From 8785bd7759df7ba9c199dcdf398edd922866e3df Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Thu, 21 Dec 2017 22:12:00 +0100
Subject: doc: Document fixed-output derivations.

* doc/guix.texi (Derivations): Add paragraph on fixed-output
derivations.
---
 doc/guix.texi | 8 ++++++++
 1 file changed, 8 insertions(+)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index 6b6f8dedae..faad3ad6bb 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -4210,6 +4210,14 @@ paths}.  Derivations paths can be passed to the @code{build-derivations}
 procedure to perform the build actions they prescribe (@pxref{The
 Store}).
 
+@cindex fixed-output derivations
+Operations such as file downloads and version-control checkouts for
+which the expected content hash is known in advance are modeled as
+@dfn{fixed-output derivations}.  Unlike regular derivations, the outputs
+of a fixed-output derivation are independent of its inputs---e.g., a
+source code download produces the same result regardless of the download
+method and tools being used.
+
 The @code{(guix derivations)} module provides a representation of
 derivations as Scheme objects, along with procedures to create and
 otherwise manipulate derivations.  The lowest-level primitive to create
-- 
cgit 1.4.1


From 8faaf8d7cc466c8caa55905798c9ff9aaad9a1c9 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Wed, 20 Dec 2017 11:13:54 +0100
Subject: services: urandom-seed: Deprecate the 'urandom-seed-service'
 procedure.

* gnu/services/base.scm (urandom-seed-service-type)[default-value]: New
field.
(urandom-seed-service): Mark as deprecated.
(%base-services): Use URANDOM-SEED-SERVICE-TYPE directly.
* gnu/services/base.scm (%base-services):
* doc/guix.texi (Base Services): Document 'urandom-seed-service-type'
instead of 'urandom-seed-service'.
---
 doc/guix.texi         | 4 ++--
 gnu/services/base.scm | 5 +++--
 2 files changed, 5 insertions(+), 4 deletions(-)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index faad3ad6bb..94d4d8f92d 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -10031,12 +10031,12 @@ well as in the @var{groups} field of the @var{operating-system} record.
 @end example
 @end deffn
 
-@deffn {Scheme Procedure} urandom-seed-service
+@defvr {Scheme Variable} urandom-seed-service-type
 Save some entropy in @var{%random-seed-file} to seed @file{/dev/urandom}
 when rebooting.  It also tries to seed @file{/dev/urandom} from
 @file{/dev/hwrng} while booting, if @file{/dev/hwrng} exists and is
 readable.
-@end deffn
+@end defvr
 
 @defvr {Scheme Variable} %random-seed-file
 This is the name of the file where some random bytes are saved by
diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index 26525714a5..acc5c33f58 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -597,12 +597,13 @@ in KNOWN-MOUNT-POINTS when it is stopped."
                        ;; start until we have seeded the PRNG.
                        (service-extension user-processes-service-type
                                           (const '(urandom-seed)))))
+                (default-value #f)
                 (description
                  "Seed the @file{/dev/urandom} pseudo-random number
 generator (RNG) with the value recorded when the system was last shut
 down.")))
 
-(define (urandom-seed-service)
+(define (urandom-seed-service)                    ;deprecated
   (service urandom-seed-service-type #f))
 
 
@@ -1984,7 +1985,7 @@ This service is not part of @var{%base-services}."
                                           (ip "127.0.0.1")
                                           (provision '(loopback)))))
         (syslog-service)
-        (urandom-seed-service)
+        (service urandom-seed-service-type)
         (guix-service)
         (nscd-service)
 
-- 
cgit 1.4.1


From 3e30cdf1c35ebeb52630ec19b3b43b9e6d5ffb81 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Fri, 22 Dec 2017 23:40:57 +0100
Subject: guix build: Support '--with-source=PACKAGE@VERSION=URI'.

* guix/scripts/build.scm (numeric-extension?, tarball-base-name): New
procedures, formerly in 'package-with-source'.
(transform-package-source)[new-sources]: Look for '=' in URI.  Each
element of the list of now a (PKG VERSION SOURCE) tuple.
Pass VERSION to 'package-with-source'.
(package-with-source): Add 'version' parameter and honor it.
* tests/scripts-build.scm ("options->transformation, with-source, PKG=URI")
("options->transformation, with-source, PKG@VER=URI"): New tests.
* doc/guix.texi (Package Transformation Options): Document the new
forms.
---
 doc/guix.texi           | 16 +++++++---
 guix/scripts/build.scm  | 85 +++++++++++++++++++++++++++++++------------------
 tests/scripts-build.scm | 29 +++++++++++++++++
 3 files changed, 94 insertions(+), 36 deletions(-)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index 94d4d8f92d..4e83c76be7 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -5430,14 +5430,20 @@ without having to type in the definitions of package variants
 @table @code
 
 @item --with-source=@var{source}
-Use @var{source} as the source of the corresponding package.
+@itemx --with-source=@var{package}=@var{source}
+@itemx --with-source=@var{package}@@@var{version}=@var{source}
+Use @var{source} as the source of @var{package}, and @var{version} as
+its version number.
 @var{source} must be a file name or a URL, as for @command{guix
 download} (@pxref{Invoking guix download}).
 
-The ``corresponding package'' is taken to be the one specified on the
-command line the name of which matches the base of @var{source}---e.g.,
+When @var{package} is omitted,
+it is taken to be the package name specified on the
+command line that matches the base of @var{source}---e.g.,
 if @var{source} is @code{/src/guile-2.0.10.tar.gz}, the corresponding
-package is @code{guile}.  Likewise, the version string is inferred from
+package is @code{guile}.
+
+Likewise, when @var{version} is omitted, the version string is inferred from
 @var{source}; in the previous example, it is @code{2.0.10}.
 
 This option allows users to try out versions of packages other than the
@@ -5460,7 +5466,7 @@ guix build guile --with-source=../guile-2.0.9.219-e1bb7.tar.xz
 
 @example
 $ git clone git://git.sv.gnu.org/guix.git
-$ guix build guix --with-source=./guix
+$ guix build guix --with-source=guix@@1.0=./guix
 @end example
 
 @item --with-input=@var{package}=@var{replacement}
diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm
index 0571b874f1..57f2d82c5c 100644
--- a/guix/scripts/build.scm
+++ b/guix/scripts/build.scm
@@ -25,9 +25,12 @@
   #:use-module (guix packages)
   #:use-module (guix grafts)
 
+  #:use-module (guix utils)
+
   ;; Use the procedure that destructures "NAME-VERSION" forms.
-  #:use-module ((guix utils) #:hide (package-name->name+version))
-  #:use-module ((guix build utils) #:select (package-name->name+version))
+  #:use-module ((guix build utils)
+                #:select ((package-name->name+version
+                           . hyphen-package-name->name+version)))
 
   #:use-module (guix monads)
   #:use-module (guix gexp)
@@ -127,33 +130,37 @@ found.  Return #f if no build log was found."
 (define register-root*
   (store-lift register-root))
 
-(define (package-with-source store p uri)
+(define (numeric-extension? file-name)
+  "Return true if FILE-NAME ends with digits."
+  (string-every char-set:hex-digit (file-extension file-name)))
+
+(define (tarball-base-name file-name)
+  "Return the \"base\" of FILE-NAME, removing '.tar.gz' or similar
+extensions."
+  ;; TODO: Factorize.
+  (cond ((not (file-extension file-name))
+         file-name)
+        ((numeric-extension? file-name)
+         file-name)
+        ((string=? (file-extension file-name) "tar")
+         (file-sans-extension file-name))
+        ((file-extension file-name)
+         =>
+         (match-lambda
+           ("scm" file-name)
+           (else  (tarball-base-name (file-sans-extension file-name)))))
+        (else
+         file-name)))
+
+(define* (package-with-source store p uri #:optional version)
   "Return a package based on P but with its source taken from URI.  Extract
 the new package's version number from URI."
-  (define (numeric-extension? file-name)
-    ;; Return true if FILE-NAME ends with digits.
-    (string-every char-set:hex-digit (file-extension file-name)))
-
-  (define (tarball-base-name file-name)
-    ;; Return the "base" of FILE-NAME, removing '.tar.gz' or similar
-    ;; extensions.
-    ;; TODO: Factorize.
-    (cond ((not (file-extension file-name))
-           file-name)
-          ((numeric-extension? file-name)
-           file-name)
-          ((string=? (file-extension file-name) "tar")
-           (file-sans-extension file-name))
-          ((file-extension file-name)
-           (tarball-base-name (file-sans-extension file-name)))
-          (else
-           file-name)))
-
   (let ((base (tarball-base-name (basename uri))))
-    (let-values (((name version)
-                  (package-name->name+version base)))
+    (let-values (((_ version*)
+                  (hyphen-package-name->name+version base)))
       (package (inherit p)
-               (version (or version (package-version p)))
+               (version (or version version*
+                            (package-version p)))
 
                ;; Use #:recursive? #t to allow for directories.
                (source (download-to-store store uri
@@ -173,8 +180,23 @@ the new package's version number from URI."
 matching URIs given in SOURCES."
   (define new-sources
     (map (lambda (uri)
-           (cons (package-name->name+version (basename uri))
-                 uri))
+           (match (string-index uri #\=)
+             (#f
+              ;; Determine the package name and version from URI.
+              (call-with-values
+                  (lambda ()
+                    (hyphen-package-name->name+version
+                     (tarball-base-name (basename uri))))
+                (lambda (name version)
+                  (list name version uri))))
+             (index
+              ;; What's before INDEX is a "PKG@VER" or "PKG" spec.
+              (call-with-values
+                  (lambda ()
+                    (package-name->name+version (string-take uri index)))
+                (lambda (name version)
+                  (list name version
+                        (string-drop uri (+ 1 index))))))))
          sources))
 
   (lambda (store obj)
@@ -182,10 +204,11 @@ matching URIs given in SOURCES."
                (result   '()))
       (match obj
         ((? package? p)
-         (let ((source (assoc-ref sources (package-name p))))
-           (if source
-               (package-with-source store p source)
-               p)))
+         (match (assoc-ref sources (package-name p))
+           ((version source)
+            (package-with-source store p source version))
+           (#f
+            p)))
         (_
          obj)))))
 
diff --git a/tests/scripts-build.scm b/tests/scripts-build.scm
index a408ea6f8d..190426ed06 100644
--- a/tests/scripts-build.scm
+++ b/tests/scripts-build.scm
@@ -96,6 +96,35 @@
              (string-contains (get-output-string port)
                               "had no effect"))))))
 
+(test-assert "options->transformation, with-source, PKG=URI"
+  (let* ((p (dummy-package "foo"))
+         (s (search-path %load-path "guix.scm"))
+         (f (string-append "foo=" s))
+         (t (options->transformation `((with-source . ,f)))))
+    (with-store store
+      (let ((new (t store p)))
+        (and (not (eq? new p))
+             (string=? (package-name new) (package-name p))
+             (string=? (package-version new)
+                       (package-version p))
+             (string=? (package-source new)
+                       (add-to-store store (basename s) #t
+                                     "sha256" s)))))))
+
+(test-assert "options->transformation, with-source, PKG@VER=URI"
+  (let* ((p (dummy-package "foo"))
+         (s (search-path %load-path "guix.scm"))
+         (f (string-append "foo@42.0=" s))
+         (t (options->transformation `((with-source . ,f)))))
+    (with-store store
+      (let ((new (t store p)))
+        (and (not (eq? new p))
+             (string=? (package-name new) (package-name p))
+             (string=? (package-version new) "42.0")
+             (string=? (package-source new)
+                       (add-to-store store (basename s) #t
+                                     "sha256" s)))))))
+
 (test-assert "options->transformation, with-input"
   (let* ((p (dummy-package "guix.scm"
               (inputs `(("foo" ,(specification->package "coreutils"))
-- 
cgit 1.4.1


From fae7973e1f2eb1aba3f17c415b8886c4b00fd1a8 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Sat, 23 Dec 2017 00:04:06 +0100
Subject: doc: Add "/guix" after LOCALSTATEDIR.

Fixes <https://bugs.gnu.org/29813>.
Reported by Martin Castillo <castilma@uni-bremen.de>.

* doc/guix.texi (Invoking guix-daemon, Invoking guix package): Add
missing "/guix" after LOCALSTATEDIR.
---
 doc/guix.texi | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index 4e83c76be7..b8ace68ba7 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -1335,7 +1335,7 @@ using Unix-domain sockets along with SSH.
 
 When @code{--listen} is omitted, @command{guix-daemon} listens for
 connections on the Unix-domain socket located at
-@file{@var{localstatedir}/daemon-socket/socket}.
+@file{@var{localstatedir}/guix/daemon-socket/socket}.
 @end table
 
 
@@ -1711,7 +1711,7 @@ source "$HOME/.guix-profile/etc/profile"
 In a multi-user setup, user profiles are stored in a place registered as
 a @dfn{garbage-collector root}, which @file{$HOME/.guix-profile} points
 to (@pxref{Invoking guix gc}).  That directory is normally
-@code{@var{localstatedir}/profiles/per-user/@var{user}}, where
+@code{@var{localstatedir}/guix/profiles/per-user/@var{user}}, where
 @var{localstatedir} is the value passed to @code{configure} as
 @code{--localstatedir}, and @var{user} is the user name.  The
 @file{per-user} directory is created when @command{guix-daemon} is
-- 
cgit 1.4.1


From 28c03b4555e99da9524c697f5eba3783916050c7 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 23 Dec 2017 06:58:57 +0100
Subject: gnu: dovecot: Update to 2.3.0.

* gnu/packages/mail.scm (dovecot): Update to 2.3.0.
* gnu/services/mail.scm (dovecot-configuration)[director-doveadm-port]
[ssl-parameters-regenerate]: Delete fields.
[ssl-protocols]: Rename to...
[ssl-min-protocol]: ...this.
[mail-log-prefix, mdbox-rotate-size, ssl-cipher-list, imap-logout-format]:
Update default values.
* doc/guix.texi (Mail Services): Reflect the above changes to the service.
---
 doc/guix.texi         | 29 ++++++++---------------------
 gnu/packages/mail.scm |  4 ++--
 gnu/services/mail.scm | 30 ++++++++++--------------------
 3 files changed, 20 insertions(+), 43 deletions(-)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index b8ace68ba7..21b80a6e16 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -13072,13 +13072,6 @@ has any connections.
 Defaults to @samp{"15 min"}.
 @end deftypevr
 
-@deftypevr {@code{dovecot-configuration} parameter} non-negative-integer director-doveadm-port
-TCP/IP port that accepts doveadm connections (instead of director
-connections) If you enable this, you'll also need to add
-@samp{inet-listener} for the port.
-Defaults to @samp{0}.
-@end deftypevr
-
 @deftypevr {@code{dovecot-configuration} parameter} string director-username-hash
 How the username is translated before being hashed.  Useful values
 include %Ln if user can log in with or without @@domain, %Ld if mailboxes
@@ -13171,7 +13164,7 @@ Defaults to @samp{"%$: %s"}.
 @deftypevr {@code{dovecot-configuration} parameter} string mail-log-prefix
 Log prefix for mail processes.  See doc/wiki/Variables.txt for list
 of possible variables you can use.
-Defaults to @samp{"\"%s(%u): \""}.
+Defaults to @samp{"\"%s(%u)<%{pid}><%{session}>: \""}.
 @end deftypevr
 
 @deftypevr {@code{dovecot-configuration} parameter} string deliver-log-format
@@ -13516,7 +13509,7 @@ Defaults to @samp{0}.
 
 @deftypevr {@code{dovecot-configuration} parameter} non-negative-integer mdbox-rotate-size
 Maximum dbox file size until it's rotated.
-Defaults to @samp{2000000}.
+Defaults to @samp{10000000}.
 @end deftypevr
 
 @deftypevr {@code{dovecot-configuration} parameter} string mdbox-rotate-interval
@@ -13654,21 +13647,14 @@ x500UniqueIdentifier are the usual choices.  You'll also need to set
 Defaults to @samp{"commonName"}.
 @end deftypevr
 
-@deftypevr {@code{dovecot-configuration} parameter} hours ssl-parameters-regenerate
-How often to regenerate the SSL parameters file.  Generation is
-quite CPU intensive operation.  The value is in hours, 0 disables
-regeneration entirely.
-Defaults to @samp{168}.
-@end deftypevr
-
-@deftypevr {@code{dovecot-configuration} parameter} string ssl-protocols
-SSL protocols to use.
-Defaults to @samp{"!SSLv2"}.
+@deftypevr {@code{dovecot-configuration} parameter} string ssl-min-protocol
+Minimum SSL protocol version to accept.
+Defaults to @samp{"TLSv1"}.
 @end deftypevr
 
 @deftypevr {@code{dovecot-configuration} parameter} string ssl-cipher-list
 SSL ciphers to use.
-Defaults to @samp{"ALL:!LOW:!SSLv2:!EXP:!aNULL"}.
+Defaults to @samp{"ALL:!kRSA:!SRP:!kDHd:!DSS:!aNULL:!eNULL:!EXPORT:!DES:!3DES:!MD5:!PSK:!RC4:!ADH:!LOW@@STRENGTH"}.
 @end deftypevr
 
 @deftypevr {@code{dovecot-configuration} parameter} string ssl-crypto-device
@@ -13770,7 +13756,8 @@ total number of bytes read from client
 @item %o
 total number of bytes sent to client.
 @end table
-Defaults to @samp{"in=%i out=%o"}.
+See @file{doc/wiki/Variables.txt} for a list of all the variables you can use.
+Defaults to @samp{"in=%i out=%o deleted=%{deleted} expunged=%{expunged} trashed=%{trashed} hdr_count=%{fetch_hdr_count} hdr_bytes=%{fetch_hdr_bytes} body_count=%{fetch_body_count} body_bytes=%{fetch_body_bytes}"}.
 @end deftypevr
 
 @deftypevr {@code{dovecot-configuration} parameter} string imap-capability
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 6aedcf7c3a..3cfa7baebd 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -1137,7 +1137,7 @@ facilities for checking incoming mail.")
 (define-public dovecot
   (package
     (name "dovecot")
-    (version "2.2.33.2")
+    (version "2.3.0")
     (source
      (origin
        (method url-fetch)
@@ -1145,7 +1145,7 @@ facilities for checking incoming mail.")
                            (version-major+minor version) "/"
                            name "-" version ".tar.gz"))
        (sha256 (base32
-                "117f9i62liz2pm96zi2lpldzlj2knzj7g410zhifwmlsc1w3n7py"))))
+                "10c5myzgys866c3x6jdr1s9x9pqnjd5vpyz8z384sph21m3wnq6y"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
diff --git a/gnu/services/mail.scm b/gnu/services/mail.scm
index 6305f06f85..ab90942739 100644
--- a/gnu/services/mail.scm
+++ b/gnu/services/mail.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2015 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au>
+;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -745,12 +746,6 @@ allowed too, like 10.0.0.10-10.0.0.30.")
    "How long to redirect users to a specific server after it no longer
 has any connections.")
 
-  (director-doveadm-port
-   (non-negative-integer 0)
-   "TCP/IP port that accepts doveadm connections (instead of director
-connections) If you enable this, you'll also need to add
-@samp{inet-listener} for the port.")
-
   (director-username-hash
    (string "%Lu")
    "How the username is translated before being hashed.  Useful values
@@ -831,7 +826,7 @@ string.")
 string, %$ contains the data we want to log.")
 
   (mail-log-prefix
-   (string "\"%s(%u): \"")
+   (string "\"%s(%u)<%{pid}><%{session}>: \"")
    "Log prefix for mail processes.  See doc/wiki/Variables.txt for list
 of possible variables you can use.")
 
@@ -1145,7 +1140,7 @@ files.  If an index file already exists it's still read, just not
 updated.")
 
   (mdbox-rotate-size
-   (non-negative-integer #e2e6)
+   (non-negative-integer #e10e6)
    "Maximum dbox file size until it's rotated.")
 
   (mdbox-rotate-interval
@@ -1262,18 +1257,12 @@ it, set @samp{auth-ssl-require-client-cert? #t} in auth section.")
 x500UniqueIdentifier are the usual choices.  You'll also need to set
 @samp{auth-ssl-username-from-cert? #t}.")
 
-  (ssl-parameters-regenerate
-   (hours 168)
-   "How often to regenerate the SSL parameters file.  Generation is
-quite CPU intensive operation.  The value is in hours, 0 disables
-regeneration entirely.")
-
-  (ssl-protocols
-   (string "!SSLv2")
-   "SSL protocols to use.")
+  (ssl-min-protocol
+   (string "TLSv1")
+   "Minimum SSL protocol version to accept.")
 
   (ssl-cipher-list
-   (string "ALL:!LOW:!SSLv2:!EXP:!aNULL")
+   (string "ALL:!kRSA:!SRP:!kDHd:!DSS:!aNULL:!eNULL:!EXPORT:!DES:!3DES:!MD5:!PSK:!RC4:!ADH:!LOW@STRENGTH")
    "SSL ciphers to use.")
 
   (ssl-crypto-device
@@ -1356,14 +1345,15 @@ get \"Too long argument\" or \"IMAP command line too large\" errors
 often.")
 
   (imap-logout-format
-   (string "in=%i out=%o")
+   (string "in=%i out=%o deleted=%{deleted} expunged=%{expunged} trashed=%{trashed} hdr_count=%{fetch_hdr_count} hdr_bytes=%{fetch_hdr_bytes} body_count=%{fetch_body_count} body_bytes=%{fetch_body_bytes}")
    "IMAP logout format string:
 @table @code
 @item %i
 total number of bytes read from client
 @item %o
 total number of bytes sent to client.
-@end table")
+@end table
+See @file{doc/wiki/Variables.txt} for a list of all the variables you can use.")
 
   (imap-capability
    (string "")
-- 
cgit 1.4.1


From 90d8923bf92cab8696d8395ef68c98d9775b110c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 23 Dec 2017 15:39:33 +0100
Subject: doc: Properly escape brackets.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This fixes a build failure reported by Catonano <catonano@gmail.com>.

* doc/guix.texi (Mail Services): Escape ‘{’ and ‘}’ everywhere.
---
 doc/guix.texi | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index 21b80a6e16..8ecefa26e4 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -13164,7 +13164,7 @@ Defaults to @samp{"%$: %s"}.
 @deftypevr {@code{dovecot-configuration} parameter} string mail-log-prefix
 Log prefix for mail processes.  See doc/wiki/Variables.txt for list
 of possible variables you can use.
-Defaults to @samp{"\"%s(%u)<%{pid}><%{session}>: \""}.
+Defaults to @samp{"\"%s(%u)<%@{pid@}><%@{session@}>: \""}.
 @end deftypevr
 
 @deftypevr {@code{dovecot-configuration} parameter} string deliver-log-format
@@ -13757,7 +13757,7 @@ total number of bytes read from client
 total number of bytes sent to client.
 @end table
 See @file{doc/wiki/Variables.txt} for a list of all the variables you can use.
-Defaults to @samp{"in=%i out=%o deleted=%{deleted} expunged=%{expunged} trashed=%{trashed} hdr_count=%{fetch_hdr_count} hdr_bytes=%{fetch_hdr_bytes} body_count=%{fetch_body_count} body_bytes=%{fetch_body_bytes}"}.
+Defaults to @samp{"in=%i out=%o deleted=%@{deleted@} expunged=%@{expunged@} trashed=%@{trashed@} hdr_count=%@{fetch_hdr_count@} hdr_bytes=%@{fetch_hdr_bytes@} body_count=%@{fetch_body_count@} body_bytes=%@{fetch_body_bytes@}"}.
 @end deftypevr
 
 @deftypevr {@code{dovecot-configuration} parameter} string imap-capability
-- 
cgit 1.4.1


From 7459cb9305ff8ae7e72ca29aad0f8f8e1e807641 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 24 Dec 2017 00:51:08 +0100
Subject: services: messaging: Use HTTPS for prosody.im URLs.

* gnu/services/messaging.scm (prosody-configuration): Use HTTPS whenever
referring to prosody.im URLs in documentation.
* doc/guix.texi (Messaging Services): Likewise.
---
 doc/guix.texi              | 48 +++++++++++++++++++++++-----------------------
 gnu/services/messaging.scm | 46 ++++++++++++++++++++++----------------------
 2 files changed, 47 insertions(+), 47 deletions(-)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index 8ecefa26e4..7572ab8768 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -13956,7 +13956,7 @@ definitions for messaging services: currently only Prosody is supported.
 @subsubheading Prosody Service
 
 @deffn {Scheme Variable} prosody-service-type
-This is the type for the @uref{http://prosody.im, Prosody XMPP
+This is the type for the @uref{https://prosody.im, Prosody XMPP
 communication server}.  Its value must be a @code{prosody-configuration}
 record as in this example:
 
@@ -14021,13 +14021,13 @@ The Prosody package.
 
 @deftypevr {@code{prosody-configuration} parameter} file-name data-path
 Location of the Prosody data storage directory.  See
-@url{http://prosody.im/doc/configure}.
+@url{https://prosody.im/doc/configure}.
 Defaults to @samp{"/var/lib/prosody"}.
 @end deftypevr
 
 @deftypevr {@code{prosody-configuration} parameter} file-name-list plugin-paths
 Additional plugin directories.  They are searched in all the specified
-paths in order.  See @url{http://prosody.im/doc/plugins_directory}.
+paths in order.  See @url{https://prosody.im/doc/plugins_directory}.
 Defaults to @samp{()}.
 @end deftypevr
 
@@ -14040,15 +14040,15 @@ Defaults to @samp{"/etc/prosody/certs"}.
 
 @deftypevr {@code{prosody-configuration} parameter} string-list admins
 This is a list of accounts that are admins for the server.  Note that you
-must create the accounts separately.  See @url{http://prosody.im/doc/admins} and
-@url{http://prosody.im/doc/creating_accounts}.
+must create the accounts separately.  See @url{https://prosody.im/doc/admins} and
+@url{https://prosody.im/doc/creating_accounts}.
 Example: @code{(admins '("user1@@example.com" "user2@@example.net"))}
 Defaults to @samp{()}.
 @end deftypevr
 
 @deftypevr {@code{prosody-configuration} parameter} boolean use-libevent?
 Enable use of libevent for better performance under high load.  See
-@url{http://prosody.im/doc/libevent}.
+@url{https://prosody.im/doc/libevent}.
 Defaults to @samp{#f}.
 @end deftypevr
 
@@ -14056,7 +14056,7 @@ Defaults to @samp{#f}.
 This is the list of modules Prosody will load on startup.  It looks for
 @code{mod_modulename.lua} in the plugins folder, so make sure that exists too.
 Documentation on modules can be found at:
-@url{http://prosody.im/doc/modules}.
+@url{https://prosody.im/doc/modules}.
 Defaults to @samp{("roster" "saslauth" "tls" "dialback" "disco" "carbons" "private" "blocklist" "vcard" "version" "uptime" "time" "ping" "pep" "register" "admin_adhoc")}.
 @end deftypevr
 
@@ -14069,13 +14069,13 @@ Defaults to @samp{()}.
 @deftypevr {@code{prosody-configuration} parameter} file-name groups-file
 Path to a text file where the shared groups are defined.  If this path is
 empty then @samp{mod_groups} does nothing.  See
-@url{http://prosody.im/doc/modules/mod_groups}.
+@url{https://prosody.im/doc/modules/mod_groups}.
 Defaults to @samp{"/var/lib/prosody/sharedgroups.txt"}.
 @end deftypevr
 
 @deftypevr {@code{prosody-configuration} parameter} boolean allow-registration?
 Disable account creation by default, for security.  See
-@url{http://prosody.im/doc/creating_accounts}.
+@url{https://prosody.im/doc/creating_accounts}.
 Defaults to @samp{#f}.
 @end deftypevr
 
@@ -14083,7 +14083,7 @@ Defaults to @samp{#f}.
 These are the SSL/TLS-related settings.  Most of them are disabled so to
 use Prosody's defaults.  If you do not completely understand these options, do
 not add them to your config, it is easy to lower the security of your server
-using them.  See @url{http://prosody.im/doc/advanced_ssl_config}.
+using them.  See @url{https://prosody.im/doc/advanced_ssl_config}.
 
 Available @code{ssl-configuration} fields are:
 
@@ -14154,7 +14154,7 @@ Password for encrypted private keys.
 
 @deftypevr {@code{prosody-configuration} parameter} boolean c2s-require-encryption?
 Whether to force all client-to-server connections to be encrypted or not.
-See @url{http://prosody.im/doc/modules/mod_tls}.
+See @url{https://prosody.im/doc/modules/mod_tls}.
 Defaults to @samp{#f}.
 @end deftypevr
 
@@ -14166,7 +14166,7 @@ Defaults to @samp{("DIGEST-MD5")}.
 
 @deftypevr {@code{prosody-configuration} parameter} boolean s2s-require-encryption?
 Whether to force all server-to-server connections to be encrypted or not.
-See @url{http://prosody.im/doc/modules/mod_tls}.
+See @url{https://prosody.im/doc/modules/mod_tls}.
 Defaults to @samp{#f}.
 @end deftypevr
 
@@ -14174,7 +14174,7 @@ Defaults to @samp{#f}.
 Whether to require encryption and certificate authentication.  This
 provides ideal security, but requires servers you communicate with to support
 encryption AND present valid, trusted certificates.  See
-@url{http://prosody.im/doc/s2s#security}.
+@url{https://prosody.im/doc/s2s#security}.
 Defaults to @samp{#f}.
 @end deftypevr
 
@@ -14182,14 +14182,14 @@ Defaults to @samp{#f}.
 Many servers don't support encryption or have invalid or self-signed
 certificates.  You can list domains here that will not be required to
 authenticate using certificates.  They will be authenticated using DNS.  See
-@url{http://prosody.im/doc/s2s#security}.
+@url{https://prosody.im/doc/s2s#security}.
 Defaults to @samp{()}.
 @end deftypevr
 
 @deftypevr {@code{prosody-configuration} parameter} string-list s2s-secure-domains
 Even if you leave @code{s2s-secure-auth?} disabled, you can still require
 valid certificates for some domains by specifying a list here.  See
-@url{http://prosody.im/doc/s2s#security}.
+@url{https://prosody.im/doc/s2s#security}.
 Defaults to @samp{()}.
 @end deftypevr
 
@@ -14197,20 +14197,20 @@ Defaults to @samp{()}.
 Select the authentication backend to use.  The default provider stores
 passwords in plaintext and uses Prosody's configured data storage to store the
 authentication data.  If you do not trust your server please see
-@url{http://prosody.im/doc/modules/mod_auth_internal_hashed} for information
+@url{https://prosody.im/doc/modules/mod_auth_internal_hashed} for information
 about using the hashed backend.  See also
-@url{http://prosody.im/doc/authentication}
+@url{https://prosody.im/doc/authentication}
 Defaults to @samp{"internal_plain"}.
 @end deftypevr
 
 @deftypevr {@code{prosody-configuration} parameter} maybe-string log
 Set logging options.  Advanced logging configuration is not yet supported
-by the GuixSD Prosody Service.  See @url{http://prosody.im/doc/logging}.
+by the GuixSD Prosody Service.  See @url{https://prosody.im/doc/logging}.
 Defaults to @samp{"*syslog"}.
 @end deftypevr
 
 @deftypevr {@code{prosody-configuration} parameter} file-name pidfile
-File to write pid in.  See @url{http://prosody.im/doc/modules/mod_posix}.
+File to write pid in.  See @url{https://prosody.im/doc/modules/mod_posix}.
 Defaults to @samp{"/var/run/prosody/prosody.pid"}.
 @end deftypevr
 
@@ -14237,7 +14237,7 @@ instance can serve many domains, each one defined as a VirtualHost entry in
 Prosody's configuration.  Conversely a server that hosts a single domain would
 have just one VirtualHost entry.
 
-See @url{http://prosody.im/doc/configure#virtual_host_settings}.
+See @url{https://prosody.im/doc/configure#virtual_host_settings}.
 
 Available @code{virtualhost-configuration} fields are:
 
@@ -14258,7 +14258,7 @@ Internal components are implemented with Prosody-specific plugins.  To add an
 internal component, you simply fill the hostname field, and the plugin you wish
 to use for the component.
 
-See @url{http://prosody.im/doc/components}.
+See @url{https://prosody.im/doc/components}.
 Defaults to @samp{()}.
 
 Available @code{int-component-configuration} fields are:
@@ -14277,10 +14277,10 @@ Multi-user chat (MUC) is Prosody's module for allowing you to create
 hosted chatrooms/conferences for XMPP users.
 
 General information on setting up and using multi-user chatrooms can be found
-in the "Chatrooms" documentation (@url{http://prosody.im/doc/chatrooms}),
+in the "Chatrooms" documentation (@url{https://prosody.im/doc/chatrooms}),
 which you should read if you are new to XMPP chatrooms.
 
-See also @url{http://prosody.im/doc/modules/mod_muc}.
+See also @url{https://prosody.im/doc/modules/mod_muc}.
 
 Available @code{mod-muc-configuration} fields are:
 
@@ -14311,7 +14311,7 @@ Defaults to @samp{20}.
 @deftypevr {@code{prosody-configuration} parameter} ext-component-configuration-list ext-components
 External components use XEP-0114, which most standalone components
 support.  To add an external component, you simply fill the hostname field.  See
-@url{http://prosody.im/doc/components}.
+@url{https://prosody.im/doc/components}.
 Defaults to @samp{()}.
 
 Available @code{ext-component-configuration} fields are:
diff --git a/gnu/services/messaging.scm b/gnu/services/messaging.scm
index d57a7562a2..a9820ed21f 100644
--- a/gnu/services/messaging.scm
+++ b/gnu/services/messaging.scm
@@ -320,13 +320,13 @@ can create such a file with:
     (data-path
      (file-name "/var/lib/prosody")
      "Location of the Prosody data storage directory.  See
-@url{http://prosody.im/doc/configure}."
+@url{https://prosody.im/doc/configure}."
      global)
 
     (plugin-paths
      (file-name-list '())
      "Additional plugin directories.  They are searched in all the specified
-paths in order.  See @url{http://prosody.im/doc/plugins_directory}."
+paths in order.  See @url{https://prosody.im/doc/plugins_directory}."
      global)
 
     (certificates
@@ -339,15 +339,15 @@ certificates/keys from the directory specified here."
     (admins
      (string-list '())
      "This is a list of accounts that are admins for the server.  Note that you
-must create the accounts separately.  See @url{http://prosody.im/doc/admins} and
-@url{http://prosody.im/doc/creating_accounts}.
+must create the accounts separately.  See @url{https://prosody.im/doc/admins} and
+@url{https://prosody.im/doc/creating_accounts}.
 Example: @code{(admins '(\"user1@@example.com\" \"user2@@example.net\"))}"
      common)
 
     (use-libevent?
      (boolean #f)
      "Enable use of libevent for better performance under high load.  See
-@url{http://prosody.im/doc/libevent}."
+@url{https://prosody.im/doc/libevent}."
      common)
 
     (modules-enabled
@@ -355,7 +355,7 @@ Example: @code{(admins '(\"user1@@example.com\" \"user2@@example.net\"))}"
      "This is the list of modules Prosody will load on startup.  It looks for
 @code{mod_modulename.lua} in the plugins folder, so make sure that exists too.
 Documentation on modules can be found at:
-@url{http://prosody.im/doc/modules}."
+@url{https://prosody.im/doc/modules}."
      common)
 
     (modules-disabled
@@ -368,13 +368,13 @@ should you want to disable them then add them to this list."
      (file-name "/var/lib/prosody/sharedgroups.txt")
      "Path to a text file where the shared groups are defined.  If this path is
 empty then @samp{mod_groups} does nothing.  See
-@url{http://prosody.im/doc/modules/mod_groups}."
+@url{https://prosody.im/doc/modules/mod_groups}."
      common)
 
     (allow-registration?
      (boolean #f)
      "Disable account creation by default, for security.  See
-@url{http://prosody.im/doc/creating_accounts}."
+@url{https://prosody.im/doc/creating_accounts}."
      common)
 
     (ssl
@@ -382,13 +382,13 @@ empty then @samp{mod_groups} does nothing.  See
      "These are the SSL/TLS-related settings.  Most of them are disabled so to
 use Prosody's defaults.  If you do not completely understand these options, do
 not add them to your config, it is easy to lower the security of your server
-using them.  See @url{http://prosody.im/doc/advanced_ssl_config}."
+using them.  See @url{https://prosody.im/doc/advanced_ssl_config}."
      common)
 
     (c2s-require-encryption?
      (boolean #f)
      "Whether to force all client-to-server connections to be encrypted or not.
-See @url{http://prosody.im/doc/modules/mod_tls}."
+See @url{https://prosody.im/doc/modules/mod_tls}."
      common)
 
     (disable-sasl-mechanisms
@@ -400,7 +400,7 @@ See @url{http://prosody.im/doc/modules/mod_tls}."
     (s2s-require-encryption?
      (boolean #f)
      "Whether to force all server-to-server connections to be encrypted or not.
-See @url{http://prosody.im/doc/modules/mod_tls}."
+See @url{https://prosody.im/doc/modules/mod_tls}."
      common)
 
     (s2s-secure-auth?
@@ -408,7 +408,7 @@ See @url{http://prosody.im/doc/modules/mod_tls}."
      "Whether to require encryption and certificate authentication.  This
 provides ideal security, but requires servers you communicate with to support
 encryption AND present valid, trusted certificates.  See
-@url{http://prosody.im/doc/s2s#security}."
+@url{https://prosody.im/doc/s2s#security}."
      common)
 
     (s2s-insecure-domains
@@ -416,14 +416,14 @@ encryption AND present valid, trusted certificates.  See
      "Many servers don't support encryption or have invalid or self-signed
 certificates.  You can list domains here that will not be required to
 authenticate using certificates.  They will be authenticated using DNS.  See
-@url{http://prosody.im/doc/s2s#security}."
+@url{https://prosody.im/doc/s2s#security}."
      common)
 
     (s2s-secure-domains
      (string-list '())
      "Even if you leave @code{s2s-secure-auth?} disabled, you can still require
 valid certificates for some domains by specifying a list here.  See
-@url{http://prosody.im/doc/s2s#security}."
+@url{https://prosody.im/doc/s2s#security}."
      common)
 
     (authentication
@@ -431,21 +431,21 @@ valid certificates for some domains by specifying a list here.  See
      "Select the authentication backend to use.  The default provider stores
 passwords in plaintext and uses Prosody's configured data storage to store the
 authentication data.  If you do not trust your server please see
-@url{http://prosody.im/doc/modules/mod_auth_internal_hashed} for information
+@url{https://prosody.im/doc/modules/mod_auth_internal_hashed} for information
 about using the hashed backend.  See also
-@url{http://prosody.im/doc/authentication}"
+@url{https://prosody.im/doc/authentication}"
      common)
 
     ;; TODO: Handle more complicated log structures.
     (log
      (maybe-string "*syslog")
      "Set logging options.  Advanced logging configuration is not yet supported
-by the GuixSD Prosody Service.  See @url{http://prosody.im/doc/logging}."
+by the GuixSD Prosody Service.  See @url{https://prosody.im/doc/logging}."
      common)
 
     (pidfile
      (file-name "/var/run/prosody/prosody.pid")
-     "File to write pid in.  See @url{http://prosody.im/doc/modules/mod_posix}."
+     "File to write pid in.  See @url{https://prosody.im/doc/modules/mod_posix}."
      global)
 
     (http-max-content-size
@@ -476,7 +476,7 @@ instance can serve many domains, each one defined as a VirtualHost entry in
 Prosody's configuration.  Conversely a server that hosts a single domain would
 have just one VirtualHost entry.
 
-See @url{http://prosody.im/doc/configure#virtual_host_settings}."
+See @url{https://prosody.im/doc/configure#virtual_host_settings}."
      global)
 
     (int-components
@@ -490,14 +490,14 @@ Internal components are implemented with Prosody-specific plugins.  To add an
 internal component, you simply fill the hostname field, and the plugin you wish
 to use for the component.
 
-See @url{http://prosody.im/doc/components}."
+See @url{https://prosody.im/doc/components}."
      global)
 
     (ext-components
      (ext-component-configuration-list '())
      "External components use XEP-0114, which most standalone components
 support.  To add an external component, you simply fill the hostname field.  See
-@url{http://prosody.im/doc/components}."
+@url{https://prosody.im/doc/components}."
      global)
 
     (component-secret
@@ -536,10 +536,10 @@ support.  To add an external component, you simply fill the hostname field.  See
 hosted chatrooms/conferences for XMPP users.
 
 General information on setting up and using multi-user chatrooms can be found
-in the \"Chatrooms\" documentation (@url{http://prosody.im/doc/chatrooms}),
+in the \"Chatrooms\" documentation (@url{https://prosody.im/doc/chatrooms}),
 which you should read if you are new to XMPP chatrooms.
 
-See also @url{http://prosody.im/doc/modules/mod_muc}."
+See also @url{https://prosody.im/doc/modules/mod_muc}."
      int-component)
 
     (hostname
-- 
cgit 1.4.1


From e9960d8cbae74a7660988e0d5724ffc96a016137 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 24 Dec 2017 01:01:21 +0100
Subject: gnu, doc: Use HTTPS for cran.r-project.org home pages.

* gnu/packages/bioinformatics.scm (r-sparql, r-acsnminer, r-gkmsvm)
(r-maldiquant, r-gprofiler)[home-page]: Use HTTPS.
* gnu/packages/cran.scm (r-colorspace, r-auc, r-calibrate, r-shape)
(r-compare, r-proxy, r-sp, r-rmtstat, r-lmtest, r-inline, r-bbmle)
(r-lpsolve, r-energy, r-suppdists, r-ksamples, r-cvst, r-drr, r-prodlim)
(r-ddalpha, r-rcpproll, r-ipred, r-psych, r-truncnorm, r-rsolnp, r-laeken)
(r-vcd, r-ica, r-scatterplot3d)[home-page]: Likewise.
* gnu/packages/machine-learning.scm (r-adaptivesparsity, r-kernlab)
[home-page]: Likewise.
* gnu/packages/maths.scm (r-quadprog, r-pracma)[home-page]: Likewise.
* gnu/packages/statistics.scm (r-boot, r-cluster, r-codetools, r-foreign)
(r-kernsmooth, r-nlme, r-mgcv, r-rpart, r-dichromat, r-estimability)
(r-pheatmap, r-labeling, r-magrittr, r-munsell, r-rcolorbrewer, r-sendmailr)
(r-gdtools, r-acepack, r-formula, r-locfit, r-chron, r-coda, r-backports)
(r-brew, r-commonmark, r-rstudioapi, r-plotrix, r-gridbase, r-bitops)
(r-catools, r-xnomial, r-lambda-r, r-whoreadsthis, r-futile-options)
(r-futile-logger, r-segmented, r-snow, r-iterators, r-foreach, r-doparallel)
(r-domc, r-irlba, r-registry, r-e1071, r-bigmemory-sri, r-r-methodss3)
(r-tidyselect, r-base64, r-runit, r-sfsmisc, r-gtools, r-gdata, r-gplots)
(r-ztable, r-vipor, r-sourcetools, r-statmod, r-compquadform, r-mixtools)
(r-fastica, r-diptest, r-modeltools, r-flexmix, r-deoptimr, r-pcapp)
(r-rrcov, r-fit-models, r-robust, r-trimcluster, r-fpc, r-fnn)
(r-modelmetrics, r-nloptr, r-lme4, r-tclust, r-lubridate)[home-page]:
Likewise.
* gnu/packages/web.scm (r-htmltools, r-hwriter, r-rjson, r-rook)[home-page]:
Likewise.
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Likewise.
---
 doc/guix.texi                     |   4 +-
 gnu/packages/bioinformatics.scm   |  10 +--
 gnu/packages/cran.scm             |  58 +++++++--------
 gnu/packages/machine-learning.scm |   4 +-
 gnu/packages/maths.scm            |   4 +-
 gnu/packages/statistics.scm       | 150 +++++++++++++++++++-------------------
 gnu/packages/web.scm              |   8 +-
 7 files changed, 119 insertions(+), 119 deletions(-)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index 7572ab8768..cb6754a4bc 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -6032,7 +6032,7 @@ guix import cpan Acme::Boolean
 @item cran
 @cindex CRAN
 @cindex Bioconductor
-Import metadata from @uref{http://cran.r-project.org/, CRAN}, the
+Import metadata from @uref{https://cran.r-project.org/, CRAN}, the
 central repository for the @uref{http://r-project.org, GNU@tie{}R
 statistical and graphical environment}.
 
@@ -6403,7 +6403,7 @@ the updater for packages hosted on kernel.org;
 @item elpa
 the updater for @uref{http://elpa.gnu.org/, ELPA} packages;
 @item cran
-the updater for @uref{http://cran.r-project.org/, CRAN} packages;
+the updater for @uref{https://cran.r-project.org/, CRAN} packages;
 @item bioconductor
 the updater for @uref{https://www.bioconductor.org/, Bioconductor} R packages;
 @item cpan
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 30eae3e0b4..660c7b408b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6367,7 +6367,7 @@ track.  The database is exposed as a @code{TxDb} object.")
   (propagated-inputs
    `(("r-rcurl" ,r-rcurl)
      ("r-xml" ,r-xml)))
-  (home-page "http://cran.r-project.org/web/packages/SPARQL")
+  (home-page "https://cran.r-project.org/web/packages/SPARQL")
   (synopsis "SPARQL client for R")
   (description "This package provides an interface to use SPARQL to pose
 SELECT or UPDATE queries to an end-point.")
@@ -6601,7 +6601,7 @@ BLAST, KEGG, GenBank, MEDLINE and GO.")
     (propagated-inputs
       `(("r-ggplot2" ,r-ggplot2)
         ("r-gridextra" ,r-gridextra)))
-    (home-page "http://cran.r-project.org/web/packages/ACSNMineR")
+    (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
     (synopsis "Gene enrichment analysis")
     (description
      "This package provides tools to compute and represent gene set enrichment
@@ -8497,7 +8497,7 @@ factors bound at the specific regions.")
        ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)
        ("r-seqinr" ,r-seqinr)))
-    (home-page "http://cran.r-project.org/web/packages/gkmSVM")
+    (home-page "https://cran.r-project.org/web/packages/gkmSVM")
     (synopsis "Gapped-kmer support vector machine")
     (description
      "This R package provides tools for training gapped-kmer SVM classifiers
@@ -9090,7 +9090,7 @@ trait.")
          "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z"))))
     (properties `((upstream-name . "MALDIquant")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/MALDIquant")
+    (home-page "https://cran.r-project.org/web/packages/MALDIquant")
     (synopsis "Quantitative analysis of mass spectrometry data")
     (description
      "This package provides a complete analysis pipeline for matrix-assisted
@@ -9997,7 +9997,7 @@ interval to data view, mismatch pileup, and several splicing summaries.")
     (propagated-inputs
      `(("r-plyr" ,r-plyr)
        ("r-rcurl" ,r-rcurl)))
-    (home-page "http://cran.r-project.org/web/packages/gProfileR/")
+    (home-page "https://cran.r-project.org/web/packages/gProfileR/")
     (synopsis "Interface to the g:Profiler toolkit")
     (description
      "This package provides tools for functional enrichment analysis,
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9b80b68984..9359b7f736 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -42,7 +42,7 @@
        (sha256
         (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/colorspace")
+    (home-page "https://cran.r-project.org/web/packages/colorspace")
     (synopsis "Color space manipulation")
     (description
      "This package carries out a mapping between assorted color spaces
@@ -170,7 +170,7 @@ bindings that call a C++ function.")
          "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
     (properties `((upstream-name . "AUC")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/AUC")
+    (home-page "https://cran.r-project.org/web/packages/AUC")
     (synopsis "Compute the area under the curve of selected measures")
     (description
      "This package includes functions to compute the area under the curve of
@@ -195,7 +195,7 @@ is provided.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)))
-    (home-page "http://cran.r-project.org/web/packages/calibrate")
+    (home-page "https://cran.r-project.org/web/packages/calibrate")
     (synopsis "Calibration of scatterplot and biplot axes")
     (description
      "This is a package for drawing calibrated scales with tick marks
@@ -214,7 +214,7 @@ on (non-orthogonal) variable vectors in scatterplots and biplots.")
         (base32
          "1v9xp60p813rnx41vchkh32qmcb4z2zp9l7r1a8a6f8aqylnq3vj"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/shape")
+    (home-page "https://cran.r-project.org/web/packages/shape")
     (synopsis "Functions for plotting graphical shapes")
     (description
      "This package provides functions for plotting graphical shapes such as
@@ -308,7 +308,7 @@ approach is used to estimate the lower cut-off for the scaling region.")
         (base32
          "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/compare")
+    (home-page "https://cran.r-project.org/web/packages/compare")
     (synopsis "Comparing objects for differences")
     (description
      "This package provides functions to compare a model object to a
@@ -550,7 +550,7 @@ plot networks.")
         (base32
          "15g6dacdmlbkcnimblscghl23aj732cn6qwbs583r4im9v5nvbla"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/proxy")
+    (home-page "https://cran.r-project.org/web/packages/proxy")
     (synopsis "Distance and similarity measures")
     (description
      "This package provides an extensible framework for the efficient
@@ -572,7 +572,7 @@ most popular ones.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
-    (home-page "http://cran.r-project.org/web/packages/sp")
+    (home-page "https://cran.r-project.org/web/packages/sp")
     (synopsis "Classes and methods for spatial data")
     (description
      "This package provides classes and methods for spatial data; the classes
@@ -595,7 +595,7 @@ print, summary, etc.")
          "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
     (properties `((upstream-name . "RMTstat")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/RMTstat")
+    (home-page "https://cran.r-project.org/web/packages/RMTstat")
     (synopsis "Distributions, statistics and tests derived from random matrix theory")
     (description
      "This package provides functions for working with the Tracy-Widom laws
@@ -710,7 +710,7 @@ or excesses over a high threshold.")
      `(("r-zoo" ,r-zoo)))
     (native-inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/lmtest")
+    (home-page "https://cran.r-project.org/web/packages/lmtest")
     (synopsis "Testing linear regression models")
     (description
      "This package provides a collection of tests, data sets, and examples for
@@ -730,7 +730,7 @@ tools for inference in parametric models are provided.")
                (base32
                 "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/inline")
+    (home-page "https://cran.r-project.org/web/packages/inline")
     (synopsis "Functions to inline C, C++, Fortran function calls from R")
     (description
      "This package provides functionality to dynamically define R functions
@@ -755,7 +755,7 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
      `(("r-lattice" ,r-lattice)
        ("r-mass" ,r-mass)
        ("r-numderiv" ,r-numderiv)))
-    (home-page "http://cran.r-project.org/web/packages/bbmle")
+    (home-page "https://cran.r-project.org/web/packages/bbmle")
     (synopsis "Tools for General Maximum Likelihood Estimation")
     (description
      "This package provides methods and functions for fitting maximum
@@ -805,7 +805,7 @@ topics for ecologists (ISBN 978-0-691-12522-0).")
          "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m"))))
     (properties `((upstream-name . "lpSolve")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/lpSolve")
+    (home-page "https://cran.r-project.org/web/packages/lpSolve")
     (synopsis "R interface to Lp_solve to solve linear/integer programs")
     (description
      "Lp_solve is software for solving linear, integer and mixed integer
@@ -832,7 +832,7 @@ transportation problems.")
        ("r-mass" ,r-mass)
        ("r-quadprog" ,r-quadprog)))
     (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/limSolve")
+    (home-page "https://cran.r-project.org/web/packages/limSolve")
     (synopsis "Solving linear inverse models")
     (description
      "This package provides functions that:
@@ -891,7 +891,7 @@ data).  Weighted versions of MLE, MME and QME are available.")
     (propagated-inputs
      `(("r-boot" ,r-boot)
        ("r-rcpp" ,r-rcpp)))
-    (home-page "http://cran.r-project.org/web/packages/energy")
+    (home-page "https://cran.r-project.org/web/packages/energy")
     (synopsis "Multivariate inference via the energy of data")
     (description
      "This package provides e-statistics (energy) tests and statistics for
@@ -918,7 +918,7 @@ statistics/methods are implemented.")
          "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
     (properties `((upstream-name . "SuppDists")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/SuppDists")
+    (home-page "https://cran.r-project.org/web/packages/SuppDists")
     (synopsis "Supplementary distributions")
     (description
      "This package provides ten distributions supplementing those built into
@@ -944,7 +944,7 @@ George Marsaglia are included.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-suppdists" ,r-suppdists)))
-    (home-page "http://cran.r-project.org/web/packages/kSamples")
+    (home-page "https://cran.r-project.org/web/packages/kSamples")
     (synopsis "K-Sample rank tests and their combinations")
     (description
      "This package provides tools to compares k samples using the
@@ -973,7 +973,7 @@ samples.")
     (propagated-inputs
      `(("r-kernlab" ,r-kernlab)
        ("r-matrix" ,r-matrix)))
-    (home-page "http://cran.r-project.org/web/packages/CVST")
+    (home-page "https://cran.r-project.org/web/packages/CVST")
     (synopsis "Fast cross-validation via sequential testing")
     (description
      "This package implements the fast cross-validation via sequential
@@ -1027,7 +1027,7 @@ variable models.")
      `(("r-cvst" ,r-cvst)
        ("r-kernlab" ,r-kernlab)
        ("r-matrix" ,r-matrix)))
-    (home-page "http://cran.r-project.org/web/packages/DRR")
+    (home-page "https://cran.r-project.org/web/packages/DRR")
     (synopsis "Dimensionality reduction via regression")
     (description
      "This package provides an implementation of dimensionality reduction via
@@ -1051,7 +1051,7 @@ regression using Kernel Ridge Regression.")
        ("r-lava" ,r-lava)
        ("r-rcpp" ,r-rcpp)
        ("r-survival" ,r-survival)))
-    (home-page "http://cran.r-project.org/web/packages/prodlim")
+    (home-page "https://cran.r-project.org/web/packages/prodlim")
     (synopsis "Product-limit estimation for censored event history analysis")
     (description
      "This package provides a fast and user-friendly implementation of
@@ -1123,7 +1123,7 @@ calendar objects.")
        ("r-sfsmisc" ,r-sfsmisc)))
     (native-inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/ddalpha")
+    (home-page "https://cran.r-project.org/web/packages/ddalpha")
     (synopsis "Depth-Based classification and calculation of data depth")
     (description
      "This package contains procedures for depth-based supervised learning,
@@ -1172,7 +1172,7 @@ Core algorithms are executed in parallel on systems supporting OpenMP.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)))
-    (home-page "http://cran.r-project.org/web/packages/RcppRoll")
+    (home-page "https://cran.r-project.org/web/packages/RcppRoll")
     (synopsis "Efficient rolling and windowed operations")
     (description
      "This package provides fast and efficient routines for common rolling /
@@ -1200,7 +1200,7 @@ provided.")
        ("r-prodlim" ,r-prodlim)
        ("r-rpart" ,r-rpart)
        ("r-survival" ,r-survival)))
-    (home-page "http://cran.r-project.org/web/packages/ipred")
+    (home-page "https://cran.r-project.org/web/packages/ipred")
     (synopsis "Improved predictors")
     (description
      "This package provides improved predictive models by indirect
@@ -1225,7 +1225,7 @@ problems as well as resampling based estimators of prediction error.")
        ("r-lattice" ,r-lattice)
        ("r-mnormt" ,r-mnormt)
        ("r-nlme" ,r-nlme)))
-    (home-page "http://cran.r-project.org/web/packages/psych/")
+    (home-page "https://cran.r-project.org/web/packages/psych/")
     (synopsis "Procedures for psychological, psychometric, and personality research")
     (description
      "This package provides a general purpose toolbox for personality,
@@ -1456,7 +1456,7 @@ imputations.")
         (base32
          "1qac05z50618y4bw1d7yznsli1bv82s0g8h37iacrjrdkv87bmy7"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/truncnorm/")
+    (home-page "https://cran.r-project.org/web/packages/truncnorm/")
     (synopsis "Truncated normal distribution")
     (description "This package provides functions for the truncated normal
 distribution with mean equal to @code{mean} and standard deviation equal to
@@ -1479,7 +1479,7 @@ functions, as well as a random generation function.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-truncnorm" ,r-truncnorm)))
-    (home-page "http://cran.r-project.org/web/packages/Rsolnp/")
+    (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
     (synopsis "General non-linear optimization")
     (description "The Rsolnp package implements a general non-linear augmented
 Lagrange multiplier method solver, a @dfn{sequential quadratic
@@ -1654,7 +1654,7 @@ where possible.")
     (propagated-inputs
      `(("r-boot" ,r-boot)
        ("r-mass" ,r-mass)))
-    (home-page "http://cran.r-project.org/web/packages/laeken/")
+    (home-page "https://cran.r-project.org/web/packages/laeken/")
     (synopsis "Estimation of indicators on social exclusion and poverty")
     (description "This package provides tools for the estimation of indicators
 on social exclusion and poverty, as well as an implementation of Pareto tail
@@ -1677,7 +1677,7 @@ modeling for empirical income distributions.")
      `(("r-colorspace" ,r-colorspace)
        ("r-lmtest" ,r-lmtest)
        ("r-mass" ,r-mass)))
-    (home-page "http://cran.r-project.org/web/packages/vcd/")
+    (home-page "https://cran.r-project.org/web/packages/vcd/")
     (synopsis "Visualizing categorical data")
     (description "This package provides visualization techniques, data sets,
 summary and inference procedures aimed particularly at categorical data.
@@ -1699,7 +1699,7 @@ Analysis with R\" by Michael Friendly and David Meyer (2015).")
         (base32
          "1bkl4a72l0k6gm82l3jxnib898z20cw17zg81jj39l9dn65rlmcq"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/ica/")
+    (home-page "https://cran.r-project.org/web/packages/ica/")
     (synopsis "Independent component analysis")
     (description "This package provides tools for @dfn{Independent Component
 Analysis} (ICA) using various algorithms: FastICA,
@@ -1766,7 +1766,7 @@ statistics, etc.")
         (base32
          "0ababcj87kx7860mica9y2ydlhskxmgj9n46crx036cila512jc2"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/scatterplot3d/")
+    (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
     (synopsis "3D scatter plot")
     (description "This package provides an implementation of scatter plots for
 plotting.  a three dimensional point cloud.")
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index c8bd5d7747..dbd2af1ea4 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -492,7 +492,7 @@ in terms of new algorithms.")
        ("r-rcpparmadillo" ,r-rcpparmadillo)))
     (inputs
      `(("armadillo" ,armadillo)))
-    (home-page "http://cran.r-project.org/web/packages/AdaptiveSparsity")
+    (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
     (synopsis "Adaptive sparsity models")
     (description
      "This package implements the Figueiredo machine learning algorithm for
@@ -512,7 +512,7 @@ geometric models.")
         (base32
          "0qnaq9x3j2xc6jrmmd98wc6hkzch487s4p3a9lnc00xvahkhgpmr"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/kernlab")
+    (home-page "https://cran.r-project.org/web/packages/kernlab")
     (synopsis "Kernel-based machine learning tools")
     (description
      "This package provides kernel-based machine learning methods for
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index b1a497c36b..e8c7707408 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1885,7 +1885,7 @@ sparse system of linear equations A x = b using Guassian elimination.")
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/quadprog")
+    (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
@@ -1904,7 +1904,7 @@ programming problems.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-quadprog" ,r-quadprog)))
-    (home-page "http://cran.r-project.org/web/packages/pracma")
+    (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
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f92f6d3904..7fb125cad1 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -305,7 +305,7 @@ available, greatly increasing its breadth and scope.")
         (base32
          "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/boot")
+    (home-page "https://cran.r-project.org/web/packages/boot")
     (synopsis "Bootstrap functions for R")
     (description
      "This package provides functions and datasets for bootstrapping from the
@@ -371,7 +371,7 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
     (build-system r-build-system)
     (inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/cluster")
+    (home-page "https://cran.r-project.org/web/packages/cluster")
     (synopsis "Methods for cluster analysis")
     (description
      "This package provides methods for cluster analysis.  It is a much
@@ -391,7 +391,7 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
         (base32
          "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/codetools")
+    (home-page "https://cran.r-project.org/web/packages/codetools")
     (synopsis "Code analysis tools for R")
     (description "This package provides code analysis tools for R to check R
 code for possible problems.")
@@ -410,7 +410,7 @@ code for possible problems.")
         (base32
          "0s1lxmd85dd0kxx8hwk02w9l7pmpk4bpy7787fbyh2dbq5g9ys0k"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/foreign")
+    (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")
     (description
      "This package provides functions for reading and writing data stored by
@@ -433,7 +433,7 @@ for reading and writing some dBase files.")
     (build-system r-build-system)
     (inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/KernSmooth")
+    (home-page "https://cran.r-project.org/web/packages/KernSmooth")
     (synopsis "Functions for kernel smoothing")
     (description
      "This package provides functions for kernel smoothing (and density
@@ -500,7 +500,7 @@ and operations on them using LAPACK and SuiteSparse.")
      `(("r-lattice" ,r-lattice)))
     (native-inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/nlme")
+    (home-page "https://cran.r-project.org/web/packages/nlme")
     (synopsis "Linear and nonlinear mixed effects models")
     (description
      "This package provides tools to fit and compare Gaussian linear and
@@ -522,7 +522,7 @@ nonlinear mixed-effects models.")
    (propagated-inputs
     `(("r-matrix" ,r-matrix)
       ("r-nlme" ,r-nlme)))
-   (home-page "http://cran.r-project.org/web/packages/mgcv")
+   (home-page "https://cran.r-project.org/web/packages/mgcv")
    (synopsis "Mixed generalised additive model computation")
    (description
     "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
@@ -562,7 +562,7 @@ single hidden layer, and for multinomial log-linear models.")
         (base32
          "165djqj7lk81jr7z5fwccq3h7ayys26hx1kj9hndvg2rkyaq1arq"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/rpart")
+    (home-page "https://cran.r-project.org/web/packages/rpart")
     (synopsis "Recursive partitioning and regression trees")
     (description
      "This package provides recursive partitioning functions for
@@ -693,7 +693,7 @@ caching.")
        (sha256
         (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/dichromat")
+    (home-page "https://cran.r-project.org/web/packages/dichromat")
     (synopsis "Color schemes for dichromats")
     (description
      "Dichromat collapses red-green or green-blue distinctions to simulate the
@@ -741,7 +741,7 @@ OpenSSL should be used.")
                (base32
                 "13b80bpnbrarazjvnpnk91ljjsqgfm2fm3gy66aj09cmmsmv199h"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/estimability")
+    (home-page "https://cran.r-project.org/web/packages/estimability")
     (synopsis "Tools for assessing estimability of linear predictions")
     (description "Provides tools for determining estimability of linear
 functions of regression coefficients, and 'epredict' methods that handle
@@ -765,7 +765,7 @@ non-estimable cases correctly.")
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-scales" ,r-scales)))
     (home-page
-     "http://cran.r-project.org/web/packages/pheatmap")
+     "https://cran.r-project.org/web/packages/pheatmap")
     (synopsis "Pretty heatmaps")
     (description
      "This package provides an implementation of heatmaps that offers more
@@ -783,7 +783,7 @@ control over dimensions and appearance.")
        (sha256
         (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/labeling")
+    (home-page "https://cran.r-project.org/web/packages/labeling")
     (synopsis "Axis labeling algorithms")
     (description "The labeling package provides a range of axis labeling
 algorithms.")
@@ -800,7 +800,7 @@ algorithms.")
        (sha256
         (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/magrittr/index.html")
+    (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
     (synopsis "A forward-pipe operator for R")
     (description
      "Magrittr provides a mechanism for chaining commands with a new
@@ -823,7 +823,7 @@ see package vignette.  To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-colorspace" ,r-colorspace)))
-    (home-page "http://cran.r-project.org/web/packages/munsell")
+    (home-page "https://cran.r-project.org/web/packages/munsell")
     (synopsis "Munsell colour system")
     (description
      "The Munsell package contains Functions for exploring and using the
@@ -904,7 +904,7 @@ prototype-based, rather than class-based object oriented ideas.")
        (sha256
         (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/RColorBrewer")
+    (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
     (synopsis "ColorBrewer palettes")
     (description
      "This package provides color schemes for maps (and other graphics)
@@ -928,7 +928,7 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org")
     (propagated-inputs
      `(("r-base64enc" ,r-base64enc)))
     (home-page
-     "http://cran.r-project.org/web/packages/sendmailR")
+     "https://cran.r-project.org/web/packages/sendmailR")
     (synopsis "Send email using R")
     (description
      "This package contains a simple SMTP client which provides a portable
@@ -1112,7 +1112,7 @@ agnes cluster diagrams.")
      `(("cairo" ,cairo)))
     (propagated-inputs
      `(("r-withr" ,r-withr)))
-    (home-page "http://cran.r-project.org/web/packages/gdtools")
+    (home-page "https://cran.r-project.org/web/packages/gdtools")
     (synopsis "Utilities for graphical rendering")
     (description
      "The @code{gdtools} package provides functionalities to get font metrics
@@ -1668,7 +1668,7 @@ features require SQL translation to be provided by the package author.")
     (build-system r-build-system)
     (inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/acepack")
+    (home-page "https://cran.r-project.org/web/packages/acepack")
     (synopsis "Functions for regression transformations")
     (description
      "This package provides ACE and AVAS methods for choosing regression
@@ -1688,7 +1688,7 @@ transformations.")
          "0ad49bzip1zqmpj1d8jajwl4bd81fm3k6dq8p26x6mvlzc04dvwd"))))
     (properties `((upstream-name . "Formula")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/Formula")
+    (home-page "https://cran.r-project.org/web/packages/Formula")
     (synopsis "Extended model formulas")
     (description
      "This package provides a new class @code{Formula}, which extends the base
@@ -1711,7 +1711,7 @@ side.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
-    (home-page "http://cran.r-project.org/web/packages/locfit")
+    (home-page "https://cran.r-project.org/web/packages/locfit")
     (synopsis "Local regression, likelihood and density estimation")
     (description
      "This package provides functions used for local regression, likelihood
@@ -1729,7 +1729,7 @@ and density estimation.")
                (base32
                 "05aznigw9nwv3hbwjnjbvqhfjqkwsw2csgrjx8500gzr2fvla5w8"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/chron")
+    (home-page "https://cran.r-project.org/web/packages/chron")
     (synopsis "Chronological R objects which can handle dates and times")
     (description
      "This package provides chronological R objects which can handle dates and
@@ -1890,7 +1890,7 @@ inference for statistical models.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
-    (home-page "http://cran.r-project.org/web/packages/coda")
+    (home-page "https://cran.r-project.org/web/packages/coda")
     (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
     (description "This package provides functions for summarizing and plotting
 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
@@ -2021,7 +2021,7 @@ limited to R.")
         (base32
          "0mml9h3xagi7144pyb3jj9zbh9qzns7izkhdg7df20v7bikr6nz8"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/backports")
+    (home-page "https://cran.r-project.org/web/packages/backports")
     (synopsis "Reimplementations of functions introduced since R 3.0.0")
     (description
      "Provides implementations of functions which have been introduced in R
@@ -2141,7 +2141,7 @@ SLURM and Sun Grid Engine.  Multicore and SSH systems are also supported.")
                (base32
                 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/brew")
+    (home-page "https://cran.r-project.org/web/packages/brew")
     (synopsis "Templating framework for report generation")
     (description
      "The brew package implements a templating framework for mixing text and R
@@ -2186,7 +2186,7 @@ other packages.")
         (base32
          "1vb8r9khpvcf0q7acv8rsplfjjwcll302bg5kp596cvn6aacypl6"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/commonmark")
+    (home-page "https://cran.r-project.org/web/packages/commonmark")
     (synopsis "CommonMark and Github Markdown Rendering in R")
     (description
      "The CommonMark specification defines a rationalized version of markdown
@@ -2317,7 +2317,7 @@ pure C implementation of the Git core methods.")
                (base32
                 "133s75q2hr6jg28m1wvs96qrbc9c4vw87migwhkjqb88xxvbqhd5"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/rstudioapi")
+    (home-page "https://cran.r-project.org/web/packages/rstudioapi")
     (synopsis "Safely access the RStudio API")
     (description
      "This package provides functions to access the RStudio API and provide
@@ -2428,7 +2428,7 @@ disk (or a connection).")
                (base32
                 "0rw81n9p3d2i03b4pgcfj5blryc94f29bm9a4j9bnp5h8qjj6pry"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/plotrix")
+    (home-page "https://cran.r-project.org/web/packages/plotrix")
     (synopsis "Various plotting functions")
     (description
      "This package provides lots of plotting, various labeling, axis and color
@@ -2446,7 +2446,7 @@ scaling functions for R.")
                (base32
                 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/gridBase")
+    (home-page "https://cran.r-project.org/web/packages/gridBase")
     (synopsis "Integration of base and grid graphics")
     (description
      "This package provides an integration of base and grid graphics for R.")
@@ -2517,7 +2517,7 @@ the header files from the templated Armadillo library.")
                (base32
                 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/bitops")
+    (home-page "https://cran.r-project.org/web/packages/bitops")
     (synopsis "Bitwise operations")
     (description
      "This package provides functions for bitwise operations on integer
@@ -2538,7 +2538,7 @@ vectors.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bitops" ,r-bitops)))
-    (home-page "http://cran.r-project.org/web/packages/caTools")
+    (home-page "https://cran.r-project.org/web/packages/caTools")
     (synopsis "Various tools including functions for moving window statistics")
     (description
      "This package contains several basic utility functions including:
@@ -2778,7 +2778,7 @@ offers access to an XPath \"interpreter\".")
                "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
     (properties (quasiquote ((upstream-name . "XNomial"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/XNomial")
+    (home-page "https://cran.r-project.org/web/packages/XNomial")
     (synopsis "Goodness-of-Fit test for multinomial data")
     (description
      "This package provides an exact Goodness-of-Fit test for
@@ -2806,7 +2806,7 @@ plotted and compared with the asymptotic curve.")
                 "0vql32np716dpd0kjn7s7wgawd02ysgp2a5il4kb19nlw661ii3x"))))
     (properties `((upstream-name . "lambda.r")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/lambda.r")
+    (home-page "https://cran.r-project.org/web/packages/lambda.r")
     (synopsis "Functional programming extension for R")
     (description
      "This package provides a language extension to efficiently write
@@ -2828,7 +2828,7 @@ safety.")
     (properties
      `((upstream-name . "futile.options")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/futile.options")
+    (home-page "https://cran.r-project.org/web/packages/futile.options")
     (synopsis "Options management framework")
     (description
      "The futile.options subsystem provides an easy user-defined options
@@ -2852,7 +2852,7 @@ options defined in other packages.")
     (propagated-inputs
      `(("r-futile-options" ,r-futile-options)
        ("r-lambda-r" ,r-lambda-r)))
-    (home-page "http://cran.r-project.org/web/packages/futile.logger")
+    (home-page "https://cran.r-project.org/web/packages/futile.logger")
     (synopsis "Logging utility for R")
     (description
      "This package provides a simple yet powerful logging utility.  Based
@@ -2873,7 +2873,7 @@ statements.")
         (base32
          "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/segmented")
+    (home-page "https://cran.r-project.org/web/packages/segmented")
     (synopsis "Regression models with breakpoints estimation")
     (description
      "Given a regression model, segmented updates the model by adding one or
@@ -2892,7 +2892,7 @@ multiple breakpoints are allowed.")
                (base32
                 "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/snow")
+    (home-page "https://cran.r-project.org/web/packages/snow")
     (synopsis "Support for simple parallel computing in R")
     (description
      "The snow package provides support for simple parallel computing on a
@@ -2937,7 +2937,7 @@ standard R subsetting and Kronecker products.")
         (base32
          "16sycjq912ix52fjxjhcwiaqr0yj1v5iqmrvjljd3z857031w06y"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/iterators")
+    (home-page "https://cran.r-project.org/web/packages/iterators")
     (synopsis "Iterator construct for R")
     (description
      "This package provides support for iterators, which allow a programmer to
@@ -2960,7 +2960,7 @@ data.")
     (propagated-inputs
      `(("r-codetools" ,r-codetools)
        ("r-iterators" ,r-iterators)))
-    (home-page "http://cran.r-project.org/web/packages/foreach")
+    (home-page "https://cran.r-project.org/web/packages/foreach")
     (synopsis "Foreach looping construct for R")
     (description
      "This package provides support for the @code{foreach} looping construct.
@@ -2989,7 +2989,7 @@ parallel.")
     (propagated-inputs
      `(("r-foreach" ,r-foreach)
        ("r-iterators" ,r-iterators)))
-    (home-page "http://cran.r-project.org/web/packages/doParallel")
+    (home-page "https://cran.r-project.org/web/packages/doParallel")
     (synopsis "Foreach parallel adaptor for the 'parallel' package")
     (description
      "This package provides a parallel backend for the @code{%dopar%} function
@@ -3012,7 +3012,7 @@ using the parallel package.")
     (propagated-inputs
      `(("r-foreach" ,r-foreach)
        ("r-iterators" ,r-iterators)))
-    (home-page "http://cran.r-project.org/web/packages/doMC")
+    (home-page "https://cran.r-project.org/web/packages/doMC")
     (synopsis "Foreach parallel adaptor for the 'parallel' package")
     (description
      "This package provides a parallel backend for the @code{%dopar%} function
@@ -3085,7 +3085,7 @@ flexible than the orphaned \"base64\" package.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
-    (home-page "http://cran.r-project.org/web/packages/irlba")
+    (home-page "https://cran.r-project.org/web/packages/irlba")
     (synopsis "Methods for eigendecomposition of large matrices")
     (description
      "This package provides fast and memory efficient methods for truncated
@@ -3158,7 +3158,7 @@ options and registries, vignette, unit test and bibtex related utilities.")
          (base32
           "1yqfl1g6vsl28zn8brzc39659k8lqsmfms7900j7p64ilydyb2sx"))))
      (build-system r-build-system)
-     (home-page "http://cran.r-project.org/web/packages/registry")
+     (home-page "https://cran.r-project.org/web/packages/registry")
      (synopsis "Infrastructure for R package registries")
      (description
       "This package provides a generic infrastructure for creating and using R
@@ -3229,7 +3229,7 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)))
-    (home-page "http://cran.r-project.org/web/packages/e1071")
+    (home-page "https://cran.r-project.org/web/packages/e1071")
     (synopsis "Miscellaneous functions for probability theory")
     (description
      "This package provides functions for latent class analysis, short time
@@ -3250,7 +3250,7 @@ computation, bagged clustering, naive Bayes classifier, and more.")
     (properties
      `((upstream-name . "bigmemory.sri")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/bigmemory.sri")
+    (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
     (synopsis "Shared resource interface for the bigmemory package")
     (description "This package provides a shared resource interface for the
 bigmemory and synchronicity packages.")
@@ -3357,7 +3357,7 @@ performing parallel computations on multicore machines.")
                 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
     (properties `((upstream-name . "R.methodsS3")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/R.methodsS3")
+    (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
     (synopsis "S3 methods simplified")
     (description
      "This package provides methods that simplify the setup of S3 generic
@@ -3583,7 +3583,7 @@ the 'lite' version of the more complete @code{viridis} package.")
        ("r-purrr" ,r-purrr)
        ("r-rcpp" ,r-rcpp)
        ("r-rlang" ,r-rlang)))
-    (home-page "http://cran.r-project.org/web/packages/tidyselect")
+    (home-page "https://cran.r-project.org/web/packages/tidyselect")
     (synopsis "Select from a set of strings")
     (description
      "This package provides a backend for the selecting functions of the
@@ -3865,7 +3865,7 @@ following problems:
     (build-system r-build-system)
     (propagated-inputs
      `(("r-openssl" ,r-openssl)))
-    (home-page "http://cran.r-project.org/web/packages/base64")
+    (home-page "https://cran.r-project.org/web/packages/base64")
     (synopsis "Base64 encoder and decoder")
     (description
      "This package is a compatibility wrapper to replace the orphaned package
@@ -3929,7 +3929,7 @@ conversion of R objects to LaTeX code, and recoding variables.")
          "1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx"))))
     (properties `((upstream-name . "RUnit")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/RUnit")
+    (home-page "https://cran.r-project.org/web/packages/RUnit")
     (synopsis "R unit test framework")
     (description
      "This package provides R functions implementing a standard unit testing
@@ -4015,7 +4015,7 @@ existing packages provide.")
         (base32
          "0jzmbywlyzfxs7hlmyd0iynghfc9qp5sa5lnhr73y8r360yv1ahf"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/sfsmisc")
+    (home-page "https://cran.r-project.org/web/packages/sfsmisc")
     (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
     (description
      "This package provides useful utilities from Seminar fuer Statistik ETH
@@ -4034,7 +4034,7 @@ Zurich, including many that are related to graphics.")
         (base32
          "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/gtools")
+    (home-page "https://cran.r-project.org/web/packages/gtools")
     (synopsis "Various R programming tools")
     (description
      "This package contains a collection of various functions to assist in R
@@ -4060,7 +4060,7 @@ tests for whether a value is missing, empty or contains only @code{NA} and
      `(("perl" ,perl)))
     (propagated-inputs
      `(("r-gtools" ,r-gtools)))
-    (home-page "http://cran.r-project.org/web/packages/gdata")
+    (home-page "https://cran.r-project.org/web/packages/gdata")
     (synopsis "Various R programming tools for data manipulation")
     (description
      "This package provides various R programming tools for data manipulation,
@@ -4101,7 +4101,7 @@ including:
        ("r-gdata" ,r-gdata)
        ("r-gtools" ,r-gtools)
        ("r-kernsmooth" ,r-kernsmooth)))
-    (home-page "http://cran.r-project.org/web/packages/gplots")
+    (home-page "https://cran.r-project.org/web/packages/gplots")
     (synopsis "Various R programming tools for plotting data")
     (description
      "This package provides various R programming tools for plotting data,
@@ -4185,7 +4185,7 @@ series of numeric vectors/matrices and factors.")
                (base32
                 "1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/ztable")
+    (home-page "https://cran.r-project.org/web/packages/ztable")
     (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
     (description
      "This package provides functions to make zebra-striped tables (tables
@@ -4206,7 +4206,7 @@ with alternating row colors) in LaTeX and HTML formats easily from
                (base32
                 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/vipor")
+    (home-page "https://cran.r-project.org/web/packages/vipor")
     (synopsis "Plot categorical data using noise and density estimates")
     (description
      "This package provides tools to generate a violin point plot, a
@@ -4245,7 +4245,7 @@ closely-packed, non-overlapping points.")
         (base32
          "0l8c6fql82cb246qh7hfgxb4s35qn0qfgy6dzvkx0zkz1cpqvx69"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/sourcetools")
+    (home-page "https://cran.r-project.org/web/packages/sourcetools")
     (synopsis "Tools for reading, tokenizing and parsing R code")
     (description
      "The sourcetools package provides both an R and C++ interface for the
@@ -4312,7 +4312,7 @@ Wall Street Journal, among others.  This package also provides
                (base32
                 "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/statmod")
+    (home-page "https://cran.r-project.org/web/packages/statmod")
     (native-inputs
      `(("gfortran" ,gfortran)))
     (synopsis "Statistical modeling")
@@ -4388,7 +4388,7 @@ published by the statistics blog FiveThirtyEight.")
          "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
     (properties `((upstream-name . "CompQuadForm")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/CompQuadForm")
+    (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
     (synopsis "Distribution function of quadratic forms in normal variables")
     (description
      "This package provides functions to compute the distribution function of
@@ -4437,7 +4437,7 @@ letters, as is often required for scientific publications.")
      `(("r-mass" ,r-mass)
        ("r-segmented" ,r-segmented)
        ("r-survival" ,r-survival)))
-    (home-page "http://cran.r-project.org/web/packages/mixtools")
+    (home-page "https://cran.r-project.org/web/packages/mixtools")
     (synopsis "Tools for analyzing finite mixture models")
     (description
      "This package provides a collection of R functions for analyzing finite
@@ -4483,7 +4483,7 @@ regression.")
          "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
     (properties `((upstream-name . "fastICA")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/fastICA")
+    (home-page "https://cran.r-project.org/web/packages/fastICA")
     (synopsis "FastICA algorithms to perform ICA and projection pursuit")
     (description
      "This package provides an implementation of the FastICA algorithm to
@@ -4525,7 +4525,7 @@ forest of trees using random inputs, for classification and regression.")
         (base32
          "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/diptest")
+    (home-page "https://cran.r-project.org/web/packages/diptest")
     (synopsis "Hartigan's dip test statistic for unimodality")
     (description
      "This package computes Hartigan's dip test statistic for unimodality,
@@ -4545,7 +4545,7 @@ original public code has been corrected.")
         (base32
          "0ynds453xprxv0jqqzi3blnv5w6vrdww9pvd1sq4lrr5ar3k3cq7"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/modeltools")
+    (home-page "https://cran.r-project.org/web/packages/modeltools")
     (synopsis "Tools and classes for statistical models")
     (description
      "This package provides a collection of tools to deal with statistical
@@ -4569,7 +4569,7 @@ to change in the future.")
      `(("r-lattice" ,r-lattice)
        ("r-modeltools" ,r-modeltools)
        ("r-nnet" ,r-nnet)))
-    (home-page "http://cran.r-project.org/web/packages/flexmix")
+    (home-page "https://cran.r-project.org/web/packages/flexmix")
     (synopsis "Flexible mixture modeling")
     (description
      "This package implements a general framework for finite mixtures of
@@ -4639,7 +4639,7 @@ data for species delimitation, nearest neighbor based noise detection.")
          "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
     (properties `((upstream-name . "DEoptimR")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/DEoptimR")
+    (home-page "https://cran.r-project.org/web/packages/DEoptimR")
     (synopsis "Differential evolution optimization in pure R")
     (description
      "This package provides a differential evolution (DE) stochastic
@@ -4687,7 +4687,7 @@ regression methodology including model selections and multivariate statistics.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mvtnorm" ,r-mvtnorm)))
-    (home-page "http://cran.r-project.org/web/packages/pcaPP")
+    (home-page "https://cran.r-project.org/web/packages/pcaPP")
     (synopsis "Robust PCA by projection pursuit")
     (description
      "This package provides functions for robust @dfn{principal component
@@ -4714,7 +4714,7 @@ analysis} (PCA) by projection pursuit.")
        ("r-robustbase" ,r-robustbase)))
     (native-inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/rrcov")
+    (home-page "https://cran.r-project.org/web/packages/rrcov")
     (synopsis "Scalable robust estimators with high breakdown Point")
     (description
      "This package provides an implementation of robust location and scatter
@@ -4736,7 +4736,7 @@ estimation and robust multivariate analysis with high breakdown point.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
-    (home-page "http://cran.r-project.org/web/packages/fit.models")
+    (home-page "https://cran.r-project.org/web/packages/fit.models")
     (synopsis "Compare fitted models")
     (description
      "The @code{fit.models} function and its associated methods (coefficients, print,
@@ -4769,7 +4769,7 @@ generally.")
        ("r-rrcov" ,r-rrcov)))
     (native-inputs
      `(("gfortran" ,gfortran)))
-    (home-page "http://cran.r-project.org/web/packages/robust")
+    (home-page "https://cran.r-project.org/web/packages/robust")
     (synopsis "Port of the S+ \"Robust Library\"")
     (description
      "This package is a port of the S+ \"Robust Library\".  It provides
@@ -4789,7 +4789,7 @@ multivariate analysis.")
         (base32
          "0lsgbg93hm0w1rdb813ry0ks2l0jfpyqzqkf3h3bj6fch0avcbv2"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/trimcluster")
+    (home-page "https://cran.r-project.org/web/packages/trimcluster")
     (synopsis "Cluster analysis with trimming")
     (description
      "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
@@ -4822,7 +4822,7 @@ of the points.")
        ("r-prabclus" ,r-prabclus)
        ("r-robustbase" ,r-robustbase)
        ("r-trimcluster" ,r-trimcluster)))
-    (home-page "http://cran.r-project.org/web/packages/fpc")
+    (home-page "https://cran.r-project.org/web/packages/fpc")
     (synopsis "Flexible procedures for clustering")
     (description
      "This package provides various methods for clustering and cluster validation.
@@ -4890,7 +4890,7 @@ showing the progress is useful e.g. bootstrap.")
          "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
     (properties `((upstream-name . "FNN")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/FNN")
+    (home-page "https://cran.r-project.org/web/packages/FNN")
     (synopsis "Fast nearest neighbor search algorithms and applications")
     (description
      "This package provides cover-tree and kd-tree fast k-nearest neighbor
@@ -4961,7 +4961,7 @@ decompositions of such matrices, and solutions of linear systems.")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)))
-    (home-page "http://cran.r-project.org/web/packages/ModelMetrics")
+    (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
     (synopsis "Rapid calculation of model metrics")
     (description
      "Written in C++ using @code{Rcpp}, this package provides a collection of
@@ -5034,7 +5034,7 @@ expected shortfall risk are also included.")
      `(("pkg-config" ,pkg-config)))
     (inputs
      `(("nlopt" ,nlopt)))
-    (home-page "http://cran.r-project.org/web/packages/nloptr")
+    (home-page "https://cran.r-project.org/web/packages/nloptr")
     (synopsis "R interface to NLopt")
     (description
      "This package is interface to NLopt, a library for nonlinear
@@ -5066,7 +5066,7 @@ algorithms.")
        ("r-nloptr" ,r-nloptr)
        ("r-mass" ,r-mass)
        ("r-nlme" ,r-nlme)))
-    (home-page "http://cran.r-project.org/web/packages/lme4")
+    (home-page "https://cran.r-project.org/web/packages/lme4")
     (synopsis "Linear mixed-effects models using eigen and S4")
     (description
       "This package provides fit linear and generalized linear mixed-effects
@@ -5262,7 +5262,7 @@ multivariate case.")
        ("r-mclust" ,r-mclust)
        ("r-mvtnorm" ,r-mvtnorm)
        ("r-sn" ,r-sn)))
-    (home-page "http://cran.r-project.org/web/packages/tclust")
+    (home-page "https://cran.r-project.org/web/packages/tclust")
     (synopsis "Robust trimmed clustering")
     (description
      "This package implements different robust clustering
@@ -5364,7 +5364,7 @@ is supported.")
      `(("r-rcpp" ,r-rcpp)
        ("r-stringr" ,r-stringr)))
     (home-page
-     "http://cran.r-project.org/web/packages/lubridate")
+     "https://cran.r-project.org/web/packages/lubridate")
     (synopsis "Make dealing with dates a little easier")
     (description
      "This package provides functions to work with date-times and time-spans:
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 54f210873e..a31801f7b4 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3844,7 +3844,7 @@ directory.")
     (propagated-inputs
      `(("r-digest" ,r-digest)
        ("r-rcpp" ,r-rcpp)))
-    (home-page "http://cran.r-project.org/web/packages/htmltools")
+    (home-page "https://cran.r-project.org/web/packages/htmltools")
     (synopsis "R tools for HTML")
     (description
      "This package provides tools for HTML generation and output in R.")
@@ -3959,7 +3959,7 @@ callback or connection interfaces.")
         (base32
          "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/hwriter")
+    (home-page "https://cran.r-project.org/web/packages/hwriter")
     (synopsis "Output R objects in HTML format")
     (description
      "This package provides easy-to-use and versatile functions to output R
@@ -3978,7 +3978,7 @@ objects in HTML format.")
         (base32
          "1vzjyvf57k1fjizlk28rby65y5lsww5qnfvgnhln74qwda7hvl3p"))))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/rjson")
+    (home-page "https://cran.r-project.org/web/packages/rjson")
     (synopsis "JSON library for R")
     (description
      "This package provides functions to convert R objects into JSON objects
@@ -5424,7 +5424,7 @@ files).  It currently supports linked brushing and filtering.")
     (properties `((upstream-name . "Rook")))
     (build-system r-build-system)
     (propagated-inputs `(("r-brew" ,r-brew)))
-    (home-page "http://cran.r-project.org/web/packages/Rook")
+    (home-page "https://cran.r-project.org/web/packages/Rook")
     (synopsis "Web server interface for R")
     (description
      "This package contains the Rook specification and convenience software
-- 
cgit 1.4.1


From d2c3be991c4e6c9ee1753475391efe571053a32e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 26 Dec 2017 12:59:44 +0000
Subject: doc: Fix typo.

* doc/guix.texi (Application Setup): Transpose words.
---
 doc/guix.texi | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index cb6754a4bc..d925b4edac 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -1509,7 +1509,7 @@ either in @file{$HOME/.guix-profile/share/emacs/site-lisp/} or in
 sub-directories of
 @file{$HOME/.guix-profile/share/emacs/site-lisp/guix.d/}.  The latter
 directory exists because potentially there may exist thousands of Emacs
-packages and storing all their files in a single directory may be not
+packages and storing all their files in a single directory may not be
 reliable (because of name conflicts).  So we think using a separate
 directory for each package is a good idea.  It is very similar to how
 the Emacs package system organizes the file structure (@pxref{Package
-- 
cgit 1.4.1


From db8ed7cee81cbd60b0f8d89a7bee377b369fdac1 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 31 Oct 2017 21:38:21 +0100
Subject: services: networking: Add a dependency override mechanism to
 <static-networking>.

* gnu/services/networking.scm (<static-networking>)[requirement]: New field.
(static-networking-shepherd-service): Don't override requirement for loopback.
(static-networking-service): Expose 'requirement' parameter.  Default to UDEV.
* gnu/services/base.scm (%base-services): Add (requirement '()) for loopback service.
* doc/guix.texi (Networking Services): Document it.
---
 doc/guix.texi               |  5 ++++-
 gnu/services/base.scm       |  1 +
 gnu/services/networking.scm | 14 +++++++++-----
 3 files changed, 14 insertions(+), 6 deletions(-)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index d925b4edac..ad018ffc8e 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -10392,9 +10392,12 @@ This is the type for statically-configured network interfaces.
 
 @deffn {Scheme Procedure} static-networking-service @var{interface} @var{ip} @
        [#:netmask #f] [#:gateway #f] [#:name-servers @code{'()}]
+       [#:requirement @code{'(udev)}]
 Return a service that starts @var{interface} with address @var{ip}.  If
 @var{netmask} is true, use it as the network mask.  If @var{gateway} is true,
-it must be a string specifying the default network gateway.
+it must be a string specifying the default network gateway.  @var{requirement}
+can be used to declare a dependency on another service before configuring the
+interface.
 
 This procedure can be called several times, one for each network
 interface of interest.  Behind the scenes what it does is extend
diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index 7fc8f6aa7e..f4681c804d 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -1986,6 +1986,7 @@ This service is not part of @var{%base-services}."
         (service static-networking-service-type
                  (list (static-networking (interface "lo")
                                           (ip "127.0.0.1")
+                                          (requirement '())
                                           (provision '(loopback)))))
         (syslog-service)
         (service urandom-seed-service-type)
diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm
index b0c23aafc7..c3ba0787c0 100644
--- a/gnu/services/networking.scm
+++ b/gnu/services/networking.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
+;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -51,6 +52,7 @@
             static-networking-ip
             static-networking-netmask
             static-networking-gateway
+            static-networking-requirement
 
             static-networking-service
             static-networking-service-type
@@ -145,22 +147,21 @@ fe80::1%lo0 apps.facebook.com\n")
            (default #f))
   (provision static-networking-provision
              (default #f))
+  (requirement static-networking-requirement
+               (default '()))
   (name-servers static-networking-name-servers    ;FIXME: doesn't belong here
                 (default '())))
 
 (define static-networking-shepherd-service
   (match-lambda
     (($ <static-networking> interface ip netmask gateway provision
-                            name-servers)
+                            requirement name-servers)
      (let ((loopback? (and provision (memq 'loopback provision))))
        (shepherd-service
 
-        ;; Unless we're providing the loopback interface, wait for udev to be up
-        ;; and running so that INTERFACE is actually usable.
-        (requirement (if loopback? '() '(udev)))
-
         (documentation
          "Bring up the networking interface using a static IP address.")
+        (requirement requirement)
         (provision (or provision
                        (list (symbol-append 'networking-
                                             (string->symbol interface)))))
@@ -263,6 +264,8 @@ network interface.")))
 (define* (static-networking-service interface ip
                                     #:key
                                     netmask gateway provision
+                                    ;; Most interfaces require udev to be usable.
+                                    (requirement '(udev))
                                     (name-servers '()))
   "Return a service that starts @var{interface} with address @var{ip}.  If
 @var{netmask} is true, use it as the network mask.  If @var{gateway} is true,
@@ -277,6 +280,7 @@ to handle."
                   (list (static-networking (interface interface) (ip ip)
                                            (netmask netmask) (gateway gateway)
                                            (provision provision)
+                                           (requirement requirement)
                                            (name-servers name-servers)))))
 
 (define dhcp-client-service-type
-- 
cgit 1.4.1


From 431703ffd022e77c50e09ceedfa110a7eb7e4ee5 Mon Sep 17 00:00:00 2001
From: ng0 <ng0@infotropique.org>
Date: Sat, 30 Dec 2017 22:52:54 +0100
Subject: gnu: services: Add MATE desktop service.

* gnu/services/desktop.scm (<mate-desktop-configuration>,
mate-desktop-service-type): New variable.
(mate-desktop-service): New public variable.

* doc/guix.texi (Desktop Services): Document the service.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
---
 doc/guix.texi            | 26 +++++++++++++++++++-------
 gnu/services/desktop.scm | 33 +++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+), 7 deletions(-)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index ad018ffc8e..2289d8201d 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -26,7 +26,7 @@ Copyright @copyright{} 2016 Ben Woodcroft@*
 Copyright @copyright{} 2016, 2017 Chris Marusich@*
 Copyright @copyright{} 2016, 2017 Efraim Flashner@*
 Copyright @copyright{} 2016 John Darrington@*
-Copyright @copyright{} 2016 ng0@*
+Copyright @copyright{} 2016, 2017 ng0@*
 Copyright @copyright{} 2016, 2017 Jan Nieuwenhuizen@*
 Copyright @copyright{} 2016 Julien Lepiller@*
 Copyright @copyright{} 2016 Alex ter Weele@*
@@ -12106,7 +12106,7 @@ The @code{(gnu services desktop)} module provides services that are
 usually useful in the context of a ``desktop'' setup---that is, on a
 machine running a graphical display server, possibly with graphical user
 interfaces, etc.  It also defines services that provide specific desktop
-environments like GNOME and XFCE.
+environments like GNOME, XFCE or MATE.
 
 To simplify things, the module defines a variable containing the set of
 services that users typically expect on a machine with a graphical
@@ -12131,9 +12131,10 @@ The @var{%desktop-services} variable can be used as the @code{services}
 field of an @code{operating-system} declaration (@pxref{operating-system
 Reference, @code{services}}).
 
-Additionally, the @code{gnome-desktop-service} and
-@code{xfce-desktop-service} procedures can add GNOME and/or XFCE to a
-system.  To ``add GNOME'' means that system-level services like the
+Additionally, the @code{gnome-desktop-service},
+@code{xfce-desktop-service} and @code{mate-desktop-service}
+procedures can add GNOME, XFCE and/or MATE to a system.
+To ``add GNOME'' means that system-level services like the
 backlight adjustment helpers and the power management utilities are
 added to the system, extending @code{polkit} and @code{dbus}
 appropriately, allowing GNOME to operate with elevated privileges on a
@@ -12144,6 +12145,11 @@ not only adds the @code{xfce} metapackage to the system profile, but it
 also gives the Thunar file manager the ability to open a ``root-mode''
 file management window, if the user authenticates using the
 administrator's password via the standard polkit graphical interface.
+To ``add MATE'' means that @code{polkit} and @code{dbus} are extended
+appropriately, allowing MATE to operate with elevated privileges on a
+limited number of special-purpose system interfaces.  Additionally,
+adding a service made by @code{mate-desktop-service} adds the MATE
+metapackage to the system profile.
 
 @deffn {Scheme Procedure} gnome-desktop-service
 Return a service that adds the @code{gnome} package to the system
@@ -12158,9 +12164,15 @@ file system as root from within a user session, after the user has
 authenticated with the administrator's password.
 @end deffn
 
-Because the GNOME and XFCE desktop services pull in so many packages,
+@deffn {Scheme Procedure} mate-desktop-service
+Return a service that adds the @code{mate} package to the system
+profile, and extends polkit with the actions from
+@code{mate-settings-daemon}.
+@end deffn
+
+Because the GNOME, XFCE and MATE desktop services pull in so many packages,
 the default @code{%desktop-services} variable doesn't include either of
-them by default.  To add GNOME or XFCE, just @code{cons} them onto
+them by default.  To add GNOME, XFCE orMATE, just @code{cons} them onto
 @code{%desktop-services} in the @code{services} field of your
 @code{operating-system}:
 
diff --git a/gnu/services/desktop.scm b/gnu/services/desktop.scm
index 78530b3454..64b999caba 100644
--- a/gnu/services/desktop.scm
+++ b/gnu/services/desktop.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2017 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2017 ng0 <ng0@infotropique.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -42,6 +43,7 @@
   #:use-module (gnu packages suckless)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages libusb)
+  #:use-module (gnu packages mate)
   #:use-module (guix records)
   #:use-module (guix packages)
   #:use-module (guix store)
@@ -82,6 +84,11 @@
             gnome-desktop-service
             gnome-desktop-service-type
 
+            mate-desktop-configuration
+            mate-desktop-configuration?
+            mate-desktop-service
+            mate-desktop-service-type
+
             xfce-desktop-configuration
             xfce-desktop-configuration?
             xfce-desktop-service
@@ -817,6 +824,32 @@ rules."
 and extends polkit with the actions from @code{gnome-settings-daemon}."
   (service gnome-desktop-service-type config))
 
+;; MATE Desktop service.
+;; TODO: Add mate-screensaver.
+
+(define-record-type* <mate-desktop-configuration> mate-desktop-configuration
+  make-mate-desktop-configuration
+  mate-desktop-configuration
+  (mate-package mate-package (default mate)))
+
+(define mate-desktop-service-type
+  (service-type
+   (name 'mate-desktop)
+   (extensions
+    (list (service-extension polkit-service-type
+                             (compose list
+                                      (package-direct-input-selector
+                                       "mate-settings-daemon")
+                                      mate-package))
+          (service-extension profile-service-type
+                             (compose list
+                                      mate-package))))))
+
+(define* (mate-desktop-service #:key (config (mate-desktop-configuration)))
+  "Return a service that adds the @code{mate} package to the system profile,
+and extends polkit with the actions from @code{mate-settings-daemon}."
+  (service mate-desktop-service-type config))
+
 
 ;;;
 ;;; XFCE desktop service.
-- 
cgit 1.4.1


From 1c27f72fc2770d68243dd95b7c05adc3b2b02ea4 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 30 Dec 2017 21:05:09 -0500
Subject: doc: Fix typo.

* doc/guix.texi (Desktop Services): "orMATE" --> "or MATE".
---
 doc/guix.texi | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'doc')

diff --git a/doc/guix.texi b/doc/guix.texi
index 2289d8201d..1d1f30f000 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -12172,7 +12172,7 @@ profile, and extends polkit with the actions from
 
 Because the GNOME, XFCE and MATE desktop services pull in so many packages,
 the default @code{%desktop-services} variable doesn't include either of
-them by default.  To add GNOME, XFCE orMATE, just @code{cons} them onto
+them by default.  To add GNOME, XFCE or MATE, just @code{cons} them onto
 @code{%desktop-services} in the @code{services} field of your
 @code{operating-system}:
 
-- 
cgit 1.4.1