Merge branch 'master' into core-updates

build-aux/hydra/gnu-system.scm

@@ -330,12 +330,11 @@ (define (load-manifest manifest)
        (set-current-module (make-user-module '((guix profiles) (gnu))))
        (primitive-load manifest))))
 
-  (parameterize ((%graft? #f))
+  (delete-duplicates!
-    (delete-duplicates!
+   (map manifest-entry-item
-     (map manifest-entry-item
+        (append-map (compose manifest-entries
-          (append-map (compose manifest-entries
+                             load-manifest)
-                               load-manifest)
+                    manifests))))
-                      manifests)))))
 
 
 ;;;

doc/guix.texi

@@ -7268,6 +7268,36 @@ The following options can be used to customize GnuPG operation:
 Use @var{command} as the GnuPG 2.x command.  @var{command} is searched
 for in @code{$PATH}.
 
+@item --keyring=@var{file}
+Use @var{file} as the keyring for upstream keys.  @var{file} must be in the
+@dfn{keybox format}.  Keybox files usually have a name ending in @file{.kbx}
+and the GNU@tie{}Privacy Guard (GPG) can manipulate these files
+(@pxref{kbxutil, @command{kbxutil},, gnupg, Using the GNU Privacy Guard}, for
+information on a tool to manipulate keybox files).
+
+When this option is omitted, @command{guix refresh} uses
+@file{~/.config/guix/upstream/trustedkeys.kbx} as the keyring for upstream
+signing keys.  OpenPGP signatures are checked against keys from this keyring;
+missing keys are downloaded to this keyring as well (see
+@option{--key-download} below.)
+
+You can export keys from your default GPG keyring into a keybox file using
+commands like this one:
+
+@example
+gpg --export rms@@gnu.org | kbxutil --import-openpgp >> mykeyring.kbx
+@end example
+
+Likewise, you can fetch keys to a specific keybox file like this:
+
+@example
+gpg --no-default-keyring --keyring mykeyring.kbx \
+  --recv-keys @value{OPENPGP-SIGNING-KEY-ID}
+@end example
+
+@ref{GPG Configuration Options, @option{--keyring},, gnupg, Using the GNU
+Privacy Guard}, for more information on GPG's @option{--keyring} option.
+
 @item --key-download=@var{policy}
 Handle missing OpenPGP keys according to @var{policy}, which may be one
 of:
@@ -7711,6 +7741,13 @@ This is useful to precisely refer to a package, as in this example:
 @example
 guix graph -e '(@@@@ (gnu packages commencement) gnu-make-final)'
 @end example
+
+@item --system=@var{system}
+@itemx -s @var{system}
+Display the graph for @var{system}---e.g., @code{i686-linux}.
+
+The package dependency graph is largely architecture-independent, but there
+are some architecture-dependent bits that this option allows you to visualize.
 @end table
 
 
@@ -11575,6 +11612,54 @@ Thus, it can be instantiated like this:
 @end lisp
 @end defvr
 
+@cindex iptables
+@defvr {Scheme Variable} iptables-service-type
+This is the service type to set up an iptables configuration. iptables is a
+packet filtering framework supported by the Linux kernel.  This service
+supports configuring iptables for both IPv4 and IPv6.  A simple example
+configuration rejecting all incoming connections except those to the ssh port
+22 is shown below.
+
+@lisp
+(service iptables-service-type
+         (iptables-configuration
+          (ipv4-rules (plain-file "iptables.rules" "*filter
+:INPUT ACCEPT
+:FORWARD ACCEPT
+:OUTPUT ACCEPT
+-A INPUT -p tcp --dport 22 -j ACCEPT
+-A INPUT -j REJECT --reject-with icmp-port-unreachable
+COMMIT
+"))
+          (ipv6-rules (plain-file "ip6tables.rules" "*filter
+:INPUT ACCEPT
+:FORWARD ACCEPT
+:OUTPUT ACCEPT
+-A INPUT -p tcp --dport 22 -j ACCEPT
+-A INPUT -j REJECT --reject-with icmp6-port-unreachable
+COMMIT
+"))))
+@end lisp
+@end defvr
+
+@deftp {Data Type} iptables-configuration
+The data type representing the configuration of iptables.
+
+@table @asis
+@item @code{iptables} (default: @code{iptables})
+The iptables package that provides @code{iptables-restore} and
+@code{ip6tables-restore}.
+@item @code{ipv4-rules} (default: @code{%iptables-accept-all-rules})
+The iptables rules to use.  It will be passed to @code{iptables-restore}.
+This may be any ``file-like'' object (@pxref{G-Expressions, file-like
+objects}).
+@item @code{ipv6-rules} (default: @code{%iptables-accept-all-rules})
+The ip6tables rules to use.  It will be passed to @code{ip6tables-restore}.
+This may be any ``file-like'' object (@pxref{G-Expressions, file-like
+objects}).
+@end table
+@end deftp
+
 @cindex NTP
 @cindex real time clock
 @deffn {Scheme Procedure} ntp-service [#:ntp @var{ntp}] @

gnu/bootloader/u-boot.scm

@@ -31,7 +31,7 @@ (define-module (gnu bootloader u-boot)
             u-boot-a20-olinuxino-lime-bootloader
             u-boot-a20-olinuxino-lime2-bootloader
             u-boot-a20-olinuxino-micro-bootloader
-            u-boot-banana-pi-m2-ultra-bootloader
+            u-boot-bananapi-m2-ultra-bootloader
             u-boot-beaglebone-black-bootloader
             u-boot-mx6cuboxi-bootloader
             u-boot-nintendo-nes-classic-edition-bootloader
@@ -148,10 +148,10 @@ (define u-boot-a20-olinuxino-micro-bootloader
    (inherit u-boot-allwinner-bootloader)
    (package u-boot-a20-olinuxino-micro)))
 
-(define u-boot-banana-pi-m2-ultra-bootloader
+(define u-boot-bananapi-m2-ultra-bootloader
   (bootloader
    (inherit u-boot-allwinner-bootloader)
-   (package u-boot-banana-pi-m2-ultra)))
+   (package u-boot-bananapi-m2-ultra)))
 
 (define u-boot-mx6cuboxi-bootloader
   (bootloader

gnu/local.mk

@@ -1012,7 +1012,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/openocd-nrf52.patch			\
   %D%/packages/patches/opensmtpd-fix-crash.patch		\
   %D%/packages/patches/openssl-runpath.patch			\
-  %D%/packages/patches/openssl-1.1.0-c-rehash-in.patch		\
+  %D%/packages/patches/openssl-1.1-c-rehash-in.patch		\
   %D%/packages/patches/openssl-c-rehash-in.patch		\
   %D%/packages/patches/orpheus-cast-errors-and-includes.patch	\
   %D%/packages/patches/osip-CVE-2017-7853.patch			\
@@ -1231,7 +1231,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/xapian-revert-5489fb2f8.patch		\
   %D%/packages/patches/xboing-CVE-2004-0149.patch		\
   %D%/packages/patches/xf86-video-ark-remove-mibstore.patch	\
-  %D%/packages/patches/xf86-video-ast-remove-mibstore.patch	\
   %D%/packages/patches/xf86-video-geode-glibc-2.20.patch	\
   %D%/packages/patches/xf86-video-i128-remove-mibstore.patch	\
   %D%/packages/patches/xf86-video-mach64-glibc-2.20.patch	\

gnu/packages/admin.scm

@@ -963,7 +963,7 @@ (define-public rottlog
 (define-public sudo
   (package
     (name "sudo")
-    (version "1.8.25")
+    (version "1.8.25p1")
     (source (origin
               (method url-fetch)
               (uri
@@ -973,7 +973,7 @@ (define-public sudo
                                     version ".tar.gz")))
               (sha256
                (base32
-                "0hfw6pcwjvv1vvnhb4n1p210306jm4npz99p9cfhbd33yrhhzkwx"))
+                "0nqri46d4dpycj96zin2f2wszmhm7q9mr68hhj9sp81pgmx9rjcx"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1236,7 +1236,7 @@ (define-public wakelan
 (define-public dmidecode
   (package
     (name "dmidecode")
-    (version "3.1")
+    (version "3.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1244,7 +1244,7 @@ (define-public dmidecode
                     version ".tar.xz"))
               (sha256
                (base32
-                "1h0sg0lxa15nzf8s7884p6q7p6md9idm0c79wyqmk32l4ndwwrnp"))))
+                "1pcfhcgs2ifdjwp7amnsr3lq95pgxpr150bjhdinvl505px0cw07"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases (delete 'configure))
@@ -2779,6 +2779,8 @@ (define-public python-pyudev
                #t))))))
     (inputs
      `(("eudev" ,eudev)))
+    (propagated-inputs
+     `(("python-six" ,python-six)))
     (native-inputs
      `(("python-docutils" ,python-docutils)
        ("python-hypothesis" ,python-hypothesis)

gnu/packages/bioinformatics.scm

@@ -13699,3 +13699,27 @@ (define-public python-pygenometracks
 options), bedgraph, links (represented as arcs), and Hi-C matrices.
 pyGenomeTracks can make plots with or without Hi-C data.")
     (license license:gpl3+)))
+
+(define-public python-hic2cool
+  (package
+    (name "python-hic2cool")
+    (version "0.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "hic2cool" version))
+       (sha256
+        (base32
+         "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl"))))
+    (build-system python-build-system)
+    (arguments '(#:tests? #f)) ; no tests included
+    (propagated-inputs
+     `(("python-cooler" ,python-cooler)))
+    (home-page "https://github.com/4dn-dcic/hic2cool")
+    (synopsis "Converter for .hic and .cool files")
+    (description
+     "This package provides a converter between @code{.hic} files (from
+juicer) and single-resolution or multi-resolution @code{.cool} files (for
+cooler).  Both @code{hic} and @code{cool} files describe Hi-C contact
+matrices.")
+    (license license:expat)))

gnu/packages/bootloaders.scm

@@ -382,7 +382,7 @@ (define u-boot
        ("sdl" ,sdl)
        ("swig" ,swig)))
     (build-system  gnu-build-system)
-    (home-page "http://www.denx.de/wiki/U-Boot/")
+    (home-page "https://www.denx.de/wiki/U-Boot/")
     (synopsis "ARM bootloader")
     (description "U-Boot is a bootloader used mostly for ARM boards. It
 also initializes the boards (RAM etc).")
@@ -571,7 +571,7 @@ (define-public u-boot-pine64-plus
        `(("firmware" ,arm-trusted-firmware-pine64-plus)
          ,@(package-native-inputs base))))))
 
-(define-public u-boot-banana-pi-m2-ultra
+(define-public u-boot-bananapi-m2-ultra
   (make-u-boot-package "Bananapi_M2_Ultra" "arm-linux-gnueabihf"))
 
 (define-public u-boot-a20-olinuxino-lime

gnu/packages/busybox.scm

@@ -31,7 +31,7 @@ (define-module (gnu packages busybox)
 (define-public busybox
   (package
     (name "busybox")
-    (version "1.29.1")
+    (version "1.29.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -39,7 +39,7 @@ (define-public busybox
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1hqlr5b3bsyb6avadz1z4za6pyl32r1krnpcpwwqilhnx8q0f9gw"))))
+                "1dzg45vgy2w1xcd3p6h8d76ykhabbvk1h0lf8yb24ikrwlv8cr4p"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases

gnu/packages/cdrom.scm

@@ -152,14 +152,14 @@ (define-public libcdio-paranoia
 (define-public xorriso
   (package
     (name "xorriso")
-    (version "1.4.8")
+    (version "1.5.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/xorriso/xorriso-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "10c44yr3dpmwxa7rf23mwfsy1bahny3jpcg9ig0xjv090jg0d0pc"))))
+               "0aq6lvlwlkxz56l5sbvgycr6j5c82ch2bv6zrnc2345ibfpafgx9"))))
     (build-system gnu-build-system)
     (inputs
      `(("acl" ,acl)
@@ -727,14 +727,14 @@ (define-public ccd2cue
 (define-public libburn
   (package
     (name "libburn")
-    (version "1.4.8")
+    (version "1.5.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://files.libburnia-project.org/releases/"
                                  "libburn-" version ".tar.gz"))
              (sha256
               (base32
-               "19lxnzn8bz70glrrrn2hs43gf5g7gfbcka9rcbckhv1pb7is509y"))))
+               "1gg2kgnqvaa2fwghai62prxz6slpak1f6bvgjh8m4dn16v114asq"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -749,14 +749,14 @@ (define-public libburn
 (define-public libisofs
   (package
     (name "libisofs")
-    (version "1.4.8")
+    (version "1.5.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://files.libburnia-project.org/releases/"
                                  "libisofs-" version ".tar.gz"))
              (sha256
               (base32
-               "0scvqb72qq24wcg814p1iw1dknldl21hr1hxsc1wy9vc6vgyk7fw"))))
+               "001l3akf3wb6msl9man776w560iqyvsbwwzs7d7y7msx13irspys"))))
     (build-system gnu-build-system)
     (inputs
      `(("zlib" ,zlib)

gnu/packages/cinnamon.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -50,13 +51,10 @@ (define-public cinnamon-desktop
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
+         (add-before 'bootstrap 'skip-premature-configure
            (lambda _
-             (mkdir-p "m4")
+             (setenv "NOCONFIGURE" "set")
-             (zero?
+             #t)))))
-              (and (system* "glib-gettextize" "--force" "--copy")
-                   (system* "intltoolize" "--force" "--copy" "--automake")
-                   (system* "autoreconf" "--verbose" "--force" "--install"))))))))
     ;; TODO: package 'libgsystem'.
     (inputs
      `(("accountsservice" ,accountsservice)

gnu/packages/cran.scm

@@ -5797,3 +5797,81 @@ (define-public r-abjutils
 It also implements functions for text cleaning, such as accentuation
 removal.")
     (license license:expat)))
+
+(define-public r-abnormality
+  (package
+    (name "r-abnormality")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abnormality" version))
+       (sha256
+        (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)))
+    (home-page "https://cran.r-project.org/web/packages/abnormality/")
+    (synopsis "Measure a subject's abnormality with respect to a reference population")
+    (description
+     "This package contains functions to implement the methodology and
+considerations laid out by Marks et al. in the article \"Measuring abnormality
+in high dimensional spaces: applications in biomechanical gait analysis\".
+Using high-dimensional datasets to measure a subject's overall level of
+abnormality as compared to a reference population is often needed in outcomes
+research.")
+    (license license:expat)))
+
+(define-public r-abodoutlier
+  (package
+    (name "r-abodoutlier")
+    (version "0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abodOutlier" version))
+       (sha256
+        (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
+    (properties `((upstream-name . "abodOutlier")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cluster" ,r-cluster)))
+    (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
+    (synopsis "Angle-based outlier detection")
+    (description
+     "This package performs angle-based outlier detection on a given data
+frame.  It offers three methods to process data:
+@enumerate
+@item full but slow implementation using all the data that has cubic
+  complexity;
+@item a fully randomized method;
+@item a method using k-nearest neighbours.
+@end enumerate
+These algorithms are well suited for high dimensional data outlier
+detection.")
+    (license license:expat)))
+
+(define-public r-abps
+  (package
+    (name "r-abps")
+    (version "0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ABPS" version))
+       (sha256
+        (base32 "1k3f5i34f4w2khkszb4qhwwcpiy7gsfh82vjr6rypwg6rx5rjclq"))))
+    (properties `((upstream-name . "ABPS")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-kernlab" ,r-kernlab)))
+    (home-page "https://cran.r-project.org/web/packages/ABPS/")
+    (synopsis "Abnormal blood profile score to detect blood doping")
+    (description
+     "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
+The ABPS is a part of the Athlete biological passport program of the World
+anti-doping agency, which combines several blood parameters into a single
+score in order to detect blood doping.  The package also contains functions to
+calculate other scores used in anti-doping programs, such as the ratio of
+hemoglobin to reticulocytes (OFF-score), as well as example data.")
+    (license license:gpl2+)))

gnu/packages/cups.scm

@@ -574,14 +574,14 @@ (define-public foomatic-filters
 (define-public foo2zjs
   (package
     (name "foo2zjs")
-    (version "20171202")
+    (version "20180910")
     (source (origin
               (method url-fetch)
               ;; XXX: This is an unversioned URL!
               (uri "http://foo2zjs.rkkda.com/foo2zjs.tar.gz")
               (sha256
                (base32
-                "10m1ksbzqsrsl4faqyl73ahfnj2hv1y3zrmr366zvjg7w3l6ag5n"))))
+                "1clddqy4y4vvws0lllv1v90dfiihihdc23bn93c544yb3fvmwmr6"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases

gnu/packages/electronics.scm

@@ -60,7 +60,7 @@ (define-public libserialport
 (define-public libsigrokdecode
   (package
     (name "libsigrokdecode")
-    (version "0.5.1")
+    (version "0.5.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -68,7 +68,7 @@ (define-public libsigrokdecode
                     version ".tar.gz"))
               (sha256
                (base32
-                "07mmb6s62ncqqgsc6szilj2yxixf6gg99ggbzsjlbhp4b9aqnga9"))))
+                "1w434nl1syjkvwl08lji3r9sr60lbxp1nqys8hqwzv2lgiwrx3g0"))))
     (outputs '("out" "doc"))
     (arguments
      `(#:phases

gnu/packages/emacs.scm

@@ -579,16 +579,16 @@ (define-public magit-svn
 (define-public emacs-magit-popup
   (package
     (name "emacs-magit-popup")
-    (version "2.12.3")
+    (version "2.12.4")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append
+              (uri (git-reference
-                    "https://github.com/magit/magit-popup/archive/v"
+                    (url "https://github.com/magit/magit-popup.git")
-                    version ".tar.gz"))
+                    (commit (string-append "v" version))))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1kz6vj67awkwf9y2wj6m3l2him3znm08z6bkdvnmfr6rwd96dr39"))))
+                "08952nzn0cb6gxscqyiljk4fq2zxjvr3ism0lvgw0gs9hl5phiwx"))))
     (build-system emacs-build-system)
     (arguments
      `(#:phases
@@ -7182,6 +7182,28 @@ (define-public emacs-dired-hacks
 @end itemize\n")
       (license license:gpl3+))))
 
+(define-public emacs-dired-sidebar
+  (let ((commit "06bd0d40bab812c61a668129daf29ba359424454")
+        (revision "0"))
+    (package
+      (name "emacs-dired-sidebar")
+      (home-page "https://github.com/jojojames/dired-sidebar")
+      (version (git-version "0.0.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference (url home-page) (commit commit)))
+                (sha256
+                 (base32
+                  "0lvwvq6sl80sha9fq5m4568sg534dhmifyjqw75bqddcbf3by84x"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-dired-subtree" ,emacs-dired-hacks)))
+      (synopsis "Sidebar for Emacs using Dired")
+      (description
+       "This package provides a sidebar for Emacs similar to @code{NeoTree}
+or @code{treemacs}, but leveraging @code{Dired} to do the job of display.")
+      (license license:gpl3+))))
+
 (define-public emacs-which-key
   (package
     (name "emacs-which-key")

gnu/packages/enlightenment.scm

@@ -62,7 +62,7 @@ (define-module (gnu packages enlightenment)
 (define-public efl
   (package
     (name "efl")
-    (version "1.21.0")
+    (version "1.21.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -70,7 +70,7 @@ (define-public efl
                     version ".tar.xz"))
               (sha256
                (base32
-                "0jxfrcz2aq1synxzd6sh9nhxz7fg9qgz0idr8zj6gaiplmwbwrby"))))
+                "0a5907h896pvpix7a6idc2fspzy6d78xrzf84k8y9fyvnd14nxs4"))))
     (outputs '("out"       ; 49 MB
                "include")) ; 17 MB
     (build-system gnu-build-system)
@@ -251,7 +251,7 @@ (define-public rage
 (define-public enlightenment
   (package
     (name "enlightenment")
-    (version "0.22.3")
+    (version "0.22.4")
     (source (origin
               (method url-fetch)
               (uri
@@ -259,7 +259,7 @@ (define-public enlightenment
                               name "/" name "-" version ".tar.xz"))
               (sha256
                (base32
-                "16zydv7z94aw3rywmb9gr8ya85k7b75h22wng95lfx1x0y1yb0ad"))
+                "0ygy891rrw5c7lhk539nhif77j88phvz2h0fhx172iaridy9kx2r"))
               (patches (search-patches "enlightenment-fix-setuid-path.patch"))))
     (build-system gnu-build-system)
     (arguments

gnu/packages/games.scm

@@ -2694,7 +2694,7 @@ (define-public einstein
 (define-public powwow
   (package
     (name "powwow")
-    (version "1.2.17")
+    (version "1.2.18")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2703,11 +2703,11 @@ (define-public powwow
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1xmsg2y7qcvj67i9ilnih0mvfxcpni7fzrz343x9rdfnkkzf3pp8"))))
+                "1gf0jc1vfv05lxij51n3c1dqn3aiiy2kj1v6q14an3wm7yl7cllp"))))
     (inputs
      `(("ncurses" ,ncurses)))
     (build-system gnu-build-system)
-    (home-page "http://www.hoopajoo.net/projects/powwow.html")
+    (home-page "https://www.hoopajoo.net/projects/powwow.html")
     (synopsis "MUD and telnet client")
     (description
      "POWWOW is a client software which can be used for telnet as well as for

gnu/packages/gnome.scm

@@ -4156,7 +4156,7 @@ (define-public eolie
        ("gtkspell3" ,gtkspell3)
        ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
        ("webkitgtk" ,webkitgtk)))
-    (home-page "https://github.com/gnumdk/eolie/")
+    (home-page "https://wiki.gnome.org/Apps/Eolie")
     (synopsis "Web browser for GNOME")
     (description
      "Eolie is a new web browser for GNOME.  It features Firefox sync support,
@@ -4438,7 +4438,7 @@ (define-public gexiv2
 (define-public shotwell
   (package
     (name "shotwell")
-    (version "0.28.0")
+    (version "0.28.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -4446,7 +4446,7 @@ (define-public shotwell
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1d797nmlz9gs6ri0h65b76s40ss6ma6h6405xqx03lhg5xni3kmg"))))
+                "03k7n2kmzqn11kf3733w7m6xjh2b5q9xr84za2hli11fjymzaxm9"))))
     (build-system glib-or-gtk-build-system)
     (propagated-inputs
      `(("dconf" ,dconf)))

gnu/packages/golang.scm

@@ -389,7 +389,7 @@ (define-public go-1.10
   (package
     (inherit go-1.9)
     (name "go")
-    (version "1.10.3")
+    (version "1.10.4")
     (source
      (origin
        (method url-fetch)
@@ -397,7 +397,7 @@ (define-public go-1.10
                            name version ".src.tar.gz"))
        (sha256
         (base32
-         "1wjmw65nfkkzz084695gdgn13sbjcaafy2y5370d214pdk31qysn"))))
+         "10ap5pan71y2hdwzv4cg8wx4sy8fkcz5520rm1ldjg25xmjlkr3g"))))
     (arguments
      (substitute-keyword-arguments (package-arguments go-1.9)
        ((#:phases phases)

gnu/packages/guile.scm

@@ -2175,4 +2175,31 @@ (define-public guile-sparql
 using S-expressions.")
    (license license:gpl3+)))
 
+(define-public guile-debbugs
+  (package
+    (name "guile-debbugs")
+    (version "0.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnu/guile-debbugs/guile-debbugs-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "16l8910p57im6s3j93xhdaqvgfy6ms5n97177mrch3y961z5hy0i"))
+              (modules '((guix build utils)))
+              (snippet
+               '(substitute* "Makefile.in"
+                  (("^godir = (.*)/ccache" _ prefix)
+                   (string-append "godir = " prefix "/site-ccache"))))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("guile" ,guile-2.2)
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://savannah.gnu.org/projects/guile-debbugs/")
+    (synopsis "Guile interface to the Debbugs bug tracking service")
+    (description
+     "This package provides a Guile library to communicate with a Debbugs bug
+tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
+    (license license:gpl3+)))
+
 ;;; guile.scm ends here

gnu/packages/image-viewers.scm

@@ -60,7 +60,7 @@ (define-module (gnu packages image-viewers)
 (define-public feh
   (package
     (name "feh")
-    (version "2.27.1")
+    (version "2.28")
     (home-page "https://feh.finalrewind.org/")
     (source (origin
               (method url-fetch)
@@ -68,7 +68,7 @@ (define-public feh
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "10zk76l491s22qrv86rax6cvpgwyl3qq0izl2pbk0k1z1kw3ihvf"))))
+                "1nfka7w6pzj2bbwx8vydr2wwm7z8mrbqiy1xrq97c1g5bxy2vlhk"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases (delete 'configure))

gnu/packages/image.scm

@@ -267,8 +267,16 @@ (define-public libjpeg
     "Libjpeg implements JPEG image encoding, decoding, and transcoding.
 JPEG is a standardized compression method for full-color and gray-scale
 images.
-The included programs provide conversion between the JPEG format and
+It also includes programs that provide conversion between the JPEG format and
-image files in PBMPLUS PPM/PGM, GIF, BMP, and Targa file formats.")
+image files in PBMPLUS PPM/PGM, GIF, BMP, and Targa file formats, as well as
+lossless JPEG manipulations such as rotation, scaling or cropping:
+@enumerate
+@item cjpeg
+@item djpeg
+@item jpegtran
+@item rdjpgcom
+@item wrjpgcom
+@end enumerate")
    (license license:ijg)
    (home-page "http://www.ijg.org/")))
 
@@ -1350,8 +1358,9 @@ (define-public libiptcdata
     (build-system gnu-build-system)
     (home-page "http://libiptcdata.sourceforge.net/")
     (synopsis "IPTC metadata manipulation library")
-    (description "Libiptcdata is a C library for manipulating the International
+    (description
-Press Telecommunications Council (IPTC) metadata stored within multimedia files
+     "Libiptcdata is a C library for manipulating the International Press
+Telecommunications Council (@dfn{IPTC}) metadata stored within multimedia files
 such as images.  This metadata can include captions and keywords, often used by
 popular photo management applications.  The library provides routines for
 parsing, viewing, modifying, and saving this metadata.")

gnu/packages/libreoffice.scm

@@ -654,19 +654,19 @@ (define-public libodfgen
 (define-public libmwaw
   (package
     (name "libmwaw")
-    (version "0.3.12")
+    (version "0.3.14")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://sourceforge/" name "/" name "/" name "-"
                           version "/" name "-" version ".tar.xz"))
       (sha256 (base32
-               "1ryi1v38lgy5kv84fzjqkawidrg30y4hlqrz1v262792wzkad4bn"))))
+               "1s9wyf8pyh3fbazq2d2b6fgi7s7bid60viw2xbdkmn2ywlfbza5c"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
        ("pkg-config" ,pkg-config)))
-    (propagated-inputs ; in Requires field of .pkg
+    (propagated-inputs                  ; in Requires field of .pkg
      `(("librevenge" ,librevenge)))
     (inputs
      `(("boost" ,boost)
@@ -676,7 +676,7 @@ (define-public libmwaw
     (description "Libmwaw contains some import filters for old Macintosh
 text documents (MacWrite, ClarisWorks, ... ) and for some graphics and
 spreadsheet documents.")
-    (license (list mpl2.0 lgpl2.1+)))) ; dual license
+    (license (list mpl2.0 lgpl2.1+))))  ; dual license
 
 (define-public libstaroffice
   (package
@@ -704,19 +704,19 @@ (define-public libstaroffice
 (define-public libwps
   (package
     (name "libwps")
-    (version "0.4.9")
+    (version "0.4.10")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://sourceforge/" name "/" name "/"
                           name "-" version "/" name "-" version ".tar.xz"))
       (sha256 (base32
-               "08j9nxnrzxsnq35d9l824ad8w8az42fivaxn8ajl85dv6g3v1ghk"))))
+               "1ji9zd4wxmas03g8jyx0ih0amrqfazm5874a2v9rd7va50sf088l"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
        ("pkg-config" ,pkg-config)))
-    (propagated-inputs ; in Requires field of .pkg
+    (propagated-inputs                  ; in Requires field of .pkg
      `(("librevenge" ,librevenge)))
     (inputs
      `(("boost" ,boost)
@@ -725,7 +725,7 @@ (define-public libwps
     (synopsis "Import library for Microsoft Works text documents")
     (description "Libwps is a library for importing files in the Microsoft
 Works word processor file format.")
-    (license (list mpl2.0 lgpl2.1+)))) ; dual license
+    (license (list mpl2.0 lgpl2.1+))))  ; dual license
 
 (define-public libzmf
   (package

gnu/packages/linux.scm

@@ -399,8 +399,8 @@ (define %linux-compatible-systems '("x86_64-linux" "i686-linux" "armhf-linux" "a
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.7")
+(define %linux-libre-version "4.18.8")
-(define %linux-libre-hash "1gn3ip2blczfr5hl20x6c93z8v7h528kl423pzkcn22hin6717wd")
+(define %linux-libre-hash "163awpba1yd0x33xzj5dczimk4y96xc28syc4w2ad0qafgapng8l")
 
 (define %linux-libre-4.18-patches
   (list %boot-logo-patch
@@ -430,8 +430,8 @@ (define-public linux-libre
                     #:patches %linux-libre-4.18-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.69")
+(define %linux-libre-4.14-version "4.14.70")
-(define %linux-libre-4.14-hash "08pw5hywlx3rsavj74qa17fm9hmhaw2rb1d3ahaqmd1zzsddb3qf")
+(define %linux-libre-4.14-hash "138v51m6k57wnvlf9c22dad0w819mfb8f95i6w99mlg69qpwdvag")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
@@ -440,14 +440,14 @@ (define-public linux-libre-4.14
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.126"
+  (make-linux-libre "4.9.127"
-                    "0qa9zxa7isn20b9sbjcyrqfynd00phddv3yindp5dmvsng1kwxj8"
+                    "0q7h5gnl3ikic0pvwrxp78pz56yvijhz6s84gb92xywi1v3dd8mh"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.155"
+  (make-linux-libre "4.4.156"
-                    "1gcnwrgv0xghr550lcl6dmxdl59drzbi02mwp78g8vjql6ihdfys"
+                    "13j4jb4hifh3fah2ysy2425fakwqqdh2z23lf4i0frxa1xl974h2"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

gnu/packages/lisp.scm

@@ -8,6 +8,7 @@
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Benjamin Slade <slade@jnanam.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -62,6 +63,7 @@ (define-module (gnu packages lisp)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages xorg)
+  #:use-module (gnu packages perl)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1))
 
@@ -1009,8 +1011,8 @@ (define-public ecl-stumpwm
 ;; we expose the union of these as `sbcl-slynk'.  The following variable
 ;; describes the base module.
 (define sbcl-slynk-boot0
-  (let ((revision "1")
+  (let ((revision "2")
-        (commit "5706cd45d484a4f25795abe8e643509d31968aa2"))
+        (commit "cbf84c36c4eca8b032e3fd16177a7bc02df3ec4c"))
     (package
       (name "sbcl-slynk-boot0")
       (version (string-append "1.0.0-beta-" revision "." (string-take commit 7)))
@@ -1022,7 +1024,7 @@ (define sbcl-slynk-boot0
            (url "https://github.com/joaotavora/sly.git")
            (commit commit)))
          (sha256
-          (base32 "0h4gg3sndl2bf6jdnx9nrf14p9hhi43hagrl0f4v4l11hczl8w81"))
+          (base32 "13dyhsravn591p7g6is01mp2ynzjnnj7pwgi57r6xqmd4611y9vh"))
          (file-name (string-append "slynk-" version "-checkout"))
          (modules '((guix build utils)
                     (ice-9 ftw)))
@@ -1033,14 +1035,19 @@ (define sbcl-slynk-boot0
              (substitute* "slynk/slynk.asd"
                (("\\.\\./contrib")
                 "contrib")
-               (("\\(defsystem :slynk-util")
+               (("\\(defsystem :slynk/util")
-                "(defsystem :slynk-util :depends-on (:slynk)"))
+                "(defsystem :slynk/util :depends-on (:slynk)")
+               ((":depends-on \\(:slynk :slynk/util\\)")
+                ":depends-on (:slynk :slynk-util)"))
              (substitute* "contrib/slynk-trace-dialog.lisp"
                (("\\(slynk::reset-inspector\\)") ; Causes problems on load
                 "nil"))
              (substitute* "contrib/slynk-profiler.lisp"
                (("slynk:to-line")
                 "slynk-pprint-to-line"))
+             (substitute* "contrib/slynk-fancy-inspector.lisp"
+               (("slynk/util") "slynk-util")
+               ((":compile-toplevel :load-toplevel") ""))
              (rename-file "contrib" "slynk/contrib")
              ;; Move slynk's contents into the base directory for easier
              ;; access
@@ -1080,15 +1087,20 @@ (define sbcl-slynk-arglists
     (arguments
      (substitute-keyword-arguments (package-arguments sbcl-slynk-boot0)
        ((#:asd-file _ "") "slynk.asd")
-       ((#:asd-system-name _ #f) #f)))))
+       ((#:asd-system-name _ #f) "slynk/arglists")))))
 
 (define ecl-slynk-arglists
   (sbcl-package->ecl-package sbcl-slynk-arglists))
 
 (define sbcl-slynk-util
   (package
-    (inherit sbcl-slynk-arglists)
+    (inherit sbcl-slynk-boot0)
-    (name "sbcl-slynk-util")))
+    (name "sbcl-slynk-util")
+    (inputs `(("slynk" ,sbcl-slynk-boot0)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments sbcl-slynk-boot0)
+       ((#:asd-file _ "") "slynk.asd")
+       ((#:asd-system-name _ #f) "slynk/util")))))
 
 (define ecl-slynk-util
   (sbcl-package->ecl-package sbcl-slynk-util))
@@ -1098,7 +1110,10 @@ (define sbcl-slynk-fancy-inspector
     (inherit sbcl-slynk-arglists)
     (name "sbcl-slynk-fancy-inspector")
     (inputs `(("slynk-util" ,sbcl-slynk-util)
-              ,@(package-inputs sbcl-slynk-arglists)))))
+              ,@(package-inputs sbcl-slynk-arglists)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments sbcl-slynk-arglists)
+       ((#:asd-system-name _ #f) "slynk/fancy-inspector")))))
 
 (define ecl-slynk-fancy-inspector
   (sbcl-package->ecl-package sbcl-slynk-fancy-inspector))
@@ -1106,15 +1121,21 @@ (define ecl-slynk-fancy-inspector
 (define sbcl-slynk-package-fu
   (package
     (inherit sbcl-slynk-arglists)
-    (name "sbcl-slynk-package-fu")))
+    (name "sbcl-slynk-package-fu")
+    (arguments
+     (substitute-keyword-arguments (package-arguments sbcl-slynk-arglists)
+       ((#:asd-system-name _ #f) "slynk/package-fu")))))
 
 (define ecl-slynk-package-fu
   (sbcl-package->ecl-package sbcl-slynk-package-fu))
 
 (define sbcl-slynk-mrepl
   (package
-    (inherit sbcl-slynk-arglists)
+    (inherit sbcl-slynk-fancy-inspector)
-    (name "sbcl-slynk-mrepl")))
+    (name "sbcl-slynk-mrepl")
+    (arguments
+     (substitute-keyword-arguments (package-arguments sbcl-slynk-arglists)
+       ((#:asd-system-name _ #f) "slynk/mrepl")))))
 
 (define ecl-slynk-mrepl
   (sbcl-package->ecl-package sbcl-slynk-mrepl))
@@ -1122,7 +1143,10 @@ (define ecl-slynk-mrepl
 (define sbcl-slynk-trace-dialog
   (package
     (inherit sbcl-slynk-arglists)
-    (name "sbcl-slynk-trace-dialog")))
+    (name "sbcl-slynk-trace-dialog")
+    (arguments
+     (substitute-keyword-arguments (package-arguments sbcl-slynk-arglists)
+       ((#:asd-system-name _ #f) "slynk/trace-dialog")))))
 
 (define ecl-slynk-trace-dialog
   (sbcl-package->ecl-package sbcl-slynk-trace-dialog))
@@ -1130,7 +1154,10 @@ (define ecl-slynk-trace-dialog
 (define sbcl-slynk-profiler
   (package
     (inherit sbcl-slynk-arglists)
-    (name "sbcl-slynk-profiler")))
+    (name "sbcl-slynk-profiler")
+    (arguments
+     (substitute-keyword-arguments (package-arguments sbcl-slynk-arglists)
+       ((#:asd-system-name _ #f) "slynk/profiler")))))
 
 (define ecl-slynk-profiler
   (sbcl-package->ecl-package sbcl-slynk-profiler))
@@ -1138,7 +1165,10 @@ (define ecl-slynk-profiler
 (define sbcl-slynk-stickers
   (package
     (inherit sbcl-slynk-arglists)
-    (name "sbcl-slynk-stickers")))
+    (name "sbcl-slynk-stickers")
+    (arguments
+     (substitute-keyword-arguments (package-arguments sbcl-slynk-arglists)
+       ((#:asd-system-name _ #f) "slynk/stickers")))))
 
 (define ecl-slynk-stickers
   (sbcl-package->ecl-package sbcl-slynk-stickers))
@@ -1146,7 +1176,10 @@ (define ecl-slynk-stickers
 (define sbcl-slynk-indentation
   (package
     (inherit sbcl-slynk-arglists)
-    (name "sbcl-slynk-indentation")))
+    (name "sbcl-slynk-indentation")
+    (arguments
+     (substitute-keyword-arguments (package-arguments sbcl-slynk-arglists)
+       ((#:asd-system-name _ #f) "slynk/indentation")))))
 
 (define ecl-slynk-indentation
   (sbcl-package->ecl-package sbcl-slynk-indentation))
@@ -1154,7 +1187,10 @@ (define ecl-slynk-indentation
 (define sbcl-slynk-retro
   (package
     (inherit sbcl-slynk-arglists)
-    (name "sbcl-slynk-retro")))
+    (name "sbcl-slynk-retro")
+    (arguments
+     (substitute-keyword-arguments (package-arguments sbcl-slynk-arglists)
+       ((#:asd-system-name _ #f) "slynk/retro")))))
 
 (define ecl-slynk-retro
   (sbcl-package->ecl-package sbcl-slynk-retro))
@@ -1442,3 +1478,47 @@ (define-public uglify-js
      `(("sbcl" ,sbcl)
        ("sbcl-cl-uglify-js" ,sbcl-cl-uglify-js)))
     (synopsis "JavaScript compressor")))
+
+(define-public confusion-mdl
+  (let* ((commit "12a055581fc262225272df43287dae48281900f5"))
+    (package
+      (name "confusion-mdl")
+      (version "0.2")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url (string-append "https://gitlab.com/emacsomancer/" name))
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1zi8kflzvwqg97ha1sa5xjisbjs5z1mvbpa772vfxiv5ksnpxp0d"))
+                (file-name (git-file-name name version))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                    ; there are no tests
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (replace 'build
+             (lambda* (#:key (make-flags '()) #:allow-other-keys)
+               (apply invoke "make" "CC=gcc" make-flags)))
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (bin (string-append out "/bin")))
+                 (install-file "mdli" bin)
+                 #t))))))
+      (native-inputs
+       `(("perl" ,perl)))
+      (inputs
+       `(("libgc" ,libgc)))
+      (synopsis "Interpreter for the MIT Design Language (MDL)")
+      (description "MDL (the MIT Design Language) is a descendant of Lisp.  It
+was originally developed in 1971 on the PDP-10 computer under the Incompatible
+Timesharing System (ITS) to provide high level language support for the
+Dynamic Modeling Group at MIT's Project MAC.  Infocom built the original
+PDP-10 Zork in MDL and their later ZIL (Zork Implementation Language) was
+based on a subset of MDL.  Confusion is a MDL interpreter that works just well
+enough to play the original mainframe Zork all the way through.")
+      (home-page "http://www.russotto.net/git/mrussotto/confusion/src/master/src/README")
+      (license license:gpl3+))))

gnu/packages/llvm.scm

@@ -417,15 +417,7 @@ (define-public python-llvmlite
                                              "twine_cfg_undefined_behavior.patch"))
                          (sha256
                           (base32
-                           "07h71n2m1mn9zcfgw04zglffknplb233zqbcd6pckq0wygkrxflp")))
+                           "07h71n2m1mn9zcfgw04zglffknplb233zqbcd6pckq0wygkrxflp")))))))))))
-                       (origin
-                         (method url-fetch)
-                         (uri (string-append "https://raw.githubusercontent.com/numba/"
-                                             "llvmlite/v" version "/conda-recipes/"
-                                             "0001-Transforms-Add-missing-header-for-InstructionCombini.patch"))
-                         (sha256
-                          (base32
-                           "1pp0z9696l6j4dwz7ypjrm4vvkj0d3mlf1g8zmiyk08akw5lz0cb")))))))))))
     (home-page "http://llvmlite.pydata.org")
     (synopsis "Wrapper around basic LLVM functionality")
     (description

gnu/packages/mail.scm

@@ -947,14 +947,15 @@ (define-public getmail
 (define-public libetpan
   (package
     (name "libetpan")
-    (version "1.8")
+    (version "1.9.1")
     (source (origin
-             (method url-fetch)
+             (method git-fetch)
-             (uri (string-append "https://github.com/dinhviethoa/" name
+             (uri (git-reference
-                   "/archive/" version ".tar.gz"))
+                   (url  "https://github.com/dinhviethoa/libetpan.git")
-             (file-name (string-append name "-" version ".tar.gz"))
+                   (commit version)))
+             (file-name (git-file-name name version))
              (sha256
-               (base32 "1sxnaglp5hb0z78sgnfzva4x8m4flqhicvm1dz0krkxdmfsafrsf"))))
+               (base32 "1628lb1qvxixl64ifvjjr839hmirpx532klhv2mr7m6gmn7nlci5"))))
     (build-system gnu-build-system)
     (native-inputs `(("autoconf" ,autoconf-wrapper)
                      ("automake" ,automake)
@@ -978,7 +979,7 @@ (define-public libetpan
               (invoke "sh" "autogen.sh"))))
         #:configure-flags
         '("--disable-static" "--disable-db")))
-    (home-page "http://www.etpan.org/libetpan.html")
+    (home-page "https://www.etpan.org/libetpan.html")
     (synopsis "Portable middleware for email access")
     (description
      "The purpose of this mail library is to provide a portable, efficient

gnu/packages/maths.scm

@@ -27,6 +27,7 @@
 ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
 ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -459,16 +460,15 @@ (define-public cddlib
 (define-public arpack-ng
   (package
     (name "arpack-ng")
-    (version "3.6.2")
+    (version "3.6.3")
     (home-page "https://github.com/opencollab/arpack-ng")
-    (source
+    (source (origin
-     (origin
+              (method git-fetch)
-       (method url-fetch)
+              (uri (git-reference (url home-page) (commit version)))
-       (uri (string-append home-page "/archive/" version ".tar.gz"))
+              (file-name (git-file-name name version))
-       (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
-       (sha256
+               (base32
-        (base32
+                "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
-         "16jrvdl0gh78rrfnvrcxwys4slwfh6qmwwjhfc9d6vwrvq184g37"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -2084,7 +2084,8 @@ (define-public ruby-asciimath
            (lambda _
              (substitute* "spec/parser_spec.rb"
                (("\\\\\"")
-                "\"")))))))
+                "\""))
+             #t)))))
     (native-inputs
      `(("bundler" ,bundler)
        ("ruby-rspec" ,ruby-rspec)))
@@ -2873,6 +2874,18 @@ (define-public openblas
      "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
     (license license:bsd-3)))
 
+(define-public openblas-ilp64
+  (package (inherit openblas)
+    (name "openblas-ilp64")
+    (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
+    (arguments
+     (substitute-keyword-arguments (package-arguments openblas)
+       ((#:make-flags flags '())
+        `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
+                 ,flags))))
+    (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
+    (license license:bsd-3)))
+
 (define* (make-blis implementation #:optional substitutable?)
   "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
 source tree for a list of implementations.)
@@ -3217,7 +3230,7 @@ (define-public atlas
 (define-public glm
   (package
     (name "glm")
-    (version "0.9.9.1")
+    (version "0.9.9.2")
     (source
      (origin
        (method url-fetch)
@@ -3225,7 +3238,7 @@ (define-public glm
                            version  "/glm-" version ".zip"))
        (sha256
         (base32
-         "042a23hmxfs429czkmlg5ixf28aikzfbw18780prj2gcd4flgw8h"))))
+         "1m2gws1d7l6h4mdn0ap74pfnm3vva3kk8rybdqd5x4lksd1mk6r0"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("unzip" ,unzip)))

gnu/packages/mpd.scm

@@ -33,6 +33,7 @@ (define-module (gnu packages mpd)
   #:use-module (guix build-system python)
   #:use-module (gnu packages avahi)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gtk)
@@ -185,7 +186,7 @@ (define-public mpd-mpc
 (define-public ncmpc
   (package
     (name "ncmpc")
-    (version "0.29")
+    (version "0.30")
     (source (origin
               (method url-fetch)
               (uri
@@ -194,12 +195,23 @@ (define-public ncmpc
                               "/ncmpc-" version ".tar.xz"))
               (sha256
                (base32
-                "04jzv1hfdvgbn391523jb2h3yhq9a40pjrg41sl3wf3jf6vajs7g"))))
+                "18qj3cgqczgfk334x0ywxwa1ckrk9fbjyp34n4zzcxwaifshrzp3"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags
-       (list "-Dcurses=ncurses")))
+       (list "-Dcurses=ncurses")
-    (inputs `(("glib" ,glib)
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'expand-C++-include-path
+           ;; Make <gcc>/include/c++/ext/string_conversions.h find <stdlib.h>.
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let* ((path "CPLUS_INCLUDE_PATH")
+                    (gcc  (assoc-ref inputs "gcc"))
+                    (c++  (string-append gcc "/include/c++")))
+               (setenv path (string-append c++ ":" (getenv path)))
+               #t))))))
+    (inputs `(("gcc", gcc-8)            ; for its C++14 support
+              ("glib" ,glib)
               ("libmpdclient" ,libmpdclient)
               ("ncurses" ,ncurses)))
     (native-inputs `(("gettext" ,gettext-minimal) ; for xgettext

gnu/packages/mtools.scm

@@ -49,7 +49,7 @@ (define-public mtools
 (define-public exfat-utils
   (package
     (name "exfat-utils")
-    (version "1.2.8")
+    (version "1.3.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -57,7 +57,7 @@ (define-public exfat-utils
                     version "/" name "-" version ".tar.gz"))
               (sha256
                (base32
-                "09yf41mgwp8wg0psq347d5razllilx1sd4ij9173nri47p9465jw"))))
+                "0da8f8mm1sbwqp7prh78qk33xm0b8kk2d5is7mh2szlhgdxd1syz"))))
     (build-system gnu-build-system)
     (home-page "https://github.com/relan/exfat")
     (synopsis "Utilities to manipulate exFAT file systems")

gnu/packages/nutrition.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -62,9 +63,9 @@ (define-public gourmet
        (modify-phases %standard-phases
          (replace 'install
            (lambda* (#:key make-flags #:allow-other-keys)
-             (zero? (system* "python" "setup.py" "install" "--prefix"
+             (invoke "python" "setup.py" "install" "--prefix"
-                             (assoc-ref %outputs "out"))))))))
+                     (assoc-ref %outputs "out")))))))
-    (home-page "http://thinkle.github.io/gourmet/")
+    (home-page "https://thinkle.github.io/gourmet/")
     (synopsis "Recipe organizer")
     (description
      "Gourmet Recipe Manager is a recipe organizer that allows you to collect,

gnu/packages/ocaml.scm

@@ -457,7 +457,7 @@ (define-public hevea
 (define-public coq
   (package
     (name "coq")
-    (version "8.8.0")
+    (version "8.8.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/coq/coq/archive/V"
@@ -465,7 +465,7 @@ (define-public coq
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0g96k2x6lbddlmkmdaczvcpb2gwqi1ydbq9bv4gf9q38kv9w3xya"))))
+                "13cyvbg8cgqkg9wz0ax7jq03srj9k0lyvny97fcka4ai1zrzwln8"))))
     (native-search-paths
      (list (search-path-specification
             (variable "COQPATH")
@@ -486,16 +486,16 @@ (define-public coq
              (let* ((out (assoc-ref outputs "out"))
                     (mandir (string-append out "/share/man"))
                     (browser "icecat -remote \"OpenURL(%s,new-tab)\""))
-               (zero? (system* "./configure"
+               (invoke "./configure"
-                               "-prefix" out
+                       "-prefix" out
-                               "-mandir" mandir
+                       "-mandir" mandir
-                               "-browser" browser
+                       "-browser" browser
-                               "-coqide" "opt")))))
+                       "-coqide" "opt"))))
          (replace 'build
            (lambda _
-             (zero? (system* "make" "-j" (number->string
+             (invoke "make"
-                                          (parallel-job-count))
+                     "-j" (number->string (parallel-job-count))
-                             "world"))))
+                     "world")))
          (delete 'check)
          (add-after 'install 'check
            (lambda _
@@ -505,7 +505,7 @@ (define-public coq
                (delete-file-recursively "coq-makefile/timing")
                ;; This one fails because we didn't build coqtop.byte.
                (delete-file-recursively "coq-makefile/findlib-package")
-               (zero? (system* "make"))))))))
+               (invoke "make")))))))
     (home-page "https://coq.inria.fr")
     (synopsis "Proof assistant for higher-order logic")
     (description
@@ -924,21 +924,20 @@ (define-public ocaml4.01-findlib
 (define-public ocaml-ounit
   (package
     (name "ocaml-ounit")
-    (version "2.0.0")
+    (version "2.0.8")
     (source (origin
               (method url-fetch)
-              (uri (ocaml-forge-uri "ounit" version 1258))
+              (uri (ocaml-forge-uri "ounit" version 1749))
               (sha256
                (base32
-                "118xsadrx84pif9vaq13hv4yh22w9kmr0ypvhrs0viir1jr0ajjd"))))
+                "03ifp9hjcxg4m5j190iy373jcn4039d3vy10kmd8p4lfciwzwc1f"))))
     (build-system ocaml-build-system)
     (native-inputs
-     `(("libxml2" ,libxml2))) ; for xmllint
+     `(("libxml2" ,libxml2)))           ; for xmllint
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         ;; Tests are done during build.
+         (delete 'check))))             ; tests are run during build
-         (delete 'check))))
     (home-page "http://ounit.forge.ocamlcore.org")
     (synopsis "Unit testing framework for OCaml")
     (description "Unit testing framework for OCaml.  It is similar to JUnit and

gnu/packages/patches/openssl-1.1-c-rehash-in.patch

@@ -6,14 +6,14 @@ to create symbolic links to certificates, for instance in the 'nss-certs'
 package.
 
 diff --git a/tools/c_rehash.in b/tools/c_rehash.in
-index 2fef627..9d40eae 100644
+index 421fd89208..93aca4e168 100644
 --- a/tools/c_rehash.in
 +++ b/tools/c_rehash.in
 @@ -1,4 +1,6 @@
--#!{- $config{hashbangperl} -}
+-#!{- $config{HASHBANGPERL} -}
 +eval '(exit $?0)' && eval 'exec perl -wS "$0" ${1+"$@"}'
 +  & eval 'exec perl -wS "$0" $argv:q'
 +    if 0;
  
  # {- join("\n# ", @autowarntext) -}
- # Copyright 1999-2016 The OpenSSL Project Authors. All Rights Reserved.
+ # Copyright 1999-2018 The OpenSSL Project Authors. All Rights Reserved.

gnu/packages/patches/xf86-video-ast-remove-mibstore.patch

@@ -1,90 +0,0 @@
-Removes references to mibstore.h and miInitializeBackingStore, which
-have been removed from xorg-server.  Zack Rusin <zackr@vmware.com>
-wrote: "It was a noop for at least 5 years and it has been removed."
-See: http://patches.openembedded.org/patch/46133/
-
-diff -ru xf86-video-ast-0.93.10.orig/src/ast_2dtool.c xf86-video-ast-0.93.10/src/ast_2dtool.c
---- xf86-video-ast-0.93.10.orig/src/ast_2dtool.c	2012-03-23 21:40:56.000000000 -0400
-+++ xf86-video-ast-0.93.10/src/ast_2dtool.c	2014-12-19 02:42:32.422383728 -0500
-@@ -27,7 +27,6 @@
- #include "xf86_OSproc.h"
- #include "xf86cmap.h"
- #include "compiler.h"
--#include "mibstore.h"
- #include "vgaHW.h"
- #include "mipointer.h"
- #include "micmap.h"
-diff -ru xf86-video-ast-0.93.10.orig/src/ast_accel.c xf86-video-ast-0.93.10/src/ast_accel.c
---- xf86-video-ast-0.93.10.orig/src/ast_accel.c	2012-03-23 21:40:56.000000000 -0400
-+++ xf86-video-ast-0.93.10/src/ast_accel.c	2014-12-19 02:41:55.534200809 -0500
-@@ -27,7 +27,6 @@
- #include "xf86_OSproc.h"
- #include "xf86cmap.h"
- #include "compiler.h"
--#include "mibstore.h"
- #include "vgaHW.h"
- #include "mipointer.h"
- #include "micmap.h"
-diff -ru xf86-video-ast-0.93.10.orig/src/ast_cursor.c xf86-video-ast-0.93.10/src/ast_cursor.c
---- xf86-video-ast-0.93.10.orig/src/ast_cursor.c	2012-03-23 21:40:56.000000000 -0400
-+++ xf86-video-ast-0.93.10/src/ast_cursor.c	2014-12-19 02:42:37.258407708 -0500
-@@ -27,7 +27,6 @@
- #include "xf86_OSproc.h"
- #include "xf86cmap.h"
- #include "compiler.h"
--#include "mibstore.h"
- #include "vgaHW.h"
- #include "mipointer.h"
- #include "micmap.h"
-diff -ru xf86-video-ast-0.93.10.orig/src/ast_driver.c xf86-video-ast-0.93.10/src/ast_driver.c
---- xf86-video-ast-0.93.10.orig/src/ast_driver.c	2012-03-23 21:40:56.000000000 -0400
-+++ xf86-video-ast-0.93.10/src/ast_driver.c	2014-12-19 02:42:50.710474414 -0500
-@@ -31,7 +31,6 @@
- #endif
- #include "xf86cmap.h"
- #include "compiler.h"
--#include "mibstore.h"
- #include "vgaHW.h"
- #include "mipointer.h"
- #include "micmap.h"
-@@ -865,7 +864,6 @@
-    }
- #endif /* end of Accel_2D */
-      
--   miInitializeBackingStore(pScreen);
-    xf86SetBackingStore(pScreen);
-    xf86SetSilkenMouse(pScreen);
- 
-diff -ru xf86-video-ast-0.93.10.orig/src/ast_mode.c xf86-video-ast-0.93.10/src/ast_mode.c
---- xf86-video-ast-0.93.10.orig/src/ast_mode.c	2012-03-23 21:40:56.000000000 -0400
-+++ xf86-video-ast-0.93.10/src/ast_mode.c	2014-12-19 02:42:24.894346398 -0500
-@@ -27,7 +27,6 @@
- #include "xf86_OSproc.h"
- #include "xf86cmap.h"
- #include "compiler.h"
--#include "mibstore.h"
- #include "vgaHW.h"
- #include "mipointer.h"
- #include "micmap.h"
-diff -ru xf86-video-ast-0.93.10.orig/src/ast_tool.c xf86-video-ast-0.93.10/src/ast_tool.c
---- xf86-video-ast-0.93.10.orig/src/ast_tool.c	2012-03-23 21:40:56.000000000 -0400
-+++ xf86-video-ast-0.93.10/src/ast_tool.c	2014-12-19 02:42:03.930242443 -0500
-@@ -27,7 +27,6 @@
- #include "xf86_OSproc.h"
- #include "xf86cmap.h"
- #include "compiler.h"
--#include "mibstore.h"
- #include "vgaHW.h"
- #include "mipointer.h"
- #include "micmap.h"
-diff -ru xf86-video-ast-0.93.10.orig/src/ast_vgatool.c xf86-video-ast-0.93.10/src/ast_vgatool.c
---- xf86-video-ast-0.93.10.orig/src/ast_vgatool.c	2012-03-23 21:40:56.000000000 -0400
-+++ xf86-video-ast-0.93.10/src/ast_vgatool.c	2014-12-19 02:42:18.406314226 -0500
-@@ -27,7 +27,6 @@
- #include "xf86_OSproc.h"
- #include "xf86cmap.h"
- #include "compiler.h"
--#include "mibstore.h"
- #include "vgaHW.h"
- #include "mipointer.h"
- #include "micmap.h"

gnu/packages/perl.scm

@@ -2588,6 +2588,30 @@ (define-public perl-devel-checkbin
 particular command is available.")
     (license (package-license perl))))
 
+(define-public perl-devel-checklib
+  (package
+    (name "perl-devel-checklib")
+    (version "1.13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://cpan/authors/id/M/MA/MATTN/Devel-CheckLib-"
+             version ".tar.gz"))
+       (sha256
+        (base32 "1a19qkwxwz3wqb16cdabymfbf9kiydiifw90nd5srpq5hy8gvb94"))))
+    (build-system perl-build-system)
+    (native-inputs
+     `(("perl-io-captureoutput" ,perl-io-captureoutput)
+       ("perl-mock-config" ,perl-mock-config)))
+    (home-page "https://metacpan.org/release/Devel-CheckLib")
+    (synopsis "Check that a library is available")
+    (description
+     "@code{Devel::CheckLib} is a Perl module that checks whether a particular
+C library and its headers are available.  You can also check for the presence of
+particular functions in a library, or even that those functions return
+particular results.")
+    (license perl-license)))
+
 (define-public perl-devel-checkcompiler
   (package
   (name "perl-devel-checkcompiler")

gnu/packages/php.scm

@@ -53,7 +53,7 @@ (define-module (gnu packages php)
 (define-public php
   (package
     (name "php")
-    (version "7.2.8")
+    (version "7.2.10")
     (home-page "https://secure.php.net/")
     (source (origin
               (method url-fetch)
@@ -61,7 +61,7 @@ (define-public php
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "03zv1y8ygzsir60617hinpji3f4irk79zbp3ar1b8zcapq40gfjk"))
+                "1w0432i5wjga9z8x3rhc72h2ij1jd2aimg5xmhc0hg4f7951bhh1"))
               (modules '((guix build utils)))
               (snippet
                '(with-directory-excursion "ext"
@@ -227,6 +227,7 @@ (define-public php
                          ;; but with different error messages.
                          ;; Expects "illegal character", instead gets "unknown error (84)".
                          "ext/iconv/tests/bug52211.phpt"
+                         "ext/iconv/tests/bug60494.phpt"
                          ;; Expects "wrong charset", gets unknown error (22).
                          "ext/iconv/tests/iconv_mime_decode_variation3.phpt"
                          "ext/iconv/tests/iconv_strlen_error2.phpt"

gnu/packages/python.scm

@@ -4907,6 +4907,57 @@ (define-public python-urwidtrees
 (define-public python2-urwidtrees
   (package-with-python2 python-urwidtrees))
 
+(define-public python-ua-parser
+  (package
+    (name "python-ua-parser")
+    (version "0.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ua-parser" version))
+       (sha256
+        (base32
+         "1jwdf58rhchjzzrad405pviv0iq24xa2xmmmdgcm2c8s6b4wzfwp"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f))                    ;no test suite in release
+    (native-inputs
+     `(("python-pyyaml" ,python-pyyaml)))
+    (home-page "https://github.com/ua-parser/uap-python")
+    (synopsis "User agent parser")
+    (description
+     "@code{ua-parser} is a Python port of Browserscope's user agent parser.")
+    (license license:asl2.0)))
+
+(define-public python2-ua-parser
+  (package-with-python2 python-ua-parser))
+
+(define-public python-user-agents
+  (package
+    (name "python-user-agents")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "user-agents" version))
+       (sha256
+        (base32
+         "0fc00cd3j8dahq1zzn8pkgfgd7lq37bp2scmdma2n1c049vicgb4"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f))                  ;missing devices.json test file in release
+    (propagated-inputs
+     `(("python-ua-parser" ,python-ua-parser)))
+    (home-page "https://github.com/selwin/python-user-agents")
+    (synopsis "User Agent strings parsing library")
+  (description
+   "A library to identify devices (phones, tablets) and their capabilities by
+parsing (browser/HTTP) user agent strings.")
+  (license license:expat)))
+
+(define-public python2-user-agents
+  (package-with-python2 python-user-agents))
+
 (define-public python-dbus
   (package
     (name "python-dbus")
@@ -5118,13 +5169,13 @@ (define-public python-datrie
 (define-public snakemake
   (package
     (name "snakemake")
-    (version "5.2.2")
+    (version "5.2.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "snakemake" version))
        (sha256
-        (base32 "18x36n78ph5v1fxk54gvdbc3d8nfncha78phifg3lqaa9gifgzxd"))))
+        (base32 "0gj0xxgiq3mp9qyyrbfzldiaq1giliqw0in64nqiz7vx49myqj7z"))))
     (build-system python-build-system)
     (arguments
      ;; TODO: Package missing test dependencies.
@@ -5142,7 +5193,8 @@ (define-public snakemake
                                "/bin/snakemake")))
              #t)))))
     (propagated-inputs
-     `(("python-wrapt" ,python-wrapt)
+     `(("python-gitpython" ,python-gitpython)
+       ("python-wrapt" ,python-wrapt)
        ("python-requests" ,python-requests)
        ("python-appdirs" ,python-appdirs)
        ("python-configargparse" ,python-configargparse)
@@ -10762,6 +10814,37 @@ (define-public python-ddt
 (define-public python2-ddt
   (package-with-python2 python-ddt))
 
+(define-public python-pycountry
+  (package
+    (name "python-pycountry")
+    (version "18.5.26")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pycountry" version))
+       (sha256
+        (base32
+         "15q9j047s3yc9cfcxq1ch8b71f81na44cr6dydd5gxk0ki9a4akz"))))
+    (build-system python-build-system)
+    (home-page "https://bitbucket.org/flyingcircus/pycountry")
+    (synopsis "ISO databases for languages, countries, currencies, etc.")
+    (description
+     "@code{pycountry} provides the ISO databases for the standards:
+@enumerate
+@item 639-3 (Languages)
+@item 3166 (Countries)
+@item 3166-3 (Deleted Countries)
+@item 3166-2 (Subdivisions of countries)
+@item 4217 (Currencies)
+@item 15924 (Scripts)
+@end enumerate
+It includes a copy from Debian’s pkg-isocodes and makes the data accessible
+through a Python API.")
+    (license license:lgpl2.1+)))
+
+(define-public python2-pycountry
+  (package-with-python2 python-pycountry))
+
 (define-public python-pycosat
   (package
     (name "python-pycosat")
@@ -11455,17 +11538,15 @@ (define-public python2-diff-match-patch
 (define-public python-dirsync
   (package
     (name "python-dirsync")
-    (version "2.2.2")
+    (version "2.2.3")
     (source
       (origin
         (method url-fetch)
-        (uri (pypi-uri "dirsync" version ".zip"))
+        (uri (pypi-uri "dirsync" version))
         (sha256
          (base32
-          "1hcdvmkwd5512zbxpin0k7bx5bkgzy3swjx7d0kj1y45af6r75v2"))))
+          "1r40fkanksagcszf1ag85mdr8w7rgc7196n6s1qlsk2abw6i7v0z"))))
     (build-system python-build-system)
-    (native-inputs
-     `(("unzip" ,unzip)))
     (propagated-inputs
      `(("six" ,python-six)))
     (home-page "https://bitbucket.org/tkhyn/dirsync")
@@ -13716,16 +13797,16 @@ (define-public python2-gdrivefs
 (define-public pybind11
   (package
     (name "pybind11")
-    (version "2.2.3")
+    (version "2.2.4")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append
+              (uri (git-reference
-                    "https://github.com/pybind/pybind11/archive/v"
+                    (url "https://github.com/pybind/pybind11.git")
-                    version ".tar.gz"))
+                    (commit (string-append "v" version))))
               (sha256
                (base32
-                "1sj0x4fwsbnwdai5sxpw1l1vh8m5hpbkfk3zanxcbcgs39jpnfrs"))
+                "0pa79ymcasv8br5ifbx7878id5py2jpjac3i20cqxr6gs9l6ivlv"))
-              (file-name (string-append name "-" version ".tar.gz"))))
+              (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (native-inputs
      `(("python" ,python)

gnu/packages/rails.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Matthew Jordan <matthewjordandevops@yandex.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -80,14 +81,11 @@ (define-public ruby-debug-inspector
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (and
+             (invoke "rake" "compile")
-              (zero? (system* "rake" "compile"))
+             (invoke "ruby" "-Ilib" "-e"
-              (zero?
+                     (string-append
-               (system*
+                      "require 'debug_inspector'; RubyVM::DebugInspector."
-                "ruby" "-Ilib" "-e"
+                      "open{|dc| p dc.backtrace_locations}")))))))
-                (string-append
-                 "require 'debug_inspector'; RubyVM::DebugInspector."
-                 "open{|dc| p dc.backtrace_locations}")))))))))
     (synopsis "Ruby wrapper for the MRI 2.0 debug_inspector API")
     (description
      "This package provides a Ruby wrapper for the MRI 2.0 debug_inspector

gnu/packages/ruby.scm

@@ -1114,7 +1114,7 @@ (define-public ruby-permutation
             #t))
          (replace 'check
           (lambda _
-            (zero? (system* "ruby" "-Ilib" "test/test.rb")))))))
+            (invoke "ruby" "-Ilib" "test/test.rb"))))))
     (synopsis "Library to perform operations with sequence permutations")
     (description "This package provides a Ruby library to perform different
 operations with permutations of sequences, such as strings and arrays.")
@@ -1618,7 +1618,7 @@ (define-public ruby-blankslate
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
-          (lambda _ (zero? (system* "rspec" "spec/")))))))
+          (lambda _ (invoke "rspec" "spec/"))))))
     (native-inputs
      `(("bundler" ,bundler)
        ("ruby-rspec" ,ruby-rspec)))
@@ -2028,7 +2028,7 @@ (define-public ruby-minitest-pretty-diff
          (modify-phases %standard-phases
            (replace 'check
              (lambda _
-               (zero? (system* "script/test")))))))
+               (invoke "script/test"))))))
       (native-inputs
        `(("bundler" ,bundler)
          ("ruby-turn" ,ruby-turn)))
@@ -2289,23 +2289,66 @@ (define-public ruby-multipart-post
 (define-public ruby-multi-json
   (package
     (name "ruby-multi-json")
-    (version "1.12.2")
+    (version "1.13.1")
     (source
      (origin
        (method url-fetch)
-       (uri (rubygems-uri "multi_json" version))
+       ;; Tests are not distributed at rubygems.org so download from GitHub
+       ;; instead.
+       (uri (string-append "https://github.com/intridea/multi_json/archive/v"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1raim9ddjh672m32psaa9niw67ywzjbxbdb8iijx3wv9k5b0pk2x"))))
+         "1s64xqvrnrxmb59v6b2kchnisawg5ai9ky1w60dy6z6ws9la1xv4"))))
     (build-system ruby-build-system)
     (arguments
-     '(#:tests? #f)) ;; No testsuite included in the gem.
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'remove-signing-key-reference
+           (lambda _
+             (substitute* "multi_json.gemspec"
+               ((".*spec.signing_key.*") ""))
+             #t)))))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-rspec" ,ruby-rspec)
+       ("ruby-yard" ,ruby-yard)
+       ("ruby-json-pure" ,ruby-json-pure)
+       ("ruby-oj" ,ruby-oj)
+       ("ruby-yajl-ruby" ,ruby-yajl-ruby)))
     (synopsis "Common interface to multiple JSON libraries for Ruby")
     (description
      "This package provides a common interface to multiple JSON libraries,
 including Oj, Yajl, the JSON gem (with C-extensions), the pure-Ruby JSON gem,
 NSJSONSerialization, gson.rb, JrJackson, and OkJson.")
-    (home-page "http://github.com/intridea/multi_json")
+    (home-page "https://github.com/intridea/multi_json")
+    (license license:expat)))
+
+(define-public ruby-multi-test
+  (package
+    (name "ruby-multi-test")
+    (version "0.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "multi_test" version))
+       (sha256
+        (base32
+         "1sx356q81plr67hg16jfwz9hcqvnk03bd9n75pmdw8pfxjfy1yxd"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(;; Tests require different sets of specific gem versions to be available,
+       ;; and there is no gemfile that specifies the newest versions of
+       ;; dependencies to be tested.
+       #:tests? #f))
+    (synopsis
+     "Interface to testing libraries loaded into a running Ruby process")
+    (description
+     "@code{multi_test} provides a uniform interface onto whatever testing
+libraries that have been loaded into a running Ruby process to help control
+rogue test/unit/autorun requires.")
+    (home-page "https://github.com/cucumber/multi_test")
     (license license:expat)))
 
 (define-public ruby-arel
@@ -2560,7 +2603,7 @@ (define-public ruby-guard
             #t))
          (replace 'build
           (lambda _
-            (zero? (system* "gem" "build" "guard.gemspec")))))))
+            (invoke "gem" "build" "guard.gemspec"))))))
     (propagated-inputs
      `(("ruby-formatador" ,ruby-formatador)
        ("ruby-listen" ,ruby-listen)
@@ -2675,7 +2718,7 @@ (define-public ruby-rb-inotify
          ;; list of files.
          (replace 'build
           (lambda _
-            (zero? (system* "gem" "build" "rb-inotify.gemspec")))))))
+            (invoke "gem" "build" "rb-inotify.gemspec"))))))
     (propagated-inputs
      `(("ruby-ffi" ,ruby-ffi)))
     (native-inputs
@@ -2768,7 +2811,7 @@ (define-public ruby-tins
             ;; causes an error.
             (substitute* "tins.gemspec"
               (("\"lib/spruz\", ") ""))
-            (zero? (system* "gem" "build" "tins.gemspec")))))))
+            (invoke "gem" "build" "tins.gemspec"))))))
     (synopsis "Assorted tools for Ruby")
     (description "Tins is a Ruby library providing assorted tools.")
     (home-page "https://github.com/flori/tins")
@@ -2793,7 +2836,7 @@ (define-public ruby-gem-hadar
        (modify-phases %standard-phases
          (replace 'build
           (lambda _
-            (zero? (system* "gem" "build" "gem_hadar.gemspec")))))))
+            (invoke "gem" "build" "gem_hadar.gemspec"))))))
     (propagated-inputs
      `(("git" ,git)
        ("ruby-tins" ,ruby-tins)
@@ -2870,7 +2913,7 @@ (define-public ruby-term-ansicolor
        (modify-phases %standard-phases
          (replace 'build
           (lambda _
-            (zero? (system* "gem" "build" "term-ansicolor.gemspec")))))))
+            (invoke "gem" "build" "term-ansicolor.gemspec"))))))
     (propagated-inputs
      `(("ruby-tins" ,ruby-tins)))
     (native-inputs
@@ -2978,7 +3021,7 @@ (define-public ruby-json-pure
            (lambda _
              ;; Regenerate gemspec so loosened dependency constraints are
              ;; propagated.
-             (zero? (system* "rake" "gemspec")))))))
+             (invoke "rake" "gemspec"))))))
     (native-inputs
      `(("bundler" ,bundler)
        ("ragel" ,ragel)
@@ -3062,8 +3105,8 @@ (define-public ruby-activesupport
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             ;; There is no tests, instead attempt to load the library.
+             ;; There are no tests, instead attempt to load the library.
-             (zero? (system* "ruby" "-Ilib" "-r" "active_support")))))))
+             (invoke "ruby" "-Ilib" "-r" "active_support"))))))
     (propagated-inputs
      `(("ruby-concurrent" ,ruby-concurrent)
        ("ruby-i18n" ,ruby-i18n)
@@ -3193,6 +3236,43 @@ (define-public ruby-sanitize
     (home-page "https://github.com/rgrove/sanitize/")
     (license license:expat)))
 
+(define-public ruby-oj
+  (package
+    (name "ruby-oj")
+    (version "3.6.7")
+    (source
+     (origin
+       (method url-fetch)
+       ;; Version on rubygems.org does not contain Rakefile, so download from
+       ;; GitHub instead.
+       (uri (string-append "https://github.com/ohler55/oj/archive/v"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1x28ga72jxlnmsd8g8c0fw81vlh54r0qgagw2lxsd3x3la091g2h"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:test-target "test_all"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'disable-bundler
+           (lambda _
+             (substitute* "Rakefile"
+               (("Bundler\\.with_clean_env") "1.times")
+               (("bundle exec ") "")))))))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-rspec" ,ruby-rspec)
+       ("ruby-rake-compiler" ,ruby-rake-compiler)))
+    (synopsis "JSON parser for Ruby optimized for speed")
+    (description
+     "Oj is a JSON parser and generator for Ruby, where the encoding and
+decoding of JSON is implemented as a C extension to Ruby.")
+    (home-page "http://www.ohler.com/oj")
+    (license (list license:expat     ; Ruby code
+                   license:bsd-3)))) ; extension code
+
 (define-public ruby-ox
   (package
     (name "ruby-ox")
@@ -3236,7 +3316,7 @@ (define-public ruby-redcloth
          ;; existing gemspec.
          (replace 'build
           (lambda _
-            (zero? (system* "gem" "build" "redcloth.gemspec")))))))
+            (invoke "gem" "build" "redcloth.gemspec"))))))
     (native-inputs
      `(("bundler" ,bundler)
        ("ruby-diff-lcs" ,ruby-diff-lcs)
@@ -3314,9 +3394,9 @@ (define-public ruby-netrc
            ;; There is no Rakefile and minitest can only run one file at once,
            ;; so we have to iterate over all test files.
            (lambda _
-             (and (map (lambda (file)
+             (map (lambda (file)
-                         (zero? (system* "ruby" "-Itest" file)))
+                    (invoke "ruby" "-Itest" file))
-                       (find-files "./test" "test_.*\\.rb"))))))))
+                  (find-files "./test" "test_.*\\.rb")))))))
     (native-inputs
      `(("ruby-minitest" ,ruby-minitest)))
     (synopsis "Library to read and update netrc files")
@@ -3341,7 +3421,7 @@ (define-public ruby-unf-ext
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'build 'build-ext
-           (lambda _ (zero? (system* "rake" "compile:unf_ext")))))))
+           (lambda _ (invoke "rake" "compile:unf_ext"))))))
     (native-inputs
      `(("bundler" ,bundler)
        ("ruby-rake-compiler" ,ruby-rake-compiler)
@@ -3658,6 +3738,42 @@ (define-public ruby-bio-logger
     (home-page "https://github.com/pjotrp/bioruby-logger-plugin")
     (license license:expat)))
 
+(define-public ruby-yajl-ruby
+  (package
+    (name "ruby-yajl-ruby")
+    (version "1.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "yajl-ruby" version))
+       (sha256
+        (base32
+         "16v0w5749qjp13xhjgr2gcsvjv6mf35br7iqwycix1n2h7kfcckf"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:test-target "spec"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'patch-test-to-update-load-path
+           (lambda _
+             (substitute* "spec/parsing/large_number_spec.rb"
+               (("require \"yajl\"")
+                "$LOAD_PATH << 'lib'; require 'yajl'"))
+             #t)))))
+     (native-inputs
+      `(("ruby-rake-compiler" ,ruby-rake-compiler)
+        ("ruby-rspec" ,ruby-rspec)))
+     (synopsis "Streaming JSON parsing and encoding library for Ruby")
+     (description
+      "Ruby C bindings to the Yajl JSON stream-based parser library.  The API
+is compatible with the JSON gem, so yajl-ruby can act as a drop in
+replacement.
+
+A modified copy of yajl is used, and included in the package.")
+     (home-page "https://github.com/brianmario/yajl-ruby")
+     (license (list license:expat     ; Ruby code, yajl_ext.c and yajl_ext.h
+                    license:bsd-3)))) ; Included, modified copy of yajl
+
 (define-public ruby-yard
   (package
     (name "ruby-yard")
@@ -3681,7 +3797,7 @@ (define-public ruby-yard
              ;; $HOME needs to be set to somewhere writeable for tests to run
              (setenv "HOME" "/tmp")
              ;; Run tests without using 'rake' to avoid dependencies.
-             (zero? (system* "rspec")))))))
+             (invoke "rspec"))))))
     (native-inputs
      `(("ruby-rspec" ,ruby-rspec)
        ("ruby-rack" ,ruby-rack)))
@@ -3868,7 +3984,7 @@ (define-public ruby-turn
          ;; without issue.
          (replace 'check
            (lambda _
-             (zero? (system* "ruby" "-Ilib" "bin/turn" "-h")))))))
+             (invoke "ruby" "-Ilib" "bin/turn" "-h"))))))
     (propagated-inputs
      `(("ruby-ansi" ,ruby-ansi)
        ("ruby-minitest" ,ruby-minitest-4)))
@@ -4008,7 +4124,7 @@ (define-public ruby-sqlite3
              #t))
          (add-before 'check 'add-gemtest-file
            ;; This file exists in the repository but is not distributed.
-           (lambda _ (zero? (system* "touch" ".gemtest")))))))
+           (lambda _ (invoke "touch" ".gemtest"))))))
     (inputs
      `(("sqlite" ,sqlite)))
     (native-inputs
@@ -4042,7 +4158,7 @@ (define-public ruby-shoulda-context
            (lambda _
              ;; Do not run tests to avoid circular dependence with rails.
              ;; Instead just import the library to test.
-             (zero? (system* "ruby" "-Ilib" "-r" "shoulda-context")))))))
+             (invoke "ruby" "-Ilib" "-r" "shoulda-context"))))))
     (synopsis "Test::Unit context framework extracted from Shoulda")
     (description
      "@code{shoulda-context} is the context framework extracted from Shoulda.
@@ -4071,7 +4187,7 @@ (define-public ruby-shoulda-matchers
            (lambda _
              ;; Do not run tests to avoid circular dependence with rails.  Instead
              ;; just import the library to test.
-             (zero? (system* "ruby" "-Ilib" "-r" "shoulda-matchers")))))))
+             (invoke "ruby" "-Ilib" "-r" "shoulda-matchers"))))))
     (propagated-inputs
      `(("ruby-activesupport" ,ruby-activesupport)))
     (synopsis "Collection of testing matchers extracted from Shoulda")
@@ -4111,7 +4227,7 @@ (define-public ruby-shoulda
          (replace 'check
            ;; Don't run tests to avoid circular dependence with rails.  Instead
            ;; just import the library to test.
-           (lambda _ (zero? (system* "ruby" "-Ilib" "-r" "shoulda")))))))
+           (lambda _ (invoke "ruby" "-Ilib" "-r" "shoulda"))))))
     (propagated-inputs
      `(("ruby-shoulda-context" ,ruby-shoulda-context)
        ("ruby-shoulda-matchers" ,ruby-shoulda-matchers-2)))
@@ -4264,10 +4380,9 @@ (define-public ruby-httpclient
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (if tests?
-                 (zero?
+                 (invoke "ruby"
-                  (system* "ruby"
+                         "-Ilib"
-                           "-Ilib"
+                         "test/runner.rb")
-                           "test/runner.rb"))
                  #t))))))
     (native-inputs
      `(("ruby-rack" ,ruby-rack)))
@@ -4306,7 +4421,7 @@ (define-public ruby-ansi
          ;; be require'd.
          (replace 'check
            (lambda _
-             (zero? (system* "ruby" "-Ilib" "-r" "ansi"))))
+             (invoke "ruby" "-Ilib" "-r" "ansi")))
          (add-before 'validate-runpath 'replace-broken-symlink
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -4377,7 +4492,7 @@ (define-public ruby-bio-commandeer
            ;; Run test without calling 'rake' so that jeweler is
            ;; not required as an input.
            (lambda _
-             (zero? (system* "rspec" "spec/bio-commandeer_spec.rb")))))))
+             (invoke "rspec" "spec/bio-commandeer_spec.rb"))))))
     (propagated-inputs
      `(("ruby-bio-logger" ,ruby-bio-logger)
        ("ruby-systemu" ,ruby-systemu)))
@@ -4414,7 +4529,7 @@ (define-public ruby-rubytest
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (zero? (system* "ruby" "-Ilib" "-r" "rubytest")))))))
+             (invoke "ruby" "-Ilib" "-r" "rubytest"))))))
     (propagated-inputs
      `(("ruby-ansi" ,ruby-ansi)))
     (synopsis "Universal test harness for Ruby")
@@ -4444,7 +4559,7 @@ (define-public ruby-brass
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (zero? (system* "ruby" "-Ilib" "-r" "brass")))))))
+             (invoke "ruby" "-Ilib" "-r" "brass"))))))
     (synopsis "Basic foundational assertions framework")
     (description
      "BRASS (Bare-Metal Ruby Assertion System Standard) is a basic
@@ -4472,7 +4587,7 @@ (define-public ruby-qed
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (zero? (system* "ruby" "-Ilib" "bin/qed" "--copyright")))))))
+             (invoke "ruby" "-Ilib" "bin/qed" "--copyright"))))))
     (propagated-inputs
      `(("ruby-ansi" ,ruby-ansi)
        ("ruby-brass" ,ruby-brass)))
@@ -4506,7 +4621,7 @@ (define-public ruby-ae
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _ (zero? (system* "qed"))))
+           (lambda _ (invoke "qed")))
          (add-before 'validate-runpath 'replace-broken-symlink
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -4544,7 +4659,7 @@ (define-public ruby-lemon
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (replace 'check (lambda _ (zero? (system* "qed")))))))
+         (replace 'check (lambda _ (invoke "qed"))))))
     (propagated-inputs
      `(("ruby-ae" ,ruby-ae)
        ("ruby-ansi" ,ruby-ansi)
@@ -4600,8 +4715,8 @@ (define-public ruby-hashery
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (and (zero? (system* "qed"))
+             (invoke "qed")
-                  (zero? (system* "rubytest" "-Ilib" "-Itest" "test/"))))))))
+             (invoke "rubytest" "-Ilib" "-Itest" "test/"))))))
     (native-inputs
      `(("ruby-rubytest-cli" ,ruby-rubytest-cli)
        ("ruby-qed" ,ruby-qed)
@@ -4635,7 +4750,7 @@ (define-public ruby-rc4
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (zero? (system* "rspec" "spec/rc4_spec.rb")))))))
+             (invoke "rspec" "spec/rc4_spec.rb"))))))
     (native-inputs
      `(("ruby-rspec" ,ruby-rspec-2)))
     (synopsis "Implementation of the RC4 algorithm")
@@ -4889,7 +5004,7 @@ (define-public ruby-concurrent
          (add-before 'check 'rake-compile
            ;; Fix the test error described at
            ;; https://github.com/ruby-concurrency/concurrent-ruby/pull/408
-           (lambda _ (zero? (system* "rake" "compile"))))
+           (lambda _ (invoke "rake" "compile")))
          (add-before 'check 'remove-timecop-dependency
            ;; Remove timecop-dependent tests as having timecop as a depedency
            ;; causes circular depedencies.
@@ -5757,7 +5872,7 @@ (define-public ruby-heredoc-unindent
     (synopsis "Heredoc indentation cleaner")
     (description "This gem removes common margin from indented strings, such
 as the ones produced by indented heredocs.  In other words, it strips out
-leading whitespace chars at the beggining of each line, but only as much as
+leading whitespace chars at the beginning of each line, but only as much as
 the line with the smallest margin.
 
 It is acknowledged that many strings defined by heredocs are just code and

gnu/packages/rust.scm

@@ -200,7 +200,7 @@ (define-public mrustc
          ("rustc"
           ,(rust-source "1.19.0" "0l8c14qsf42rmkqy92ahij4vf356dbyspxcips1aswpvad81y8qm"))))
       (arguments
-       `(#:tests? #f
+       `(#:test-target "local_tests"
          #:make-flags (list (string-append "LLVM_CONFIG="
                                            (assoc-ref %build-inputs "llvm")
                                            "/bin/llvm-config"))
@@ -250,6 +250,7 @@ (define-public mrustc
                       (gcc (assoc-ref inputs "gcc")))
                  ;; These files are not reproducible.
                  (for-each delete-file (find-files "output" "\\.txt$"))
+                 (delete-file-recursively "output/local_tests")
                  (mkdir-p lib)
                  (copy-recursively "output" lib/rust)
                  (mkdir-p bin)
@@ -410,6 +411,8 @@ (define rust-1.19
                                    "output/rustc-build/rustc"
                                    "-C" (string-append "linker="
                                                        (getenv "CC"))
+                                   ;; Required for libterm.
+                                   "-Z" "force-unstable-if-unmarked"
                                    "-L" "output/target-libs"
                                    (string-append "src/" name "/lib.rs")
                                    "-o"
@@ -429,7 +432,13 @@ (define rust-1.19
                            ("libpanic_unwind")
                            ;; Uses "cc" to link.
                            ("libstd" "-l" "dl" "-l" "rt" "-l" "pthread")
-                           ("libarena")))
+                           ("libarena")
+
+                           ;; Test dependencies:
+
+                           ("libgetopts")
+                           ("libterm")
+                           ("libtest")))
                #t)))
          ;; This phase is overridden by newer versions.
          (replace 'check
@@ -790,8 +799,8 @@ (define-public rust-1.26
 
 (define-public rust
   (let ((base-rust
-         (rust-bootstrapped-package rust-1.26 "1.27.0"
+         (rust-bootstrapped-package rust-1.26 "1.27.2"
-                                    "089d7rhw55zpvnw71dj8vil6qrylvl4xjr4m8bywjj83d4zq1f9c"
+                                    "0pg1s37bhx9zqbynxyydq5j6q7kij9vxkcv8maz0m25prm88r0cs"
                                     #:patches
                                     '("rust-coresimd-doctest.patch"
                                       "rust-bootstrap-stage0-test.patch"

gnu/packages/scheme.scm

@@ -532,7 +532,7 @@ (define-public racket
 (define-public gambit-c
   (package
     (name "gambit-c")
-    (version "4.8.9")
+    (version "4.9.0")
     (source
      (origin
        (method url-fetch)
@@ -542,25 +542,14 @@ (define-public gambit-c
              (string-map (lambda (c) (if (char=? c #\.) #\_ c)) version)
              ".tgz"))
        (sha256
-        (base32 "16sg1s8myzxqpimj5ry6lfza0qfs157zj28bvmxwwgy89jd9m5v7"))))
+        (base32 "19862w9ij0g5xrkskl4g89xbs17gp9cc6cfcdca6dlfkb3lk6xhp"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags
        ;; According to the ./configure script, this makes the build slower and
        ;; use >= 1 GB memory, but makes Gambit much faster.
-       '("--enable-single-host")
+       '("--enable-single-host")))
-       #:phases
+    (home-page "http://gambitscheme.org")
-       (modify-phases %standard-phases
-         (add-before 'check 'fix-tests
-           (lambda _
-             (substitute* '("tests/makefile")
-               ;; '-:' is how run-time options are set.  'tl' sets some terminal
-               ;; option, which makes it fail in our build environment.  It
-               ;; recommends using 'd-' as a solution, which sets the REPL
-               ;; interaction channel to stdin/stdout.
-               (("gsi -:tl") "gsi -:d-,tl"))
-             #t)))))
-    (home-page "http://www.iro.umontreal.ca/~gambit/")
     (synopsis "Efficient Scheme interpreter and compiler")
     (description
      "Gambit consists of two main programs: gsi, the Gambit Scheme

gnu/packages/scsi.scm

@@ -27,28 +27,37 @@ (define-module (gnu packages scsi)
 (define-public sg3-utils
   (package
     (name "sg3-utils")
-    (version "1.43")
+    (version "1.44")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://sg.danny.cz/sg/p/sg3_utils-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "04l58wvncqk6lfh4lashsl3ccsa1114hkd6vwi1h1cbmq2fw9c8v"))))
+                "01avlgrbxlij8spish4i69ji1m49biz4mbayzzc2qx0hcl8ar56a"))))
     (build-system gnu-build-system)
     (home-page "http://sg.danny.cz/sg/sg3_utils.html")
     (synopsis "SCSI device utilities")
     (description
      "sg3-utils is a collection of utilities for devices that use the Small
-Computer System Interface (SCSI) command set.  It includes utilities to read
+Computer System Interface (@dfn{SCSI}) command set.  It includes utilities to
-data from, write data to, control, modify, and query the state of SCSI
+read data from, write data to, control, modify, and query the state of SCSI
-devices.  For example, this package provides command-line tools to copy data
+devices.
-based on @code{dd} syntax and semantics (called @code{sg_dd}, @code{sgp_dd}
+
-and @code{sgm_dd}), check INQUIRY data and VPD pages (@code{sg_inq}), check
+For example, this package provides command-line tools to:
-mode and log pages (@code{sginfo}, @code{sg_modes} and @code{sg_logs}), spin
+@itemize
-up and down disks (@code{sg_start}), do self tests (@code{sg_senddiag}), parse
+@item copy data based on @code{dd} syntax and semantics (called @command{sg_dd},
-sense data (@code{sg_decode_sense}), and perform various other functions.  In
+@command{sgp_dd}, and @command{sgm_dd})
-addition, this package includes a library, called libsgutils, which can be
+@item check @code{INQUIRY} data and @code{VPD pages} (@command{sg_inq})
+@item check mode and log pages (@command{sginfo}, @command{sg_modes}, and
+@command{sg_logs})
+@item spin up and down disks (@command{sg_start})
+@item do self-tests (@code{sg_senddiag})
+@item parse sense data (@code{sg_decode_sense})
+@item and perform various other functions.
+@end itemize
+
+In addition, this package includes a library, called libsgutils, which can be
 used in C and C++ programs to interact with SCSI devices.")
     ;; See README: "All utilities and libraries have either a "2 clause" BSD
     ;;   license or are "GPL-2ed". [...] That BSD license was updated from the

gnu/packages/security-token.scm

@@ -56,7 +56,7 @@ (define-module (gnu packages security-token)
 (define-public ccid
   (package
     (name "ccid")
-    (version "1.4.29")
+    (version "1.4.30")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -64,7 +64,7 @@ (define-public ccid
                     name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "0kdqmbma6sclsrbxy9w85h7cs0v11if4nc2r9v09613k8pl2lhx5"))))
+                "0z7zafdg75fr1adlv2x0zz34s07gljcjg2lsz76s1048w1xhh5xc"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags (list (string-append "--enable-usbdropdir=" %output
@@ -77,7 +77,7 @@ (define-public ccid
                (("/bin/echo") (which "echo")))
              #t)))))
     (native-inputs
-     `(("pcsc-lite" ,pcsc-lite) ; only required for headers
+     `(("pcsc-lite" ,pcsc-lite)         ; only required for headers
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)))
     (inputs
@@ -220,7 +220,7 @@ (define-public ykclient
 (define-public opensc
   (package
     (name "opensc")
-    (version "0.18.0")
+    (version "0.19.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -228,7 +228,7 @@ (define-public opensc
                     version "/opensc-" version ".tar.gz"))
               (sha256
                (base32
-                "0mrpik6ifzh27ws7h0viv8nwgcdj3fp5whaldmj0zhfi1l1zzh4v"))))
+                "09jqzl18z5qfrf4vf2nvbpdm3mphpgfkl3ww1clkaxh2z56hwnic"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/shells.scm

@@ -155,23 +155,18 @@ (define-public rc
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/rakitzis/rc.git")
-                    ;; commit name 'release: rc-1.7.4'
+                    (commit (string-append "v" version))))
-                    (commit "c884da53a7c885d46ace2b92de78946855b18e92")))
               (sha256
                (base32
-                "00mgzvrrh9w96xa85g4gjbsvq02f08k4jwjcdnxq7kyh5xgiw95l"))
+                "0vj1h4pcg13vxsiydmmk87dr2sra9h4gwx0c4q6fjsiw4in78rrd"))
-              (file-name (string-append name "-" version "-checkout"))))
+              (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
        '("--with-edit=gnu")
        #:phases
        (modify-phases %standard-phases
-         (add-after
+         (add-before 'bootstrap 'patch-trip.rc
-          'unpack 'autoreconf
-          (lambda _ (zero? (system* "autoreconf" "-vfi"))))
-         (add-before
-          'autoreconf 'patch-trip.rc
           (lambda _
             (substitute* "trip.rc"
               (("/bin/pwd") (which "pwd"))
@@ -292,7 +287,7 @@ (define-public tcsh
 (define-public zsh
   (package
     (name "zsh")
-    (version "5.6.1")
+    (version "5.6.2")
     (source (origin
               (method url-fetch)
               (uri (list (string-append
@@ -303,7 +298,7 @@ (define-public zsh
                            ".tar.xz")))
               (sha256
                (base32
-                "1s5kzfbfvixibb1sbzmmlrrx898zqwi5cfmnnq4bhcbx64zparlm"))))
+                "17iffliqcj4hv91g0bd2sxsyfcz51mfyh97sp2iyrs2p0mndc2x5"))))
     (build-system gnu-build-system)
     (arguments `(#:configure-flags '("--with-tcsetpgrp" "--enable-pcre")
                  #:phases
@@ -422,7 +417,7 @@ (define-public scsh
                #t))
            (add-after 'unpack 'autoreconf
              (lambda _
-               (zero? (system* "autoreconf")))))))
+               (invoke "autoreconf"))))))
       (inputs
        `(("scheme48" ,scheme48)
          ("scheme48-rx" ,scheme48-rx)))
@@ -628,7 +623,7 @@ (define-public mksh
          (replace 'build
            (lambda _
              (setenv "CC" "gcc")
-             (zero? (system* (which "sh") "Build.sh"))))
+             (invoke (which "sh") "Build.sh")))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -637,7 +632,8 @@ (define-public mksh
                (install-file "mksh" bin)
                (with-directory-excursion bin
                  (symlink "mksh" "ksh"))
-               (install-file "mksh.1" man)))))))
+               (install-file "mksh.1" man)
+               #t))))))
     (home-page "https://www.mirbsd.org/mksh.htm")
     (synopsis "Korn Shell from MirBSD")
     (description "mksh is an actively developed free implementation of the

gnu/packages/telephony.scm

@@ -7,7 +7,7 @@
 ;;; Copyright © 2016 Francesco Frassinelli <fraph24@gmail.com>
 ;;; Copyright © 2016, 2017 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Jovany Leandro G.C <bit4bit@riseup.net>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -314,7 +314,7 @@ (define-public libiax2
        `(#:phases (modify-phases %standard-phases
                     (add-after 'unpack 'autoconf
                       (lambda _
-                        (zero? (system* "autoreconf" "-vfi")))))))
+                        (invoke "autoreconf" "-vfi"))))))
       (home-page "https://gitlab.savoirfairelinux.com/sflphone/libiax2")
       (synopsis "Inter-Asterisk-Protocol library")
       (description "LibIAX2 implements the Inter-Asterisk-Protocol for relaying
@@ -393,27 +393,27 @@ (define-public mumble
        (modify-phases %standard-phases
          (replace 'configure
            (lambda* (#:key outputs #:allow-other-keys)
-             (zero? (system* "qmake" "main.pro" "-recursive"
+             (invoke "qmake" "main.pro" "-recursive"
-                             (string-append "CONFIG+="
+                     (string-append "CONFIG+="
-                                            (string-join
+                                    (string-join
-                                             (list "no-update"
+                                     (list "no-update"
-                                                   "no-ice"
+                                           "no-ice"
-                                                   "no-embed-qt-translations"
+                                           "no-embed-qt-translations"
-                                                   "no-bundled-speex"
+                                           "no-bundled-speex"
-                                                   "pch"
+                                           "pch"
-                                                   "no-bundled-opus"
+                                           "no-bundled-opus"
-                                                   "no-celt"
+                                           "no-celt"
-                                                   "no-alsa"
+                                           "no-alsa"
-                                                   "no-oss"
+                                           "no-oss"
-                                                   "no-portaudio"
+                                           "no-portaudio"
-                                                   "speechd"
+                                           "speechd"
-                                                   "no-g15"
+                                           "no-g15"
-                                                   "no-bonjour"
+                                           "no-bonjour"
-                                                   "release")))
+                                           "release")))
-                             (string-append "DEFINES+="
+                     (string-append "DEFINES+="
-                                            "PLUGIN_PATH="
+                                    "PLUGIN_PATH="
-                                            (assoc-ref outputs "out")
+                                    (assoc-ref outputs "out")
-                                            "/lib/mumble")))))
+                                    "/lib/mumble"))))
          (add-before 'configure 'fix-libspeechd-include
            (lambda _
              (substitute* "src/mumble/TextToSpeech_unix.cpp"

gnu/packages/time.scm

@@ -243,14 +243,14 @@ (define-public python2-isodate
 (define-public python-iso8601
   (package
     (name "python-iso8601")
-    (version "0.1.11")
+    (version "0.1.12")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "iso8601" version))
        (sha256
         (base32
-         "0c7gh3lsdjds262h0v1sqc66l7hqgfwbakn96qrhdbl0i3vm5yz8"))))
+         "10nyvvnrhw2w3p09v1ica4lgj6f4g9j3kkfx17qmraiq3w7b5i29"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-pytest" ,python-pytest)))

gnu/packages/tls.scm

@@ -394,7 +394,7 @@ (define-public openssl-next
   (package
     (inherit openssl)
     (name "openssl")
-    (version "1.1.0i")
+    (version "1.1.1")
     (source (origin
              (method url-fetch)
              (uri (list (string-append "https://www.openssl.org/source/openssl-"
@@ -404,13 +404,13 @@ (define-public openssl-next
                         (string-append "ftp://ftp.openssl.org/source/old/"
                                        (string-trim-right version char-set:letter)
                                        "/" name "-" version ".tar.gz")))
-              (patches (search-patches "openssl-1.1.0-c-rehash-in.patch"))
+              (patches (search-patches "openssl-1.1-c-rehash-in.patch"))
               (sha256
                (base32
-                "16fgaf113p6s5ixw227sycvihh3zx6f6rf0hvjjhxk68m12cigzb"))))
+                "0gbab2fjgms1kx5xjvqx8bxhr98k4r8l2fa8vw7kvh491xd8fdi8"))))
     (outputs '("out"
-               "doc"        ; 1.3MiB of man3 pages
+               "doc"        ; 6.7 MiB of man3 pages and full HTML documentation
-               "static"))   ; 5.5MiB of .a files
+               "static"))   ; 6.4 MiB of .a files
     (arguments
      (substitute-keyword-arguments (package-arguments openssl)
        ((#:phases phases)
@@ -423,6 +423,11 @@ (define-public openssl-next
              (lambda* (#:key outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
                       (lib (string-append out "/lib")))
+                 ;; It's not a shebang so patch-source-shebangs misses it.
+                 (substitute* "config"
+                   (("/usr/bin/env")
+                    (string-append (assoc-ref %build-inputs "coreutils")
+                                   "/bin/env")))
                  (invoke "./config"
                          "shared"       ;build shared libraries
                          "--libdir=lib"
@@ -444,6 +449,21 @@ (define-public openssl-next
                                '("-mfpu=vfpv3")
                                '())))))
 
+           (delete 'move-man3-pages)
+           (add-after 'install 'move-extra-documentation
+             (lambda* (#:key outputs #:allow-other-keys)
+               ;; Move man3 pages and full HTML documentation to "doc".
+               (let* ((out    (assoc-ref outputs "out"))
+                      (man3   (string-append out "/share/man/man3"))
+                      (html (string-append out "/share/doc/openssl"))
+                      (doc    (assoc-ref outputs "doc"))
+                      (man-target (string-append doc "/share/man/man3"))
+                      (html-target (string-append doc "/share/doc/openssl")))
+                 (copy-recursively man3 man-target)
+                 (delete-file-recursively man3)
+                 (copy-recursively html html-target)
+                 (delete-file-recursively html)
+                 #t)))
            ;; XXX: Duplicate this phase to make sure 'version' evaluates
            ;; in the current scope and not the inherited one.
            (replace 'remove-miscellany
@@ -806,7 +826,7 @@ (define-public acme-client
 (define-public mbedtls-apache
   (package
     (name "mbedtls-apache")
-    (version "2.7.5")
+    (version "2.7.6")
     (source
      (origin
        (method url-fetch)
@@ -816,7 +836,7 @@ (define-public mbedtls-apache
                            version "-apache.tgz"))
        (sha256
         (base32
-         "0h4vks2z68bkwzg093mn0a7aqsva8rxr4m971n4bkasa17cjlc51"))))
+         "0fl2nrxvlgx9ja7yy3kd1zadpr98fxbvn3f6fl2mj87gryhkfqlk"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags

gnu/packages/version-control.scm

@@ -309,6 +309,13 @@ (define-public git
             (let* ((netrc (assoc-ref outputs "credential-netrc")))
               (install-file "contrib/credential/netrc/git-credential-netrc"
                             (string-append netrc "/bin"))
+              ;; Previously, Git.pm was automatically found by netrc.
+              ;; Perl 5.26 changed how it locates modules so that @INC no
+              ;; longer includes the current working directory (the Perl
+              ;; community calls this "dotless @INC").
+              (wrap-program (string-append netrc "/bin/git-credential-netrc")
+                `("PERL5LIB" ":" prefix
+                  (,(string-append (assoc-ref outputs "out") "/share/perl5"))))
               #t)))
         (add-after 'install 'split
           (lambda* (#:key inputs outputs #:allow-other-keys)

gnu/packages/video.scm

@@ -1427,16 +1427,16 @@ (define-public you-get
 (define-public youtube-viewer
   (package
     (name "youtube-viewer")
-    (version "3.3.4")
+    (version "3.4.1")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append
+              (uri (git-reference
-                    "https://github.com/trizen/youtube-viewer/archive/"
+                    (url "https://github.com/trizen/youtube-viewer.git")
-                    version ".tar.gz"))
+                    (commit version)))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1dqaxkz5svv0lmxds6lppcpzhkq6gar2raw9gx6imrd7yz02fpgn"))))
+                "0axgb95lx81psgrb2a5rfdd8gl4mhsrzf41jas6l58d1xkaj54ri"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-module-build" ,perl-module-build)))

gnu/packages/virtualization.scm

@@ -873,7 +873,7 @@ (define-public runc
 (define-public umoci
   (package
     (name "umoci")
-    (version "0.4.0")
+    (version "0.4.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -882,7 +882,7 @@ (define-public umoci
               (file-name (string-append "umoci-" version ".tar.xz"))
               (sha256
                (base32
-                "0hg7hs4dagj2fgymm4b4s68k1v2k2093s3jg0d94j0ixhfmyg9nd"))))
+                "1rq5jxcss9cmy05x9b2kh9ld57ribi8hgnx2w67jpmf343b83m4q"))))
     (build-system go-build-system)
     (arguments
      '(#:import-path "github.com/openSUSE/umoci"

gnu/packages/wine.scm

@@ -71,7 +71,7 @@ (define-module (gnu packages wine)
 (define-public wine
   (package
     (name "wine")
-    (version "3.0.2")
+    (version "3.0.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://dl.winehq.org/wine/source/"
@@ -79,7 +79,7 @@ (define-public wine
                                   "/wine-" version ".tar.xz"))
               (sha256
                (base32
-                "1zv3nk31s758ghp4795ym3w8l5868c2dllmjx9245qh9ahvp3mya"))))
+                "18add8wqqz7y1aj8x0dcba7pqj9jkbhngwjv4yjmar3gxacmjr7b"))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)
                      ("gettext" ,gettext-minimal)
@@ -225,7 +225,7 @@ (define-public wine64
 (define-public wine-staging-patchset-data
   (package
    (name "wine-staging-patchset-data")
-   (version "3.15")
+   (version "3.16")
    (source
     (origin
       (method git-fetch)
@@ -235,7 +235,7 @@ (define-public wine-staging-patchset-data
       (file-name (git-file-name name version))
       (sha256
        (base32
-        "1rgbx4qnxaarkq5n8nvj57q0rhxcqbwm5897ws962fgxh6zymg9n"))))
+        "0c1bs9qpxlvld6jkwjri2v8jaixxn1r5b0m9r5hnkfrnpl7z7cfv"))))
    (build-system trivial-build-system)
    (native-inputs
     `(("bash" ,bash)
@@ -281,7 +281,7 @@ (define-public wine-staging
               (file-name (string-append name "-" version ".tar.xz"))
               (sha256
                (base32
-                "07mmd8r70ciqrxzdg2m2mg34kcnb43dk9nw1ljm8jbcznsawv8ic"))))
+                "0g55l41apiwgblfk9ihzd96003gd32w5ng79f96hmiwhyzwbqhxd"))))
     (inputs `(("autoconf" ,autoconf) ; for autoreconf
               ("gtk+" ,gtk+)
               ("libva" ,libva)

gnu/packages/xdisorg.scm

@@ -476,9 +476,8 @@ (define-public scrot
              (let* ((out (assoc-ref outputs "out"))
                     (doc (string-append out "/share/doc/scrot")))
                (mkdir-p doc)
-               (zero?
+               (invoke "make" "install"
-                (system* "make" "install"
+                        (string-append "docsdir=" doc))))))))
-                         (string-append "docsdir=" doc)))))))))
     (inputs
      `(("libx11" ,libx11)
        ("giblib" ,giblib)))
@@ -585,10 +584,9 @@ (define-public unclutter
                     (man1 (string-append out "/share/man/man1")))
                (mkdir-p bin)
                (mkdir-p man1)
-               (zero?
+               (invoke "make" "install" "install.man"
-                 (system* "make" "install" "install.man"
+                       (string-append "BINDIR=" bin)
-                          (string-append "BINDIR=" bin)
+                       (string-append "MANDIR=" man1))))))))
-                          (string-append "MANDIR=" man1)))))))))
     (inputs `(("libx11" ,libx11)))
     (home-page "http://ftp.x.org/contrib/utilities/")
     (synopsis "Hide idle mouse cursor")
@@ -1344,7 +1342,7 @@ (define-public nxbelld
                  #:phases (modify-phases %standard-phases
                            (add-before 'configure 'autoreconf
                              (lambda _
-                               (zero? (system* "autoreconf" "-vfi")))))))
+                               (invoke "autoreconf" "-vfi"))))))
    (native-inputs `(("autoconf" ,autoconf)
                     ("automake" ,automake)
                     ("pkg-config" ,pkg-config)
@@ -1403,7 +1401,7 @@ (define-public xautolock
                #t)))
          (add-after 'install 'install/man
            (lambda _
-             (zero? (system* "make" "install.man")))))))
+             (invoke "make" "install.man"))))))
     (home-page "http://ibiblio.org/pub/Linux/X11/screensavers/")
     (synopsis "Program launcher for idle X sessions")
     (description "Xautolock monitors input devices under the X Window

gnu/packages/xiph.scm

@@ -387,7 +387,7 @@ (define opus-tools
 (define opusfile
   (package
     (name "opusfile")
-    (version "0.10")
+    (version "0.11")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -395,7 +395,7 @@ (define opusfile
                     ".tar.gz"))
               (sha256
                (base32
-                "0bs1376sd131qdh7198jp64vv5d17az5wyy4y7srrvw7p8k3bq28"))))
+                "1gq3aszzl5glgbajw5p1f5a1kdyf23w5vjdmwwrk246syin9pkkl"))))
     (build-system gnu-build-system)
     (propagated-inputs
      `(("opus" ,opus)))

gnu/packages/xorg.scm

@@ -2645,33 +2645,27 @@ (define-public xf86-video-ark
      "xf86-video-ark is an Ark Logic video driver for the Xorg X server.")
     (license license:x11)))
 
-;; This driver depends on XAA which has been removed from xorg-server.
+(define-public xf86-video-ast
-;;
+  (package
-;; (define-public xf86-video-ast
+    (name "xf86-video-ast")
-;;   (package
+    (version "1.1.5")
-;;     (name "xf86-video-ast")
+    (home-page "https://cgit.freedesktop.org/xorg/driver/xf86-video-ast/")
-;;     (version "0.93.10")
+    (source (origin
-;;     (source
+              (method url-fetch)
-;;       (origin
+              (uri (string-append
-;;         (method url-fetch)
+                    "mirror://xorg/individual/driver/xf86-video-ast-"
-;;         (uri (string-append
+                    version ".tar.bz2"))
-;;                "mirror://xorg/individual/driver/xf86-video-ast-"
+              (sha256
-;;                version
+               (base32
-;;                ".tar.bz2"))
+                "1pm2cy81ma7ldsw0yfk28b33h9z2hcj5rccrxhfxfgvxsiavrnqy"))))
-;;         (sha256
+    (build-system gnu-build-system)
-;;           (base32
+    (inputs `(("xorg-server" ,xorg-server)))
-;;            "1q64z8qqa0ix3cymqiwk1s3sphd1fvvz30lvyxhgkgciygz6dm69"))
+    (native-inputs `(("pkg-config" ,pkg-config)))
-;;         (patches (search-patches "xf86-video-ast-remove-mibstore.patch"))))
+    (synopsis "ASpeed Technologies video driver for X server")
-;;     (build-system gnu-build-system)
+    (description
-;;     (inputs `(("xorg-server" ,xorg-server)))
+     "xf86-video-ast is an ASpeed Technologies video driver for the Xorg
-;;     (native-inputs `(("pkg-config" ,pkg-config)))
+X server.")
-;;     (home-page "https://www.x.org/wiki/")
+    (license license:x11)))
-;;     (synopsis "ASpeed Technologies video driver for X server")
-;;     (description
-;;      "xf86-video-ast is an ASpeed Technologies video driver for the Xorg
-;; X server.")
-;;     (license license:x11)))
-
 
 (define-public xf86-video-ati
   (package

gnu/services/base.scm

@@ -1846,16 +1846,9 @@ (define udev-shepherd-service
 
          (documentation "Populate the /dev directory, dynamically.")
          (start #~(lambda ()
-                    (define find
-                      (@ (srfi srfi-1) find))
-
                     (define udevd
-                      ;; Choose the right 'udevd'.
+                      ;; 'udevd' from eudev.
-                      (find file-exists?
+                      #$(file-append udev "/sbin/udevd"))
-                            (map (lambda (suffix)
-                                   (string-append #$udev suffix))
-                                 '("/libexec/udev/udevd" ;udev
-                                   "/sbin/udevd"))))     ;eudev
 
                     (define (wait-for-udevd)
                       ;; Wait until someone's listening on udevd's control
@@ -1891,24 +1884,20 @@ (define (wait-for-udevd)
                       (make-static-device-nodes directory)
                       (umask old-umask))
 
-                    (let ((pid (primitive-fork)))
+                    (let ((pid (fork+exec-command (list udevd))))
-                      (case pid
+                      ;; Wait until udevd is up and running.  This appears to
-                        ((0)
+                      ;; be needed so that the events triggered below are
-                         (exec-command (list udevd)))
+                      ;; actually handled.
-                        (else
+                      (wait-for-udevd)
-                         ;; Wait until udevd is up and running.  This
-                         ;; appears to be needed so that the events
-                         ;; triggered below are actually handled.
-                         (wait-for-udevd)
 
-                         ;; Trigger device node creation.
+                      ;; Trigger device node creation.
-                         (system* #$(file-append udev "/bin/udevadm")
+                      (system* #$(file-append udev "/bin/udevadm")
-                                  "trigger" "--action=add")
+                               "trigger" "--action=add")
 
-                         ;; Wait for things to settle down.
+                      ;; Wait for things to settle down.
-                         (system* #$(file-append udev "/bin/udevadm")
+                      (system* #$(file-append udev "/bin/udevadm")
-                                  "settle")
+                               "settle")
-                         pid)))))
+                      pid)))
          (stop #~(make-kill-destructor))
 
          ;; When halting the system, 'udev' is actually killed by
@@ -2133,7 +2122,7 @@ (define static-networking-shepherd-service
                                              AF_INET INADDR_ANY 0)))
                     (set-network-interface-flags sock #$interface 0)
                     (close-port sock)
-:                    #f)))
+                    #f)))
         (respawn? #f))))))
 
 (define (static-networking-etc-files interfaces)

gnu/services/networking.scm

@@ -8,6 +8,7 @@
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Chris Marusich <cmmarusich@gmail.com>
+;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -103,7 +104,14 @@ (define-module (gnu services networking)
             wpa-supplicant-service-type
 
             openvswitch-service-type
-            openvswitch-configuration))
+            openvswitch-configuration
+
+            iptables-configuration
+            iptables-configuration?
+            iptables-configuration-iptables
+            iptables-configuration-ipv4-rules
+            iptables-configuration-ipv6-rules
+            iptables-service-type))
 
 ;;; Commentary:
 ;;;
@@ -1108,4 +1116,50 @@ (define openvswitch-service-type
 switch designed to enable massive network automation through programmatic
 extension.")))
 
+;;;
+;;; iptables
+;;;
+
+(define %iptables-accept-all-rules
+  (plain-file "iptables-accept-all.rules"
+              "*filter
+:INPUT ACCEPT
+:FORWARD ACCEPT
+:OUTPUT ACCEPT
+COMMIT
+"))
+
+(define-record-type* <iptables-configuration>
+  iptables-configuration make-iptables-configuration iptables-configuration?
+  (iptables iptables-configuration-iptables
+            (default iptables))
+  (ipv4-rules iptables-configuration-ipv4-rules
+              (default %iptables-accept-all-rules))
+  (ipv6-rules iptables-configuration-ipv6-rules
+              (default %iptables-accept-all-rules)))
+
+(define iptables-shepherd-service
+  (match-lambda
+    (($ <iptables-configuration> iptables ipv4-rules ipv6-rules)
+     (let ((iptables-restore (file-append iptables "/sbin/iptables-restore"))
+           (ip6tables-restore (file-append iptables "/sbin/ip6tables-restore")))
+       (shepherd-service
+        (documentation "Packet filtering framework")
+        (provision '(iptables))
+        (start #~(lambda _
+                   (invoke #$iptables-restore #$ipv4-rules)
+                   (invoke #$ip6tables-restore #$ipv6-rules)))
+        (stop #~(lambda _
+                  (invoke #$iptables-restore #$%iptables-accept-all-rules)
+                  (invoke #$ip6tables-restore #$%iptables-accept-all-rules))))))))
+
+(define iptables-service-type
+  (service-type
+   (name 'iptables)
+   (description
+    "Run @command{iptables-restore}, setting up the specified rules.")
+   (extensions
+    (list (service-extension shepherd-root-service-type
+                             (compose list iptables-shepherd-service))))))
+
 ;;; networking.scm ends here

gnu/system/install.scm

@@ -47,7 +47,7 @@ (define-module (gnu system install)
             a20-olinuxino-lime-installation-os
             a20-olinuxino-lime2-emmc-installation-os
             a20-olinuxino-micro-installation-os
-            banana-pi-m2-ultra-installation-os
+            bananapi-m2-ultra-installation-os
             beaglebone-black-installation-os
             mx6cuboxi-installation-os
             nintendo-nes-classic-edition-installation-os
@@ -448,8 +448,8 @@ (define a20-olinuxino-micro-installation-os
                             "/dev/mmcblk0" ; SD card storage
                             "ttyS0"))
 
-(define banana-pi-m2-ultra-installation-os
+(define bananapi-m2-ultra-installation-os
-  (embedded-installation-os u-boot-banana-pi-m2-ultra-bootloader
+  (embedded-installation-os u-boot-bananapi-m2-ultra-bootloader
                             "/dev/mmcblk1" ; eMMC storage
                             "ttyS0"))
 

gnu/tests/networking.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Chris Marusich <cmmarusich@gmail.com>
+;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,9 +30,11 @@ (define-module (gnu tests networking)
   #:use-module (guix store)
   #:use-module (guix monads)
   #:use-module (gnu packages bash)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages networking)
   #:use-module (gnu services shepherd)
-  #:export (%test-inetd %test-openvswitch %test-dhcpd %test-tor))
+  #:use-module (ice-9 match)
+  #:export (%test-inetd %test-openvswitch %test-dhcpd %test-tor %test-iptables))
 
 (define %inetd-os
   ;; Operating system with 2 inetd services.
@@ -434,3 +437,127 @@ (define %test-tor
    (name "tor")
    (description "Test a running Tor daemon configuration.")
    (value (run-tor-test))))
+
+(define* (run-iptables-test)
+  "Run tests of 'iptables-service-type'."
+  (define iptables-rules
+    "*filter
+:INPUT ACCEPT
+:FORWARD ACCEPT
+:OUTPUT ACCEPT
+-A INPUT -p tcp -m tcp --dport 7 -j REJECT --reject-with icmp-port-unreachable
+COMMIT
+")
+
+  (define ip6tables-rules
+    "*filter
+:INPUT ACCEPT
+:FORWARD ACCEPT
+:OUTPUT ACCEPT
+-A INPUT -p tcp -m tcp --dport 7 -j REJECT --reject-with icmp6-port-unreachable
+COMMIT
+")
+
+  (define inetd-echo-port 7)
+
+  (define os
+    (marionette-operating-system
+     (simple-operating-system
+      (dhcp-client-service)
+      (service inetd-service-type
+               (inetd-configuration
+                (entries (list
+                          (inetd-entry
+                           (name "echo")
+                           (socket-type 'stream)
+                           (protocol "tcp")
+                           (wait? #f)
+                           (user "root"))))))
+      (service iptables-service-type
+               (iptables-configuration
+                (ipv4-rules (plain-file "iptables.rules" iptables-rules))
+                (ipv6-rules (plain-file "ip6tables.rules" ip6tables-rules)))))
+     #:imported-modules '((gnu services herd))
+     #:requirements '(inetd iptables)))
+
+  (define test
+    (with-imported-modules '((gnu build marionette))
+      #~(begin
+          (use-modules (srfi srfi-64)
+                       (gnu build marionette))
+          (define marionette
+            (make-marionette (list #$(virtual-machine os))))
+
+          (define (dump-iptables iptables-save marionette)
+            (marionette-eval
+             `(begin
+                (use-modules (ice-9 popen)
+                             (ice-9 rdelim)
+                             (ice-9 regex))
+                (call-with-output-string
+                  (lambda (out)
+                    (call-with-port
+                     (open-pipe* OPEN_READ ,iptables-save)
+                     (lambda (in)
+                       (let loop ((line (read-line in)))
+                         ;; iptables-save does not output rules in the exact
+                         ;; same format we loaded using iptables-restore. It
+                         ;; adds comments, packet counters, etc. We remove
+                         ;; these additions.
+                         (unless (eof-object? line)
+                           (cond
+                            ;; Remove comments
+                            ((string-match "^#" line) #t)
+                            ;; Remove packet counters
+                            ((string-match "^:([A-Z]*) ([A-Z]*) .*" line)
+                             => (lambda (match-record)
+                                  (format out ":~a ~a~%"
+                                          (match:substring match-record 1)
+                                          (match:substring match-record 2))))
+                            ;; Pass other lines without modification
+                            (else (display line out)
+                                  (newline out)))
+                           (loop (read-line in)))))))))
+             marionette))
+
+          (mkdir #$output)
+          (chdir #$output)
+
+          (test-begin "iptables")
+
+          (test-equal "iptables-save dumps the same rules that were loaded"
+            (dump-iptables #$(file-append iptables "/sbin/iptables-save")
+                           marionette)
+            #$iptables-rules)
+
+          (test-equal "ip6tables-save dumps the same rules that were loaded"
+            (dump-iptables #$(file-append iptables "/sbin/ip6tables-save")
+                           marionette)
+            #$ip6tables-rules)
+
+          (test-error "iptables firewall blocks access to inetd echo service"
+                      'misc-error
+                      (wait-for-tcp-port inetd-echo-port marionette #:timeout 5))
+
+          ;; TODO: This test freezes up at the login prompt without any
+          ;; relevant messages on the console. Perhaps it is waiting for some
+          ;; timeout. Find and fix this issue.
+          ;; (test-assert "inetd echo service is accessible after iptables firewall is stopped"
+          ;;   (begin
+          ;;     (marionette-eval
+          ;;      '(begin
+          ;;         (use-modules (gnu services herd))
+          ;;         (stop-service 'iptables))
+          ;;      marionette)
+          ;;     (wait-for-tcp-port inetd-echo-port marionette #:timeout 5)))
+
+          (test-end)
+          (exit (= (test-runner-fail-count (test-runner-current)) 0)))))
+
+  (gexp->derivation "iptables" test))
+
+(define %test-iptables
+  (system-test
+   (name "iptables")
+   (description "Test a running iptables daemon.")
+   (value (run-iptables-test))))

guix/build/lisp-utils.scm

@@ -81,6 +81,20 @@ (define (normalize-string str)
   "Replace invalid characters in STR with a hyphen."
   (string-join (string-tokenize str valid-char-set) "-"))
 
+(define (normalize-dependency dependency)
+  "Normalize the name of DEPENDENCY.  Handles dependency definitions of the
+dependency-def form described by
+<https://common-lisp.net/project/asdf/asdf.html#The-defsystem-grammar>."
+  (match dependency
+    ((':version name rest ...)
+     `(:version ,(normalize-string name) ,@rest))
+    ((':feature feature-specification dependency-specification)
+     `(:feature
+       ,feature-specification
+       ,(normalize-dependency dependency-specification)))
+    ((? string? name) (normalize-string name))
+    (require-specification require-specification)))
+
 (define (inputs->asd-file-map inputs)
   "Produce a hash table of the form (system . asd-file), where system is the
 name of an ASD system, and asd-file is the full path to its definition."
@@ -105,9 +119,9 @@ (define (wrap-output-translations translations)
 
 (define (lisp-eval-program program)
   "Evaluate PROGRAM with a given LISP implementation."
-  (unless (zero? (apply system*
+  (define invocation (lisp-invocation program))
-                        (lisp-invocation program)))
+  (format #t "Invoking ~a: ~{~s ~}~%" (%lisp-type) invocation)
-    (error "lisp-eval-program failed!" (%lisp) program)))
+  (apply invoke invocation))
 
 (define (spread-statements program argument-name)
   "Return a list with the statements from PROGRAM spread between
@@ -138,8 +152,7 @@ (define (compile-system system asd-file)
 first."
   (lisp-eval-program
    `((require :asdf)
-     (let ((*package* (find-package :asdf)))
+     (asdf:load-asd (truename ,asd-file) :name ,(normalize-string system))
-       (load ,asd-file))
      (asdf:operate 'asdf:compile-bundle-op ,system))))
 
 (define (system-dependencies system asd-file)
@@ -148,8 +161,7 @@ (define (system-dependencies system asd-file)
   (define deps-file ".deps.sexp")
   (define program
     `((require :asdf)
-      (let ((*package* (find-package :asdf)))
+      (asdf:load-asd (truename ,asd-file) :name ,(normalize-string system))
-        (load ,asd-file))
       (with-open-file
        (stream ,deps-file :direction :output)
        (format stream
@@ -189,19 +201,18 @@ (define (test-system system asd-file test-asd-file)
 Also load TEST-ASD-FILE if necessary."
   (lisp-eval-program
    `((require :asdf)
-     (let ((*package* (find-package :asdf)))
+     (asdf:load-asd (truename ,asd-file) :name ,(normalize-string system))
-       (load ,asd-file)
+     ,@(if test-asd-file
-       ,@(if test-asd-file
+           `((asdf:load-asd (truename ,test-asd-file)))
-             `((load ,test-asd-file))
+           ;; Try some likely files.
-             ;; Try some likely files.
+           (map (lambda (file)
-             (map (lambda (file)
+                  `(when (uiop:file-exists-p ,file)
-                    `(when (uiop:file-exists-p ,file)
+                     (asdf:load-asd (truename ,file))))
-                       (load ,file)))
+                (list
-                  (list
+                 (string-append system "-tests.asd")
-                   (string-append system "-tests.asd")
+                 (string-append system "-test.asd")
-                   (string-append system "-test.asd")
+                 "tests.asd"
-                   "tests.asd"
+                 "test.asd")))
-                   "test.asd"))))
      (asdf:test-system ,system))))
 
 (define (string->lisp-keyword . strings)
@@ -273,16 +284,24 @@ (define dependencies
            (system-dependencies system system-asd-file)))
       (if (eq? 'NIL deps)
           '()
-          (map normalize-string deps))))
+          (map normalize-dependency deps))))
 
   (define lisp-input-map
     (inputs->asd-file-map inputs))
 
+  (define dependency-name
+    (match-lambda
+      ((':version name _ ...) name)
+      ((':feature _ dependency-specification)
+       (dependency-name dependency-specification))
+      ((? string? name) name)
+      (_ #f)))
+
   (define registry
     (filter-map hash-get-handle
                 (make-list (length dependencies)
                            lisp-input-map)
-                dependencies))
+                (map dependency-name dependencies)))
 
   (call-with-output-file asd-file
     (lambda (port)

guix/channels.scm

@@ -207,10 +207,16 @@ (define core-instance
             (guix-channel? (channel-instance-channel instance)))
           instances))
 
-  ;; Guile-Gcrypt is a dependency of CORE-INSTANCE.
+  (define dependencies
-  (define guile-gcrypt
+    ;; Dependencies of CORE-INSTANCE.
-    (module-ref (resolve-interface '(gnu packages gnupg))
+    ;; FIXME: It would be best not to hard-wire this information here and
-                'guile-gcrypt))
+    ;; instead query it to CORE-INSTANCE.
+    (list (module-ref (resolve-interface '(gnu packages gnupg))
+                      'guile-gcrypt)
+          (module-ref (resolve-interface '(gnu packages guile))
+                      'guile-git)
+          (module-ref (resolve-interface '(gnu packages guile))
+                      'guile-bytestructures)))
 
   (mlet %store-monad ((core (build-channel-instance core-instance)))
     (mapm %store-monad
@@ -218,7 +224,7 @@ (define guile-gcrypt
             (if (eq? instance core-instance)
                 (return core)
                 (build-channel-instance instance
-                                        (list core guile-gcrypt))))
+                                        (cons core dependencies))))
           instances)))
 
 (define (whole-package-for-legacy name modules)

guix/git-download.scm

@@ -179,24 +179,28 @@ (define (git-file-list directory)
 
 (define (git-predicate directory)
   "Return a predicate that returns true if a file is part of the Git checkout
-living at DIRECTORY.  Upon Git failure, return #f instead of a predicate.
+living at DIRECTORY.  If DIRECTORY does not lie within a Git checkout, and
+upon Git errors, return #f instead of a predicate.
 
 The returned predicate takes two arguments FILE and STAT where FILE is an
 absolute file name and STAT is the result of 'lstat'."
-  (let* ((files  (git-file-list directory))
+  (catch 'git-error
-         (inodes (fold (lambda (file result)
+    (lambda ()
-                         (let ((stat
+      (let* ((files  (git-file-list directory))
-                                (lstat (string-append directory "/"
+             (inodes (fold (lambda (file result)
-                                                      file))))
+                             (let ((stat
-                           (vhash-consv (stat:ino stat) (stat:dev stat)
+                                    (lstat (string-append directory "/"
-                                        result)))
+                                                          file))))
-                       vlist-null
+                               (vhash-consv (stat:ino stat) (stat:dev stat)
-                       files)))
+                                            result)))
-    (lambda (file stat)
+                           vlist-null
-      ;; Comparing file names is always tricky business so we rely on inode
+                           files)))
-      ;; numbers instead.
+        (lambda (file stat)
-      (match (vhash-assv (stat:ino stat) inodes)
+          ;; Comparing file names is always tricky business so we rely on inode
-        ((_ . dev) (= dev (stat:dev stat)))
+          ;; numbers instead.
-        (#f        #f)))))
+          (match (vhash-assv (stat:ino stat) inodes)
+            ((_ . dev) (= dev (stat:dev stat)))
+            (#f        #f)))))
+    (const #f)))
 
 ;;; git-download.scm ends here

guix/git.scm

@@ -36,7 +36,8 @@ (define-module (guix git)
             latest-repository-commit))
 
 (define %repository-cache-directory
-  (make-parameter "/var/cache/guix/checkouts"))
+  (make-parameter (string-append (cache-directory #:ensure? #f)
+                                 "/checkouts")))
 
 (define-syntax-rule (with-libgit2 thunk ...)
   (begin

guix/gnupg.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2010, 2011, 2013, 2014, 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2010, 2011, 2013, 2014, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -24,9 +24,12 @@ (define-module (guix gnupg)
   #:use-module (ice-9 rdelim)
   #:use-module (ice-9 i18n)
   #:use-module (srfi srfi-1)
-  #:use-module (guix ui)
+  #:use-module (guix i18n)
+  #:use-module ((guix utils) #:select (config-directory))
+  #:use-module ((guix build utils) #:select (mkdir-p))
   #:export (%gpg-command
             %openpgp-key-server
+            current-keyring
             gnupg-verify
             gnupg-verify*
             gnupg-status-good-signature?
@@ -42,13 +45,25 @@ (define %gpg-command
   ;; The GnuPG 2.x command-line program name.
   (make-parameter (or (getenv "GUIX_GPG_COMMAND") "gpg")))
 
+(define %gpgv-command
+  ;; The 'gpgv' program.
+  (make-parameter (or (getenv "GUIX_GPGV_COMMAND") "gpgv")))
+
+(define current-keyring
+  ;; The default keyring of "trusted keys".
+  (make-parameter (string-append (config-directory #:ensure? #f)
+                                 "/gpg/trustedkeys.kbx")))
+
 (define %openpgp-key-server
   ;; The default key server.  Note that keys.gnupg.net appears to be
   ;; unreliable.
   (make-parameter "pgp.mit.edu"))
 
-(define (gnupg-verify sig file)
+(define* (gnupg-verify sig file
-  "Verify signature SIG for FILE.  Return a status s-exp if GnuPG failed."
+                       #:optional (keyring (current-keyring)))
+  "Verify signature SIG for FILE against the keys in KEYRING.  All the keys in
+KEYRING as assumed to be \"trusted\", whether or not they expired or were
+revoked.  Return a status s-exp if GnuPG failed."
 
   (define (status-line->sexp line)
     ;; See file `doc/DETAILS' in GnuPG.
@@ -117,8 +132,8 @@ (define (parse-status input)
           (loop (read-line input)
                 (cons (status-line->sexp line) result)))))
 
-  (let* ((pipe   (open-pipe* OPEN_READ (%gpg-command) "--status-fd=1"
+  (let* ((pipe   (open-pipe* OPEN_READ (%gpgv-command) "--status-fd=1"
-                             "--verify" sig file))
+                             "--keyring" keyring sig file))
          (status (parse-status pipe)))
     ;; Ignore PIPE's exit status since STATUS above should contain all the
     ;; info we need.
@@ -145,12 +160,21 @@ (define (gnupg-status-missing-key? status)
            (_ #f)))
        status))
 
-(define (gnupg-receive-keys key-id server)
+(define* (gnupg-receive-keys key-id server
-  (system* (%gpg-command) "--keyserver" server "--recv-keys" key-id))
+                             #:optional (keyring (current-keyring)))
+  (unless (file-exists? keyring)
+    (mkdir-p (dirname keyring))
+    (call-with-output-file keyring (const #t)))   ;create an empty keybox
+
+  (system* (%gpg-command) "--keyserver" server
+           "--no-default-keyring" "--keyring" keyring
+           "--recv-keys" key-id))
 
 (define* (gnupg-verify* sig file
-                        #:key (key-download 'interactive)
+                        #:key
-                              (server (%openpgp-key-server)))
+                        (key-download 'interactive)
+                        (server (%openpgp-key-server))
+                        (keyring (current-keyring)))
   "Like `gnupg-verify', but try downloading the public key if it's missing.
 Return #t if the signature was good, #f otherwise.  KEY-DOWNLOAD specifies a
 download policy for missing OpenPGP keys; allowed values: 'always', 'never',
@@ -161,15 +185,17 @@ (define* (gnupg-verify* sig file
           (define (download-and-try-again)
             ;; Download the missing key and try again.
             (begin
-              (gnupg-receive-keys missing server)
+              (gnupg-receive-keys missing server keyring)
-              (gnupg-status-good-signature? (gnupg-verify sig file))))
+              (gnupg-status-good-signature? (gnupg-verify sig file
+                                                          keyring))))
 
           (define (receive?)
             (let ((answer
-                   (begin (format #t (G_ "~a~a~%")
+                   (begin
-                                  "Would you like to download this key "
+                     (format #t (G_ "Would you like to add this key \
-                                  "and add it to your keyring?")
+to keyring '~a'?~%")
-                          (read-line))))
+                             keyring)
+                     (read-line))))
               (string-match (locale-yes-regexp) answer)))
 
           (and missing

guix/scripts/describe.scm

@@ -134,8 +134,10 @@ (define number
                     ;; Show most recently installed packages last.
                     (reverse
                      (manifest-entries
-                      (profile-manifest (generation-file-name profile
+                      (profile-manifest
-                                                              number)))))))))
+                       (if (zero? number)
+                           profile
+                           (generation-file-name profile number))))))))))
   (display-package-search-path fmt))
 
 

guix/scripts/graph.scm

@@ -439,6 +439,10 @@ (define %options
         (option '(#\e "expression") #t #f
                 (lambda (opt name arg result)
                   (alist-cons 'expression arg result)))
+        (option '(#\s "system") #t #f
+                (lambda (opt name arg result)
+                  (alist-cons 'system arg
+                              (alist-delete 'system result eq?))))
         (option '(#\h "help") #f #f
                 (lambda args
                   (show-help)
@@ -462,6 +466,8 @@ (define (show-help)
       --list-types       list the available graph types"))
   (display (G_ "
   -e, --expression=EXPR  consider the package EXPR evaluates to"))
+  (display (G_ "
+  -s, --system=SYSTEM    consider the graph for SYSTEM--e.g., \"i686-linux\""))
   (newline)
   (display (G_ "
   -h, --help             display this help and exit"))
@@ -472,7 +478,8 @@ (define (show-help)
 
 (define %default-options
   `((node-type . ,%package-node-type)
-    (backend   . ,%graphviz-backend)))
+    (backend   . ,%graphviz-backend)
+    (system    . ,(%current-system))))
 
 
 ;;;
@@ -508,7 +515,8 @@ (define (guix-graph . args)
               (export-graph (concatenate nodes)
                             (current-output-port)
                             #:node-type type
-                            #:backend backend)))))))
+                            #:backend backend))
+            #:system (assq-ref opts 'system))))))
   #t)
 
 ;;; graph.scm ends here

guix/scripts/pull.scm

@@ -176,17 +176,18 @@ (define (honor-lets-encrypt-certificates! store)
          (certs (string-append (derivation->output-path drv)
                                "/etc/ssl/certs")))
     (build-derivations store (list drv))
+    (set-tls-certificate-locations! certs)))
 
-    ;; In the past Guile-Git would not provide this procedure.
+(define (honor-x509-certificates store)
-    (if (module-defined? (resolve-interface '(git))
+  "Use the right X.509 certificates for Git checkouts over HTTPS."
-                         'set-tls-certificate-locations!)
+  (let ((file      (getenv "SSL_CERT_FILE"))
-        (set-tls-certificate-locations! certs)
+        (directory (or (getenv "SSL_CERT_DIR") "/etc/ssl/certs")))
-        (begin
+    (if (or (and file (file-exists? file))
-          ;; In this case we end up using whichever certificates OpenSSL
+            (and=> (stat directory #f)
-          ;; chooses to use: $SSL_CERT_FILE, $SSL_CERT_DIR, or /etc/ssl/certs.
+                   (lambda (st)
-          (warning (G_ "cannot enforce use of the Let's Encrypt \
+                     (> (stat:nlink st) 2))))
-certificates~%"))
+        (set-tls-certificate-locations! directory file)
-          (warning (G_ "please upgrade Guile-Git~%"))))))
+        (honor-lets-encrypt-certificates! store))))
 
 (define (report-git-error error)
   "Report the given Guile-Git error."
@@ -233,7 +234,9 @@ (define (display-profile-content profile number)
             ;; Show most recently installed packages last.
             (reverse
              (manifest-entries
-              (profile-manifest (generation-file-name profile number))))))
+              (profile-manifest (if (zero? number)
+                                    profile
+                                    (generation-file-name profile number)))))))
 
 (define (indented-string str indent)
   "Return STR with each newline preceded by IDENT spaces."
@@ -431,13 +434,7 @@ (define (guix-pull . args)
                 (parameterize ((%graft? (assoc-ref opts 'graft?))
                                (%repository-cache-directory cache))
                   (set-build-options-from-command-line store opts)
-
+                  (honor-x509-certificates store)
-                  ;; When certificates are already installed, use them.
-                  ;; Otherwise, use the Let's Encrypt certificates, which we
-                  ;; know Savannah uses.
-                  (let ((certs (or (getenv "SSL_CERT_DIR") "/etc/ssl/certs")))
-                    (unless (file-exists? certs)
-                      (honor-lets-encrypt-certificates! store)))
 
                   (let ((instances (latest-channel-instances store channels)))
                     (format (current-error-port)

guix/scripts/refresh.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Alex Kost <alezost@gmail.com>
@@ -89,6 +89,9 @@ (define %options
                 (lambda (opt name arg result)
                   (alist-cons 'list-dependent? #t result)))
 
+        (option '("keyring") #t #f
+                (lambda (opt name arg result)
+                  (alist-cons 'keyring arg result)))
         (option '("key-server") #t #f
                 (lambda (opt name arg result)
                   (alist-cons 'key-server arg result)))
@@ -138,6 +141,8 @@ (define (show-help)
   -l, --list-dependent   list top-level dependent packages that would need to
                          be rebuilt as a result of upgrading PACKAGE..."))
   (newline)
+  (display (G_ "
+      --keyring=FILE     use FILE as the keyring of upstream OpenPGP keys"))
   (display (G_ "
       --key-server=HOST  use HOST as the OpenPGP key server"))
   (display (G_ "
@@ -437,7 +442,11 @@ (define core-package?
                                 (%openpgp-key-server)))
                            (%gpg-command
                             (or (assoc-ref opts 'gpg-command)
-                                (%gpg-command))))
+                                (%gpg-command)))
+                           (current-keyring
+                            (or (assoc-ref opts 'keyring)
+                                (string-append (config-directory)
+                                               "/upstream/trustedkeys.kbx"))))
               (for-each
                (cut update-package store <> updaters
                     #:key-download key-download

guix/store.scm

@@ -770,6 +770,7 @@ (define total 0)
 
   (define (flush)
     (put-bytevector port buffer 0 total)
+    (force-output port)
     (set! total 0))
 
   (define (write bv offset count)
@@ -927,6 +928,7 @@ (define add-to-store
              (write-int (if recursive? 1 0) port)
              (write-string hash-algo port)
              (write-file file-name port #:select? select?)
+             (write-buffered-output server)
              (let loop ((done? (process-stderr server)))
                (or done? (loop (process-stderr server))))
              (read-store-path port)))))
@@ -1042,6 +1044,7 @@ (define cache
                            #:file-port file-port
                            #:symlink-target symlink-target
                            #:directory-entries directory-entries)
+          (write-buffered-output server)
           (let loop ((done? (process-stderr server)))
             (or done? (loop (process-stderr server))))
           (let ((result (read-store-path port)))

tests/pack.scm

@@ -51,7 +51,12 @@ (define %tar-bootstrap %bootstrap-coreutils&co)
 
 (test-begin "pack")
 
-(unless (network-reachable?) (test-skip 1))
+;; FIXME: The following test would rebuild the world (and likely fail) as a
+;; consequence of commit c45477d2a1a651485feede20fe0f3d15aec48b39 (and related
+;; changes) that made guile-sqlite3 a dependency of the derivation.
+;; See <https://bugs.gnu.org/32184>.
+(test-skip 1)
+
 (test-assertm "self-contained-tarball"
   (mlet* %store-monad
       ((profile (profile-derivation (packages->manifest