Merge branch 'master' into core-updates

Makefile.am

@@ -274,10 +274,10 @@ dist_noinst_DATA = guix/tests.scm guix/tests/http.scm
 # Auxiliary files for packages.
 AUX_FILES =						\
   gnu/packages/aux-files/emacs/guix-emacs.el		\
-  gnu/packages/aux-files/linux-libre/4.16-arm.conf	\
+  gnu/packages/aux-files/linux-libre/4.17-arm.conf	\
-  gnu/packages/aux-files/linux-libre/4.16-arm64.conf	\
+  gnu/packages/aux-files/linux-libre/4.17-arm64.conf	\
-  gnu/packages/aux-files/linux-libre/4.16-i686.conf	\
+  gnu/packages/aux-files/linux-libre/4.17-i686.conf	\
-  gnu/packages/aux-files/linux-libre/4.16-x86_64.conf	\
+  gnu/packages/aux-files/linux-libre/4.17-x86_64.conf	\
   gnu/packages/aux-files/linux-libre/4.14-arm.conf	\
   gnu/packages/aux-files/linux-libre/4.14-i686.conf	\
   gnu/packages/aux-files/linux-libre/4.14-x86_64.conf	\

doc/guix.texi

@@ -16405,7 +16405,11 @@ saved to @code{/etc/letsencrypt/live/@var{name}/privkey.pem}.
 The @code{(gnu services dns)} module provides services related to the
 @dfn{domain name system} (DNS).  It provides a server service for hosting
 an @emph{authoritative} DNS server for multiple zones, slave or master.
-This service uses @uref{https://www.knot-dns.cz/, Knot DNS}.
+This service uses @uref{https://www.knot-dns.cz/, Knot DNS}.  And also a
+caching and forwarding DNS server for the LAN, which uses
+@uref{http://www.thekelleys.org.uk/dnsmasq/doc.html, dnsmasq}.
+
+@subsubheading Knot Service
 
 An example configuration of an authoritative server for two zones, one master
 and one slave, is:
@@ -16800,6 +16804,59 @@ The list of knot-zone-configuration used by this configuration.
 @end table
 @end deftp
 
+@subsubheading Dnsmasq Service
+
+@deffn {Scheme Variable} dnsmasq-service-type
+This is the type of the dnsmasq service, whose value should be an
+@code{dnsmasq-configuration} object as in this example:
+
+@example
+(service dnsmasq-service-type
+         (dnsmasq-configuration
+           (no-resolv? #t)
+           (servers '("192.168.1.1"))))
+@end example
+@end deffn
+
+@deftp {Data Type} dnsmasq-configuration
+Data type representing the configuration of dnsmasq.
+
+@table @asis
+@item @code{package} (default: @var{dnsmasq})
+Package object of the dnsmasq server.
+
+@item @code{no-hosts?} (default: @code{#f})
+When true, don't read the hostnames in /etc/hosts.
+
+@item @code{port} (default: @code{53})
+The port to listen on.  Setting this to zero completely disables DNS
+funtion, leaving only DHCP and/or TFTP.
+
+@item @code{local-service?} (default: @code{#t})
+Accept DNS queries only from hosts whose address is on a local subnet,
+ie a subnet for which an interface exists on the server.
+
+@item @code{listen-addresses} (default: @code{'()})
+Listen on the given IP addresses.
+
+@item @code{resolv-file} (default: @code{"/etc/resolv.conf"})
+The file to read the IP address of the upstream nameservers from.
+
+@item @code{no-resolv?} (default: @code{#f})
+When true, don't read @var{resolv-file}.
+
+@item @code{servers} (default: @code{'()})
+Specify IP address of upstream servers directly.
+
+@item @code{cache-size} (default: @code{150})
+Set the size of dnsmasq's cache.  Setting the cache size to zero
+disables caching.
+
+@item @code{no-negcache?} (default: @code{#f})
+When true, disable negative caching.
+
+@end table
+@end deftp
 
 @node VPN Services
 @subsubsection VPN Services

gnu/packages/bioinformatics.scm

@@ -13185,3 +13185,54 @@ Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
 include Markov models of discrete and continuous trait evolution and constant
 rate speciation and extinction.")
     (license license:gpl2+)))
+
+(define-public sjcount
+  ;; There is no tag for version 3.2, nor is there a release archive.
+  (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")
+        (revision "1"))
+    (package
+      (name "sjcount")
+      (version (git-version "3.2" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/pervouchine/sjcount-full.git")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "0gdgj35j249f04rqgq8ymcc1xg1vi9kzbajnjqpaq2wpbh8bl234"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                    ; requires a 1.4G test file
+         #:make-flags
+         (list (string-append "SAMTOOLS_DIR="
+                              (assoc-ref %build-inputs "samtools")
+                              "/lib/"))
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'configure
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "makefile"
+                 (("-I \\$\\{SAMTOOLS_DIR\\}")
+                  (string-append "-I" (assoc-ref inputs "samtools")
+                                 "/include/samtools"))
+                 (("-lz ") "-lz -lpthread "))
+               #t))
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (for-each (lambda (tool)
+                           (install-file tool
+                                         (string-append (assoc-ref outputs "out")
+                                                        "/bin")))
+                         '("j_count" "b_count" "sjcount"))
+               #t)))))
+      (inputs
+       `(("samtools" ,samtools-0.1)
+         ("zlib" ,zlib)))
+      (home-page "https://github.com/pervouchine/sjcount-full/")
+      (synopsis "Annotation-agnostic splice junction counting pipeline")
+      (description "Sjcount is a utility for fast quantification of splice
+junctions in RNA-seq data.  It is annotation-agnostic and offset-aware.  This
+version does count multisplits.")
+      (license license:gpl3+))))

gnu/packages/linux.scm

@@ -395,8 +395,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.16.13")
+(define %linux-libre-version "4.17")
-(define %linux-libre-hash "1frpqxv5ykf87hrmh62b8nxxcpv64a5w7lxw51z4vs82799inmng")
+(define %linux-libre-hash "0abbqrq96kn97jr02mf4ahqg7hl9vhq95c1l2z0s7jqrmhv1n8pb")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
@@ -404,8 +404,8 @@ It has been modified to remove all non-free binary blobs.")
                     %linux-compatible-systems
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.47")
+(define %linux-libre-4.14-version "4.14.48")
-(define %linux-libre-4.14-hash "1hm1vk6cdrwr971g5rcbq425fadn49580xa27zp1h6jz40n119wd")
+(define %linux-libre-4.14-hash "011lkq30gpvbgvg2p1nw2kqkig9a3qridy678rkx3fpah0ya4rhd")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
@@ -414,8 +414,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.105"
+  (make-linux-libre "4.9.106"
-                    "0kzznalr69c3z63y4gs38zs6cb0jmn41ggvz4i1gp2sqpmjm6ybb"
+                    "0wgyv15x2czd4nyw4smzp9923cl1ix7pjcry4zn3y61ivqxbqini"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

gnu/packages/music.scm

@@ -1987,7 +1987,7 @@ capabilities, custom envelopes, effects, etc.")
 (define-public yoshimi
   (package
     (name "yoshimi")
-    (version "1.5.7")
+    (version "1.5.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/yoshimi/"
@@ -1995,7 +1995,7 @@ capabilities, custom envelopes, effects, etc.")
                                   "/yoshimi-" version ".tar.bz2"))
               (sha256
                (base32
-                "1w916mmi6hh547a7icrgx6qr2kwxlxwlm6ampql427rshcz9r61k"))))
+                "0gwsr5srzy28hwqhfzrc8pswysmyra8kbww3bxfx8bq4mdjifdj6"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ; there are no tests
@@ -2189,16 +2189,28 @@ from the command line.")
 (define-public qtractor
   (package
     (name "qtractor")
-    (version "0.9.0")
+    (version "0.9.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://downloads.sourceforge.net/qtractor/"
                                   "qtractor-" version ".tar.gz"))
               (sha256
                (base32
-                "03892177k3jn2bsi366dhq28rcdsc1p9v5qqc0k6hg3cnrkh23na"))))
+                "07csbqr7q4m1j0pqg89kn7jdw0snd5lwna5rha0986s4plq4z1qb"))))
     (build-system gnu-build-system)
-    (arguments `(#:tests? #f)) ; no "check" target
+    (arguments
+     `(#:tests? #f  ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-build-with-qt-5.11
+           (lambda _
+             (substitute* "src/qtractorMeter.h"
+               (("#include <QFrame>" m)
+                (string-append "#include <QAction>\n" m)))
+             (substitute* "src/qtractorTrackButton.h"
+               (("#include <QPushButton>" m)
+                (string-append "#include <QAction>\n" m)))
+             #t)))))
     (inputs
      `(("qt" ,qtbase)
        ("qtx11extras" ,qtx11extras)

gnu/services/dns.scm

@@ -27,6 +27,7 @@
   #:use-module (guix records)
   #:use-module (guix gexp)
   #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-26)
   #:use-module (srfi srfi-34)
   #:use-module (srfi srfi-35)
   #:use-module (ice-9 match)
@@ -41,7 +42,10 @@
             knot-configuration
             define-zone-entries
             zone-file
-            zone-entry))
+            zone-entry
+
+            dnsmasq-service-type
+            dnsmasq-configuration))
 
 ;;;
 ;;; Knot DNS.
@@ -591,3 +595,76 @@
                                            knot-activation)
                         (service-extension account-service-type
                                            (const %knot-accounts))))))
+
+
+;;;
+;;; Dnsmasq.
+;;;
+
+(define-record-type* <dnsmasq-configuration>
+  dnsmasq-configuration make-dnsmasq-configuration
+  dnsmasq-configuration?
+  (package          dnsmasq-configuration-package
+                    (default dnsmasq))  ;package
+  (no-hosts?        dnsmasq-configuration-no-hosts?
+                    (default #f))       ;boolean
+  (port             dnsmasq-configuration-port
+                    (default 53))       ;integer
+  (local-service?   dnsmasq-configuration-local-service?
+                    (default #t))       ;boolean
+  (listen-addresses dnsmasq-configuration-listen-address
+                    (default '()))      ;list of string
+  (resolv-file      dnsmasq-configuration-resolv-file
+                    (default "/etc/resolv.conf")) ;string
+  (no-resolv?       dnsmasq-configuration-no-resolv?
+                    (default #f))       ;boolean
+  (servers          dnsmasq-configuration-servers
+                    (default '()))      ;list of string
+  (cache-size       dnsmasq-configuration-cache-size
+                    (default 150))      ;integer
+  (no-negcache?     dnsmasq-configuration-no-negcache?
+                    (default #f)))      ;boolean
+
+(define dnsmasq-shepherd-service
+  (match-lambda
+    (($ <dnsmasq-configuration> package
+                                no-hosts?
+                                port local-service? listen-addresses
+                                resolv-file no-resolv? servers
+                                cache-size no-negcache?)
+     (shepherd-service
+      (provision '(dnsmasq))
+      (requirement '(networking))
+      (documentation "Run the dnsmasq DNS server.")
+      (start #~(make-forkexec-constructor
+                '(#$(file-append package "/sbin/dnsmasq")
+                  "--keep-in-foreground"
+                  "--pid-file=/run/dnsmasq.pid"
+                  #$@(if no-hosts?
+                         '("--no-hosts")
+                         '())
+                  #$(format #f "--port=~a" port)
+                  #$@(if local-service?
+                         '("--local-service")
+                         '())
+                  #$@(map (cut format #f "--listen-address=~a" <>)
+                          listen-addresses)
+                  #$(format #f "--resolv-file=~a" resolv-file)
+                  #$@(if no-resolv?
+                         '("--no-resolv")
+                         '())
+                  #$@(map (cut format #f "--server=~a" <>)
+                          servers)
+                  #$(format #f "--cache-size=~a" cache-size)
+                  #$@(if no-negcache?
+                         '("--no-negcache")
+                         '()))
+                #:pid-file "/run/dnsmasq.pid"))
+      (stop #~(make-kill-destructor))))))
+
+(define dnsmasq-service-type
+  (service-type
+   (name 'dnsmasq)
+   (extensions
+    (list (service-extension shepherd-root-service-type
+                             (compose list dnsmasq-shepherd-service))))))