patch			\
   %D%/packages/patches/pyqt-public-sip.patch			\
+  %D%/packages/patches/pyqt-unbundled-qt.patch			\
   %D%/packages/patches/python-2-deterministic-build-info.patch	\
   %D%/packages/patches/python-2.7-adjust-tests.patch		\
   %D%/packages/patches/python-2.7-search-paths.patch		\
@@ -1268,6 +1281,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-3-deterministic-build-info.patch	\
   %D%/packages/patches/python-3-search-paths.patch		\
   %D%/packages/patches/python-3-fix-tests.patch			\
+  %D%/packages/patches/python-3.8-search-paths.patch		\
+  %D%/packages/patches/python-3.8-fix-tests.patch		\
   %D%/packages/patches/python-CVE-2018-14647.patch		\
   %D%/packages/patches/python-axolotl-AES-fix.patch		\
   %D%/packages/patches/python-cairocffi-dlopen-path.patch	\
@@ -1296,7 +1311,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-waitress-fix-tests.patch		\
   %D%/packages/patches/qemu-glibc-2.27.patch 			\
   %D%/packages/patches/qt4-ldflags.patch			\
-  %D%/packages/patches/qtbase-old-kernel.patch			\
   %D%/packages/patches/qtbase-use-TZDIR.patch			\
   %D%/packages/patches/qtscript-disable-tests.patch		\
   %D%/packages/patches/quagga-reproducible-build.patch          \
@@ -1319,6 +1333,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
   %D%/packages/patches/rtags-separate-rct.patch			\
   %D%/packages/patches/racket-store-checksum-override.patch	\
+  %D%/packages/patches/retroarch-disable-online-updater.patch	\
   %D%/packages/patches/ruby-rubygems-276-for-ruby24.patch	\
   %D%/packages/patches/ruby-rack-ignore-failing-test.patch      \
   %D%/packages/patches/ruby-safe-yaml-add-require-time.patch	\
@@ -1336,6 +1351,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/scotch-build-parallelism.patch		\
   %D%/packages/patches/scotch-integer-declarations.patch	\
   %D%/packages/patches/sdl-libx11-1.6.patch			\
+  %D%/packages/patches/sdl2-mesa-compat.patch			\
   %D%/packages/patches/seahorse-gkr-use-0-on-empty-flags.patch	\
   %D%/packages/patches/seq24-rename-mutex.patch			\
   %D%/packages/patches/sharutils-CVE-2018-1000097.patch		\
@@ -1382,7 +1398,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/texi2html-document-encoding.patch	\
   %D%/packages/patches/texi2html-i18n.patch			\
   %D%/packages/patches/thefuck-test-environ.patch		\
-  %D%/packages/patches/thermald-make-int-max32-visible.patch	\
   %D%/packages/patches/tidy-CVE-2015-5522+5523.patch		\
   %D%/packages/patches/tinyxml-use-stl.patch			\
   %D%/packages/patches/tipp10-fix-compiling.patch		\
@@ -1396,6 +1411,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/tuxpaint-stamps-path.patch		\
   %D%/packages/patches/txr-shell.patch				\
   %D%/packages/patches/u-boot-fix-mkimage-header-verification.patch	\
+  %D%/packages/patches/ucx-tcp-iface-ioctl.patch		\
   %D%/packages/patches/udiskie-no-appindicator.patch		\
   %D%/packages/patches/unzip-CVE-2014-8139.patch		\
   %D%/packages/patches/unzip-CVE-2014-8140.patch		\
@@ -1454,8 +1470,11 @@ dist_patch_DATA =						\
   %D%/packages/patches/xf86-video-voodoo-pcitag.patch		\
   %D%/packages/patches/xfce4-panel-plugins.patch		\
   %D%/packages/patches/xfce4-settings-defaults.patch		\
-  %D%/packages/patches/xinetd-fix-fd-leak.patch			\
+  %D%/packages/patches/xsane-fix-memory-leak.patch		\
-  %D%/packages/patches/xinetd-CVE-2013-4342.patch
+  %D%/packages/patches/xsane-fix-pdf-floats.patch		\
+  %D%/packages/patches/xsane-fix-snprintf-buffer-length.patch	\
+  %D%/packages/patches/xsane-support-ipv6.patch			\
+  %D%/packages/patches/xsane-tighten-default-umask.patch
 
 MISC_DISTRO_FILES =				\
   %D%/packages/ld-wrapper.in

gnu/machine/ssh.scm

@@ -54,6 +54,7 @@
             machine-ssh-configuration-authorize?
             machine-ssh-configuration-port
             machine-ssh-configuration-user
+            machine-ssh-configuration-host-key
             machine-ssh-configuration-session))
 
 ;;; Commentary:
@@ -87,6 +88,8 @@
   (identity       machine-ssh-configuration-identity       ; path to a private key
                   (default #f))
   (session        machine-ssh-configuration-session        ; session
+                  (default #f))
+  (host-key       machine-ssh-configuration-host-key       ; #f | string
                   (default #f)))
 
 (define (machine-ssh-session machine)
@@ -98,11 +101,13 @@ one from the configuration's parameters if one was not provided."
         (let ((host-name (machine-ssh-configuration-host-name config))
               (user (machine-ssh-configuration-user config))
               (port (machine-ssh-configuration-port config))
-              (identity (machine-ssh-configuration-identity config)))
+              (identity (machine-ssh-configuration-identity config))
+              (host-key (machine-ssh-configuration-host-key config)))
           (open-ssh-session host-name
                             #:user user
                             #:port port
-                            #:identity identity)))))
+                            #:identity identity
+                            #:host-key host-key)))))
 
 
 ;;;

gnu/packages/admin.scm

@@ -27,6 +27,8 @@
 ;;; Copyright © 2019 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2019 Jakob L. Kreuze <zerodaysfordays@sdf.lonestar.org>
 ;;; Copyright © 2019 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2019 Alex Griffin <a@ajgrf.com>
+;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -60,13 +62,16 @@
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
+  #:use-module (gnu packages c)
   #:use-module (gnu packages check)
   #:use-module (gnu packages crypto)
+  #:use-module (gnu packages cryptsetup)
   #:use-module (gnu packages cyrus-sasl)
   #:use-module (gnu packages dns)
   #:use-module (gnu packages file)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages libbsd)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages lua)
   #:use-module (gnu packages guile)
@@ -87,6 +92,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages openldap)
   #:use-module (gnu packages mcrypt)
+  #:use-module (gnu packages patchutils)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages popt)
   #:use-module (gnu packages python)
@@ -620,6 +626,64 @@ and exploration tool, since it can create almost any kind of connection you
 would need and has several interesting built-in capabilities.")
     (license license:gpl2+)))
 
+(define-public netcat-openbsd
+  (package
+    (name "netcat-openbsd")
+    (version "1.203-2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://salsa.debian.org/debian/netcat-openbsd.git")
+                    (commit (string-append "debian/" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0j85gzbjzs6yrhgabh3zkwzd27qkr5s0zjjczl0hah8q7yhrjk3m"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no test suite
+       #:make-flags
+       (list "CC=gcc"
+             (string-append "CFLAGS=-I" (assoc-ref %build-inputs "libbsd") "/include")
+             "LDFLAGS=-lbsd")
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'build 'patch
+           (lambda _
+             (setenv "QUILT_PATCHES" "debian/patches")
+             (invoke "quilt" "push" "-a")
+             #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (man (string-append out "/share/man/man1"))
+                    (doc (string-append out "/share/doc/netcat-openbsd-" ,version))
+                    (examples (string-append doc "/examples")))
+               (install-file "nc" bin)
+               (install-file "nc.1" man)
+               (install-file "debian/copyright" doc)
+               (copy-recursively "debian/examples" examples)
+               #t))))))
+    (inputs `(("libbsd" ,libbsd)))
+    (native-inputs `(("pkg-config" ,pkg-config)
+                     ("quilt" ,quilt)))
+    (home-page "https://packages.debian.org/sid/netcat-openbsd")
+    (synopsis "Read and write data over TCP/IP")
+    (description
+     "Netcat is a simple Unix utility which reads and writes data across
+network connections using TCP or UDP protocol.  It is designed to be a reliable
+\"back-end\" tool that can be used directly or easily driven by other programs
+and scripts.  At the same time it is a feature-rich network debugging and
+exploration tool, since it can create almost any kind of connection you would
+need and has several interesting built-in capabilities.
+
+This package contains the OpenBSD rewrite of netcat, including support for
+IPv6, proxies, and Unix sockets.")
+    (license (list license:bsd-3
+                   license:bsd-2))))  ; atomicio.*, socks.c
+
 (define-public sipcalc
   (package
     (name "sipcalc")
@@ -689,7 +753,7 @@ connection alive.")
 (define-public isc-dhcp
   (let* ((bind-major-version "9")
          (bind-minor-version "11")
-         (bind-patch-version "11")
+         (bind-patch-version "13")
          (bind-release-type "")         ; for patch release, use "-P"
          (bind-release-version "")      ; for patch release, e.g. "6"
          (bind-version (string-append bind-major-version
@@ -830,7 +894,7 @@ connection alive.")
                                         "/bind-" bind-version ".tar.gz"))
                     (sha256
                      (base32
-                      "0swavslyli3vcrkcm2ip11s6p58g3k7r4gjs2b899r25cqrk0lk1"))))
+                      "0z8g81xinqx8j3y2fclxa31dq7zsi9cj9srmvd9agnpwzk4kqgzx"))))
 
                 ;; When cross-compiling, we need the cross Coreutils and sed.
                 ;; Otherwise just use those from %FINAL-INPUTS.
@@ -1378,14 +1442,14 @@ command.")
 (define-public hostapd
   (package
     (name "hostapd")
-    (version "2.8")
+    (version "2.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://w1.fi/releases/hostapd-" version
                                   ".tar.gz"))
               (sha256
                (base32
-                "1c74rrazkhy4lr7pwgwa2igzca7h9l4brrs7672kiv7fwqmm57wj"))))
+                "1mrbvg4v7vm7mknf0n29mf88k3s4a4qj6r4d51wq8hmjj1m7s7c8"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -1511,7 +1575,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
 (define-public acpica
   (package
     (name "acpica")
-    (version "20190816")
+    (version "20191018")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1519,7 +1583,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0lipy3jwl498lvgwzj6xcvmg61myl7hhilpallh1cf3ppgrq13l8"))))
+                "0k6xr9v46pnw8kl7jh23zfafs2vq3gk2sgkmjdf9a8jx8n3aifgd"))))
     (build-system gnu-build-system)
     (native-inputs `(("flex" ,flex)
                      ("bison" ,bison)))
@@ -2453,7 +2517,7 @@ produce uniform output across heterogeneous networks.")
 (define-public cbatticon
   (package
     (name "cbatticon")
-    (version "1.6.9")
+    (version "1.6.10")
     (source
      (origin
        (method git-fetch)
@@ -2461,7 +2525,7 @@ produce uniform output across heterogeneous networks.")
              (url "https://github.com/valr/cbatticon.git")
              (commit version)))
        (sha256
-        (base32 "0kw09d678sd3m18fmi4380sl4a2m5lkfmq0kps16cdmq7z80rvaf"))
+        (base32 "0ivm2dzhsa9ir25ry418r2qg2llby9j7a6m3arbvq5c3kaj8m9jr"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
@@ -2565,11 +2629,7 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.")
     ;; clause requiring us to give all recipients a copy.
     (license license:gpl1+)))
 
-(define-public sunxi-tools
+(define (sunxi-tools-source version)
-  (package
-    (name "sunxi-tools")
-    (version "1.4.2")
-    (source
      (origin
        (method git-fetch)
        (uri (git-reference
@@ -2584,14 +2644,49 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.")
         '(begin
            (delete-file-recursively "bin")
            #t))
-       (file-name (git-file-name name version))))
+       (file-name (git-file-name "sunxi-tools" version))))
+
+(define sunxi-target-tools
+  (package
+    (name "sunxi-target-tools")
+    (version "1.4.2")
+    (build-system gnu-build-system)
+    (source
+     (sunxi-tools-source version))
+    (arguments
+     `(#:system "armhf-linux"
+       #:tests? #f
+       #:make-flags (list (string-append "PREFIX="
+                                         (assoc-ref %outputs "out"))
+                          (string-append "CROSS_COMPILE=")
+                          "CC=gcc")
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'build
+           (lambda* (#:key make-flags #:allow-other-keys)
+             (apply invoke "make" "target-tools" make-flags)))
+         (replace 'install
+           (lambda* (#:key make-flags #:allow-other-keys)
+             (apply invoke "make" "install-target-tools"
+                    make-flags))))))
+    (home-page "https://github.com/linux-sunxi/sunxi-tools")
+    (synopsis "Hardware management tools for Allwinner computers")
+    (description "This package contains tools for Allwinner devices:
+@enumerate
+@item @command{sunxi-meminfo}: Prints memory bus settings.
+@end enumerate")
+    (license license:gpl2+)))
+
+(define-public sunxi-tools
+  (package
+    (name "sunxi-tools")
+    (version "1.4.2")
+    (source
+     (sunxi-tools-source version))
     (native-inputs
-     `(("pkg-config" ,pkg-config)
+     `(("sunxi-target-tools" ,sunxi-target-tools)
-       ("cross-gcc" ,(cross-gcc "arm-linux-gnueabihf"
+       ("pkg-config" ,pkg-config)))
-                                #:xbinutils (cross-binutils "arm-linux-gnueabihf")
-                                #:libc (cross-libc "arm-linux-gnueabihf")))
-       ("cross-libc" ,(cross-libc "arm-linux-gnueabihf")) ; header files
-       ("cross-libc-static" ,(cross-libc "arm-linux-gnueabihf") "static")))
     (inputs
      `(("libusb" ,libusb)))
     (build-system gnu-build-system)
@@ -2599,50 +2694,22 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.")
      `(#:tests? #f                      ; no tests exist
        #:make-flags (list (string-append "PREFIX="
                                          (assoc-ref %outputs "out"))
-                          (string-append "CROSS_COMPILE="
+                          (string-append "CROSS_COMPILE=disabled")
-                                         "arm-linux-gnueabihf-")
                           "CC=gcc")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
-         (add-before 'build 'set-environment-up
-           (lambda* (#:key make-flags #:allow-other-keys)
-             (define (cross? x)
-               (string-contains x "cross-arm-linux"))
-             (define (filter-environment! filter-predicate
-                                          environment-variable-names)
-               (for-each
-                (lambda (env-name)
-                  (when (getenv env-name)
-                    (let* ((env-value (getenv env-name))
-                           (search-path (search-path-as-string->list env-value))
-                           (new-search-path (filter filter-predicate
-                                                    search-path))
-                           (new-env-value (list->search-path-as-string
-                                           new-search-path ":")))
-                      (setenv env-name new-env-value))))
-                environment-variable-names))
-             (setenv "CROSS_CPATH" (getenv "CPATH"))
-             (setenv "CROSS_C_INCLUDE_PATH" (getenv "C_INCLUDE_PATH"))
-             (setenv "CROSS_CPLUS_INCLUDE_PATH" (getenv "CPLUS_INCLUDE_PATH"))
-             (setenv "CROSS_LIBRARY_PATH" (getenv "LIBRARY_PATH"))
-             (filter-environment! cross?
-              '("CROSS_CPATH" "CROSS_C_INCLUDE_PATH" "CROSS_CPLUS_INCLUDE_PATH"
-                "CROSS_LIBRARY_PATH"))
-             (filter-environment! (lambda (e) (not (cross? e)))
-              '("CPATH" "C_INCLUDE_PATH" "CPLUS_INCLUDE_PATH"
-                "LIBRARY_PATH"))
-             #t))
          (replace 'build
            (lambda* (#:key make-flags #:allow-other-keys)
              (apply invoke "make" "tools" "misc" make-flags)))
-         (add-after 'build 'build-armhf
-           (lambda* (#:key make-flags #:allow-other-keys)
-             (setenv "LIBRARY_PATH" #f)
-             (apply invoke "make" "target-tools" make-flags)))
          (replace 'install
-           (lambda* (#:key make-flags #:allow-other-keys)
+           (lambda* (#:key inputs outputs make-flags #:allow-other-keys)
-             (apply invoke "make" "install-all" "install-misc"
+             ;; Those tools have been built for armhf but are part of the
+             ;; installation in the upstream package.  So do the same
+             ;; here.
+             (copy-recursively (assoc-ref inputs "sunxi-target-tools")
+                               (assoc-ref outputs "out"))
+             (apply invoke "make" "install-tools" "install-misc"
                     make-flags))))))
     (home-page "https://github.com/linux-sunxi/sunxi-tools")
     (synopsis "Hardware management tools for Allwinner computers")
@@ -2915,14 +2982,14 @@ everyone's screenshots nowadays.")
 (define-public nnn
   (package
     (name "nnn")
-    (version "2.6")
+    (version "2.7")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/jarun/nnn/releases/download/v"
                            version "/nnn-v" version ".tar.gz"))
        (sha256
-        (base32 "0xb6crd9vig3xgjwl8m4bmgcs4azfmfdpx3g8pdpzs28jdg7i3rr"))))
+        (base32 "1wvh11iw7s3r8c985s99fqm2l7cn7dkbx7ah3xpk34jvry7j3vg5"))))
     (build-system gnu-build-system)
     (inputs
      `(("ncurses" ,ncurses)
@@ -2951,7 +3018,7 @@ make it a perfect utility on modern distros.")
 (define-public thermald
   (package
     (name "thermald")
-    (version "1.8")
+    (version "1.9")
     (source
      (origin
       (method git-fetch)
@@ -2960,9 +3027,7 @@ make it a perfect utility on modern distros.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "1g1l7k8yxj8bl1ysdx8v6anv1s7xk9j072y44gwki70dy48n7j92"))
+       (base32 "1ajhivl9jifcf12nbk281yayk7666v65m249aclyli0bz1kh8cfs"))))
-      (patches
-       (search-patches "thermald-make-int-max32-visible.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -3238,7 +3303,7 @@ support forum.  It runs with the @code{/exec} command in most IRC clients.")
 (define-public pscircle
   (package
     (name "pscircle")
-    (version "1.3.0")
+    (version "1.3.1")
     (source
      (origin
        (method git-fetch)
@@ -3247,8 +3312,7 @@ support forum.  It runs with the @code{/exec} command in most IRC clients.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32
+        (base32 "1sm99423hh90kr4wdjqi9sdrrpk65j2vz2hzj65zcxfxyr6khjci"))))
-         "0qsif00dkqa8ky3vl2ycx5anx2yk62nrv47f5lrlqzclz91f00fx"))))
     (build-system meson-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -3452,3 +3516,68 @@ IGMP and Raw, across a wide variety of interface types, and understands BPF
 filter logic in the same fashion as more common packet sniffing tools, such as
 tcpdump and snoop.")
     (license license:bsd-3)))
+
+(define-public pam-mount
+  (package
+    (name "pam-mount")
+    (version "2.16")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/pam-mount/pam_mount/"
+                           version "/pam_mount-" version ".tar.xz"))
+       (sha256
+        (base32
+         "1rvi4irb7ylsbhvx1cr6islm2xxw1a4b19q6z4a9864ndkm0f0mf"))
+       (patches
+        ;; Patch adding support for encrypted volumes in LUKS2 format.
+        ;; It comes from the Gentoo package definition for sys-auth/pam_mount.
+        (search-patches "pam-mount-luks2-support.patch"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("perl" ,perl)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("cryptsetup" ,cryptsetup)
+       ("libhx" ,libhx)
+       ("libxml2" ,libxml2)
+       ("linux-pam" ,linux-pam)
+       ("lvm2" ,lvm2)
+       ("openssl" ,openssl)
+       ("pcre" ,pcre)
+       ("util-linux" ,util-linux)))
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-slibdir=" %output "/lib")
+             (string-append "--with-ssbindir=" %output "/sbin"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-program-paths
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((util-linux (assoc-ref inputs "util-linux"))
+                   (out (assoc-ref outputs "out")))
+               (substitute* "src/mtcrypt.c"
+                 (("\"mount\";")
+                  (string-append "\"" util-linux "/bin/mount\";"))
+                 (("\"umount\";")
+                  (string-append "\"" util-linux "/bin/umount\";"))
+                 (("\"fsck\",")
+                  (string-append "\"" util-linux "/sbin/fsck\",")))
+               (substitute* "src/rdconf1.c"
+                 (("\"mount\", \"")
+                  (string-append "\"" util-linux "/bin/mount\", \""))
+                 (("\"umount\", \"")
+                  (string-append "\"" util-linux "/bin/umount\", \""))
+                 (("\"fsck\", \"")
+                  (string-append "\"" util-linux "/sbin/fsck\", \""))
+                 (("\"pmvarrun\", \"")
+                  (string-append "\"" out "/sbin/pmvarrun\", \""))))
+             #t)))))
+    (home-page "http://pam-mount.sourceforge.net")
+    (synopsis "PAM module to mount volumes for a user session")
+    (description
+     "Pam-mount is a PAM module that can mount volumes when a user logs in.
+It supports mounting local filesystems of any kind the normal mount utility
+supports.  It can also mount encrypted LUKS volumes using the password
+supplied by the user when logging in.")
+    (license (list license:gpl2+ license:lgpl2.1+))))

gnu/packages/agda.scm

@@ -37,7 +37,7 @@
 (define-public agda
   (package
     (name "agda")
-    (version "2.5.4.2")
+    (version "2.6.0.1")
     (source
      (origin
        (method url-fetch)
@@ -46,10 +46,11 @@
              version ".tar.gz"))
        (sha256
         (base32
-         "07wvawpfjhx3gw2w53v27ncv1bl0kkx08wkm6wzxldbslkcasign"))))
+         "1s600ry1qwizr3ynyj05rvlx7jdcw9a1viyc0ycjamm5sjf8mf3v"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-alex" ,ghc-alex)
+     `(("ghc-aeson" ,ghc-aeson)
+       ("ghc-alex" ,ghc-alex)
        ("ghc-async" ,ghc-async)
        ("ghc-blaze-html" ,ghc-blaze-html)
        ("ghc-boxes" ,ghc-boxes)
@@ -57,6 +58,7 @@
        ("ghc-edisoncore" ,ghc-edisoncore)
        ("ghc-edit-distance" ,ghc-edit-distance)
        ("ghc-equivalence" ,ghc-equivalence)
+       ("ghc-exceptions" ,ghc-exceptions)
        ("ghc-filemanip" ,ghc-filemanip)
        ("ghc-geniplate-mirror" ,ghc-geniplate-mirror)
        ("ghc-gitrev" ,ghc-gitrev)
@@ -66,7 +68,6 @@
        ("ghc-ieee754" ,ghc-ieee754)
        ("ghc-murmur-hash" ,ghc-murmur-hash)
        ("ghc-uri-encode" ,ghc-uri-encode)
-       ("ghc-parallel" ,ghc-parallel)
        ("ghc-regex-tdfa" ,ghc-regex-tdfa)
        ("ghc-strict" ,ghc-strict)
        ("ghc-unordered-containers" ,ghc-unordered-containers)

gnu/packages/algebra.scm

@@ -346,7 +346,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "1.5.0-69")
+    (version "1.5.0-75")
     (source (origin
               (method url-fetch)
               ;; "~parisse/giac" is not used because the maintainer regularly
@@ -358,7 +358,7 @@ precision.")
                                   "source/giac_" version ".tar.gz"))
               (sha256
                (base32
-                "05l1qa2kfmvsbp0iqjmg3ixkcqa3h9ry1mjpcps52bxw05s3k1z9"))))
+                "1k94xl6hvy9xqwc3ccgnhpdqgq3lkjbgpgq0njizmlg514dh2jhq"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)

gnu/packages/android.scm

@@ -500,9 +500,14 @@ that is safe to use for user space.  It also includes
        ;; pcre is inlined by our package.
        ("pcre" ,pcre)))
     (home-page "https://developer.android.com/")
-    (synopsis (package-synopsis libselinux))
+    (synopsis "Android version of the SELinux libraries and utilities")
-    (description (package-description libselinux))
+    (description
-    (license (package-license libselinux))))
+     "The libselinux library provides an API for SELinux applications to get
+and set process and file security contexts, and to obtain security policy
+decisions.  It is required for any applications that use the SELinux API, and
+used by all applications that are SELinux-aware.  This package also includes
+the core SELinux management utilities.")
+    (license license:public-domain)))
 
 (define-public android-ext4-utils
   (package

gnu/packages/assembly.scm

@@ -52,7 +52,7 @@
     (source (origin
               (method url-fetch)
               (uri (string-append "http://www.nasm.us/pub/nasm/releasebuilds/"
-                                  version "/" name "-" version ".tar.xz"))
+                                  version "/nasm-" version ".tar.xz"))
               (sha256
                (base32
                 "1xg8dfr49py15vbwk1rzcjc3zpqydmr49ahlijm56wlgj8zdwjp2"))))

gnu/packages/astronomy.scm

@@ -120,7 +120,7 @@ header.")
 (define-public gnuastro
   (package
     (name "gnuastro")
-    (version "0.10")
+    (version "0.11")
     (source
      (origin
        (method url-fetch)
@@ -128,7 +128,7 @@ header.")
                            version ".tar.lz"))
        (sha256
         (base32
-         "0gmhmh0yddb2aql4hd5ffrr0d4hrmh4pa3yln0n186hslqinp81b"))))
+         "0c1yc2qb7vrqad96savfn06rn01izlfz0va738signv93qqj5k3v"))))
     (inputs
      `(("cfitsio" ,cfitsio)
        ("gsl" ,gsl)
@@ -149,7 +149,7 @@ programs for the manipulation and analysis of astronomical data.")
 (define-public stellarium
   (package
     (name "stellarium")
-    (version "0.19.1")
+    (version "0.19.2")
     (source
      (origin
        (method url-fetch)
@@ -157,7 +157,7 @@ programs for the manipulation and analysis of astronomical data.")
                            "/releases/download/v" version
                            "/stellarium-" version ".tar.gz"))
        (sha256
-        (base32 "0s7v5iyhah258k83kvy2a91a3mdf34r150lcar4mmdsrrcmas98g"))))
+        (base32 "10b05slj5fjakrjb20m68xql68plb64mwn0165dy2fry8z2hbl74"))))
     (build-system cmake-build-system)
     (inputs
      `(("qtbase" ,qtbase)

gnu/packages/audio.scm

@@ -24,6 +24,8 @@
 ;;; Copyright © 2019 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2019 Alexandros Theodotou <alex@zrythm.org>
+;;; Copyright © 2019 Christopher Lemmer Webber <cwebber@dustycloud.org>
+;;; Copyright © 2019 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -552,14 +554,14 @@ plugins are provided.")
 (define-public calf
   (package
     (name "calf")
-    (version "0.90.2")
+    (version "0.90.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://calf-studio-gear.org/files/calf-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0bn4j1klw2yfxz8clbmasaydifq25rdfsv0n6iisxrzcj1lx7sgh"))))
+                "17x4hylgq4dn9qycsdacfxy64f5cv57n2qgkvsdp524gnqzw4az3"))))
     (build-system gnu-build-system)
     (inputs
      `(("fluidsynth" ,fluidsynth)
@@ -2299,6 +2301,29 @@ aimed at audio/musical applications.")
                  (base32
                   "04fajrass3ymr72flx5js5vxc601ccrmx8ny8scp0rw7j0igyjdr")))))))
 
+(define-public resample
+  (package
+    (name "resample")
+    (version "1.8.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://ccrma.stanford.edu/~jos/gz/resample-"
+                                  version
+                                  ".tar.gz"))
+              (sha256 (base32
+                       "074zj8ydp05yy1hjcglfv3hkvj4cm50f9nralka1992pm6yf8yvy"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("pkg-config" ,pkg-config)
+       ("libtool" ,libtool)))
+    (synopsis "Real-time library for sampling rate conversion")
+    (description "The @command{resample} software package contains free
+sampling-rate conversion and filter design utilities.")
+    (home-page "https://ccrma.stanford.edu/~jos/resample/Free_Resampling_Software.html")
+    (license license:lgpl2.1+)))
+
 (define-public rubberband
   (package
     (name "rubberband")
@@ -2681,7 +2706,7 @@ Tracker 3 S3M and Impulse Tracker IT files.")
        ("automake" ,automake)
        ("libtool" ,libtool)
        ("file" ,file)))
-    (home-page "http://www.surina.net/soundtouch/")
+    (home-page "https://www.surina.net/soundtouch/")
     (synopsis
      "Audio processing library for changing tempo, pitch and playback rate")
     (description
@@ -3170,21 +3195,23 @@ with support for HD extensions.")
 (define-public bs1770gain
   (package
     (name "bs1770gain")
-    (version "0.6.0")
+    (version "0.6.5")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/bs1770gain/bs1770gain/"
                            version "/bs1770gain-" version ".tar.gz"))
        (sha256
-        (base32 "0nnqixvw3x7i22nsr54n4bgm35z9nh3d9qj5s75cfd3ajjsjndyh"))
+        (base32 "15nvlh9bg0a52cpg2mii17mlzmxszwivjjalbb4np1v5nj8l5fk6"))
        (modules '((guix build utils)))
        (snippet
         '(begin
            ;; XXX
+           (substitute* (find-files "." "\\.[ch]$")
+             (("^ \\* N..o.*") ""))
            (substitute* "libbg/bgx.c"
-             (("#define BS.* ") "#define BS ")
+             (("#define BG.* ") "#define BS ")
-             (("BS.*NO?.*N.*S.*E.*N.*SE?") "NO")
+             (("BG.*NO?.*N.*S.*E.*N.*SE?") "NO")
              (("\"( #|N).*\"") "\"\""))
            (substitute* (list "config.h"
                               "configure.ac"
@@ -3353,14 +3380,14 @@ on the ALSA software PCM plugin.")
 (define-public snd
   (package
     (name "snd")
-    (version "19.6")
+    (version "19.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "ftp://ccrma-ftp.stanford.edu/pub/Lisp/"
                                   "snd-" version ".tar.gz"))
               (sha256
                (base32
-                "0s2qv8sznvw6559bi39qj9p072azh9qcb2b86w6w8clz2azjaa76"))))
+                "13s8fahpsjygjdrcwmprcrz23ny3klaj2rh2xzdv3bfs69gxvhys"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
@@ -3811,3 +3838,102 @@ therefore satisfying any requirements they may have to be self contained,
 as is the case with audio plugins.")
     (home-page "https://gitlab.com/geontime/redkite")
     (license license:gpl3+)))
+
+(define-public carla
+  (package
+    (name "carla")
+    (version "2.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri
+        (git-reference
+         (url "https://github.com/falkTX/Carla.git")
+         (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0fqgncqlr86n38yy7pa118mswfacmfczj7w9xx6c6k0jav3wk29k"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; no "check" target
+       #:make-flags
+       (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'set-CC-variable-and-show-features
+           (lambda _
+             (setenv "CC" "gcc")
+             (invoke "make" "features")))
+         (delete 'configure))))
+    (inputs
+     `(("alsa-lib" ,alsa-lib)
+       ("ffmpeg" ,ffmpeg)
+       ("fluidsynth" ,fluidsynth)
+       ("file" ,file)
+       ("liblo" ,liblo)
+       ("libsndfile" ,libsndfile)
+       ("gtk+" ,gtk+)
+       ("python-pyliblo" ,python-pyliblo)
+       ("python-pyqt" ,python-pyqt)
+       ("python-rdflib" ,python-rdflib)
+       ;; python-pyqt shows the following error without python-wrapper:
+       ;; Error while finding module specification for 'PyQt5.uic.pyuic'
+       ;; (ModuleNotFoundError: No module named 'PyQt5')
+       ("python-wrapper" ,python-wrapper)
+       ("libx11" ,libx11)
+       ("qtbase" ,qtbase)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://kx.studio/Applications:Carla")
+    (synopsis "Audio plugin host")
+    (description "Carla is a modular audio plugin host, with features like
+transport control, automation of parameters via MIDI CC and remote control
+over OSC.  Carla currently supports LADSPA (including LRDF), DSSI, LV2, VST2,
+and VST3 plugin formats, plus SF2 and SFZ file support.  It uses JACK as the
+default and preferred audio driver but also supports native drivers like ALSA.")
+    (license license:gpl2+)))
+
+(define-public ecasound
+  (package
+    (name "ecasound")
+    (version "2.9.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://nosignal.fi/download/ecasound-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32 "15rcs28fq2wfvfs66p5na7adq88b55qszbhshpizgdbyqzgr2jf1"))))
+    (build-system gnu-build-system)
+    (native-inputs `(("pkg-config" ,pkg-config)))
+    ;; would be nice to add mikmod to inputs if that gets packaged
+    ;; eventually
+    (inputs `(("alsa-lib" ,alsa-lib)
+              ("jack" ,jack-1)
+              ("mpg123" ,mpg123)
+              ("lame" ,lame)
+              ("vorbis-tools" ,vorbis-tools)
+              ("faad2" ,faad2)
+              ("flac" ,flac)
+              ("timidity++" ,timidity++)
+              ("libsndfile" ,libsndfile)
+              ("libsamplerate" ,libsamplerate)
+              ("ncurses" ,ncurses)
+              ("ladspa" ,ladspa)
+              ("lilv" ,lilv)))
+    (home-page "http://nosignal.fi/ecasound/index.php")
+    (synopsis "Multitrack audio processing")
+    (description "Ecasound is a software package designed for multitrack audio
+processing. It can be used for simple tasks like audio playback, recording and
+format conversions, as well as for multitrack effect processing, mixing,
+recording and signal recycling. Ecasound supports a wide range of audio inputs,
+outputs and effect algorithms. Effects and audio objects can be combined in
+various ways, and their parameters can be controlled by operator objects like
+oscillators and MIDI-CCs. A versatile console mode user-interface is included
+in the package.")
+    ;; As an exception to the above, the C, C++ and python implementations
+    ;; of the Ecasound Control Interface (ECI) are licensed under the LGPL
+    ;; (see the file 'COPYING.LGPL'). This allows writing ECI applications
+    ;; that are not licensed under GPL.
+    (license (list license:gpl2 license:lgpl2.1))))

gnu/packages/aux-files/emacs/guix-emacs.el

@@ -2,6 +2,7 @@
 
 ;; Copyright © 2014, 2015, 2016, 2017 Alex Kost <alezost@gmail.com>
 ;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
+;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 
 ;; This file is part of GNU Guix.
 
@@ -24,91 +25,39 @@
 ;; installed with Guix.
 
 ;;; Code:
-
+(require 'seq)
-(require 'cl-lib)
-
-(defvar guix-user-profile (expand-file-name "~/.guix-profile"))
-
-(defvar guix-emacs-autoloads nil
-  "List of the last loaded Emacs autoloads.")
 
 (defvar guix-emacs-autoloads-regexp
-  (rx (group (* any) "-autoloads")
+  (rx (* any) "-autoloads.el" (zero-or-one "c") string-end)
-      ".el" (zero-or-one "c") string-end)
   "Regexp to match Emacs 'autoloads' file.")
 
-(defun guix-emacs-directory (&optional profile)
-  "Return directory with Emacs packages installed in PROFILE.
-If PROFILE is nil, use `guix-user-profile'."
-  (expand-file-name "share/emacs/site-lisp"
-                    (or profile guix-user-profile)))
-
 (defun guix-emacs-find-autoloads (directory)
   "Return a list of Emacs 'autoloads' files in DIRECTORY.
 The files in the list do not have extensions (.el, .elc)."
-  (cl-remove-duplicates
+  ;; `directory-files' doesn't honor group in regexp.
-   (delq nil
+  (mapcar #'file-name-sans-extension
-        (mapcar (lambda (file)
+          (directory-files directory 'full-name guix-emacs-autoloads-regexp)))
-                  (when (string-match guix-emacs-autoloads-regexp file)
-                    (match-string 1 file)))
-                (directory-files directory 'full-name nil 'no-sort)))
-   :test #'string=))
-
-(defun guix-emacs-subdirs (directory)
-  "Return list of DIRECTORY subdirectories."
-  (cl-remove-if (lambda (file)
-                  (or (string-match-p (rx "/." string-end) file)
-                      (string-match-p (rx "/.." string-end) file)
-                      (not (file-directory-p file))))
-                (directory-files directory 'full-name nil 'no-sort)))
-
-(defun guix-emacs-directories (&optional profile)
-  "Return the list of directories under PROFILE that contain Emacs packages.
-This includes both `share/emacs/site-lisp/guix.d/PACKAGE'
-sub-directories and `share/emacs/site-lisp' itself.
-
-If PROFILE is nil, use `guix-user-profile'.
-Return nil, if Emacs packages are not installed in PROFILE."
-  (let ((root-dir (guix-emacs-directory (or profile guix-user-profile))))
-    (when (file-directory-p root-dir)
-      (let* ((pkgs-dir  (expand-file-name "guix.d" root-dir))
-             (pkgs-dirs (when (file-directory-p pkgs-dir)
-                          (guix-emacs-subdirs pkgs-dir))))
-        (cons root-dir pkgs-dirs)))))
 
 ;;;###autoload
-(defun guix-emacs-autoload-packages (&rest profiles)
+(defun guix-emacs-autoload-packages ()
-  "Autoload Emacs packages installed in PROFILES.
+  "Autoload Emacs packages found in EMACSLOADPATH.
-If PROFILES are not specified, use a default user and system
-profiles.
 
-'Autoload' means add directories with Emacs packages to
+'Autoload' means to load the 'autoloads' files matching
-`load-path' and load 'autoloads' files matching
 `guix-emacs-autoloads-regexp'."
-  (interactive (list (if (fboundp 'guix-read-package-profile)
+  ;; FIXME: The autoloads generated by the emacs-build-system are not byte
-                         (funcall 'guix-read-package-profile)
+  ;; compiled.
-                       guix-user-profile)))
+  (interactive)
-  (let* ((env      (getenv "GUIX_ENVIRONMENT"))
+  (let* ((emacs-non-core-load-path-directories
-         (profiles (or profiles
+          ;; Filter out core Elisp directories, which are already autoloaded
-                       (append (list "/run/current-system/profile"
+          ;; by Emacs.
-                                     guix-user-profile)
+          (seq-filter (lambda (dir)
-                               (and env (list env))))))
+                        (string-match-p "/share/emacs/site-lisp" dir))
-    (dolist (profile profiles)
+                      load-path))
-      (let ((dirs (guix-emacs-directories profile)))
+         (autoloads (mapcan #'guix-emacs-find-autoloads
-        (when dirs
+                            emacs-non-core-load-path-directories)))
-          (let* ((autoloads     (cl-mapcan #'guix-emacs-find-autoloads
+    (mapc (lambda (f)
-                                           dirs))
+            (load f 'noerror))
-                 (new-autoloads (cl-nset-difference autoloads
+          autoloads)))
-                                                    guix-emacs-autoloads
-                                                    :test #'string=)))
-            (dolist (dir dirs)
-              (cl-pushnew (directory-file-name dir)
-                          load-path
-                          :test #'string=))
-            (dolist (file new-autoloads)
-              (load file 'noerror))
-            (setq guix-emacs-autoloads
-                  (append new-autoloads guix-emacs-autoloads))))))))
 
 (provide 'guix-emacs)
 

gnu/packages/backup.scm

@@ -842,7 +842,7 @@ is like a time machine for your data. ")
 (define-public restic
   (package
     (name "restic")
-    (version "0.9.5")
+    (version "0.9.6")
     ;; TODO Try packaging the bundled / vendored dependencies in the 'vendor/'
     ;; directory.
     (source (origin
@@ -853,7 +853,7 @@ is like a time machine for your data. ")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0afl3dv7gzwdc9klikk3fsb57d0px2fwihb0xxb7zq7d8vlhh8p2"))))
+                "1zmh42aah32ah8w5n6ilz9bci0y2xrf8p7qshy3yf1lzm5gnbj0w"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/restic/restic"

gnu/packages/base.scm

@@ -1196,7 +1196,7 @@ command.")
 (define-public tzdata
   (package
     (name "tzdata")
-    (version "2019b")
+    (version "2019c")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -1204,7 +1204,7 @@ command.")
                    version ".tar.gz"))
              (sha256
               (base32
-               "0r0clnlslwm15m1c61dinf1fi9ffgl6aipng7i7yryfwj0n0kn85"))))
+               "0z7w1yv37cfk8yhix2cillam091vgp1j4g8fv84261q9mdnq1ivr"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f
@@ -1254,7 +1254,7 @@ command.")
                                 version ".tar.gz"))
                           (sha256
                            (base32
-                            "0vbmswvv3li25s31shyllq5v24449lxnrki9hr043nipjd09sirf"))))))
+                            "1m3y2rnf1nggxxhxplab5zdd5whvar3ijyrv7lifvm82irkd7szn"))))))
     (home-page "https://www.iana.org/time-zones")
     (synopsis "Database of current and historical time zones")
     (description "The Time Zone Database (often called tz or zoneinfo)
@@ -1272,7 +1272,25 @@ and daylight-saving rules.")
 (define-public tzdata-for-tests
   (hidden-package
    (package
-     (inherit tzdata))))
+     (inherit tzdata)
+     (version "2019b")
+     (source (origin
+               (method url-fetch)
+               (uri (string-append
+                     "https://data.iana.org/time-zones/releases/tzdata"
+                     version ".tar.gz"))
+               (sha256
+                (base32
+                 "0r0clnlslwm15m1c61dinf1fi9ffgl6aipng7i7yryfwj0n0kn85"))))
+     (inputs
+      `(("tzcode" ,(origin
+                     (method url-fetch)
+                     (uri (string-append
+                           "https://data.iana.org/time-zones/releases/tzcode"
+                           version ".tar.gz"))
+                     (sha256
+                      (base32
+                       "0vbmswvv3li25s31shyllq5v24449lxnrki9hr043nipjd09sirf")))))))))
 
 (define-public libiconv
   (package

gnu/packages/benchmark.scm

@@ -35,6 +35,7 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages storage)
   #:use-module (ice-9 match))

gnu/packages/bioconductor.scm

@@ -76,21 +76,14 @@ objects.")
     (version "1.4.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "BSgenome.Celegans.UCSC.ce10_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
     (properties
      `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
     (build-system r-build-system)
-    ;; As this package provides little more than a very large data file it
-    ;; doesn't make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
@@ -108,21 +101,14 @@ objects.")
     (version "1.4.1")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "BSgenome.Dmelanogaster.UCSC.dm6_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
     (properties
      `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
     (build-system r-build-system)
-    ;; As this package provides little more than a very large data file it
-    ;; doesn't make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
@@ -140,21 +126,14 @@ objects.")
     (version "1.4.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "BSgenome.Dmelanogaster.UCSC.dm3_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
     (properties
      `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
     (build-system r-build-system)
-    ;; As this package provides little more than a very large data file it
-    ;; doesn't make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
@@ -172,12 +151,8 @@ Biostrings objects.")
     (version "1.3.99")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "http://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
@@ -207,21 +182,14 @@ Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
     (version "0.99.1")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "BSgenome.Hsapiens.1000genomes.hs37d5_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
     (properties
      `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
     (build-system r-build-system)
-    ;; As this package provides little more than a very large data file it
-    ;; doesn't make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
@@ -238,12 +206,8 @@ Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
     (version "1.3.99")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "http://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "BSgenome.Hsapiens.UCSC.hg19.masked_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
@@ -273,21 +237,14 @@ default.")
     (version "1.4.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "BSgenome.Mmusculus.UCSC.mm9_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
     (properties
      `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
     (build-system r-build-system)
-    ;; As this package provides little more than a very large data file it
-    ;; doesn't make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
@@ -304,12 +261,8 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
     (version "1.3.99")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "http://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "BSgenome.Mmusculus.UCSC.mm9.masked_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
@@ -339,21 +292,14 @@ default."  )
     (version "1.4.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "BSgenome.Mmusculus.UCSC.mm10_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
     (properties
      `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
     (build-system r-build-system)
-    ;; As this package provides little more than a very large data file it
-    ;; doesn't make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
@@ -371,11 +317,7 @@ in Biostrings objects.")
     (version "3.7.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "org.Ce.eg.db_" version ".tar.gz"))
               (sha256
                (base32
                 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
@@ -397,11 +339,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
     (version "3.7.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "org.Dm.eg.db_" version ".tar.gz"))
               (sha256
                (base32
                 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
@@ -423,11 +361,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
     (version "3.7.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "org.Dr.eg.db_" version ".tar.gz"))
               (sha256
                (base32
                 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
@@ -449,11 +383,7 @@ based on mapping using Entrez Gene identifiers.")
     (version "3.7.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "org.Hs.eg.db_" version ".tar.gz"))
               (sha256
                (base32
                 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
@@ -475,11 +405,7 @@ on mapping using Entrez Gene identifiers.")
     (version "3.7.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "org.Mm.eg.db_" version ".tar.gz"))
               (sha256
                (base32
                 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
@@ -501,21 +427,14 @@ annotations for the genome of the model mouse Mus musculus.")
     (version "1.4.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "BSgenome.Hsapiens.UCSC.hg19_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
     (properties
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
     (build-system r-build-system)
-    ;; As this package provides little more than a very large data file it
-    ;; doesn't make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)))
     (home-page
@@ -555,11 +474,7 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.")
     (source
      (origin
        (method url-fetch)
-       ;; We cannot use bioconductor-uri here because this tarball is
+       (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
-       ;; located under "data/experiment/" instead of "bioc/".
-       (uri (string-append "https://bioconductor.org/packages/"
-                           "release/data/experiment/src/contrib"
-                           "/geneLenDataBase_" version ".tar.gz"))
        (sha256
         (base32
          "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
@@ -582,21 +497,14 @@ genomes and gene ID formats, largely based on the UCSC table browser.")
     (version "3.2.2")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib"
-                                  "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
     (properties
      `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
     (build-system r-build-system)
-    ;; As this package provides little more than a very large data file it
-    ;; doesn't make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
     (propagated-inputs
      `(("r-genomicfeatures" ,r-genomicfeatures)))
     (home-page
@@ -614,12 +522,8 @@ track.  The database is exposed as a @code{TxDb} object.")
     (version "3.4.6")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib"
-                                  "/TxDb.Hsapiens.UCSC.hg38.knownGene_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
@@ -643,12 +547,8 @@ track.  The database is exposed as a @code{TxDb} object.")
     (version "3.2.2")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib"
-                                  "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
@@ -673,21 +573,14 @@ database is exposed as a @code{TxDb} object.")
     (version "3.4.7")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "TxDb.Mmusculus.UCSC.mm10.knownGene_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
     (properties
      `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
     (build-system r-build-system)
-    ;; As this package provides little more than a very large data file it
-    ;; doesn't make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
     (propagated-inputs
      `(("r-bsgenome" ,r-bsgenome)
        ("r-genomicfeatures" ,r-genomicfeatures)
@@ -733,12 +626,8 @@ by exposing these as TxDb objects.")
     (version "2.2.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "FDb.InfiniumMethylation.hg19_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
@@ -765,12 +654,8 @@ annotations.")
     (version "0.3.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
-              ;; located under "data/annotation/" instead of "bioc/".
+                                     version 'annotation))
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "IlluminaHumanMethylationEPICmanifest_"
-                                  version ".tar.gz"))
               (sha256
                (base32
                 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
@@ -791,11 +676,7 @@ annotations.")
     (version "2.9")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "DO.db" version 'annotation))
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/"
-                                  "DO.db_" version ".tar.gz"))
               (sha256
                (base32
                 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
@@ -872,11 +753,7 @@ species.")
     (version "1.12.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "ABAData" version 'experiment))
-              ;; located under "data/experiment/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/experiment/src/contrib/"
-                                  "ABAData_" version ".tar.gz"))
               (sha256
                (base32
                 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
@@ -909,11 +786,7 @@ All datasets are restricted to protein coding genes.")
     (version "1.18.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "ARRmData" version 'experiment))
-              ;; located under "data/experiment/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/experiment/src/contrib/"
-                                  "ARRmData_" version ".tar.gz"))
               (sha256
                (base32
                 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
@@ -933,11 +806,7 @@ from Illumina 450k methylation arrays.")
     (version "1.2.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
-              ;; located under "data/experiment/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/experiment/src/contrib/"
-                                  "HSMMSingleCell_" version ".tar.gz"))
               (sha256
                (base32
                 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
@@ -966,11 +835,7 @@ resulting in a complete gene expression profile for each cell.")
     (version "1.26.0")
     (source (origin
               (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
+              (uri (bioconductor-uri "ALL" version 'experiment))
-              ;; located under "data/experiment/" instead of "bioc/".
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/experiment/src/contrib/"
-                                  "ALL_" version ".tar.gz"))
               (sha256
                (base32
                 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))

gnu/packages/bioinformatics.scm

@@ -84,10 +84,10 @@
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages java)
   #:use-module (gnu packages java-compression)
+  #:use-module (gnu packages javascript)
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages dlang)
   #:use-module (gnu packages linux)
-  #:use-module (gnu packages lisp)
   #:use-module (gnu packages logging)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages man)
@@ -105,6 +105,7 @@
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-compression)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
@@ -983,16 +984,17 @@ e.g. microbiome samples, genomes, metagenomes.")
       (version "1.7.0")
       (source
        (origin
-         (method url-fetch)
+         (method git-fetch)
-         (uri (string-append "https://github.com/bioperl/bioperl-live/"
+         (uri (git-reference
-                             "archive/release-"
+                (url "https://github.com/bioperl/bioperl-live")
-                             (string-map (lambda (c)
+                (commit (string-append "release-"
-                                           (if (char=? c #\.)
+                                       (string-map (lambda (c)
-                                               #\- c)) version)
+                                                     (if (char=? c #\.)
-                             ".tar.gz"))
+                                                         #\- c)) version)))))
+         (file-name (git-file-name name version))
          (sha256
           (base32
-           "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06"))))
+           "0wl8yvzcls59pwwk6m8ahy87pwg6nnibzy5cldbvmcwg2x2w7783"))))
       (build-system perl-build-system)
       (arguments
        `(#:phases
@@ -11271,7 +11273,8 @@ models.  TADbit is complemented by TADkit for visualizing 3D models.")
        ("tcsh" ,tcsh)
        ("perl" ,perl)
        ("libpng" ,libpng)
-       ("mariadb" ,mariadb)
+       ("mariadb" ,mariadb "lib")
+       ("mariadb-dev" ,mariadb "dev")
        ("openssl" ,openssl)))
     (home-page "http://genome.cse.ucsc.edu/index.html")
     (synopsis "Assorted bioinformatics utilities")
@@ -11571,35 +11574,6 @@ provide this functionality without the necessity of drawing in a heavy-weight
 dependency like SeqAn.")
     (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt"))))
 
-(define-public libdivsufsort
-  (package
-    (name "libdivsufsort")
-    (version "2.0.1")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/y-256/libdivsufsort.git")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
-    (build-system cmake-build-system)
-    (arguments
-     '(#:tests? #f                      ; there are no tests
-       #:configure-flags
-       ;; Needed for rapmap and sailfish.
-       '("-DBUILD_DIVSUFSORT64=ON")))
-    (home-page "https://github.com/y-256/libdivsufsort")
-    (synopsis "Lightweight suffix-sorting library")
-    (description "libdivsufsort is a software library that implements a
-lightweight suffix array construction algorithm.  This library provides a
-simple and an efficient C API to construct a suffix array and a
-Burrows-Wheeler transformed string from a given string over a constant-size
-alphabet.  The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
-bytes of memory space, where n is the length of the string.")
-    (license license:expat)))
-
 (define-public sailfish
   (package
     (name "sailfish")
@@ -13890,7 +13864,7 @@ datasets.")
 (define-public ngless
   (package
     (name "ngless")
-    (version "0.9.1")
+    (version "1.0.1")
     (source
      (origin
        (method git-fetch)
@@ -13900,7 +13874,7 @@ datasets.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0mc2gi7h4lx74zylvyp76mvc0w6706j858ii9vlgzqsw6acpr117"))))
+         "06ygv8q2zjqsnrid1302yrlhhvb8ik48nq6n0higk3i1mdc8r0dg"))))
     (build-system haskell-build-system)
     (arguments
      `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1:
@@ -13908,7 +13882,24 @@ datasets.")
                      ; import Options.Applicative
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'create-cabal-file
+         (add-after 'unpack 'create-Versions.hs
+           (lambda _
+             (substitute* "Makefile"
+               (("BWA_VERSION = .*")
+                (string-append "BWA_VERSION = "
+                               ,(package-version bwa) "\n"))
+               (("SAM_VERSION = .*")
+                (string-append "SAM_VERSION = "
+                               ,(package-version samtools) "\n"))
+               (("PRODIGAL_VERSION = .*")
+                (string-append "PRODIGAL_VERSION = "
+                               ,(package-version prodigal) "\n"))
+               (("MINIMAP2_VERSION = .*")
+                (string-append "MINIMAP2_VERSION = "
+                               ,(package-version minimap2) "\n")))
+             (invoke "make" "NGLess/Dependencies/Versions.hs")
+             #t))
+         (add-after 'create-Versions.hs 'create-cabal-file
            (lambda _ (invoke "hpack") #t))
          ;; These tools are expected to be installed alongside ngless.
          (add-after 'install 'link-tools
@@ -13937,15 +13928,15 @@ datasets.")
        ("ghc-async" ,ghc-async)
        ("ghc-atomic-write" ,ghc-atomic-write)
        ("ghc-bytestring-lexing" ,ghc-bytestring-lexing)
-       ("ghc-chart" ,ghc-chart)
-       ("ghc-chart-cairo" ,ghc-chart-cairo)
        ("ghc-conduit" ,ghc-conduit)
        ("ghc-conduit-algorithms" ,ghc-conduit-algorithms)
-       ("ghc-conduit-combinators" ,ghc-conduit-combinators)
        ("ghc-conduit-extra" ,ghc-conduit-extra)
        ("ghc-configurator" ,ghc-configurator)
        ("ghc-convertible" ,ghc-convertible)
        ("ghc-data-default" ,ghc-data-default)
+       ("ghc-diagrams-core" ,ghc-diagrams-core)
+       ("ghc-diagrams-lib" ,ghc-diagrams-lib)
+       ("ghc-diagrams-svg" ,ghc-diagrams-svg)
        ("ghc-double-conversion" ,ghc-double-conversion)
        ("ghc-edit-distance" ,ghc-edit-distance)
        ("ghc-either" ,ghc-either)
@@ -13966,6 +13957,7 @@ datasets.")
        ("ghc-safeio" ,ghc-safeio)
        ("ghc-strict" ,ghc-strict)
        ("ghc-tar" ,ghc-tar)
+       ("ghc-tar-conduit" ,ghc-tar-conduit)
        ("ghc-unliftio" ,ghc-unliftio)
        ("ghc-unliftio-core" ,ghc-unliftio-core)
        ("ghc-vector" ,ghc-vector)

gnu/packages/boost.scm

@@ -211,6 +211,23 @@ across a broad spectrum of applications.")
                              (symlink "libboost_python37.so" "libboost_python3.so"))
                            #t)))))))))
 
+(define-public boost-static
+  (package
+    (inherit boost)
+    (name "boost-static")
+    (arguments
+     (substitute-keyword-arguments (package-arguments boost)
+       ((#:make-flags flags)
+        `(cons "link=static" (delete "link=shared" ,flags)))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (replace 'provide-libboost_python
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out")))
+                 (with-directory-excursion (string-append out "/lib")
+                   (symlink "libboost_python27.a" "libboost_python.a"))
+                 #t)))))))))
+
 (define-public boost-for-mysql
   ;; Older version for MySQL 5.7.23.
   (package

gnu/packages/build-tools.scm

@@ -80,7 +80,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
 (define-public bear
   (package
     (name "bear")
-    (version "2.3.13")
+    (version "2.4.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -89,7 +89,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0imvvs22gyr1v6ydgp5yn2nq8fb8llmz0ra1m733ikjaczl3jm7z"))))
+                "1w1kyjzvvy5lj16kn3yyf7iil2cqlfkszi8kvagql7f5h5l6w9b1"))))
     (build-system cmake-build-system)
     (inputs
      `(("python" ,python-wrapper)))

gnu/packages/busybox.scm

@@ -113,7 +113,7 @@ any small or embedded system.")
 (define-public toybox
   (package
     (name "toybox")
-    (version "0.8.1")
+    (version "0.8.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -121,7 +121,7 @@ any small or embedded system.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "1czxzvyggm157z8wgxbk8k0n675p1gig9xvrcijsplh9p1i1xi0s"))))
+                "1mgya8zxgf30i5w3rhsb3n70kwlhifxbajh6wqdsz6rf8kx609ws"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases

gnu/packages/c.scm

@@ -4,6 +4,8 @@
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
+;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -78,6 +80,13 @@
                                      `("--triplet=arm-linux-gnueabihf")
                                      '()))
        #:test-target "test"))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "CPATH")
+            (files '("include")))
+           (search-path-specification
+            (variable "LIBRARY_PATH")
+            (files '("lib" "lib64")))))
     ;; Fails to build on MIPS: "Unsupported CPU"
     (supported-systems (delete "mips64el-linux" %supported-systems))
     (synopsis "Tiny and fast C compiler")
@@ -90,66 +99,6 @@ standard.")
     ;; (if ever) complete.  See the RELICENSING file for more information.
     (license license:lgpl2.1+)))
 
-(define-public tcc-wrapper
-  (package
-    (inherit tcc)
-    (name "tcc-wrapper")
-    (build-system trivial-build-system)
-    (native-inputs '())
-    (inputs `(("tcc" ,tcc)
-              ("guile" ,guile-2.2)))
-
-    ;; By default TCC does not honor any search path environment variable.
-    ;; This wrapper adds them.
-    ;;
-    ;; FIXME: TCC includes its own linker so our 'ld-wrapper' hack to set the
-    ;; RUNPATH is ineffective here.  We should modify TCC itself.
-    (native-search-paths
-     (list (search-path-specification
-            (variable "TCC_CPATH")
-            (files '("include")))
-           (search-path-specification
-            (variable "TCC_LIBRARY_PATH")
-            (files '("lib" "lib64")))))
-
-    (arguments
-     '(#:builder
-       (let* ((out   (assoc-ref %outputs "out"))
-              (bin   (string-append out "/bin"))
-              (tcc   (assoc-ref %build-inputs "tcc"))
-              (guile (assoc-ref %build-inputs "guile")))
-         (mkdir out)
-         (mkdir bin)
-         (call-with-output-file (string-append bin "/cc")
-           (lambda (port)
-             (format port "#!~a/bin/guile --no-auto-compile~%!#~%" guile)
-             (write
-              `(begin
-                 (use-modules (ice-9 match)
-                              (srfi srfi-26))
-
-                 (define (split path)
-                   (string-tokenize path (char-set-complement
-                                          (char-set #\:))))
-
-                 (apply execl ,(string-append tcc "/bin/tcc")
-                        ,(string-append tcc "/bin/tcc") ;argv[0]
-                        (append (cdr (command-line))
-                                (match (getenv "TCC_CPATH")
-                                  (#f '())
-                                  (str
-                                   (map (cut string-append "-I" <>)
-                                        (split str))))
-                                (match (getenv "TCC_LIBRARY_PATH")
-                                  (#f '())
-                                  (str
-                                   (map (cut string-append "-L" <>)
-                                        (split str)))))))
-              port)
-             (chmod port #o777)))
-         #t)))
-    (synopsis "Wrapper providing the 'cc' command for TCC")))
-
 (define-public pcc
   (package
     (name "pcc")
@@ -183,7 +132,7 @@ compiler while still keeping it small, simple, fast and understandable.")
 (define-public libbytesize
   (package
     (name "libbytesize")
-    (version "1.4")
+    (version "2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -191,52 +140,17 @@ compiler while still keeping it small, simple, fast and understandable.")
                     "download/" version "/libbytesize-" version ".tar.gz"))
               (sha256
                (base32
-                "0bbqzln1nhjxl71aydq9k4jg3hvki9lqsb4w10s1i27jgibxqkdv"))
+                "1bpz9cpb8s47kqplkkiz6ryfahas2ma95g9rh2axnfjp6w1d9ixc"))))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; This Makefile hard-codes MSGMERGE et al. instead of
-                  ;; honoring what 'configure' detected.  Fix that.
-                  (substitute* "po/Makefile.in"
-                    (("^MSGMERGE = msgmerge")
-                     "MSGMERGE = @MSGMERGE@\n"))
-                  #t))))
     (build-system gnu-build-system)
     (arguments
-     ;; When running "make", the POT files are built with the build time as
+     `(#:tests? #f))
-     ;; their "POT-Creation-Date".  Later on, "make" notices that .pot
-     ;; files were updated and goes on to run "msgmerge"; as a result, the
-     ;; non-deterministic POT-Creation-Date finds its way into .po files,
-     ;; and then in .gmo files.  To avoid that, simply make sure 'msgmerge'
-     ;; never runs.  See <https://bugs.debian.org/792687>.
-     '(#:configure-flags '("ac_cv_path_MSGMERGE=true")
-
-       #:phases (modify-phases %standard-phases
-                  (add-after 'configure 'create-merged-po-files
-                    (lambda _
-                      ;; Create "merged PO" (.mpo) files so that 'msgmerge'
-                      ;; doesn't need to run.
-                      (for-each (lambda (po-file)
-                                  (let ((merged-po
-                                         (string-append (dirname po-file) "/"
-                                                        (basename po-file
-                                                                  ".po")
-                                                        ".mpo")))
-                                    (copy-file po-file merged-po)))
-                                (find-files "po" "\\.po$"))
-                      #t)))
-
-       ;; One test fails because busctl (systemd only?) and python2-pocketlint
-       ;; are missing.  Should we fix it, we would need the "python-2" ,
-       ;; "python2-polib" and "python2-six" native-inputs.
-       #:tests? #f))
     (native-inputs
      `(("gettext" ,gettext-minimal)
        ("pkg-config" ,pkg-config)
        ("python" ,python)))
     (inputs
      `(("mpfr" ,mpfr)
-       ("pcre" ,pcre)))
+       ("pcre2" ,pcre2)))
     (home-page "https://github.com/storaged-project/libbytesize")
     (synopsis "Tiny C library for working with arbitrary big sizes in bytes")
     (description
@@ -316,3 +230,25 @@ Its three main components are:
      "The purpose of libfixposix is to offer replacements for parts of POSIX
 whose behaviour is inconsistent across *NIX flavours.")
     (license license:boost1.0)))
+
+(define-public libhx
+  (package
+    (name "libhx")
+    (version "3.24")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/libhx/libHX/"
+                           "libHX-" version ".tar.xz"))
+       (sha256
+        (base32
+         "0i8v2464p830c15myknvvs6bhxaf663lrqgga95l94ygfynkw6x5"))))
+    (build-system gnu-build-system)
+    (home-page "http://libhx.sourceforge.net")
+    (synopsis "C library with common data structures and functions")
+    (description
+     "This is a C library (with some C++ bindings available) that provides data
+structures and functions commonly needed, such as maps, deques, linked lists,
+string formatting and autoresizing, option and config file parsing, type
+checking casts and more.")
+    (license license:lgpl2.1+)))

gnu/packages/calcurse.scm

@@ -30,14 +30,14 @@
 (define-public calcurse
   (package
     (name "calcurse")
-    (version "4.5.0")
+    (version "4.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://calcurse.org/files/calcurse-"
                            version ".tar.gz"))
        (sha256
-        (base32 "1vjwcmp51h7dsvwn0qx93w9chp3wp970v7d9mjhk7jyamcbfywn3"))))
+        (base32 "0cgkd285x5pk62lmdx9fjxl46c5lj8wj2cqbxq7d99yb4il5fdjk"))))
     (build-system gnu-build-system)
     (inputs `(("ncurses" ,ncurses)))
     (native-inputs `(("tzdata" ,tzdata-for-tests)))

gnu/packages/calendar.scm

@@ -50,7 +50,7 @@
 (define-public libical
   (package
     (name "libical")
-    (version "3.0.5")
+    (version "3.0.6")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -58,7 +58,7 @@
                     version "/libical-" version ".tar.gz"))
               (sha256
                (base32
-                "1rkq9qkvbv76n6k6kc8pxhwj9vhyigkb6flfcn1rk6wwqk451mbs"))))
+                "15sdmh8w4vszd7jhv9fdpd48anpkniq2k1jw7siy9v1jnz1232jw"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; test suite appears broken

gnu/packages/cdrom.scm

@@ -104,14 +104,14 @@ caching facility provided by the library.")
 (define-public libcdio
   (package
     (name "libcdio")
-    (version "2.0.0")
+    (version "2.1.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/libcdio/libcdio-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "0jr8ppdm80c533nzmrpz3iffnpc6nhvsria1di9f4jg1l19a03fd"))))
+               "0avi6apv5ydjy6b9c3z9a46rvp5i57qyr09vr7x4nndxkmcfjl45"))))
     (build-system gnu-build-system)
     (inputs
      `(("ncurses" ,ncurses)
@@ -134,14 +134,14 @@ extraction from CDs.")
 (define-public libcdio-paranoia
   (package
     (name "libcdio-paranoia")
-    (version "10.2+0.94+2")
+    (version "10.2+2.0.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/libcdio/libcdio-paranoia-"
-                                 version ".tar.gz"))
+                                 version ".tar.bz2"))
              (sha256
               (base32
-               "0h8rr1ir05r29rgawa1ccw335668k4s3zq4yg9095svyx7n843yn"))))
+               "1h8k8z9r75h3p697f77z9j1blwb6gf2d5rik6z2q6420my6c2ra5"))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)))
     (propagated-inputs `(("libcdio" ,libcdio)))
@@ -790,14 +790,14 @@ laid out on the image.")
 (define-public libburn
   (package
     (name "libburn")
-    (version "1.5.0")
+    (version "1.5.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://files.libburnia-project.org/releases/"
                                  "libburn-" version ".tar.gz"))
              (sha256
               (base32
-               "1gg2kgnqvaa2fwghai62prxz6slpak1f6bvgjh8m4dn16v114asq"))))
+               "09sjrvq8xsj1gnl2wwyv4lbmicyzzl6x1ac2rrn53xnp34bxnckv"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

gnu/packages/cedille.scm

@@ -44,7 +44,7 @@
     (inputs
      `(("agda" ,agda)
        ("agda-ial" ,agda-ial)
-       ("ghc" ,ghc-8.4)
+       ("ghc" ,ghc)
        ("ghc-alex" ,ghc-alex)
        ("ghc-happy" ,ghc-happy)))
     (build-system emacs-build-system)

gnu/packages/certs.scm

@@ -76,7 +76,7 @@
 (define-public nss-certs
   (package
     (name "nss-certs")
-    (version "3.45")
+    (version "3.46.1")
     (source (origin
               (method url-fetch)
               (uri (let ((version-with-underscores
@@ -87,7 +87,7 @@
                       "nss-" version ".tar.gz")))
               (sha256
                (base32
-                "12sfq9xvpwpc22qnjsg1if1lmchiy33byrh92wn91phz7li0abqi"))))
+                "0l9ns44rlkp1bpblplspfbqmyhb8rhvc89y56kqh725rgpny1xrv"))))
     (build-system gnu-build-system)
     (outputs '("out"))
     (native-inputs

gnu/packages/check.scm

@@ -264,7 +264,7 @@ problem, and shows the differences.")
 (define-public cmocka
   (package
     (name "cmocka")
-    (version "1.1.3")
+    (version "1.1.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://cmocka.org/files/"
@@ -272,7 +272,7 @@ problem, and shows the differences.")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "1bxzzafjlwzgldcb07hjnlnqvh88wh21r2kw7z8f704w5bvvrsj3"))))
+                "1dm8pdvkyfa8dsbz9bpq7wwgixjij4sii9bbn5sgvqjm5ljdik7h"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))                    ; no test target
@@ -497,7 +497,7 @@ test coverage and has a web user interface that will refresh automatically.")
     (arguments
      `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")))
     (native-inputs
-     `(("python-2" ,python-2)))
+     `(("python" ,python-wrapper)))
     (home-page "https://github.com/google/googletest/")
     (synopsis "Test discovery and XUnit test framework")
     (description "Google Test features an XUnit test framework, automated test
@@ -2249,7 +2249,7 @@ portable to just about any platform.")
 (define-public libfaketime
   (package
     (name "libfaketime")
-    (version "0.9.7")
+    (version "0.9.8")
     (home-page "https://github.com/wolfcw/libfaketime")
     (source (origin
               (method git-fetch)
@@ -2258,7 +2258,7 @@ portable to just about any platform.")
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "1cin1pqwpsswcv7amiwijirvcg3x1zf2l00s1x84nxc5602fzr5c"))
+                "1mfdl82ppgbdvy1ny8mb7xii7p0g7awvn4bn36jb8v4r545slmjc"))
               (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments

gnu/packages/chemistry.scm

@@ -243,13 +243,14 @@ analogy is that InChI is the bar-code for chemistry and chemical structures.")
     (version "3.0.11")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://bitbucket.org/khinsen/"
+       (uri (git-reference
-                           "nmoldyn3/downloads/nMOLDYN-"
+             (url "https://github.com/khinsen/nMOLDYN3")
-                           version ".tar.gz"))
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1mvmz3lkr217kdrd8cvdr1d82y58wp1403c9rnd943mijgq8xb5a"))))
+         "016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r"))))
     (build-system python-build-system)
     (inputs
      `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))

gnu/packages/chromium.scm

@@ -242,8 +242,8 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %chromium-version "78.0.3904.97")
+(define %chromium-version "78.0.3904.108")
-(define %ungoogled-revision "acaf16383f264d8a2f24142ad054c9b4355771d3")
+(define %ungoogled-revision "8f065138317a6152b20decc224027a5192ba76b1")
 (define %debian-revision "e43d74632091324774a5049668782dba7b09cf72")
 (define package-revision "0")
 (define %package-version (string-append %chromium-version "-"
@@ -258,7 +258,7 @@ from forcing GEXP-PROMISE."
                         %chromium-version ".tar.xz"))
     (sha256
      (base32
-      "01wx5bi397d80za0sdfwgfbjj6n2ad2i31zmcrhm6wzryjwrmx6i"))))
+      "03jvfz68nvmmrplygf96sh0l347p4h03c8vpw8yrglh6ycwkiigr"))))
 
 (define %ungoogled-origin
   (origin
@@ -269,7 +269,7 @@ from forcing GEXP-PROMISE."
                               (string-take %ungoogled-revision 7)))
     (sha256
      (base32
-      "1gqbch6dnww3c3vn1i4nb07iz1f78mws9dsxscj3rsrkcgwhsdz8"))))
+      "0zix90jz82hpym9jmyf99yw19swaf13ps6szi60wccmz1gccv77g"))))
 
 (define %debian-origin
   (origin
@@ -660,8 +660,8 @@ from forcing GEXP-PROMISE."
                ;; their current status for convenience.
                (format #t "Dumping configure flags...\n")
                (invoke "gn" "args" "out/Release" "--list"))))
-         (replace 'build
+         (add-before 'build 'increase-resource-limits
-           (lambda* (#:key (parallel-build? #t) #:allow-other-keys)
+           (lambda _
              ;; XXX: Chromiums linking step requires a lot of simultaneous file
              ;; accesses.  Having a too low ulimit will result in bogus linker
              ;; errors such as "foo.a: error adding symbols: malformed archive".
@@ -677,7 +677,9 @@ from forcing GEXP-PROMISE."
                    (format #t
                            "increased maximum number of open files from ~d to ~d~%"
                            soft (if hard (min hard 4096) 4096)))))
-
+             #t))
+         (replace 'build
+           (lambda* (#:key (parallel-build? #t) #:allow-other-keys)
              (invoke "ninja" "-C" "out/Release"
                      "-j" (if parallel-build?
                               (number->string (parallel-job-count))

gnu/packages/cinnamon.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 ng0 <ng0@n0.is>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,6 +22,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
@@ -40,13 +42,14 @@
     (name "cinnamon-desktop")
     (version "3.4.2")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/linuxmint/cinnamon-desktop/"
+              (uri (git-reference
-                                  "archive/" version ".tar.gz"))
+                     (url "https://github.com/linuxmint/cinnamon-desktop")
-              (file-name (string-append name "-" version ".tar.gz"))
+                     (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1jf24csrbfi9aiza1g70jpvsbjiqwphk0i5wilxq9kpjjsl99maq"))))
+                "18mjy80ly9361npjhxpm3n0pkmrwviaqr2kixjb7hyxa6kzzh5xw"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/code.scm

@@ -11,6 +11,7 @@
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2019 Hartmut Goebel <h.goebel@goebel-consult.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -598,21 +599,38 @@ Objective@tie{}C, D, Java, Pawn, and Vala).  Features:
        #:make-flags (list (string-append "prefix=" %output)
                           "INSTALL=install"
                           "all")
+       #:modules ((guix build gnu-build-system) ;; FIXME use %default-modules
+                  (guix build utils)
+                  (ice-9 regex))
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
            (lambda _ (chdir "build/gcc") #t))
          (add-after 'install 'install-libs
            (lambda* (#:key outputs #:allow-other-keys)
-             ;; Libraries are not installed by default
+             ;; Libraries and includes are not installed by default
              (let* ((output (assoc-ref outputs "out"))
+                    (incdir (string-append output "/include"))
                     (libdir (string-append output "/lib")))
-               (begin
+               (define (make-so-link sofile strip-pattern)
-                 (mkdir-p libdir)
+                 (symlink
-                 (for-each (lambda (l)
+                  (basename sofile)
-                             (copy-file
+                  (regexp-substitute #f
-                              l (string-append libdir "/" (basename l))))
+                                     (string-match strip-pattern sofile)
-                           (find-files "bin" "lib*"))))
+                                     'pre)))
+               (mkdir-p incdir)
+               (copy-file "../../src/astyle.h"
+                          (string-append incdir "/astyle.h"))
+               (mkdir-p libdir)
+               (for-each (lambda (l)
+                           (copy-file
+                            l (string-append libdir "/" (basename l))))
+                         (find-files "bin" "lib*"))
+               (for-each
+                (lambda (sofile)
+                  (make-so-link sofile "(\\.[0-9]){3}$")  ;; link .so
+                  (make-so-link sofile "(\\.[0-9]){2}$")) ;; link .so.3
+                (find-files libdir "lib.*\\.so\\..*")))
              #t)))))
     (home-page "http://astyle.sourceforge.net/")
     (synopsis "Source code indenter, formatter, and beautifier")

gnu/packages/compression.scm

@@ -650,13 +650,14 @@ This package is mostly for compatibility and historical interest.")
     (name "sfarklib")
     (version "2.24")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/raboof/sfArkLib/archive/"
+              (uri (git-reference
-                                  version ".tar.gz"))
+                     (url "https://github.com/raboof/sfArkLib.git")
-              (file-name (string-append name "-" version ".tar.gz"))
+                     (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0bzs2d98rk1xw9qwpnc7gmlbxwmwc3dg1rpn310afy9pq1k9clzi"))))
+                "0jrxy24gak7q5ml06p5jjgzk9i5r2mkfjk4ycirkp4kg7k5a237w"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
@@ -735,7 +736,7 @@ decompression of some loosely related file formats used by Microsoft.")
 (define-public lz4
   (package
     (name "lz4")
-    (version "1.9.1")
+    (version "1.9.2")
     (source
      (origin
        (method git-fetch)
@@ -743,10 +744,13 @@ decompression of some loosely related file formats used by Microsoft.")
                            (commit (string-append "v" version))))
        (sha256
         (base32
-         "1l1caxrik1hqs40vj3bpv1pikw6b74cfazv5c0v6g48zpcbmshl0"))
+         "0lpaypmk70ag2ks3kf2dl4ac3ba40n5kc1ainkp9wfjawz76mh61"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
-    (native-inputs `(("valgrind" ,valgrind)))    ;for tests
+    (native-inputs
+     `(;; For tests.
+       ("python" ,python)
+       ("valgrind" ,valgrind)))
     (arguments
      `(#:test-target "test"
        #:make-flags (list "CC=gcc"
@@ -1106,12 +1110,13 @@ well as bzip2.")
     (version "1.1.7")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/google/snappy/archive/"
+       (uri (git-reference
-                           version ".tar.gz"))
+              (url "https://github.com/google/snappy.git")
-       (file-name (string-append "snappy-" version ".tar.gz"))
+              (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1m7rcdqzkys5lspj8jcsaah8w33zh28s771bw0ga2lgzfgl05yix"))
+        (base32 "1x7r8sjmdqlqjz0xfiwdyrqpgaj5yrvrgb28ivgpvnxgar5qv6m2"))
        (patches (search-patches "snappy-add-O2-flag-in-CmakeLists.txt.patch"))))
     (build-system cmake-build-system)
     (arguments
@@ -1178,7 +1183,7 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
              (invoke "make" "test")
              (invoke "make" "test_7z")
              (invoke "make" "test_7zr"))))))
-    (inputs
+    (native-inputs
      (let ((system (or (%current-target-system)
                        (%current-system))))
        `(,@(cond ((string-prefix? "x86_64" system)
@@ -1300,13 +1305,14 @@ or junctions, and always follows hard links.")
     (name "unshield")
     (version "1.4.3")
     (source
-     (origin (method url-fetch)
+     (origin (method git-fetch)
-             (uri (string-append "http://github.com/twogood/unshield/archive/"
+             (uri (git-reference
-                                 version ".tar.gz"))
+                    (url "http://github.com/twogood/unshield.git")
-             (file-name (string-append name "-" version ".tar.gz"))
+                    (commit version)))
+             (file-name (git-file-name name version))
              (sha256
               (base32
-               "1avv5c11jbmzwizq10pwvlh1dmyna8ccvpgacv95h4gbq26rg35a"))))
+               "19wn22vszhci8dfcixx5rliz7phx3lv5ablvhjlclvj75k2vsdqd"))))
     (build-system cmake-build-system)
     (inputs
      `(("zlib" ,zlib)
@@ -1652,7 +1658,9 @@ recreates the stored directory structure by default.")
     (native-inputs
      `(("perl" ,perl)))
     (inputs
-     `(("zlib" ,zlib)))
+     `(("gnutls" ,gnutls)
+       ("openssl" ,openssl)
+       ("zlib" ,zlib)))
     (build-system cmake-build-system)
     (home-page "https://libzip.org")
     (synopsis "C library for reading, creating, and modifying zip archives")
@@ -1810,16 +1818,16 @@ single-member files which can't be decompressed in parallel.")
 (define-public innoextract
   (package
    (name "innoextract")
-   (version "1.7")
+   (version "1.8")
    (source
     (origin
      (method url-fetch)
-     (uri (string-append "https://github.com/dscharrer/innoextract/archive/"
+     (uri (string-append "https://github.com/dscharrer/innoextract/releases"
-                         version ".tar.gz"))
+                         "/download/" version
+                         "/innoextract-" version ".tar.gz"))
      (sha256
       (base32
-       "0khwi9f0q0h6xfbixrrc1rfpgj0b7ajwilq7yhmxnn5lpc807f6x"))
+       "0saj50n8ds85shygy4mq1h6s99510r9wgjjdll4dmvhra4lzcy2y"))))
-     (file-name (string-append name "-" version ".tar.gz"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f

gnu/packages/coq.scm

@@ -377,13 +377,14 @@ theorems between the two libraries.")
     (name "coq-bignums")
     (version "8.9.0")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/coq/bignums/archive/V"
+              (uri (git-reference
-                                  version ".tar.gz"))
+                     (url "https://github.com/coq/bignums.git")
-              (file-name (string-append name "-" version ".tar.gz"))
+                     (commit (string-append "V" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0pmk9smw7a14wrfkvjlvmpxim4bsv6xnm5xkrlld2faqy74a044g"))))
+                "03qz1w2xb2j5p06liz5yyafl0fl9vprcqm6j0iwi7rxwghl00p01"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml" ,ocaml)

gnu/packages/cpp.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2019 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -209,7 +210,7 @@ as ordering relation.")
 (define-public json-modern-cxx
   (package
     (name "json-modern-cxx")
-    (version "3.7.0")
+    (version "3.7.3")
     (home-page "https://github.com/nlohmann/json")
     (source
      (origin
@@ -218,7 +219,7 @@ as ordering relation.")
                            (commit (string-append "v" version))))
        (sha256
         (base32
-         "0v7xih4zjixxxfvkfbs7a8j9qcvpwlsv4vrkbyns3hc7b44nb8ap"))
+         "04rry1xzis71z5gj1ylcj8b4li5q18zxhcwaviwvi3hx0frzxl9w"))
        (file-name (git-file-name name version))
        (modules '((guix build utils)))
        (snippet
@@ -252,6 +253,9 @@ as ordering relation.")
 intuitive syntax and trivial integration.")
     (license license:expat)))
 
+(define-public nlohmann-json-cpp
+  (deprecated-package "nlohmann-json-cpp" json-modern-cxx))
+
 (define-public xtl
   (package
     (name "xtl")
@@ -289,7 +293,7 @@ tools (containers, algorithms) used by other QuantStack packages.")
 (define-public ccls
   (package
     (name "ccls")
-    (version "0.20190823.3")
+    (version "0.20190823.5")
     (source
      (origin
        (method git-fetch)
@@ -297,7 +301,7 @@ tools (containers, algorithms) used by other QuantStack packages.")
              (url "https://github.com/MaskRay/ccls")
              (commit version)))
        (sha256
-        (base32 "1sx31zp6q2qc6fz3r78rx34zp2x4blrqzxwbpww71vb6lp1clmdm"))
+        (base32 "0b2pkpzn576b92zcxpwchpkyw2fww6s69818rx4g9z34kzm35zy5"))
        (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (arguments
@@ -375,3 +379,34 @@ for style issues following Google’s C++ style guide.  While Google maintains
 it's own version of the tool, this is a fork that aims to be more responsive
 and make @code{cpplint} usable in wider contexts.")
     (license license:bsd-3)))
+
+(define-public sobjectizer
+  (package
+    (name "sobjectizer")
+    (version "5.6.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Stiffstream/sobjectizer.git")
+             (commit (string-append "v." version))))
+       (sha256
+        (base32 "0jfai7sqxnnjkms38krm7mssj5l79nb3pllkbyj4j581a7l5j6l5"))
+       (file-name (git-file-name name version))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'change-directory
+           (lambda _
+             (chdir "dev")
+             #t)))))
+    (home-page "https://stiffstream.com/en/products/sobjectizer.html")
+    (synopsis "Cross-platform actor framework for C++")
+    (description
+     "SObjectizer is a cross-platform \"actor frameworks\" for C++.
+SObjectizer supports not only the Actor Model but also the Publish-Subscribe
+Model and CSP-like channels.  The goal of SObjectizer is to simplify
+development of concurrent and multithreaded applications in C++.")
+    (license license:bsd-3)))

gnu/packages/cran.scm

@@ -1,7 +1,8 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
-;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
@@ -13,6 +14,7 @@
 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
@@ -60,7 +62,6 @@
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages java)
   #:use-module (gnu packages javascript)
-  #:use-module (gnu packages lisp)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
@@ -95,6 +96,56 @@
 the system clipboards.")
     (license license:gpl3)))
 
+(define-public r-scales
+  (package
+    (name "r-scales")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "scales" version))
+       (sha256
+        (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-farver" ,r-farver)
+       ("r-labeling" ,r-labeling)
+       ("r-lifecycle" ,r-lifecycle)
+       ("r-munsell" ,r-munsell)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-r6" ,r-r6)
+       ("r-viridislite" ,r-viridislite)))
+    (home-page "https://github.com/hadley/scales")
+    (synopsis "Scale functions for visualization")
+    (description
+     "This package provides graphical scales that map data to aesthetics, and
+provides methods for automatically determining breaks and labels for axes and
+legends.")
+    (license license:expat)))
+
+(define-public r-pheatmap
+  (package
+    (name "r-pheatmap")
+    (version "1.0.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pheatmap" version))
+       (sha256
+        (base32
+         "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gtable" ,r-gtable)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-scales" ,r-scales)))
+    (home-page "https://cran.r-project.org/web/packages/pheatmap")
+    (synopsis "Pretty heatmaps")
+    (description
+     "This package provides an implementation of heatmaps that offers more
+control over dimensions and appearance.")
+    (license license:gpl2+)))
+
 (define-public r-ellipsis
   (package
     (name "r-ellipsis")
@@ -243,14 +294,14 @@ data types as well.")
 (define-public r-tidyverse
   (package
     (name "r-tidyverse")
-    (version "1.2.1")
+    (version "1.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyverse" version))
        (sha256
         (base32
-         "0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd"))))
+         "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
@@ -267,6 +318,7 @@ data types as well.")
        ("r-lubridate" ,r-lubridate)
        ("r-magrittr" ,r-magrittr)
        ("r-modelr" ,r-modelr)
+       ("r-pillar" ,r-pillar)
        ("r-purrr" ,r-purrr)
        ("r-readr" ,r-readr)
        ("r-readxl" ,r-readxl)
@@ -314,14 +366,13 @@ scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
 (define-public r-selectr
   (package
     (name "r-selectr")
-    (version "0.4-1")
+    (version "0.4-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "selectr" version))
        (sha256
-        (base32
+        (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
-         "1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-stringr" ,r-stringr)
@@ -601,13 +652,13 @@ LaTeX.")
 (define-public r-curl
   (package
     (name "r-curl")
-    (version "4.2")
+    (version "4.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "curl" version))
               (sha256
                (base32
-                "0xh227gvb056wlipjxxbf555z1i1qcs7rr1igvs6k6645y9irrlp"))))
+                "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -906,14 +957,13 @@ application framework for R, making it easy to create attractive dashboards.")
 (define-public r-shinyfiles
   (package
     (name "r-shinyfiles")
-    (version "0.7.3")
+    (version "0.7.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyFiles" version))
        (sha256
-        (base32
+        (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
-         "01as3l9ffj5dwac0vviais2x5l3027zxlj67kcvkdwxaj5hql33i"))))
     (properties `((upstream-name . "shinyFiles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1254,6 +1304,26 @@ applications.  That is, compute distances and related measures for angular
 (longitude/latitude) locations.")
     (license license:gpl3+)))
 
+(define-public r-jpeg
+  (package
+    (name "r-jpeg")
+    (version "0.1-8.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "jpeg" version))
+       (sha256
+        (base32
+         "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
+    (build-system r-build-system)
+    (inputs `(("libjpeg" ,libjpeg)))
+    (home-page "http://www.rforge.net/jpeg/")
+    (synopsis "Read and write JPEG images with R")
+    (description "This package provides a way to read, write and display
+bitmap images stored in the JPEG format with R.  It can read and write both
+files and in-memory raw vectors.")
+    (license license:gpl2+)))
+
 (define-public r-ggmap
   (package
     (name "r-ggmap")
@@ -1813,14 +1883,14 @@ rows, dropping names) to see if the modified versions are identical.")
 (define-public r-dendextend
   (package
     (name "r-dendextend")
-    (version "1.12.0")
+    (version "1.13.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dendextend" version))
        (sha256
         (base32
-         "0mgsc9qkr5p6hss3wychdjvk263ay48yx543wawj72l7q7cgx1xl"))))
+         "1iclvd9cyckd4djpa87ynm05fk6zl4b4m735za1w4irimc130m3r"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -2175,14 +2245,14 @@ SpatialVx.")
 (define-public r-extremes
   (package
     (name "r-extremes")
-    (version "2.0-10")
+    (version "2.0-11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "extRemes" version))
        (sha256
         (base32
-         "08fj72gpq2d6695hbm3cgwgal64z009ykrirby7g6r0akfcsx5ic"))))
+         "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
     (properties `((upstream-name . "extRemes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2339,14 +2409,14 @@ transportation problems.")
 (define-public r-limsolve
   (package
     (name "r-limsolve")
-    (version "1.5.5.3")
+    (version "1.5.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "limSolve" version))
        (sha256
         (base32
-         "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg"))))
+         "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
     (properties `((upstream-name . "limSolve")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2584,14 +2654,14 @@ regression using Kernel Ridge Regression.")
 (define-public r-prodlim
   (package
     (name "r-prodlim")
-    (version "2019.10.13")
+    (version "2019.11.13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "prodlim" version))
        (sha256
         (base32
-         "0rsyfpz667y5cijmq33l318mrdw8r340khp72gcg8n490b1g0176"))))
+         "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-kernsmooth" ,r-kernsmooth)
@@ -2688,7 +2758,8 @@ dimensioned arrays.")
     (properties `((upstream-name . "RMySQL")))
     (build-system r-build-system)
     (inputs
-     `(("mariadb" ,mariadb)
+     `(("mariadb" ,mariadb "lib")
+       ("mariadb-dev" ,mariadb "dev")
        ("zlib" ,zlib)))
     (propagated-inputs
      `(("r-dbi" ,r-dbi)))
@@ -3395,14 +3466,14 @@ structure.")
 (define-public r-vioplot
   (package
     (name "r-vioplot")
-    (version "0.3.2")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vioplot" version))
        (sha256
         (base32
-         "13kfjp747bnzksai8j39y2hyl3ljc6n53c2cfhaw78q3d63x0lbv"))))
+         "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-sm" ,r-sm)
@@ -3585,14 +3656,14 @@ normalizations, minimum variance matching, and so on.")
 (define-public r-sdmtools
   (package
     (name "r-sdmtools")
-    (version "1.1-221.1")
+    (version "1.1-221.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "SDMTools" version))
        (sha256
         (base32
-         "1fsgnlc7glawimzijp11j53g5bnfp1mdq9wb0754idmxcdi8a99q"))))
+         "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
     (properties `((upstream-name . "SDMTools")))
     (build-system r-build-system)
     (propagated-inputs `(("r-r-utils" ,r-r-utils)))
@@ -3826,14 +3897,14 @@ of merit, ordering functions, and enhanced versions of @code{pairs} and
 (define-public r-webshot
   (package
     (name "r-webshot")
-    (version "0.5.1")
+    (version "0.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "webshot" version))
        (sha256
         (base32
-         "08sb1xi376pfy1vwilk2d68zljsg9yiv04n2dkqz383gdhh0sxdr"))))
+         "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -4078,14 +4149,14 @@ published results; and a routine for graphical display.")
 (define-public r-network
   (package
     (name "r-network")
-    (version "1.15")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "network" version))
        (sha256
         (base32
-         "1cscw5978fyixhkicf06c4b2g1yf6gyi8vx86cz3dy75d41mrgjw"))))
+         "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-magrittr" ,r-magrittr)
@@ -4842,14 +4913,13 @@ the application.")
 (define-public r-algdesign
   (package
     (name "r-algdesign")
-    (version "1.1-7.3")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "AlgDesign" version))
        (sha256
-        (base32
+        (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
-         "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz"))))
     (properties `((upstream-name . "AlgDesign")))
     (build-system r-build-system)
     (home-page "https://github.com/jvbraun/AlgDesign")
@@ -5326,14 +5396,14 @@ simple method for converting between file types.")
 (define-public r-maptools
   (package
     (name "r-maptools")
-    (version "0.9-8")
+    (version "0.9-9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "maptools" version))
        (sha256
         (base32
-         "1ix3cg74w0w6cj8nwi0r9n3y5q9ljc21hm8xq6yqqngs57prvn2x"))))
+         "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreign" ,r-foreign)
@@ -5762,14 +5832,14 @@ 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
@@ -5777,6 +5847,8 @@ 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)
@@ -6052,14 +6124,14 @@ to help insert or delete content at a specific location in the document.")
 (define-public r-abn
   (package
     (name "r-abn")
-    (version "2.1")
+    (version "2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abn" version))
        (sha256
         (base32
-         "08jlvb6i5f7ry2dwm0jgrnn2w95vr0l67dpx13n9878lz9ld131b"))))
+         "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
     (build-system r-build-system)
     (inputs
      `(("gsl" ,gsl)))
@@ -6203,14 +6275,14 @@ other add-on packages.")
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.6.0")
+    (version "0.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "1izqh4j0gzyk25cga67gs0i6rl0j471h5y2c3y1maz79r32fs7fd"))))
+         "0scjmr8qvwaswb9wfq2lxp1v5fl72way8cid9agrf0z1agp0adad"))))
     (build-system r-build-system)
     (home-page "https://easystats.github.io/insight/")
     (synopsis "Easy access to model information for various model objects")
@@ -6368,14 +6440,14 @@ 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")
@@ -8017,14 +8089,14 @@ 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)
@@ -8113,14 +8185,14 @@ correlation, censored, ordered and multivariate problems.")
 (define-public r-bayesplot
   (package
     (name "r-bayesplot")
-    (version "1.7.0")
+    (version "1.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayesplot" version))
        (sha256
         (base32
-         "0h23sbfny2hcipvvfhq5aiwdh1vanizn7f8lpb9kffypxhcd7v7w"))))
+         "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
     (build-system r-build-system)
     (inputs
      `(("pandoc" ,ghc-pandoc)
@@ -8175,14 +8247,13 @@ detection, parallelism through BLAS and parallel user templates.")
 (define-public r-sjstats
   (package
     (name "r-sjstats")
-    (version "0.17.6")
+    (version "0.17.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjstats" version))
        (sha256
-        (base32
+        (base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6"))))
-         "11z1wfi0d74d1rld0320l3vmv6rl41wa0v9bjc44rk06yc90wld2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)
@@ -8332,22 +8403,47 @@ are also supported.  The two main functions are @code{ggpredict()} and
 results using @code{ggplot2}.")
     (license license:gpl3)))
 
+(define-public r-effectsize
+  (package
+    (name "r-effectsize")
+    (version "0.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "effectsize" version))
+       (sha256
+        (base32
+         "07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb"))))
+    (properties `((upstream-name . "effectsize")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bayestestr" ,r-bayestestr)
+       ("r-insight" ,r-insight)
+       ("r-parameters" ,r-parameters)))
+    (home-page "https://github.com/easystats/effectsize")
+    (synopsis "Indices of effect size and standardized parameters")
+    (description
+     "This package provides utilities to work with indices of effect size and
+standardized parameters for a wide variety of models, allowing computation and
+conversion of indices such as Cohen's d, r, odds, etc.")
+    (license license:gpl3)))
+
 (define-public r-sjplot
   (package
     (name "r-sjplot")
-    (version "2.7.2")
+    (version "2.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjPlot" version))
        (sha256
-        (base32 "1kx1qqgp4fhwwwpqn9mv8m1pnpjxfs7ww36ns7j1ja4a7ydwn2hp"))))
+        (base32 "0rmfc2pq80w0kxh6icljhqm31q580s0czvllsfxk6crmpyfgxkp7"))))
     (properties `((upstream-name . "sjPlot")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)
-       ("r-broom" ,r-broom)
        ("r-dplyr" ,r-dplyr)
+       ("r-effectsize" ,r-effectsize)
        ("r-forcats" ,r-forcats)
        ("r-ggeffects" ,r-ggeffects)
        ("r-ggplot2" ,r-ggplot2)
@@ -8359,7 +8455,7 @@ results using @code{ggplot2}.")
        ("r-magrittr" ,r-magrittr)
        ("r-mass" ,r-mass)
        ("r-modelr" ,r-modelr)
-       ("r-nlme" ,r-nlme)
+       ("r-parameters" ,r-parameters)
        ("r-performance" ,r-performance)
        ("r-psych" ,r-psych)
        ("r-purrr" ,r-purrr)
@@ -9047,14 +9143,13 @@ netCDF files.")
 (define-public r-biocmanager
   (package
     (name "r-biocmanager")
-    (version "1.30.9")
+    (version "1.30.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "BiocManager" version))
        (sha256
-        (base32
+        (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
-         "1l9b2mr99nhpvk1wkd93397i0d6z4vvbq3zm8dk86gb1pfci26sx"))))
     (properties `((upstream-name . "BiocManager")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/BiocManager/")
@@ -9581,13 +9676,13 @@ maps.")
 (define-public r-tidytree
   (package
     (name "r-tidytree")
-    (version "0.2.9")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidytree" version))
        (sha256
-        (base32 "1l9rk71dzlwg8736l0g4rdlq3pghxkfzmlxyln8y4bxx7ym51i6g"))))
+        (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ape" ,r-ape)
@@ -9608,13 +9703,13 @@ manipulate tree data.")
 (define-public r-rvcheck
   (package
     (name "r-rvcheck")
-    (version "0.1.6")
+    (version "0.1.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rvcheck" version))
        (sha256
-        (base32 "11n3qxapxcqsa0771s9q8n95kxmfyflya1d6wz4mm0lz0i6q55ia"))))
+        (base32 "1a3xlzi4n1rqiapfa180aif7n7nws8pbg8k3nk7ccaczvmni38aw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocmanager" ,r-biocmanager)
@@ -9821,14 +9916,14 @@ definiteness of a matrix.")
 (define-public r-rspectra
   (package
     (name "r-rspectra")
-    (version "0.15-0")
+    (version "0.16-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RSpectra" version))
        (sha256
         (base32
-         "1ab975scdqaxdna9sayjl6l14hz991y0pc8c8ah48w000616km8s"))))
+         "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
     (properties `((upstream-name . "RSpectra")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9970,14 +10065,14 @@ Touzet and Varre (2007).")
 (define-public r-rnifti
   (package
     (name "r-rnifti")
-    (version "0.11.1")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RNifti" version))
        (sha256
         (base32
-         "0jcgdg5k2swmi57aqj347kfi1fc4nvag7pxdfz61kc0vqqamm0wg"))))
+         "0hfid40pgfi1ykqka8y3v0m7h0iyd6fbvycvqlad3ibmbg621f0w"))))
     (properties `((upstream-name . "RNifti")))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -10083,14 +10178,14 @@ 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
@@ -10107,14 +10202,14 @@ 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
@@ -10138,18 +10233,17 @@ 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
@@ -11146,19 +11240,16 @@ library.")
 (define-public r-protviz
   (package
     (name "r-protviz")
-    (version "0.4.0")
+    (version "0.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "protViz" version))
        (sha256
         (base32
-         "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1"))))
+         "0cznzm1ijlq33yd5wsa61prav77y2vi698w0n2fx1xcv504c4bjv"))))
     (properties `((upstream-name . "protViz")))
     (build-system r-build-system)
-    (inputs
-     `(("perl" ,perl)
-       ("python-2" ,python-2)))
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
     (home-page "https://github.com/protViz/protViz/")
     (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
@@ -11225,14 +11316,14 @@ model with finite state space using the Aalen-Johansen estimator.")
 (define-public r-epi
   (package
     (name "r-epi")
-    (version "2.38")
+    (version "2.40")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Epi" version))
        (sha256
         (base32
-         "0ald9fjynrlyah8nzwfs49a08j4myd3c5bm56zn61gg5pyyhi8hd"))))
+         "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
     (properties `((upstream-name . "Epi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11407,14 +11498,14 @@ them in distributed compute environments.")
 (define-public r-future
   (package
     (name "r-future")
-    (version "1.15.0")
+    (version "1.15.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future" version))
        (sha256
         (base32
-         "1cbp7agb9lipjxsh7xm1yphh8a4hrjy7wrbkvhsxn1swh0c4s3b7"))))
+         "101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -13124,14 +13215,13 @@ lspec, polyclass, and polymars.")
 (define-public r-rms
   (package
     (name "r-rms")
-    (version "5.1-3.1")
+    (version "5.1-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rms" version))
        (sha256
-        (base32
+        (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
-         "0drbr3g0x5pbxyzy50wnf92rbal8izizrcqslqhg0gsfg9adjih9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -13360,13 +13450,13 @@ SELECT or UPDATE queries to an end-point.")
 (define-public r-bookdown
   (package
     (name "r-bookdown")
-    (version "0.15")
+    (version "0.16")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "bookdown" version))
               (sha256
                (base32
-                "0pgkabaqsckaz8z1nlza84jp172jyzv17kx5dily43jfx5psy2ap"))))
+                "1gwgvx1yg6q3wccnhidr3gshdvlgr42i4pvlg4h29kpsa7smjiv1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-htmltools" ,r-htmltools)
@@ -15362,13 +15452,13 @@ 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
@@ -15539,14 +15629,14 @@ in pipelines.")
 (define-public r-parameters
   (package
     (name "r-parameters")
-    (version "0.2.0")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parameters" version))
        (sha256
         (base32
-         "1mgggb3l67wgjiccq4y84wbs2dw9qk01akd553yiwbwky9rpawgh"))))
+         "0ifb9g1h8sn661q7jf9d8glk58gxdcym5ywbmx7phwn0y3is5wdv"))))
     (properties `((upstream-name . "parameters")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15566,13 +15656,13 @@ 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
@@ -15673,3 +15763,112 @@ unique identifiers, and whether it is a certain length.  In addition,
 files and to efficiently import multiple tabular data files into one
 data.table.")
     (license license:gpl3)))
+
+(define-public r-quadprog
+  (package
+    (name "r-quadprog")
+    (version "1.5-8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "quadprog" version))
+       (sha256
+        (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/quadprog")
+    (synopsis "Functions to solve quadratic programming problems")
+    (description
+     "This package contains routines and documentation for solving quadratic
+programming problems.")
+    (license license:gpl3+)))
+
+(define-public r-desolve
+  (package
+    (name "r-desolve")
+    (version "1.25")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "deSolve" version))
+       (sha256
+        (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp"))))
+    (properties `((upstream-name . "deSolve")))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://desolve.r-forge.r-project.org/")
+    (synopsis "Solvers for initial value problems of differential equations")
+    (description "This package provides functions that solve initial
+value problems of a system of first-order ordinary differential equations (ODE),
+of partial differential equations (PDE), of differential algebraic equations
+(DAE), and of delay differential equations.  The functions provide an interface
+to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
+to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
+the Runge-Kutta family with fixed or variable time steps.  The package contains
+routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
+differential equations (PDE) that have been converted to ODEs by numerical
+differencing.")
+    (license license:gpl2+)))
+
+(define-public r-pracma
+  (package
+    (name "r-pracma")
+    (version "2.2.5")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "pracma" version))
+              (sha256
+               (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/pracma/")
+    (synopsis "Practical numerical math functions")
+    (description "This package provides functions for numerical analysis and
+linear algebra, numerical optimization, differential equations, plus some
+special functions.  It uses Matlab function names where appropriate to simplify
+porting.")
+    (license license:gpl3+)))
+
+(define-public r-subplex
+  (package
+    (name "r-subplex")
+    (version "1.5-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "subplex" version))
+       (sha256
+        (base32
+         "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/subplex")
+    (synopsis "Unconstrained optimization using the subplex algorithm")
+    (description
+     "This package implements the Subplex optimization algorithm.
+It solves unconstrained optimization problems using a simplex method on
+subspaces.  The method is well suited for optimizing objective functions that
+are noisy or are discontinuous at the solution.")
+    (license license:gpl3+)))
+
+(define-public r-txtplot
+  (package
+    (name "r-txtplot")
+    (version "1.0-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "txtplot" version))
+       (sha256
+        (base32
+         "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/txtplot/")
+    (synopsis "Text-based plotting")
+    (description "This package provides functions to produce rudimentary ASCII
+graphics directly in the terminal window.  This package provides a basic
+plotting function (and equivalents of curve, density, acf and barplot) as well
+as a boxplot function.")
+    (license license:lgpl3+)))

gnu/packages/crypto.scm

@@ -535,19 +535,18 @@ generator.")
 (define-public perl-crypt-random-source
   (package
     (name "perl-crypt-random-source")
-    (version "0.12")
+    (version "0.14")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/"
                            "Crypt-Random-Source-" version ".tar.gz"))
        (sha256
-        (base32
+        (base32 "1rpdds3sy5l1fhngnkrsgwsmwd54wpicx3i9ds69blcskwkcwkpc"))))
-         "00mw5m52sbz9nqp3f6axyrgcrihqxn7k8gv0vi1kvm1j1nc9g29h"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-module-build-tiny" ,perl-module-build-tiny)
-       ("perl-test-exception" ,perl-test-exception)))
+       ("perl-test-fatal" ,perl-test-fatal)))
     (propagated-inputs
      `(("perl-capture-tiny" ,perl-capture-tiny)
        ("perl-module-find" ,perl-module-find)

gnu/packages/cups.scm

@@ -58,7 +58,7 @@
 (define-public cups-filters
   (package
     (name "cups-filters")
-    (version "1.25.1")
+    (version "1.25.11")
     (source(origin
               (method url-fetch)
               (uri
@@ -66,7 +66,7 @@
                               "cups-filters-" version ".tar.xz"))
               (sha256
                (base32
-                "0nlq44jnjcnrbdv0dv5myg5kaycmk6a4klynpvj65xvn3l9cq28s"))
+                "0ni8krr4rf5833livn9401cd41gspjvxj0iiqnc1rfg3x90i0fxh"))
               (modules '((guix build utils)))
               (snippet
                ;; install backends, banners and filters to cups-filters output
@@ -187,7 +187,7 @@ filters for the PDF-centric printing workflow introduced by OpenPrinting.")
 (define-public cups-minimal
   (package
     (name "cups-minimal")
-    (version "2.2.11")
+    (version "2.3.0")
     (source
      (origin
        (method url-fetch)
@@ -195,7 +195,7 @@ filters for the PDF-centric printing workflow introduced by OpenPrinting.")
                            version "/cups-" version "-source.tar.gz"))
        (sha256
         (base32
-         "0v5p10lyv8wv48s8ghkhjmdrxg6iwj8hn36v1ilkz46n7y0i107m"))))
+         "19d1jpdpxy0fclq37pchi7ldnw9dssxx3zskcgqai3h0rwlh5bxc"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -225,7 +225,7 @@ filters for the PDF-centric printing workflow introduced by OpenPrinting.")
                #t)))
          (add-before 'build 'patch-tests
            (lambda _
-             (substitute* "test/ippserver.c"
+             (substitute* "tools/ippeveprinter.c"
                (("#  else /\\* HAVE_AVAHI \\*/")
                 "#elif defined(HAVE_AVAHI)"))
              #t)))))
@@ -245,7 +245,8 @@ networked printers, and printers can be shared from one computer to another.
 Internally, CUPS uses PostScript Printer Description (@dfn{PPD}) files to
 describe printer capabilities and features, and a wide variety of generic and
 device-specific programs to convert and print many types of files.")
-    (license license:gpl2)))
+    ;; CUPS is Apache 2.0 with exceptions, see the NOTICE file.
+    (license license:asl2.0)))
 
 (define-public cups
   (package (inherit cups-minimal)

gnu/packages/databases.scm

@@ -37,6 +37,7 @@
 ;;; Copyright © 2019 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2019 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
+;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -96,6 +97,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rdf)
   #:use-module (gnu packages readline)
@@ -715,9 +717,11 @@ Language.")
                                     (find-files "pcre") (find-files "zlib")))
                   #t))))
     (build-system cmake-build-system)
+    (outputs '("out" "lib" "dev"))
     (arguments
      `(#:configure-flags
-       '("-DBUILD_CONFIG=mysql_release"
+       (list
+         "-DBUILD_CONFIG=mysql_release"
          ;; Linking with libarchive fails, like this:
 
          ;; ld: /gnu/store/...-libarchive-3.2.2/lib/libarchive.a(archive_entry.o):
@@ -741,15 +745,26 @@ Language.")
          "-DDEFAULT_COLLATION=utf8_general_ci"
          "-DMYSQL_DATADIR=/var/lib/mysql"
          "-DMYSQL_UNIX_ADDR=/run/mysqld/mysqld.sock"
-         "-DINSTALL_INFODIR=share/mysql/docs"
+         (string-append "-DCMAKE_INSTALL_PREFIX=" (assoc-ref %outputs "lib"))
-         "-DINSTALL_MANDIR=share/man"
+         (string-append "-DCMAKE_INSTALL_RPATH=" (assoc-ref %outputs "lib")
+                        "/lib")
+         (string-append "-DINSTALL_INFODIR=" (assoc-ref %outputs "out")
+                        "/share/mysql/docs")
+         (string-append "-DINSTALL_MANDIR=" (assoc-ref %outputs "out")
+                        "/share/man")
+         (string-append "-DINSTALL_SCRIPTDIR=" (assoc-ref %outputs "out") "/bin")
+         (string-append "-DINSTALL_BINDIR=" (assoc-ref %outputs "out") "/bin")
+         "-DCMAKE_INSTALL_LIBDIR=lib"
          "-DINSTALL_PLUGINDIR=lib/mysql/plugin"
-         "-DINSTALL_SCRIPTDIR=bin"
+         (string-append "-DINSTALL_INCLUDEDIR=" (assoc-ref %outputs "dev")
-         "-DINSTALL_INCLUDEDIR=include/mysql"
+                        "/include/mysql")
-         "-DINSTALL_DOCREADMEDIR=share/mysql/docs"
+         (string-append "-DINSTALL_DOCREADMEDIR=" (assoc-ref %outputs "out")
-         "-DINSTALL_SUPPORTFILESDIR=share/mysql/support-files"
+                        "/share/mysql/docs")
+         (string-append "-DINSTALL_DOCDIR=" (assoc-ref %outputs "out")
+                        "/share/mysql/docs")
+         (string-append "-DINSTALL_SUPPORTFILESDIR=" (assoc-ref %outputs "out")
+                        "/share/mysql/support-files")
          "-DINSTALL_MYSQLSHAREDIR=share/mysql"
-         "-DINSTALL_DOCDIR=share/mysql/docs"
          "-DINSTALL_SHAREDIR=share")
        #:phases
        (modify-phases %standard-phases
@@ -832,19 +847,29 @@ Language.")
           'install 'post-install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out     (assoc-ref outputs "out"))
-                   (test    (assoc-ref outputs "test")))
+                   (dev     (assoc-ref outputs "dev"))
+                   (lib     (assoc-ref outputs "lib")))
               (substitute* (string-append out "/bin/mysql_install_db")
                 (("basedir=\"\"")
                  (string-append "basedir=\"" out "\"")))
               ;; Remove unneeded files for testing.
-              (with-directory-excursion out
+              (with-directory-excursion lib
                 (for-each delete-file-recursively
-                          '("data" "mysql-test" "sql-bench"
+                          '("data" "mysql-test" "sql-bench"))
-                            "share/man/man1/mysql-test-run.pl.1"))
-                ;; 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$")))
+              (with-directory-excursion out
+                (delete-file "share/man/man1/mysql-test-run.pl.1")
+                ;; Delete huge and unnecessary executables.
+                (for-each delete-file (find-files "bin" "(test|embedded)")))
+              (mkdir-p (string-append dev "/share"))
+              (mkdir-p (string-append dev "/bin"))
+              (rename-file (string-append lib "/bin/mysqld")
+                           (string-append out "/bin/mysqld"))
+              (rename-file (string-append lib "/share/pkgconfig")
+                           (string-append dev "/share/pkgconfig"))
+              (rename-file (string-append out "/bin/mysql_config")
+                           (string-append dev "/bin/mysql_config"))
               #t))))))
     (native-inputs
      `(("bison" ,bison)
@@ -1609,7 +1634,8 @@ columns, primary keys, unique constraints and relationships.")
        #:tests? #f))
     (propagated-inputs
      `(("perl-dbi" ,perl-dbi)
-       ("mysql" ,mariadb)))
+       ("mysql" ,mariadb "lib")
+       ("mysql-dev" ,mariadb "dev")))
     (home-page "https://metacpan.org/release/DBD-mysql")
     (synopsis "DBI MySQL interface")
     (description "This package provides a MySQL driver for the Perl5
@@ -2727,7 +2753,8 @@ database).")
        ("mock" ,python-mock)
        ("py.test" ,python-pytest)))
     (inputs
-     `(("mysql" ,mariadb)
+     `(("mysql" ,mariadb "lib")
+       ("mysql-dev" ,mariadb "dev")
        ("libz" ,zlib)
        ("openssl" ,openssl)))
     (home-page "https://github.com/PyMySQL/mysqlclient-python")
@@ -3170,3 +3197,92 @@ NumPy, and other traditional Python scientific computing packages.")
 It implements the Python DB API 2.0 specification and includes support for
 SQLAlchemy.")
     (license license:asl2.0)))
+
+(define-public libdbi
+  (package
+    (name "libdbi")
+    (version "0.9.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/libdbi/libdbi/libdbi-"
+                                  version "/libdbi-" version ".tar.gz"))
+              (sha256
+               (base32
+                "00s5ra7hdlq25iv23nwf4h1v3kmbiyzx0v9bhggjiii4lpf6ryys"))))
+    (build-system gnu-build-system)
+    (synopsis "Database independent abstraction layer in C")
+    (description
+     "This library implements a database independent abstraction layer in C,
+similar to the DBI/DBD layer in Perl.  Writing one generic set of code,
+programmers can leverage the power of multiple databases and multiple
+simultaneous database connections by using this framework.")
+    (home-page "http://libdbi.sourceforge.net/")
+    (license license:lgpl2.1+)))
+
+(define-public libdbi-drivers
+  (package
+    (name "libdbi-drivers")
+    (version "0.9.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/libdbi-drivers/"
+                                  "libdbi-drivers/libdbi-drivers-" version
+                                  "/libdbi-drivers-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0m680h8cc4428xin4p733azysamzgzcmv4psjvraykrsaz6ymlj3"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("inetutils" ,inetutils)
+       ("glibc-locales" ,glibc-locales)))
+    (inputs
+     `(("libdbi" ,libdbi)
+       ("mysql" ,mariadb)
+       ("postgresql" ,postgresql)
+       ("sqlite" ,sqlite)))
+    (arguments
+     `(#:configure-flags
+       (let ((libdbi (assoc-ref %build-inputs "libdbi"))
+             (mysql (assoc-ref %build-inputs "mysql"))
+             (postgresql (assoc-ref %build-inputs "postgresql"))
+             (sqlite (assoc-ref %build-inputs "sqlite")))
+         (list "--disable-docs"
+               (string-append "--with-dbi-incdir=" libdbi "/include")
+               (string-append "--with-dbi-libdir=" libdbi "/lib")
+               "--with-mysql"
+               (string-append "--with-mysql-incdir=" mysql "/include/mysql")
+               (string-append "--with-mysql-libdir=" mysql "/lib")
+               "--with-pgsql"
+               (string-append "--with-pgsql-incdir=" postgresql "/include")
+               (string-append "--with-pgsql-libdir=" postgresql "/lib")
+               "--with-sqlite3"
+               (string-append "--with-sqlite-incdir=" sqlite "/include")
+               (string-append "--with-sqlite-libdir=" sqlite "/lib")))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-tests
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "tests/test_mysql.sh"
+               (("^MYMYSQLD=.*")
+                (string-append "MYMYSQLD="
+                               (assoc-ref inputs "mysql")
+                               "/bin/mysqld")))
+             #t))
+         (add-after 'install 'remove-empty-directories
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((var (string-append (assoc-ref outputs "out") "/var")))
+               (delete-file-recursively var))
+             #t)))))
+    (synopsis "Database drivers for the libdbi framework")
+    (description
+     "The @code{libdbi-drivers} library provides the database specific drivers
+for the @code{libdbi} framework.
+
+The drivers officially supported by @code{libdbi} are:
+@itemize
+@item MySQL,
+@item PostgreSQL,
+@item SQLite.
+@end itemize")
+    (home-page "http://libdbi-drivers.sourceforge.net/")
+    (license license:lgpl2.1+)))

gnu/packages/datastructures.scm

@@ -1,7 +1,8 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
+;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -20,7 +21,6 @@
 
 (define-module (gnu packages datastructures)
   #:use-module (gnu packages)
-  #:use-module (gnu packages documentation)
   #:use-module (gnu packages perl)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
@@ -80,12 +80,14 @@ library.")
     (name "sparsehash")
     (version "2.0.3")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/sparsehash/sparsehash/"
+              (uri (git-reference
-                                  "archive/sparsehash-" version ".tar.gz"))
+                     (url "https://github.com/sparsehash/sparsehash.git")
+                     (commit (string-append name "-" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "133szz0ldwch0kd91l0sa57qsnl020njn622szd9cxrjqyjqds85"))))
+                "0m3f0cnpnpf6aak52wn8xbrrdw8p0yhq8csgc8nlvf9zp8c402na"))))
     (build-system gnu-build-system)
     (synopsis "Memory-efficient hashtable implementations")
     (description
@@ -211,10 +213,31 @@ to the structure and choosing one or more fields to act as the key.")
                                   ".tar.gz.offline.install.gz"))
               (sha256
                (base32
-                "1v86ivv3mmdy802i9xkjpxb4cggj3s27wb19ja4sw1klnivjj69g"))))
+                "1v86ivv3mmdy802i9xkjpxb4cggj3s27wb19ja4sw1klnivjj69g"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (delete-file-recursively "external") #t))
+              (patches
+                (list (origin
+                        (method url-fetch)
+                        (uri "https://salsa.debian.org/science-team/libsdsl/raw/debian/2.1.1+dfsg-2/debian/patches/0001-Patch-cmake-files.patch")
+                        (file-name "sdsl-lite-dont-use-bundled-libraries.patch")
+                        (sha256
+                         (base32
+                          "0m542xpys54bni29zibgrfpgpd0zgyny4h131virxsanixsbz52z")))))))
     (build-system cmake-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-static-library
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (copy-file "lib/libsdsl_static.a"
+                          (string-append out "/lib/libsdsl.a")))
+             #t)))))
     (native-inputs
-     `(("doxygen" ,doxygen)))
+     `(("libdivsufsort" ,libdivsufsort)))
     (home-page "https://github.com/simongog/sdsl-lite")
     (synopsis "Succinct data structure library")
     (description "The Succinct Data Structure Library (SDSL) is a powerful and
@@ -226,3 +249,32 @@ operations of the original object efficiently.  The theoretical time
 complexity of an operation performed on the classical data structure and the
 equivalent succinct data structure are (most of the time) identical.")
     (license license:gpl3+)))
+
+(define-public libdivsufsort
+  (package
+    (name "libdivsufsort")
+    (version "2.0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/y-256/libdivsufsort.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:tests? #f                      ; there are no tests
+       #:configure-flags
+       ;; Needed for rapmap and sailfish.
+       '("-DBUILD_DIVSUFSORT64=ON")))
+    (home-page "https://github.com/y-256/libdivsufsort")
+    (synopsis "Lightweight suffix-sorting library")
+    (description "libdivsufsort is a software library that implements a
+lightweight suffix array construction algorithm.  This library provides a
+simple and an efficient C API to construct a suffix array and a
+Burrows-Wheeler transformed string from a given string over a constant-size
+alphabet.  The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
+bytes of memory space, where n is the length of the string.")
+    (license license:expat)))

gnu/packages/dc.scm

@@ -33,14 +33,14 @@
 (define-public ncdc
   (package
     (name "ncdc")
-    (version "1.22")
+    (version "1.22.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "http://dev.yorhel.nl/download/ncdc-" version
                            ".tar.gz"))
-       (sha256 (base32
+       (sha256
-                "0n9sn4rh4zhmzjknsvyp4bfh925abz93ln43gl8a1v63rs2yyhgx"))))
+        (base32 "1bdgqd07f026qk6vpbxqsin536znd33931m3b4z44prlm9wd6pyi"))))
     (build-system gnu-build-system)
     (inputs
      `(("bzip2" ,bzip2)

gnu/packages/debug.scm

@@ -325,7 +325,7 @@ conditions.")
       ;; stress-make wrapper is under BSD-3-modifications-must-be-indicated,
       ;; and patched GNU Make is under its own license.
       (license (list (non-copyleft "LICENSE.md")
-                     (package-license gnu-make))))))
+                     gpl3+)))))
 
 (define-public zzuf
   (package

gnu/packages/dictionaries.scm

@@ -219,7 +219,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
 (define-public grammalecte
   (package
     (name "grammalecte")
-    (version "1.5.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch/zipbomb)
@@ -227,7 +227,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
                            "Grammalecte-fr-v" version ".zip"))
        (sha256
         (base32
-         "0byh578apbyq2jdpgmbaw01izlkyw2h5nsr28az44rvaqrsndy0z"))))
+         "0kz13gx2hd23xd6bfr4z73lh18slj3vbvs2xcb7qvhramxjqzqcn"))))
     (build-system python-build-system)
     (home-page "https://grammalecte.net")
     (synopsis "French spelling and grammar checker")

gnu/packages/diffoscope.scm

@@ -67,7 +67,7 @@
   #:use-module (ice-9 match))
 
 (define-public diffoscope
-  (let ((version "129"))
+  (let ((version "131"))
     (package
       (name "diffoscope")
       (version version)
@@ -79,7 +79,7 @@
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1r8hq93gga9n4jv4fyf1divc9cwvvjadkzl47lazzrfy3nn1qjwr"))))
+                  "0jai3kycjlrc64f4vg8yklri6ds1451qy6r6sw2646bhjr0gs233"))))
       (build-system python-build-system)
       (arguments
        `(#:phases (modify-phases %standard-phases

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/display-managers.scm

@@ -27,6 +27,7 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system qt)
   #:use-module (guix build-system gnu)
   #:use-module (guix packages)
   #:use-module (guix utils)
@@ -62,7 +63,7 @@
               (sha256
                (base32
                 "0nilrhwlyvkngjgxfc08n73c16azgmw80pvx0a78xqww9y3hv4xh"))))
-    (build-system cmake-build-system)
+    (build-system qt-build-system)
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
        ("pkg-config" ,pkg-config)
@@ -102,27 +103,16 @@
                        (assoc-ref %build-inputs "shadow")
                        "/etc/login.defs")
         (string-append "-DQT_IMPORTS_DIR="
-                       (assoc-ref %outputs "out") "/qml")
+                       (assoc-ref %outputs "out") "/lib/qt5/qml")
         (string-append "-DCMAKE_INSTALL_SYSCONFDIR="
                        (assoc-ref %outputs "out") "/etc"))
-       #:modules ((guix build cmake-build-system)
-                  (guix build qt-utils)
-                  (guix build utils))
-       #:imported-modules (,@%cmake-build-system-modules
-                           (guix build qt-utils))
        #:phases
-       (modify-phases %standard-phases
+       (modify-phases (@ (guix build qt-build-system) %standard-phases)
          (add-after 'unpack 'embed-loginctl-reference
            (lambda _
              (substitute* "CMakeLists.txt"
                (("/usr/bin/loginctl") (which "loginctl")))
-             #t))
+               #t)))))
-         (add-after 'install 'wrap-programs
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (wrap-qt-program out "sddm")
-               (wrap-qt-program out "sddm-greeter")
-               #t))))))
     (synopsis "QML based X11 and Wayland display manager")
     (description "SDDM is a display manager for X11 and Wayland aiming to be
 fast, simple and beautiful.  SDDM is themeable and puts no restrictions on the

gnu/packages/django.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 ng0 <ng0@n0.is>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
@@ -348,14 +348,14 @@ account authentication.")
     (version "1.10.1")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append
+       (uri (git-reference
-             "https://github.com/jazzband/django-debug-toolbar/archive/"
+             (url "https://github.com/jazzband/django-debug-toolbar.git")
-             version ".tar.gz"))
+             (commit version)))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1rww056hyzks8spbgf4h7kf6ybxlc5p08a2b6gn1nqrrzs4yx9sy"))))
+         "0zr6yjsms97wlvvd17rdbrx01irkg887dn9x70c1hzfjmfvp9afk"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-sqlparse" ,python-sqlparse)
@@ -456,14 +456,14 @@ merging, minifying and compiling CSS and Javascript files.")
     (version "2.4.1")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append
+       (uri (git-reference
-             "https://github.com/niwinz/django-jinja/archive/"
+             (url "https://github.com/niwinz/django-jinja.git")
-             version ".tar.gz"))
+             (commit version)))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0bzrb4m6wx9ph5cpvz7wpvg5k6ksvj0dnxlg0nhhqskhvp46brs1"))))
+         "1fcrxlznlq1xvl26y3j1r22vvy6m08r5l97xi2wj50rdmxhfvhis"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-django" ,python-django)
@@ -695,6 +695,9 @@ project.")
              (or
               (not tests?)
               (begin
+                (setenv "PYTHONPATH"
+                        (string-append (getcwd) ":"
+                                       (getenv "PYTHONPATH")))
                 (setenv "DJANGO_SETTINGS_MODULE" "tests.settings")
                 (invoke "django-admin" "test" "tests"))))))))
     (propagated-inputs

gnu/packages/dns.scm

@@ -114,7 +114,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
 (define-public isc-bind
   (package
     (name "bind")
-    (version "9.14.7")
+    (version "9.14.8")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -122,7 +122,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
                     "/bind-" version ".tar.gz"))
               (sha256
                (base32
-                "07998nx0yv3xy8c62b1ira9qygsgvpljwcgb47ypzxq8b57gb86f"))))
+                "0xm0xrpgxq6gk6r6aa2w0lygnq02y1p614dmyjdmlsfnrrsslig5"))))
     (build-system gnu-build-system)
     (outputs `("out" "utils"))
     (inputs
@@ -320,14 +320,14 @@ asynchronous fashion.")
 (define-public nsd
   (package
     (name "nsd")
-    (version "4.2.2")
+    (version "4.2.3")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.nlnetlabs.nl/downloads/nsd/nsd-"
                            version ".tar.gz"))
        (sha256
-        (base32 "1ys608jyp5scc957q4brm094c97sxlwymina7d2nvzi51aa37cw3"))))
+        (base32 "1664wpglrwqk627xma10f9qa652vzmf90gsjd8pribyj74xrczc1"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -595,14 +595,15 @@ Extensions} (DNSSEC).")
 (define-public knot
   (package
     (name "knot")
-    (version "2.9.0")
+    (version "2.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://secure.nic.cz/files/knot-dns/"
                            "knot-" version ".tar.xz"))
        (sha256
-        (base32 "18i1kdyaqaskjyhmq888wml4d2p4ic1sbjynlb6ggfxsxzm38x6z"))
+        (base32
+         "0kd0v2w1c2by1l8jw91x16wkyyy9wh9lyr93g4w0qdmadjaj34gi"))
        (modules '((guix build utils)))
        (snippet
         '(begin

gnu/packages/education.scm

@@ -58,6 +58,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python)
+  #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
   #:use-module (srfi srfi-1))
 
@@ -167,7 +168,7 @@ of categories with some of the activities available in that category.
        ("gettext" ,gettext-minimal)
        ("perl" ,perl)
        ("qttools" ,qttools)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("openssl" ,openssl)
        ("python-2" ,python-2)
@@ -253,7 +254,7 @@ easy.")
 (define-public snap
   (package
     (name "snap")
-    (version "5.2.5")
+    (version "5.3.8")
     (source
      (origin
        (method git-fetch)
@@ -263,7 +264,7 @@ easy.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0smlqxd8gqy26dlsal197848lhynv74m8myxs6fdlnzgva1f3zzw"))))
+         "1lm5vvykdzgn667kvnsv0ab5bl0kjsr05kvcd18a7pn0g8sykfpc"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))
@@ -487,14 +488,14 @@ letters of the alphabet, spelling, eye-hand coordination, etc.")
 (define-public fet
   (package
     (name "fet")
-    (version "5.40.2")
+    (version "5.41.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.lalescu.ro/liviu/fet/download/"
                                   "fet-" version ".tar.bz2"))
               (sha256
                (base32
-                "068zdvb3rys7vvkq33i2jh89c7svvdaqp0548k99jmhbd24xnhgh"))))
+                "0ppa5h1p0y0z8x4xpn45b0x3nl1khyh56m22v6xysk3znxlak4q7"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -554,7 +555,7 @@ language and very flexible regarding to new or unknown keyboard layouts.")
 (define-public ktouch
   (package
     (name "ktouch")
-    (version "19.08.1")
+    (version "19.08.2")
     (source
       (origin
         (method url-fetch)
@@ -562,16 +563,11 @@ language and very flexible regarding to new or unknown keyboard layouts.")
                             version "/src/ktouch-" version ".tar.xz"))
         (sha256
          (base32
-          "19rdk94pls75hdvx11hnfk3qpm6l28p9q45q5f04sknxagrfaznr"))))
+          "0dm6xcwai0bx2h16rny1xa9n1509mfxvy39kfxx5qih53p15jrnk"))))
-    (build-system cmake-build-system)
+    (build-system qt-build-system)
     (arguments
-     `(#:modules ((guix build cmake-build-system)
+     `(#:phases
-                  (guix build qt-utils)
+       (modify-phases (@ (guix build qt-build-system) %standard-phases)
-                  (guix build utils))
-       #:imported-modules (,@%cmake-build-system-modules
-                            (guix build qt-utils))
-       #:phases
-       (modify-phases %standard-phases
          (add-after 'configure 'patch-makefiles
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((qtdec (assoc-ref inputs "qtdeclarative")))
@@ -579,11 +575,6 @@ language and very flexible regarding to new or unknown keyboard layouts.")
                               "src/CMakeFiles/ktouch.dir/build.make")
                  (("/gnu/store/.*qmlcachegen")
                   (string-append qtdec "/bin/qmlcachegen"))))
-             #t))
-         (add-after 'install 'wrap-executable
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (wrap-qt-program out "ktouch"))
              #t)))))
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)

gnu/packages/efi.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2019 Danny Milosavljevic <dannym@scratchpost.org>
 ;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -36,18 +37,17 @@
 (define-public gnu-efi
   (package
     (name "gnu-efi")
-    (version "3.0.9")
+    (version "3.0.11")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/gnu-efi/"
-                           name "-" version ".tar.bz2"))
+                           "gnu-efi-" version ".tar.bz2"))
        (sha256
-        (base32
+        (base32 "1ffnc4xbzfggs37ymrgfx76j56kk2644c081ivhr2bjkla9ag3gj"))))
-         "1w3p4aqlc5j93q44la7dc8cr3hky20zvsd0h0k2lyzhwmrzfl5b7"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ; None exist.
+     `(#:tests? #f                      ; none exist
        #:make-flags
        (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
        #:phases

gnu/packages/elixir.scm

@@ -33,7 +33,7 @@
 (define-public elixir
   (package
     (name "elixir")
-    (version "1.8.2")
+    (version "1.9.4")
     (source
      (origin
        (method git-fetch)
@@ -42,7 +42,7 @@
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1n77cpcl2b773gmj3m9s24akvj9gph9byqbmj2pvlsmby4aqwckq"))
+        (base32 "1l4318g35y4h0vi2w07ayc3jizw1xc3s7hdb47w6j3iw33y06g6b"))
        (patches (search-patches "elixir-path-length.patch"))))
     (build-system gnu-build-system)
     (arguments
@@ -63,9 +63,21 @@
                               "lib/mix/lib/mix/scm/git.ex")
                  (("(cmd\\(['\"])git" _ prefix)
                   (string-append prefix (which "git"))))
+               (substitute* '("lib/mix/lib/mix/release.ex"
+                              "lib/mix/lib/mix/tasks/release.init.ex")
+                 (("#!/bin/sh")
+                  (string-append "#!" (which "sh"))))
                (substitute* "bin/elixir"
-                 (("ERL_EXEC=\"erl\"")
+                 (("ERTS_BIN=")
-                  (string-append "ERL_EXEC=" (which "erl"))))
+                  (string-append
+                    "ERTS_BIN="
+                    ;; Elixir Releases will prepend to ERTS_BIN the path of a copy of erl.
+                    ;; We detect if a release is being generated by checking the initial ERTS_BIN
+                    ;; value: if it's empty, we are not in release mode and can point to the actual
+                    ;; erl binary in Guix store.
+                    "\nif [ -z \"$ERTS_BIN\" ]; then ERTS_BIN="
+                    (string-drop-right (which "erl") 3)
+                    "; fi")))
                (substitute* "bin/mix"
                  (("#!/usr/bin/env elixir")
                   (string-append "#!" out "/bin/elixir"))))

gnu/packages/elm.scm

@@ -47,9 +47,25 @@
         (base32 "0s93z9vr0vp5w894ghc5s34nsq09sg1msf59zfiba87sid5vgjqy"))
        (patches
         (search-patches "elm-compiler-disable-reactor.patch"
-                        "elm-compiler-relax-glsl-bound.patch"
                         "elm-compiler-fix-map-key.patch"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'update-constraints
+           (lambda _
+             (substitute* "elm.cabal"
+               (("ansi-terminal >= 0\\.8 && < 0\\.9,")
+                "ansi-terminal >= 0.8 && < 0.10,")
+               (("containers >= 0\\.5\\.8\\.2 && < 0\\.6,")
+                "containers >= 0.5.8.2 && < 0.7,")
+               (("http-client >= 0\\.5 && < 0\\.6,")
+                "http-client >= 0.5 && < 0.7,")
+               (("language-glsl >= 0\\.0\\.2 && < 0\\.3,")
+                "language-glsl >= 0.0.2 && < 0.4,")
+               (("network >= 2\\.4 && < 2\\.7,")
+                "network >= 2.4 && < 2.9,"))
+             #t)))))
     (inputs
      `(("ghc-ansi-terminal" ,ghc-ansi-terminal)
        ("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint)

gnu/packages/emacs-xyz.scm

@@ -79,6 +79,7 @@
   #:use-module (guix cvs-download)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix hg-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system emacs)
@@ -126,6 +127,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages acl)
   #:use-module (gnu packages mail)
+  #:use-module (gnu packages messaging)
   #:use-module (gnu packages package-management)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pdf)
@@ -1005,6 +1007,30 @@ skip set strings, which are arguments to @code{skip-chars-forward} and
 and reused.")
       (license license:gpl3+))))
 
+(define-public emacs-ample-theme
+  (let ((commit "536966adf882446165a1f756830028faa792c7a9")
+        (revision "1"))
+    (package
+      (name "emacs-ample-theme")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/jordonbiondo/ample-theme")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "07bpv8dag40qjnm5000pgzpazj4whfxf93x2vprz26sg3mjfx0nf"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/jordonbiondo/ample-theme")
+      (synopsis "Theme for Emacs providing dark, light, and flat versions")
+      (description "Ample themes is a collection of three themes sharing a
+similar pallet with a light, dark and flat versions with a focus on being easy
+on the eyes during night and day.  They only support GUI and 256 colour
+terminals.")
+      (license license:gpl3+))))
+
 (define-public emacs-reformatter
   (package
     (name "emacs-reformatter")
@@ -1635,15 +1661,14 @@ a set of simplified face specifications and a user-supplied color palette")
 (define-public emacs-howm
   (package
     (name "emacs-howm")
-    (version "1.4.4")
+    (version "1.4.5")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "http://howm.sourceforge.jp/a/howm-"
+       (uri (string-append "https://howm.sourceforge.jp/a/howm-"
                            version ".tar.gz"))
        (sha256
-        (base32
+        (base32 "1kvr5pxpc9rwhkza9025mdi0wvh0f0rpawl21rzirjk1x10903yi"))))
-         "0ddm91l6z58j7x59fa966j6q1rg4cinyza4r8ibg80hprn5h31qk"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("emacs" ,emacs-minimal)))
@@ -1661,7 +1686,7 @@ a set of simplified face specifications and a user-supplied color palette")
        (modify-phases %standard-phases
          (add-after 'install 'make-autoloads
            (assoc-ref emacs:%standard-phases 'make-autoloads)))))
-    (home-page "http://howm.osdn.jp/")
+    (home-page "https://howm.osdn.jp/")
     (synopsis "Note-taking tool for Emacs")
     (description "Howm is a note-taking tool for Emacs.  Like
 code@{emacs-wiki.el}, it facilitates using hyperlinks and doing full-text
@@ -1974,9 +1999,9 @@ filters, new key bindings and faces.  It can be enabled by
              ;; upgrading" that pdf-tools tries to perform.
              (emacs-substitute-variables "pdf-tools.el"
                ("pdf-tools-handle-upgrades" '()))))
-         (add-after 'emacs-patch-variables 'emacs-set-emacs-load-path
+         (add-after 'emacs-patch-variables 'emacs-add-source-to-load-path
-           (assoc-ref emacs:%standard-phases 'set-emacs-load-path))
+           (assoc-ref emacs:%standard-phases 'add-source-to-load-path))
-         (add-after 'emacs-set-emacs-load-path 'emacs-install
+         (add-after 'emacs-add-source-to-load-path 'emacs-install
            (assoc-ref emacs:%standard-phases 'install))
          (add-after 'emacs-install 'emacs-build
            (assoc-ref emacs:%standard-phases 'build))
@@ -2049,14 +2074,14 @@ type, for example: packages, buffers, files, etc.")
 (define-public emacs-guix
   (package
     (name "emacs-guix")
-    (version "0.5.1.1")
+    (version "0.5.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://emacs-guix.gitlab.io/website/"
                                   "releases/emacs-guix-" version ".tar.gz"))
               (sha256
                (base32
-                "1gxg7lan3njc2yg2d02b2zij0d2cm2pv2q08nqz86s85jk3b6m03"))))
+                "0yz64c0z4ygi2k4af18k4r1ncgys18jb8icywkp2g5pgmpn5l7ps"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -2217,7 +2242,7 @@ a command.")
 (define-public emacs-olivetti
   (package
     (name "emacs-olivetti")
-    (version "1.8.0")
+    (version "1.8.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2226,7 +2251,7 @@ a command.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0ba30swqxxbpa8866chymywnahby1hk670zzkz44q49328i2wksj"))))
+                "1fbj9s49y5yx5i429awv9rybacfgvhwp7v5h0zw67bpgx4qs44pa"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/rnkn/olivetti")
     (synopsis "Emacs minor mode for a nice writing environment")
@@ -3333,7 +3358,7 @@ word (to avoid repetitions for example).")
 (define-public emacs-elisp-demos
   (package
     (name "emacs-elisp-demos")
-    (version "2019.08.16")
+    (version "2019.12.01")
     (source
      (origin
        (method git-fetch)
@@ -3343,7 +3368,7 @@ word (to avoid repetitions for example).")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0lybadq66bl4snkwph9i1y0qxln29wyfjn222ii3nfwany28cj66"))))
+         "097d8xhvq0770z96wlhiv4gz98cq89pwx5fa42zpfh4p85qj4q9z"))))
     (build-system emacs-build-system)
     (arguments
      `(#:include '("\\.el$" "\\.org$")
@@ -3465,14 +3490,14 @@ source code using IPython.")
 (define-public emacs-debbugs
   (package
     (name "emacs-debbugs")
-    (version "0.20")
+    (version "0.21")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://elpa.gnu.org/packages/debbugs-"
                                   version ".tar"))
               (sha256
                (base32
-                "03mmb1zvbqlsznl5agq8k3xrlcz310vnsa2zn0y8myanm4ra51zm"))))
+                "1xx1wjfpsnwx2fpydqhwy9k1b5kjk8dqbkzf8lqaj9c4rvjbn50a"))))
     (build-system emacs-build-system)
     (arguments '(#:include '("\\.el$" "\\.wsdl$" "\\.info$")))
     (propagated-inputs
@@ -3619,7 +3644,7 @@ These are distributed in separate files and can be used individually.")
 (define-public emacs-irony-mode
   (package
     (name "emacs-irony-mode")
-    (version "1.2.0")
+    (version "1.4.0")
     (home-page "https://github.com/Sarcasm/irony-mode")
     (source (origin
               (method git-fetch)
@@ -3629,7 +3654,7 @@ These are distributed in separate files and can be used individually.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0nhjrnlmss535jbshjjd30vydbr8py21vkx4p294w6d8vg2rssf8"))))
+                "0n2nfcq58md1p2xdhq1smh8v7lsyj0ci7ma5xyd6bkg5rvhsh10i"))))
     (build-system emacs-build-system)
     (inputs `(("server" ,emacs-irony-mode-server)))
     (arguments `(#:phases
@@ -4092,11 +4117,11 @@ to a key in your preferred mode.")
                (substitute* "el/CMakeLists.txt"
                  (("share/emacs/site-lisp/SuperCollider")
                   (string-append
-                   "share/emacs/site-lisp/guix.d/scel-" ,version)))
+                   "share/emacs/site-lisp")))
                ((assoc-ref cmake:%standard-phases 'configure)
                 #:outputs outputs
                 #:configure-flags '("-DSC_EL_BYTECOMPILE=OFF"))))
-           (add-after 'set-emacs-load-path 'add-el-dir-to-emacs-load-path
+           (add-after 'add-source-to-load-path 'add-el-dir-to-emacs-load-path
              (lambda _
                (setenv "EMACSLOADPATH"
                        (string-append (getcwd) "/el:" (getenv "EMACSLOADPATH")))
@@ -4789,13 +4814,14 @@ variants.")
     (name "emacs-solarized-theme")
     (version "1.2.2")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/bbatsov/solarized-emacs/"
+              (uri (git-reference
-                                  "archive/v"  version ".tar.gz"))
+                     (url "https://github.com/bbatsov/solarized-emacs/")
-              (file-name (string-append name "-" version ".tar.gz"))
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1ha3slc6d9wi9ilkhmwrzkvf308n6ph7b0k69pk369s9304awxzx"))))
+                "0zcj9jf8nlsj9vms888z2vs76q54n8g8r9sh381xad3x8d6lrlb3"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-dash" ,emacs-dash)))
@@ -5225,7 +5251,7 @@ after buffer changes.")
      `(#:tests? #t
        #:phases
        (modify-phases %standard-phases
-         (add-after 'set-emacs-load-path 'fix-autogen-script
+         (add-after 'unpack 'fix-autogen-script
            (lambda _
              (substitute* "autogen.sh"
                (("./configure") "sh configure"))))
@@ -5911,13 +5937,14 @@ possible to query other endpoints like DBPedia.")
     (version "0.1.3")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/technomancy/better-defaults"
+       (uri (git-reference
-                           "/archive/" version ".tar.gz"))
+              (url "https://github.com/technomancy/better-defaults")
-       (file-name (string-append name "-" version ".tar.gz"))
+              (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "08fg4zslzlxbvyil5g4gwvwd22fh4zsgqprs5wh9hv1rgc6757m2"))))
+         "1rxznx2l0cdpiz8mad8s6q17m1fngpgb1cki7ch6yh18r3qz8ysr"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/technomancy/better-defaults")
     (synopsis "Better defaults for Emacs")
@@ -6670,16 +6697,16 @@ of its name.")
 (define-public emacs-rainbow-mode
   (package
     (name "emacs-rainbow-mode")
-    (version "1.0.1")
+    (version "1.0.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://elpa.gnu.org/packages/rainbow-mode-" version ".el"))
+                    "https://elpa.gnu.org/packages/rainbow-mode-" version ".el"))
               (sha256
                (base32
-                "0cpga4ax635rfpj7y2vmh7ank0yw00dcy20gjg1mj74r97by8csf"))))
+                "1zfqj63sr07pdlwy7caz4fxsjhmbhh939n81z6jxq9xggm8ajxkd"))))
     (build-system emacs-build-system)
-    (home-page "http://elpa.gnu.org/packages/rainbow-mode.html")
+    (home-page "https://elpa.gnu.org/packages/rainbow-mode.html")
     (synopsis "Colorize color names in buffers")
     (description
      "This minor mode sets background color to strings that match color
@@ -7920,14 +7947,14 @@ passive voice.")
     (version "0.5.2")
     (home-page "https://github.com/jaypei/emacs-neotree")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append
+              (uri (git-reference
-                    "https://github.com/jaypei/" name
+                     (url home-page)
-                    "/archive/" version ".tar.gz"))
+                     (commit version)))
               (sha256
                (base32
-                "1zd6dchwyijnf7kgchfcp51gs938l204dk9z6mljrfqf2zy0gp12"))
+                "0hx72fq10772bbyqrj7mhhp02k26cccjxdadiqm1ykainhfmn1x0"))
-              (file-name (string-append name "-" version ".tar.gz"))))
+              (file-name (git-file-name name version))))
     (build-system emacs-build-system)
     (synopsis "Folder tree view for Emacs")
     (description "This Emacs package provides a folder tree view.")
@@ -7987,7 +8014,7 @@ programming and reproducible research.")
                                  string=? contrib-files org+contrib-files)))
                (with-directory-excursion
                    (string-append
-                    out "/share/emacs/site-lisp/guix.d/org-contrib-" ,version)
+                    out "/share/emacs/site-lisp")
                  (for-each delete-file duplicates))
                #t))))))
     (propagated-inputs
@@ -8008,13 +8035,14 @@ files that you would find in @file{contrib/} from the git repository.")))
     (version "0.6.1")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/lewang/"
+       (uri (git-reference
-                           "flx/archive/v" version ".tar.gz"))
+              (url "https://github.com/lewang/flx.git")
+              (commit (string-append "v" version))))
        (sha256
         (base32
-         "0bkcpnf1j4i2fcc2rllwbz62l00sw2mcia6rm5amgwvlkqavmkv6"))
+         "0sjybrcnb2sl33swy3q664vqrparajcl0m455gciiih2j87hwadc"))
-       (file-name (string-append name "-" version ".tar.gz"))))
+       (file-name (git-file-name name version))))
     (build-system emacs-build-system)
     (home-page "https://github.com/lewang/flx")
     (synopsis "Fuzzy matching for Emacs")
@@ -8032,13 +8060,14 @@ Flx has support for ido (interactively do things) through flx-ido.")
     (version "1.19")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/n3mo/cyberpunk-theme.el/"
+       (uri (git-reference
-                           "archive/" version ".tar.gz"))
+              (url "https://github.com/n3mo/cyberpunk-theme.el/")
+              (commit version)))
        (sha256
         (base32
-         "05l5fxw1mn5py6mfhxrzyqjq0d8m5m1akfi46vrgh13r414jffvv"))
+         "1npwrw3pgdmvqhihcqcfi2yrs178iiip5fcj8zhpp6cr9yqsvvgi"))
-       (file-name (string-append name "-" version ".tar.gz"))))
+       (file-name (git-file-name name version))))
     (build-system emacs-build-system)
     (home-page "https://github.com/n3mo/cyberpunk-theme.el")
     (synopsis "Cyberpunk theme for emacs built-in color theme support")
@@ -8106,13 +8135,14 @@ by zenburn, sinburn and similar themes, but slowly diverging from them.")
     (version "1.5.1")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/auto-complete/"
+       (uri (git-reference
-                           "auto-complete/archive/v" version ".tar.gz"))
+              (url "https://github.com/auto-complete/auto-complete.git")
+              (commit (string-append "v" version))))
        (sha256
         (base32
-         "1jvq4lj00hwml75lpmlciazy8f3bbg13gffsfnl835p4qd8l7yqv"))
+         "04i9b11iksg6acn885wl3qgi5xpsm3yszlqmd2x21yhprndlz7gb"))
-       (file-name (string-append name "-" version ".tar.gz"))))
+       (file-name (git-file-name name version))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-popup" ,emacs-popup)))
@@ -8442,13 +8472,14 @@ been adapted to work with mu4e.")
     (version "2.0.3")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/akatov/pretty-mode/"
+       (uri (git-reference
-                           "archive/" version ".tar.gz"))
+              (url "https://github.com/akatov/pretty-mode/")
-       (file-name (string-append name "-" version ".tar.gz"))
+              (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1fan7m4vnqs8kpg7r54kx3g7faadkpkf9kzarfv8n57kq8w157pl"))))
+         "013fig9i4fyx16krp2vfv953p3rwdzr38zs6i50af4pqz4vrcfvh"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/akatov/pretty-mode")
     (synopsis "Redisplay parts of the buffer as Unicode symbols")
@@ -8917,7 +8948,7 @@ actually changing the buffer's text.")
 (define-public emacs-diff-hl
   (package
     (name "emacs-diff-hl")
-    (version "1.8.6")
+    (version "1.8.7")
     (source
      (origin
        (method git-fetch)
@@ -8926,8 +8957,7 @@ actually changing the buffer's text.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32
+        (base32 "0i7x6qgr3nydcwhw72sbc8z9x9dfhgkf0dqj9nakvx36vn1bblbq"))))
-         "1xlsg728mz3cwhrsqvisa0aidic67nymd9g7h4c1h3q63j39yb2s"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/dgutov/diff-hl")
     (synopsis
@@ -9831,8 +9861,7 @@ Emacs.")
                  (substitute* "bin/ert-runner"
                    (("ERT_RUNNER=\"\\$\\(dirname \\$\\(dirname \\$0\\)\\)")
                     (string-append "ERT_RUNNER=\"" out
-                                   "/share/emacs/site-lisp/guix.d/ert-runner-"
+                                   "/share/emacs/site-lisp")))
-                                   ,version)))
                  (install-file "bin/ert-runner" (string-append out "/bin"))
                  (wrap-program (string-append out "/bin/ert-runner")
                    (list "EMACSLOADPATH" ":" 'prefix
@@ -10223,6 +10252,30 @@ list of commands is displayed in a handy popup.")
 characters from end of lines.")
     (license license:gpl3+)))
 
+(define-public emacs-openwith
+  (let ((changeset "aeb78782ec87680ea9f082a3f20a3675b3770cf9")
+        (revision "0"))
+    (package
+      (name "emacs-openwith")
+      (home-page "https://bitbucket.org/jpkotta/openwith")
+      (version (git-version "0.0.1" revision changeset))
+      (source (origin
+                (method hg-fetch)
+                (uri (hg-reference (url home-page) (changeset changeset)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1wl6gnxsyhaad4cl9bxjc0qbc5jzvlwbwjbajs0n1s6qr07d6r01"))))
+      (build-system emacs-build-system)
+      (synopsis "Open external applications for files with Emacs")
+      (description
+       "This package enables you to associate file name patterns with external
+applications that are automatically invoked when you use commands like
+@code{find-file}.  For example, you can have it open @code{png} files with
+@code{feh} and @code{mp4} files with @code{mpv}.  This is especially useful
+when browsing files with Dired.")
+      (license license:gpl2+))))
+
 (define-public emacs-org-edit-latex
   (package
     (name "emacs-org-edit-latex")
@@ -11171,14 +11224,14 @@ supports multiple backends such as @code{vlc}, @code{mpg123},
     (name "emacs-groovy-modes")
     (version "2.0")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append
+              (uri (git-reference
-                    "https://github.com/Groovy-Emacs-Modes/groovy-emacs-modes"
+                     (url "https://github.com/Groovy-Emacs-Modes/groovy-emacs-modes")
-                    "/archive/" version ".tar.gz"))
+                     (commit version)))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "15j0hnkx9nppjzda5cqsxxz5f3bq9hc4xfyjcdypzqiypcvmpa39"))))
+                "0c1d4cbnlny8gpcd20zr1wxx6ggf28jgh7sgd5r1skpsvjpbfqx2"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-s" ,emacs-s)))
@@ -11897,13 +11950,13 @@ object has been freed.")
                (install-file "sqlite/emacsql-sqlite"
                              (string-append out "/bin"))
                (for-each (cut install-file <>
-                              (string-append out "/share/emacs/site-lisp/guix.d/"
+                              (string-append out "/share/emacs/site-lisp"))
-                                             "emacsql" "-" ,version))
                          (find-files "." "\\.elc*$")))
              #t)))))
     (inputs
      `(("emacs-minimal" ,emacs-minimal)
-       ("mariadb" ,mariadb)
+       ("mariadb" ,mariadb "lib")
+       ("mariadb-dev" ,mariadb "dev")
        ("postgresql" ,postgresql)))
     (propagated-inputs
      `(("emacs-finalize" ,emacs-finalize)
@@ -12605,13 +12658,14 @@ region instead.")
     (name "emacs-validate")
     (version "1.0.5")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/Malabarba/validate.el"
+              (uri (git-reference
-                                  "/archive/" version ".tar.gz"))
+                     (url "https://github.com/Malabarba/validate.el")
-              (file-name (string-append name "-" version ".tar.gz"))
+                     (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "125mbd111f1h1baw0z3fzm48y1bvaigljyzvvnqgrn0shxbj0khg"))))
+                "1l12ibx6cw4mgicgjpw71fb4fr4sd0k54lvbpq7ngc29br3j6i4v"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/Malabarba/validate.el")
     (synopsis "Emacs library for scheme validation")
@@ -12978,13 +13032,14 @@ confused by comments or @code{foo-bar} matching @code{foo}.")
     (version "0.15")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/phillord/m-buffer-el"
+       (uri (git-reference
-                           "/archive/" "v" version ".tar.gz"))
+              (url "https://github.com/phillord/m-buffer-el")
-       (file-name (string-append name "-" version ".tar.gz"))
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "17vdcc8q37q9db98jyww1c0ivinmwfcw4l04zccfacalra63a214"))))
+         "1sx76i59razwccvn6x7rx5a124bfyjw9fcbxf4gj7nsg33qiq809"))))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -13305,13 +13360,14 @@ grouping buffers by their projectile root directory.")
     (version "1.0.0")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/istib/helm-mode-manager/"
+       (uri (git-reference
-                           "archive/" version ".tar.gz"))
+              (url "https://github.com/istib/helm-mode-manager")
-       (file-name (string-append name "-" version ".tar.gz"))
+              (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0wllj321z16hgrx0ddwzk5wz4mnnx5am7w5nclqclfc5dfdn92wm"))))
+         "1srx5f0s9x7zan7ayqd6scxfhcvr3nkd4yzs96hphd87rb18apzk"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-helm" ,emacs-helm)))
@@ -13995,13 +14051,14 @@ split to display more windows and more buffers, the buffer exits
     (name "emacs-rsw-elisp")
     (version "1.0.5")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/rswgnu/rsw-elisp"
+              (uri (git-reference
-                                  "/archive/" version ".tar.gz"))
+                     (url "https://github.com/rswgnu/rsw-elisp")
-              (file-name (string-append name "-" version ".tar.gz"))
+                     (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1jnn7xfwl3wxc87v44ccsf1wwp80par3xgcvfb1icd6zchjmlcps"))))
+                "0dfq8myg0r91900bk1s70amsmm4mjk2qsg12v5pk7lla5d2vnyaf"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/rswgnu/rsw-elisp")
     (synopsis "Improved expressions that interactively evaluate Emacs Lisp")
@@ -14214,13 +14271,14 @@ compilation/grep buffers.  Works with @code{wgrep}, @code{ack}, @code{ag},
     (version "0.1")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/alezost/shift-number.el"
+       (uri (git-reference
-                           "/archive/" "v" version ".tar.gz"))
+              (url "https://github.com/alezost/shift-number.el")
-       (file-name (string-append name "-" version ".tar.gz"))
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1g79m0hqn9jgpm565vvh8pdfzndc4vw7xisnh5qysj55qfg8cb1x"))))
+         "0zlwmzsxkv4mkggylxfx2fkrwgz7dz3zbg2gkn2rxcpy2k2gla64"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/alezost/shift-number.el")
     (synopsis "Increase or decrease the number at point")
@@ -14430,7 +14488,7 @@ Emacs minor mode to escape sequences in code.")
 (define-public emacs-dashboard
   (package
     (name "emacs-dashboard")
-    (version "1.5.0")
+    (version "1.6.0")
     (source
      (origin
        (method git-fetch)
@@ -14439,7 +14497,7 @@ Emacs minor mode to escape sequences in code.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0ihpcagwgc9qy70lf2y3dvx2bm5h9lnqh4sx6643cr8pp06ysbvq"))))
+        (base32 "1g6g8vad1kdmv1zxp95a8sn70idl26isqjb3xk1r95pqnx1cn591"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-page-break-lines" ,emacs-page-break-lines)))
@@ -14805,7 +14863,7 @@ appropriate directory if no @code{eshell} session is active.")
 (define-public emacs-eshell-z
   (package
     (name "emacs-eshell-z")
-    (version "0.3.2")
+    (version "0.4")
     (source
      (origin
        (method git-fetch)
@@ -14815,7 +14873,7 @@ appropriate directory if no @code{eshell} session is active.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1aac4m814jgxwpz7lbyx5r4z5dmawp4sk7pwbx0zqpnbcsaq5wwc"))))
+         "13dwaq8q23rwmrkpy3gvf7aswrkk6b9ak5221xl7n0bld4wdhq3j"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/xuchunyang/eshell-z")
     (synopsis "Quick navigation to frequently visited directories")
@@ -14857,7 +14915,7 @@ autosuggestions with:
 (define-public emacs-desktop-environment
   (package
     (name "emacs-desktop-environment")
-    (version "0.2.2")
+    (version "0.3.0")
     (source
      (origin
        (method git-fetch)
@@ -14867,7 +14925,7 @@ autosuggestions with:
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "14ija2rrz3zjhjbzxg84j5fq6xph4ah7w9bkqnq37by040cydvhw"))))
+         "195n99xvxyh4cfxjpfa1h1maalqrxf7nyi0bh3lqa1z6z5bdb6x2"))))
     (build-system emacs-build-system)
     (home-page "https://gitlab.petton.fr/DamienCassou/desktop-environment")
     (synopsis "Control your GNU/Linux desktop environment from Emacs")
@@ -15820,7 +15878,8 @@ Pandoc, the document-conversion tool.")
            "1qgfxc5d1hb32ks1fxpx7agpw7dvnkz99wydlflc9fqq75g8v142"))))
       (build-system emacs-build-system)
       (propagated-inputs
-       `(("emacs-dash" ,emacs-dash)
+       `(("ccls" ,ccls)
+         ("emacs-dash" ,emacs-dash)
          ("emacs-projectile" ,emacs-projectile)
          ("emacs-lsp-mode" ,emacs-lsp-mode)))
       (home-page "https://github.com/MaskRay/emacs-ccls")
@@ -17743,19 +17802,14 @@ as Emacs Lisp.")
          #:imported-modules (,@%gnu-build-system-modules
                              (guix build emacs-utils))
          #:tests? #f                   ; tests are not included in the release
-         #:make-flags (list "lisp" "info"
+         #:make-flags (list "lisp" "info")
-                            (string-append "LOAD_PATH=-L . -L "
-                                           (assoc-ref %build-inputs "dash")
-                                           "/share/emacs/site-lisp/guix.d/dash-"
-                                           ,(package-version emacs-dash)))
          #:phases
          (modify-phases %standard-phases
            (delete 'configure)
            (replace 'install
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
-                      (lisp (string-append out "/share/emacs/site-lisp/guix.d/"
+                      (lisp (string-append out "/share/emacs/site-lisp"))
-                                           "transient" "-" ,version))
                       (info (string-append out "/share/info")))
                  (for-each (cut install-file <> lisp)
                            (find-files "." "\\.elc*$"))
@@ -17817,9 +17871,7 @@ a suffix) we prefer to call it just a \"transient\".")
              (lambda _
                (substitute* "./Makefile"
                  (("lisp docs") "lisp"))))
-           (add-after 'delete-doc-targets 'emacs-set-emacs-load-path
+           (add-after 'delete-doc-targets 'chdir-lisp
-             (assoc-ref emacs:%standard-phases 'set-emacs-load-path))
-           (add-after 'emacs-set-emacs-load-path 'chdir-lisp
              (lambda _
                (chdir "lisp")))
            (add-after 'chdir-lisp 'emacs-install
@@ -19892,3 +19944,140 @@ Google guidelines.")
       (description "Helm Fish Completion is a Helm interface for Emacs
 fish-completion.  It can be used in both Eshell and M-x shell.")
       (license license:gpl3+))))
+
+(define-public emacs-telega
+  (let ((commit "019e923f933370d75dbe0a8473a18eb66fe94c0e")
+	(revision "1")
+	(version "0.4.4"))
+    (package
+      (name "emacs-telega")
+      (version (git-version version revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/zevlg/telega.el.git")
+               (commit commit)))
+         (sha256
+          (base32
+           "058814agkq8mp9ajpj8sz51rm9nigs2xpsdij05wjkxhfq30kqva"))
+         (file-name (git-file-name name version))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f
+         #:modules ((guix build gnu-build-system)
+                    ((guix build emacs-build-system) #:prefix emacs:)
+                    (guix build utils)
+                    (guix build emacs-utils))
+         #:imported-modules (,@%gnu-build-system-modules
+                             (guix build emacs-build-system)
+                             (guix build emacs-utils))
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'unpack-patch
+             (lambda _
+               (substitute* "server/Makefile"
+                 (("CC=cc")
+                  "CC=gcc")
+                 (("INSTALL_PREFIX=\\$\\(HOME\\)/.telega")
+                  (string-append "INSTALL_PREFIX=" (assoc-ref %outputs "out")
+                                 "/bin")))
+               #t))
+           (delete 'configure)
+
+           ;; Build emacs-side using `emacs-build-system'
+           (add-after 'compress-documentation 'emacs-add-source-to-load-path
+             (assoc-ref emacs:%standard-phases 'add-source-to-load-path))
+           (add-after 'emacs-set-emacs-load-path 'emacs-install
+             (assoc-ref emacs:%standard-phases 'install))
+           (add-after 'emacs-install 'emacs-build
+             (assoc-ref emacs:%standard-phases 'build))
+           (add-after 'emacs-install 'emacs-make-autoloads
+             (assoc-ref emacs:%standard-phases 'make-autoloads)))))
+      (propagated-inputs
+       `(("emacs-visual-fill-column" ,emacs-visual-fill-column)))
+      (native-inputs
+       `(("tdlib" ,tdlib)
+         ("emacs" ,emacs-minimal)))
+      (synopsis "GNU Emacs client for the Telegram messenger")
+      (description
+       "Telega is full-featured, unofficial client for the Telegram messaging
+platform for GNU Emacs.")
+      (home-page "https://github.com/zevlg/telega.el")
+      (license license:gpl3+))))
+
+(define-public emacs-doom-modeline
+  (package
+    (name "emacs-doom-modeline")
+    (version "2.8.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/seagle0128/doom-modeline.git")
+                    (commit (string-append "v" version))))
+              (sha256
+               (base32
+                "12zksk0rwpgpdc00km3z0hmc8wm1j1r8lbwn4kivniw56mgy0n22"))
+              (file-name (git-file-name name version))))
+    (build-system emacs-build-system)
+    (arguments
+     `(#:test-command '("ert-runner")))
+    (native-inputs `(("emacs-ert-runner" ,emacs-ert-runner)))
+    (propagated-inputs
+     `(("emacs-all-the-icons" ,emacs-all-the-icons)
+       ("emacs-shrink-path" ,emacs-shrink-path)))
+    (synopsis "Fancy and fast mode-line inspired by minimalism design")
+    (description "Doom modeline is a complete modeline for GNU Emacs inspired
+by the Doom theme collection.  This modeline features support for mode-specific
+icon support, git integration, and several other utilities.")
+    (home-page "https://github.com/seagle0128/doom-modeline/")
+    (license license:gpl3+)))
+
+(define-public emacs-shrink-path
+  (package
+    (name "emacs-shrink-path")
+    (version "0.3.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/bennya/shrink-path.el.git")
+             (commit (string-append "v" version))))
+       (sha256
+        (base32
+         "0kx0c4syd7k6ff9j463bib32pz4wq0rzjlg6b0yqnymlzfr1mbki"))
+       (file-name (git-file-name name version))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-s" ,emacs-s)
+       ("emacs-dash" ,emacs-dash)
+       ("emacs-f" ,emacs-f)))
+    (home-page "https://gitlab.com/bennya/shrink-path.el")
+    (synopsis "Fish-style path truncation in emacs-lisp")
+    (description "This package provides utility functions that allow for
+Fish-style truncated directories in eshell and various modelines.")
+    (license license:gpl3+)))
+
+(define-public emacs-org-present
+  (let ((commit "d13acd70eff6a1608bc991920232146a0de76b21"))
+    (package
+      (name "emacs-org-present")
+      (version "0.0.1")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/rlister/org-present.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0jz8xiny3rv9ql0p623byz32pip1b82j2c2nyfz2wd114kiabb6q"))))
+      (build-system emacs-build-system)
+      (synopsis "Ultra-minimalist presentation minor-mode for Emacs org-mode")
+      (description "Org-present is an extremely minimalist presentation tool
+for Emacs org-mode.  Simply layout your presentation with each slide under a
+top-level header, start the minor mode with @code{org-present}, and page through
+each slide with left/right keys.")
+      (home-page "https://github.com/rlister/org-present")
+      (license license:gpl2))))

gnu/packages/emacs.scm

@@ -9,7 +9,7 @@
 ;;; Copyright © 2016 David Thompson <dthompson2@worcester.edu>
 ;;; Copyright © 2016 ng0 <ng0@n0.is>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2017 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2017, 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
@@ -185,6 +185,11 @@
 
     (native-search-paths
      (list (search-path-specification
+            (variable "EMACSLOADPATH")
+            ;; The versioned entry is for the Emacs' builtin libraries.
+            (files (list (string-append "share/emacs/" version "/lisp")
+                         "share/emacs/site-lisp")))
+           (search-path-specification
             (variable "INFOPATH")
             (files '("share/info")))))
 

gnu/packages/embedded.scm

@@ -4,7 +4,7 @@
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018, 2019 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,6 +30,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (guix build utils)
   #:use-module (gnu packages)
@@ -47,6 +48,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages xorg)
@@ -1162,3 +1164,31 @@ raw USB commands.")
     ;; The flashloaders/stm32l0x.s and flashloaders/stm32lx.s source files are
     ;; licensed under the GPLv2+.
     (license (list license:bsd-3 license:gpl2+))))
+
+(define-public west
+  (package
+    (name "west")
+    (version "0.6.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "west" version))
+       (sha256
+        (base32
+         "0ql6ij1hrj2ir5wkxm96zgig5qwvfwa75w77wh2y13w6b9cqcr4b"))))
+    (propagated-inputs
+     `(("python-colorama" ,python-colorama)
+       ("python-configobj" ,python-configobj)
+       ("python-pykwalify" ,python-pykwalify)
+       ("python-pyyaml" ,python-pyyaml)))
+    (build-system python-build-system)
+    (home-page "https://github.com/zephyrproject-rtos/west")
+    (synopsis "Zephyr RTOS Project meta-tool")
+    (description "West is the swiss-army knife command line tool of the Zephyr
+project.  Its built-in commands provide a multiple repository management
+system with features inspired by Google’s Repo tool and Git submodules.  West
+simplifies configuration and is also pluggable: you can write your own west
+\"extension commands\" which add additional features to west.  Zephyr uses
+this feature to provide conveniences for building applications, flashing and
+debugging them, and more.")
+    (license license:expat)))

gnu/packages/emulators.scm

@@ -1062,7 +1062,18 @@ emulation community.  It provides highly accurate emulation.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0y7rcpz7psf8k3agsrq277jdm651vbnn9xpqvmj2in1a786idya7"))))
+        (base32 "0y7rcpz7psf8k3agsrq277jdm651vbnn9xpqvmj2in1a786idya7"))
+       (patches
+        (search-patches "retroarch-disable-online-updater.patch"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Don't suggest using the Online Updater if available: it never
+           ;; is.  This disables translation of this particular message.
+           (substitute* (find-files "menu/drivers" "\\.c$")
+             (("msg_hash_to_str\\(MSG_MISSING_ASSETS\\)")
+              "\"Warning: Missing assets, go get some\""))
+           #t))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
@@ -1074,7 +1085,7 @@ emulation community.  It provides highly accurate emulation.")
                     (etc (string-append out "/etc"))
                     (vulkan (assoc-ref inputs "vulkan-loader"))
                     (wayland-protocols (assoc-ref inputs "wayland-protocols")))
-               ;; Hard-code the path to libvulkan.so.
+               ;; Hard-code some store file names.
                (substitute* "gfx/common/vulkan_common.c"
                  (("libvulkan.so") (string-append vulkan "/lib/libvulkan.so")))
                (substitute* "gfx/common/wayland/generate_wayland_protos.sh"
@@ -1082,10 +1093,12 @@ emulation community.  It provides highly accurate emulation.")
                  (string-append wayland-protocols "/share/wayland-protocols")))
                (substitute* "qb/qb.libs.sh"
                  (("/bin/true") (which "true")))
+
                ;; Use shared zlib.
                (substitute* '("libretro-common/file/archive_file_zlib.c"
                               "libretro-common/streams/trans_stream_zlib.c")
                  (("<compat/zlib.h>") "<zlib.h>"))
+
                ;; The configure script does not yet accept the extra arguments
                ;; (like ‘CONFIG_SHELL=’) passed by the default configure phase.
                (invoke
@@ -1095,7 +1108,8 @@ emulation community.  It provides highly accurate emulation.")
                        '("--enable-neon" "--enable-floathard")
                        '())
                  (string-append "--prefix=" out)
-                 (string-append "--global-config-dir=" etc))))))))
+                 (string-append "--global-config-dir=" etc)
+                 "--disable-builtinminiupnpc")))))))
     (inputs
      `(("alsa-lib" ,alsa-lib)
        ("ffmpeg" ,ffmpeg)
@@ -1106,6 +1120,7 @@ emulation community.  It provides highly accurate emulation.")
        ("libxrandr" ,libxrandr)
        ("libxv" ,libxv)
        ("mesa" ,mesa)
+       ("miniupnpc" ,miniupnpc)
        ("openal" ,openal)
        ("pulseaudio" ,pulseaudio)
        ("python" ,python)
@@ -1132,7 +1147,7 @@ multi-system game/emulator system.")
 (define-public scummvm
   (package
     (name "scummvm")
-    (version "2.0.0")
+    (version "2.1.0")
     (source
      (origin
        (method url-fetch)
@@ -1140,10 +1155,10 @@ multi-system game/emulator system.")
                            "/scummvm-" version ".tar.xz"))
        (sha256
         (base32
-         "0q6aiw97wsrf8cjw9vjilzhqqsr2rw2lll99s8i5i9svan6l314p"))))
+         "09zp2mxmida6sz5vrr5bzyv8c3yjvq2xqmpmcllbadhmd9cwcl3b"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f                      ;require "git"
+     `(#:tests? #f                                 ;require "git"
        #:configure-flags (list "--enable-release") ;for optimizations
        #:phases
        (modify-phases %standard-phases
@@ -1165,6 +1180,7 @@ multi-system game/emulator system.")
        ("faad2" ,faad2)
        ("fluidsynth" ,fluidsynth)
        ("freetype" ,freetype)
+       ("liba52" ,liba52)
        ("libflac" ,flac)
        ("libjpeg-turbo" ,libjpeg-turbo)
        ("libmad" ,libmad)
@@ -1174,7 +1190,7 @@ multi-system game/emulator system.")
        ("libtheora" ,libtheora)
        ("libvorbis" ,libvorbis)
        ("nasm" ,nasm)
-       ("sdl2" ,sdl2)
+       ("sdl2" ,(sdl-union (list sdl2 sdl2-net)))
        ("zlib" ,zlib)))
     (home-page "https://www.scummvm.org/")
     (synopsis "Engine for several graphical adventure games")
@@ -1188,7 +1204,7 @@ play them on systems for which they were never designed!")
 (define-public mame
   (package
     (name "mame")
-    (version "0.215")
+    (version "0.216")
     (source
      (origin
        (method git-fetch)
@@ -1198,7 +1214,7 @@ play them on systems for which they were never designed!")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1fj2qahi0fpn41zxph06wdgjashy6vsgj0gqfly8hvcmv99r3d65"))
+         "1q3mrlinkg3hxry7ssl5713lclz3k243q30933flxh99fnzgajwc"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled libraries.
@@ -1213,6 +1229,8 @@ play them on systems for which they were never designed!")
     (arguments
      `(#:make-flags
        (cons*
+        ;; A 'strict-overflow' error pops up on i686 so disable '-Werror'.
+        "NOWERROR=1"
         (string-append "QT_HOME=" (assoc-ref %build-inputs "qtbase"))
         (string-append "SDL_INI_PATH="
                        (assoc-ref %outputs "out")

gnu/packages/engineering.scm

@@ -373,7 +373,7 @@ features.")))
        ("imagemagick" ,imagemagick)
        ("gerbv" ,gerbv)
        ("ghostscript" ,ghostscript)
-       ("xvfb" ,xorg-server)))
+       ("xvfb" ,xorg-server-for-tests)))
     (home-page "http://pcb.geda-project.org/")
     (synopsis "Design printed circuit board layouts")
     (description
@@ -1771,7 +1771,7 @@ parallel computing platforms.  It also supports serial execution.")
          ("python" ,python-2) ; for tests
          ("matplotlib" ,python2-matplotlib) ; for tests
          ("numpy" ,python2-numpy) ; for tests
-         ("xorg-server" ,xorg-server))) ; for tests
+         ("xorg-server" ,xorg-server-for-tests))) ; for tests
       (inputs
        `(("adms" ,adms)
          ("asco" ,asco)
@@ -2174,7 +2174,7 @@ specification can be downloaded at @url{http://3mf.io/specification/}.")
        ("imagemagick" ,imagemagick)
        ("ps" ,procps)
        ("python" ,python)
-       ("xvfb" ,xorg-server)))
+       ("xvfb" ,xorg-server-for-tests)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases

gnu/packages/erlang.scm

@@ -223,7 +223,7 @@ built-in support for concurrency, distribution and fault tolerance.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'set-emacs-load-path 'change-working-directory
+         (add-before 'add-source-to-load-path 'change-working-directory
            (lambda _ (chdir "lib/tools/emacs") #t)))))
     (home-page "https://www.erlang.org/")
     (synopsis "Erlang major mode for Emacs")

gnu/packages/fabric-management.scm

@@ -190,7 +190,8 @@ testing InfiniBand networks.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0x3clvy716i7va4m4adgx6ihjsfnzrkdizhxz5v52944dkglpc8n"))))
+                "0x3clvy716i7va4m4adgx6ihjsfnzrkdizhxz5v52944dkglpc8n"))
+              (patches (search-patches "ucx-tcp-iface-ioctl.patch"))))
     (build-system gnu-build-system)
     (arguments
      '( ;; These are some of the flags found in 'contrib/configure-release'.

gnu/packages/finance.scm

@@ -77,6 +77,7 @@
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages textutils)
+  #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages upnp)
   #:use-module (gnu packages version-control)
@@ -442,7 +443,7 @@ other machines/servers.  Electrum does not download the Bitcoin blockchain.")
   (package
     (inherit electrum)
     (name "electron-cash")
-    (version "4.0.7")
+    (version "4.0.10")
     (source
      (origin
        (method url-fetch)
@@ -453,13 +454,17 @@ other machines/servers.  Electrum does not download the Bitcoin blockchain.")
                            ".tar.gz"))
        (sha256
         (base32
-         "0xswmr68cm1c77lzisi3z812jzqczm9dfrshfhdq42zz5kaz4gnn"))
+         "1rcywlma6hk52ymisx536jvkdwa73rhn1jxhsbs4wbvajl90w9s8"))
        (modules '((guix build utils)))
        (snippet
         '(begin
            ;; Delete the bundled dependencies.
            (delete-file-recursively "packages")
            #t))))
+    (inputs
+     `(,@(package-inputs electrum)
+       ("python-dateutil", python-dateutil)
+       ("python-dnspython", python-dnspython)))
     (home-page "https://electroncash.org/")
     (synopsis "Bitcoin Cash wallet")
     (description
@@ -477,7 +482,7 @@ other machines/servers.  Electroncash does not download the Bitcoin Cash blockch
   ;; the system's dynamically linked library.
   (package
     (name "monero")
-    (version "0.15.0.0")
+    (version "0.15.0.1")
     (source
      (origin
        (method git-fetch)
@@ -498,7 +503,7 @@ other machines/servers.  Electroncash does not download the Bitcoin Cash blockch
            #t))
        (sha256
         (base32
-         "19y4kcj4agws7swfa3draysb1y18c3xb13r8cg0faxx1dlm0zbnr"))))
+         "0sypa235lf2bbib4b71xpaw39h9304slgsvnsz8wmy9fq1zx009m"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
@@ -592,7 +597,7 @@ the Monero command line client and daemon.")
 (define-public monero-gui
   (package
     (name "monero-gui")
-    (version "0.15.0.0")
+    (version "0.15.0.1")
     (source
      (origin
        (method git-fetch)
@@ -602,7 +607,7 @@ the Monero command line client and daemon.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1shpnly2dym5jhvk8zk10p69mz062dihx979djg74q6hgkhhhqsh"))))
+         "08j8kkncdn57xql0bhmlzjpjkdfhqbpda1p07r797q8qi0nl4w8n"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)

gnu/packages/flashing-tools.scm

@@ -211,14 +211,15 @@ firmware from it.")
   (let ((commit "f289b7a2e5627464044249f0e5742830e052e360"))
     (package
       (name "teensy-loader-cli")
-      (version (string-append "2.1-1." (string-take commit 7)))
+      (version (git-version "2.1" "1" commit))
       (source
        (origin
-         (method url-fetch)
+         (method git-fetch)
-         (uri (string-append "https://github.com/PaulStoffregen/"
+         (uri (git-reference
-                             "teensy_loader_cli/archive/" commit ".tar.gz"))
+                (url "https://github.com/PaulStoffregen/teensy_loader_cli.git")
-         (sha256 (base32 "17wqc2q4fa473cy7f5m2yiyb9nq0qw7xal2kzrxzaikgm9rabsw8"))
+                (commit commit)))
-         (file-name (string-append "teensy-loader-cli-" version ".tar.gz" ))
+         (sha256 (base32 "0sssim56pwsxp5cp5dlf6mi9h5fx2592m6j1g7abnm0s09b0lpdx"))
+         (file-name (git-file-name name version))
          (modules '((guix build utils)))
          (snippet
           `(begin
@@ -294,13 +295,14 @@ RK3036, RK3066, RK312X, RK3168, RK3188, RK3288, RK3368.")
     (name "heimdall")
     (version "1.4.2")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/Benjamin-Dobell/Heimdall"
+              (uri (git-reference
-                                  "/archive/v" version ".tar.gz"))
+                     (url "https://gitlab.com/BenjaminDobell/Heimdall.git")
-              (file-name (string-append name "-" version ".tar.gz"))
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1y7gwg3lipyp2zcysm2vid1qg5nwin9bxbvgzs28lz2rya4fz6sq"))))
+                "1ygn4snvcmi98rgldgxf5hwm7zzi1zcsihfvm6awf9s6mpcjzbqz"))))
     (build-system cmake-build-system)
     (arguments
      `(#:build-type "Release"
@@ -327,7 +329,7 @@ RK3036, RK3066, RK312X, RK3168, RK3188, RK3288, RK3368.")
      `(("libusb" ,libusb)
        ("qtbase" ,qtbase)
        ("zlib" ,zlib)))
-    (home-page "http://glassechidna.com.au/heimdall/")
+    (home-page "https://glassechidna.com.au/heimdall/")
     (synopsis "Flash firmware onto Samsung mobile devices")
     (description "@command{heimdall} is a tool suite used to flash firmware (aka
 ROMs) onto Samsung mobile devices.  Heimdall connects to a mobile device over
@@ -415,13 +417,14 @@ Management Engine (ME).  You need to @code{sudo rmmod mei_me} and
     (name "me-cleaner")
     (version "1.2")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/corna/me_cleaner/"
+              (uri (git-reference
-                                  "archive/v" version ".tar.gz"))
+                     (url "https://github.com/corna/me_cleaner.git")
+                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "0hdnay1ai0r6l69z63jkiz6yfwdsqc2mrfyj77hgadv7xxxqm6na"))
+                "1bdj2clm13ir441vn7sv860xsc5gh71ja5lc2wn0gggnff0adxj4"))
-              (file-name (string-append name "-" version ".tar.gz"))))
+              (file-name (git-file-name name version))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -444,15 +447,16 @@ ME as far as possible (it only edits ME firmware image files).")
 (define-public uefitool
   (package
     (name "uefitool")
-    (version "0.22.4")
+    (version "0.26.0")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/LongSoft/UEFITool/archive/"
+              (uri (git-reference
-                                  version ".tar.gz"))
+                     (url "https://github.com/LongSoft/UEFITool.git")
+                     (commit version)))
               (sha256
                (base32
-                "05jmhv7jpq08kqbd1477y1lgyjvcic3njrd0bmzdy7v7b7lnhl82"))
+                "1ka7i12swm9r5bmyz5vjr82abd2f3lj8p35f4208byalfbx51yq7"))
-              (file-name (string-append name "-" version ".tar.gz"))))
+              (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/fonts.scm

@@ -27,6 +27,7 @@
 ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2019 Baptiste Strazzulla <bstrazzull@hotmail.fr>
 ;;; Copyright © 2019 Alva <alva@skogen.is>
+;;; Copyright © 2019 Alexandros Theodotou <alex@zrythm.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1524,3 +1525,43 @@ Symbols stand out from common text.  Dots and commas are easily seen, and
 operators are clear even when not surrounded by spaces.  Similar characters
 have been designed to be very distinguishable from each other.")
     (license license:silofl1.1)))
+
+(define-public font-dseg
+  (package
+    (name "font-dseg")
+    (version "0.45")
+    (source
+      (origin
+        (method url-fetch/zipbomb)
+        (uri
+          (string-append "https://github.com/keshikan/DSEG/"
+                         "releases/download/v" version
+                         "/fonts-DSEG_v"
+                         (string-concatenate (string-split version #\.))
+                         ".zip"))
+        (sha256
+          (base32
+            "0v8sghh4vl286faf8pvi74znz07pyf0qii8z4wjllisqwc35sx72"))))
+    (build-system font-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (font-dir (string-append out "/share/fonts"))
+                    (truetype-dir (string-append font-dir "/truetype")))
+               (with-directory-excursion
+                 (string-append "fonts-DSEG_v"
+                                (apply string-append (string-split ,version
+                                                                   #\.)))
+                 (for-each (lambda (f) (install-file f truetype-dir))
+                           (find-files "." "\\.ttf$"))
+               #t)))))))
+    (home-page "https://www.keshikan.net/fonts-e.html")
+    (synopsis "DSEG: 7-segment and 14-segment fonts")
+    (description
+     "DSEG is a font family that imitates seven- and fourteen-segment LCD
+displays (7SEG, 14SEG).  DSEG includes the roman alphabet and symbol glyphs.
+This package provides the TrueType fonts.")
+    (license license:silofl1.1)))

gnu/packages/freedesktop.scm

@@ -155,14 +155,14 @@ freedesktop.org project.")
 (define-public libinput
   (package
     (name "libinput")
-    (version "1.13.4")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://freedesktop.org/software/libinput/"
                                   "libinput-" version ".tar.xz"))
               (sha256
                (base32
-                "07a0w7rak7rvnh6g4j0akwjxwinxfszc1xi9mrx12fv82k3mgsyk"))))
+                "0w7fas37mp2k06f12i3lnj717lw73asziknj6z51kh1m50ja6cz3"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags '("-Ddocumentation=false")
@@ -879,13 +879,13 @@ message bus.")
   (package
     (name "accountsservice")
     (version "0.6.50")
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              (uri (string-append "https://www.freedesktop.org/software/"
+       (method url-fetch)
-                                  name "/" name "-" version ".tar.xz"))
+       (uri (string-append "https://www.freedesktop.org/software/"
-              (sha256
+                           "accountsservice/accountsservice-" version ".tar.xz"))
-               (base32
+       (sha256
-                "0jn7vg1z4vxnna0hl33hbcb4bb3zpilxc2vyclh24vx4vvsjhn83"))))
+        (base32 "0jn7vg1z4vxnna0hl33hbcb4bb3zpilxc2vyclh24vx4vvsjhn83"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f ; XXX: tests require DocBook 4.1.2

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>
@@ -463,13 +463,14 @@ want what you have.")
     (name "cowsay")
     (version "3.04")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/tnalpgge/"
+              (uri (git-reference
-                                  "rank-amateur-cowsay/archive/"
+                     (url "https://github.com/tnalpgge/rank-amateur-cowsay.git")
-                                  "cowsay-" version ".tar.gz"))
+                     (commit (string-append name "-" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "12w7apbf6a9qffk92r32b16w22na2fjcqbl32rn0n7zw5hrp3f6q"))))
+                "06455kq37hvq1xb7adyiwrx0djs50arsxvjgixyxks16lm1rlc7n"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -1880,30 +1881,38 @@ match, cannon keep, and grave-itation pit.")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                     (url "https://github.com/minetest/minetest")
+                    (url "https://github.com/minetest/minetest")
-                     (commit version)))
+                    (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
                 "184n9gxfa7yr0j85z2x736maaymsnppd5jzm326wlqri3c0qqy3z"))
               (modules '((guix build utils)))
               (snippet
-                '(begin
+               '(begin
-                   (delete-file-recursively "lib") #t))))
+                  ;; Mimic upstream commit 706b6aad06, for compatibility with
+                  ;; newer jsoncpp.  Remove this for > 5.1.0.
+                  (substitute* "cmake/Modules/FindJson.cmake"
+                    (("features\\.h")
+                     "allocator.h"))
+
+                  ;; Delete bundled libraries.
+                  (delete-file-recursively "lib")
+                  #t))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags
-         (list "-DRUN_IN_PLACE=0"
+       (list "-DRUN_IN_PLACE=0"
-               "-DENABLE_FREETYPE=1"
+             "-DENABLE_FREETYPE=1"
-               "-DENABLE_GETTEXT=1"
+             "-DENABLE_GETTEXT=1"
-               "-DENABLE_SYSTEM_JSONCPP=TRUE"
+             "-DENABLE_SYSTEM_JSONCPP=TRUE"
-               (string-append "-DIRRLICHT_INCLUDE_DIR="
+             (string-append "-DIRRLICHT_INCLUDE_DIR="
-                              (assoc-ref %build-inputs "irrlicht")
+                            (assoc-ref %build-inputs "irrlicht")
-                              "/include/irrlicht")
+                            "/include/irrlicht")
-               (string-append "-DCURL_INCLUDE_DIR="
+             (string-append "-DCURL_INCLUDE_DIR="
-                              (assoc-ref %build-inputs "curl")
+                            (assoc-ref %build-inputs "curl")
-                              "/include/curl"))
+                            "/include/curl"))
-       #:tests? #f)) ; no check target
+       #:tests? #f))                    ;no check target
     (native-search-paths
      (list (search-path-specification
             (variable "MINETEST_SUBGAME_PATH")
@@ -3787,13 +3796,14 @@ Linux / Mac OS X servers, and an auto mapper with a VT100 map display.")
     (name "laby")
     (version "0.6.4")
     (source
-     (origin (method url-fetch)
+     (origin (method git-fetch)
-             (uri (string-append
+             (uri (git-reference
-                   "https://github.com/sgimenez/laby/archive/"
+                    (url "https://github.com/sgimenez/laby.git")
-                   "laby-" version ".tar.gz"))
+                    (commit (string-append name "-" version))))
+             (file-name (git-file-name name version))
              (sha256
               (base32
-               "0gyrfa95l1qka7gbjf7l6mk7mbfvph00l0c995ia272qdw7rjhyf"))
+               "12fq9hhrxpzgfinmj9ra9ckss9yficwdlrmgjvvsq7agvh3sgyl1"))
              (patches (search-patches "laby-make-install.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -3830,29 +3840,22 @@ programmers may also add their own favorite language.")
 (define-public bambam
   (package
     (name "bambam")
-    (version "0.6")
+    (version "1.0.0")
     (source
       (origin
         (method git-fetch)
         (uri (git-reference
               (url "https://github.com/porridge/bambam")
-              (commit version)))
+              (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32
+         (base32 "18cwd1wpyyx8y61cags9bkdhx9x858xicc4y1c9c2s0xjmgzhl3i"))))
-          "08hcd0gzia3pz7fzk4pqc5kbq1074j4q0jcmbpgvr7n623nj2xa5"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2
+     `(#:tests? #f                      ; no tests
-       #:tests? #f ; no tests
        #:phases
        (modify-phases %standard-phases
-         (delete 'build)
+         (delete 'build)                ; nothing to build
-         (add-before 'install 'patch-data-dir-location
-           (lambda _
-             (substitute* "bambam.py"
-               (("'data'") "'../share/bambam/data'"))
-             #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out   (assoc-ref outputs "out"))
@@ -3943,7 +3946,7 @@ throwing people around in pseudo-randomly generated buildings.")
 (define-public hyperrogue
   (package
     (name "hyperrogue")
-    (version "10.5d")
+    (version "11.2d")
     ;; When updating this package, be sure to update the "hyperrogue-data"
     ;; origin in native-inputs.
     (source (origin
@@ -3954,7 +3957,7 @@ throwing people around in pseudo-randomly generated buildings.")
                     "-src.tgz"))
               (sha256
                (base32
-                "1ls055v4pv2xmn2a8lav7wl370zn0wsd91q41bk0amxd168kcndy"))))
+                "1b532s94zv1jsni7bvh848m42arxcclsr0x3n7c689iamwqzrxmn"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no check target
@@ -4032,7 +4035,7 @@ throwing people around in pseudo-randomly generated buildings.")
              "-win.zip"))
            (sha256
             (base32
-             "13n9hcvf9yv7kjghm5jhjpwq1kh94i4bgvcczky9kvdvw1y9278n"))))
+             "0vq4l1xaqpjj3hmxn1vn2b3bbkn1hrag42ck9f30blinv347bwhf"))))
        ("unzip" ,unzip)))
     (inputs
      `(("font-dejavu" ,font-dejavu)
@@ -4935,9 +4938,9 @@ fight against their plot and save his fellow rabbits from slavery.")
     (home-page "https://play0ad.com")
     (license (list (license:fsdg-compatible
                     "http://tavmjong.free.fr/FONTS/ArevCopyright.txt"
-                    (license:license-comment
+                    "Similar to the license of the Bitstream Vera fonts.")
-                     (package-license font-bitstream-vera)))
+                   (license:fsdg-compatible
-                   (package-license font-bitstream-vera)
+                    "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts")
                    license:cc-by-sa3.0
                    license:expat
                    license:gfl1.0
@@ -5136,7 +5139,7 @@ Crowther & Woods, its original authors, in 1995.  It has been known as
 (define-public tome4
   (package
     (name "tome4")
-    (version "1.6.0")
+    (version "1.6.4")
     (synopsis "Single-player, RPG roguelike game set in the world of Eyal")
     (source
      (origin
@@ -5145,7 +5148,7 @@ Crowther & Woods, its original authors, in 1995.  It has been known as
                            version ".tar.bz2"))
        (sha256
         (base32
-         "1z1w4ycgl5wbm0sv7577vcdfwwf4k7vaf2njzyb21rvqjizpbkwr"))
+         "1hrh79aqmvwwd7idlr3lzpdpc9dgm1k5p7w2462chcjvd8vhfhb7"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -5436,14 +5439,14 @@ making Yamagi Quake II one of the most solid Quake II implementations available.
     (version "0.9.3.1")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append
+       (uri (git-reference
-             "https://github.com/the-butterfly-effect/tbe/archive/"
+              (url "https://github.com/the-butterfly-effect/tbe.git")
-             "v" version ".tar.gz"))
+              (commit (string-append "v" version))))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "18qkp7fgdvyl3haqqa693mgyic7afsznsxgz98z9wn4csaqxsnby"))))
+         "1ag2cp346f9bz9qy6za6q54id44d2ypvkyhvnjha14qzzapwaysj"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -5787,7 +5790,7 @@ affect gameplay).")
   (package
     (inherit chocolate-doom)
     (name "crispy-doom")
-    (version "5.5.2")
+    (version "5.6.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5795,7 +5798,7 @@ affect gameplay).")
                     (commit (string-append "crispy-doom-" version))))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "1a60ns0blhvml6gzj9qx18c18pbf02rq7vypaajd6nqy5h4fz3cn"))))
+               (base32 "0f319979wqfgm4pvsa6y5clg30p55l441kmrr8db0p5smyv3x2s4"))))
     (native-inputs
      (append
       (package-native-inputs chocolate-doom)
@@ -6803,7 +6806,7 @@ where the player draws runes in real time to effect the desired spell.")
 (define-public edgar
   (package
     (name "edgar")
-    (version "1.31")
+    (version "1.32")
     (source
      (origin
        (method url-fetch)
@@ -6811,7 +6814,7 @@ where the player draws runes in real time to effect the desired spell.")
         (string-append "https://github.com/riksweeney/edgar/releases/download/"
                        version "/edgar-" version "-1.tar.gz"))
        (sha256
-        (base32 "0i4851ci8a86ql4bhdq3xdfmf4b9z5zrd4xpc6vhi06697zgm13i"))))
+        (base32 "12lam6qcscc5ima1w2ksd1cvsvxbd17h6mqkgsqpzx8ap43p2r5p"))))
     (build-system gnu-build-system)
     (arguments '(#:tests? #f            ; there are no tests
                  #:make-flags
@@ -6879,6 +6882,22 @@ 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 _
@@ -6930,7 +6949,7 @@ 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.")
@@ -7331,14 +7350,14 @@ play with up to four players simultaneously.  It has network support.")
 (define-public hedgewars
   (package
     (name "hedgewars")
-    (version "0.9.25")
+    (version "1.0.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.hedgewars.org/download/releases/"
                                   "hedgewars-src-" version ".tar.bz2"))
               (sha256
                (base32
-                "08x7fqpy0hpnbfq2k06g522xayi7s53bca819zfhalvqnqs76pdk"))))
+                "0nqm9w02m0xkndlsj6ys3wr0ik8zc14zgilq7k6fwjrf3zk385i1"))))
     (build-system cmake-build-system)
     (arguments
      ;; XXX: Engine is built as Pascal source code, requiring Free Pascal
@@ -7347,32 +7366,8 @@ play with up to four players simultaneously.  It has network support.")
      `(#:configure-flags (list "-DBUILD_ENGINE_C=ON")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'remove-failing-test
-           ;; XXX: Remove single failing test.  Note: it is marked
-           ;; a "non-critical" test.
-           (lambda _
-             (delete-file-recursively "tests/lua_noncritical")
-             #t))
-         (add-after 'unpack 'fix-compiler
-           ;; XXX: Flag BUILD_ENGINE_C, as set above, implies using Clang to
-           ;; compile files.  However, using `clang' globally leads to the
-           ;; error: qtbase-5.11.3/include/qt5/QtCore/qglobal.h:45:12: fatal
-           ;; error: 'type_traits' file not found.
-           ;;
-           ;; Therefore, we make sure to use `c++' everywhere but in the
-           ;; engine.
-           (lambda _
-             (substitute* "project_files/hwc/CMakeLists.txt"
-               (("find_package\\(SDL2_ttf 2 REQUIRED\\)" all)
-                (string-append all "\n"
-                               "set(CMAKE_C_COMPILER ${CLANG_EXECUTABLE})\n"
-                               "set(CMAKE_CXX_COMPILER ${CLANG_EXECUTABLE})")))
-             (substitute* "CMakeLists.txt"
-               (("set\\(CMAKE_C(XX)?_COMPILER" all) (string-append "#" all)))
-             #t))
          (replace 'check
-           (lambda _
+           (lambda _ (invoke "ctest"))))))
-             (invoke "ctest"))))))
     (inputs
      `(("ffmpeg" ,ffmpeg)
        ("freeglut" ,freeglut)
@@ -7813,3 +7808,84 @@ remake of that series or any other game.")
 the AlphaGo Zero paper.  The current best network weights file for the engine
 can be downloaded from @url{https://zero.sjeng.org/best-network}.")
    (license license:gpl3+)))
+
+(define-public q5go
+  (package
+   (name "q5go")
+   (version "1.0")
+   (source (origin
+            (method git-fetch)
+            (uri (git-reference
+                  (url "https://github.com/bernds/q5Go.git")
+                  (commit (string-append "q5go-" version))))
+            (file-name (git-file-name name version))
+            (sha256
+             (base32
+              "1gdlfqcqkqv7vph3qwq78d0qz6dhmdsranxq9bmixiisbzkqby31"))))
+   (build-system gnu-build-system)
+   (native-inputs
+    `(("pkg-config" ,pkg-config)))
+   (inputs
+    `(("qtbase" ,qtbase)
+      ("qtmultimedia" ,qtmultimedia)
+      ("qtsvg" ,qtsvg)))
+   (arguments
+    '(#:phases
+      (modify-phases %standard-phases
+        (add-after 'unpack 'fix-configure-script
+          (lambda _
+            ;; Bypass the unavailable qtchooser program.
+            (substitute* "configure"
+              (("test -z \"QTCHOOSER\"")
+               "false")
+              (("qtchooser -run-tool=(.*) -qt=qt5" _ command)
+               command))
+            #t))
+        (add-after 'unpack 'fix-paths
+          (lambda _
+            (substitute* '("src/pics/Makefile.in"
+                           "src/translations/Makefile.in")
+              (("\\$\\(datadir\\)/qGo/")
+               "$(datadir)/q5go/"))
+            #t))
+        (add-after 'install 'install-desktop-file
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let* ((out (assoc-ref outputs "out"))
+                   (apps (string-append out "/share/applications"))
+                   (pics (string-append out "/share/q5go/pics")))
+              (delete-file-recursively (string-append out "/share/applnk"))
+              (delete-file-recursively (string-append out "/share/mimelnk"))
+              (install-file "../source/src/pics/Bowl.ico" pics)
+              (mkdir-p apps)
+              (with-output-to-file (string-append apps "/q5go.desktop")
+                (lambda _
+                  (format #t
+                          "[Desktop Entry]~@
+                           Name=q5go~@
+                           Exec=~a/bin/q5go~@
+                           Icon=~a/Bowl.ico~@
+                           Categories=Game;~@
+                           Comment=Game of Go~@
+                           Comment[de]=Spiel des Go~@
+                           Comment[eo]=Goo~@
+                           Comment[es]=Juego de Go~@
+                           Comment[fr]=Jeu de Go~@
+                           Comment[ja]=囲碁~@
+                           Comment[ko]=바둑~@
+                           Comment[zh]=围棋~@
+                           Terminal=false~@
+                           Type=Application~%"
+                          out pics))))
+             #t)))))
+   (synopsis "Qt GUI to play the game of Go")
+   (description
+    "This a tool for Go players which performs the following functions:
+@itemize
+@item SGF editor,
+@item Analysis frontend for Leela Zero (or compatible engines),
+@item GTP interface (to play against an engine),
+@item IGS client (to play on the internet),
+@item Export games to a variety of formats.
+@end itemize")
+   (home-page "https://github.com/bernds/q5Go")
+   (license license:gpl2+)))

gnu/packages/gdb.scm

@@ -34,17 +34,17 @@
   #:use-module (guix download)
   #:use-module (guix build-system gnu))
 
-(define-public gdb-8.2
+(define-public gdb-8.3
   (package
     (name "gdb")
-    (version "8.2.1")
+    (version "8.3.1")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/gdb/gdb-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "00i27xqawjv282a07i73lp1l02n0a3ywzhykma75qg500wll6sha"))))
+               "1i2pjwaafrlz7wqm40b4znr77ai32rjsxkpl2az38yyarpbv8m8y"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; FIXME "make check" fails on single-processor systems.
@@ -106,19 +106,19 @@ the program is running to try to fix bugs.  It can be used to debug programs
 written in C, C++, Ada, Objective-C, Pascal and more.")
     (license gpl3+)))
 
-(define-public gdb-8.3
+(define-public gdb-8.2
-  (package
+  (package/inherit
-    (inherit gdb-8.2)
+   gdb-8.3
-    (version "8.3.1")
+   (version "8.2.1")
-    (source (origin
+   (source (origin
-              (method url-fetch)
+             (method url-fetch)
-              (uri (string-append "mirror://gnu/gdb/gdb-"
+             (uri (string-append "mirror://gnu/gdb/gdb-"
-                                  version ".tar.xz"))
+                                 version ".tar.xz"))
-              (sha256
+             (sha256
-               (base32
+              (base32
-                "1i2pjwaafrlz7wqm40b4znr77ai32rjsxkpl2az38yyarpbv8m8y"))))))
+               "00i27xqawjv282a07i73lp1l02n0a3ywzhykma75qg500wll6sha"))))))
 
 (define-public gdb
   ;; This is the fixed version that packages depend on.  Update it rarely
   ;; enough to avoid massive rebuilds.
-  gdb-8.2)
+  gdb-8.3)

gnu/packages/gl.scm

@@ -229,7 +229,7 @@ also known as DXTn or DXTC) for Mesa.")
 (define-public mesa
   (package
     (name "mesa")
-    (version "19.1.4")
+    (version "19.2.1")
     (source
       (origin
         (method url-fetch)
@@ -241,9 +241,10 @@ also known as DXTn or DXTC) for Mesa.")
                                   version "/mesa-" version ".tar.xz")))
         (sha256
          (base32
-          "1yvb7ja09i36zjifpyrf8jmbm9z0wqs2w3x8dlmxkkzdv6knilm6"))
+          "1s81kwcjkkahnf5y5mshmd3q9j057hhsai7awpq6yb6im2hkriac"))
         (patches
-         (search-patches "mesa-skip-disk-cache-test.patch"))))
+         (search-patches "mesa-skip-disk-cache-test.patch"
+                         "mesa-timespec-test-32bit.patch"))))
     (build-system meson-build-system)
     (propagated-inputs
       `(;; The following are in the Requires.private field of gl.pc.
@@ -277,13 +278,11 @@ also known as DXTn or DXTC) for Mesa.")
         ("gettext" ,gettext-minimal)
         ,@(match (%current-system)
             ((or "x86_64-linux" "i686-linux")
-             `(("glslang" ,glslang)
+             `(("glslang" ,glslang)))
-               ("vulkan-headers" ,vulkan-headers)
-               ("vulkan-loader" ,vulkan-loader)))
             (_
              `()))
         ("pkg-config" ,pkg-config)
-        ("python" ,python)
+        ("python" ,python-wrapper)
         ("python-mako" ,python-mako)
         ("which" ,(@ (gnu packages base) which))))
     (arguments

gnu/packages/glib.scm

@@ -347,6 +347,7 @@ shared NFS home directories.")
            (variable "GIO_EXTRA_MODULES")
            (files '("lib/gio/modules")))))
    (search-paths native-search-paths)
+   (properties '((hidden? . #t)))
 
    (synopsis "Thread-safe general utility library; basis of GTK+ and GNOME")
    (description
@@ -356,6 +357,34 @@ dynamic loading, and an object system.")
    (home-page "https://developer.gnome.org/glib/")
    (license license:lgpl2.1+)))
 
+(define-public glib-with-documentation
+  ;; glib's doc must be built in a separate package since it requires gtk-doc,
+  ;; which in turn depends on glib.
+  (package
+    (inherit glib)
+    (properties (alist-delete 'hidden? (package-properties glib)))
+    (outputs (cons "doc" (package-outputs glib))) ; 20 MiB of GTK-Doc reference
+    (native-inputs
+     `(("gtk-doc" ,gtk-doc)             ; for the doc
+       ("docbook-xml" ,docbook-xml)
+       ("libxml2" ,libxml2)
+       ,@(package-native-inputs glib)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments glib)
+       ((#:configure-flags flags ''())
+        `(cons "-Dgtk_doc=true" ,flags))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'install 'move-doc
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out"))
+                     (doc (assoc-ref outputs "doc"))
+                     (html (string-append "/share/gtk-doc")))
+                 (copy-recursively (string-append out html)
+                                   (string-append doc html))
+                 (delete-file-recursively (string-append out html))
+                 #t)))))))))
+
 (define gobject-introspection
   (package
     (name "gobject-introspection")

gnu/packages/gnome.scm

@@ -75,6 +75,7 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages crates-io)
   #:use-module (gnu packages cups)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages cyrus-sasl)
@@ -165,6 +166,7 @@
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages xorg)
   #:use-module (gnu artwork)
+  #:use-module (guix build-system cargo)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
@@ -177,6 +179,8 @@
   #:use-module (guix packages)
   #:use-module (guix utils)
   #:use-module (guix gexp)
+  #:use-module (guix monads)
+  #:use-module (guix store)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1))
 
@@ -861,8 +865,21 @@ on the GNOME Desktop with a single simple application.")
        (base32
         "0bshwm49cd01ighsxqlbqn10q0ch71ff99gcrx8pr2gyky2ad3pq"))))
     (build-system gnu-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'set-adwaita-theme-file-name
+                    (lambda* (#:key inputs #:allow-other-keys)
+                      ;; Provide the correct file name of the default GNOME
+                      ;; background, 'adwaita-timed.xml'.
+                      (let ((theme (assoc-ref inputs "gnome-backgrounds")))
+                        (substitute* (find-files "schemas"
+                                                 "\\.gschema\\.xml\\.in$")
+                          (("@datadir@/backgrounds/gnome")
+                           (string-append theme "/share/backgrounds/gnome")))
+                        #t))))))
     (inputs
-     `(("glib" ,glib)))
+     `(("glib" ,glib)
+       ("gnome-backgrounds" ,gnome-backgrounds)))
     (native-inputs
      `(("intltool" ,intltool)
        ("glib" ,glib "bin")                       ; glib-compile-schemas, etc.
@@ -1403,37 +1420,231 @@ dealing with different structured file formats.")
 library.")
     (license license:lgpl2.0+)))
 
+(define* (computed-origin-method gexp-promise hash-algo hash
+                                 #:optional (name "source")
+                                 #:key (system (%current-system))
+                                 (guile (default-guile)))
+  "Return a derivation that executes the G-expression that results
+from forcing GEXP-PROMISE."
+  (mlet %store-monad ((guile (package->derivation guile system)))
+    (gexp->derivation (or name "computed-origin")
+                      (force gexp-promise)
+                      #:graft? #f       ;nothing to graft
+                      #:system system
+                      #:guile-for-build guile)))
+
+(define librsvg-next-source
+  (let* ((version         "2.46.3")
+         (upstream-source (origin
+                           (method url-fetch)
+                           (uri (string-append "mirror://gnome/sources/librsvg/"
+                                               (version-major+minor version)  "/"
+                                               "librsvg-" version ".tar.xz"))
+                           (sha256
+                            (base32
+                             "1s3a96i7f4pynjwxxvhysp4b6r7kyi8nasdxfyi62hc7gm34d3kn")))))
+    (origin
+      (method computed-origin-method)
+      (file-name (string-append "librsvg-" version ".tar.xz"))
+      (sha256 #f)
+      (uri
+       (delay
+        (with-imported-modules '((guix build utils))
+          #~(begin
+              (use-modules (guix build utils))
+              (set-path-environment-variable
+               "PATH" '("bin")
+               (list "/tmp"
+                     #+(canonical-package xz)
+                     #+(canonical-package gzip)
+                     #+(canonical-package tar)))
+              (invoke "tar" "xvf" #+upstream-source)
+              (with-directory-excursion (string-append "librsvg-" #$version)
+                (for-each
+                  (lambda (crate)
+                    (delete-file-recursively (string-append "vendor/" (car crate)))
+                    (invoke "tar" "xvf" (cdr crate) "-C" "vendor"))
+                  '(
+;; aho-corasick 0.7
+;; alga 0.9
+;; approx 0.3
+;; arrayvec 0.4
+                    ("atty" . #+(package-source rust-atty-0.2))
+                    ("autocfg" . #+(package-source rust-autocfg-0.1))
+                    ("bitflags" . #+(package-source rust-bitflags-1))
+;; block 0.1
+;; bstr 0.2
+;; byteorder 1.3
+;; cairo-rs 0.7
+;; cairo-sys-rs 0.9
+;; cast 0.2
+                    ("cfg-if" . #+(package-source rust-cfg-if-0.1))
+                    ("clap" . #+(package-source rust-clap-2))
+                    ;("cloudabi" . #+(package-source rust-cloudabi-0.0))
+;; criterion 0.2
+;; criterion-plot 0.3
+;; crossbeam-deque 0.7
+;; crossbeam-epoch 0.7
+;; crossbeam-queue 0.1
+;; crossbeam-utils 0.6
+;; cssparser 0.25
+;; cssparser-macros 0.3
+;; csv 1.1
+;; csv-core 0.1
+;; data-url 0.1
+;; downcast-rs 1.0
+                    ("dtoa" . #+(package-source rust-dtoa-0.4))
+;; dtoa-short 0.3
+;; either 1.5
+;; encoding 0.2
+;; encoding-index-japanese 1.20141219.5
+;; encoding-index-korean 1.20141219.5
+;; encoding-index-simpchinese 1.20141219.5
+;; encoding-index-singlebyte 1.20141219.5
+;; encoding-index-tradchinese 1.20141219.5
+;; encoding_index_tests 0.1
+;; float-cmp 0.5
+;; fragile 0.3
+                    ;("fuchsia-cprng" . #+(package-source rust-fuchsia-cprng-0.1))
+;; futf 0.1
+;; gdk-pixbuf 0.7
+;; gdk-pixbuf-sys 0.9
+;; generic-array 0.12
+;; gio 0.7
+;; gio-sys 0.9
+;; glib 0.8
+;; glib-sys 0.9
+;; gobject-sys 0.9
+;; idna 0.2
+;; itertools 0.8
+                    ("itoa" . #+(package-source rust-itoa-0.4))
+                    ;("language-tags" . #+(package-source rust-language-tags-0.2))
+                    ("lazy_static" . #+(package-source rust-lazy-static-1.3))
+                    ("libc" . #+(package-source rust-libc-0.2))
+;; libm 0.1
+;; locale_config 0.3
+                    ("log" . #+(package-source rust-log-0.4))
+;; mac 0.1
+;; malloc_buf 0.0
+;; markup5ever 0.9
+                    ;("matches" . #+(package-source rust-matches-0.1))
+;; matrixmultiply 0.2
+;; memchr 2.2
+;; memoffset 0.5
+;; nalgebra 0.18
+;; new_debug_unreachable 1.0
+                    ("nodrop" . #+(package-source rust-nodrop-0.1))
+;; num-complex 0.2
+                    ("num-integer" . #+(package-source rust-num-integer-0.1))
+;; num-rational 0.2
+                    ("num-traits" . #+(package-source rust-num-traits-0.2))
+                    ("num_cpus" . #+(package-source rust-num-cpus-1.10))
+;; objc 0.2
+;; objc-foundation 0.1
+;; objc_id 0.1
+;; pango 0.7
+;; pango-sys 0.9
+;; pangocairo 0.8
+;; pangocairo-sys 0.10
+                    ("percent-encoding" . #+(package-source rust-percent-encoding-2.1))
+;; phf 0.7.24
+;; phf_codegen 0.7.24
+;; phf_generator 0.7.24
+;; phf_shared 0.7.24
+                    ;("pkg-config" . #+(package-source rust-pkg-config-0.3))
+;; precomputed-hash 0.1
+                    ("proc-macro2" . #+(package-source rust-proc-macro2-1.0))
+;; procedural-masquerade 0.1
+                    ("quote" . #+(package-source rust-quote-1.0))
+                    ;("rand" . #+(package-source rust-rand-0.6))
+                    ("rand_chacha" . #+(package-source rust-rand-chacha-0.1))
+                    ("rand_core-0.3.1" . #+(package-source rust-rand-core-0.3))
+                    ("rand_core" . #+(package-source rust-rand-core-0.4))
+                    ("rand_hc" . #+(package-source rust-rand-hc-0.1))
+                    ("rand_isaac" . #+(package-source rust-rand-isaac-0.1))
+                    ("rand_jitter" . #+(package-source rust-rand-jitter-0.1))
+                    ("rand_os" . #+(package-source rust-rand-os-0.1))
+                    ("rand_pcg" . #+(package-source rust-rand-pcg-0.1))
+                    ("rand_xorshift" . #+(package-source rust-rand-xorshift-0.1))
+;; rand_xoshiro 0.1
+                    ;("rawpointer" . #+(package-source rust-rawpointer-0.1))
+;; rayon 1.2
+;; rayon-core 1.6
+;; rctree 0.3
+                    ("rdrand" . #+(package-source rust-rdrand-0.4))
+;; regex 1.3
+;; regex-automata 0.1
+                    ;("regex-syntax" . #+(package-source rust-regex-syntax-0.6))
+;; rustc_version 0.2
+                    ("ryu" . #+(package-source rust-ryu-1.0))
+                    ("same-file" . #+(package-source rust-same-file-1.0))
+                    ("scopeguard" . #+(package-source rust-scopeguard-1.0))
+;; semver 0.9
+                    ;("semver-parser" . #+(package-source rust-semver-parser-0.7))
+                    ("serde" . #+(package-source rust-serde-1.0))
+                    ("serde_derive" . #+(package-source rust-serde-derive-1.0))
+                    ("serde_json" . #+(package-source rust-serde-json-1.0))
+;; siphasher 0.2
+;; smallvec 0.6
+;; string_cache 0.7
+;; string_cache_codegen 0.4
+;; string_cache_shared 0.3
+                    ("syn" . #+(package-source rust-syn-1.0))
+;; tendril 0.4
+                    ("textwrap" . #+(package-source rust-textwrap-0.11))
+                    ;("thread_local" . #+(package-source rust-thread-local-0.3))
+;; tinytemplate 1.0
+                    ;("typenum" . #+(package-source rust-typenum-1.10))
+;; unicode-bidi 0.3
+;; unicode-normalization 0.1
+                    ("unicode-width" . #+(package-source rust-unicode-width-0.1))
+                    ("unicode-xid" . #+(package-source rust-unicode-xid-0.2))
+;; url 2.1
+;; utf-8 0.7
+                    ("walkdir" . #+(package-source rust-walkdir-2.2))
+                    ("winapi" . #+(package-source rust-winapi-0.3))
+                    ;("winapi-i686-pc-windows-gnu" . #+(package-source rust-winapi-i686-pc-windows-gnu-0.4))
+                    ("winapi-util" . #+(package-source rust-winapi-util-0.1))
+                    ;("winapi-x86_64-pc-windows-gnu" . #+(package-source rust-winapi-x86-64-pc-windows-gnu-0.4))
+;; xml-rs 0.8
+                    )))
+              (format #t "Replacing vendored crates in the tarball and repacking ...~%")
+              (force-output)
+              (invoke "tar" "cfa" #$output
+                      ;; Avoid non-determinism in the archive.  We set the
+                      ;; mtime of files in the archive to early 1980 because
+                      ;; the build process fails if the mtime of source
+                      ;; files is pre-1980, due to the creation of zip
+                      ;; archives.
+                      "--mtime=@315619200" ; 1980-01-02 UTC
+                      "--owner=root:0"
+                      "--group=root:0"
+                      "--sort=name"
+                      (string-append "librsvg-" #$version))
+              #t)))))))
+
 (define-public librsvg-next
   (package
     (name "librsvg")
-    (version "2.46.0")
+    (version "2.46.3")
-    (source (origin
+    (source librsvg-next-source)
-              (method url-fetch)
-              (uri (string-append "mirror://gnome/sources/" name "/"
-                                  (version-major+minor version)  "/"
-                                  name "-" version ".tar.xz"))
-              (sha256
-               (base32
-                "1la3az2af2ccm6rp86b6wh0kq7kxzl4n8pli5qxhyic1rd91xj4n"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
        (list "--disable-static"
              "--enable-vala") ; needed for e.g. gnome-mines
        #:make-flags '("CC=gcc")
+       #:imported-modules ,%cargo-utils-modules ;for `generate-all-checksums'
        #:phases
        (modify-phases %standard-phases
-         ;; Don't patch anything in vendor/ to avoid having to recompute
+         (add-after 'configure 'patch-cargo-checksums
-         ;; checksums for the bundled Cargo "crates".  TODO: Unbundle those.
-         (delete 'patch-source-shebangs)
-         (delete 'patch-generated-file-shebangs)
-         (delete 'patch-usr-bin-file)
-         (add-before 'configure 'patch-all-the-things
            (lambda _
-             (for-each patch-shebang '("tap-driver.sh" "tap-test"))
+             (use-modules (guix build cargo-utils))
-             (patch-/usr/bin/file "configure")
+             (substitute* "librsvg/Cargo.toml"
-             (patch-makefile-SHELL "po/Makefile.in.in")
+               (("bitflags .*") "bitflags = \"1\"\n")) ; 1.2 is vendored
-             #t))
+             (generate-all-checksums "vendor")
+             (delete-file "Cargo.lock")
+             (invoke "cargo" "generate-lockfile")))
          (add-before 'configure 'pre-configure
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "gdk-pixbuf-loader/Makefile.in"
@@ -1492,7 +1703,7 @@ library.")
     (description
      "Librsvg is a C library to render SVG files using the Cairo 2D graphics
 library.")
-    (license license:lgpl2.0+)))
+    (license license:lgpl2.1+)))
 
 (define-public libidl
   (package
@@ -2012,7 +2223,7 @@ since ca. 2006, when GTK+ itself incorporated printing support.")
     (native-inputs
      `(("glib" ,glib "bin")             ; for glib-genmarshal, etc.
        ("intltool" ,intltool)
-       ("xorg-server" ,xorg-server) ; For running the tests
+       ("xorg-server" ,xorg-server-for-tests) ; For running the tests
        ("pkg-config" ,pkg-config)))
     (home-page "https://developer.gnome.org/libbonoboui/")
     (synopsis "Some user interface controls using Bonobo")
@@ -2325,28 +2536,28 @@ libraries written in C.")
 (define-public vte
   (package
     (name "vte")
-    (version "0.56.3")
+    (version "0.58.3")
     (source (origin
               (method url-fetch)
-              (uri (string-append "mirror://gnome/sources/" name "/"
+              (uri (string-append "mirror://gnome/sources/vte/"
                                   (version-major+minor version) "/"
-                                  name "-" version ".tar.xz"))
+                                  "vte-" version ".tar.xz"))
               (sha256
                (base32
-                "0j166gic5znssdb9r45qazq4kb4v9fial82czand5wa8i2yd988p"))))
+                "0xa9ipwic4jnhhbzlnqbhssz10xkzv61cpkl1ammc6mdq95bbp12"))))
-    (build-system gnu-build-system)
+    (build-system meson-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("intltool" ,intltool)
        ("vala" ,vala)
        ("gobject-introspection" ,gobject-introspection)
-       ("glib" ,glib "bin") ; for glib-genmarshal, etc.
+       ("glib" ,glib "bin")             ; for glib-genmarshal, etc.
        ("gperf" ,gperf)
        ("xmllint" ,libxml2)))
     (propagated-inputs
-     `(("gtk+" ,gtk+)                             ;required by vte-2.91.pc
+     `(("gtk+" ,gtk+)                   ; required by vte-2.91.pc
-       ("gnutls" ,gnutls)                         ;ditto
+       ("gnutls" ,gnutls)               ; ditto
-       ("pcre2" ,pcre2)))                         ;ditto
+       ("pcre2" ,pcre2)))               ; ditto
     (home-page "https://www.gnome.org/")
     (synopsis "Virtual Terminal Emulator")
     (description
@@ -2418,6 +2629,7 @@ 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
@@ -4361,7 +4573,7 @@ USB transfers with your high-level application or system daemon.")
 (define-public simple-scan
   (package
     (name "simple-scan")
-    (version "3.34.1")
+    (version "3.34.2")
     (source
      (origin
        (method url-fetch)
@@ -4369,7 +4581,7 @@ USB transfers with your high-level application or system daemon.")
                            (version-major+minor version) "/"
                            "simple-scan-" version ".tar.xz"))
        (sha256
-        (base32 "0glzskxdc7p9z7nwcakqc7qzij4l79adlvvb2cj5fmis731zw9yq"))))
+        (base32 "1fk3g4f9slckqfwm576jrjq1d1qihw0dlgzdf00ns7qbhzb0kxsp"))))
     (build-system meson-build-system)
     ;; TODO: Fix icons in home screen, About dialogue, and scan menu.
     (arguments
@@ -4578,7 +4790,7 @@ principles are simplicity and standards compliance.")
        ("pkg-config" ,pkg-config)
        ("python-pep8" ,python-pep8)
        ("xmllint" ,libxml2)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("gobject-introspection" ,gobject-introspection)
        ("gtk+" ,gtk+)
@@ -7158,13 +7370,13 @@ like GNOME, Unity, Budgie, Pantheon, XFCE, Mate, etc.")
     (version "4.3")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/moka-project/"
+       (uri (git-reference
-                           name "/archive/v" version ".tar.gz"))
+             (url "https://github.com/snwh/faba-icon-theme.git")
-       (file-name (string-append name "-" version ".tar.gz"))
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32
+        (base32 "0xh6ppr73p76z60ym49b4d0liwdc96w41cc5p07d48hxjsa6qd6n"))))
-         "18ln06xl60qzvzz61zq9q72hdbfgjsza3flph8i2asyzx3dffz68"))))
     (build-system meson-build-system)
     (arguments
      `(#:phases
@@ -7189,15 +7401,15 @@ Moka")
     (inherit faba-icon-theme)
     (name "moka-icon-theme")
     (version "5.4.0")
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              (uri (string-append "https://github.com/moka-project"
+       (method git-fetch)
-                                  "/moka-icon-theme/archive/v"
+       (uri (git-reference
-                                  version ".tar.gz"))
+             (url "https://github.com/snwh/moka-icon-theme.git")
-              (file-name (string-append name "-" version ".tar.gz"))
+             (commit (string-append "v" version))))
-              (sha256
+       (file-name (git-file-name name version))
-               (base32
+       (sha256
-                "1nbwdjj268hxv9lfagd9aylily9f0hhallp841v0i3imljp84bmk"))))
+        (base32 "015l02im4mha5z91dbchxf6xkp66d346bg3xskwg0rh3lglhjsrd"))))
     (propagated-inputs
      ;; Moka is based on Faba by using it as a fallback icon set instead of
      ;; bundling it, so we need to add it as a propagated input.
@@ -7212,14 +7424,15 @@ simple and consistent.")
   (package
     (name "arc-icon-theme")
     (version "20161122")
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              (uri (string-append "https://github.com/horst3180/arc-icon-theme"
+       (method git-fetch)
-                                  "/archive/" version ".tar.gz"))
+       (uri (git-reference
-              (file-name (string-append name "-" version ".tar.gz"))
+             (url "https://github.com/horst3180/arc-icon-theme.git")
-              (sha256
+             (commit version)))
-               (base32
+       (file-name (git-file-name name version))
-                "1ya1cqvv8q847c0rpcg6apzky87q3h04y8jz5nmi52qk6kg8si0b"))))
+       (sha256
+        (base32 "1ch3hp08qri93510hypzz6m2x4xgg2h15wvnhjwh1x1s1b7jvxjd"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -7739,7 +7952,7 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).")
 
        ;; For tests.
        ("aspell-dict-en" ,aspell-dict-en)
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (propagated-inputs
      `(("enchant" ,enchant)))            ;enchant.pc is required by gspell-1.pc
     (home-page "https://wiki.gnome.org/Projects/gspell")
@@ -8154,7 +8367,7 @@ hexadecimal or ASCII.  It is useful for editing binary files in general.")
      `(("glib" ,glib "bin")             ; glib-compile-resources
        ("pkg-config" ,pkg-config)
        ;; For tests.
-       ("xorg-server" ,xorg-server)))
+       ("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("glib" ,glib)
        ("gobject-introspection" ,gobject-introspection)
@@ -8244,7 +8457,7 @@ functionality.")
 (define-public gthumb
   (package
     (name "gthumb")
-    (version "3.8.1")
+    (version "3.8.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/gthumb/"
@@ -8252,7 +8465,7 @@ functionality.")
                                   "gthumb-" version ".tar.xz"))
               (sha256
                (base32
-                "184zn79w4s9y1zy42ar31p3jsg8rmkxy8k6iry51nz8aizbcs7jb"))))
+                "15wqks35ks5dm7zj046dfd45vvrilan2ayfy2sxiprv7q74cip2q"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t
@@ -8376,9 +8589,9 @@ advanced image management tool")
        ("gtk-doc" ,gtk-doc)
        ("pkg-config" ,pkg-config)
        ("gettext" ,gettext-minimal)
-       ("xorg-server" ,xorg-server)
 
        ;; Test suite dependencies.
+       ("xorg-server" ,xorg-server-for-tests)
        ("hicolor-icon-theme" ,hicolor-icon-theme)))
     (home-page "https://source.puri.sm/Librem5/libhandy")
     (synopsis "Library full of GTK+ widgets for mobile phones")

gnu/packages/gnucash.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2017 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -33,6 +34,7 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cmake)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages gnome)
@@ -70,6 +72,8 @@
        ("icu4c" ,icu4c)
        ("glib" ,glib)
        ("gtk" ,gtk+)
+       ("libdbi" ,libdbi)
+       ("libdbi-drivers" ,libdbi-drivers)
        ("libgnomecanvas" ,libgnomecanvas)
        ("libxml2" ,libxml2)
        ("libxslt" ,libxslt)
@@ -89,8 +93,7 @@
     (arguments
      `(#:test-target "check"
        #:configure-flags
-       (list "-DWITH_OFX=OFF"           ; libofx is not available yet
+       (list "-DWITH_OFX=OFF")          ; libofx is not available yet
-             "-DWITH_SQL=OFF")          ; without dbi.h
        #:make-flags '("GUILE_AUTO_COMPILE=0")
        #:modules ((guix build cmake-build-system)
                   ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
@@ -147,6 +150,10 @@
              (for-each (lambda (prog)
                          (wrap-program (string-append (assoc-ref outputs "out")
                                                       "/bin/" prog)
+                           `("GNC_DBD_DIR" =
+                             (,(string-append
+                                (assoc-ref inputs "libdbi-drivers")
+                                "/lib/dbd")))
                            `("PERL5LIB" ":" prefix
                              ,(map (lambda (o)
                                      (string-append o "/lib/perl5/site_perl/"

gnu/packages/gnunet.scm

@@ -55,7 +55,9 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages upnp)
   #:use-module (gnu packages video)
+  #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xiph)
   #:use-module (gnu packages backup)
@@ -232,7 +234,7 @@ supports HTTP, HTTPS and GnuTLS.")
 (define-public gnunet
   (package
    (name "gnunet")
-   (version "0.10.1")
+   (version "0.11.8")
    (source
     (origin
       (method url-fetch)
@@ -240,53 +242,67 @@ supports HTTP, HTTPS and GnuTLS.")
                           ".tar.gz"))
       (sha256
        (base32
-        "04wxzm3wkgqbn42b8ksr4cx6m5cckyig5cls1adh0nwdczwvnp7n"))))
+        "1zkmcq75sfr3iyg8rgxp9dbl7fwsvc1a71rc0vgisghcbrx1n7yj"))))
    (build-system gnu-build-system)
    (inputs
-    `(("glpk" ,glpk)
+    `(("bluez" ,bluez)
+      ("glpk" ,glpk)
       ("gnurl" ,gnurl)
-      ("gstreamer" ,gstreamer)
-      ("gst-plugins-base" ,gst-plugins-base)
       ("gnutls" ,gnutls/dane)
+      ("gstreamer" ,gstreamer)
+      ("jansson" ,jansson)
       ("libextractor" ,libextractor)
+      ("libidn" ,libidn2)
       ("libgcrypt" ,libgcrypt)
-      ("libidn" ,libidn)
-      ("libmicrohttpd" ,libmicrohttpd) ; hostlist, pt, contrib, and more
       ("libltdl" ,libltdl)
-      ("libunistring" ,libunistring) ; fs and more
+      ("libmicrohttpd" ,libmicrohttpd)
-      ("openssl" ,openssl) ; transport, certificate creation, contribs
+      ("libogg" ,libogg)
-      ("opus" ,opus) ; gnunet-conversation
+      ("libunistring" ,libunistring)
-      ("pulseaudio" ,pulseaudio) ; conversation
+      ("miniupnpc" ,miniupnpc)
-      ("sqlite" ,sqlite) ; sqlite bindings, *store
+      ("opus" ,opus)
-      ("zlib" ,zlib)
+      ("pulseaudio" ,pulseaudio)
-      ("perl" ,perl) ; doxygen and more
+      ("sqlite" ,sqlite)
-      ("jansson" ,jansson) ; identity, taler (external), gnunet-json, gns
+      ("zbar" ,zbar)
-      ("nss" ,nss) ; gns
+      ("zlib" ,zlib)))
-      ("gmp" ,gmp) ; util
-      ("bluez" ,bluez) ; gnunet-transport
-      ("glib" ,glib)
-      ("libogg" ,libogg) ; gnunet-conversation
-      ("python-2" ,python-2))) ; tests, gnunet-qr
    (native-inputs
-    `(("pkg-config" ,pkg-config)))
+    `(("pkg-config" ,pkg-config)
+      ("python" ,python)
+      ("xxd" ,xxd)
+      ("which" ,(@ (gnu packages base) which))))
    (arguments
-    '(#:configure-flags
+    '(#:parallel-tests? #f ; Parallel tests aren't supported.
-      (list (string-append "--with-nssdir=" %output "/lib"))
-      #:parallel-tests? #f
-      ;; test_gnunet_service_arm fails; reported upstream
-      #:tests? #f
       #:phases
       (modify-phases %standard-phases
-        ;; swap check and install phases and set paths to installed binaries
+        (add-after 'configure 'remove-failing-tests
+          ;; These tests fail in Guix's building envrionment.
+          (lambda _
+            (substitute* "src/transport/Makefile"
+              (("test_transport_api_udp_nat\\$\\(EXEEXT\\) \\\\\n") "")
+              (("test_transport_api_manipulation_cfg\\$\\(EXEEXT\\) \\\\\n") ""))
+            (substitute* "src/topology/Makefile"
+              (("^check_PROGRAMS.*") "\n")
+              (("test_gnunet_daemon_topology\\$\\(EXEEXT\\)\n") ""))
+            (substitute* "src/namestore/Makefile"
+              (("\\$\\(am__append_2\\)") ""))
+            (substitute* "src/gns/Makefile"
+              (("\\$\\(am__append_4\\)") ""))
+            (substitute* "contrib/Makefile"
+              (("^check_PROGRAMS.*") "\n"))
+            ;; 'test' from coreutils doesn't behave as the test expects.
+            (substitute* '("src/gns/gnunet-gns-proxy-setup-ca.in"
+                           "src/transport/gnunet-transport-certificate-creation.in")
+              (("gnutls-certtool") "certtool"))
+            #t))
+        ;; Swap 'check and 'install phases and add installed binaries to $PATH.
         (add-before 'check 'set-path-for-check
           (lambda* (#:key outputs #:allow-other-keys)
            (let ((out (assoc-ref outputs "out")))
              (setenv "GNUNET_PREFIX" (string-append out "/lib"))
              (setenv "PATH" (string-append (getenv "PATH") ":" out "/bin")))
            #t))
+        (delete 'check)
         (add-after 'install 'check
-          (assoc-ref %standard-phases 'check))
+          (assoc-ref %standard-phases 'check)))))
-        (delete 'check))))
    (synopsis "Secure, decentralized, peer-to-peer networking framework")
    (description
      "GNUnet is a framework for secure peer-to-peer networking.  The
@@ -333,14 +349,14 @@ services.")
 (define-public gnunet-gtk
   (package (inherit gnunet)
     (name "gnunet-gtk")
-    (version (package-version gnunet))
+    (version "0.11.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/gnunet/gnunet-gtk-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1p38k1s6a2fmcfc9a7cf1zrdycm9h06kqdyand4s3k500nj6mb4g"))))
+                "061ifhqk6q9kx71z5404fm4d60yj2dihlwwmdqmhkn5nn4bvcwb5"))))
     (arguments
      `(#:configure-flags
        (list "--with-libunique"
@@ -348,14 +364,17 @@ services.")
              (string-append "--with-gnunet="
                             (assoc-ref %build-inputs "gnunet")))))
     (inputs
-     `(("gnunet" ,gnunet)
+     `(("glade3" ,glade3)
-       ("libgcrypt" ,libgcrypt)
+       ("gnunet" ,gnunet)
+       ("gnutls" ,gnutls/dane)
        ("gtk+" ,gtk+)
        ("libextractor" ,libextractor)
-       ("glade3" ,glade3)
+       ("libgcrypt" ,libgcrypt)
-       ("qrencode" ,qrencode)
+       ("libunique" ,libunique)
-       ("libunique" ,libunique)))
+       ("qrencode" ,qrencode)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("libglade" ,libglade)))
-    (synopsis "Graphical front-end tools for GNUnet")))
+    (synopsis "Graphical front-end tools for GNUnet")
+    (properties '((ftp-server . "ftp.gnu.org")
+                  (ftp-directory . "/gnunet")))))

gnu/packages/gnupg.scm

@@ -260,14 +260,14 @@ compatible to GNU Pth.")
 (define-public gnupg
   (package
     (name "gnupg")
-    (version "2.2.17")
+    (version "2.2.18")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnupg/gnupg/gnupg-" version
                                   ".tar.bz2"))
               (sha256
                (base32
-                "056mgy09lvsi03531a437qj58la1j2x1y1scvfi53diris3658mg"))))
+                "02pcdmb9p4a8hil88gyd86mnc85jldss3cl02jvbkcjmrbi7rlrh"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -934,15 +934,15 @@ passphrase when @code{gpg} is run and needs it.")))
 (define-public paperkey
   (package
     (name "paperkey")
-    (version "1.5")
+    (version "1.6")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://www.jabberwocky.com/"
+              (uri (string-append "https://www.jabberwocky.com/"
                                   "software/paperkey/paperkey-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1prd2jaf4zjad3xhv160hmi5n408ssljfg7iz90jxs9w111pjwy4"))))
+                "1xq5gni6gksjkd5avg0zpd73vsr97appksfx0gx2m38s4w9zsid2"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -953,7 +953,7 @@ passphrase when @code{gpg} is run and needs it.")))
                             "checks/roundtrip-raw.sh")
                (("/bin/echo") "echo"))
              #t)))))
-    (home-page "http://www.jabberwocky.com/software/paperkey/")
+    (home-page "https://www.jabberwocky.com/software/paperkey/")
     (synopsis "Backup OpenPGP keys to paper")
     (description
      "Paperkey extracts the secret bytes from an OpenPGP (GnuPG, PGP, etc) key
@@ -1073,7 +1073,7 @@ files, to verify signatures, and to manage the private and public keys.")
        ("perl-xml-twig" ,perl-xml-twig)
        ("torsocks" ,torsocks)))
     (native-inputs
-     `(("xorg-server" ,xorg-server)))
+     `(("xorg-server" ,xorg-server-for-tests)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases

gnu/packages/gnuzilla.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
-;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 ng0 <ng0@n0.is>
@@ -550,8 +550,8 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %icecat-version "68.2.0-guix0-preview3")
+(define %icecat-version "68.3.0-guix0-preview1")
-(define %icecat-build-id "20191031000000") ;must be of the form YYYYMMDDhhmmss
+(define %icecat-build-id "20191204000000") ;must be of the form YYYYMMDDhhmmss
 
 ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
 ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
@@ -573,11 +573,11 @@ from forcing GEXP-PROMISE."
                   "firefox-" upstream-firefox-version ".source.tar.xz"))
             (sha256
              (base32
-              "0f3gf5gwhxabm6xs29nlxmfqdw3fs7v458vq1fydrglfyvmc5wc5"))))
+              "0sfwp9vyjizj1lkvj6z51r85dl41q3l8380fkdyqdbp7f2d18cg1"))))
 
-         (upstream-icecat-base-version "68.2.0") ; maybe older than base-version
+         (upstream-icecat-base-version "68.3.0") ; maybe older than base-version
          ;;(gnuzilla-commit (string-append "v" upstream-icecat-base-version))
-         (gnuzilla-commit "930298e1efff3e40721659d8fd7118cdd2477bd4")
+         (gnuzilla-commit "85e99badac11983f6d50b0d9942f66a30f55b8e5")
          (gnuzilla-source
           (origin
             (method git-fetch)
@@ -589,10 +589,8 @@ from forcing GEXP-PROMISE."
                                       (string-take gnuzilla-commit 8)))
             (sha256
              (base32
-              "14g57b0262qq5s0w8b1lrk8wkvg7m068dfi0ilvhg2q5jrxk3cd0"))))
+              "00mb734yvm0r7i64mbg7hvrvhbwkcii9f9hjgwi37aizd9k0n78a"))))
 
-         (gnuzilla-fixes-patch
-          (local-file (search-patch "icecat-gnuzilla-fixes.patch")))
          (makeicecat-patch
           (local-file (search-patch "icecat-makeicecat.patch"))))
 
@@ -638,8 +636,6 @@ from forcing GEXP-PROMISE."
 
                 (with-directory-excursion "/tmp/gnuzilla"
                   (make-file-writable "makeicecat")
-                  (invoke "patch" "--force" "--no-backup-if-mismatch"
-                          "-p1" "--input" #+gnuzilla-fixes-patch)
                   (invoke "patch" "--force" "--no-backup-if-mismatch"
                           "-p1" "--input" #+makeicecat-patch)
                   (patch-shebang "makeicecat")
@@ -658,8 +654,6 @@ from forcing GEXP-PROMISE."
                      (string-append "FFSUB=" #$sub-version "\n"))
                     (("^DATA=.*")
                      "DATA=/tmp/gnuzilla/data\n")
-                    (("^find extensions/gnu/ ")
-                     "find extensions/gnu/ | sort ")
                     (("/bin/sed")
                      #+(file-append (canonical-package sed) "/bin/sed"))))
 
@@ -703,7 +697,7 @@ from forcing GEXP-PROMISE."
                   (force-output)
                   (invoke "bash" "/tmp/gnuzilla/makeicecat"))
 
-                (format #t "Packing new IceCat tarball...~%")
+                (format #t "Packing IceCat source tarball...~%")
                 (force-output)
                 (invoke "tar" "cfa" #$output
                         ;; Avoid non-determinism in the archive.  We set the
@@ -811,6 +805,10 @@ from forcing GEXP-PROMISE."
 
                            "--with-distribution-id=org.gnu"
 
+                           ;; Do not require addons in the global app
+                           ;; directory to be signed by Mozilla.
+                           "--with-unsigned-addon-scopes=app"
+
                            "--enable-startup-notification"
                            "--enable-pulseaudio"
 
@@ -877,7 +875,7 @@ from forcing GEXP-PROMISE."
                            ;; "--with-system-png"
                            )
 
-       #:imported-modules ,%cargo-utils-modules ;for `generate-checksums'
+       #:imported-modules ,%cargo-utils-modules ;for `generate-all-checksums'
 
        #:modules ((ice-9 ftw)
                   (ice-9 rdelim)
@@ -979,15 +977,7 @@ from forcing GEXP-PROMISE."
                (substitute* '("Cargo.lock" "gfx/wr/Cargo.lock")
                  (("(\"checksum .* = )\".*\"" all name)
                   (string-append name "\"" null-hash "\"")))
-               (for-each
+               (generate-all-checksums "third_party/rust"))
-                (lambda (filename)
-                  (delete-file filename)
-                  (let ((dir (dirname filename)))
-                    (display (string-append
-                              "patch-cargo-checksums: generate-checksums for "
-                              dir "\n"))
-                    (generate-checksums dir)))
-                (find-files "third_party/rust" ".cargo-checksum.json")))
              #t))
          (add-before 'configure 'augment-CPLUS_INCLUDE_PATH
            (lambda* (#:key build inputs #:allow-other-keys)

gnu/packages/graph.scm

@@ -43,6 +43,7 @@
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages statistics)
@@ -107,14 +108,14 @@ 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")
@@ -758,7 +762,7 @@ realistic reflections, shading, perspective and other effects.")
        ("graphviz" ,graphviz)
        ("intltool" ,intltool)
        ("pkg-config" ,pkg-config)
-       ("xvfb" ,xorg-server)))
+       ("xvfb" ,xorg-server-for-tests)))
     (home-page "https://rapicorn.testbit.org/")
     (synopsis "Toolkit for rapid development of user interfaces")
     (description
@@ -1055,7 +1059,7 @@ requirements.")
                       (setenv "DISPLAY" ":1")
                       #t)))))
     (native-inputs
-     `(("xorg-server" ,xorg-server)))
+     `(("xorg-server" ,xorg-server-for-tests)))
     (inputs
      `(("glew" ,glew)
        ("libxrandr" ,libxrandr)

gnu/packages/gstreamer.scm

@@ -29,6 +29,7 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system meson)
   #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages audio)
@@ -68,19 +69,20 @@
 (define-public orc
   (package
     (name "orc")
-    (version "0.4.29")
+    (version "0.4.30")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gstreamer.freedesktop.org/data/src/"
                                   "orc/orc-" version ".tar.xz"))
+              (patches (search-patches "orc-typedef-enum.patch"))
               (sha256
                (base32
-                "1cisbbn69p9c8vikn0nin14q0zscby5m8cyvzxyw2pjb2kwh32ag"))))
+                "0wj93im7i8a6546q2r8sp39yjfbxflkc0ygb0b8iqsd58qhvjhds"))))
-    (build-system gnu-build-system)
+    (build-system meson-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'check 'disable-faulty-test
+         (add-after 'unpack 'disable-faulty-test
            (lambda _
              ;; XXX Disable the 'test-limits' and 'exec_opcodes_sys'
              ;; tests, which fail on some machines.  See:
@@ -90,6 +92,8 @@
                (("if \\(error\\) return 1;")
                 "if (error) return 77;"))
              #t)))))
+    (native-inputs
+     `(("gtk-doc" ,gtk-doc)))
     (home-page "https://gstreamer.freedesktop.org/modules/orc.html")
     (synopsis "Oil runtime compiler")
     (description
@@ -103,17 +107,16 @@ arrays of data.")
 (define-public gstreamer
   (package
     (name "gstreamer")
-    (version "1.16.0")
+    (version "1.16.1")
     (source
      (origin
       (method url-fetch)
       (uri (string-append
             "https://gstreamer.freedesktop.org/src/gstreamer/gstreamer-"
             version ".tar.xz"))
-      (patches (search-patches "gstreamer-buffer-reset-offset.patch"))
       (sha256
        (base32
-        "003wy1p1in85p9sr5jsyhbnwqaiwz069flwkhyx7qhxy31qjz3hf"))))
+        "0z9pyhf6zm1r0spw6zym80bvbyx6h8xg9h6535csbnn48ws1q882"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (arguments
@@ -152,7 +155,7 @@ This package provides the core library and elements.")
 (define-public gst-plugins-base
   (package
     (name "gst-plugins-base")
-    (version "1.16.0")
+    (version "1.16.1")
     (source
      (origin
       (method url-fetch)
@@ -160,7 +163,7 @@ This package provides the core library and elements.")
                           name "-" version ".tar.xz"))
       (sha256
        (base32
-        "1bmmdwbyy89ayb85xc48y217f6wdmpz96f30zm6v53z2a5xsm4s0"))))
+        "0aybbwnzm15074smdk2bamj3ssck3hjvmilvgh49f19xjf4w8g2w"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (propagated-inputs
@@ -211,7 +214,7 @@ for the GStreamer multimedia library.")
 (define-public gst-plugins-good
   (package
     (name "gst-plugins-good")
-    (version "1.16.0")
+    (version "1.16.1")
     (source
      (origin
       (method url-fetch)
@@ -220,7 +223,7 @@ for the GStreamer multimedia library.")
             name "-" version ".tar.xz"))
       (sha256
        (base32
-        "1zdhif1mhf0ihkjpjyrh65g2iz2cawkjjb3h5w8h9ml06grxwjk5"))))
+        "07wgz9anf4ram2snp8n1wv6l0q3pd00iaw8bvw3wgklg05lvxflz"))))
     (build-system gnu-build-system)
     (inputs
      `(("aalib" ,aalib)
@@ -274,14 +277,14 @@ developers consider to have good quality code and correct functionality.")
 (define-public gst-plugins-bad
   (package
     (name "gst-plugins-bad")
-    (version "1.16.0")
+    (version "1.16.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gstreamer.freedesktop.org/src/"
                                   name "/" name "-" version ".tar.xz"))
               (sha256
                (base32
-                "019b0yqjrcg6jmfd4cc336h1bz5p4wxl58yz1c4sdb96avirs4r2"))))
+                "1dddqacxgp77f3nl153x5a6139wdphc9phds2fpqb2cv6faiqj2n"))))
     (outputs '("out" "doc"))
     (build-system gnu-build-system)
     (arguments
@@ -354,7 +357,7 @@ par compared to the rest.")
 (define-public gst-plugins-ugly
   (package
     (name "gst-plugins-ugly")
-    (version "1.16.0")
+    (version "1.16.1")
     (source
      (origin
        (method url-fetch)
@@ -362,7 +365,7 @@ par compared to the rest.")
                            name "/" name "-" version ".tar.xz"))
        (sha256
         (base32
-         "1hm46c1fy9vl1wfwipsj41zp79cm7in1fpmjw24j5hriy32n82g3"))))
+         "07cajqjs8pqchpf2sm87hljx4ibwvkiavqxmacxsr5airar17yab"))))
     (build-system gnu-build-system)
     (inputs
      `(("gst-plugins-base" ,gst-plugins-base)
@@ -389,7 +392,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.")
 (define-public gst-libav
   (package
     (name "gst-libav")
-    (version "1.16.0")
+    (version "1.16.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -397,7 +400,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.")
                     name "-" version ".tar.xz"))
               (sha256
                (base32
-                "16ixqpfrr7plaaz14n3vagr2q5xbfkv7gpmcsyndrkx98f813b6z"))
+                "1i31ra0l77cfahb6k5xpx45zwvpskzm848aijsbbx9x4x65799g8"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -425,7 +428,7 @@ compression formats through the use of the libav library.")
 (define-public python-gst
   (package
     (name "python-gst")
-    (version "1.16.0")
+    (version "1.16.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -433,7 +436,7 @@ compression formats through the use of the libav library.")
                     "gst-python-" version ".tar.xz"))
               (sha256
                (base32
-                "0f1d9rvy2qxlymmfzyknnfr5rz1vx69jv17gp7wnamc5s6p7mp2m"))))
+                "12bl6kc0ny2vyf6klas2bwqcv0pi55q9ns5zw261px16a6awhsdl"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((guix build gnu-build-system)

gnu/packages/gtk.scm

@@ -360,7 +360,7 @@ diagrams.")
        ("glib" ,glib "bin")             ; for glib-genmarshal, etc.
        ("pkg-config" ,pkg-config)
        ;; For testing.
-       ("xorg-server" ,xorg-server)
+       ("xorg-server" ,xorg-server-for-tests)
        ("shared-mime-info" ,shared-mime-info)))
     (propagated-inputs
      ;; As per the pkg-config file.
@@ -431,7 +431,7 @@ printing and other features typical of a source code editor.")
       ("pkg-config" ,pkg-config)
       ("vala" ,vala)
       ;; For testing.
-      ("xorg-server" ,xorg-server)
+      ("xorg-server" ,xorg-server-for-tests)
       ("shared-mime-info" ,shared-mime-info)))
    (propagated-inputs
     ;; gtksourceview-3.0.pc refers to all these.
@@ -461,7 +461,7 @@ highlighting and other features typical of a source code editor.")
 (define-public gdk-pixbuf
   (package
    (name "gdk-pixbuf")
-   (version "2.38.1")
+   (version "2.40.0")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnome/sources/" name "/"
@@ -469,7 +469,7 @@ highlighting and other features typical of a source code editor.")
                                 name "-" version ".tar.xz"))
             (sha256
              (base32
-              "0fmbjgjcyym3qg46f64qgl7icdm4ii77flyc1mhk244rp8vgi7zi"))))
+              "1rnlx9yfw970maxi2x6niaxmih5la11q1ilr7gzshz2kk585k0hm"))))
    (build-system meson-build-system)
    (arguments
     `(#:configure-flags '("-Dinstalled_tests=false")
@@ -495,16 +495,7 @@ highlighting and other features typical of a source code editor.")
             '((replace 'check
               (lambda _
                 (invoke "meson" "test" "--timeout-multiplier" "5"))))
-            '())
+            '()))))
-        (add-before 'configure 'aid-install-script
-          (lambda* (#:key outputs #:allow-other-keys)
-            ;; "build-aux/post-install.sh" invokes `gdk-pixbuf-query-loaders`
-            ;; for updating loader.cache, but it's not on PATH.  Make it use
-            ;; the one we're installing.  XXX: Won't work when cross-compiling.
-            (substitute* "build-aux/post-install.sh"
-              (("gdk-pixbuf-query-loaders" match)
-               (string-append (assoc-ref outputs "out") "/bin/" match)))
-            #t)))))
    (propagated-inputs
     `(;; Required by gdk-pixbuf-2.0.pc
       ("glib" ,glib)
@@ -731,7 +722,7 @@ application suites.")
 (define-public gtk+
   (package (inherit gtk+-2)
    (name "gtk+")
-   (version "3.24.10")
+   (version "3.24.12")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnome/sources/" name "/"
@@ -739,7 +730,7 @@ application suites.")
                                 name "-" version ".tar.xz"))
             (sha256
              (base32
-              "00qvq1r96ikdalv7xzgng1kad9i0rcahqk01gwhxl3xrw83z3a1m"))
+              "10xyyhlfb0yk4hglngxh2zsv9xrxkqv343df8h01dvagc6jyp10k"))
             (patches (search-patches "gtk3-respect-GUIX_GTK3_PATH.patch"
                                      "gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch"))))
    (outputs '("out" "bin" "doc"))
@@ -753,6 +744,7 @@ application suites.")
       ("libxinerama" ,libxinerama)
       ("libxkbcommon" ,libxkbcommon)
       ("libxdamage" ,libxdamage)
+      ("libxrandr" ,libxrandr)
       ("mesa" ,mesa)
       ("pango" ,pango)
       ("wayland" ,wayland)
@@ -1295,7 +1287,7 @@ write GNOME applications.")
 (define-public perl-cairo
   (package
     (name "perl-cairo")
-    (version "1.106")
+    (version "1.107")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1303,7 +1295,7 @@ write GNOME applications.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "1i25kks408c54k2zxskvg54l5k3qadzm8n72ffga9jy7ic0h6j76"))))
+                "0sg1gf1f2pjq7pji0zsv4rbi3bzpsx82z98k7yqxafzrvlkf27ay"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-extutils-depends" ,perl-extutils-depends)
@@ -1384,15 +1376,16 @@ and routines to assist in editing internationalized text.")
 (define-public girara
   (package
     (name "girara")
-    (version "0.3.2")
+    (version "0.3.3")
-    (source (origin
+    (source
-              (method url-fetch)
+     (origin
-              (uri
+       (method git-fetch)
-               (string-append "https://pwmt.org/projects/girara/download/girara-"
+       (uri (git-reference
-                              version ".tar.xz"))
+             (url "https://git.pwmt.org/pwmt/girara")
-              (sha256
+             (commit version)))
-               (base32
+       (file-name (git-file-name name version))
-                "1kc6n1mxjxa7wvwnqy94qfg8l9jvx9qrvrr2kc7m4g0z20x3a00p"))))
+       (sha256
+        (base32 "0q0yfv2777s72p473lw0ll435n7vz4v204cmp9naq8am7a6i6avn"))))
     (native-inputs `(("pkg-config" ,pkg-config)
                      ("check" ,check)
                      ("gettext" ,gettext-minimal)

gnu/packages/guile-xyz.scm

@@ -22,6 +22,7 @@
 ;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2019 swedebugia <swedebugia@riseup.net>
 ;;; Copyright © 2019 Amar Singh <nly@disroot.org>
+;;; Copyright © 2019 Timothy Sample <samplet@ngyro.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1921,17 +1922,22 @@ is no support for parsing block and inline level HTML.")
 (define-public mcron
   (package
     (name "mcron")
-    (version "1.1.2")
+    (version "1.1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/mcron/mcron-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "069m3ri7nc8lgy3h9ka7gj3v3anqj69x9jw4l3cfq65nqkxsch4g"))))
+                "00kv7fgllzjpis0g1m9csycp4f6l11774m09dqy255cvmim2g743"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'fix-finding-guile
+                    (lambda _
+                      (substitute* "configure"
+                        (("2\\.0") "2.2 2.0"))
+                      #t))
                   (add-before 'check 'adjust-tests
                     (lambda _
                       (substitute* "tests/job-specifier.scm"
@@ -1948,11 +1954,7 @@ is no support for parsing block and inline level HTML.")
                         (("\\(test-equal \"next-year\"" all)
                          (string-append "(test-skip 4)\n" all)))
                       #t)))))
-    (native-inputs `(("autoconf" ,autoconf)
+    (native-inputs `(("pkg-config" ,pkg-config)
-                     ("automake" ,automake)
-                     ("help2man" ,help2man)
-                     ("pkg-config" ,pkg-config)
-                     ("texinfo" ,texinfo)
                      ("tzdata" ,tzdata-for-tests)))
     (inputs `(("guile" ,guile-2.2)))
     (home-page "https://www.gnu.org/software/mcron/")
@@ -2253,22 +2255,32 @@ list of components.  This module takes care of that for you.")
 (define-public guile-gi
   (package
     (name "guile-gi")
-    (version "0.2.0")
+    (version "0.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://lonelycactus.com/tarball/guile_gi-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1n4pbrmbrjkrx826a4m31ag5c35rgkj1sirqh4qalk7gg67cfb41"))))
+                "1ah5bmkzplsmkrk7v9vlxlqch7i91qv4cq2d2nar9xshbpcrj484"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:configure-flags '("--with-gnu-filesystem-hierarchy")))
+     `(#:configure-flags '("--with-gnu-filesystem-hierarchy")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'start-xorg-server
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; The init_check test requires a running X server.
+             (system (format #f "~a/bin/Xvfb :1 &"
+                             (assoc-ref inputs "xorg-server")))
+             (setenv "DISPLAY" ":1")
+             #t)))))
     (native-inputs
      `(("gettext" ,gnu-gettext)
        ("glib:bin" ,glib "bin") ; for glib-compile-resources
        ("libtool" ,libtool)
-       ("pkg-config" ,pkg-config)))
+       ("pkg-config" ,pkg-config)
+       ("xorg-server" ,xorg-server)))
     (propagated-inputs
      `(("glib" ,glib)
        ("gobject-introspection" ,gobject-introspection)
@@ -2617,8 +2629,8 @@ clean and easy to use high level API.")
     (license license:gpl3+)))
 
 (define-public guile-ffi-fftw
-  (let ((commit "95d7ffb55860f3163c5283ecec1ef43bc3d174dd")
+  (let ((commit "294ad9e7491dcb40026d2fec9be2af05263be1c0")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "guile-ffi-fftw")
       (version (git-version "0" revision commit))
@@ -2630,7 +2642,7 @@ clean and easy to use high level API.")
                 (file-name (git-file-name "guile-ffi-fftw" version))
                 (sha256
                  (base32
-                  "0v9vk9cr4x9gn36lihi9gfkxyiqak0i598v5li6qw8bg95004p49"))))
+                  "08j40a5p6a8pgvhffmzb5rfdnrav2mksy3gfjkdqy93jfj1z5afg"))))
       (build-system guile-build-system)
       (arguments
        `(#:source-directory "mod"
@@ -2656,6 +2668,56 @@ library's ‘guru interface’.  It provides two functions: @code{fftw-dft! rank
 sign in out} and @code{fftw-dft rank sign in}.  These bindings being minimal,
 there is no support for computing & reusing plans, or split r/i transforms, or
 anything other than straight complex DFTs.")
-      ;; TODO: This might actually be LGPLv3+
+      (license license:lgpl3+))))
-      ;; See https://github.com/lloda/guile-ffi-fftw/issues/1
+
-      (license license:gpl3+))))
+(define-public srfi-64-driver
+  (package
+    (name "srfi-64-driver")
+    (version "0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://files.ngyro.com/srfi-64-driver/"
+                                  "srfi-64-driver-" version ".tar.gz"))
+              (sha256
+               (base32
+                "188b6mb7sjjg0a8zldikinglf40ky8mg8rwh5768gjmch6gkk3ph"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'build))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("guile" ,guile-2.2)))
+    (home-page "https://ngyro.com/software/srfi-64-driver.html")
+    (synopsis "Automake test driver for SRFI 64 test suites")
+    (description "This package provides an Automake test driver that can
+run SRFI 64 test suites.  It gives Automake insight into the individual
+tests being run, resulting clearer and more specific output.")
+    (license license:gpl3+)))
+
+(define-public guile-semver
+  (package
+    (name "guile-semver")
+    (version "0.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://files.ngyro.com/guile-semver/"
+                                  "guile-semver-" version ".tar.gz"))
+              (sha256
+               (base32
+                "06b66rj7nyhr6i3dpkwvfw1xb10w2pngrsw2hxfxkznwsbh9byfz"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("srfi-64-driver" ,srfi-64-driver)))
+    (inputs
+     `(("guile" ,guile-2.2)))
+    (home-page "https://ngyro.com/software/guile-semver.html")
+    (synopsis "Semantic Versioning (SemVer) for Guile")
+    (description "This Guile library provides tools for reading,
+comparing, and writing Semantic Versions.  It also includes ranges in
+the style of the Node Package Manager (NPM).")
+    (license license:gpl3+)))

gnu/packages/guile.scm

@@ -276,14 +276,14 @@ without requiring the source code to be rewritten.")
   (package
     (inherit guile-2.2)
     (name "guile-next")
-    (version "2.9.4")
+    (version "2.9.5")
     (source (origin
               (inherit (package-source guile-2.2))
               (uri (string-append "ftp://alpha.gnu.org/gnu/guile/guile-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "1milviqhipyfx400pqhngxpxyajalzwmp597dxn5514pkk0g7v0p"))))
+                "1db91mhvphzmiyw6f41ks9haysphygngv400ivgqf23lg22wn5zr"))))
     (native-search-paths
      (list (search-path-specification
             (variable "GUILE_LOAD_PATH")
@@ -543,7 +543,15 @@ Guile's foreign function interface.")
                 "1nv8j7wk6b5n4p22szyi8lv8fs31rrzxhzz16gyj8r38c1fyp9qp"))
               (file-name (string-append name "-" version "-checkout"))
               (patches
-               (search-patches "guile-sqlite3-fix-cross-compilation.patch"))))
+               (search-patches "guile-sqlite3-fix-cross-compilation.patch"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Allow builds with Guile 3.0.
+                  (substitute* "configure.ac"
+                    (("^GUILE_PKG.*")
+                     "GUILE_PKG([3.0 2.2 2.0])\n"))
+                  #t))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -561,6 +569,9 @@ Guile's foreign function interface.")
 (define-public guile2.0-sqlite3
   (package-for-guile-2.0 guile-sqlite3))
 
+(define-public guile3.0-sqlite3
+  (package-for-guile-3.0 guile-sqlite3))
+
 (define-public guile-bytestructures
   (package
     (name "guile-bytestructures")
@@ -607,7 +618,21 @@ type system, elevating types to first-class status.")
               (sha256
                (base32
                 "018hmfsh0rjwfvr4h7y10jc6k8a2k9xsirngghy3pjasin4nd2yz"))
-              (file-name (git-file-name name version))))
+              (file-name (git-file-name name version))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Allow builds with Guile 3.0.
+                  (substitute* "configure.ac"
+                    (("^GUILE_PKG.*")
+                     "GUILE_PKG([3.0 2.2 2.0])\n"))
+
+                  ;; The 'guile.m4' that's shipped is too old and fails to
+                  ;; recognize Guile 2.9/3.0.  Delete it and pick the one
+                  ;; provided by the Guile we're using.
+                  (delete-file "m4/guile.m4")
+
+                  #t))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -625,8 +650,19 @@ type system, elevating types to first-class status.")
 manipulate repositories of the Git version control system.")
     (license license:gpl3+)))
 
+(define-public guile3.0-git
+  (package-for-guile-3.0 guile-git))
+
 (define-public guile2.0-git
-  (package-for-guile-2.0 guile-git))
+  (let ((base (package-for-guile-2.0 guile-git)))
+    (package
+      (inherit base)
+      ;; Libgit2's Guile test driver requires (ice-9 textual-ports), which is
+      ;; not in Guile 2.0.  Thus, keep LIBGIT2 as-is here (i.e., built against
+      ;; Guile 2.2).
+      (inputs `(("libgit2" ,libgit2)
+                ,@(srfi-1:alist-delete "libgit2"
+                                       (package-inputs base)))))))
 
 ;;; guile.scm ends here
 

gnu/packages/haskell-apps.scm

@@ -49,10 +49,14 @@
   #:use-module (gnu packages rsync)
   #:use-module (gnu packages version-control))
 
+;; In Stackage LTS 14, this package is at 2.4.1.0.  However, that
+;; version requires version 2.4.1.0 of the 'Cabal' package, which is
+;; provided by GHC 8.6.5 at version 2.4.0.1.  Hence, we use an older
+;; version to match the compiler's library.
 (define-public cabal-install
  (package
   (name "cabal-install")
-   (version "2.2.0.0")
+   (version "2.4.0.0")
    (source
     (origin
      (method url-fetch)
@@ -61,9 +65,19 @@
             version
             ".tar.gz"))
       (sha256
-       (base32 "1nd3ch7qr4dpfxhgkcq2lnhvszx2kjgnn1kwb44vk9y5jgfs4mn8"))))
+       (base32 "1xmyl0x8wqfrnray6ky5wy0g0samv4264fbdlzxhqsvk9dbfja8k"))))
-   (arguments `(#:tests? #f)) ; FIXME: testing libraries are missing.
    (build-system haskell-build-system)
+   (arguments
+    `(#:cabal-revision
+      ("2" "1xil5pim6j1ckqj61zz6l7xpfxxr3rkw2hvpws2f7pr9shk645dl")
+      #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "cabal-install.cabal"
+               (("zip-archive >= 0\\.3\\.2\\.5 && < 0\\.4,")
+                "zip-archive >= 0.3.2.5 && <= 0.4.1,"))
+             #t)))))
    (inputs
     `(("ghc-async" ,ghc-async)
       ("ghc-base16-bytestring" ,ghc-base16-bytestring)
@@ -78,6 +92,7 @@
       ("ghc-random" ,ghc-random)
       ("ghc-resolv" ,ghc-resolv)
       ("ghc-tar" ,ghc-tar)
+      ("ghc-zip-archive" ,ghc-zip-archive)
       ("ghc-zlib" ,ghc-zlib)))
    (home-page "https://www.haskell.org/cabal/")
    (synopsis "Command-line interface for Cabal and Hackage")
@@ -172,7 +187,9 @@ unlit literate code files; and an option to turn off macro-expansion.")
            #t))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags '("-fpkgconfig" "-fcurl" "-flibiconv" "-fthreaded"
+     `(#:cabal-revision
+       ("1" "0xl7j5cm704pbl2ms0dkydh7jvrz0ym76d725ifpg4h902m1zkhg")
+       #:configure-flags '("-fpkgconfig" "-fcurl" "-flibiconv" "-fthreaded"
                            "-fnetwork-uri" "-fhttp" "--flag=executable"
                            "--flag=library")
        #:phases
@@ -181,6 +198,12 @@ unlit literate code files; and an option to turn off macro-expansion.")
            (lambda _
              (substitute* "tests/issue538.sh"
                (("/bin/sh") (which "sh")))
+             #t))
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "darcs.cabal"
+               (("QuickCheck   >= 2\\.8\\.2 && < 2\\.13,")
+                "QuickCheck   >= 2.8.2 && < 2.14,"))
              #t)))))
     (inputs
      `(("ghc-cmdargs" ,ghc-cmdargs)
@@ -391,7 +414,7 @@ used to keep a folder in sync between computers.")
 (define-public hlint
   (package
     (name "hlint")
-    (version "2.1.10")
+    (version "2.1.26")
     (source
      (origin
        (method url-fetch)
@@ -400,7 +423,7 @@ used to keep a folder in sync between computers.")
              "/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "19as2m9g75cr6n1agzvsij0cvqhb0wbjlk31w4y5d5mns87dki0w"))))
+         "16zkkpbfrd69853cdqf597fva969lirfc86b039i9zd7ghlrcayc"))))
     (build-system haskell-build-system)
     (inputs
      `(("cpphs" ,cpphs)
@@ -416,6 +439,7 @@ used to keep a folder in sync between computers.")
        ("ghc-extra" ,ghc-extra)
        ("ghc-refact" ,ghc-refact)
        ("ghc-aeson" ,ghc-aeson)
+       ("ghc-lib-parser" ,ghc-lib-parser)
        ("hscolour" ,hscolour)))
     (home-page "http://community.haskell.org/~ndm/hlint/")
     (synopsis "Suggest improvements for Haskell source code")
@@ -427,7 +451,7 @@ unwanted suggestions, and to add your own custom suggestions.")
 (define-public hoogle
   (package
     (name "hoogle")
-    (version "5.0.17.3")
+    (version "5.0.17.11")
     (source
      (origin
        (method url-fetch)
@@ -437,18 +461,19 @@ unwanted suggestions, and to add your own custom suggestions.")
          version ".tar.gz"))
        (sha256
         (base32
-         "174gp41v0krzj37m75pnr3aawyhkbk2wq4q6zk2z3zh0avvvmgk6"))))
+         "1svp8z9pad8z2j386pr0dda0ds8ddxab0salnz4gm51q877w93p1"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-network-uri" ,ghc-network-uri)
+     `(("ghc-quickcheck" ,ghc-quickcheck)
-       ("ghc-network" ,ghc-network)
-       ("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-aeson" ,ghc-aeson)
+       ("ghc-blaze-html" ,ghc-blaze-html)
+       ("ghc-blaze-markup" ,ghc-blaze-markup)
        ("ghc-cmdargs" ,ghc-cmdargs)
        ("ghc-conduit" ,ghc-conduit)
        ("ghc-conduit-extra" ,ghc-conduit-extra)
        ("ghc-connection" ,ghc-connection)
        ("ghc-extra" ,ghc-extra)
+       ("ghc-foundation" ,ghc-foundation)
        ("ghc-old-locale" ,ghc-old-locale)
        ("ghc-haskell-src-exts" ,ghc-haskell-src-exts)
        ("ghc-http-conduit" ,ghc-http-conduit)
@@ -502,16 +527,16 @@ and mIRC chat codes.")
 (define-public kmonad
   (package
     (name "kmonad")
-    (version "0.2.0")
+    (version "0.3.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/david-janssen/kmonad.git")
-             (commit "06d7b8c709efa695be35df9bde91275cbb2ba099")))
+             (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1rjr4h5yq63x3kad6yn4p8v26389sd9dgr5n2w73s1chafapzwwd"))))
+        (base32 "1g40nkpldih6h1rlxjx5yf9iavr3qs1f2b6j0gd8135p5hkg8d8n"))))
     (build-system haskell-build-system)
     (arguments
      `(#:phases
@@ -543,7 +568,7 @@ and mIRC chat codes.")
        ("ghc-exceptions" ,ghc-exceptions)
        ("ghc-hashable" ,ghc-hashable)
        ("ghc-lens" ,ghc-lens)
-       ("ghc-megaparsec" ,ghc-megaparsec-7)
+       ("ghc-megaparsec" ,ghc-megaparsec)
        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
        ("ghc-unagi-chan" ,ghc-unagi-chan)
        ("ghc-unliftio" ,ghc-unliftio)

gnu/packages/haskell-check.scm

@@ -10,6 +10,7 @@
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Tonton <tonton@riseup.net>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2019 Timothy Sample <samplet@ngyro.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -39,7 +40,7 @@
 (define-public ghc-tasty-ant-xml
   (package
     (name "ghc-tasty-ant-xml")
-    (version "1.1.4")
+    (version "1.1.6")
     (source
      (origin
        (method url-fetch)
@@ -49,7 +50,7 @@
              ".tar.gz"))
        (sha256
         (base32
-         "0v0gsb90kh6hwlgxbclzawsskywc6yf7n8xhiifia97l4y0yx2m8"))))
+         "13qqpl1prr9dda87dp45mqybay24n8rhxxgvpc9j34kh72g8j5qw"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-generic-deriving" ,ghc-generic-deriving)
@@ -95,7 +96,7 @@ Haskell test framework.")
 (define-public ghc-tasty-quickcheck
   (package
     (name "ghc-tasty-quickcheck")
-    (version "0.10")
+    (version "0.10.1")
     (source
      (origin
        (method url-fetch)
@@ -104,7 +105,7 @@ Haskell test framework.")
              "tasty-quickcheck-" version ".tar.gz"))
        (sha256
         (base32
-         "0vr6szbbz3s5461i0zr8zpq347zfvidfzv5gf3xwxhm0yk731z8h"))))
+         "0k4vvd5vmrncv1s6gdf03l4xijwlk428sb9jfx8n1zaz02971msh"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)
@@ -156,7 +157,7 @@ contains the correct result for the test.")
 (define-public ghc-tasty
   (package
     (name "ghc-tasty")
-    (version "1.1.0.3")
+    (version "1.2.3")
     (source
      (origin
        (method url-fetch)
@@ -166,7 +167,7 @@ contains the correct result for the test.")
              ".tar.gz"))
        (sha256
         (base32
-         "14riid753hjqr6lca1kgxpnvq0wykf0k3qc5jpag42hh8bszav22"))))
+         "0qpn0avpw4w1qq5r2gwh2piipj0llqq6ylagr3xnqiraq6mhg8cc"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-tagged" ,ghc-tagged)
@@ -184,10 +185,40 @@ you combine your unit tests, golden tests, QuickCheck/SmallCheck properties,
 and any other types of tests into a single test suite.")
     (license license:expat)))
 
+(define-public ghc-tasty-hedgehog
+  (package
+    (name "ghc-tasty-hedgehog")
+    (version "1.0.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "tasty-hedgehog/tasty-hedgehog-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1mbg5q0c0xfrk4npfj60pi693igb7r5l78x6xf9fk2jglw0nmxhz"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-tagged" ,ghc-tagged)
+       ("ghc-tasty" ,ghc-tasty)
+       ("ghc-hedgehog" ,ghc-hedgehog)))
+    (native-inputs
+     `(("ghc-tasty-expected-failure" ,ghc-tasty-expected-failure)))
+    (arguments
+     `(#:cabal-revision
+       ("1" "1n6797fm8swyrk8cw7zxz593gq82wx8dayvm204rmgcz75bslcpn")))
+    (home-page "https://github.com/qfpl/tasty-hedgehog")
+    (synopsis "Integration for tasty and hedgehog")
+    (description "This package provides the means for integrating the
+@url{https://hackage.haskell.org/package/hedgehog, hedgehog testing library}
+with the @url{https://hackage.haskell.org/package/tasty, tasty testing
+framework}.")
+    (license license:bsd-3)))
+
 (define-public ghc-tasty-hunit
   (package
     (name "ghc-tasty-hunit")
-    (version "0.10.0.1")
+    (version "0.10.0.2")
     (source
      (origin
        (method url-fetch)
@@ -197,7 +228,7 @@ and any other types of tests into a single test suite.")
              ".tar.gz"))
        (sha256
         (base32
-         "0j3hgga6c3s8h5snzivb8a75h96207ia2rlbxzj07xbf4zpkp44g"))))
+         "1xvf5xs0r8xqkcg354klz4wyzwyzvinalyl6f4fnxwqmzrgch8s8"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-call-stack" ,ghc-call-stack-boot)
@@ -231,6 +262,31 @@ test framework.")
 tasty.")
     (license license:expat)))
 
+(define-public ghc-tasty-lua
+  (package
+    (name "ghc-tasty-lua")
+    (version "0.2.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "tasty-lua/tasty-lua-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0xlj36rrhkx312h7smx6ay20rhlhxvw2ma2ckdnzv1pvmdn6p5qx"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-file-embed" ,ghc-file-embed)
+       ("ghc-hslua" ,ghc-hslua)
+       ("ghc-tasty" ,ghc-tasty)))
+    (native-inputs
+     `(("ghc-tasty-hunit" ,ghc-tasty-hunit)))
+    (home-page "https://github.com/hslua/tasty-lua")
+    (synopsis "Write tests in Lua, integrate into tasty")
+    (description "This package gives users the ability to define tasty tests
+from Lua.")
+    (license license:expat)))
+
 (define-public ghc-tasty-th
   (package
     (name "ghc-tasty-th")
@@ -261,7 +317,7 @@ test-framework.")
 (define-public ghc-tasty-rerun
   (package
     (name "ghc-tasty-rerun")
-    (version "1.1.12")
+    (version "1.1.14")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -269,7 +325,7 @@ test-framework.")
                     "tasty-rerun-" version ".tar.gz"))
               (sha256
                (base32
-                "05lp4zy6lwd916snq6hs43848n62j9vdfl3s8sfivqydrax0vvd8"))))
+                "0s0zj8ds4g1w2cjzm2lh25ivg962jigqdrbj08v3dbz64lx4mlzr"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-optparse-applicative" ,ghc-optparse-applicative)
@@ -288,7 +344,7 @@ been added since previous test run.")
 (define-public ghc-tasty-expected-failure
   (package
     (name "ghc-tasty-expected-failure")
-    (version "0.11.1.1")
+    (version "0.11.1.2")
     (source
      (origin
        (method url-fetch)
@@ -297,7 +353,7 @@ been added since previous test run.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1i2s809m644b7hgiblqay9j364r3fjj1rwbrahsn1pgr5q6mr6ji"))))
+         "175gdk1mkslcwjxajkbl4zmaigzf8h4svzd7va5qb519y0dxk28n"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-tagged" ,ghc-tagged)
@@ -314,7 +370,7 @@ development.")
 (define-public ghc-quickcheck-instances
   (package
     (name "ghc-quickcheck-instances")
-    (version "0.3.18")
+    (version "0.3.22")
     (source
      (origin
        (method url-fetch)
@@ -324,11 +380,11 @@ development.")
              version ".tar.gz"))
        (sha256
         (base32
-         "1bh1pzz5fdcqvzdcirqxna6fnjms02min5md716299g5niz46w55"))))
+         "14asr9r7da3w7p4hjj51w2yb002nz8x0np8hdz9z4yjvi60vyrax"))))
     (build-system haskell-build-system)
     (arguments
      `(#:cabal-revision
-       ("1" "1sngfq3v71bvgjsl8cj5kh65m3fziwy8dkvwjzs0kxfrzr87faly")))
+       ("2" "1ia5fjhpg7rz793552v88gv2iqx7hl9mi2g09m0llasy1cpzc9jr")))
     (inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-base-compat" ,ghc-base-compat)
@@ -337,6 +393,7 @@ development.")
        ("ghc-old-time" ,ghc-old-time)
        ("ghc-scientific" ,ghc-scientific)
        ("ghc-tagged" ,ghc-tagged)
+       ("ghc-time-compat" ,ghc-time-compat)
        ("ghc-transformers-compat" ,ghc-transformers-compat)
        ("ghc-unordered-containers" ,ghc-unordered-containers)
        ("ghc-uuid-types" ,ghc-uuid-types)
@@ -397,7 +454,7 @@ use HUnit assertions as QuickCheck properties.")
 (define-public ghc-quickcheck
   (package
     (name "ghc-quickcheck")
-    (version "2.11.3")
+    (version "2.13.2")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -408,12 +465,13 @@ use HUnit assertions as QuickCheck properties.")
              ".tar.gz"))
        (sha256
         (base32
-         "0xhqk35fkzlbjcqbabg6962jkv8d688nzmz7ng4bm84x2d95d328"))))
+         "0426j43af8v3qmdjjqxivazsvr3a2brac8yw09vpgpjkb2m0nmkv"))))
     (build-system haskell-build-system)
     (arguments
      `(#:tests? #f))  ; FIXME: currently missing libraries used for tests.
     (inputs
      `(("ghc-random" ,ghc-random)
+       ("ghc-splitmix" ,ghc-splitmix-bootstrap)
        ("ghc-tf-random" ,ghc-tf-random)))
     (home-page "https://github.com/nick8325/quickcheck")
     (synopsis "Automatic testing of Haskell programs")
@@ -440,13 +498,8 @@ expressed in Haskell, using combinators defined in the QuickCheck library.")
     (build-system haskell-build-system)
     (arguments
      `(#:tests? #f  ; FIXME: Tests do not build.
-       #:phases
+       #:cabal-revision
-       (modify-phases %standard-phases
+       ("5" "18g92ajx3ghznd6k3ihj22ln29n676ailzwx3k0f1kj3bmpilnh6")))
-         (add-before 'configure 'update-constraints
-           (lambda _
-             (substitute* "test-framework.cabal"
-               (("QuickCheck     >= 2\\.3 && < 2\\.10")
-                "QuickCheck     >= 2.3 && < 2.12")))))))
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)
        ("ghc-quickcheck" ,ghc-quickcheck)))
@@ -500,7 +553,7 @@ reporting and test statistics output.")
 (define-public ghc-test-framework-quickcheck2
   (package
     (name "ghc-test-framework-quickcheck2")
-    (version "0.3.0.4")
+    (version "0.3.0.5")
     (source
      (origin
        (method url-fetch)
@@ -509,11 +562,11 @@ reporting and test statistics output.")
                            "test-framework-quickcheck2-" version ".tar.gz"))
        (sha256
         (base32
-         "0vj834337r6jzr3258cv68ly2sv5999mklpsrfngyk51kywsyqyp"))))
+         "0ngf9vvby4nrdf1i7dxf5m9jn0g2pkq32w48xdr92n9hxka7ixn9"))))
     (build-system haskell-build-system)
     (arguments
      `(#:cabal-revision
-       ("1" "147ngmfdkskyg7mwsp5w73a4dbx3rp5s38bci3z03kn1m093lxff")))
+       ("1" "1vmpk70h1594h9s216d3ngkb399fpny1d3sh4gg0vrc75p4as68d")))
     (inputs
      `(("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
        ("ghc-quickcheck" ,ghc-quickcheck)
@@ -588,7 +641,7 @@ JUnit tool for Java.")
 (define-public hspec-discover
   (package
     (name "hspec-discover")
-    (version "2.5.5")
+    (version "2.7.1")
     (source
      (origin
        (method url-fetch)
@@ -597,7 +650,7 @@ JUnit tool for Java.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "04aidzi91ccr9bygmfkjzshz34z9vh8wvqj4zinx2clxq6r7gqfz"))))
+         "0r47fm94wa6qrhp8cc1zzkjrxc32rnagfn9m9ga4dm6p6ydw4c8b"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)
@@ -611,7 +664,7 @@ runs Hspec tests.")
 (define-public ghc-hspec-core
   (package
     (name "ghc-hspec-core")
-    (version "2.5.5")
+    (version "2.7.1")
     (source
      (origin
        (method url-fetch)
@@ -619,19 +672,19 @@ runs Hspec tests.")
                            "hspec-core-" version ".tar.gz"))
        (sha256
         (base32
-         "1vfrqlpn32s9wiykmkxbnrnd5p56yznw20pf8fwzw78ar4wpz55x"))))
+         "08vk8588lap00hsln8zl64dazbb28lzk4b4h5vnm7xvhg7r21k1c"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: testing libraries are missing.
     (inputs
      `(("ghc-setenv" ,ghc-setenv)
        ("ghc-ansi-terminal" ,ghc-ansi-terminal)
-       ("ghc-async" ,ghc-async)
        ("ghc-clock" ,ghc-clock)
        ("ghc-quickcheck-io" ,ghc-quickcheck-io)
        ("ghc-hunit" ,ghc-hunit)
        ("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-hspec-expectations" ,ghc-hspec-expectations)
-       ("ghc-silently" ,ghc-silently)))
+       ("ghc-silently" ,ghc-silently)
+       ("ghc-tf-random" ,ghc-tf-random)))
     (home-page "https://hspec.github.io/")
     (synopsis "Testing framework for Haskell")
     (description "This library exposes internal types and functions that can
@@ -641,7 +694,7 @@ be used to extend Hspec's functionality.")
 (define-public ghc-hspec-meta
   (package
     (name "ghc-hspec-meta")
-    (version "2.4.6")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
@@ -649,13 +702,13 @@ be used to extend Hspec's functionality.")
                            "hspec-meta-" version ".tar.gz"))
        (sha256
         (base32
-         "0qmvk01n79j6skn79r6zalg2pd0x0nqqn9qn8mhg0pgyzcdnfc9b"))))
+         "1n1a4633wfivylglji8920f67mx7qz8j4q58n8p7dxk6yg4h3mz6"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-hunit" ,ghc-hunit)
        ("ghc-ansi-terminal" ,ghc-ansi-terminal)
-       ("ghc-async" ,ghc-async)
+       ("ghc-clock" ,ghc-clock)
        ("ghc-hspec-expectations" ,ghc-hspec-expectations)
        ("ghc-setenv" ,ghc-setenv)
        ("ghc-random" ,ghc-random)
@@ -669,7 +722,7 @@ used to test the in-development version of Hspec.")
 (define-public ghc-hspec
   (package
     (name "ghc-hspec")
-    (version "2.5.5")
+    (version "2.7.1")
     (source
      (origin
        (method url-fetch)
@@ -677,7 +730,7 @@ used to test the in-development version of Hspec.")
                            "hspec-" version ".tar.gz"))
        (sha256
         (base32
-         "1yv4k5b5kkig2q3waj28587sq28wms7wfav5a3lq4dra6jybimfm"))))
+         "1x8rcr7j1azcaw0fg1xzp8j0gr4ias36z09aj24i4xp8pnyfp341"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hspec-core" ,ghc-hspec-core)
@@ -696,7 +749,7 @@ Haskell, inspired by the Ruby library RSpec.")
 (define-public ghc-hspec-contrib
   (package
     (name "ghc-hspec-contrib")
-    (version "0.5.0")
+    (version "0.5.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -704,7 +757,7 @@ Haskell, inspired by the Ruby library RSpec.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "13579xdqwbsy8k0vxdcvgy932d4p76mij1rzkzbpqbspfn7399yv"))))
+                "0hhzxaa3fxz5mk5qcsrnfr98a7bn3szx2ydgr0x9mbqmm1jg06rc"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hspec-core" ,ghc-hspec-core)
@@ -798,7 +851,7 @@ implementations of cryptographic ciphers.")
 (define-public ghc-hedgehog
   (package
     (name "ghc-hedgehog")
-    (version "0.6.1")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
@@ -808,13 +861,14 @@ implementations of cryptographic ciphers.")
              ".tar.gz"))
        (sha256
         (base32
-         "0xz10ycdm5vk9nrcym1fi83k19frfwqz18bz8bnpzwvaj0j41yfj"))))
+         "1qc7hkqbnsk3f5r26wc35r3qiy941nmcxhfqgcq9027kw4gs0bi0"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-ansi-terminal" ,ghc-ansi-terminal)
        ("ghc-async" ,ghc-async)
        ("ghc-concurrent-output" ,ghc-concurrent-output)
        ("ghc-exceptions" ,ghc-exceptions)
+       ("ghc-fail" ,ghc-fail)
        ("ghc-lifted-async" ,ghc-lifted-async)
        ("ghc-mmorph" ,ghc-mmorph)
        ("ghc-monad-control" ,ghc-monad-control)
@@ -841,7 +895,7 @@ To get started quickly, see the examples:
 (define-public cabal-doctest
   (package
     (name "cabal-doctest")
-    (version "1.0.6")
+    (version "1.0.8")
     (source
      (origin
        (method url-fetch)
@@ -850,11 +904,8 @@ To get started quickly, see the examples:
                            version ".tar.gz"))
        (sha256
         (base32
-         "0bgd4jdmzxq5y465r4sf4jv2ix73yvblnr4c9wyazazafddamjny"))))
+         "03if74imlhhk7m56nci5f1wclniwqdmwl4hl177040j1gnlac9i0"))))
     (build-system haskell-build-system)
-    (arguments
-     `(#:cabal-revision
-       ("1" "1bk85avgc93yvcggwbk01fy8nvg6753wgmaanhkry0hz55h7mpld")))
     (home-page "https://github.com/phadej/cabal-doctest")
     (synopsis "Setup.hs helper for running doctests")
     (description
@@ -862,3 +913,53 @@ To get started quickly, see the examples:
 configuration.  This library provides the common bits for writing custom
 @file{Setup.hs} files.")
     (license license:bsd-3)))
+
+(define-public ghc-testing-type-modifiers
+  (package
+    (name "ghc-testing-type-modifiers")
+    (version "0.1.0.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://hackage.haskell.org/package/"
+                            "testing-type-modifiers/testing-type-modifiers-"
+                            version ".tar.gz"))
+        (sha256
+          (base32
+            "1wh2n95n39ivv6kbqn42vbzrj8zagsmk6f2al2qj40bg5kgdl2q5"))))
+    (build-system haskell-build-system)
+    (home-page "https://hackage.haskell.org/package/testing-type-modifiers")
+    (synopsis "Data type modifiers for property based testing")
+    (description "Property based testing libraries such as QuickCheck tend to
+include type modifiers.  Most of them are used to quantify over subsets of a
+type.  This library is intended to supply these modifiers to be used by
+testing libraries, in an effort to make properties more portable between
+testing frameworks.")
+    (license license:unlicense)))
+
+(define-public ghc-testing-feat
+  (package
+    (name "ghc-testing-feat")
+    (version "1.1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://hackage.haskell.org/package/"
+                            "testing-feat/testing-feat-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1v2qzzpf1s008g7q6q67glf7vbm1pkpq4rc3ii74f4g6vhfx610r"))))
+    (build-system haskell-build-system)
+    (inputs
+      `(("ghc-quickcheck" ,ghc-quickcheck)
+        ("ghc-size-based" ,ghc-size-based)
+        ("ghc-testing-type-modifiers" ,ghc-testing-type-modifiers)
+        ("ghc-semigroups" ,ghc-semigroups)))
+    (home-page "https://github.com/JonasDuregard/testing-feat")
+    (synopsis "Functional Enumeration of Algebraic Types")
+    (description "Feat (Functional Enumeration of Algebraic Types)
+provides enumerations as functions from natural numbers to
+values (similar to @code{toEnum} but for any algebraic data type).  This
+can be used for SmallCheck-style systematic testing, QuickCheck-style
+random testing, and hybrids of the two.")
+    (license license:bsd-3)))

gnu/packages/haskell-crypto.scm

@@ -36,7 +36,7 @@
 (define-public ghc-asn1-types
   (package
     (name "ghc-asn1-types")
-    (version "0.3.2")
+    (version "0.3.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -44,7 +44,7 @@
                                   version ".tar.gz"))
               (sha256
                (base32
-                "05vjchyqiy9n275cygffhn0ma7fz7jx52j0dcdm9qm8h9bziymqc"))))
+                "162lacdl9jr42pdhaj9hxqlba6hjxm6g866anna74q6v3cvw5ssp"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-memory" ,ghc-memory)
@@ -59,7 +59,7 @@ format.")
 (define-public ghc-asn1-encoding
   (package
     (name "ghc-asn1-encoding")
-    (version "0.9.5")
+    (version "0.9.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -67,7 +67,7 @@ format.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0adgbamyq0mj1l1hdq4zyyllay714bac1wl0rih3fv1z6vykp1hy"))))
+                "02nsr30h5yic1mk7znf0q4z3n560ip017n60hg7ya25rsfmxxy6r"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hourglass" ,ghc-hourglass)
@@ -85,7 +85,7 @@ supports for high level forms of ASN1 (BER, and DER).")
 (define-public ghc-asn1-parse
   (package
     (name "ghc-asn1-parse")
-    (version "0.9.4")
+    (version "0.9.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -93,7 +93,7 @@ supports for high level forms of ASN1 (BER, and DER).")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "025prsihk5g6rdv9xlfmj0zpa0wa3qjzj5i4ilzvg7f6f3sji8y6"))))
+                "17pk8y3nwv9b9i5j15qlmwi7fmq9ab2z4kfpjk2rvcrh9lsf27wg"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-asn1-types" ,ghc-asn1-types)
@@ -212,7 +212,7 @@ that hides the C implementation.")
     (build-system haskell-build-system)
     (arguments
      `(#:cabal-revision
-       ("2" "0vyb9cfvpfxpslxvvhd48gw37i9g8ry5x63xwxd9q7xfiqhs7p3a")
+       ("4" "0gzaibjkipijwj9m9l6wrhfk5s3kdvfbhdl7cl1373cjfs41v0m3")
        #:tests? #f)) ; tests require old version of ghc-hunit (0.9)
     (native-inputs `(("ghc-base16-bytestring" ,ghc-base16-bytestring)
                      ("ghc-puremd5" ,ghc-puremd5)
@@ -240,7 +240,7 @@ that hides the C implementation.")
     (build-system haskell-build-system)
     (arguments
      `(#:cabal-revision
-       ("2" "0xas0nbq9bfdzlj6k565ibizv1cqvzfzsdj6q9pdiiwyxqblqc3m")
+       ("4" "0qb2wasfc4dpf6f9ahvhlv8njb3p3p9iwblg4032ssi95cg85718")
        #:tests? #f)) ; tests require old version of ghc-hunit (0.9)
     (native-inputs `(("ghc-base16-bytestring" ,ghc-base16-bytestring)
                      ("ghc-sha" ,ghc-sha)
@@ -274,7 +274,7 @@ the C implementation.")
     (build-system haskell-build-system)
     (arguments
      `(#:cabal-revision
-       ("1" "19birnmwga1yh82l4jqc3fygqkqcf5y8dlldnxfswngkzc3rvwp3")
+       ("3" "1arhz4y792kx439s2zv9x291gvvl2zxcfx9sq0nxsjlz7c3hpyp1")
        #:tests? #f)) ; tests require old version of ghc-hunit (0.9)
     (inputs
      `(("ghc-base16-bytestring" ,ghc-base16-bytestring)))
@@ -358,7 +358,7 @@ are implemented as FFI bindings to efficient code from zlib.")
 (define-public ghc-entropy
   (package
     (name "ghc-entropy")
-    (version "0.4.1.4")
+    (version "0.4.1.5")
     (source
      (origin
        (method url-fetch)
@@ -366,7 +366,7 @@ are implemented as FFI bindings to efficient code from zlib.")
                            "entropy-" version "/"
                            "entropy-" version ".tar.gz"))
        (sha256
-        (base32 "1fgf47l9klwn1xssbcbq6by651vikd8hlfxhiwd5bqzxr1jnlgrf"))))
+        (base32 "0szf8hi1pi8g0kxnkcymh65gk1b0niyl1nnkckzdqyar87qal0jm"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/TomMD/entropy")
     (synopsis "Provides platform independent entropy source for Haskell")
@@ -780,7 +780,7 @@ extensions.")
 (define-public ghc-hsopenssl
   (package
     (name "ghc-hsopenssl")
-    (version "0.11.4.15")
+    (version "0.11.4.17")
     (source
      (origin
        (method url-fetch)
@@ -788,14 +788,11 @@ extensions.")
                            "HsOpenSSL/HsOpenSSL-" version ".tar.gz"))
        (sha256
         (base32
-         "0idmak6d8mpbxphyq9hkxkmby2wnzhc1phywlgm0zw6q47pwxgff"))))
+         "0qivl9clmybfglwxqp2sq308rv4ia4rhwshcsc8b029bvpp0mpsi"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-network" ,ghc-network)
        ("openssl" ,openssl)))
-    (arguments
-     `(#:cabal-revision
-       ("1" "0bkcw2pjfgv1bhgkrpncvwq9czfr7cr4ak14n0v8c2y33i33wk5z")))
     (home-page "https://github.com/vshabanov/HsOpenSSL")
     (synopsis "Partial OpenSSL binding for Haskell")
     (description "HsOpenSSL is an OpenSSL binding for Haskell.  It can
@@ -811,7 +808,7 @@ implementation of SSL.")
 (define-public ghc-openssl-streams
   (package
     (name "ghc-openssl-streams")
-    (version "1.2.1.3")
+    (version "1.2.2.0")
     (source
      (origin
        (method url-fetch)
@@ -820,7 +817,7 @@ implementation of SSL.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0pwghr7ygv59k572xsj1j97rilkbjz66qaiyj0ra2wfg6pl70wfw"))))
+         "0rplym6ayydkpr7x9mw3l13p0vzzfzzxw244d7sd3jcvaxpv0rmr"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hsopenssl" ,ghc-hsopenssl)
@@ -830,9 +827,6 @@ implementation of SSL.")
      `(("ghc-hunit" ,ghc-hunit)
        ("ghc-test-framework" ,ghc-test-framework)
        ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))
-    (arguments
-     `(#:cabal-revision
-       ("2" "1004kgdryflpkp19dv4ikilhcn0xbfc5dsp6v3ib34580pcfj7wy")))
     (home-page "http://hackage.haskell.org/package/openssl-streams")
     (synopsis "OpenSSL network support for io-streams")
     (description "This library contains io-streams routines for secure

gnu/packages/haskell-web.scm

@@ -39,7 +39,7 @@
 (define-public ghc-tagsoup
   (package
     (name "ghc-tagsoup")
-    (version "0.14.6")
+    (version "0.14.8")
     (source
      (origin
        (method url-fetch)
@@ -47,7 +47,7 @@
                            "tagsoup-" version ".tar.gz"))
        (sha256
         (base32
-         "1yv3dbyb0i1yqm796jgc4jj5kxkla1sxb3b2klw5ks182kdx8kjb"))))
+         "1m9sx6gr9y9yxvkmcap8xsks8cnhznvma1mrfl39zljkv005azms"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)))
@@ -95,7 +95,7 @@ for screen-scraping.")
 (define-public ghc-httpd-shed
   (package
     (name "ghc-httpd-shed")
-    (version "0.4.0.3")
+    (version "0.4.1.1")
     (source
      (origin
        (method url-fetch)
@@ -103,10 +103,11 @@ for screen-scraping.")
                            "httpd-shed-" version ".tar.gz"))
        (sha256
         (base32
-         "064jy1mqhnf1hvq6s04wlhmp916rd522x58djb9qixv13vc8gzxh"))))
+         "19dgdimpzr7pxk7pqvyin6j87gmvnf0rm35gzhmna8qr835wy3sr"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-network-uri" ,ghc-network-uri)
+     `(("ghc-network-bsd" ,ghc-network-bsd)
+       ("ghc-network-uri" ,ghc-network-uri)
        ("ghc-network" ,ghc-network)))
     (home-page "https://hackage.haskell.org/package/httpd-shed")
     (synopsis "Simple web-server with an interact style API")
@@ -146,7 +147,7 @@ both client and server code).")
 (define-public ghc-http
   (package
     (name "ghc-http")
-    (version "4000.3.12")
+    (version "4000.3.14")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -155,7 +156,7 @@ both client and server code).")
                            "HTTP-" version ".tar.gz"))
        (sha256
         (base32
-         "140r6qy1ay25piv0z3hih11zhigyi08nkwc32097j43pjff6mzx3"))))
+         "0yv8mbjicpl7l2017c4dhm49117lblgwpy1llv368wci1vrxf0m6"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-httpd-shed" ,ghc-httpd-shed)
@@ -185,7 +186,7 @@ responses coming back.")
 (define-public ghc-http-client
   (package
     (name "ghc-http-client")
-    (version "0.5.13.1")
+    (version "0.6.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -193,7 +194,7 @@ responses coming back.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0szwbgvkkdz56lgi91armkagmb7nnfwbpp4j7cm9zhmffv3ba8g1"))))
+                "1n9rnbp8lwkd4whi2anniywi4y1bn9kx6nzfigfvz28d7pn7i4in"))))
     (build-system haskell-build-system)
     ;; Tests require access to the web.
     (arguments `(#:tests? #f))
@@ -285,7 +286,7 @@ Date in Haskell.")
 (define-public ghc-http2
   (package
     (name "ghc-http2")
-    (version "1.6.3")
+    (version "1.6.5")
     (source
      (origin
        (method url-fetch)
@@ -294,14 +295,14 @@ Date in Haskell.")
                            "http2-" version ".tar.gz"))
        (sha256
         (base32
-         "0hww0rfsv6lqx62qzycbcqy5q6rh9k09qkyjkdm5m1sp1z50wqk1"))))
+         "1vlmy8vnp6ml2n2pr11aa5fzigldsscgzmibrni64ykgfvpd3sqn"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-bytestring-builder" ,ghc-bytestring-builder)
+     `(("ghc-case-insensitive" ,ghc-case-insensitive)
-       ("ghc-case-insensitive" ,ghc-case-insensitive)
+       ("ghc-network-byte-order" ,ghc-network-byte-order)
        ("ghc-aeson" ,ghc-aeson)
        ("ghc-aeson-pretty" ,ghc-aeson-pretty)
-       ("ghc-hex" ,ghc-hex)
+       ("ghc-base16-bytestring" ,ghc-base16-bytestring)
        ("ghc-unordered-containers" ,ghc-unordered-containers)
        ("ghc-vector" ,ghc-vector)
        ("ghc-word8" ,ghc-word8)
@@ -320,7 +321,7 @@ and HPACK.  Currently HTTP/2 16 framing and HPACK 10 is supported.")
 (define-public ghc-http-conduit
   (package
     (name  "ghc-http-conduit")
-    (version "2.3.2")
+    (version "2.3.7.3")
     (source
      (origin
        (method url-fetch)
@@ -329,7 +330,7 @@ and HPACK.  Currently HTTP/2 16 framing and HPACK 10 is supported.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1iay4hr0mj8brkxvgkv1liqa8irl9axfc3qhn8qsvcyq4n1l95km"))))
+         "00rshi1y0h8y4rvsnnad0bppxgpvp40sk7lw1kxmdwy8pi8xrvbs"))))
     (build-system haskell-build-system)
     ;; FIXME: `httpLbs TLS` in test-suite `test` fails with
     ;; ConnectionFailure getProtocolByName: does not exist (no such protocol
@@ -379,7 +380,7 @@ which allow you to avoid direct usage of conduits.")
 (define-public ghc-wai
   (package
     (name "ghc-wai")
-    (version "3.2.1.2")
+    (version "3.2.2.1")
     (source
      (origin
        (method url-fetch)
@@ -389,7 +390,7 @@ which allow you to avoid direct usage of conduits.")
              ".tar.gz"))
        (sha256
         (base32
-         "0jr3b2789wa4m6mxkz12ynz4lfsqmgbrcy0am8karyqr3x3528r8"))))
+         "058871axlq6r0gcqxbjw37w57df9xbv81dmz99b1zq59wf329xzy"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-bytestring-builder" ,ghc-bytestring-builder)
@@ -413,7 +414,7 @@ communication between web applications and web servers.")
 (define-public ghc-wai-logger
   (package
     (name "ghc-wai-logger")
-    (version "2.3.2")
+    (version "2.3.5")
     (source
      (origin
        (method url-fetch)
@@ -423,7 +424,7 @@ communication between web applications and web servers.")
              ".tar.gz"))
        (sha256
         (base32
-         "0w5ldq4gplc16zzk5ikmbbjw79imaqvw8p6lylaw3hlsbn3zzm4d"))))
+         "05gbipyw0672irynsc3wqvvgzqixhmq69ay2mxh2phb734r8bcmm"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: Tests cannot find libraries exported
                                ; by propagated-inputs.
@@ -446,7 +447,7 @@ communication between web applications and web servers.")
 (define-public ghc-wai-extra
   (package
     (name "ghc-wai-extra")
-    (version "3.0.24.2")
+    (version "3.0.28")
     (source
      (origin
        (method url-fetch)
@@ -456,13 +457,12 @@ communication between web applications and web servers.")
              ".tar.gz"))
        (sha256
         (base32
-         "07gcgq59dki5drkjci9ka34xjsy3bqilbsx0lsc4905w9jlyfbci"))))
+         "0iky7k4kirngvk1p2nz19zgzffb5hppfaxdjan80v06ikc8w1wm7"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-ansi-terminal" ,ghc-ansi-terminal)
        ("ghc-base64-bytestring" ,ghc-base64-bytestring)
        ("ghc-cookie" ,ghc-cookie)
-       ("ghc-blaze-builder" ,ghc-blaze-builder)
        ("ghc-network" ,ghc-network)
        ("ghc-lifted-base" ,ghc-lifted-base)
        ("ghc-streaming-commons" ,ghc-streaming-commons)
@@ -476,6 +476,7 @@ communication between web applications and web servers.")
        ("ghc-void" ,ghc-void)
        ("ghc-wai" ,ghc-wai)
        ("ghc-http-types" ,ghc-http-types)
+       ("ghc-http2" ,ghc-http2)
        ("ghc-case-insensitive" ,ghc-case-insensitive)
        ("ghc-data-default-class" ,ghc-data-default-class)
        ("ghc-unix-compat" ,ghc-unix-compat)
@@ -519,7 +520,7 @@ Haskell's Web Application Interface (WAI).")
 (define-public ghc-bsb-http-chunked
   (package
     (name "ghc-bsb-http-chunked")
-    (version "0.0.0.2")
+    (version "0.0.0.4")
     (source
      (origin
        (method url-fetch)
@@ -529,10 +530,21 @@ Haskell's Web Application Interface (WAI).")
              version ".tar.gz"))
        (sha256
         (base32
-         "1x6m6xkrcw6jiaig1bb2wb5pqyw31x8xr9k9pxgq2g3ng44pbjr8"))))
+         "0z0f18yc6zlwh29c6175ivfcin325lvi4irpvv0n3cmq7vi0k0ql"))))
     (build-system haskell-build-system)
-    (inputs
+    (arguments
-     `(("ghc-bytestring-builder" ,ghc-bytestring-builder)))
+     `(;; XXX: As of 0.0.4, one property test ("Identical output as Blaze")
+       ;; fails on i686-linux.
+       #:tests? ,(not (string-prefix? "i686" (or (%current-target-system)
+                                                 (%current-system))))))
+    (native-inputs
+     `(("ghc-attoparsec" ,ghc-attoparsec)
+       ("ghc-blaze-builder" ,ghc-blaze-builder)
+       ("ghc-hedgehog" ,ghc-hedgehog)
+       ("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-hedgehog" ,ghc-tasty-hedgehog)
+       ("ghc-tasty-hunit" ,ghc-tasty-hunit)
+       ("ghc-doctest" ,ghc-doctest)))
     (home-page "http://github.com/sjakobi/bsb-http-chunked")
     (synopsis "Chunked HTTP transfer encoding for bytestring builders")
     (description "This Haskell library contains functions for encoding
@@ -543,7 +555,7 @@ transfers.")
 (define-public ghc-warp
   (package
     (name "ghc-warp")
-    (version "3.2.27")
+    (version "3.2.28")
     (source
      (origin
        (method url-fetch)
@@ -551,7 +563,7 @@ transfers.")
                            "warp-" version "/" "warp-" version
                            ".tar.gz"))
        (sha256
-        (base32 "0p2w88q0zd55ms20qylipbi0qzbf324i9r8b9qqxyds5yc1anq76"))))
+        (base32 "0w2w3aiccpb2f8zssqiszcxzqdysihqi5xply23lwif5arz4saw7"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-async" ,ghc-async)
@@ -563,6 +575,7 @@ transfers.")
        ("ghc-iproute" ,ghc-iproute)
        ("ghc-network" ,ghc-network)
        ("ghc-streaming-commons" ,ghc-streaming-commons)
+       ("ghc-time-manager" ,ghc-time-manager)
        ("ghc-unix-compat" ,ghc-unix-compat)
        ("ghc-vault" ,ghc-vault)
        ("ghc-wai" ,ghc-wai)
@@ -589,7 +602,7 @@ based WAI (Web Application Interface in Haskell).")
 (define-public ghc-tls-session-manager
   (package
   (name "ghc-tls-session-manager")
-  (version "0.0.0.2")
+  (version "0.0.3")
   (source
     (origin
       (method url-fetch)
@@ -599,7 +612,7 @@ based WAI (Web Application Interface in Haskell).")
              version ".tar.gz"))
       (sha256
         (base32
-          "0rvmln545vghsx8zhxp44f0f6pzma8cylarmfhhysy55ipywr1n5"))))
+          "0k57flqp2b4bipafiyfipnqmdqv04ky39yr4s4s9sx577zz2j2yi"))))
   (build-system haskell-build-system)
   (inputs
     `(("ghc-auto-update" ,ghc-auto-update)
@@ -615,7 +628,7 @@ limitation, automatic pruning, energy saving and replay resistance.")
 (define-public ghc-warp-tls
   (package
     (name "ghc-warp-tls")
-    (version "3.2.4.3")
+    (version "3.2.8")
     (source
      (origin
        (method url-fetch)
@@ -624,7 +637,7 @@ limitation, automatic pruning, energy saving and replay resistance.")
                            "warp-tls-" version ".tar.gz"))
        (sha256
         (base32
-         "17gj295fr98l7mkz2gdz6kahdnmja0sql3kvy2zab6q168g53kc4"))))
+         "1z5jzl40x1gp249fk8h51gkw6m3hzxchm2bp3kbpqdgmw8r5im8y"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-cryptonite" ,ghc-cryptonite)
@@ -699,7 +712,7 @@ Haskell.")
 (define-public ghc-mime-types
   (package
     (name "ghc-mime-types")
-    (version "0.1.0.8")
+    (version "0.1.0.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -707,7 +720,7 @@ Haskell.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "14ccl2842ya17zyj0bpc7vzklbyqvvydpbypn69h2fmhgji192x8"))))
+                "1lkipa4v73z3l5lqs6sdhl898iq41kyxv2jb9agsajzgd58l6cha"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/yesodweb/wai")
     (synopsis "Basic MIME type handling types and functions")
@@ -741,7 +754,7 @@ documents.")
 (define-public ghc-blaze-html
   (package
     (name "ghc-blaze-html")
-    (version "0.9.1.1")
+    (version "0.9.1.2")
     (source
      (origin
        (method url-fetch)
@@ -750,7 +763,7 @@ documents.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "06xv8fqhclfjj61z74cgggn4lmx1s7diakxg84mnkgfvk11983pa"))))
+         "0k1r1hddjgqighazcazxrx6xfhvy2gm8il8l82ainv3cai13yl30"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-blaze-builder" ,ghc-blaze-builder)
@@ -769,7 +782,7 @@ documents.")
 (define-public ghc-aeson
   (package
     (name "ghc-aeson")
-    (version "1.3.1.1")
+    (version "1.4.5.0")
     (source
      (origin
        (method url-fetch)
@@ -779,7 +792,7 @@ documents.")
              ".tar.gz"))
        (sha256
         (base32
-         "1i1ig840fvsb1lnklcv32zsc0zscirc301lw1mpfxhc6h4pk0gw4"))))
+         "1jhabz1lbbv6yqxqiybifi86cb5xlsadrn368n5dd0wzzc7ja4iz"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: testing libraries are missing.
     (inputs
@@ -815,7 +828,7 @@ naming: in Greek mythology, Aeson was the father of Jason.)")
 (define-public ghc-aeson-pretty
   (package
     (name "ghc-aeson-pretty")
-    (version "0.8.7")
+    (version "0.8.8")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -823,7 +836,7 @@ naming: in Greek mythology, Aeson was the father of Jason.)")
                     version ".tar.gz"))
               (sha256
                (base32
-                "1m977gs0s9gf3lwzlbs5y7bl6ansc5pywmn2qjk09l5bwg2yrhf1"))))
+                "09n7gs91y1fbw6gjszrd2na3isnvk3y5rsi90lzjrwywnqfadkl1"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-aeson" ,ghc-aeson)
@@ -1011,7 +1024,7 @@ avoid any issues with characters.")
 (define-public ghc-yesod-core
   (package
     (name "ghc-yesod-core")
-    (version "1.6.6")
+    (version "1.6.16.1")
     (source
      (origin
        (method url-fetch)
@@ -1020,7 +1033,7 @@ avoid any issues with characters.")
                            "yesod-core-" version ".tar.gz"))
        (sha256
         (base32
-         "0xahf6m5c7mkl74p0gimy4wb5w4s3lh92wwxmk517fbq666c92kb"))))
+         "0a0yv7wkwvb0n6iia532y9nzrirgnm09pjc8hpm0lx4ff609pgd2"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-wai" ,ghc-wai)
               ("ghc-extra" ,ghc-extra)
@@ -1080,7 +1093,7 @@ functions, widgets, etc.")
 (define-public ghc-yesod-persistent
   (package
     (name "ghc-yesod-persistent")
-    (version "1.6.0")
+    (version "1.6.0.2")
     (source
      (origin
        (method url-fetch)
@@ -1089,7 +1102,7 @@ functions, widgets, etc.")
                            "yesod-persistent-" version ".tar.gz"))
        (sha256
         (base32
-         "1gd59xf7b6v3cald58mzwnfbdzjr49cz60rm4wc5w9pvfx12pgj2"))))
+         "17adw0aaj29ia7ii3jka301442860b5wvfrms079q973gzahz5fd"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: hspec-discover not available in PATH.
     (inputs `(("ghc-yesod-core" ,ghc-yesod-core)
@@ -1112,7 +1125,7 @@ from Yesod.")
 (define-public ghc-yesod-form
     (package
     (name "ghc-yesod-form")
-    (version "1.6.2")
+    (version "1.6.7")
     (source
       (origin
         (method url-fetch)
@@ -1122,7 +1135,7 @@ from Yesod.")
                ".tar.gz"))
         (sha256
           (base32
-            "1p1x1hffvarplc82ykdk7rm6p5isqgqf78bvxzpfhncxs4kwx057"))))
+            "0mny71dyp6cp5akyp5wvmrhmip5rkqi8ibdn3lipvmajx9h58r5d"))))
     (build-system haskell-build-system)
     (inputs
       `(("ghc-yesod-core" ,ghc-yesod-core)
@@ -1198,7 +1211,7 @@ whereas most of the core code lives in @code{ghc-yesod-core}.")
 (define-public ghc-hxt-charproperties
   (package
     (name "ghc-hxt-charproperties")
-    (version "9.2.0.1")
+    (version "9.4.0.0")
     (source
      (origin
        (method url-fetch)
@@ -1207,7 +1220,7 @@ whereas most of the core code lives in @code{ghc-yesod-core}.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1mml8wglvagqq891rchgli6r8rnkwrqhgsxfl6kb5403pzb18rp4"))))
+         "1bk88hj2pqlvcnyfncqyb9j7w9vvdxcq3cgr0w2l09c0abas23pm"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/UweSchmidt/hxt")
     (synopsis "Character properties and classes for XML and Unicode")
@@ -1273,7 +1286,7 @@ derivations of regular expressions.")
 (define-public ghc-hxt
   (package
     (name "ghc-hxt")
-    (version "9.3.1.16")
+    (version "9.3.1.18")
     (source
      (origin
        (method url-fetch)
@@ -1283,7 +1296,7 @@ derivations of regular expressions.")
              ".tar.gz"))
        (sha256
         (base32
-         "1qq3ykgn355rx242xjcbqqksgvwr6k2fdj5phw4iv28qqxff6m8d"))))
+         "0836k65px3w9c5h1h2bmzq5a7mp6ajxwvfg3pfr2kbxwkgc0j63j"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hxt-charproperties" ,ghc-hxt-charproperties)
@@ -1364,7 +1377,7 @@ deal with the result.")
 (define-public ghc-snap-core
   (package
     (name "ghc-snap-core")
-    (version "1.0.3.2")
+    (version "1.0.4.0")
     (source
      (origin
        (method url-fetch)
@@ -1372,7 +1385,7 @@ deal with the result.")
                            "snap-core/snap-core-" version ".tar.gz"))
        (sha256
         (base32
-         "136q7l4hd5yn5hb507q1ziqx124ma1lkzh5dx0n150p8dx3rhhsc"))))
+         "0dklxgrbqhnb6bc4ic358g4fyj11ywmjrkxxhqcjmci2hhpn00mr"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-old-locale" ,ghc-old-locale)
@@ -1400,9 +1413,6 @@ deal with the result.")
        ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
        ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
        ("ghc-zlib" ,ghc-zlib)))
-    (arguments
-     `(#:cabal-revision
-       ("3" "0wlhn33r7c9g7j23y006ddq9d87lkmianvvfrbl8jd8mvjvj2gfa")))
     (home-page "http://snapframework.com/")
     (synopsis "Haskell Web Framework (core interfaces and types)")
     (description "Snap is a simple and fast web development framework
@@ -1414,7 +1424,7 @@ contains the core definitions and types for the Snap framework.")
 (define-public ghc-snap-server
   (package
     (name "ghc-snap-server")
-    (version "1.1.0.0")
+    (version "1.1.1.1")
     (source
      (origin
        (method url-fetch)
@@ -1422,7 +1432,7 @@ contains the core definitions and types for the Snap framework.")
                            "snap-server/snap-server-" version ".tar.gz"))
        (sha256
         (base32
-         "0vvw9n8xs272qdlrf3dxhnva41zh3awi7pf022rrjj75lj8a77i4"))))
+         "0lw475wp0lnrbgc3jcfif3qjjc3pmrh2k74d8cgpnc1304g6a2s5"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-attoparsec" ,ghc-attoparsec)
@@ -1453,7 +1463,7 @@ contains the core definitions and types for the Snap framework.")
        ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
     (arguments
      `(#:cabal-revision
-       ("3" "0a9d3nqb5rvgm25nak68lp6yj9m6cwhbgdbg5l7ib5i2czcg7yjh")))
+       ("1" "094b7ll47lxd4lvr6kd59jyw0vz686gw5cx16w758d6fli0cy3x3")))
     (home-page "http://snapframework.com/")
     (synopsis "Web server for the Snap Framework")
     (description "Snap is a simple and fast web development framework

gnu/packages/haskell.scm

@@ -604,7 +604,7 @@ interactive environment for the functional language Haskell.")
                                 (file-pattern ".*\\.conf\\.d$")
                                 (file-type 'directory))))))
 
-(define-public ghc-8 ghc-8.4)
+(define-public ghc-8 ghc-8.6)
 
 (define-public ghc ghc-8)
 

gnu/packages/idris.scm

@@ -70,8 +70,8 @@
        ("ghc-fsnotify" ,ghc-fsnotify)
        ("ghc-ieee754" ,ghc-ieee754)
        ("ghc-libffi" ,ghc-libffi)
-       ("ghc-megaparsec" ,ghc-megaparsec-7)
+       ("ghc-megaparsec" ,ghc-megaparsec)
-       ("ghc-network" ,ghc-network-2.8)
+       ("ghc-network" ,ghc-network)
        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
        ("ghc-regex-tdfa" ,ghc-regex-tdfa)
        ("ghc-safe" ,ghc-safe)
@@ -90,6 +90,11 @@
              "-fFFI" "-fGMP")
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'update-constraints
+           (lambda _
+             (substitute* "idris.cabal"
+               (("ansi-terminal < 0\\.9") "ansi-terminal < 0.10"))
+             #t))
          (add-before 'configure 'set-cc-command
            (lambda _
              (setenv "CC" "gcc")

gnu/packages/image-processing.scm

@@ -75,7 +75,7 @@
 (define-public dcmtk
   (package
     (name "dcmtk")
-    (version "3.6.4")
+    (version "3.6.5")
     (source
      (origin
        (method url-fetch)
@@ -84,7 +84,7 @@
                        "dcmtk" (string-join (string-split version #\.) "")
                        "/dcmtk-" version ".tar.gz"))
        (sha256
-        (base32 "1h22z8g0kmvhg8lgkbikyzyphhvxvq6018a00yd6i4g0z9ag6gx9"))))
+        (base32 "1fdyz5wwjp4grys61mxb2ia9fi6i3ax6s43l16xnv291bxk7hld0"))))
     (build-system cmake-build-system)
     (inputs
      `(;; Our ICU is too recent: “error: ‘UChar’ does not name a type“.
@@ -373,7 +373,7 @@ integrates with various databases on GUI toolkits such as Qt and Tk.")
              (zero? (system (format #f "~a/bin/Xvfb ~a &" xorg-server disp)))))))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("xorg-server" ,xorg-server) ; For running the tests
+       ("xorg-server" ,xorg-server-for-tests) ; For running the tests
        ("opencv-extra"
         ,(origin
            (method git-fetch)

gnu/packages/image-viewers.scm

@@ -11,6 +11,7 @@
 ;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2019 Guy Fleury Iteriteka <hoonandon@gmail.com>
+;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -64,7 +65,7 @@
 (define-public feh
   (package
     (name "feh")
-    (version "3.2.1")
+    (version "3.3")
     (home-page "https://feh.finalrewind.org/")
     (source (origin
               (method url-fetch)
@@ -72,7 +73,7 @@
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "070axq8jpibcabmjfv4fmjmpk3k349vzvh4qhsi4n62bkcwl35wg"))))
+                "04c8cgwzkax481sz7lbzy23mk79bqmjy3qpvr7vxa4c14mc9k5gk"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases (delete 'configure))

gnu/packages/image.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2015 Amirouche Boubekki <amirouche@hypermove.net>
 ;;; Copyright © 2014, 2017 John Darrington <jmd@gnu.org>
 ;;; Copyright © 2016, 2017, 2018 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016, 2017 Arun Isaac <arunisaac@systemreboot.net>
@@ -19,7 +19,7 @@
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
-;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018, 2019 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <contact@parouby.fr>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
@@ -51,8 +51,6 @@
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
-  ;; To provide gcc@5 and gcc@6, to work around <http://bugs.gnu.org/24703>.
-  #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages gl)
@@ -63,6 +61,8 @@
   #:use-module (gnu packages man)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mcrypt)
+  #:use-module (gnu packages mp3)
+  #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages photo)
   #:use-module (gnu packages pkg-config)
@@ -80,7 +80,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system python)
-  #:use-module (guix build-system r)
   #:use-module (guix build-system scons)
   #:use-module (srfi srfi-1))
 
@@ -298,7 +297,7 @@ Currently all documentation resides in @file{pnglite.h}.")
 (define-public libimagequant
   (package
     (name "libimagequant")
-    (version "2.12.3")
+    (version "2.12.5")
     (source
      (origin
        (method git-fetch)
@@ -307,17 +306,17 @@ Currently all documentation resides in @file{pnglite.h}.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0qsfq1kv1m5jzn9v9iz0bac66k4clcis1c9877qabnwzwmwma5v0"))))
+        (base32 "0cp68w04ja5pv77ssfafsn958w9hh9zb8crrlb5j3gsrcmdc032k"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:tests? #f)) ; no check target
+     '(#:tests? #f))                    ; no check target
     (home-page "https://pngquant.org/lib/")
     (synopsis "Image palette quantization library")
     (description "libimagequant is a small, portable C library for
 high-quality conversion of RGBA images to 8-bit indexed-color (palette)
 images.  This library can significantly reduces file sizes and powers pngquant
 and other PNG optimizers.")
-   (license license:gpl3+)))
+    (license license:gpl3+)))
 
 (define-public pngquant
   (package
@@ -853,7 +852,7 @@ compose, and analyze GIF images.")
 (define-public imlib2
   (package
     (name "imlib2")
-    (version "1.5.1")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -861,19 +860,21 @@ compose, and analyze GIF images.")
                     "/imlib2-" version ".tar.bz2"))
               (sha256
                (base32
-                "1bms2iwmvnvpz5jqq3r52glarqkafif47zbh1ykz8hw85d2mfkps"))))
+                "07b9v3ycwhici35fnczvpyjpgkc7gbcdhajpl9dwhpzdzbfl1i6g"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkgconfig" ,pkg-config)))
     (inputs
-     `(("libx11" ,libx11)
+     `(("bzip2" ,bzip2)
-       ("libxext" ,libxext)
        ("freetype" ,freetype)
+       ("giflib" ,giflib)
+       ("libid3tag" ,libid3tag)
        ("libjpeg" ,libjpeg)
        ("libpng" ,libpng)
        ("libtiff" ,libtiff)
-       ("giflib" ,giflib)
+       ("libx11" ,libx11)
-       ("bzip2" ,bzip2)))
+       ("libxext" ,libxext)
+       ("libwebp" ,libwebp)))
     (home-page "https://sourceforge.net/projects/enlightenment/")
     (synopsis
      "Loading, saving, rendering and manipulating image files")
@@ -1127,11 +1128,7 @@ language bindings to VIGRA.")
     (arguments
      '(#:configure-flags '("--enable-libwebpmux"
                            "--enable-libwebpdemux"
-                           "--enable-libwebpdecoder")
+                           "--enable-libwebpdecoder")))
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'bootstrap
-                    (lambda _
-                      (invoke "autoreconf" "-vif"))))))
     (home-page "https://developers.google.com/speed/webp/")
     (synopsis "Lossless and lossy image compression")
     (description
@@ -1490,6 +1487,7 @@ is hereby granted."))))
   (package
     (name "libjpeg-turbo")
     (version "2.0.2")
+    (replacement libjpeg-turbo/fixed)
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/libjpeg-turbo/"
@@ -1519,6 +1517,20 @@ and decompress to 32-bit and big-endian pixel buffers (RGBX, XBGR, etc.).")
                    license:ijg          ;the libjpeg library and associated tools
                    license:zlib))))     ;the libjpeg-turbo SIMD extensions
 
+;; Replacement package to fix CVE-2019-13960 and CVE-2019-2201.
+(define libjpeg-turbo/fixed
+  (package
+    (inherit libjpeg-turbo)
+    (version "2.0.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/libjpeg-turbo/"
+                                  version "/libjpeg-turbo-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1ds16bnj17v6hzd43w8pzijz3imd9am4hw75ir0fxm240m8dwij2"))
+              (patches (search-patches "libjpeg-turbo-CVE-2019-2201.patch"))))))
+
 (define-public niftilib
   (package
     (name "niftilib")
@@ -1668,26 +1680,6 @@ Features:
 @end itemize\n")
     (license license:gpl3+)))
 
-(define-public r-jpeg
-  (package
-   (name "r-jpeg")
-   (version "0.1-8.1")
-   (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "jpeg" version))
-       (sha256
-        (base32
-         "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
-   (build-system r-build-system)
-   (inputs `(("libjpeg" ,libjpeg)))
-   (home-page "http://www.rforge.net/jpeg/")
-   (synopsis "Read and write JPEG images with R")
-   (description "This package provides a way to read, write and display bitmap
-images stored in the JPEG format with R.  It can read and write both files and
-in-memory raw vectors.")
-   (license license:gpl2+)))
-
 (define-public gifsicle
   (package
    (name "gifsicle")
@@ -1734,28 +1726,24 @@ lightweight animated-GIF viewer, and @command{gifdiff} compares two GIFs for
 identical visual appearance.")
    (license license:gpl2+)))
 
+;; 1.0.7 is buggy and reverted in git repository.
 (define-public jp2a
   (package
     (name "jp2a")
-    (version "1.0.7")
+    (version "1.0.6")
     (source
      (origin
-       (method git-fetch)
+       (method url-fetch)
-       (uri (git-reference
+       (uri (string-append "mirror://debian/pool/main/j/jp2a/jp2a_"
-             (url "https://github.com/cslarsen/jp2a.git")
+                           version ".orig.tar.gz"))
-             (commit (string-append "v" version))))
+        (sha256
-       (file-name (git-file-name name version))
+         (base32
-       (sha256
+          "076frk3pa16s4r1b10zgy81vdlz0385zh3ykbnkaij25jn5aqc09"))))
-        (base32
-         "12a1z9ba2j16y67f41y8ax5sgv1wdjd71pg7circdxkj263n78ql"))))
     (build-system gnu-build-system)
     (inputs
-     `(("libjpeg" ,libjpeg)
+     `(("curl" ,curl)
-       ("curl" ,curl)))
+       ("libjpeg" ,libjpeg)
-    (native-inputs
+       ("ncurses" ,ncurses)))
-     `(("autoconf" ,autoconf)
-       ("automake" ,automake)
-       ("pkg-config" ,pkg-config)))
     (home-page "https://csl.name/jp2a/")
     (synopsis "Convert JPEG images to ASCII")
     (description