Merge branch 'master' into core-updates

build-aux/hydra/gnu-system.scm

@@ -330,12 +330,11 @@ valid."
        (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 @@
             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 @@
    (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 @@ system administrator.")
 (define-public sudo
   (package
     (name "sudo")
-    (version "1.8.25")
+    (version "1.8.25p1")
     (source (origin
               (method url-fetch)
               (uri
@@ -973,7 +973,7 @@ system administrator.")
                                     version ".tar.gz")))
               (sha256
                (base32
-                "0hfw6pcwjvv1vvnhb4n1p210306jm4npz99p9cfhbd33yrhhzkwx"))
+                "0nqri46d4dpycj96zin2f2wszmhm7q9mr68hhj9sp81pgmx9rjcx"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1236,7 +1236,7 @@ network, which causes enabled computers to power on.")
 (define-public dmidecode
   (package
     (name "dmidecode")
-    (version "3.1")
+    (version "3.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1244,7 +1244,7 @@ network, which causes enabled computers to power on.")
                     version ".tar.xz"))
               (sha256
                (base32
-                "1h0sg0lxa15nzf8s7884p6q7p6md9idm0c79wyqmk32l4ndwwrnp"))))
+                "1pcfhcgs2ifdjwp7amnsr3lq95pgxpr150bjhdinvl505px0cw07"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases (delete 'configure))
@@ -2779,6 +2779,8 @@ support forum.  It runs with the @code{/exec} command in most IRC clients.")
                #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 @@ are highly customizable.  Currently, it is possible to plot: bigwig, bed (many
 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 @@ tree binary files.  These are board description files used by Linux and BSD.")
        ("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 @@ board-independent tools.")))
        `(("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-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 @@
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1hqlr5b3bsyb6avadz1z4za6pyl32r1krnpcpwwqilhnx8q0f9gw"))))
+                "1dzg45vgy2w1xcd3p6h8d76ykhabbvk1h0lf8yb24ikrwlv8cr4p"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases

gnu/packages/cdrom.scm

@@ -152,14 +152,14 @@ libcdio.")
 (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 @@ laid out on the image.")
 (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 @@ DVD-RW, DVD-R, DVD-R/DL, BD-R, and BD-RE.")
 (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 @@
     (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 @@ sampling and basic manipulation of Brazilian lawsuits identification number.
 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 @@ printer/driver specific, but spooler-independent PPD file.")
 (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 @@ to take care of the OS-specific details when writing software that uses serial p
 (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 @@ to take care of the OS-specific details when writing software that uses serial p
                     version ".tar.gz"))
               (sha256
                (base32
-                "07mmb6s62ncqqgsc6szilj2yxixf6gg99ggbzsjlbhp4b9aqnga9"))))
+                "1w434nl1syjkvwl08lji3r9sr60lbxp1nqys8hqwzv2lgiwrx3g0"))))
     (outputs '("out" "doc"))
     (arguments
      `(#:phases

gnu/packages/emacs.scm

@@ -579,16 +579,16 @@ support for Git-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 @@ the actual transformations.")
 @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-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 @@
                     version ".tar.xz"))
               (sha256
                (base32
-                "0jxfrcz2aq1synxzd6sh9nhxz7fg9qgz0idr8zj6gaiplmwbwrby"))))
+                "0a5907h896pvpix7a6idc2fspzy6d78xrzf84k8y9fyvnd14nxs4"))))
     (outputs '("out"       ; 49 MB
                "include")) ; 17 MB
     (build-system gnu-build-system)
@@ -251,7 +251,7 @@ Libraries with some extra bells and whistles.")
 (define-public enlightenment
   (package
     (name "enlightenment")
-    (version "0.22.3")
+    (version "0.22.4")
     (source (origin
               (method url-fetch)
               (uri
@@ -259,7 +259,7 @@ Libraries with some extra bells and whistles.")
                               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 @@ is attributed to Albert 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 @@ is attributed to Albert Einstein.")
               (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 @@ work and the interface is well tested.")
        ("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 @@ metadata in photo and video files of various formats.")
 (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 @@ metadata in photo and video files of various formats.")
                                   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 @@ in the style of communicating sequential processes (@dfn{CSP}).")
   (package
     (inherit go-1.9)
     (name "go")
-    (version "1.10.3")
+    (version "1.10.4")
     (source
      (origin
        (method url-fetch)
@@ -397,7 +397,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                            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 @@ endpoint.  Additionally, it provides an interface to write SPARQL queries
 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-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 @@
                                   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 @@ files.  It can compress them as much as 40% losslessly.")
     "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 @@ medical image data, e.g. magnetic resonance image (MRI) and functional MRI
     (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 @@ text documents, vector drawings, presentations and spreadsheets.")
 (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 @@ text documents, vector drawings, presentations and spreadsheets.")
     (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 @@ from the old StarOffice (.sdc, .sdw, ...).")
 (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 @@ from the old StarOffice (.sdc, .sdw, ...).")
     (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 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.7")
+(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 @@ It has been modified to remove all non-free binary blobs.")
                     #: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 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.126"
+  (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 @@
   #: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 @@ productive, customizable lisp based systems.")
 ;; 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 @@ productive, customizable lisp based systems.")
            (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 @@ productive, customizable lisp based systems.")
              (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 @@ multiple inspectors with independent history.")
     (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 @@ multiple inspectors with independent history.")
     (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 @@ multiple inspectors with independent history.")
 (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 @@ multiple inspectors with independent history.")
 (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 @@ multiple inspectors with independent history.")
 (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 @@ multiple inspectors with independent history.")
 (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 @@ multiple inspectors with independent history.")
 (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 @@ multiple inspectors with independent history.")
 (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 @@ compressor.  It works on data produced by @code{parse-js} to generate a
      `(("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 @@ code analysis tools.")
                                              "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 @@ useful features.")
 (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 @@ useful features.")
               (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 @@ computing convex hulls.")
 (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 @@ porting.")
            (lambda _
              (substitute* "spec/parser_spec.rb"
                (("\\\\\"")
-                "\"")))))))
+                "\""))
+             #t)))))
     (native-inputs
      `(("bundler" ,bundler)
        ("ruby-rspec" ,ruby-rspec)))
@@ -2873,6 +2874,18 @@ parts of it.")
      "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 @@ Failure to do so will result in a library with poor performance.")
 (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 @@ Failure to do so will result in a library with poor performance.")
                            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 @@
   #: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 @@ player daemon.")
 (define-public ncmpc
   (package
     (name "ncmpc")
-    (version "0.29")
+    (version "0.30")
     (source (origin
               (method url-fetch)
               (uri
@@ -194,12 +195,23 @@ player daemon.")
                               "/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 @@ FAT-specific file attributes.")
 (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 @@ FAT-specific file attributes.")
                     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 @@
        (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 @@ written in Objective Caml.")
 (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 @@ written in Objective Caml.")
               (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 @@ written in Objective Caml.")
              (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 @@ written in Objective Caml.")
                (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 @@ compilers that can directly deal with packages.")
 (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 @@ the appropriate objects.")
 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-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 @@
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "03zv1y8ygzsir60617hinpji3f4irk79zbp3ar1b8zcapq40gfjk"))
+                "1w0432i5wjga9z8x3rhc72h2ij1jd2aimg5xmhc0hg4f7951bhh1"))
               (modules '((guix build utils)))
               (snippet
                '(with-directory-excursion "ext"
@@ -227,6 +227,7 @@
                          ;; 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 @@ toolkit.  Use it to build trees of widgets.")
 (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 @@ Python.")
 (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 @@ Python.")
                                "/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 @@ cases.")
 (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 @@ perform the operations required for synchronizing plain text.")
 (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 @@ under Python 2.7.")
 (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 @@ migration.")
        (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 @@ and inspect the environment.")
             #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 @@ objects.")
      `(#: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 @@ is to be run.")
          (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 @@ net/http library.")
 (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 @@ invocation, and source and documentation browsing.")
             #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 @@ IANA Time Zone database packaged as Ruby modules for use with @code{TZInfo}.")
          ;; 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 @@ documentation for Ruby code.")
             ;; 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 @@ documentation for Ruby code.")
        (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 @@ Ruby's large and slower test/unit.")
        (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 @@ a native C extension.")
            (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 @@ you about the changes.")
        (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 @@ unacceptable HTML and/or CSS from a string.")
     (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 @@ alternative to Marshal for Object serialization. ")
          ;; 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 @@ other things and it comes with a command line interface.")
            ;; 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 @@ including comments and whitespace.")
      `(#: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 @@ features such as filtering and fine grained logging.")
     (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 @@ features such as filtering and fine grained logging.")
              ;; $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 @@ name and provides query methods such as @{RubyEngine.mri?}.")
          ;; 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 @@ neither too verbose nor too minimal.")
              #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 @@ engine.")
            (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 @@ names.")
            (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 @@ more complex, and error-prone.")
          (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 @@ It has built-in support for the legacy @code{cookies.txt} and
          (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 @@ requests either using arguments or with an interactive prompt.")
          ;; 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 @@ subprocess.")
            ;; 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 @@ detail to ease debugging.")
        (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 @@ single pass.")
        (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 @@ make use of.")
        (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 @@ requirement specifications systems like Cucumber.")
      `(#: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 @@ for reuse by other test frameworks.")
     (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 @@ Rubytest-based test frameworks.  It provides the @code{rubytest} executable.")
        (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 @@ specific use case.")
        (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 @@ call.")
          (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 @@ hashes more powerful.")
     (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 @@ in turn be used to build the final Rust.")
          ("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 @@ in turn be used to build the final Rust.")
                       (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 @@ test = { path = \"../libtest\" }
                                    "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 @@ test = { path = \"../libtest\" }
                            ("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 @@ jemalloc = \"" jemalloc "/lib/libjemalloc_pic.a" "\"
 
 (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 @@ of libraries.")
 (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 @@ of libraries.")
              (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-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-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 @@
                     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 @@
                (("/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 @@ website for more information about Yubico and the YubiKey.")
 (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 @@ website for more information about Yubico and the YubiKey.")
                     version "/opensc-" version ".tar.gz"))
               (sha256
                (base32
-                "0mrpik6ifzh27ws7h0viv8nwgcdj3fp5whaldmj0zhfi1l1zzh4v"))))
+                "09jqzl18z5qfrf4vf2nvbpdm3mphpgfkl3ww1clkaxh2z56hwnic"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/shells.scm

@@ -155,23 +155,18 @@ and syntax highlighting.")
               (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 @@ history mechanism, job control and a C-like syntax.")
 (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 @@ history mechanism, job control and a C-like syntax.")
                            ".tar.xz")))
               (sha256
                (base32
-                "1s5kzfbfvixibb1sbzmmlrrx898zqwi5cfmnnq4bhcbx64zparlm"))))
+                "17iffliqcj4hv91g0bd2sxsyfcz51mfyh97sp2iyrs2p0mndc2x5"))))
     (build-system gnu-build-system)
     (arguments `(#:configure-flags '("--with-tcsetpgrp" "--enable-pcre")
                  #:phases
@@ -422,7 +417,7 @@ use of experts and novices alike.")
                #t))
            (add-after 'unpack 'autoreconf
              (lambda _
-               (zero? (system* "autoreconf")))))))
+               (invoke "autoreconf"))))))
       (inputs
        `(("scheme48" ,scheme48)
          ("scheme48-rx" ,scheme48-rx)))
@@ -628,7 +623,7 @@ interactive POSIX shell targeted at resource-constrained systems.")
          (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 @@ interactive POSIX shell targeted at resource-constrained systems.")
                (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 @@ protocol (RFC 3550).")
        `(#: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 @@ address of one of the participants.")
        (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 @@ ISO 8601 dates, time and duration.")
 (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 @@ required structures.")
   (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 @@ required structures.")
                         (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 @@ required structures.")
              (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 @@ required structures.")
                                '("-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 @@ then ported to the GNU / Linux environment.")
 (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 @@ then ported to the GNU / Linux environment.")
                            version "-apache.tgz"))
        (sha256
         (base32
-         "0h4vks2z68bkwzg093mn0a7aqsva8rxr4m971n4bkasa17cjlc51"))))
+         "0fl2nrxvlgx9ja7yy3kd1zadpr98fxbvn3f6fl2mj87gryhkfqlk"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags

gnu/packages/version-control.scm

@@ -309,6 +309,13 @@ as well as the classic centralized workflow.")
             (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 @@ audio, images) from the Web.  It can use either mpv or vlc for playback.")
 (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 @@ Open Container Initiative specification.")
 (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 @@ Open Container Initiative specification.")
               (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-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 @@
                                   "/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 @@ integrate Windows applications into your desktop.")
 (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 @@ integrate Windows applications into your desktop.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-        "1rgbx4qnxaarkq5n8nvj57q0rhxcqbwm5897ws962fgxh6zymg9n"))))
+        "0c1bs9qpxlvld6jkwjri2v8jaixxn1r5b0m9r5hnkfrnpl7z7cfv"))))
    (build-system trivial-build-system)
    (native-inputs
     `(("bash" ,bash)
@@ -281,7 +281,7 @@ integrate Windows applications into your desktop.")
               (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 @@ move windows, switch between desktops, etc.).")
              (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 @@ include cursor in the resulting image.")
                     (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 @@ invert colors on a specific display/screen.")
                  #: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 @@ or playing a PCM encoded WAVE file.")
                #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 @@ decoding .opus files.")
 (define opusfile
   (package
     (name "opusfile")
-    (version "0.10")
+    (version "0.11")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -395,7 +395,7 @@ decoding .opus files.")
                     ".tar.gz"))
               (sha256
                (base32
-                "0bs1376sd131qdh7198jp64vv5d17az5wyy4y7srrvw7p8k3bq28"))))
+                "1gq3aszzl5glgbajw5p1f5a1kdyf23w5vjdmwwrk246syin9pkkl"))))
     (build-system gnu-build-system)
     (propagated-inputs
      `(("opus" ,opus)))

gnu/packages/xorg.scm

@@ -2645,33 +2645,27 @@ as USB mice.")
      "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 @@ item of @var{packages}."
 
          (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 @@ item of @var{packages}."
                       (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 @@ This service is not part of @var{%base-services}."
                                              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 @@
             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 @@ networking."))))
 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 @@
             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 @@ The bootloader BOOTLOADER is installed to BOOTLOADER-TARGET."
                             "/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 @@
   #: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 @@ subnet 192.168.1.0 netmask 255.255.255.0 {
    (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 @@
   "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 @@ name of an ASD system, and asd-file is the full path to its definition."
 
 (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 @@ with PROGRAM."
 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 @@ asdf:system-depends-on.  First load the system's 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 @@ asdf:system-depends-on.  First load the system's 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 @@ system to find its dependencies, as described by GENERATE-DEPENDENCY-LINKS."
            (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 @@ INSTANCES."
             (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 @@ INSTANCES."
             (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 @@ are relative to DIRECTORY, which is not necessarily the root of the checkout."
 
 (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 @@
             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 @@
   #: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 @@
   ;; 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 @@
           (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 @@ missing key."
            (_ #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 @@ and 'interactive' (default)."
           (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 @@ in the format specified by FMT."
                     ;; 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 @@ package modules, while attempting to retain user package modules."
         (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 @@ Emit a representation of the dependency graph of PACKAGE...\n"))
       --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 @@ Emit a representation of the dependency graph of PACKAGE...\n"))
 
 (define %default-options
   `((node-type . ,%package-node-type)
-    (backend   . ,%graphviz-backend)))
+    (backend   . ,%graphviz-backend)
+    (system    . ,(%current-system))))
 
 
 ;;;
@@ -508,7 +515,8 @@ Emit a representation of the dependency graph of PACKAGE...\n"))
               (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 @@ Download and deploy the latest version of Guix.\n"))
          (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 @@ way and displaying details about the channel's source code."
             ;; 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 @@ Use '~/.config/guix/channels.scm' instead."))
                 (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 @@
                 (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 @@ specified with `--select'.\n"))
   -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 @@ update would trigger a complete rebuild."
                                 (%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 @@ bytevector) as its internal buffer, and a thunk to flush this output port."
 
   (define (flush)
     (put-bytevector port buffer 0 total)
+    (force-output port)
     (set! total 0))
 
   (define (write bv offset count)
@@ -927,6 +928,7 @@ path."
              (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 @@ an arbitrary directory layout in the store without creating a derivation."
                            #: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 @@
 
 (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