Merge branch 'master' into core-updates

HACKING

@@ -5,6 +5,7 @@
 Copyright © 2012, 2013, 2014, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 Copyright © 2015, 2017 Mathieu Lirzin <mthl@gnu.org>
 Copyright © 2017 Leo Famulari <leo@famulari.name>
+Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 
   Copying and distribution of this file, with or without modification,
   are permitted in any medium without royalty provided the copyright
@@ -61,3 +62,12 @@ after two weeks, and if you’re confident, it’s OK to commit.
 
 That last part is subject to being adjusted, allowing individuals to commit
 directly on non-controversial changes on parts they’re familiar with.
+
+* Using emacs-debbugs
+
+Bug reports and patches are tracked using debbugs. If you are on emacs, you
+can use emacs-debbugs.
+
+List all open bug reports on guix-patches with
+
+C-u M-x debbugs-gnu <RET> <RET> guix-patches <RET> n y

Makefile.am

@@ -577,7 +577,7 @@ GUIXSD_SUPPORTED_SYSTEMS ?= x86_64-linux i686-linux
 GUIXSD_VM_SYSTEMS ?= x86_64-linux
 
 # Prefix of the GuixSD installation image file name.
-GUIXSD_IMAGE_BASE = guixsd-usb-install-$(PACKAGE_VERSION)
+GUIXSD_IMAGE_BASE = guixsd-install-$(PACKAGE_VERSION)
 
 # Prefix of the GuixSD VM image file name.
 GUIXSD_VM_IMAGE_BASE = guixsd-vm-image-$(PACKAGE_VERSION)
@@ -628,6 +628,7 @@ release: dist
 	for system in $(GUIXSD_SUPPORTED_SYSTEMS) ; do					\
 	  image=`$(top_builddir)/pre-inst-env						\
 	    guix system disk-image							\
+	    --file-system-type=iso9660							\
             --system=$$system								\
 	    gnu/system/install.scm` ;							\
 	  if [ ! -f "$$image" ] ; then							\

doc/guix.texi

@@ -216,7 +216,7 @@ Services
 * X Window::                    Graphical display.
 * Printing Services::           Local and remote printer support.
 * Desktop Services::            D-Bus and desktop services.
-* Database Services::           SQL databases.
+* Database Services::           SQL databases, key-value stores, etc.
 * Mail Services::               IMAP, POP3, SMTP, and all that.
 * Messaging Services::          Messaging services.
 * Monitoring Services::         Monitoring services.
@@ -2630,7 +2630,7 @@ configuration triplets,, autoconf, Autoconf}).
 @item --compression=@var{tool}
 @itemx -C @var{tool}
 Compress the resulting tarball using @var{tool}---one of @code{gzip},
-@code{bzip2}, @code{xz}, or @code{lzip}.
+@code{bzip2}, @code{xz}, @code{lzip}, or @code{none} for no compression.
 
 @item --symlink=@var{spec}
 @itemx -S @var{spec}
@@ -7465,6 +7465,7 @@ available.
 * Limitations::                 What you can expect.
 * Hardware Considerations::     Supported hardware.
 * USB Stick Installation::      Preparing the installation medium.
+* DVD Installation::            Preparing the installation medium.
 * Preparing for Installation::  Networking, partitioning, etc.
 * Proceeding with the Installation::  The real thing.
 * Installing GuixSD in a VM::   GuixSD playground.
@@ -7554,7 +7555,7 @@ about their support in GNU/Linux.
 @subsection USB Stick Installation
 
 An installation image for USB sticks can be downloaded from
-@indicateurl{ftp://alpha.gnu.org/gnu/guix/guixsd-usb-install-@value{VERSION}.@var{system}.xz},
+@indicateurl{ftp://alpha.gnu.org/gnu/guix/guixsd-install-@value{VERSION}.@var{system}.xz},
 where @var{system} is one of:
 
 @table @code
@@ -7570,8 +7571,8 @@ Make sure to download the associated @file{.sig} file and to verify the
 authenticity of the image against it, along these lines:
 
 @example
-$ wget ftp://alpha.gnu.org/gnu/guix/guixsd-usb-install-@value{VERSION}.@var{system}.xz.sig
+$ wget ftp://alpha.gnu.org/gnu/guix/guixsd-install-@value{VERSION}.@var{system}.xz.sig
-$ gpg --verify guixsd-usb-install-@value{VERSION}.@var{system}.xz.sig
+$ gpg --verify guixsd-install-@value{VERSION}.@var{system}.xz.sig
 @end example
 
 If that command fails because you do not have the required public key,
@@ -7585,9 +7586,8 @@ $ gpg --keyserver pgp.mit.edu --recv-keys @value{OPENPGP-SIGNING-KEY-ID}
 and rerun the @code{gpg --verify} command.
 @c end duplication
 
-This image contains a single partition with the tools necessary for an
+This image contains the tools necessary for an installation.
-installation.  It is meant to be copied @emph{as is} to a large-enough
+It is meant to be copied @emph{as is} to a large-enough USB stick or DVD.
-USB stick.
 
 To copy the image to a USB stick, follow these steps:
 
@@ -7596,7 +7596,7 @@ To copy the image to a USB stick, follow these steps:
 Decompress the image using the @command{xz} command:
 
 @example
-xz -d guixsd-usb-install-@value{VERSION}.@var{system}.xz
+xz -d guixsd-install-@value{VERSION}.@var{system}.xz
 @end example
 
 @item
@@ -7605,7 +7605,7 @@ its device name.  Assuming that the USB stick is known as @file{/dev/sdX},
 copy the image with:
 
 @example
-dd if=guixsd-usb-install-@value{VERSION}.x86_64 of=/dev/sdX
+dd if=guixsd-install-@value{VERSION}.x86_64 of=/dev/sdX
 sync
 @end example
 
@@ -7619,12 +7619,79 @@ UEFI boot menu, where you can choose to boot from the USB stick.
 @xref{Installing GuixSD in a VM}, if, instead, you would like to install
 GuixSD in a virtual machine (VM).
 
+@node DVD Installation
+@subsection DVD Installation
+
+An installation image for DVDs can be downloaded from
+@indicateurl{ftp://alpha.gnu.org/gnu/guix/guixsd-install-@value{VERSION}.@var{system}.xz},
+where @var{system} is one of:
+
+@table @code
+@item x86_64-linux
+for a GNU/Linux system on Intel/AMD-compatible 64-bit CPUs;
+
+@item i686-linux
+for a 32-bit GNU/Linux system on Intel-compatible CPUs.
+@end table
+
+@c start duplication of authentication part from ``Binary Installation''
+Make sure to download the associated @file{.sig} file and to verify the
+authenticity of the image against it, along these lines:
+
+@example
+$ wget ftp://alpha.gnu.org/gnu/guix/guixsd-install-@value{VERSION}.@var{system}.xz.sig
+$ gpg --verify guixsd-install-@value{VERSION}.@var{system}.xz.sig
+@end example
+
+If that command fails because you do not have the required public key,
+then run this command to import it:
+
+@example
+$ gpg --keyserver pgp.mit.edu --recv-keys @value{OPENPGP-SIGNING-KEY-ID}
+@end example
+
+@noindent
+and rerun the @code{gpg --verify} command.
+@c end duplication
+
+This image contains the tools necessary for an installation.
+It is meant to be copied @emph{as is} to a large-enough USB stick or DVD.
+
+To copy the image to a DVD, follow these steps:
+
+@enumerate
+@item
+Decompress the image using the @command{xz} command:
+
+@example
+xz -d guixsd-install-@value{VERSION}.@var{system}.xz
+@end example
+
+@item
+Insert a blank DVD into your machine, and determine
+its device name.  Assuming that the DVD drive is known as @file{/dev/srX},
+copy the image with:
+
+@example
+growisofs -dvd-compat -Z /dev/srX=guixsd-install-@value{VERSION}.x86_64
+@end example
+
+Access to @file{/dev/srX} usually requires root privileges.
+@end enumerate
+
+Once this is done, you should be able to reboot the system and boot from
+the DVD.  The latter usually requires you to get in the BIOS or
+UEFI boot menu, where you can choose to boot from the DVD.
+
+@xref{Installing GuixSD in a VM}, if, instead, you would like to install
+GuixSD in a virtual machine (VM).
+
 @node Preparing for Installation
 @subsection Preparing for Installation
 
-Once you have successfully booted the image on the USB stick, you should
+Once you have successfully booted your computer using the installation medium,
-end up with a root prompt.  Several console TTYs are configured and can
+you should end up with a root prompt.  Several console TTYs are configured
-be used to run commands as root.  TTY2 shows this documentation,
+and can be used to run commands as root.  TTY2 shows this documentation,
 browsable using the Info reader commands (@pxref{Top,,, info-stnd,
 Stand-alone GNU Info}).  The installation system runs the GPM mouse
 daemon, which allows you to select text with the left mouse button and
@@ -7979,7 +8046,7 @@ Boot the USB installation image in an VM:
 @example
 qemu-system-x86_64 -m 1024 -smp 1 \
   -net user -net nic,model=virtio -boot menu=on \
-  -drive file=guixsd-usb-install-@value{VERSION}.@var{system} \
+  -drive file=guixsd-install-@value{VERSION}.@var{system} \
   -drive file=guixsd.img
 @end example
 

gnu/bootloader/grub.scm

@@ -389,7 +389,20 @@ (define install-grub
         (unless (zero? (system* grub "--no-floppy"
                                 "--boot-directory" install-dir
                                 device))
-          (error "failed to install GRUB")))))
+          (error "failed to install GRUB (BIOS)")))))
+
+(define install-grub-efi
+  #~(lambda (bootloader efi-dir mount-point)
+      ;; Install GRUB onto the EFI partition mounted at EFI-DIR, for the
+      ;; system whose root is mounted at MOUNT-POINT.
+      (let ((grub-install (string-append bootloader "/sbin/grub-install"))
+            (install-dir (string-append mount-point "/boot")))
+        ;; Tell 'grub-install' that there might be a LUKS-encrypted /boot or
+        ;; root partition.
+        (setenv "GRUB_ENABLE_CRYPTODISK" "y")
+        (unless (zero? (system* grub-install "--boot-directory" install-dir
+                                "--efi-directory" efi-dir))
+          (error "failed to install GRUB (EFI)")))))
 
 
 
@@ -408,6 +421,7 @@ (define grub-bootloader
 (define* grub-efi-bootloader
   (bootloader
    (inherit grub-bootloader)
+   (installer install-grub-efi)
    (name 'grub-efi)
    (package grub-efi)))
 

gnu/local.mk

@@ -196,6 +196,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/gv.scm				\
   %D%/packages/gxmessage.scm			\
   %D%/packages/haskell.scm			\
+  %D%/packages/ham-radio.scm			\
   %D%/packages/hexedit.scm			\
   %D%/packages/hugs.scm				\
   %D%/packages/hurd.scm				\
@@ -527,6 +528,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/awesome-reproducible-png.patch		\
   %D%/packages/patches/azr3.patch				\
   %D%/packages/patches/bash-completion-directories.patch	\
+  %D%/packages/patches/bcftools-regidx-unsigned-char.patch	\
   %D%/packages/patches/binutils-ld-new-dtags.patch		\
   %D%/packages/patches/binutils-loongson-workaround.patch	\
   %D%/packages/patches/blast+-fix-makefile.patch		\
@@ -670,6 +672,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \
   %D%/packages/patches/gobject-introspection-cc.patch		\
   %D%/packages/patches/gobject-introspection-girepository.patch	\
+  %D%/packages/patches/graphicsmagick-CVE-2017-12935.patch	\
+  %D%/packages/patches/graphicsmagick-CVE-2017-12936.patch	\
+  %D%/packages/patches/graphicsmagick-CVE-2017-12937.patch	\
   %D%/packages/patches/graphite2-ffloat-store.patch		\
   %D%/packages/patches/grep-gnulib-lock.patch                   \
   %D%/packages/patches/grep-timing-sensitive-test.patch		\
@@ -822,7 +827,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/lvm2-static-link.patch			\
   %D%/packages/patches/lxsession-use-gapplication.patch         \
   %D%/packages/patches/lxterminal-CVE-2016-10369.patch		\
-  %D%/packages/patches/lz4-fix-test-failures.patch		\
   %D%/packages/patches/make-impure-dirs.patch			\
   %D%/packages/patches/mars-install.patch			\
   %D%/packages/patches/mars-sfml-2.3.patch			\
@@ -859,6 +863,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/netsurf-system-utf8proc.patch		\
   %D%/packages/patches/netsurf-y2038-tests.patch		\
   %D%/packages/patches/netsurf-longer-test-timeout.patch	\
+  %D%/packages/patches/newsbeuter-CVE-2017-12904.patch		\
   %D%/packages/patches/ngircd-handle-zombies.patch		\
   %D%/packages/patches/ninja-zero-mtime.patch			\
   %D%/packages/patches/node-9077.patch				\
@@ -953,7 +958,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch	\
   %D%/packages/patches/python-statsmodels-fix-tests.patch	\
   %D%/packages/patches/python-configobj-setuptools.patch	\
-  %D%/packages/patches/python-cython-fix-tests-32bit.patch	\
   %D%/packages/patches/python-faker-fix-build-32bit.patch	\
   %D%/packages/patches/python-pandas-skip-failing-tests.patch	\
   %D%/packages/patches/python-paste-remove-website-test.patch	\
@@ -990,7 +994,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/reptyr-fix-gcc-7.patch			\
   %D%/packages/patches/ripperx-missing-file.patch		\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
-  %D%/packages/patches/rpm-CVE-2014-8118.patch			\
   %D%/packages/patches/rsem-makefile.patch			\
   %D%/packages/patches/ruby-concurrent-ignore-broken-test.patch	\
   %D%/packages/patches/ruby-concurrent-test-arm.patch		\
@@ -1060,6 +1063,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/util-linux-tests.patch			\
   %D%/packages/patches/upower-builddir.patch			\
   %D%/packages/patches/valgrind-enable-arm.patch		\
+  %D%/packages/patches/vinagre-revert-1.patch                   \
+  %D%/packages/patches/vinagre-revert-2.patch                   \
   %D%/packages/patches/virglrenderer-CVE-2017-6386.patch 	\
   %D%/packages/patches/vorbis-tools-CVE-2014-9638+CVE-2014-9639.patch		\
   %D%/packages/patches/vorbis-tools-CVE-2014-9640.patch		\
@@ -1091,6 +1096,7 @@ dist_patch_DATA =						\
   %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	\
+  %D%/packages/patches/xf86-video-siliconmotion-fix-ftbfs.patch \
   %D%/packages/patches/xf86-video-tga-remove-mibstore.patch	\
   %D%/packages/patches/xfce4-panel-plugins.patch		\
   %D%/packages/patches/xfce4-session-fix-xflock4.patch		\

gnu/packages/admin.scm

@@ -1793,14 +1793,14 @@ (define-public di
 (define-public cbatticon
   (package
     (name "cbatticon")
-    (version "1.6.5")
+    (version "1.6.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/valr/"
                                   name "/archive/" version ".tar.gz"))
               (sha256
                (base32
-                "0xzz1faqgm57bwlkw6sjdfbckf5hck81879zbfk18p7xn9vhvixv"))
+                "1rxlrwd817f2zl4fsc5ha43wjzfidq3yyagq4lgyi150qg36svv3"))
               (file-name (string-append name "-" version ".tar.gz"))))
     (build-system gnu-build-system)
     (arguments

gnu/packages/algebra.scm

@@ -207,7 +207,7 @@ (define-public gp2c
 (define-public giac-xcas
   (package
     (name "giac-xcas")
-    (version "1.2.3-51")
+    (version "1.2.3-57")
     (source (origin
               (method url-fetch)
               ;; "~parisse/giac" is not used because the maintainer regularly
@@ -219,7 +219,7 @@ (define-public giac-xcas
                                   "source/giac_" version ".tar.gz"))
               (sha256
                (base32
-                "1w7d4sdjbvqiibnfkhrqy9np3smsysilfba9pry3q1qn5g5y6nrp"))))
+                "0a7c1r2rgsin671qy98yvwgkg6a81d0pp0p4p7sydhrfi1k9xpr1"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/bioinformatics.scm

@@ -311,6 +311,7 @@ (define-public bcftools
               (sha256
                (base32
                 "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
+              (patches (search-patches "bcftools-regidx-unsigned-char.patch"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled htslib.
@@ -2114,7 +2115,7 @@ (define-public deeptools
 (define-public diamond
   (package
     (name "diamond")
-    (version "0.9.9")
+    (version "0.9.10")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2123,7 +2124,7 @@ (define-public diamond
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "04i03046g3l2vk9722z47r1p7j415g97vvz6d76ywmbawyiihcb1"))))
+                "13qqzwg54n5dqh8pm5n3v8x6gqbczzakphwwjix63qv60hcd5bqd"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no "check" target
@@ -8315,6 +8316,30 @@ (define-public r-rhdf5
 the available RAM.")
     (license license:artistic2.0)))
 
+(define-public r-annotationfilter
+  (package
+    (name "r-annotationfilter")
+    (version "1.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AnnotationFilter" version))
+              (sha256
+               (base32
+                "0pxvswjzwibdfmrkdragxmzcl844z73pmkn82z92wahwa6gjfyi7"))))
+    (properties
+     `((upstream-name . "AnnotationFilter")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genomicranges" ,r-genomicranges)
+       ("r-lazyeval" ,r-lazyeval)))
+    (home-page "https://github.com/Bioconductor/AnnotationFilter")
+    (synopsis "Facilities for filtering Bioconductor annotation resources")
+    (description
+     "This package provides classes and other infrastructure to implement
+filters for manipulating Bioconductor annotation resources.  The filters are
+used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
+    (license license:artistic2.0)))
+
 (define-public emboss
   (package
     (name "emboss")
@@ -8672,6 +8697,52 @@ (define-public r-copywriter
 number detection tools.")
     (license license:gpl2)))
 
+(define-public r-methylkit
+  (package
+    (name "r-methylkit")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "methylKit" version))
+              (sha256
+               (base32
+                "02acdjf6jl0c1glymin84pdna4farn4vv0gb6107d9iqz3y3gkmm"))))
+    (properties `((upstream-name . "methylKit")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)
+       ("r-emdbook" ,r-emdbook)
+       ("r-fastseg" ,r-fastseg)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-gtools" ,r-gtools)
+       ("r-iranges" ,r-iranges)
+       ("r-kernsmooth" ,r-kernsmooth)
+       ("r-limma" ,r-limma)
+       ("r-mclust" ,r-mclust)
+       ("r-qvalue" ,r-qvalue)
+       ("r-r-utils" ,r-r-utils)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "http://code.google.com/p/methylkit/")
+    (synopsis
+     "DNA methylation analysis from high-throughput bisulfite sequencing results")
+    (description
+     "MethylKit is an R package for DNA methylation analysis and annotation
+from high-throughput bisulfite sequencing.  The package is designed to deal
+with sequencing data from @dfn{Reduced representation bisulfite
+sequencing} (RRBS) and its variants, but also target-capture methods and whole
+genome bisulfite sequencing.  It also has functions to analyze base-pair
+resolution 5hmC data from experimental protocols such as oxBS-Seq and
+TAB-Seq.")
+    (license license:artistic2.0)))
+
 (define-public r-sva
   (package
     (name "r-sva")
@@ -8816,7 +8887,8 @@ (define-public r-mzr
     (properties `((upstream-name . "mzR")))
     (build-system r-build-system)
     (inputs
-     `(("netcdf" ,netcdf)))
+     `(("boost" ,boost)
+       ("netcdf" ,netcdf)))
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
@@ -9234,6 +9306,123 @@ (define-public r-edaseq
 global-scaling and full-quantile normalization.")
     (license license:artistic2.0)))
 
+(define-public r-interactivedisplaybase
+  (package
+    (name "r-interactivedisplaybase")
+    (version "1.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "interactiveDisplayBase" version))
+       (sha256
+        (base32
+         "12f6ap4bl3h2iwwhg8i3r9a7yyd28d8i5lb3fj1vnfvjs762r7r7"))))
+    (properties
+     `((upstream-name . "interactiveDisplayBase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-shiny" ,r-shiny)))
+    (home-page "http://bioconductor.org/packages/interactiveDisplayBase")
+    (synopsis "Base package for web displays of Bioconductor objects")
+    (description
+     "This package contains the basic methods needed to generate interactive
+Shiny-based display methods for Bioconductor objects.")
+    (license license:artistic2.0)))
+
+(define-public r-annotationhub
+  (package
+    (name "r-annotationhub")
+    (version "2.8.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "AnnotationHub" version))
+       (sha256
+        (base32
+         "1nh5si3j1nv37jcg4260582ayjg18851np47cskrm54prnvhwd9r"))))
+    (properties `((upstream-name . "AnnotationHub")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocinstaller" ,r-biocinstaller)
+       ("r-httr" ,r-httr)
+       ("r-interactivedisplaybase" ,r-interactivedisplaybase)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-yaml" ,r-yaml)))
+    (home-page "http://bioconductor.org/packages/AnnotationHub")
+    (synopsis "Client to access AnnotationHub resources")
+    (description
+     "This package provides a client for the Bioconductor AnnotationHub web
+resource.  The AnnotationHub web resource provides a central location where
+genomic files (e.g. VCF, bed, wig) and other resources from standard
+locations (e.g. UCSC, Ensembl) can be discovered.  The resource includes
+metadata about each resource, e.g., a textual description, tags, and date of
+modification.  The client creates and manages a local cache of files retrieved
+by the user, helping with quick and reproducible access.")
+    (license license:artistic2.0)))
+
+(define-public r-fastseg
+  (package
+    (name "r-fastseg")
+    (version "1.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "fastseg" version))
+       (sha256
+        (base32
+         "083wiz03q9mynwchs9frlpp6c84dncri5ncibx6h82p228cpja6h"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "http://www.bioinf.jku.at/software/fastseg/index.html")
+    (synopsis "Fast segmentation algorithm for genetic sequencing data")
+    (description
+     "Fastseg implements a very fast and efficient segmentation algorithm.
+It can segment data from DNA microarrays and data from next generation
+sequencing for example to detect copy number segments.  Further it can segment
+data from RNA microarrays like tiling arrays to identify transcripts.  Most
+generally, it can segment data given as a matrix or as a vector.  Various data
+formats can be used as input to fastseg like expression set objects for
+microarrays or GRanges for sequencing data.")
+    (license license:lgpl2.0+)))
+
+(define-public r-qvalue
+  (package
+    (name "r-qvalue")
+    (version "2.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "qvalue" version))
+       (sha256
+        (base32
+         "1dxdwa767a9r8n61r272ypi09qblcdfpzzwkmri74y5mbp1r3y4i"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-reshape2" ,r-reshape2)))
+    (home-page "http://github.com/jdstorey/qvalue")
+    (synopsis "Q-value estimation for false discovery rate control")
+    (description
+     "This package takes a list of p-values resulting from the simultaneous
+testing of many hypotheses and estimates their q-values and local @dfn{false
+discovery rate} (FDR) values.  The q-value of a test measures the proportion
+of false positives incurred when that particular test is called significant.
+The local FDR measures the posterior probability the null hypothesis is true
+given the test's p-value.  Various plots are automatically generated, allowing
+one to make sensible significance cut-offs.  The software can be applied to
+problems in genomics, brain imaging, astrophysics, and data mining.")
+    ;; Any version of the LGPL.
+    (license license:lgpl3+)))
+
 (define htslib-for-sambamba
   (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
     (package

gnu/packages/ci.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016, 2017 Mathieu Lirzin <mthl@gnu.org>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
+;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -186,8 +187,8 @@ (define-public hydra
       (license l:gpl3+))))
 
 (define-public cuirass
-  (let ((commit "870e8d6ad3415ac61c52e57095fcc6164023a0fc")
+  (let ((commit "6f85bc04f31ae5853ceaa0bb3e1dedfe8412a189")
-        (revision "6"))
+        (revision "7"))
     (package
       (name "cuirass")
       (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -199,7 +200,7 @@ (define-public cuirass
                 (file-name (string-append name "-" version))
                 (sha256
                  (base32
-                  "0lp5a5p42k7lml15lbmmd7az9i0gw5kips3sh3awd2z79h0w2knw"))))
+                  "1dglsa23z21m1s70420ar73qmg39fvdvwlz9xjz6lfp5s9mgzx15"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)
@@ -223,7 +224,8 @@ (define-public cuirass
                (let* ((out    (assoc-ref outputs "out"))
                       (json   (assoc-ref inputs "guile-json"))
                       (sqlite (assoc-ref inputs "guile-sqlite3"))
-                      (git    (assoc-ref inputs "git"))
+                      (git    (assoc-ref inputs "guile-git"))
+                      (bytes  (assoc-ref inputs "guile-bytestructures"))
                       (guix   (assoc-ref inputs "guix"))
                       (guile  (assoc-ref %build-inputs "guile"))
                       (effective (read-line
@@ -231,16 +233,19 @@ (define-public cuirass
                                               (string-append guile "/bin/guile")
                                               "-c" "(display (effective-version))")))
                       (mods   (string-append json "/share/guile/site/"
+                                             effective ":"
+                                             git "/share/guile/site/"
+                                             effective ":"
+                                             bytes "/share/guile/site/"
                                              effective ":"
                                              sqlite "/share/guile/site/"
                                              effective ":"
                                              guix "/share/guile/site/"
                                              effective)))
-                 ;; Make sure 'cuirass' can find the 'git' and 'evaluate'
+                 ;; Make sure 'cuirass' can find the 'evaluate' command, as
-                 ;; commands, as well as the relevant Guile modules.
+                 ;; well as the relevant Guile modules.
                  (wrap-program (string-append out "/bin/cuirass")
-                   `("PATH" ":" prefix (,(string-append out "/bin")
+                   `("PATH" ":" prefix (,(string-append out "/bin")))
-                                        ,(string-append git "/bin")))
                    `("GUILE_LOAD_PATH" ":" prefix (,mods))
                    `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,mods)))
                  #t))))))
@@ -248,8 +253,11 @@ (define-public cuirass
        `(("guile" ,guile-2.2)
          ("guile-json" ,guile-json)
          ("guile-sqlite3" ,guile-sqlite3)
-         ("guix" ,guix)
+         ("guile-git" ,guile-git)
-         ("git" ,git)))
+         ;; FIXME: this is propagated by "guile-git", but it needs to be among
+         ;; the inputs to add it to GUILE_LOAD_PATH.
+         ("guile-bytestructures" ,guile-bytestructures)
+         ("guix" ,guix)))
       (native-inputs
        `(("autoconf" ,autoconf)
          ("automake" ,automake)

gnu/packages/compression.scm

@@ -606,14 +606,14 @@ (define-public sfarkxtc
 (define-public libmspack
   (package
     (name "libmspack")
-    (version "0.5")
+    (version "0.6")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "http://www.cabextract.org.uk/libmspack/libmspack-"
                           version "alpha.tar.gz"))
       (sha256
-       (base32 "04413hynb7zizxnkgy9riik3612dwirkpr6fcjrnfl2za9sz4rw9"))))
+       (base32 "08gr2pcinas6bdqz3k0286g5cnksmcx813skmdwyca6bmj1fxnqy"))))
     (build-system gnu-build-system)
     (home-page "http://www.cabextract.org.uk/libmspack/")
     (synopsis "Compression tools for some formats used by Microsoft")
@@ -702,16 +702,15 @@ (define-public perl-io-compress
 (define-public lz4
   (package
     (name "lz4")
-    (version "1.7.5")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/lz4/lz4/archive/"
                            "v" version ".tar.gz"))
-       (patches (search-patches "lz4-fix-test-failures.patch"))
        (sha256
         (base32
-         "0zkykqqjfa1q3ji0qmb1ml3l9063qqfh99agyj3cnb02cg6wm401"))
+         "1xnckwwah74gl98gylf1b00vk4km1d8sgd8865h07ccvgbm8591c"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system gnu-build-system)
     (native-inputs `(("valgrind" ,valgrind)))   ; for tests
@@ -722,14 +721,14 @@ (define-public lz4
                           (string-append "PREFIX=" (assoc-ref %outputs "out")))
        #:phases (modify-phases %standard-phases
                   (delete 'configure))))        ; no configure script
-    (home-page "https://github.com/lz4/lz4")
+    (home-page "http://www.lz4.org")
     (synopsis "Compression algorithm focused on speed")
     (description "LZ4 is a lossless compression algorithm, providing
 compression speed at 400 MB/s per core (0.16 Bytes/cycle).  It also features an
 extremely fast decoder, with speed in multiple GB/s per core (0.71 Bytes/cycle).
 A high compression derivative, called LZ4_HC, is also provided.  It trades CPU
 time for compression ratio.")
-    ;; The libraries (lz4, lz4hc, and xxhash are BSD licenced. The command
+    ;; The libraries (lz4, lz4hc, and xxhash) are BSD licenced. The command
     ;; line interface programs (lz4, fullbench, fuzzer, datagen) are GPL2+.
     (license (list license:bsd-2 license:gpl2+))))
 

gnu/packages/connman.scm

@@ -42,7 +42,7 @@ (define-module (gnu packages connman)
 (define-public connman
   (package
     (name "connman")
-    (version "1.34")
+    (version "1.35")
     (source
       (origin
         (method url-fetch)
@@ -50,7 +50,7 @@ (define-public connman
                             name "-" version ".tar.xz"))
     (sha256
      (base32
-      "07n71wcy1c4cc01ca4dl9k1jpdqr5nsyr33dqf7k87wwfa681859"))))
+      "1apj5j25kj7v1bsfv3nh54aiq873nfrsjfbj85p5qm3ihfwxxmv6"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags

gnu/packages/cran.scm

@@ -21,7 +21,12 @@ (define-module (gnu packages cran)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix utils)
-  #:use-module (guix build-system r))
+  #:use-module (guix build-system r)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages web))
 
 (define-public r-colorspace
   (package
@@ -148,3 +153,778 @@ (define-public r-bindrcpp
      "This package provides an easy way to fill an environment with active
 bindings that call a C++ function.")
     (license license:expat)))
+
+(define-public r-auc
+  (package
+    (name "r-auc")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AUC" version))
+       (sha256
+        (base32
+         "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
+    (properties `((upstream-name . "AUC")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/AUC")
+    (synopsis "Compute the area under the curve of selected measures")
+    (description
+     "This package includes functions to compute the area under the curve of
+selected measures: the area under the sensitivity curve (AUSEC), the area
+under the specificity curve (AUSPC), the area under the accuracy
+curve (AUACC), and the area under the receiver operating characteristic
+curve (AUROC).  The curves can also be visualized.  Support for partial areas
+is provided.")
+    (license license:gpl2+)))
+
+(define-public r-calibrate
+  (package
+    (name "r-calibrate")
+    (version "1.7.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "calibrate" version))
+       (sha256
+        (base32
+         "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)))
+    (home-page "http://cran.r-project.org/web/packages/calibrate")
+    (synopsis "Calibration of scatterplot and biplot axes")
+    (description
+     "This is a package for drawing calibrated scales with tick marks
+on (non-orthogonal) variable vectors in scatterplots and biplots.")
+    (license license:gpl2)))
+
+(define-public r-shape
+  (package
+    (name "r-shape")
+    (version "1.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shape" version))
+       (sha256
+        (base32
+         "0yk3cmsa57svcvbnm21pyr0s0qbhnllka8nmsg4yb41frjlqph66"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/shape")
+    (synopsis "Functions for plotting graphical shapes")
+    (description
+     "This package provides functions for plotting graphical shapes such as
+ellipses, circles, cylinders, arrows, ...")
+    (license license:gpl3+)))
+
+(define-public r-globaloptions
+  (package
+    (name "r-globaloptions")
+    (version "0.0.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "GlobalOptions" version))
+       (sha256
+        (base32
+         "1abpc03cfvazbwj2sx6qgngs5pgpzysvxkana20hyvb4n7ws77f0"))))
+    (properties `((upstream-name . "GlobalOptions")))
+    (build-system r-build-system)
+    (home-page "https://github.com/jokergoo/GlobalOptions")
+    (synopsis "Generate functions to get or set global options")
+    (description
+     "This package provides more controls on the option values such as
+validation and filtering on the values, making options invisible or private.")
+    (license license:gpl2+)))
+
+(define-public r-circlize
+  (package
+    (name "r-circlize")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "circlize" version))
+       (sha256
+        (base32
+         "0p1zx1aawkblz48kzzfn5w1k3lbwv9wrk1k5gcfjrr2b4sz1pp5b"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-colorspace" ,r-colorspace)
+       ("r-globaloptions" ,r-globaloptions)
+       ("r-shape" ,r-shape)))
+    (home-page "https://github.com/jokergoo/circlize")
+    (synopsis "Circular visualization")
+    (description
+     "Circular layout is an efficient way for the visualization of huge
+amounts of information.  This package provides an implementation of circular
+layout generation in R as well as an enhancement of available software.  The
+flexibility of the package is based on the usage of low-level graphics
+functions such that self-defined high-level graphics can be easily implemented
+by users for specific purposes.  Together with the seamless connection between
+the powerful computational and visual environment in R, it gives users more
+convenience and freedom to design figures for better understanding complex
+patterns behind multiple dimensional data.")
+    (license license:gpl2+)))
+
+(define-public r-powerlaw
+  (package
+    (name "r-powerlaw")
+    (version "0.70.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "poweRlaw" version))
+       (sha256
+        (base32
+         "1p2la3hslxq2xa8jkwvci6zcpn47cvyr9xqd5agp1riwwp2xw5gh"))))
+    (properties `((upstream-name . "poweRlaw")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-vgam" ,r-vgam)))
+    (home-page "https://github.com/csgillespie/poweRlaw")
+    (synopsis "Tools for the analysis of heavy tailed distributions")
+    (description
+     "This package provides an implementation of maximum likelihood estimators
+for a variety of heavy tailed distributions, including both the discrete and
+continuous power law distributions.  Additionally, a goodness-of-fit based
+approach is used to estimate the lower cut-off for the scaling region.")
+    ;; Any of these GPL versions.
+    (license (list license:gpl2 license:gpl3))))
+
+(define-public r-compare
+  (package
+    (name "r-compare")
+    (version "0.2-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "compare" version))
+       (sha256
+        (base32
+         "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/compare")
+    (synopsis "Comparing objects for differences")
+    (description
+     "This package provides functions to compare a model object to a
+comparison object.  If the objects are not identical, the functions can be
+instructed to explore various modifications of the objects (e.g., sorting
+rows, dropping names) to see if the modified versions are identical.")
+    (license license:gpl2+)))
+
+(define-public r-dendextend
+  (package
+    (name "r-dendextend")
+    (version "1.5.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "dendextend" version))
+       (sha256
+        (base32
+         "04jz58apibfrkjcrdmw2hmsav6qpb5cs6qdai81k1v1iznfcya42"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-fpc" ,r-fpc)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-magrittr" ,r-magrittr)
+       ("r-viridis" ,r-viridis)
+       ("r-whisker" ,r-whisker)))
+    (home-page "https://cran.r-project.org/web/packages/dendextend")
+    (synopsis "Extending 'dendrogram' functionality in R")
+    (description
+     "This package offers a set of functions for extending @code{dendrogram}
+objects in R, letting you visualize and compare trees of hierarchical
+clusterings.  You can adjust a tree's graphical parameters (the color, size,
+type, etc of its branches, nodes and labels) and visually and statistically
+compare different dendrograms to one another.")
+    ;; Any of these versions
+    (license (list license:gpl2 license:gpl3))))
+
+(define-public r-getoptlong
+  (package
+    (name "r-getoptlong")
+    (version "0.1.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "GetoptLong" version))
+       (sha256
+        (base32
+         "1d98gcvlvp9nz5lbnzr0kkpc2hbkx74hlhrnybqhg1gdwc3g09pm"))))
+    (properties `((upstream-name . "GetoptLong")))
+    (build-system r-build-system)
+    (inputs
+     `(("perl" ,perl)))
+    (propagated-inputs
+     `(("r-globaloptions" ,r-globaloptions)
+       ("r-rjson" ,r-rjson)))
+    (home-page "https://github.com/jokergoo/GetoptLong")
+    (synopsis "Parsing command-line arguments and variable interpolation")
+    (description
+     "This is yet another command-line argument parser which wraps the
+powerful Perl module @code{Getopt::Long} and with some adaptation for easier
+use in R.  It also provides a simple way for variable interpolation in R.")
+    (license license:gpl2+)))
+
+(define-public r-fastmatch
+  (package
+    (name "r-fastmatch")
+    (version "1.1-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fastmatch" version))
+       (sha256
+        (base32
+         "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
+    (build-system r-build-system)
+    (home-page "http://www.rforge.net/fastmatch")
+    (synopsis "Fast match function")
+    (description
+     "This package provides a fast @code{match} replacement for cases that
+require repeated look-ups.  It is slightly faster that R's built-in
+@code{match} function on first match against a table, but extremely fast on
+any subsequent lookup as it keeps the hash table in memory.")
+    (license license:gpl2)))
+
+(define-public r-ff
+  (package
+    (name "r-ff")
+    (version "2.2-13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ff" version))
+       (sha256
+        (base32
+         "1nvd6kx46xzyc99a44mgynd94pvd2h495m5a7b1g67k5w2phiywb"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-bit" ,r-bit)))
+    (home-page "http://ff.r-forge.r-project.org/")
+    (synopsis "Memory-efficient storage of large data on disk and access functions")
+    (description
+     "This package provides data structures that are stored on disk but
+behave (almost) as if they were in RAM by transparently mapping only a section
+in main memory.")
+    (license license:gpl2)))
+
+(define-public r-ffbase
+  (package
+    (name "r-ffbase")
+    (version "0.12.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ffbase" version))
+       (sha256
+        (base32
+         "1nz97bndxxkzp8rq6va8ff5ky9vkaib1jybm6j852awwb3n9had5"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bit" ,r-bit)
+       ("r-fastmatch" ,r-fastmatch)
+       ("r-ff" ,r-ff)))
+    (home-page "http://github.com/edwindj/ffbase")
+    (synopsis "Basic statistical functions for package 'ff'")
+    (description
+     "This package extends the out of memory vectors of @code{ff} with
+statistical functions and other utilities to ease their usage.")
+    (license license:gpl3)))
+
+(define-public r-prettyunits
+  (package
+    (name "r-prettyunits")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "prettyunits" version))
+       (sha256
+        (base32
+         "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-assertthat" ,r-assertthat)
+       ("r-magrittr" ,r-magrittr)))
+    (home-page "https://github.com/gaborcsardi/prettyunits")
+    (synopsis "Pretty, human readable formatting of quantities")
+    (description
+     "This package provides tools for pretty, human readable formatting of
+quantities.")
+    (license license:expat)))
+
+(define-public r-reshape
+  (package
+    (name "r-reshape")
+    (version "0.8.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "reshape" version))
+       (sha256
+        (base32
+         "1f1ngalc22knhdm9djv1m6abnjqpv1frdzxfkpakhph2l67bk7fq"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-plyr" ,r-plyr)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "http://had.co.nz/reshape")
+    (synopsis "Flexibly reshape data")
+    (description
+     "Flexibly restructure and aggregate data using just two functions:
+@code{melt} and @code{cast}.  This package provides them.")
+    (license license:expat)))
+
+(define-public r-progress
+  (package
+    (name "r-progress")
+    (version "1.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "progress" version))
+       (sha256
+        (base32
+         "1fxakchfjr5vj59s9sxynd7crpz97xj42438rmkhkf3rjpyspx59"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-prettyunits" ,r-prettyunits)
+       ("r-r6" ,r-r6)))
+    (home-page "https://github.com/gaborcsardi/progress")
+    (synopsis "Terminal progress bars")
+    (description
+     "This package provides configurable progress bars.  They may include
+percentage, elapsed time, and/or the estimated completion time.  They work in
+terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app.  The
+package also provides a C++ API, that works with or without Rcpp.")
+    (license license:expat)))
+
+(define-public r-ggally
+  (package
+    (name "r-ggally")
+    (version "1.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "GGally" version))
+       (sha256
+        (base32
+         "12ddab0nd0f9c7bb6cx3c22mliyvc8xsxv26aqz3cvfbla8crp3b"))))
+    (properties `((upstream-name . "GGally")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-gtable" ,r-gtable)
+       ("r-plyr" ,r-plyr)
+       ("r-progress" ,r-progress)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-reshape" ,r-reshape)))
+    (home-page "https://ggobi.github.io/ggally")
+    (synopsis "Extension to ggplot2")
+    (description
+     "The R package ggplot2 is a plotting system based on the grammar of
+graphics.  GGally extends ggplot2 by adding several functions to reduce the
+complexity of combining geometric objects with transformed data.  Some of
+these functions include a pairwise plot matrix, a two group pairwise plot
+matrix, a parallel coordinates plot, a survival plot, and several functions to
+plot networks.")
+    (license license:gpl2+)))
+
+(define-public r-proxy
+  (package
+    (name "r-proxy")
+    (version "0.4-17")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "proxy" version))
+       (sha256
+        (base32
+         "0bg1fn96qrj8whmnl7c3gv244ksm2ykxxsd0zrmw4lb6465pizl2"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/proxy")
+    (synopsis "Distance and similarity measures")
+    (description
+     "This package provides an extensible framework for the efficient
+calculation of auto- and cross-proximities, along with implementations of the
+most popular ones.")
+    (license license:gpl2)))
+
+(define-public r-sp
+  (package
+    (name "r-sp")
+    (version "1.2-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sp" version))
+       (sha256
+        (base32
+         "0crba3j00mb2xv2yk60rpa57gn97xq4ql3a6p9cjzqjxzv2cknk2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lattice" ,r-lattice)))
+    (home-page "http://cran.r-project.org/web/packages/sp")
+    (synopsis "Classes and methods for spatial data")
+    (description
+     "This package provides classes and methods for spatial data; the classes
+document where the spatial location information resides, for 2D or 3D data.
+Utility functions are provided, e.g. for plotting data as maps, spatial
+selection, as well as methods for retrieving coordinates, for subsetting,
+print, summary, etc.")
+    (license license:gpl2+)))
+
+(define-public r-rmtstat
+  (package
+    (name "r-rmtstat")
+    (version "0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RMTstat" version))
+       (sha256
+        (base32
+         "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
+    (properties `((upstream-name . "RMTstat")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/RMTstat")
+    (synopsis "Distributions, statistics and tests derived from random matrix theory")
+    (description
+     "This package provides functions for working with the Tracy-Widom laws
+and other distributions related to the eigenvalues of large Wishart
+matrices.")
+    (license license:bsd-3)))
+
+(define-public r-lmoments
+  (package
+    (name "r-lmoments")
+    (version "1.2-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Lmoments" version))
+       (sha256
+        (base32
+         "13p0r4w16jvjnyjmkhkp3dwdfr1gap2l0k4k5jy41m8nc5fvcx79"))))
+    (properties `((upstream-name . "Lmoments")))
+    (build-system r-build-system)
+    (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
+    (synopsis "L-moments and quantile mixtures")
+    (description
+     "This package contains functions to estimate L-moments and trimmed
+L-moments from the data.  It also contains functions to estimate the
+parameters of the normal polynomial quantile mixture and the Cauchy polynomial
+quantile mixture from L-moments and trimmed L-moments.")
+    (license license:gpl2)))
+
+(define-public r-distillery
+  (package
+    (name "r-distillery")
+    (version "1.0-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "distillery" version))
+       (sha256
+        (base32
+         "12m4cacvc18fd3aayc8iih5q6bwsmvf29b55fwp7vs8wp1h8nd8c"))))
+    (build-system r-build-system)
+    (home-page "http://www.ral.ucar.edu/staff/ericg")
+    (synopsis "Functions for confidence intervals and object information")
+    (description
+     "This package provides some very simple method functions for confidence
+interval calculation and to distill pertinent information from a potentially
+complex object; primarily used in common with the packages extRemes and
+SpatialVx.")
+    (license license:gpl2+)))
+
+(define-public r-extremes
+  (package
+    (name "r-extremes")
+    (version "2.0-8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "extRemes" version))
+       (sha256
+        (base32
+         "0pnpib3g2r9x8hfqhvq23j8m3jh62lp28ipnqir5yadnzv850gfm"))))
+    (properties `((upstream-name . "extRemes")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-car" ,r-car)
+       ("r-distillery" ,r-distillery)
+       ("r-lmoments" ,r-lmoments)))
+    (home-page "http://www.assessment.ucar.edu/toolkit/")
+    (synopsis "Extreme value analysis")
+    (description
+     "ExtRemes is a suite of functions for carrying out analyses on the
+extreme values of a process of interest; be they block maxima over long blocks
+or excesses over a high threshold.")
+    (license license:gpl2+)))
+
+(define-public r-lmtest
+  (package
+    (name "r-lmtest")
+    (version "0.9-35")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lmtest" version))
+       (sha256
+        (base32
+         "107br1l7p52wxvazs031f4h5ryply97qywg9dzrkw4ydnvqq4j9g"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-zoo" ,r-zoo)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://cran.r-project.org/web/packages/lmtest")
+    (synopsis "Testing linear regression models")
+    (description
+     "This package provides a collection of tests, data sets, and examples for
+diagnostic checking in linear regression models.  Furthermore, some generic
+tools for inference in parametric models are provided.")
+    ;; Either version is okay
+    (license (list license:gpl2 license:gpl3))))
+
+(define-public r-inline
+  (package
+    (name "r-inline")
+    (version "0.3.14")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "inline" version))
+              (sha256
+               (base32
+                "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/inline")
+    (synopsis "Functions to inline C, C++, Fortran function calls from R")
+    (description
+     "This package provides functionality to dynamically define R functions
+and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
+@code{.Call} calling conventions.")
+    ;; Any version of the LGPL.
+    (license license:lgpl3+)))
+
+(define-public r-bbmle
+  (package
+    (name "r-bbmle")
+    (version "1.0.19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bbmle" version))
+       (sha256
+        (base32
+         "014h6mw16gv4acs2p78dy7lla7s428n633aybsb1mbi6250dg0p8"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lattice" ,r-lattice)
+       ("r-mass" ,r-mass)
+       ("r-numderiv" ,r-numderiv)))
+    (home-page "http://cran.r-project.org/web/packages/bbmle")
+    (synopsis "Tools for General Maximum Likelihood Estimation")
+    (description
+     "Methods and functions for fitting maximum likelihood models in R.  This
+package modifies and extends the @code{mle} classes in the @code{stats4}
+package.")
+    ;; Any version of the GPL
+    (license (list license:gpl2 license:gpl3))))
+
+(define-public r-emdbook
+  (package
+    (name "r-emdbook")
+    (version "1.3.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "emdbook" version))
+       (sha256
+        (base32
+         "09xbdyw8a4pvrsg3ryr8drby0njy4avc5wsjj4ffibdaicpchy69"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bbmle" ,r-bbmle)
+       ("r-coda" ,r-coda)
+       ("r-lattice" ,r-lattice)
+       ("r-mass" ,r-mass)
+       ("r-plyr" ,r-plyr)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
+    (synopsis "Support functions and data for \"Ecological Models and Data\"")
+    (description
+     "This package provides auxiliary functions and data sets for \"Ecological
+Models and Data\", a book presenting maximum likelihood estimation and related
+topics for ecologists (ISBN 978-0-691-12522-0).")
+    ;; Any GPL version
+    (license (list license:gpl2 license:gpl3))))
+
+(define-public r-lpsolve
+  (package
+    (name "r-lpsolve")
+    (version "5.6.13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lpSolve" version))
+       (sha256
+        (base32
+         "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m"))))
+    (properties `((upstream-name . "lpSolve")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/lpSolve")
+    (synopsis "R interface to Lp_solve to solve linear/integer programs")
+    (description
+     "Lp_solve is software for solving linear, integer and mixed integer
+programs.  This implementation supplies a \"wrapper\" function in C and some R
+functions that solve general linear/integer problems, assignment problems, and
+transportation problems.")
+    (license license:lgpl2.0)))
+
+(define-public r-limsolve
+  (package
+    (name "r-limsolve")
+    (version "1.5.5.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "limSolve" version))
+       (sha256
+        (base32
+         "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg"))))
+    (properties `((upstream-name . "limSolve")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lpsolve" ,r-lpsolve)
+       ("r-mass" ,r-mass)
+       ("r-quadprog" ,r-quadprog)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://cran.r-project.org/web/packages/limSolve")
+    (synopsis "Solving linear inverse models")
+    (description
+     "This package provides functions that:
+
+@enumerate
+@item find the minimum/maximum of a linear or quadratic function,
+@item sample an underdetermined or overdetermined system,
+@item solve a linear system Ax=B for the unknown x.
+@end enumerate
+
+It includes banded and tridiagonal linear systems.  The package calls Fortran
+functions from LINPACK.")
+    ;; Any GPL version.
+    (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-fitdistrplus
+  (package
+    (name "r-fitdistrplus")
+    (version "1.0-9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fitdistrplus" version))
+       (sha256
+        (base32
+         "18x9454g598d54763k3hvi33iszifk7sxvhd1zg5r8z1vpixx3z6"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-survival" ,r-survival)))
+    (home-page "http://riskassessment.r-forge.r-project.org")
+    (synopsis "Fitting a parametric distribution from data")
+    (description
+     "This package extends the @code{fitdistr} function of the MASS package
+with several functions to help the fit of a parametric distribution to
+non-censored or censored data.  Censored data may contain left-censored,
+right-censored and interval-censored values, with several lower and upper
+bounds.  In addition to @dfn{maximum likelihood estimation} (MLE), the package
+provides moment matching (MME), quantile matching (QME) and maximum
+goodness-of-fit estimation (MGE) methods (available only for non-censored
+data).  Weighted versions of MLE, MME and QME are available.")
+    (license license:gpl2+)))
+
+(define-public r-energy
+  (package
+    (name "r-energy")
+    (version "1.7-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "energy" version))
+       (sha256
+        (base32
+         "1g4hqi6mgsnd1w4q7dd2m40ljh2jdmvad91ksbq9fscnrqpvji1x"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-boot" ,r-boot)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "http://cran.r-project.org/web/packages/energy")
+    (synopsis "Multivariate inference via the energy of data")
+    (description
+     "This package provides e-statistics (energy) tests and statistics for
+multivariate and univariate inference, including distance correlation,
+one-sample, two-sample, and multi-sample tests for comparing multivariate
+distributions, are implemented.  Measuring and testing multivariate
+independence based on distance correlation, partial distance correlation,
+multivariate goodness-of-fit tests, clustering based on energy distance,
+testing for multivariate normality, distance components (disco) for
+non-parametric analysis of structured data, and other energy
+statistics/methods are implemented.")
+    (license license:gpl2+)))
+
+(define-public r-suppdists
+  (package
+    (name "r-suppdists")
+    (version "1.1-9.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "SuppDists" version))
+       (sha256
+        (base32
+         "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
+    (properties `((upstream-name . "SuppDists")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/SuppDists")
+    (synopsis "Supplementary distributions")
+    (description
+     "This package provides ten distributions supplementing those built into
+R.  Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
+Spearman's rho, maximum F ratio, the Pearson product moment correlation
+coefficient, Johnson distributions, normal scores and generalized
+hypergeometric distributions.  In addition two random number generators of
+George Marsaglia are included.")
+    (license license:gpl2+)))
+
+(define-public r-ksamples
+  (package
+    (name "r-ksamples")
+    (version "1.2-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "kSamples" version))
+       (sha256
+        (base32
+         "1pbam0zqq44slpxdgl2s2fsfdgl7i0pgm8bzlvnm0fy0na24bgdj"))))
+    (properties `((upstream-name . "kSamples")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-suppdists" ,r-suppdists)))
+    (home-page "http://cran.r-project.org/web/packages/kSamples")
+    (synopsis "K-Sample rank tests and their combinations")
+    (description
+     "This package provides tools to compares k samples using the
+Anderson-Darling test, Kruskal-Wallis type tests with different rank score
+criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
+test.  It computes asymptotic, simulated or (limited) exact P-values, all
+valid under randomization, with or without ties, or conditionally under random
+sampling from populations, given the observed tie pattern.  Except for Steel's
+test and the JT test it also combines these tests across several blocks of
+samples.")
+    (license license:gpl2+)))

gnu/packages/crypto.scm

@@ -81,7 +81,7 @@ (define-public libsodium
 (define-public signify
   (package
     (name "signify")
-    (version "21")
+    (version "22")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/aperezdc/signify/"
@@ -89,7 +89,7 @@ (define-public signify
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0jd26kxwmmar3bylpx9x5dpqxzs17ky5dvwx8pdgcg95n4lyk223"))))
+                "0iv5bjaas70ymqchxasapin4c32c41kqzkfhc3kcjzd7rxy78msy"))))
     (build-system gnu-build-system)
     ;; TODO Build with libwaive (described in README.md), to implement something
     ;; like OpenBSD's pledge().

gnu/packages/databases.scm

@@ -17,6 +17,7 @@
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -396,7 +397,7 @@ (define-public mysql
 (define-public mariadb
   (package
     (name "mariadb")
-    (version "10.1.25")
+    (version "10.1.26")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://downloads.mariadb.org/f/"
@@ -404,7 +405,7 @@ (define-public mariadb
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1mm0n8sl6grajk5rbrx55333laz5dg2abyl8mlsn7h8vdymfq1bj"))))
+                "0ggpdcal0if9y6h9hp1yv2q65cbkjfl4p8rqk68a5pk7k75v325s"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags

gnu/packages/debug.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -166,12 +167,15 @@ (define-public american-fuzzy-lop
                             (%current-system))
                    ("x86_64-linux"   "x86_64")
                    ("i686-linux"     "i386")
+                   ("aarch64-linux"  "aarch64")
+                   ("armhf-linux"    "arm")
+                   ("mips64el-linux" "mips64el")
                    ;; Prevent errors when querying this package on unsupported
                    ;; platforms, e.g. when running "guix package --search="
                    (_                "UNSUPPORTED"))))
     (package
       (name "american-fuzzy-lop")
-      (version "2.15b")             ;It seems all releases have the 'b' suffix
+      (version "2.49b")             ;It seems all releases have the 'b' suffix
       (source
        (origin
          (method url-fetch)
@@ -179,7 +183,7 @@ (define-public american-fuzzy-lop
                              "afl-" version ".tgz"))
          (sha256
           (base32
-           "04n2jfkchpz6a07w694b0im1vcmc3220ryqcaasa7vix7784wzs2"))))
+           "1lc8mpwlbyb1iil9961yfysp8l2l4nw0s07781m1haiz4jq2rigp"))))
       (build-system gnu-build-system)
       (inputs
        `(("custom-qemu"
@@ -234,6 +238,20 @@ (define-public american-fuzzy-lop
                             "CC=gcc")
          #:phases (modify-phases %standard-phases
                     (delete 'configure)
+                    ,@(if (string=? (%current-system) (or "x86_64-linux"
+                                                          "i686-linux"))
+                        '()
+                        '((add-before 'build 'set-afl-flag
+                            (lambda _ (setenv "AFL_NO_X86" "1") #t))
+                          (add-after 'install 'remove-x86-programs
+                            (lambda* (#:key outputs #:allow-other-keys)
+                              (let* ((out (assoc-ref outputs "out"))
+                                     (bin (string-append out "/bin/")))
+                                (delete-file (string-append bin "afl-gcc"))
+                                (delete-file (string-append bin "afl-g++"))
+                                (delete-file (string-append bin "afl-clang"))
+                                (delete-file (string-append bin "afl-clang++")))
+                              #t))))
                     (add-after
                      ;; TODO: Build and install the afl-llvm tool.
                      'install 'install-qemu
@@ -243,10 +261,7 @@ (define-public american-fuzzy-lop
                          (symlink (string-append qemu "/bin/qemu-" ,machine)
                                   (string-append out "/bin/afl-qemu-trace"))
                          #t)))
-                    (delete 'check))))
+                    (delete 'check)))) ; Tests are run during 'install phase.
-      (supported-systems (fold delete
-                               %supported-systems
-                               '("armhf-linux" "mips64el-linux")))
       (home-page "http://lcamtuf.coredump.cx/afl")
       (synopsis "Security-oriented fuzzer")
       (description

gnu/packages/ebook.scm

@@ -28,10 +28,14 @@ (define-module (gnu packages ebook)
   #:use-module (gnu packages)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
+  #:use-module (gnu packages fribidi)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages icu4c)
@@ -44,6 +48,7 @@ (define-module (gnu packages ebook)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
+  #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg))
 
 (define-public chmlib
@@ -195,3 +200,80 @@ (define-public calibre
                    license:public-domain
                    license:silofl1.1
                    license:cc-by-sa3.0))))
+
+(define-public liblinebreak
+  (package
+    (name "liblinebreak")
+    (version "2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/vimgadgets"
+                                  "/liblinebreak/" version
+                                  "/liblinebreak-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1f36dbq7nc77lln1by2n1yl050g9dc63viawhs3gc3169mavm36x"))))
+    (build-system gnu-build-system)
+    (home-page "http://vimgadgets.sourceforge.net/liblinebreak/")
+    (synopsis "Library for detecting where linebreaks are allowed in text")
+    (description "@code{liblinebreak} is an implementation of the line
+breaking algorithm as described in Unicode 6.0.0 Standard Annex 14,
+Revision 26.  It breaks lines that contain Unicode characters.  It is
+designed to be used in a generic text renderer.")
+    (license license:zlib)))
+
+(define-public fbreader
+  (package
+    (name "fbreader")
+    (version "0.99.6")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/geometer/FBReader/"
+                                  "archive/" version "-freebsdport.tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0gf1nl562fqkwlzcn6rgkp1j8jcixzmfsnwxbc0sm49zh8n3zqib"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("curl" ,curl)
+       ("expat" ,expat)
+       ("fribidi" ,fribidi)
+       ("glib" ,glib)
+       ("gtk+-2" ,gtk+-2)
+       ("libjpeg" ,libjpeg)
+       ("liblinebreak" ,liblinebreak)
+       ("libxft" ,libxft)
+       ("sqlite" ,sqlite)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (arguments
+     `(#:tests? #f ; No tests exist.
+       #:make-flags `("CC=gcc" "TARGET_ARCH=desktop" "UI_TYPE=gtk"
+                      "TARGET_STATUS=release"
+                      ,(string-append "INSTALLDIR="
+                                      (assoc-ref %outputs "out"))
+                      ,(string-append "LDFLAGS=-Wl,-rpath="
+                                      (assoc-ref %outputs "out") "/lib"))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))))
+    (home-page "https://fbreader.org/")
+    (synopsis "E-Book reader")
+    (description "@code{fbreader} is an E-Book reader.  It supports the
+following formats:
+
+@enumerate
+@item CHM
+@item Docbook
+@item FB2
+@item HTML
+@item OEB
+@item PDB
+@item RTF
+@item TCR
+@item TXT
+@item XHTML
+@end enumerate")
+    (license license:gpl2+)))

gnu/packages/emacs.scm

@@ -2632,6 +2632,38 @@ (define-public emacs-smartparens
 well as completely new features.")
     (license license:gpl3+)))
 
+(define-public emacs-highlight-symbol
+  (package
+    (name "emacs-highlight-symbol")
+    (version "1.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/nschum/highlight-symbol.el/archive/"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1n7k1qns0fn0jsyc0hrjac5nzk21xw48yc30vyrhwvc51h0b9g90"))))
+    (build-system emacs-build-system)
+    (home-page "https://nschum.de/src/emacs/highlight-symbol")
+    (synopsis "Automatic and manual symbol highlighting for Emacs")
+    (description
+     "Use @code{highlight-symbol} to toggle highlighting of the symbol at
+point throughout the current buffer.  Use @code{highlight-symbol-mode} to keep
+the symbol at point highlighted.
+
+The functions @code{highlight-symbol-next}, @code{highlight-symbol-prev},
+@code{highlight-symbol-next-in-defun} and
+@code{highlight-symbol-prev-in-defun} allow for cycling through the locations
+of any symbol at point.  Use @code{highlight-symbol-nav-mode} to enable key
+bindings @code{M-p} and @code{M-p} for navigation.  When
+@code{highlight-symbol-on-navigation-p} is set, highlighting is triggered
+regardless of @code{highlight-symbol-idle-delay}.
+
+@code{highlight-symbol-query-replace} can be used to replace the symbol. ")
+    (license license:gpl2+)))
+
 (define-public emacs-hl-todo
   (package
     (name "emacs-hl-todo")

gnu/packages/fonts.scm

@@ -622,35 +622,14 @@ (define-public font-google-noto
     (name "font-google-noto")
     (version "20170403")
     (source (origin
-              (method url-fetch)
+              (method url-fetch/zipbomb)
               (uri (string-append "https://noto-website.storage.googleapis.com/"
                                   "pkgs/Noto-hinted.zip"))
+              (file-name (string-append name "-" version ".zip"))
               (sha256
                (base32
                 "1p92a6dvs7wqwjfpp1ahr9z1wz35am0l8r78521383spd77bmrfm"))))
-    (build-system trivial-build-system)
+    (build-system font-build-system)
-    (arguments
-     `(#:modules ((guix build utils))
-       #:builder (begin
-                   (use-modules (guix build utils)
-                                (srfi srfi-26))
-
-                   (let ((PATH     (string-append (assoc-ref %build-inputs
-                                                             "unzip")
-                                                  "/bin"))
-                         (font-dir (string-append %output
-                                                  "/share/fonts/truetype")))
-                     (setenv "PATH" PATH)
-                     (system* "unzip" (assoc-ref %build-inputs "source"))
-
-                     (mkdir-p font-dir)
-                     (for-each (lambda (ttf)
-                                 (install-file ttf font-dir))
-                               (find-files "." "\\.ttf$"))
-                     (for-each (lambda (otf)
-                                 (install-file otf font-dir))
-                               (find-files "." "\\.otf$"))))))
-    (native-inputs `(("unzip" ,unzip)))
     (home-page "https://www.google.com/get/noto/")
     (synopsis "Fonts to cover all languages")
     (description "Google Noto Fonts is a family of fonts designed to support

gnu/packages/freeipmi.scm

@@ -27,14 +27,14 @@ (define-module (gnu packages freeipmi)
 (define-public freeipmi
   (package
     (name "freeipmi")
-    (version "1.5.6")
+    (version "1.5.7")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/freeipmi/freeipmi-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "0p3cl32wwxhyc5vkd9spmmckb78797snkmplgh0ybc7zap2bs6ib"))))
+               "1rdxs33klk6956rg8mn2dxwkk43y5yilvgvbcka8g6v4x0r98v5l"))))
     (build-system gnu-build-system)
     (inputs
      `(("libgcrypt" ,libgcrypt)))

gnu/packages/game-development.scm

@@ -9,6 +9,7 @@
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 Julian Graham <joolean@gmail.com>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -40,11 +41,14 @@ (define-module (gnu packages game-development)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages documentation)
+  #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages fribidi)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnunet)
+  #:use-module (gnu packages graphics)
+  #:use-module (gnu packages graphviz)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages m4)
   #:use-module (gnu packages multiprecision)
@@ -934,3 +938,84 @@ (define-public ois
 robust and compatible with many systems and operating systems.")
     (home-page "https://github.com/wgois/OIS")
     (license license:zlib)))
+
+(define-public mygui
+  (package
+    (name "mygui")
+    (version "3.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "https://github.com/MyGUI/" name
+                       "/archive/MyGUI" version ".tar.gz"))
+       (sha256
+        (base32
+         "13x7cydmj7gjmsg702sqjbfi53z265iv6j7binv3r6a7ibndfa0a"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:tests? #f                      ; No test target
+       #:configure-flags
+       (list "-DMYGUI_INSTALL_DOCS=TRUE"
+             (string-append "-DOGRE_INCLUDE_DIR="
+                            (assoc-ref %build-inputs "ogre")
+                            "/include/OGRE"))))
+    (native-inputs
+     `(("boost" ,boost)
+       ("doxygen" ,doxygen)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("font-dejavu" ,font-dejavu)
+       ("freetype" ,freetype)
+       ("graphviz" ,graphviz)
+       ("libx11" ,libx11)
+       ("ogre" ,ogre)
+       ("ois" ,ois)))
+    (synopsis "Fast, flexible and simple GUI")
+    (description
+     "MyGUI is a library for creating Graphical User Interfaces (GUIs) for games
+and 3D applications.  The main goals of mygui are: speed, flexibility and ease
+of use.")
+    (home-page "http://mygui.info/")
+    (license license:expat)))
+
+(define-public openmw
+  (package
+    (name "openmw")
+    (version "0.42.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "https://github.com/OpenMW/openmw/archive/"
+                       name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1pla8016lpbg8cgm9kia318a860f26dmiayc72p3zl35mqrc7g7w"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f                      ; No test target
+       #:configure-flags
+       (list "-DDESIRED_QT_VERSION=5")))
+    (native-inputs
+     `(("boost" ,boost)
+       ("doxygen" ,doxygen)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("bullet" ,bullet)
+       ("ffmpeg" ,ffmpeg)
+       ("libxt" ,libxt)
+       ("mygui" ,mygui)
+       ("openal" ,openal)
+       ("openscenegraph" ,openscenegraph)
+       ("qtbase" ,qtbase)
+       ("sdl" ,sdl2)
+       ("unshield" ,unshield)))
+    (synopsis "Free software re-implementation of the RPG Morrowind engine")
+    (description
+     "OpenMW is a free, open source and modern engine which reimplements and
+extends the one that runs the 2002 open-world RPG Morrowind.  The engine comes
+with its own editor, called OpenMW-CS which allows the user to edit or create
+their own original games.")
+    (home-page "https://openmw.org")
+    (license license:gpl3)))

gnu/packages/games.scm

@@ -83,6 +83,7 @@ (define-module (gnu packages games)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages libcanberra)
+  #:use-module (gnu packages libedit)
   #:use-module (gnu packages libunwind)
   #:use-module (gnu packages haskell)
   #:use-module (gnu packages mp3)
@@ -433,6 +434,47 @@ (define-public gnushogi
 Chess).  It is similar to standard chess but this variant is far more complicated.")
     (license license:gpl3+)))
 
+(define-public ltris
+  (package
+    (name "ltris")
+    (version "1.0.19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://prdownloads.sourceforge.net/lgames/"
+                           name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1895wv1fqklrj4apkz47rnkcfhfav7zjknskw6p0886j35vrwslg"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(;; The code in LTris uses traditional GNU semantics for inline functions
+       #:configure-flags '("CFLAGS=-fgnu89-inline")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'set-paths 'set-sdl-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "CPATH"
+                     (string-append (assoc-ref inputs "sdl-union")
+                                    "/include/SDL"))
+             #t)))))
+    (inputs
+     `(("sdl-union" ,(sdl-union (list sdl sdl-mixer)))))
+    (home-page "http://lgames.sourceforge.net/LTris/")
+    (synopsis "Tetris clone based on the SDL library")
+    (description
+     "LTris is a tetris clone: differently shaped blocks are falling down the
+rectangular playing field and can be moved sideways or rotated by 90 degree
+units with the aim of building lines without gaps which then disappear (causing
+any block above the deleted line to fall down).  LTris has three game modes: In
+Classic you play until the stack of blocks reaches the top of the playing field
+and no new blocks can enter.  In Figures the playing field is reset to a new
+figure each level and later on tiles and lines suddenly appear.  In Multiplayer
+up to three players (either human or CPU) compete with each other sending
+removed lines to all opponents.  There is also a Demo mode in which you can
+watch your CPU playing while enjoying a cup of tea!")
+    (license license:gpl2+)))
+
 (define-public prboom-plus
   (package
    (name "prboom-plus")
@@ -2920,6 +2962,64 @@ (define-public higan
     ;; - higan/emulator/emulator.hpp
     (license license:gpl3)))
 
+(define-public mgba
+  (package
+    (name "mgba")
+    (version "0.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/mgba-emu/mgba/archive/"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "01zy2w5pihlkrmbm51icgyff6iqyqa5ha6qrm4aj8ibzznz03kyq"))
+              (modules '((guix build utils)))
+              (snippet
+               ;; Make sure we don't use the bundled software.
+               '(for-each
+                 (lambda (subdir)
+                   (let ((lib-subdir (string-append "src/third-party/" subdir)))
+                     (delete-file-recursively lib-subdir)))
+                 '("libpng" "lzma" "sqlite3" "zlib")))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f                      ;no "test" target
+       #:configure-flags
+       (list "-DUSE_LZMA=OFF"           ;do not use bundled LZMA
+             "-DUSE_LIBZIP=OFF"         ;use "zlib" instead
+             ;; Validate RUNPATH phase fails ("error: depends on
+             ;; 'libmgba.so.0.6', which cannot be found in RUNPATH") without
+             ;; the following S-exp.
+             (string-append "-DCMAKE_INSTALL_LIBDIR="
+                            (assoc-ref %outputs "out")
+                            "/lib"))))
+    (native-inputs `(("pkg-config" ,pkg-config)))
+    (inputs `(("ffmpeg" ,ffmpeg)
+              ("imagemagick" ,imagemagick)
+              ("libedit" ,libedit)
+              ("libepoxy" ,libepoxy)
+              ("libpng" ,libpng)
+              ("mesa" ,mesa)
+              ("minizip" ,minizip)
+              ("ncurses" ,ncurses)
+              ("qtbase" ,qtbase)
+              ("qtmultimedia" ,qtmultimedia)
+              ("qttools" ,qttools)
+              ("sdl2" ,sdl2)
+              ("sqlite" ,sqlite)
+              ("zlib" ,zlib)))
+    (home-page "https://mgba.io")
+    (synopsis "Game Boy Advance emulator")
+    (description
+     "mGBA is an emulator for running Game Boy Advance games.  It aims to be
+faster and more accurate than many existing Game Boy Advance emulators, as
+well as adding features that other emulators lack.  It also supports Game Boy
+and Game Boy Color games.")
+    ;; Code is mainly MPL 2.0. "blip_buf.c" is LGPL 2.1+ and "inih.c" is
+    ;; BSD-3.
+    (license (list license:mpl2.0 license:lgpl2.1+ license:bsd-3))))
+
 (define-public grue-hunter
   (package
     (name "grue-hunter")

gnu/packages/gnome.scm

@@ -6,7 +6,7 @@
 ;;; Copyright © 2014, 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2015, 2016 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
-;;; Copyright © 2015 Andy Wingo <wingo@igalia.com>
+;;; Copyright © 2015, 2017 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2015 David Hashe <david.hashe@dhashe.com>
 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017 Mark H Weaver <mhw@netris.org>
@@ -627,7 +627,7 @@ (define-public libgnome-keyring
 (define-public gnome-keyring
   (package
     (name "gnome-keyring")
-    (version "3.20.0")
+    (version "3.20.1")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnome/sources/" name "/"
@@ -635,7 +635,7 @@ (define-public gnome-keyring
                                  name "-" version ".tar.xz"))
              (sha256
               (base32
-               "16gcwwcg91ipxjmiyi4c4njvnxixmv1i278p0bilc3lafk6ww5xw"))))
+               "134ci3mn6jjap59z3lrvyiip7zf2nlw5xvanr44yajs57xr4x5lp"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;48 of 603 tests fail because /var/lib/dbus/machine-id does
@@ -2134,6 +2134,9 @@ (define-public vinagre
               (uri (string-append "mirror://gnome/sources/" name "/"
                                   (version-major+minor version) "/"
                                   name "-" version ".tar.xz"))
+              (patches ; We have to revert 2 commits to build against freerdp 1.1.
+               (search-patches "vinagre-revert-1.patch"
+                               "vinagre-revert-2.patch"))
               (sha256
                (base32
                 "10jya3jyrm18nbw3v410gbkc7677bqamax44pzgd3j15randn76d"))))
@@ -3039,7 +3042,7 @@ (define-public gnome-settings-daemon
 (define-public totem-pl-parser
  (package
    (name "totem-pl-parser")
-   (version "3.10.7")
+   (version "3.10.8")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnome/sources/totem-pl-parser/"
@@ -3047,7 +3050,7 @@ (define-public totem-pl-parser
                                 "totem-pl-parser-" version ".tar.xz"))
             (sha256
              (base32
-              "17089sqyh6w6zr8ci865ihmvqshnslcsk9fbsl4s7yii66y8b0lw"))))
+              "0ayxg0gfs5h5jhr811ja5hxlhryklzp6jlal2ach9wym2c3hmigz"))))
    (build-system gnu-build-system)
    (arguments
     ;; FIXME: Tests require gvfs.
@@ -3391,10 +3394,10 @@ (define-public gom
 queries upon that data.")
     (license license:lgpl2.1+)))
 
-(define-public libgames-support
+(define-public libgnome-games-support
   (package
-    (name "libgames-support")
+    (name "libgnome-games-support")
-    (version "1.0.2")
+    (version "1.2.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -3402,14 +3405,14 @@ (define-public libgames-support
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0rms2ksiv7j9944km7r87q22nh05si1fisn5xm3z4zy5vpcfi5mh"))))
+                "04qbgcgmc01sinhbqdljiny8q868l01nkdawj8wrnqnd1i8czvsg"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
        (modify-phases %standard-phases
          (add-before 'check 'pre-check
            (lambda _
-             ;; tests require a writable HOME.
+             ;; Tests require a writable HOME.
              (setenv "HOME" (getcwd))
              #t)))))
     (native-inputs
@@ -3417,30 +3420,16 @@ (define-public libgames-support
        ("pkg-config" ,pkg-config)
        ("vala" ,vala)))
     (propagated-inputs
-     ;; Required by libgames-support-1.0.pc
+     ;; Required by libgnome-games-support-1.0.pc
      `(("gtk+" ,gtk+)
        ("libgee" ,libgee)))
     (home-page "https://www.gnome.org/")
     (synopsis "Useful functionality shared among GNOME games")
     (description
-     "libgames-support is a small library intended for internal use by
+     "libgnome-games-support is a small library intended for internal use by
 GNOME Games, but it may be used by others.")
     (license license:lgpl3+)))
 
-(define-public libgnome-games-support
-  (package
-    (inherit libgames-support)
-    (name "libgnome-games-support")
-    (version "1.2.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://gnome/sources/" name "/"
-                                  (version-major+minor version) "/"
-                                  name "-" version ".tar.xz"))
-              (sha256
-               (base32
-                "1rsyf5hbjim7zpk1yar3gv65g1nmw6zbbc0smrmxsfk0f9n3j9m6"))))))
-
 (define-public gnome-klotski
   (package
     (name "gnome-klotski")
@@ -4357,7 +4346,7 @@ (define-public gexiv2
 (define-public shotwell
   (package
     (name "shotwell")
-    (version "0.26.2")
+    (version "0.26.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -4365,7 +4354,7 @@ (define-public shotwell
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0frjqa6nmh025clwnb74z2rzbdq65wjcp2lf9csgcbkpahyjhrag"))))
+                "1r8fd63r7c5n99hwrkzv9jlrk84z4sa15q3h70pydzfjnfqf90zv"))))
     (build-system glib-or-gtk-build-system)
     (propagated-inputs
      `(("dconf" ,dconf)))
@@ -4525,7 +4514,7 @@ (define-public gnome-session
 (define-public gjs
   (package
     (name "gjs")
-    (version "1.48.3")
+    (version "1.48.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -4533,7 +4522,7 @@ (define-public gjs
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0cqgv460wfhwkw6j1h46v6bg29bycg6dfl7c5rv0lfcqmmw7v6v6"))))
+                "04nkig077r7xq55dxg9v46w8i7p8zkkdyja92yv81grq9fx6apz8"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -5274,7 +5263,7 @@ (define-public gnome-bluetooth
 (define-public gnome-control-center
   (package
     (name "gnome-control-center")
-    (version "3.24.2")
+    (version "3.24.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -5282,7 +5271,7 @@ (define-public gnome-control-center
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0awga40jh6gvn335mn6kyl6yg79frap1znrsz3sw2m27yldlnaiq"))))
+                "18ncjqjj93a39sla2zjr9i6pw59yh87p4jla899lmvi2qajd5923"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      '(#:phases
@@ -5345,7 +5334,7 @@ (define-public gnome-control-center
 (define-public gnome-shell
   (package
     (name "gnome-shell")
-    (version "3.24.2")
+    (version "3.24.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -5353,7 +5342,7 @@ (define-public gnome-shell
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1xp2ccmdrvzlczsrcplykwqwx2v4lbmkr0rxyylb06danlw9mivh"))))
+                "1f20x36ymkp1j667hb7s7byly2gqc4m0anldy3qwp38vm8437caq"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      '(#:phases
@@ -5733,6 +5722,37 @@ (define-public dconf-editor
 software that do not provide their own configuration interface.")
     (license license:lgpl2.1+)))
 
+(define-public gnome-default-applications
+  (package
+    (name "gnome-default-applications")
+    (version "0")
+    (build-system trivial-build-system)
+    (source #f)
+    (propagated-inputs
+     `(("nautilus" ,nautilus)))
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let* ((out (assoc-ref %outputs "out"))
+                (apps (string-append out "/share/applications")))
+           (mkdir-p apps)
+           (call-with-output-file (string-append apps "/defaults.list")
+             (lambda (port)
+               (format port "[Default Applications]\n")
+               (format port "inode/directory=org.gnome.Nautilus.desktop\n")))
+           #t))))
+    (synopsis "Default MIME type associations for the GNOME desktop")
+    (description
+     "Given many installed packages which might handle a given MIME type, a
+user running the GNOME desktop probably has some preferences: for example,
+that folders be opened by default by the Nautilus file manager, not the Baobab
+disk usage analyzer.  This package establishes that set of default MIME type
+associations for GNOME.")
+    (license license:gpl3+)
+    (home-page #f)))
+
 (define-public gnome
   (package
     (name "gnome")
@@ -5746,6 +5766,7 @@ (define-public gnome
      `(("adwaita-icon-theme"        ,adwaita-icon-theme)
        ("baobab"                    ,baobab)
        ("font-cantarell"            ,font-cantarell)
+       ("font-dejavu"               ,font-dejavu)
        ("at-spi2-core"              ,at-spi2-core)
        ("dbus"                      ,dbus)
        ("dconf"                     ,dconf)
@@ -5757,13 +5778,20 @@ (define-public gnome
        ("gedit"                     ,gedit)
        ("glib-networking"           ,glib-networking)
        ("gnome-backgrounds"         ,gnome-backgrounds)
+       ("gnome-bluetooth"           ,gnome-bluetooth)
+       ("gnome-calculator"          ,gnome-calculator)
        ("gnome-control-center"      ,gnome-control-center)
+       ("gnome-disk-utility"        ,gnome-disk-utility)
+       ("gnome-default-applications" ,gnome-default-applications)
        ("gnome-keyring"             ,gnome-keyring)
+       ("gnome-online-accounts"     ,gnome-online-accounts)
        ("gnome-session"             ,gnome-session)
        ("gnome-settings-daemon"     ,gnome-settings-daemon)
        ("gnome-shell"               ,gnome-shell)
+       ("gnome-system-monitor"      ,gnome-system-monitor)
        ("gnome-terminal"            ,gnome-terminal)
        ("gnome-themes-standard"     ,gnome-themes-standard)
+       ("gucharmap"                 ,gucharmap)
        ("gvfs"                      ,gvfs)
        ("hicolor-icon-theme"        ,hicolor-icon-theme)
        ("nautilus"                  ,nautilus)

gnu/packages/gnunet.scm

@@ -186,14 +186,14 @@ (define-public libmicrohttpd
 (define-public gnurl
   (package
    (name "gnurl")
-   (version "7.55.0")
+   (version "7.55.1")
    (source (origin
             (method url-fetch)
             (uri (string-append "https://gnunet.org/sites/default/files/"
                                 name "-" version ".tar.bz2"))
             (sha256
              (base32
-              "0i9bik76rbyag3mbxbk8j383iaxs5v7lmjkn4v36ascl6bdks6vn"))))
+              "118vb2mc5ivsbrkqzg40w56raf5jdnx00cfmkh735w0mjfy6wccv"))))
    (build-system gnu-build-system)
    (outputs '("out"
               "doc"))                             ; 1.5 MiB of man3 pages

gnu/packages/gobby.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016 Andy Wingo <wingo@igalia.com>
+;;; Copyright © 2016, 2017 Andy Wingo <wingo@igalia.com>
+;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,6 +26,7 @@ (define-module (gnu packages gobby)
   #:use-module (gnu packages)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
+  #:use-module (gnu packages gsasl)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages tls)
@@ -96,7 +98,10 @@ (define-public obby
 documents in one session.  Obby is used by the Gobby collaborative editor.")
     (license license:gpl2+)))
 
-(define-public gobby
+;; Although there is a newer version of Gobby defined below, the protocols are
+;; incompatible; you need Gobby 0.4 if you want to connect to servers running
+;; the 0.4 protocol.
+(define-public gobby-0.4
   (package
     (name "gobby")
     (version "0.4.13")
@@ -127,5 +132,81 @@ (define-public gobby
     (description
      "Collaborative editor that supports multiple documents in one session and
 a multi-user chat.  Gobby allows multiple users to edit the same document
+together over the internet in real-time.
+
+This is the older 0.4 version of Gobby.  Use this version only if you need to
+connect to a server running the old 0.4 protocol.")
+    (license license:gpl2+)))
+
+(define-public gobby
+  (package
+    (name "gobby")
+    (version "0.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://releases.0x539.de/gobby/gobby-"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "165x0r668ma5blziisvbr8qig3jw9hf7i6w8r7wwvz3wsac3bswc"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("intltool" ,intltool)))
+    (inputs
+     `(("gnutls" ,gnutls)
+       ("gsasl" ,gsasl)
+       ("gtkmm-2" ,gtkmm-2)
+       ("gtksourceview-2" ,gtksourceview-2)
+       ("libinfinity" ,libinfinity)
+       ("libxml++-2" ,libxml++-2)))
+    (arguments
+     ;; Required by libsigc++.
+     `(#:configure-flags '("CXXFLAGS=-std=c++11")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'move-executable
+           (lambda* (#:key outputs #:allow-other-keys)
+             (with-directory-excursion (assoc-ref outputs "out")
+               (rename-file "bin/gobby-0.5" "bin/gobby"))
+             #t)))))
+    (home-page "https://gobby.github.io/")
+    (synopsis "Collaborative editor")
+    (description
+     "Collaborative editor that supports multiple documents in one session and
+a multi-user chat.  Gobby allows multiple users to edit the same document
 together over the internet in real-time.")
     (license license:gpl2+)))
+
+(define-public libinfinity
+  (package
+    (name "libinfinity")
+    (version "0.6.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://releases.0x539.de/libinfinity/libinfinity-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0nylsb6qz9pjw3agjp27c4za205i6zg6i5g1vgs5vbdnbh77wkhc"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("glib" ,glib)
+       ("gsasl" ,gsasl)
+       ("gtk+" ,gtk+-2)
+       ("libxml2" ,libxml2)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (arguments
+     `(#:configure-flags (list "--with-inftextgtk"
+                               "--with-infgtk")))
+    (home-page "https://gobby.github.io/")
+    (synopsis "Infininote protocol implementation")
+    (description "libinfinity is a library to build collaborative text
+editors.  Changes to the text buffers are synced to all other clients over a
+central server.  Even though a central server is involved, the local user sees
+his changes applied instantly and the merging is done on the individual
+clients.")
+    (license license:lgpl2.1+)))

gnu/packages/graphics.scm

@@ -36,11 +36,13 @@ (define-module (gnu packages graphics)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages haskell)
   #:use-module (gnu packages image)
   #:use-module (gnu packages python)
   #:use-module (gnu packages flex)
+  #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)  ;libsndfile, libsamplerate
@@ -60,6 +62,7 @@ (define-module (gnu packages graphics)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages sdl)
+  #:use-module (gnu packages swig)
   #:use-module (gnu packages video)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg))
@@ -228,6 +231,74 @@ (define-public ilmbase
 exception-handling library.")
     (license license:bsd-3)))
 
+(define-public ogre
+  (package
+    (name "ogre")
+    (version "1.10.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/OGRECave/" name
+                           "/archive/v" version ".tar.gz"))
+       (sha256
+        (base32
+         "1ab354bmwwryxr4zgxchfkm6h4z38mjgif8yn89x640rsrgw5ipj"))
+       (file-name (string-append name "-" version ".tar.gz"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'pre-configure
+           (lambda _
+             ;; It expects googletest source to be downloaded and
+             ;; be in a specific place.
+             (substitute* "Tests/CMakeLists.txt"
+               (("URL(.*)$" _ suffix)
+                (string-append "URL " suffix
+                               "\t\tURL_HASH "
+                               "MD5=16877098823401d1bf2ed7891d7dce36\n")))
+             #t))
+         (add-before 'build 'pre-build
+           (lambda* (#:key inputs #:allow-other-keys)
+             (copy-file (assoc-ref inputs "googletest-source")
+                        (string-append (getcwd)
+                                       "/Tests/googletest-prefix/src/"
+                                       "release-1.8.0.tar.gz"))
+             #t)))
+       #:configure-flags
+       (list "-DOGRE_BUILD_TESTS=TRUE"
+             (string-append "-DCMAKE_INSTALL_RPATH="
+                            (assoc-ref %outputs "out") "/lib:"
+                            (assoc-ref %outputs "out") "/lib/OGRE:"
+                            (assoc-ref %build-inputs "googletest") "/lib")
+             "-DOGRE_INSTALL_DOCS=TRUE"
+             "-DOGRE_INSTALL_SAMPLES=TRUE"
+             "-DOGRE_INSTALL_SAMPLES_SOURCE=TRUE")))
+    (native-inputs
+     `(("boost" ,boost)
+       ("doxygen" ,doxygen)
+       ("googletest-source" ,(package-source googletest))
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("font-dejavu" ,font-dejavu)
+       ("freeimage" ,freeimage)
+       ("freetype" ,freetype)
+       ("glu" ,glu)
+       ("googletest" ,googletest)
+       ("sdl2" ,sdl2)
+       ("libxaw" ,libxaw)
+       ("libxrandr" ,libxrandr)
+       ("tinyxml" ,tinyxml)
+       ("zziplib" ,zziplib)))
+    (synopsis "Scene-oriented, flexible 3D engine written in C++")
+    (description
+     "OGRE (Object-Oriented Graphics Rendering Engine) is a scene-oriented,
+flexible 3D engine written in C++ designed to make it easier and more intuitive
+for developers to produce applications utilising hardware-accelerated 3D
+graphics.")
+    (home-page "http://www.ogre3d.org/")
+    (license license:expat)))
+
 (define-public openexr
   (package
     (name "openexr")

gnu/packages/ham-radio.scm

@@ -0,0 +1,52 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages ham-radio)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (gnu packages libusb)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (guix build-system cmake))
+
+(define-public rtl-sdr
+  (package
+    (name "rtl-sdr")
+    (version "0.5.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://cgit.osmocom.org/rtl-sdr/snapshot/rtl-sdr-"
+                           version ".tar.xz"))
+       (sha256
+        (base32
+         "08awca3v28sa4lxym4r81pzf0la0j86wbmpyhv3xd53an9gkpjy9"))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("libusb" ,libusb)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (arguments
+     `(#:configure-flags '("-DDETACH_KERNEL_DRIVER=ON")
+       #:tests? #f)) ; No tests
+    (home-page "https://osmocom.org/projects/sdr/wiki/rtl-sdr")
+    (synopsis "Software defined radio driver for Realtek RTL2832U")
+    (description "DVB-T dongles based on the Realtek RTL2832U can be used as a
+cheap software defined radio, since the chip allows transferring the raw I/Q
+samples to the host.  @code{rtl-sdr} provides drivers for this purpose.")
+    (license license:gpl2+)))

gnu/packages/haskell.scm

@@ -10,6 +10,7 @@
 ;;; Copyright © 2016, 2017 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Danny Milosavljevic <dannym@scratchpost.org>
 ;;; Copyright © 2017 Peter Mikkelsen <petermikkelsen10@gmail.com>
+;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1324,7 +1325,7 @@ (define-public ghc-streaming-commons
 (define-public cpphs
   (package
     (name "cpphs")
-    (version "1.19.3")
+    (version "1.20.8")
     (source
      (origin
        (method url-fetch)
@@ -1333,7 +1334,7 @@ (define-public cpphs
              name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1njpmxgpah5pcqppcl1cxb5xicf6xlqrd162qm12khp9hainlm72"))))
+         "1bh524asqhk9v1s0wvipl0hgn7l63iy3js867yv0z3h5v2kn8vg5"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-polyparse" ,ghc-polyparse)
@@ -1807,6 +1808,26 @@ (define-public ghc-text
 in terms of large data quantities and high speed.")
     (license license:bsd-3)))
 
+(define-public ghc-strict
+  (package
+    (name "ghc-strict")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/strict/strict-"
+                           version ".tar.gz"))
+       (sha256
+        (base32 "08cjajqz9h47fkq98mlf3rc8n5ghbmnmgn8pfsl3bdldjdkmmlrc"))))
+    (build-system haskell-build-system)
+    (home-page "https://hackage.haskell.org/package/strict")
+    (synopsis "Strict data types and String IO")
+    (description
+     "This package provides strict versions of some standard Haskell data
+types, such as pairs, @code{Maybe} and @code{Either}.  It also contains strict
+IO operations.")
+    (license license:bsd-3)))
+
 (define-public ghc-hashable
   (package
     (name "ghc-hashable")
@@ -1837,6 +1858,51 @@ (define-public ghc-hashable
 combine hash values.")
     (license license:bsd-3)))
 
+(define-public ghc-data-hash
+  (package
+    (name "ghc-data-hash")
+    (version "0.2.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/data-hash"
+                           "/data-hash-" version ".tar.gz"))
+       (sha256
+        (base32 "1ghbqvc48gf9p8wiy71hdpaj7by3b9cw6wgwi3qqz8iw054xs5wi"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
+    (home-page "https://hackage.haskell.org/package/data-hash")
+    (synopsis "Combinators for building fast hashing functions")
+    (description
+     "This package provides combinators for building fast hashing functions.
+It includes hashing functions for all basic Haskell98 types.")
+    (license license:bsd-3)))
+
+(define-public ghc-murmur-hash
+  (package
+    (name "ghc-murmur-hash")
+    (version "0.1.0.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/murmur-hash"
+                           "/murmur-hash-" version ".tar.gz"))
+       (sha256
+        (base32 "1bb58kfnzvx3mpc0rc0dhqc1fk36nm8prd6gvf20gk6lxaadpfc9"))))
+    (build-system haskell-build-system)
+    (home-page "https://github.com/nominolo/murmur-hash")
+    (synopsis "MurmurHash2 implementation for Haskell")
+    (description
+     "This package provides an implementation of MurmurHash2, a good, fast,
+general-purpose, non-cryptographic hashing function.  See
+@url{https://sites.google.com/site/murmurhash/} for details.  This
+implementation is pure Haskell, so it might be a bit slower than a C FFI
+binding.")
+    (license license:bsd-3)))
+
 (define-public ghc-hunit
   (package
     (name "ghc-hunit")
@@ -3806,6 +3872,55 @@ (define-public ghc-vault
 representing a store for a single element.")
     (license license:bsd-3)))
 
+(define-public ghc-edisonapi
+  (package
+    (name "ghc-edisonapi")
+    (version "1.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/EdisonAPI"
+                           "/EdisonAPI-" version ".tar.gz"))
+       (sha256
+        (base32 "0vmmlsj8ggbpwx6fkf5fvb6jp0zpx6iba6b28m80lllr2p8bi8wm"))))
+    (build-system haskell-build-system)
+    (inputs `(("ghc-mtl" ,ghc-mtl)))
+    (home-page "http://rwd.rdockins.name/edison/home/")
+    (synopsis "Library of efficient, purely-functional data structures (API)")
+    (description
+     "Edison is a library of purely functional data structures written by
+Chris Okasaki.  It is named after Thomas Alva Edison and for the mnemonic
+value EDiSon (Efficient Data Structures).  Edison provides several families of
+abstractions, each with multiple implementations.  The main abstractions
+provided by Edison are: Sequences such as stacks, queues, and dequeues;
+Collections such as sets, bags and heaps; and Associative Collections such as
+finite maps and priority queues where the priority and element are distinct.")
+    (license license:expat)))
+
+(define-public ghc-edisoncore
+  (package
+    (name "ghc-edisoncore")
+    (version "1.3.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/EdisonCore"
+                           "/EdisonCore-" version ".tar.gz"))
+       (sha256
+        (base32 "06shxmcqxcahcn6zgl64vlqix4fnq53d97drcgsh94qp7gp201ry"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-mtl" ,ghc-mtl)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-edisonapi" ,ghc-edisonapi)))
+    (home-page "http://rwd.rdockins.name/edison/home/")
+    (synopsis "Library of efficent, purely-functional data structures")
+    (description
+     "This package provides the core Edison data structure implementations,
+including multiple sequence, set, bag, and finite map concrete implementations
+with various performance characteristics.")
+    (license license:expat)))
+
 (define-public ghc-mmorph
   (package
     (name "ghc-mmorph")
@@ -3855,6 +3970,50 @@ (define-public ghc-monad-control
 @code{catch} can be lifted from @code{IO} or any other base monad.")
     (license license:bsd-3)))
 
+(define-public ghc-fail
+  (package
+    (name "ghc-fail")
+    (version "4.9.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/fail/fail-"
+                           version ".tar.gz"))
+       (sha256
+        (base32 "18nlj6xvnggy61gwbyrpmvbdkq928wv0wx2zcsljb52kbhddnp3d"))))
+    (build-system haskell-build-system)
+    (home-page "https://prime.haskell.org/wiki/Libraries/Proposals/MonadFail")
+    (synopsis "Forward-compatible MonadFail class")
+    (description
+     "This package contains the @code{Control.Monad.Fail} module providing the
+@uref{https://prime.haskell.org/wiki/Libraries/Proposals/MonadFail, MonadFail}
+class that became available in
+@uref{https://hackage.haskell.org/package/base-4.9.0.0, base-4.9.0.0} for
+older @code{base} package versions.  This package turns into an empty package
+when used with GHC versions which already provide the
+@code{Control.Monad.Fail} module.")
+    (license license:bsd-3)))
+
+(define-public ghc-monadplus
+  (package
+    (name "ghc-monadplus")
+    (version "1.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/monadplus"
+                           "/monadplus-" version ".tar.gz"))
+       (sha256
+        (base32 "15b5320wdpmdp5slpphnc1x4rhjch3igw245dp2jxbqyvchdavin"))))
+    (build-system haskell-build-system)
+    (home-page "https://hackage.haskell.org/package/monadplus")
+    (synopsis "Filtering and folding over arbitrary MonadPlus instances")
+    (description
+     "This package generalizes many common stream operations such as
+@code{filter}, @code{catMaybes} etc, enabling filtering and folding over
+arbitrary @code{MonadPlus} instances.")
+    (license license:bsd-3)))
+
 (define-public ghc-byteorder
   (package
     (name "ghc-byteorder")
@@ -4694,6 +4853,35 @@ (define-public ghc-adjunctions
 for Haskell.")
     (license license:bsd-3)))
 
+(define-public ghc-equivalence
+  (package
+    (name "ghc-equivalence")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/equivalence"
+                           "/equivalence-" version ".tar.gz"))
+       (sha256
+        (base32 "0a85bdyyvjqs5z4kfhhf758210k9gi9dv42ik66a3jl0z7aix8kx"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-mtl" ,ghc-mtl)
+       ("ghc-stmonadtrans" ,ghc-stmonadtrans)
+       ("ghc-transformers-compat" ,ghc-transformers-compat)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
+    (home-page "https://github.com/pa-ba/equivalence")
+    (synopsis "Maintaining an equivalence relation implemented as union-find")
+    (description
+     "This is an implementation of Tarjan's Union-Find algorithm (Robert E.@:
+Tarjan.  \"Efficiency of a Good But Not Linear Set Union Algorithm\",JACM
+22(2), 1975) in order to maintain an equivalence relation.  This
+implementation is a port of the @code{union-find} package using the @code{ST}
+monad transformer (instead of the IO monad).")
+    (license license:bsd-3)))
+
 (define-public ghc-fast-logger
   (package
     (name "ghc-fast-logger")
@@ -5081,6 +5269,28 @@ (define-public ghc-aeson-pretty
 essentially the opposite of pretty-printing.")
     (license license:bsd-3)))
 
+(define-public ghc-boxes
+  (package
+    (name "ghc-boxes")
+    (version "0.1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/boxes/boxes-"
+                           version ".tar.gz"))
+       (sha256
+        (base32 "1n7xiplzd3s1a39nizwjcgsh3wi2348mp21c3fk19v98ialfjgjf"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-split" ,ghc-split)
+       ("ghc-quickcheck" ,ghc-quickcheck)))
+    (home-page "https://hackage.haskell.org/package/boxes")
+    (synopsis "2D text pretty-printing library")
+    (description
+     "Boxes is a pretty-printing library for laying out text in two dimensions,
+using a simple box model.")
+    (license license:bsd-3)))
+
 (define-public ghc-wai
   (package
     (name "ghc-wai")
@@ -5565,6 +5775,50 @@ (define-public ghc-th-orphans
 package, and that's where the version number started.")
     (license license:bsd-3)))
 
+(define-public ghc-geniplate-mirror
+  (package
+    (name "ghc-geniplate-mirror")
+    (version "0.7.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package"
+                           "/geniplate-mirror"
+                           "/geniplate-mirror-" version ".tar.gz"))
+       (sha256
+        (base32 "17vjps2118s5z3k39ij00lkmkxv3mqf8h59wv6qdamlgmhyr36si"))))
+    (build-system haskell-build-system)
+    (inputs `(("ghc-mtl" ,ghc-mtl)))
+    (home-page "https://github.com/danr/geniplate")
+    (synopsis "Use Template Haskell to generate Uniplate-like functions")
+    (description
+     "Use Template Haskell to generate Uniplate-like functions.  This is a
+maintained mirror of the @uref{https://hackage.haskell.org/package/geniplate,
+geniplate} package, written by Lennart Augustsson.")
+    (license license:bsd-3)))
+
+(define-public ghc-gitrev
+  (package
+    (name "ghc-gitrev")
+    (version "1.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/gitrev/gitrev-"
+                           version ".tar.gz"))
+       (sha256
+        (base32 "0cl3lfm6k1h8fxp2vxa6ihfp4v8igkz9h35iwyq2frzm4kdn96d8"))))
+    (build-system haskell-build-system)
+    (inputs `(("ghc-base-compat" ,ghc-base-compat)))
+    (home-page "https://github.com/acfoltzer/gitrev")
+    (synopsis "Compile git revision info into Haskell projects")
+    (description
+     "This package provides some handy Template Haskell splices for including
+the current git hash and branch in the code of your project.  This is useful
+for including in panic messages, @command{--version} output, or diagnostic
+info for more informative bug reports.")
+    (license license:bsd-3)))
+
 (define-public ghc-haskell-src-meta
   (package
     (name "ghc-haskell-src-meta")
@@ -6078,6 +6332,31 @@ (define-public ghc-asn1-parse
 when ASN1 pattern matching is not convenient.")
     (license license:bsd-3)))
 
+(define-public ghc-edit-distance
+  (package
+    (name "ghc-edit-distance")
+    (version "0.2.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/edit-distance"
+                           "/edit-distance-" version ".tar.gz"))
+       (sha256
+        (base32 "0jkca97zyv23yyilp3jydcrzxqhyk27swhzh82llvban5zp8b21y"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-random" ,ghc-random)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
+    (home-page "https://github.com/phadej/edit-distance")
+    (synopsis "Levenshtein and restricted Damerau-Levenshtein edit distances")
+    (description
+     "This package provides optimized functions to determine the edit
+distances for fuzzy matching, including Levenshtein and restricted
+Damerau-Levenshtein algorithms.")
+    (license license:bsd-3)))
+
 (define-public ghc-tasty-kat
   (package
     (name "ghc-tasty-kat")
@@ -7056,6 +7335,27 @@ (define-public ghc-transformers-0.4.2.0
                (base32
                 "0a364zfcm17mhpy0c4ms2j88sys4yvgd6071qsgk93la2wjm8mkr"))))))
 
+(define-public ghc-stmonadtrans
+  (package
+    (name "ghc-stmonadtrans")
+    (version "0.4.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/STMonadTrans"
+                           "/STMonadTrans-" version ".tar.gz"))
+       (sha256
+        (base32 "1nr26fnmi5fdjc6d00w13kjhmfyvb5b837d0006w4dj0yxndaksp"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-mtl" ,ghc-mtl)))
+    (home-page "https://hackage.haskell.org/package/STMonadTrans")
+    (synopsis "Monad transformer version of the ST monad")
+    (description
+     "This package provides a monad transformer version of the @code{ST} monad
+for strict state threads.")
+    (license license:bsd-3)))
+
 (define-public ghc-findbin
   (package
     (name "ghc-findbin")

gnu/packages/image.scm

@@ -16,6 +16,7 @@
 ;;; Copyright © 2016, 2017 Kei Kebreau <kei@openmailbox.org>
 ;;; Copyright © 2017 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -48,6 +49,8 @@ (define-module (gnu packages image)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages graphics)
+  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages lua)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mcrypt)
   #:use-module (gnu packages perl)
@@ -61,6 +64,8 @@ (define-module (gnu packages image)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system python)
+  #:use-module (guix build-system r)
   #:use-module (srfi srfi-1))
 
 (define-public libpng
@@ -177,6 +182,29 @@ (define-public libpng-1.2
        (sha256
         (base32 "1n2lrzjkm5jhfg2bs10q398lkwbbx742fi27zgdgx0x23zhj0ihg"))))))
 
+(define-public r-png
+  (package
+    (name "r-png")
+    (version "0.1-7")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "png" version))
+              (sha256
+               (base32
+                "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
+    (build-system r-build-system)
+    (inputs
+     `(("libpng" ,libpng)
+       ("zlib" ,zlib)))
+    (home-page "http://www.rforge.net/png/")
+    (synopsis "Read and write PNG images")
+    (description
+     "This package provides an easy and simple way to read, write and display
+bitmap images stored in the PNG format.  It can read and write both files and
+in-memory raw vectors.")
+    ;; Any of these GPL versions.
+    (license (list license:gpl2 license:gpl3))))
+
 (define-public pngcrunch
   (package
    (name "pngcrunch")
@@ -1157,3 +1185,46 @@ (define-public niftilib
 (fMRI) brain images.")
     (home-page "http://niftilib.sourceforge.net")
     (license license:public-domain)))
+
+(define-public gpick
+  (package
+    (name "gpick")
+    (version "0.2.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/thezbyg/gpick/archive/"
+                                  name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0mxvxk15xhk2i5vfavjhnkk4j3bnii0gpf8di14rlbpq070hd5rs"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("boost" ,boost)
+       ("gettext" ,gnu-gettext)
+       ("pkg-config" ,pkg-config)
+       ("scons" ,scons)))
+    (inputs
+     `(("expat" ,expat)
+       ("gtk2" ,gtk+-2)
+       ("lua" ,lua-5.2)))
+    (arguments
+     `(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'fix-lua-reference
+           (lambda _
+             (substitute* "SConscript"
+               (("lua5.2") "lua-5.2"))
+             #t))
+         (replace 'build
+           (lambda _
+             (zero? (system* "scons"))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((dest (assoc-ref outputs "out")))
+               (zero? (system* "scons" "install"
+                               (string-append "DESTDIR=" dest)))))))))
+    (home-page "http://www.gpick.org/")
+    (synopsis "Color picker")
+    (description "Gpick is an advanced color picker and palette editing tool.")
+    (license license:bsd-3)))

gnu/packages/imagemagick.scm

@@ -175,7 +175,11 @@ (define-public graphicsmagick
                                  "/GraphicsMagick-" version ".tar.xz")))
               (sha256
                (base32
-                "122zgs96dqrys62mnh8x5yvfff6km4d3yrnvaxzg3mg5sprib87v"))))
+                "122zgs96dqrys62mnh8x5yvfff6km4d3yrnvaxzg3mg5sprib87v"))
+              (patches
+               (search-patches "graphicsmagick-CVE-2017-12935.patch"
+                               "graphicsmagick-CVE-2017-12936.patch"
+                               "graphicsmagick-CVE-2017-12937.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags

gnu/packages/irc.scm

@@ -301,14 +301,14 @@ (define-public sic
 (define-public limnoria
   (package
     (name "limnoria")
-    (version "2017.03.30")
+    (version "2017.08.18")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "limnoria" version))
        (sha256
         (base32
-         "1q0y6iglg1cbhimgjz3afws51as3shy6rd61dck7jfm25y8pi6g8"))))
+         "1hij444l45mjli8i67iyd3syf263ijj1l0cm3irqjjxv5r3f9zjj"))))
     (build-system python-build-system)
     (inputs
      `(("python-pytz" ,python-pytz)

gnu/packages/java.scm

@@ -1064,7 +1064,7 @@ (define-public icedtea-6
     (license license:gpl2+)))
 
 (define-public icedtea-7
-  (let* ((version "2.6.10")
+  (let* ((version "2.6.11")
          (drop (lambda (name hash)
                  (origin
                    (method url-fetch)
@@ -1082,7 +1082,7 @@ (define-public icedtea-7
                       version ".tar.xz"))
                 (sha256
                  (base32
-                  "0am945k2zqrka2xn7lb5grmkad4lwncnhnwk8iq6f269birzsj8w"))
+                  "1ibp6ybqnf8g7mbs45bkbv44dwz4h2w9gr4rh15yvr1m8lqkq1i0"))
                 (modules '((guix build utils)))
                 (snippet
                  '(substitute* "Makefile.in"
@@ -1475,25 +1475,25 @@ (define (import-cert cert)
       (native-inputs
        `(("openjdk-src"
           ,(drop "openjdk"
-                 "02klsxp9hlf5sial6mxpiq53hmrhlrg6x774j7bjjfhb7hpdvadh"))
+                 "1zhr4l9kxnbzghcsgjk3vmih9qpg1wrr9qry7fx04l97svp1ylhd"))
          ("corba-drop"
           ,(drop "corba"
-                 "1vbly6khri241xda05gnwkpf2fk41d96ls96ximi084mx0a3w5rd"))
+                 "108v15ncb2rnsyzgzncjlm1f57d1sv60zd9qbpas8kqmvpp8r0gz"))
          ("jaxp-drop"
           ,(drop "jaxp"
-                 "0s8zln64vdwdxwlw1vpfzm8xbpyhgsv3nqjmnv7y36qpsszg27a5"))
+                 "0zcpcmm3g1s7m31glrbw3ys7azi97ixcvbyxd40y9xzdja3jyr52"))
          ("jaxws-drop"
           ,(drop "jaxws"
-                 "0myd66bv8ib8krzgqv754bc564rd8xwpwabvf7my1apyb86vap3n"))
+                 "1gkqm0p3sr8d0xpki3fhf7cvmgqxx8ambgl5f3jx2plfnhsg96d2"))
          ("jdk-drop"
           ,(drop "jdk"
-                 "10b4lfv10vba07zblw0wii7mhrfhf32pf7410x5nz2q0smgszl2h"))
+                 "1d9fjnzdx4m6gwkvmj2n097ag0mvkhm3lldaxjki8x8c6a5clknf"))
          ("langtools-drop"
           ,(drop "langtools"
-                 "0lvncxb5qzrlqkflrnd0l8vwy155cwj1jb07rkq10z2vx0bq7lq2"))
+                 "0zscdp9arcq7gr8j7jq4m75gq0w1i3ryxpdnrc8fl0msh4w2s2k5"))
          ("hotspot-drop"
           ,(drop "hotspot"
-                 "0q6mdgbbd3681y3n0z1v783irdjhhi73z6sn5csczpyhjm318axb"))
+                 "1y6vnssn5y50x27g4ypdb5wwpmi7zf7jdi8gqbymkwf6n8p5y1d6"))
          ("ant" ,ant-bootstrap)
          ("attr" ,attr)
          ("coreutils" ,coreutils)
@@ -1543,7 +1543,7 @@ (define (import-cert cert)
       (license license:gpl2+))))
 
 (define-public icedtea-8
-  (let* ((version "3.5.0")
+  (let* ((version "3.5.1")
          (drop (lambda (name hash)
                  (origin
                    (method url-fetch)
@@ -1552,7 +1552,7 @@ (define-public icedtea-8
                          "/icedtea8/" version "/" name ".tar.xz"))
                    (sha256 (base32 hash))))))
     (package (inherit icedtea-7)
-      (version "3.5.0")
+      (version "3.5.1")
       (source (origin
                 (method url-fetch)
                 (uri (string-append
@@ -1560,7 +1560,7 @@ (define-public icedtea-8
                       version ".tar.xz"))
                 (sha256
                  (base32
-                  "1dfa7ing61i73m6wfx2kx59q44npqdiy7cd66xmslyy0xh09xa4s"))
+                  "1j8iv0cdk9fkh3yb5is7z29m9k3s89w6y9090538j6aa7p4nmalf"))
                 (modules '((guix build utils)))
                 (snippet
                  '(begin
@@ -1632,34 +1632,34 @@ (define-public icedtea-8
        `(("jdk" ,icedtea-7 "jdk")
          ("openjdk-src"
           ,(drop "openjdk"
-                 "0di7gmyis1p6rpksmff1q21ck85i51sqcl9awqyvg7xiwggq0wsm"))
+                 "0a6yrq8y1zkzc7hm2l28rm3vzy5izfxhmmhhhvc91lhfclnqcd2q"))
          ("aarch32-drop"
           ,(drop "aarch32"
                  "0cway5a5hcfyh4pzl9zz5xr7lil4gsliy6r5iqbaasd2d9alvqiq"))
          ("corba-drop"
           ,(drop "corba"
-                 "1xk64bsdxfc66g61d8k6xrhqj8rc56vzrlxx6s23gkr45604bl8x"))
+                 "031sc6byd8lqvz3cd07phm13pqrxalxk9f3a2q8pim5n4sbsy0qb"))
          ("jaxp-drop"
           ,(drop "jaxp"
-                 "1iw9xa4s5kxijdqpf0ih4x6g0lw142yy11vrzfmz6n1y4b0ic7iw"))
+                 "1815jaj0k0w1s0g0jr1ahkajp1jx2qlb08i6l9ha4wyqqyp49a4n"))
          ("jaxws-drop"
           ,(drop "jaxws"
-                 "14p2l4j985wh5cdd4hfmm18gb5wmry73yiysdx9pg3aqpkw9qms7"))
+                 "0vh4f85cxhqvabzg86ycpz02519cdzgsn5dr75k22rkmbbxnbbl6"))
          ("jdk-drop"
           ,(drop "jdk"
-                 "1qwmb80vicn7jd801f3j23lyil7327ks54d3s87czwv8h108m40r"))
+                 "196ycqz4d9kknc6b219q4ib83l1kkl6w6l1cznw9bzaafyynqa35"))
          ("langtools-drop"
           ,(drop "langtools"
-                 "175pi2privhcvn9sbam5mhhgcvicfqbgldiw25fi5g80fqkkrza9"))
+                 "0ssnadlr5cxhmj06nmni34kdynix1sjhcvjzahm5yzfd7dfllmgy"))
          ("hotspot-drop"
           ,(drop "hotspot"
-                 "1qdyn02p4ssl3p7z9aadhzl9qdam2q7pvwddz2jkyvajcrxb0mpi"))
+                 "0f7fxf0s9kadvs80hm5ga72pyp9r0fvl8zm1wmd1wrks8kl79sd6"))
          ("nashorn-drop"
           ,(drop "nashorn"
-                 "0kzmpf5b9kwhrvnwn7m20q3dzz8s82jjvbac84606x3ff97xk5gr"))
+                 "0m95qgnd4z6p0xp9m06ihss7skx2yrm7xw69jsjsrxpriy1shiwy"))
          ("shenandoah-drop"
           ,(drop "shenandoah"
-                 "0kjc5m5jj2bzyy1vj1s59khv5xjfnkxy18z0g4bdb1kb3g21c5wi"))
+                 "0yjlcgp6mldp30hmkfl68mdwlbg3gb0m6xd5y7srczni7cln5f3i"))
          ,@(fold alist-delete (package-native-inputs icedtea-7)
                  '("jdk" "openjdk-src" "corba-drop" "jaxp-drop" "jaxws-drop"
                    "jdk-drop" "langtools-drop" "hotspot-drop")))))))

gnu/packages/kde.scm

@@ -258,7 +258,7 @@ (define-public libkomparediff2
 (define-public libksysguard
   (package
     (name "libksysguard")
-    (version "5.8.2")
+    (version "5.10.4")
     (source
      (origin
        (method url-fetch)
@@ -266,7 +266,7 @@ (define-public libksysguard
                            "/libksysguard-" version ".tar.xz"))
        (sha256
         (base32
-         "158n30wbpsgbw3axhhsc58hnwhwdd02j3zc9hhcybmnbkfl5c96l"))))
+         "01w0laywva0p0ar2lvr1k5000bhjikjfxsb4f6p30qswrchrmrh3"))))
     (native-inputs
      `(("extra-cmake-modules" ,extra-cmake-modules)
        ("pkg-config" ,pkg-config)))
@@ -303,7 +303,7 @@ (define-public libksysguard
          (replace 'check
            (lambda _         ;other tests require a display and therefore fail
              (zero? (system* "ctest" "-R" "chronotest")))))))
-    (home-page "https://www.kde.org/info/plasma-5.8.2.php")
+    (home-page "https://www.kde.org/info/plasma-5.10.4.php")
     (synopsis "Network enabled task and system monitoring")
     (description "KSysGuard can obtain information on system load and
 manage running processes.  It obtains this information by interacting

gnu/packages/libreoffice.scm

@@ -789,7 +789,7 @@ (define xmlsec-src-libreoffice
 (define-public libreoffice
   (package
     (name "libreoffice")
-    (version "5.3.2.2")
+    (version "5.3.5.2")
     (source
      (origin
       (method url-fetch)
@@ -798,7 +798,7 @@ (define-public libreoffice
           "http://download.documentfoundation.org/libreoffice/src/"
           (version-prefix version 3) "/libreoffice-" version ".tar.xz"))
       (sha256 (base32
-               "1bcy1wx2cixawpd6cpivakwcwv8ryyy25kdw0fbci319p5gaj4c8"))))
+               "1sknmb9bhm8mxyfycqbwng1jqs4avyp1ffcla7dhlpwqs1aqxvx5"))))
     (build-system gnu-build-system)
     (native-inputs
      `(;; autoreconf is run by the LibreOffice build system, since after

gnu/packages/linux.scm

@@ -101,6 +101,7 @@ (define-module (gnu packages linux)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages groff)
   #:use-module (gnu packages selinux)
+  #:use-module (gnu packages swig)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python)
@@ -366,8 +367,8 @@ (define* (make-linux-libre version hash supported-systems
 
 (define %intel-compatible-systems '("x86_64-linux" "i686-linux"))
 
-(define %linux-libre-version "4.12.7")
+(define %linux-libre-version "4.12.8")
-(define %linux-libre-hash "1sjkxkcikdgl2w5h7c5pfyqwi29g69dxp4s2z2yavw7aicc91xfq")
+(define %linux-libre-hash "1p4ah15qs94id2yj6lhp6abdycvgp7lvn3ccsfs7f6n34hdij0cm")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
@@ -376,14 +377,14 @@ (define-public linux-libre
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.43"
+  (make-linux-libre "4.9.44"
-                    "0fxid4xmnrcq966vz2wsb6spw3i02pvqp2hv8xfrx7dr3hfs9nrr"
+                    "0a92bsb5d0pyhyn5ypc8ashwxixhivdadvikcpv31376j842fmj2"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.82"
+  (make-linux-libre "4.4.83"
-                    "01bn0vn6i22hhwiqfh29m1cir1jrvz643lz13war8k9l6h0dmmwy"
+                    "1fv3j0w0v82aa9s9n4a4qyrxc5bpq2ag9riawlabx57a380x1n62"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
@@ -1466,7 +1467,52 @@ (define-public libnl
                (base32
                 "1r3lw3hjvqxi5zqyq2w1qadm3gisd9nlf71dkl4yplacmssnhm3h"))))
     (build-system gnu-build-system)
-    (native-inputs `(("flex" ,flex) ("bison" ,bison)))
+    (native-inputs
+     `(("bison" ,bison)
+       ("flex" ,flex)
+       ("pkg-config" ,pkg-config)
+       ("swig" ,swig)
+       ("libnl3-doc"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append
+                 "https://github.com/thom311/libnl/releases/download/libnl"
+                 (string-join (string-split version #\.) "_")
+                 "/libnl-doc-" version ".tar.gz"))
+           (sha256
+            (base32 "0srab805yj8wb13l64qjyp3mdbqapxg5vk46v3zlhhzpmxqw8j7r"))))))
+    (inputs
+     `(("python-2" ,python-2)
+       ("python-3" ,python-3)))
+    (outputs '("out" "doc" "python2" "python3"))
+    (arguments
+     `(#:modules ((guix build gnu-build-system)
+                  (guix build utils)
+                  (srfi srfi-1))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-python
+           (lambda* (#:key outputs #:allow-other-keys)
+             (define (python-inst python)
+               (let ((ldflags (format #f "LDFLAGS=-Wl,-rpath=~a/lib"
+                                      (assoc-ref %outputs "out")))
+                     (pyout (assoc-ref %outputs python)))
+                 (and
+                  (zero? (system (format #f "~a ~a setup.py build"
+                                         ldflags python pyout)))
+                  (zero?
+                   (system (format #f "~a ~a setup.py install --prefix=~a"
+                                   ldflags python pyout)))
+                  (zero? (system* python "setup.py" "clean")))))
+             (with-directory-excursion "./python"
+               (every python-inst '("python2" "python3")))))
+         (add-after 'install 'install-doc
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((dest (string-append (assoc-ref outputs "doc")
+                                        "/share/doc/libnl")))
+               (mkdir-p dest)
+               (zero? (system* "tar" "xf" (assoc-ref inputs "libnl3-doc")
+                               "--strip-components=1" "-C" dest))))))))
     (home-page "http://www.infradead.org/~tgr/libnl/")
     (synopsis "NetLink protocol library suite")
     (description
@@ -4263,3 +4309,34 @@ (define-public procenv
 comparing system environments.")
    (home-page "http://github.com/jamesodhunt/procenv/")
    (license license:gpl3+)))
+
+(define-public libfabric
+  (package
+    (name "libfabric")
+    (version "1.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "https://github.com/ofiwg/libfabric/releases/download/v"
+                       version "/libfabric-" version ".tar.bz2"))
+       (sha256
+        (base32 "19l2m1frna1l765z4j7wl8hp4rb9wrh0hy5496685hd183hmy5pv"))))
+    (build-system gnu-build-system)
+    (inputs `(("rdma-core" ,rdma-core)
+              ;; TODO: add psm, psm(2).
+              ("libnl" ,libnl)))
+    (home-page "https://ofiwg.github.io/libfabric/")
+    (synopsis "Open Fabric Interfaces")
+    (description
+     "OpenFabrics Interfaces (OFI) is a framework focused on exporting fabric
+communication services to applications.  OFI is best described as a collection
+of libraries and applications used to export fabric services.  The key
+components of OFI are: application interfaces, provider libraries, kernel
+services, daemons, and test applications.
+
+Libfabric is a core component of OFI.  It is the library that defines and
+exports the user-space API of OFI, and is typically the only software that
+applications deal with directly.  It works in conjunction with provider
+libraries, which are often integrated directly into libfabric.")
+    (license (list license:bsd-2 license:gpl2)))) ;dual

gnu/packages/maths.scm

@@ -585,6 +585,14 @@ (define-public hdf4
        #:configure-flags '("--enable-shared")
        #:phases
        (modify-phases %standard-phases
+         ;; This is inspired by two of Debian's patches.
+         (add-before 'configure 'add-more-aarch64-support
+           (lambda _
+             (substitute* '("mfhdf/ncgen/ncgen.l"
+                            "mfhdf/ncgen/ncgenyy.c"
+                            "mfhdf/libsrc/netcdf.h.in")
+               (("AIX5L64") "__aarch64__"))
+             #t))
          (add-before 'configure 'patchbuild
            (lambda _
              (substitute*
@@ -596,7 +604,8 @@ (define-public hdf4
 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
                (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
--R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")))))))
+-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
+             #t)))))
     (home-page "https://www.hdfgroup.org/products/hdf4/")
     (synopsis
      "Library and multi-object file format for storing and managing data")

gnu/packages/mpi.scm

@@ -126,6 +126,8 @@ (define-public openmpi
     (inputs
      `(("hwloc" ,hwloc "lib")
        ("gfortran" ,gfortran)
+       ("libfabric" ,libfabric)
+       ("rdma-core" ,rdma-core)
        ("valgrind" ,valgrind)))
     (native-inputs
      `(("pkg-config" ,pkg-config)

gnu/packages/music.scm

@@ -952,7 +952,7 @@ (define-public solfege
 (define-public powertabeditor
   (package
     (name "powertabeditor")
-    (version "2.0.0-alpha9")
+    (version "2.0.0-alpha10")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -961,7 +961,7 @@ (define-public powertabeditor
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1zjdz1qpkl83xr6dkap8airqcyjs3mxc5dzfyhrrvkyr7dics7ii"))
+                "1fr14ql0yhlqvh6y08yaanszm2nvca5i50rqym396kfvga3ky18x"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -996,20 +996,13 @@ (define-public powertabeditor
          (replace 'check
            (lambda _
              (zero? (system* "bin/pte_tests"
-                             ;; FIXME: one test fails.
+                             ;; FIXME: these tests fail
-                             "exclude:Formats/PowerTabOldImport/Directions"))))
+                             "exclude:Actions/EditStaff"
-         (add-after 'unpack 'set-target-directories
+                             "exclude:Formats/PowerTabOldImport/MergeMultiBarRests"
-           (lambda _
+                             "exclude:Score/ViewFilter/FilterRule"
-             (substitute* "cmake/PTE_Executable.cmake"
+                             "exclude:Score/ViewFilter/ViewFilter"
-               (("set\\( install_dir.*")
+                             "exclude:Formats/PowerTabOldImport/Directions"
-                "set( install_dir bin )\n"))
+                             ))))
-             (substitute* "cmake/PTE_Paths.cmake"
-               (("set\\( PTE_DATA_DIR .*")
-                "set( PTE_DATA_DIR share/powertabeditor )\n"))
-             ;; Tests hardcode the data directory as "data"
-             (substitute* "test/CMakeLists.txt"
-               (("\\$\\{PTE_DATA_DIR\\}") "data"))
-             #t))
          (add-before 'configure 'remove-third-party-libs
            (lambda* (#:key inputs #:allow-other-keys)
              ;; Link with required static libraries, because we're not
@@ -3171,3 +3164,37 @@ (define-public musescore
 sample library.")
     (home-page "https://musescore.org")
     (license license:gpl2)))
+
+(define-public dssi
+  (package
+    (name "dssi")
+    (version "1.1.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://sourceforge/dssi/dssi/" version
+                    "/dssi-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0kl1hzhb7cykzkrqcqgq1dk4xcgrcxv0jja251aq4z4l783jpj7j"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("alsa-lib" ,alsa-lib)
+       ("jack-2" ,jack-2)
+       ("ladspa" ,ladspa)
+       ("libsamplerate" ,libsamplerate)
+       ("libsndfile" ,libsndfile)
+       ("liblo" ,liblo)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (synopsis "Audio plugin API for soft synths and effects")
+    (description "DSSI is a plugin API for software instruments with user
+interfaces, permitting them to be hosted in-process by audio applications.
+It is intended to be simple, GUI-toolkit-agnostic, and slightly biased
+towards familiarity with MIDI.  The DSSI distribution package contains
+a JACK/ALSA-sequencer reference host and some plugins as well as the
+specification and header.")
+    (home-page "http://dssi.sourceforge.net/")
+    ;; The DSSI interface is LGPL2.1+, some tests and examples are GPL2+.
+    ;; The vast majority of examples are in the public domain.
+    (license (list license:lgpl2.1+ license:gpl2+))))

gnu/packages/networking.scm

@@ -6,7 +6,7 @@
 ;;; Copyright © 2016 Raimon Grau <raimonster@gmail.com>
 ;;; Copyright © 2016 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
-;;; Copyright © 2016 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2016, 2017 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016, 2017 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2016, 2017 Arun Isaac <arunisaac@systemreboot.net>
@@ -55,6 +55,7 @@ (define-module (gnu packages networking)
   #:use-module (gnu packages dejagnu)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gettext)
+  #:use-module (gnu packages glib)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages libidn)
@@ -66,7 +67,9 @@ (define-module (gnu packages networking)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages qt)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages ssh)
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages valgrind)
@@ -480,30 +483,31 @@ (define-public whois
 (define-public wireshark
   (package
     (name "wireshark")
-    (version "2.2.7")
+    (version "2.4.0")
-    (synopsis "Network traffic analyzer")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.wireshark.org/download/src/wireshark-"
-                           version ".tar.bz2"))
+                           version ".tar.xz"))
        (sha256
         (base32
-         "1dfvhra5v6xhzbp097qsxi0zvirw0srbasl4v1wjf58v49idz7b8"))))
+         "011vvrj76z1azkpvyy2j40b1x1z56ymld508zfc4xw3gh8dv82w9"))))
-    (build-system glib-or-gtk-build-system)
+    (build-system gnu-build-system)
-    (inputs `(("bison" ,bison)
+    (inputs `(("c-ares" ,c-ares)
-              ("c-ares" ,c-ares)
+              ("glib" ,glib)
-              ("flex" ,flex)
               ("gnutls" ,gnutls)
-              ("gtk+" ,gtk+)
               ("libcap" ,libcap)
               ("libgcrypt" ,libgcrypt)
               ("libnl" ,libnl)
               ("libpcap" ,libpcap)
-              ("lua" ,lua-5.2)
+              ("libssh" ,libssh)
+              ("libxml2" ,libxml2)
+              ("lua" ,lua-5.2)          ;Lua 5.3 unsupported
               ("krb5" ,mit-krb5)
               ("openssl" ,openssl)
               ("portaudio" ,portaudio)
+              ("qtbase" ,qtbase)
+              ("qttools" ,qttools)
               ("sbc" ,sbc)
               ("zlib" ,zlib)))
     (native-inputs `(("perl" ,perl)
@@ -514,19 +518,21 @@ (define-public wireshark
        (list (string-append "--with-c-ares=" (assoc-ref %build-inputs "c-ares"))
              (string-append "--with-krb5=" (assoc-ref %build-inputs "krb5"))
              (string-append "--with-libcap=" (assoc-ref %build-inputs "libcap"))
+             (string-append "--with-libssh=" (assoc-ref %build-inputs "libssh"))
              (string-append "--with-lua=" (assoc-ref %build-inputs "lua"))
              (string-append "--with-pcap=" (assoc-ref %build-inputs "libpcap"))
              (string-append "--with-portaudio="
-                             (assoc-ref %build-inputs "portaudio"))
+                            (assoc-ref %build-inputs "portaudio"))
              (string-append "--with-sbc=" (assoc-ref %build-inputs "sbc"))
              (string-append "--with-ssl=" (assoc-ref %build-inputs "openssl"))
-             (string-append "--with-zlib=" (assoc-ref %build-inputs "zlib"))
+             (string-append "--with-zlib=" (assoc-ref %build-inputs "zlib")))))
-             "--without-qt")))
+    (home-page "https://www.wireshark.org/")
+    (synopsis "Network traffic analyzer")
     (description "Wireshark is a network protocol analyzer, or @dfn{packet
 sniffer}, that lets you capture and interactively browse the contents of
 network frames.")
-    (license license:gpl2+)
+    (home-page "https://www.wireshark.org/")
-    (home-page "https://www.wireshark.org/")))
+    (license license:gpl2+)))
 
 (define-public fping
   (package

gnu/packages/package-management.scm

@@ -411,15 +411,15 @@ (define-public stow
 (define-public rpm
   (package
     (name "rpm")
-    (version "4.12.0.1")
+    (version "4.13.0.1")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://rpm.org/releases/rpm-4.12.x/rpm-"
+              (uri (string-append "http://ftp.rpm.org/releases/rpm-"
+                                  (version-major+minor version) ".x/rpm-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "0a82ym8phx7g0f3k6smvxnvzh7yv857l42xafk49689kzhld5pbp"))
+                "03cvbwbfrhm0fa02j7828k1qp05hf2m0fradwcf2nqhrsjkppz17"))))
-              (patches (search-patches "rpm-CVE-2014-8118.patch"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--with-external-db"   ;use the system's bdb

gnu/packages/patches/bcftools-regidx-unsigned-char.patch

@@ -0,0 +1,16 @@
+Description: Fix test-regidx argument parsing on archs with unsigned char
+ On architectures where char is unsigned "c >= 0" was always true.
+Author: Adrian Bunk <bunk@debian.org>
+Bug-Debian: https://bugs.debian.org/865060
+
+--- a/test/test-regidx.c
++++ b/test/test-regidx.c
+@@ -336,7 +336,7 @@
+         {"seed",1,0,'s'},
+         {0,0,0,0}
+     };
+-    char c;
++    int c;
+     int seed = (int)time(NULL);
+     while ((c = getopt_long(argc, argv, "hvs:",loptions,NULL)) >= 0) 
+     {

gnu/packages/patches/graphicsmagick-CVE-2017-12935.patch

@@ -0,0 +1,28 @@
+This patch comes from http://hg.code.sf.net/p/graphicsmagick/code/rev/cd699a44f188.
+
+diff -ur a/coders/png.c b/coders/png.c
+--- a/coders/png.c	2017-07-04 17:32:08.000000000 -0400
++++ b/coders/png.c	2017-08-19 11:16:20.933969362 -0400
+@@ -4101,11 +4101,17 @@
+                   mng_info->image=image;
+                 }
+ 
+-              if ((mng_info->mng_width > 65535L) || (mng_info->mng_height
+-                                                     > 65535L))
+-                (void) ThrowException(&image->exception,ImageError,
+-                                      WidthOrHeightExceedsLimit,
+-                                      image->filename);
++              if ((mng_info->mng_width > 65535L) ||
++                  (mng_info->mng_height > 65535L))
++                {
++                  (void) LogMagickEvent(CoderEvent,GetMagickModule(),
++                      "  MNG width or height is too large: %lu, %lu",
++                      mng_info->mng_width,mng_info->mng_height);
++                  MagickFreeMemory(chunk);
++                  ThrowReaderException(CorruptImageError,
++                     ImproperImageHeader,image);
++                }
++
+               FormatString(page_geometry,"%lux%lu+0+0",mng_info->mng_width,
+                            mng_info->mng_height);
+               mng_info->frame.left=0;

gnu/packages/patches/graphicsmagick-CVE-2017-12936.patch

@@ -0,0 +1,16 @@
+This patch comes from http://hg.code.sf.net/p/graphicsmagick/code/rev/be898b7c97bd.
+
+diff -ur a/coders/wmf.c b/coders/wmf.c
+--- a/coders/wmf.c	2016-09-05 15:20:23.000000000 -0400
++++ b/coders/wmf.c	2017-08-19 10:38:08.984187264 -0400
+@@ -2719,8 +2719,8 @@
+   if(image->exception.severity != UndefinedException)
+     ThrowException2(exception,
+                    CoderWarning,
+-                   ddata->image->exception.reason,
+-                   ddata->image->exception.description);
++                   image->exception.reason,
++                   image->exception.description);
+ 
+   if(logging)
+     (void) LogMagickEvent(CoderEvent,GetMagickModule(),"leave ReadWMFImage()");

gnu/packages/patches/graphicsmagick-CVE-2017-12937.patch

@@ -0,0 +1,28 @@
+This patch comes from http://hg.code.sf.net/p/graphicsmagick/code/rev/95d00d55e978.
+
+diff -ur a/coders/sun.c b/coders/sun.c
+--- a/coders/sun.c	2016-05-30 13:19:54.000000000 -0400
++++ b/coders/sun.c	2017-08-18 18:00:00.191023610 -0400
+@@ -1,5 +1,5 @@
+ /*
+-% Copyright (C) 2003-2015 GraphicsMagick Group
++% Copyright (C) 2003-2017 GraphicsMagick Group
+ % Copyright (C) 2002 ImageMagick Studio
+ % Copyright 1991-1999 E. I. du Pont de Nemours and Company
+ %
+@@ -577,6 +577,7 @@
+           for (bit=7; bit >= 0; bit--)
+             {
+               index=((*p) & (0x01 << bit) ? 0x01 : 0x00);
++              VerifyColormapIndex(image,index);
+               indexes[x+7-bit]=index;
+               q[x+7-bit]=image->colormap[index];
+             }
+@@ -587,6 +588,7 @@
+             for (bit=7; bit >= (long) (8-(image->columns % 8)); bit--)
+               {
+                 index=((*p) & (0x01 << bit) ? 0x01 : 0x00);
++                VerifyColormapIndex(image,index);
+                 indexes[x+7-bit]=index;
+                 q[x+7-bit]=image->colormap[index];
+               }

gnu/packages/patches/lz4-fix-test-failures.patch

@@ -1,136 +0,0 @@
-These two patches fix some bugs in lz4's test suite:
-
-https://github.com/lz4/lz4/issues/308
-
-Patches copied from upstream source repository:
-
-https://github.com/lz4/lz4/commit/b89cac7b2e92b792af98bb0a12e4d14684d07629
-https://github.com/lz4/lz4/commit/0dfb0b9dad2a8cb7cc347d2139bf9b84de7e1481
-
-From b89cac7b2e92b792af98bb0a12e4d14684d07629 Mon Sep 17 00:00:00 2001
-From: Eric Siegerman <pub08-git@davor.org>
-Date: Tue, 14 Feb 2017 14:17:06 -0500
-Subject: [PATCH] Don't use "foo && false || true"
-
-Replace it with either:
-    test ! -f $FILE_THAT_SHOULD_NOT_EXIST
-or:
-    ! $COMMAND_THAT_SHOULD_FAIL
-
-as appropriate.
----
- tests/Makefile | 38 +++++++++++++++++++-------------------
- 1 file changed, 19 insertions(+), 19 deletions(-)
-
-diff --git a/tests/Makefile b/tests/Makefile
-index 77e6ae7..ebab278 100644
---- a/tests/Makefile
-+++ b/tests/Makefile
-@@ -236,17 +236,17 @@ test-lz4-basic: lz4 datagen unlz4 lz4cat
- 	./datagen -g256MB | $(LZ4) -vqB4D | $(LZ4) -t
- 	@echo "hello world" > tmp
- 	$(LZ4) --rm -f tmp
--	ls -ls tmp         && false || true   # must fail (--rm)
--	ls -ls tmp.lz4
--	$(PRGDIR)/lz4cat tmp.lz4              # must display hello world
--	ls -ls tmp.lz4
-+	test ! -f tmp                      # must fail (--rm)
-+	test   -f tmp.lz4
-+	$(PRGDIR)/lz4cat tmp.lz4           # must display hello world
-+	test   -f tmp.lz4
- 	$(PRGDIR)/unlz4 --rm tmp.lz4
--	ls -ls tmp
--	ls -ls tmp.lz4     && false || true   # must fail (--rm)
--	ls -ls tmp.lz4.lz4 && false || true   # must fail (unlz4)
--	$(PRGDIR)/lz4cat tmp                  # pass-through mode
--	ls -ls tmp
--	ls -ls tmp.lz4     && false || true   # must fail (lz4cat)
-+	test   -f tmp
-+	test ! -f tmp.lz4                  # must fail (--rm)
-+	test ! -f tmp.lz4.lz4              # must fail (unlz4)
-+	$(PRGDIR)/lz4cat tmp               # pass-through mode
-+	test   -f tmp
-+	test ! -f tmp.lz4                  # must fail (lz4cat)
- 	$(LZ4) tmp                         # creates tmp.lz4
- 	$(PRGDIR)/lz4cat < tmp.lz4 > tmp3  # checks lz4cat works with stdin (#285)
- 	$(DIFF) -q tmp tmp3
-@@ -262,22 +262,22 @@ test-lz4-hugefile: lz4 datagen
- 
- test-lz4-testmode: lz4 datagen
- 	@echo "\n ---- bench mode ----"
--	$(LZ4) -bi1
-+	  $(LZ4) -bi1
- 	@echo "\n ---- test mode ----"
--	./datagen | $(LZ4) -t             && false || true
--	./datagen | $(LZ4) -tf            && false || true
-+	! ./datagen | $(LZ4) -t
-+	! ./datagen | $(LZ4) -tf
- 	@echo "\n ---- pass-through mode ----"
--	./datagen | $(LZ4) -d  > $(VOID)  && false || true
--	./datagen | $(LZ4) -df > $(VOID)
-+	! ./datagen | $(LZ4) -d  > $(VOID)
-+	  ./datagen | $(LZ4) -df > $(VOID)
- 	@echo "Hello World !" > tmp1
- 	$(LZ4) -dcf tmp1
- 	@echo "from underground..." > tmp2
- 	$(LZ4) -dcfm tmp1 tmp2
- 	@echo "\n ---- test cli ----"
--	$(LZ4)     file-does-not-exist    && false || true
--	$(LZ4) -f  file-does-not-exist    && false || true
--	$(LZ4) -fm file1-dne file2-dne    && false || true
--	$(LZ4) -fm file1-dne file2-dne    && false || true
-+	! $(LZ4)     file-does-not-exist
-+	! $(LZ4) -f  file-does-not-exist
-+	! $(LZ4) -fm file1-dne file2-dne
-+	! $(LZ4) -fm file1-dne file2-dne
- 
- test-lz4-opt-parser: lz4 datagen
- 	@echo "\n ---- test opt-parser ----"
--- 
-2.12.2
-
-From 0dfb0b9dad2a8cb7cc347d2139bf9b84de7e1481 Mon Sep 17 00:00:00 2001
-From: "Dmitry V. Levin" <ldv@altlinux.org>
-Date: Sun, 5 Mar 2017 23:20:10 +0000
-Subject: [PATCH] Fix test-lz4-basic
-
-When no output filename is specified and stdout is not a terminal,
-lz4 doesn't attempt to guess an output filename and uses stdout for
-output.
-
-This change fixes test-lz4-basic when run without a terminal
-by specifying output filenames.
----
- tests/Makefile | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/tests/Makefile b/tests/Makefile
-index ebab278..d68c700 100644
---- a/tests/Makefile
-+++ b/tests/Makefile
-@@ -235,19 +235,19 @@ test-lz4-basic: lz4 datagen unlz4 lz4cat
- 	./datagen -g33M   | $(LZ4) --no-frame-crc | $(LZ4) -t
- 	./datagen -g256MB | $(LZ4) -vqB4D | $(LZ4) -t
- 	@echo "hello world" > tmp
--	$(LZ4) --rm -f tmp
-+	$(LZ4) --rm -f tmp tmp.lz4
- 	test ! -f tmp                      # must fail (--rm)
- 	test   -f tmp.lz4
- 	$(PRGDIR)/lz4cat tmp.lz4           # must display hello world
- 	test   -f tmp.lz4
--	$(PRGDIR)/unlz4 --rm tmp.lz4
-+	$(PRGDIR)/unlz4 --rm tmp.lz4 tmp
- 	test   -f tmp
- 	test ! -f tmp.lz4                  # must fail (--rm)
- 	test ! -f tmp.lz4.lz4              # must fail (unlz4)
- 	$(PRGDIR)/lz4cat tmp               # pass-through mode
- 	test   -f tmp
- 	test ! -f tmp.lz4                  # must fail (lz4cat)
--	$(LZ4) tmp                         # creates tmp.lz4
-+	$(LZ4) tmp tmp.lz4                 # creates tmp.lz4
- 	$(PRGDIR)/lz4cat < tmp.lz4 > tmp3  # checks lz4cat works with stdin (#285)
- 	$(DIFF) -q tmp tmp3
- 	$(PRGDIR)/lz4cat < tmp > tmp2      # checks lz4cat works with stdin (#285)
--- 
-2.12.2
-

gnu/packages/patches/newsbeuter-CVE-2017-12904.patch

@@ -0,0 +1,34 @@
+Fix CVE-2017-12904:
+
+https://github.com/akrennmair/newsbeuter/issues/591
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=2017-12904
+
+Patch copied from the Debian package of newsbeuter, version 2.9-5+deb9u1.
+
+Adapted from upstream source repository:
+
+https://github.com/akrennmair/newsbeuter/commit/96e9506ae9e252c548665152d1b8968297128307
+
+Description: Fix a RCE vulnerability in the bookmark command
+ Newsbeuter didn't properly escape the title and description fields before
+ passing them to the bookmarking program which could lead to remote code
+ execution using the shells command substitution functionality (e.g. "$()", ``,
+ etc)
+
+Origin: upstream, https://github.com/akrennmair/newsbeuter/commit/96e9506ae9e252c548665152d1b8968297128307
+Last-Update: 2017-08-18
+
+--- newsbeuter-2.9.orig/src/controller.cpp
++++ newsbeuter-2.9/src/controller.cpp
+@@ -1274,9 +1274,10 @@ std::string controller::bookmark(const s
+ 	std::string bookmark_cmd = cfg.get_configvalue("bookmark-cmd");
+ 	bool is_interactive = cfg.get_configvalue_as_bool("bookmark-interactive");
+ 	if (bookmark_cmd.length() > 0) {
+-		std::string cmdline = utils::strprintf("%s '%s' %s %s",
++		std::string cmdline = utils::strprintf("%s '%s' '%s' '%s'",
+ 		                                       bookmark_cmd.c_str(), utils::replace_all(url,"'", "%27").c_str(),
+-		                                       stfl::quote(title).c_str(), stfl::quote(description).c_str());
++		                                       utils::replace_all(title,"'", "%27").c_str(),
++		                                       utils::replace_all(description,"'", "%27").c_str());
+ 
+ 		LOG(LOG_DEBUG, "controller::bookmark: cmd = %s", cmdline.c_str());

gnu/packages/patches/python-cython-fix-tests-32bit.patch

@@ -1,27 +0,0 @@
-This fixes a test failure on 32-bit platforms.
-
-Upstream bug URL: https://github.com/cython/cython/issues/1548
-
-Patch copied from upstream source repository:
-
-https://github.com/cython/cython/commit/d92a718a26c9354fbf35f31a17de5c069865a447
-
-From d92a718a26c9354fbf35f31a17de5c069865a447 Mon Sep 17 00:00:00 2001
-From: Robert Bradshaw <robertwb@gmail.com>
-Date: Tue, 24 Jan 2017 16:57:00 -0800
-Subject: [PATCH] Normalize possible L suffix.
-
----
- tests/run/cpdef_enums.pyx | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tests/run/cpdef_enums.pyx b/tests/run/cpdef_enums.pyx
-index 167c762..c264ec5 100644
---- a/tests/run/cpdef_enums.pyx
-+++ b/tests/run/cpdef_enums.pyx
-@@ -93,4 +93,4 @@ def verify_resolution_GH1533():
-     3
-     """
-     THREE = 100
--    return PyxEnum.THREE
-+    return int(PyxEnum.THREE)

gnu/packages/patches/python-pygit2-disable-network-tests.patch

@@ -1,64 +1,43 @@
 Disable tests trying to look up remote servers.
 
 diff --git a/test/test_credentials.py b/test/test_credentials.py
-index 92482d9..9a281e5 100644
 --- a/test/test_credentials.py
 +++ b/test/test_credentials.py
-@@ -68,39 +68,5 @@ class CredentialCreateTest(utils.NoRepoTestCase):
+@@ -68,6 +68,7 @@ class CredentialCreateTest(utils.NoRepoTestCase):
          self.assertEqual((username, None, None, None), cred.credential_tuple)
  
  
--class CredentialCallback(utils.RepoTestCase):
++@unittest.skipIf(True, "network tests are not supported in Guix")
--    def test_callback(self):
+ class CredentialCallback(utils.RepoTestCase):
--        class MyCallbacks(pygit2.RemoteCallbacks):
+     def test_callback(self):
--            @staticmethod
+         class MyCallbacks(pygit2.RemoteCallbacks):
--            def credentials(url, username, allowed):
+@@ -92,6 +93,7 @@ class CredentialCallback(utils.RepoTestCase):
--                self.assertTrue(allowed & GIT_CREDTYPE_USERPASS_PLAINTEXT)
+         remote = self.repo.create_remote("github", url)
--                raise Exception("I don't know the password")
+         self.assertRaises(TypeError, lambda: remote.fetch(callbacks=MyCallbacks()))
--
+ 
--        url = "https://github.com/github/github"
++@unittest.skipIf(True, "network tests are not supported in Guix")
--        remote = self.repo.create_remote("github", url)
+ class CallableCredentialTest(utils.RepoTestCase):
--
+ 
--        self.assertRaises(Exception, lambda: remote.fetch(callbacks=MyCallbacks()))
+     def test_user_pass(self):
--
--    def test_bad_cred_type(self):
--        class MyCallbacks(pygit2.RemoteCallbacks):
--            @staticmethod
--            def credentials(url, username, allowed):
--                self.assertTrue(allowed & GIT_CREDTYPE_USERPASS_PLAINTEXT)
--                return Keypair("git", "foo.pub", "foo", "sekkrit")
--
--        url = "https://github.com/github/github"
--        remote = self.repo.create_remote("github", url)
--        self.assertRaises(TypeError, lambda: remote.fetch(callbacks=MyCallbacks()))
--
--class CallableCredentialTest(utils.RepoTestCase):
--
--    def test_user_pass(self):
--        credentials = UserPass("libgit2", "libgit2")
--        callbacks = pygit2.RemoteCallbacks(credentials=credentials)
--
--        url = "https://bitbucket.org/libgit2/testgitrepository.git"
--        remote = self.repo.create_remote("bb", url)
--        remote.fetch(callbacks=callbacks)
--
- if __name__ == '__main__':
-     unittest.main()
 diff --git a/test/test_repository.py b/test/test_repository.py
-index cfdf01e..c0d8de4 100644
 --- a/test/test_repository.py
 +++ b/test/test_repository.py
-@@ -538,13 +538,6 @@ class CloneRepositoryTest(utils.NoRepoTestCase):
+@@ -573,6 +573,7 @@ class CloneRepositoryTest(utils.NoRepoTestCase):
          self.assertTrue('refs/remotes/custom_remote/master' in repo.listall_references())
          self.assertIsNotNone(repo.remotes["custom_remote"])
  
--    def test_clone_with_credentials(self):
++    @unittest.skipIf(True, "network tests are not supported in Guix")
--        repo = clone_repository(
+     def test_clone_with_credentials(self):
--            "https://bitbucket.org/libgit2/testgitrepository.git",
+         repo = clone_repository(
--            self._temp_dir, callbacks=pygit2.RemoteCallbacks(credentials=pygit2.UserPass("libgit2", "libgit2")))
+             "https://bitbucket.org/libgit2/testgitrepository.git",
--
+diff --git a/test/test_submodule.py b/test/test_submodule.py
--        self.assertFalse(repo.is_empty)
+--- a/test/test_submodule.py
--
++++ b/test/test_submodule.py
-     def test_clone_with_checkout_branch(self):
+@@ -42,6 +42,7 @@ SUBM_PATH = 'submodule'
-         # create a test case which isolates the remote
+ SUBM_URL = 'https://github.com/libgit2/pygit2'
-         test_repo = clone_repository('./test/data/testrepo.git',
+ SUBM_HEAD_SHA = '819cbff552e46ac4b8d10925cc422a30aa04e78e'
+ 
++@unittest.skipIf(True, "network tests are not supported in Guix")
+ class SubmoduleTest(utils.SubmoduleRepoTestCase):
+ 
+     def test_lookup_submodule(self):

gnu/packages/patches/rpm-CVE-2014-8118.patch

@@ -1,25 +0,0 @@
-Fix CVE-2014-8118 (integer overflow allowing arbitrary remote code
-execution via crafted CPIO header).
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2014-8118
-
-Source:
-https://bugzilla.redhat.com/attachment.cgi?id=962159&action=diff
-
-Adopted by Debian:
-http://anonscm.debian.org/cgit/collab-maint/rpm.git/plain/debian/patches/CVE-2014-8118.patch
-
-diff --git a/lib/cpio.c b/lib/cpio.c
-index 253ff0f..600633a 100644
---- a/lib/cpio.c
-+++ b/lib/cpio.c
-@@ -399,6 +399,9 @@ int rpmcpioHeaderRead(rpmcpio_t cpio, char ** path, int * fx)
- 
-     GET_NUM_FIELD(hdr.filesize, fsize);
-     GET_NUM_FIELD(hdr.namesize, nameSize);
-+    if (nameSize <= 0 || nameSize > 4096) {
-+        return RPMERR_BAD_HEADER;
-+    }
- 
-     char name[nameSize + 1];
-     read = Fread(name, nameSize, 1, cpio->fd);

gnu/packages/patches/vinagre-revert-1.patch

@@ -0,0 +1,56 @@
+Patch taken from Debian: revert changes that prevent building against freerdp
+version 1.1 branch.
+
+From 8ebc0685b85e0d1f70eb00171f2e7712de3d44bd Mon Sep 17 00:00:00 2001
+From: Michael Biebl <biebl@debian.org>
+Date: Thu, 22 Sep 2016 01:15:55 +0200
+Subject: [PATCH 1/2] Revert "Improve FreeRDP authentication failure handling"
+
+This reverts commit d7b4f88943e8615d252d27e1efc58cb64a9e1821.
+---
+ plugins/rdp/vinagre-rdp-tab.c | 10 ++++++----
+ 1 file changed, 6 insertions(+), 4 deletions(-)
+
+diff --git a/plugins/rdp/vinagre-rdp-tab.c b/plugins/rdp/vinagre-rdp-tab.c
+index b731f9b..8572bc3 100644
+--- a/plugins/rdp/vinagre-rdp-tab.c
++++ b/plugins/rdp/vinagre-rdp-tab.c
+@@ -1195,8 +1195,8 @@ open_freerdp (VinagreRdpTab *rdp_tab)
+   VinagreTab           *tab = VINAGRE_TAB (rdp_tab);
+   GtkWindow            *window = GTK_WINDOW (vinagre_tab_get_window (tab));
+   gboolean              success = TRUE;
++  gboolean              authentication_error = FALSE;
+   gboolean              cancelled = FALSE;
+-  guint                 authentication_errors = 0;
+ 
+   priv->events = g_queue_new ();
+ 
+@@ -1205,12 +1205,14 @@ open_freerdp (VinagreRdpTab *rdp_tab)
+ 
+   do
+     {
++      authentication_error = FALSE;
++
+       /* Run FreeRDP session */
+       success = freerdp_connect (priv->freerdp_session);
+       if (!success)
+         {
+-          authentication_errors += freerdp_get_last_error (priv->freerdp_session->context) == 0x20009 ||
+-                                   freerdp_get_last_error (priv->freerdp_session->context) == 0x2000c;
++          authentication_error = freerdp_get_last_error (priv->freerdp_session->context) == 0x20009 ||
++                                 freerdp_get_last_error (priv->freerdp_session->context) == 0x2000c;
+ 
+           cancelled = freerdp_get_last_error (priv->freerdp_session->context) == 0x2000b;
+ 
+@@ -1218,7 +1220,7 @@ open_freerdp (VinagreRdpTab *rdp_tab)
+           init_freerdp (rdp_tab);
+         }
+     }
+-  while (!success && authentication_errors < 3);
++  while (!success && authentication_error);
+ 
+   if (!success)
+     {
+-- 
+2.9.3
+

gnu/packages/patches/vinagre-revert-2.patch

@@ -0,0 +1,448 @@
+Patch taken from Debian: revert changes that prevent building against freerdp
+version 1.1 branch.
+
+From bb1828b6b7eb29bb037bcc687cf10f916ddc7561 Mon Sep 17 00:00:00 2001
+From: Michael Biebl <biebl@debian.org>
+Date: Thu, 22 Sep 2016 01:18:16 +0200
+Subject: [PATCH 2/2] Revert "Store credentials for RDP"
+
+This reverts commit 60dea279a24c7f0e398b89a0a60d45e80087ed1d.
+---
+ plugins/rdp/vinagre-rdp-connection.c |  22 +---
+ plugins/rdp/vinagre-rdp-plugin.c     |  29 +----
+ plugins/rdp/vinagre-rdp-tab.c        | 231 +++++++++++++++++------------------
+ 3 files changed, 123 insertions(+), 159 deletions(-)
+
+diff --git a/plugins/rdp/vinagre-rdp-connection.c b/plugins/rdp/vinagre-rdp-connection.c
+index f0ff02b..c5f6ed1 100644
+--- a/plugins/rdp/vinagre-rdp-connection.c
++++ b/plugins/rdp/vinagre-rdp-connection.c
+@@ -127,25 +127,9 @@ rdp_parse_item (VinagreConnection *conn, xmlNode *root)
+ static void
+ rdp_parse_options_widget (VinagreConnection *conn, GtkWidget *widget)
+ {
+-  const gchar *text;
+-  GtkWidget   *u_entry, *d_entry, *spin_button, *scaling_button;
+-  gboolean     scaling;
+-  guint        width, height;
+-
+-  d_entry = g_object_get_data (G_OBJECT (widget), "domain_entry");
+-  if (!d_entry)
+-    {
+-      g_warning ("Wrong widget passed to rdp_parse_options_widget()");
+-      return;
+-    }
+-
+-  text = gtk_entry_get_text (GTK_ENTRY (d_entry));
+-  vinagre_cache_prefs_set_string  ("rdp-connection", "domain", text);
+-
+-  g_object_set (conn,
+-		"domain", text != NULL && *text != '\0' ? text : NULL,
+-		NULL);
+-
++  GtkWidget *u_entry, *spin_button, *scaling_button;
++  gboolean   scaling;
++  guint      width, height;
+ 
+   u_entry = g_object_get_data (G_OBJECT (widget), "username_entry");
+   if (!u_entry)
+diff --git a/plugins/rdp/vinagre-rdp-plugin.c b/plugins/rdp/vinagre-rdp-plugin.c
+index 4751102..f41da37 100644
+--- a/plugins/rdp/vinagre-rdp-plugin.c
++++ b/plugins/rdp/vinagre-rdp-plugin.c
+@@ -100,7 +100,7 @@ vinagre_rdp_plugin_init (VinagreRdpPlugin *plugin)
+ static GtkWidget *
+ impl_get_connect_widget (VinagreProtocol *plugin, VinagreConnection *conn)
+ {
+-  GtkWidget *grid, *label, *u_entry, *d_entry, *spin_button, *check;
++  GtkWidget *grid, *label, *u_entry, *spin_button, *check;
+   gchar     *str;
+   gint       width, height;
+ 
+@@ -146,29 +146,10 @@ impl_get_connect_widget (VinagreProtocol *plugin, VinagreConnection *conn)
+   g_free (str);
+ 
+ 
+-  label = gtk_label_new_with_mnemonic (_("_Domain:"));
+-  gtk_misc_set_alignment (GTK_MISC (label), 0.0, 0.5);
+-  gtk_grid_attach (GTK_GRID (grid), label, 0, 3, 1, 1);
+-  gtk_widget_set_margin_left (label, 12);
+-
+-  d_entry = gtk_entry_new ();
+-  /* Translators: This is the tooltip for the domain field in a RDP connection */
+-  gtk_widget_set_tooltip_text (d_entry, _("Optional."));
+-  g_object_set_data (G_OBJECT (grid), "domain_entry", d_entry);
+-  gtk_grid_attach (GTK_GRID (grid), d_entry, 1, 3, 1, 1);
+-  gtk_label_set_mnemonic_widget (GTK_LABEL (label), d_entry);
+-  str = g_strdup (VINAGRE_IS_CONNECTION (conn) ?
+-		  vinagre_connection_get_domain (conn) :
+-		  vinagre_cache_prefs_get_string  ("rdp-connection", "domain", ""));
+-  gtk_entry_set_text (GTK_ENTRY (d_entry), str);
+-  gtk_entry_set_activates_default (GTK_ENTRY (d_entry), TRUE);
+-  g_free (str);
+-
+-
+   /* Host width */
+   label = gtk_label_new_with_mnemonic (_("_Width:"));
+   gtk_misc_set_alignment (GTK_MISC (label), 0.0, 0.5);
+-  gtk_grid_attach (GTK_GRID (grid), label, 0, 4, 1, 1);
++  gtk_grid_attach (GTK_GRID (grid), label, 0, 3, 1, 1);
+   gtk_widget_set_margin_left (label, 12);
+ 
+   spin_button = gtk_spin_button_new_with_range (MIN_SIZE, MAX_SIZE, 1);
+@@ -176,7 +157,7 @@ impl_get_connect_widget (VinagreProtocol *plugin, VinagreConnection *conn)
+   gtk_widget_set_tooltip_text (spin_button, _("Set width of the remote desktop"));
+   gtk_spin_button_set_value (GTK_SPIN_BUTTON (spin_button), DEFAULT_WIDTH);
+   g_object_set_data (G_OBJECT (grid), "width_spin_button", spin_button);
+-  gtk_grid_attach (GTK_GRID (grid), spin_button, 1, 4, 1, 1);
++  gtk_grid_attach (GTK_GRID (grid), spin_button, 1, 3, 1, 1);
+   gtk_label_set_mnemonic_widget (GTK_LABEL (label), spin_button);
+   width = VINAGRE_IS_CONNECTION (conn) ?
+           vinagre_connection_get_width (conn) :
+@@ -188,7 +169,7 @@ impl_get_connect_widget (VinagreProtocol *plugin, VinagreConnection *conn)
+   /* Host height */
+   label = gtk_label_new_with_mnemonic (_("_Height:"));
+   gtk_misc_set_alignment (GTK_MISC (label), 0.0, 0.5);
+-  gtk_grid_attach (GTK_GRID (grid), label, 0, 5, 1, 1);
++  gtk_grid_attach (GTK_GRID (grid), label, 0, 4, 1, 1);
+   gtk_widget_set_margin_left (label, 12);
+ 
+   spin_button = gtk_spin_button_new_with_range (MIN_SIZE, MAX_SIZE, 1);
+@@ -196,7 +177,7 @@ impl_get_connect_widget (VinagreProtocol *plugin, VinagreConnection *conn)
+   gtk_widget_set_tooltip_text (spin_button, _("Set height of the remote desktop"));
+   gtk_spin_button_set_value (GTK_SPIN_BUTTON (spin_button), DEFAULT_HEIGHT);
+   g_object_set_data (G_OBJECT (grid), "height_spin_button", spin_button);
+-  gtk_grid_attach (GTK_GRID (grid), spin_button, 1, 5, 1, 1);
++  gtk_grid_attach (GTK_GRID (grid), spin_button, 1, 4, 1, 1);
+   gtk_label_set_mnemonic_widget (GTK_LABEL (label), spin_button);
+   height = VINAGRE_IS_CONNECTION (conn) ?
+            vinagre_connection_get_height (conn) :
+diff --git a/plugins/rdp/vinagre-rdp-tab.c b/plugins/rdp/vinagre-rdp-tab.c
+index 8572bc3..f3d9c08 100644
+--- a/plugins/rdp/vinagre-rdp-tab.c
++++ b/plugins/rdp/vinagre-rdp-tab.c
+@@ -70,8 +70,6 @@ struct _VinagreRdpTabPrivate
+   gboolean         scaling;
+   double           scale;
+   double           offset_x, offset_y;
+-
+-  guint            authentication_attempts;
+ };
+ 
+ G_DEFINE_TYPE (VinagreRdpTab, vinagre_rdp_tab, VINAGRE_TYPE_TAB)
+@@ -611,7 +609,6 @@ frdp_post_connect (freerdp *instance)
+                               0, 0,
+                               gdi->width, gdi->height);
+ 
+-  vinagre_tab_save_credentials_in_keyring (VINAGRE_TAB (rdp_tab));
+   vinagre_tab_add_recent_used (VINAGRE_TAB (rdp_tab));
+   vinagre_tab_set_state (VINAGRE_TAB (rdp_tab), VINAGRE_TAB_STATE_CONNECTED);
+ 
+@@ -862,76 +859,114 @@ frdp_mouse_moved (GtkWidget      *widget,
+   return TRUE;
+ }
+ 
++static void
++entry_text_changed_cb (GtkEntry   *entry,
++                       GtkBuilder *builder)
++{
++  const gchar *text;
++  GtkWidget   *widget;
++  gsize        username_length;
++  gsize        password_length;
++
++  widget = GTK_WIDGET (gtk_builder_get_object (builder, "username_entry"));
++  text = gtk_entry_get_text (GTK_ENTRY (widget));
++  username_length = strlen (text);
++
++  widget = GTK_WIDGET (gtk_builder_get_object (builder, "password_entry"));
++  text = gtk_entry_get_text (GTK_ENTRY (widget));
++  password_length = strlen (text);
++
++  widget = GTK_WIDGET (gtk_builder_get_object (builder, "ok_button"));
++  gtk_widget_set_sensitive (widget, password_length > 0 && username_length > 0);
++}
++
+ static gboolean
+ frdp_authenticate (freerdp  *instance,
+                    char    **username,
+                    char    **password,
+                    char    **domain)
+ {
+-  VinagreTab           *tab = VINAGRE_TAB (((frdpContext *) instance->context)->rdp_tab);
+-  VinagreRdpTab        *rdp_tab = VINAGRE_RDP_TAB (tab);
+-  VinagreRdpTabPrivate *priv = rdp_tab->priv;
+-  VinagreConnection    *conn = vinagre_tab_get_conn (tab);
+-  GtkWindow            *window = GTK_WINDOW (vinagre_tab_get_window (tab));
+-  gboolean              save_in_keyring = FALSE;
+-  gchar                *keyring_domain = NULL;
+-  gchar                *keyring_username = NULL;
+-  gchar                *keyring_password = NULL;
++  VinagreTab        *tab = VINAGRE_TAB (((frdpContext *) instance->context)->rdp_tab);
++  VinagreConnection *conn = vinagre_tab_get_conn (tab);
++  const gchar       *user_name;
++  const gchar       *domain_name;
++  GtkBuilder        *builder;
++  GtkWidget         *dialog;
++  GtkWidget         *widget;
++  GtkWidget         *username_entry;
++  GtkWidget         *password_entry;
++  GtkWidget         *domain_entry;
++  gboolean           save_credential_check_visible;
++  gboolean           domain_label_visible;
++  gboolean           domain_entry_visible;
++  gint               response;
+ 
+-  priv->authentication_attempts++;
++  builder = vinagre_utils_get_builder ();
+ 
+-  if (priv->authentication_attempts == 1)
+-    {
+-      vinagre_tab_find_credentials_in_keyring (tab, &keyring_domain, &keyring_username, &keyring_password);
+-      if (keyring_password != NULL && keyring_username != NULL)
+-        {
+-          *domain = keyring_domain;
+-          *username = keyring_username;
+-          *password = keyring_password;
++  dialog = GTK_WIDGET (gtk_builder_get_object (builder, "auth_required_dialog"));
++  gtk_window_set_modal ((GtkWindow *) dialog, TRUE);
++  gtk_window_set_transient_for ((GtkWindow *) dialog, GTK_WINDOW (vinagre_tab_get_window (tab)));
+ 
+-          return TRUE;
+-        }
+-      else
+-        {
+-          g_free (keyring_domain);
+-          g_free (keyring_username);
+-          g_free (keyring_password);
+-        }
++  widget = GTK_WIDGET (gtk_builder_get_object (builder, "host_label"));
++  gtk_label_set_text (GTK_LABEL (widget), vinagre_connection_get_host (conn));
++
++  username_entry = GTK_WIDGET (gtk_builder_get_object (builder, "username_entry"));
++  password_entry = GTK_WIDGET (gtk_builder_get_object (builder, "password_entry"));
++  domain_entry = GTK_WIDGET (gtk_builder_get_object (builder, "domain_entry"));
++
++  if (*username != NULL && *username[0] != '\0')
++    {
++      gtk_entry_set_text (GTK_ENTRY (username_entry), *username);
++      gtk_widget_grab_focus (password_entry);
+     }
+ 
+-  if (vinagre_utils_request_credential (window,
+-                                        "RDP",
+-                                        vinagre_connection_get_host (conn),
+-                                        vinagre_connection_get_domain (conn),
+-                                        vinagre_connection_get_username (conn),
+-                                        TRUE,
+-                                        TRUE,
+-                                        TRUE,
+-                                        20,
+-                                        domain,
+-                                        username,
+-                                        password,
+-                                        &save_in_keyring))
++  g_signal_connect (username_entry, "changed", G_CALLBACK (entry_text_changed_cb), builder);
++  g_signal_connect (password_entry, "changed", G_CALLBACK (entry_text_changed_cb), builder);
++
++
++  widget = GTK_WIDGET (gtk_builder_get_object (builder, "save_credential_check"));
++  save_credential_check_visible = gtk_widget_get_visible (widget);
++  gtk_widget_set_visible (widget, FALSE);
++
++  widget = GTK_WIDGET (gtk_builder_get_object (builder, "domain_label"));
++  domain_label_visible = gtk_widget_get_visible (widget);
++  gtk_widget_set_visible (widget, TRUE);
++
++  domain_entry_visible = gtk_widget_get_visible (domain_entry);
++  gtk_widget_set_visible (domain_entry, TRUE);
++
++
++  response = gtk_dialog_run (GTK_DIALOG (dialog));
++  gtk_widget_hide (dialog);
++
++
++  widget = GTK_WIDGET (gtk_builder_get_object (builder, "save_credential_check"));
++  gtk_widget_set_visible (widget, save_credential_check_visible);
++
++  widget = GTK_WIDGET (gtk_builder_get_object (builder, "domain_label"));
++  gtk_widget_set_visible (widget, domain_label_visible);
++
++  gtk_widget_set_visible (domain_entry, domain_entry_visible);
++
++
++  if (response == GTK_RESPONSE_OK)
+     {
+-      if (*domain && **domain != '\0')
+-        vinagre_connection_set_domain (conn, *domain);
++      domain_name = gtk_entry_get_text (GTK_ENTRY (domain_entry));
++      if (g_strcmp0 (*domain, domain_name) != 0)
++        *domain = g_strdup (domain_name);
+ 
+-      if (*username && **username != '\0')
+-        vinagre_connection_set_username (conn, *username);
++      user_name = gtk_entry_get_text (GTK_ENTRY (username_entry));
++      if (g_strcmp0 (*username, user_name) != 0)
++        *username = g_strdup (user_name);
+ 
+-      if (*password && **password != '\0')
+-        vinagre_connection_set_password (conn, *password);
++      *password = g_strdup (gtk_entry_get_text (GTK_ENTRY (password_entry)));
+ 
+-      vinagre_tab_set_save_credentials (tab, save_in_keyring);
++      return TRUE;
+     }
+   else
+     {
+-      vinagre_tab_remove_from_notebook (tab);
+-
+       return FALSE;
+     }
+-
+-  return TRUE;
+ }
+ 
+ static BOOL
+@@ -1028,25 +1063,30 @@ frdp_changed_certificate_verify (freerdp *instance,
+ #endif
+ 
+ static void
+-init_freerdp (VinagreRdpTab *rdp_tab)
++open_freerdp (VinagreRdpTab *rdp_tab)
+ {
+   VinagreRdpTabPrivate *priv = rdp_tab->priv;
+-  rdpSettings          *settings;
+   VinagreTab           *tab = VINAGRE_TAB (rdp_tab);
+   VinagreConnection    *conn = vinagre_tab_get_conn (tab);
+-  gboolean              scaling;
+-  gchar                *hostname;
+-  gint                  width, height;
+-  gint                  port;
++  rdpSettings          *settings;
++  GtkWindow            *window = GTK_WINDOW (vinagre_tab_get_window (tab));
++  gboolean              success = TRUE;
++  gboolean              fullscreen, scaling;
++  gchar                *hostname, *username;
++  gint                  port, width, height;
+ 
+   g_object_get (conn,
+                 "port", &port,
+                 "host", &hostname,
+                 "width", &width,
+                 "height", &height,
++                "fullscreen", &fullscreen,
+                 "scaling", &scaling,
++                "username", &username,
+                 NULL);
+ 
++  priv->events = g_queue_new ();
++
+   /* Setup FreeRDP session */
+   priv->freerdp_session = freerdp_new ();
+   priv->freerdp_session->PreConnect = frdp_pre_connect;
+@@ -1111,6 +1151,17 @@ init_freerdp (VinagreRdpTab *rdp_tab)
+   settings->port = port;
+ #endif
+ 
++  /* Set username */
++  username = g_strstrip (username);
++  if (username != NULL && username[0] != '\0')
++    {
++#if HAVE_FREERDP_1_1
++      settings->Username = g_strdup (username);
++#else
++      settings->username = g_strdup (username);
++#endif
++    }
++
+   /* Set keyboard layout */
+ #if HAVE_FREERDP_1_1
+   freerdp_keyboard_init (KBD_US);
+@@ -1120,24 +1171,6 @@ init_freerdp (VinagreRdpTab *rdp_tab)
+ 
+   /* Allow font smoothing by default */
+   settings->AllowFontSmoothing = TRUE;
+-}
+-
+-static void
+-init_display (VinagreRdpTab *rdp_tab)
+-{
+-  VinagreRdpTabPrivate *priv = rdp_tab->priv;
+-  VinagreTab           *tab = VINAGRE_TAB (rdp_tab);
+-  VinagreConnection    *conn = vinagre_tab_get_conn (tab);
+-  GtkWindow            *window = GTK_WINDOW (vinagre_tab_get_window (tab));
+-  gboolean              fullscreen, scaling;
+-  gint                  width, height;
+-
+-  g_object_get (conn,
+-                "width", &width,
+-                "height", &height,
+-                "fullscreen", &fullscreen,
+-                "scaling", &scaling,
+-                NULL);
+ 
+   /* Setup display for FreeRDP session */
+   priv->display = gtk_drawing_area_new ();
+@@ -1186,54 +1219,20 @@ init_display (VinagreRdpTab *rdp_tab)
+   priv->key_release_handler_id = g_signal_connect (GTK_WIDGET (tab), "key-release-event",
+                                                    G_CALLBACK (frdp_key_pressed),
+                                                    rdp_tab);
+-}
+-
+-static void
+-open_freerdp (VinagreRdpTab *rdp_tab)
+-{
+-  VinagreRdpTabPrivate *priv = rdp_tab->priv;
+-  VinagreTab           *tab = VINAGRE_TAB (rdp_tab);
+-  GtkWindow            *window = GTK_WINDOW (vinagre_tab_get_window (tab));
+-  gboolean              success = TRUE;
+-  gboolean              authentication_error = FALSE;
+-  gboolean              cancelled = FALSE;
+-
+-  priv->events = g_queue_new ();
+-
+-  init_freerdp (rdp_tab);
+-  init_display (rdp_tab);
+-
+-  do
+-    {
+-      authentication_error = FALSE;
+ 
+-      /* Run FreeRDP session */
+-      success = freerdp_connect (priv->freerdp_session);
+-      if (!success)
+-        {
+-          authentication_error = freerdp_get_last_error (priv->freerdp_session->context) == 0x20009 ||
+-                                 freerdp_get_last_error (priv->freerdp_session->context) == 0x2000c;
+-
+-          cancelled = freerdp_get_last_error (priv->freerdp_session->context) == 0x2000b;
+-
+-          freerdp_free (priv->freerdp_session);
+-          init_freerdp (rdp_tab);
+-        }
+-    }
+-  while (!success && authentication_error);
++  /* Run FreeRDP session */
++  success = freerdp_connect (priv->freerdp_session);
+ 
+   if (!success)
+     {
+       gtk_window_unfullscreen (window);
+-      if (!cancelled)
+-        vinagre_utils_show_error_dialog (_("Error connecting to host."),
+-                                         NULL,
+-                                         window);
++      vinagre_utils_show_error_dialog (_("Error connecting to host."),
++                                       NULL,
++                                       window);
+       g_idle_add ((GSourceFunc) idle_close, rdp_tab);
+     }
+   else
+     {
+-      priv->authentication_attempts = 0;
+       priv->update_id = g_idle_add ((GSourceFunc) update, rdp_tab);
+     }
+ }
+-- 
+2.9.3
+

gnu/packages/patches/xf86-video-siliconmotion-fix-ftbfs.patch

@@ -0,0 +1,171 @@
+From eee8fd4c489a693344da0bba14cfa54c54610b89 Mon Sep 17 00:00:00 2001
+From: Maarten Lankhorst <maarten.lankhorst@ubuntu.com>
+Date: Thu, 9 Mar 2017 13:31:34 +0200
+Subject: [PATCH] Fix build against xorg server 1.17 on certain architectures
+
+Fixes at least arm64, likely also hppa, m68k, sh4.
+
+Signed-off-by: Maarten Lankhorst <maarten.lankhorst@ubuntu.com>
+---
+ src/regsmi.h       | 18 ++++++++++++++++++
+ src/smi.h          |  2 ++
+ src/smi_driver.c   | 19 +++++++++----------
+ src/smilynx_crtc.c |  6 +++---
+ src/smilynx_hw.c   |  5 ++---
+ 5 files changed, 34 insertions(+), 16 deletions(-)
+
+diff --git a/src/regsmi.h b/src/regsmi.h
+index 5dd0320..69205ba 100644
+--- a/src/regsmi.h
++++ b/src/regsmi.h
+@@ -64,8 +64,13 @@ VGAIN8_INDEX(SMIPtr pSmi, int indexPort, int dataPort, CARD8 index)
+ 	MMIO_OUT8(pSmi->IOBase, indexPort, index);
+ 	return(MMIO_IN8(pSmi->IOBase, dataPort));
+     } else {
++#ifdef XSERVER_LIBPCIACCESS
++	pci_io_write8(pSmi->io, indexPort, index);
++	return pci_io_read8(pSmi->io, dataPort);
++#else
+ 	outb(pSmi->PIOBase + indexPort, index);
+ 	return(inb(pSmi->PIOBase + dataPort));
++#endif
+     }
+ }
+ 
+@@ -76,8 +81,13 @@ VGAOUT8_INDEX(SMIPtr pSmi, int indexPort, int dataPort, CARD8 index, CARD8 data)
+ 	MMIO_OUT8(pSmi->IOBase, indexPort, index);
+ 	MMIO_OUT8(pSmi->IOBase, dataPort, data);
+     } else {
++#ifdef XSERVER_LIBPCIACCESS
++	pci_io_write8(pSmi->io, indexPort, index);
++	pci_io_write8(pSmi->io, dataPort, data);
++#else
+ 	outb(pSmi->PIOBase + indexPort, index);
+ 	outb(pSmi->PIOBase + dataPort, data);
++#endif
+     }
+ }
+ 
+@@ -87,7 +97,11 @@ VGAIN8(SMIPtr pSmi, int port)
+     if (pSmi->IOBase) {
+ 	return(MMIO_IN8(pSmi->IOBase, port));
+     } else {
++#ifdef XSERVER_LIBPCIACCESS
++	return pci_io_read8(pSmi->io, port);
++#else
+ 	return(inb(pSmi->PIOBase + port));
++#endif
+     }
+ }
+ 
+@@ -97,7 +111,11 @@ VGAOUT8(SMIPtr pSmi, int port, CARD8 data)
+     if (pSmi->IOBase) {
+ 	MMIO_OUT8(pSmi->IOBase, port, data);
+     } else {
++#ifdef XSERVER_LIBPCIACCESS
++	pci_io_write8(pSmi->io, port, data);
++#else
+ 	outb(pSmi->PIOBase + port, data);
++#endif
+     }
+ }
+ 
+diff --git a/src/smi.h b/src/smi.h
+index 2742c8d..1f20a2d 100644
+--- a/src/smi.h
++++ b/src/smi.h
+@@ -171,6 +171,8 @@ typedef struct
+     pciVideoPtr		PciInfo;	/* PCI info vars */
+ #ifndef XSERVER_LIBPCIACCESS
+     PCITAG		PciTag;
++#else
++    struct pci_io_handle *io;
+ #endif
+     int			Chipset;	/* Chip info, set using PCI
+ 					   above */
+diff --git a/src/smi_driver.c b/src/smi_driver.c
+index 8949cae..6bdf64d 100644
+--- a/src/smi_driver.c
++++ b/src/smi_driver.c
+@@ -446,6 +446,9 @@ SMI_PreInit(ScrnInfoPtr pScrn, int flags)
+ 	pSmi->PIOBase = hwp->PIOOffset;
+ #else
+ 	pSmi->PIOBase = 0;
++#ifdef XSERVER_LIBPCIACCESS
++	pSmi->io = hwp->io;
++#endif
+ #endif
+ 
+ 	xf86ErrorFVerb(VERBLEV, "\tSMI_PreInit vgaCRIndex=%x, vgaIOBase=%x, "
+@@ -2022,16 +2025,14 @@ SMI_EnableMmio(ScrnInfoPtr pScrn)
+ 	vgaHWSetStdFuncs(hwp);
+ 
+ 	/* Enable linear mode */
+-	outb(pSmi->PIOBase + VGA_SEQ_INDEX, 0x18);
+-	tmp = inb(pSmi->PIOBase + VGA_SEQ_DATA);
++	tmp = VGAIN8_INDEX(pSmi, VGA_SEQ_INDEX, VGA_SEQ_DATA, 0x18);
+ 	pSmi->SR18Value = tmp;					/* PDR#521 */
+-	outb(pSmi->PIOBase + VGA_SEQ_DATA, tmp | 0x11);
++	VGAOUT8_INDEX(pSmi, VGA_SEQ_INDEX, VGA_SEQ_DATA, 0x18, tmp | 0x11);
+ 
+ 	/* Enable 2D/3D Engine and Video Processor */
+-	outb(pSmi->PIOBase + VGA_SEQ_INDEX, 0x21);
+-	tmp = inb(pSmi->PIOBase + VGA_SEQ_DATA);
++	tmp = VGAIN8_INDEX(pSmi, VGA_SEQ_INDEX, VGA_SEQ_DATA, 0x21);
+ 	pSmi->SR21Value = tmp;					/* PDR#521 */
+-	outb(pSmi->PIOBase + VGA_SEQ_DATA, tmp & ~0x03);
++	VGAOUT8_INDEX(pSmi, VGA_SEQ_INDEX, VGA_SEQ_DATA, 0x21, tmp & ~0x03);
+     }
+ 
+     LEAVE();
+@@ -2050,12 +2051,10 @@ SMI_DisableMmio(ScrnInfoPtr pScrn)
+ 	vgaHWSetStdFuncs(hwp);
+ 
+ 	/* Disable 2D/3D Engine and Video Processor */
+-	outb(pSmi->PIOBase + VGA_SEQ_INDEX, 0x21);
+-	outb(pSmi->PIOBase + VGA_SEQ_DATA, pSmi->SR21Value);	/* PDR#521 */
++	VGAOUT8_INDEX(pSmi, VGA_SEQ_INDEX, VGA_SEQ_DATA, 0x21, pSmi->SR21Value);	/* PDR#521 */
+ 
+ 	/* Disable linear mode */
+-	outb(pSmi->PIOBase + VGA_SEQ_INDEX, 0x18);
+-	outb(pSmi->PIOBase + VGA_SEQ_DATA, pSmi->SR18Value);	/* PDR#521 */
++	VGAOUT8_INDEX(pSmi, VGA_SEQ_INDEX, VGA_SEQ_DATA, 0x18, pSmi->SR18Value);	/* PDR#521 */
+     }
+ 
+     LEAVE();
+diff --git a/src/smilynx_crtc.c b/src/smilynx_crtc.c
+index fb7183c..f4d8b4e 100644
+--- a/src/smilynx_crtc.c
++++ b/src/smilynx_crtc.c
+@@ -619,9 +619,9 @@ SMILynx_CrtcModeSet_bios(xf86CrtcPtr crtc,
+     xf86ExecX86int10(pSmi->pInt10);
+ 
+     /* Enable linear mode. */
+-    outb(pSmi->PIOBase + VGA_SEQ_INDEX, 0x18);
+-    tmp = inb(pSmi->PIOBase + VGA_SEQ_DATA);
+-    outb(pSmi->PIOBase + VGA_SEQ_DATA, tmp | 0x01);
++    VGAOUT8(pSmi, VGA_SEQ_INDEX, 0x18);
++    tmp = VGAIN8(pSmi, VGA_SEQ_DATA);
++    VGAOUT8(pSmi, VGA_SEQ_DATA, tmp | 0x01);
+ 
+     /* Enable DPR/VPR registers. */
+     tmp = VGAIN8_INDEX(pSmi, VGA_SEQ_INDEX, VGA_SEQ_DATA, 0x21);
+diff --git a/src/smilynx_hw.c b/src/smilynx_hw.c
+index b2ee8a5..40aa5a4 100644
+--- a/src/smilynx_hw.c
++++ b/src/smilynx_hw.c
+@@ -365,9 +365,8 @@ SMILynx_WriteMode(ScrnInfoPtr pScrn, vgaRegPtr vgaSavePtr, SMIRegPtr restore)
+ 	xf86ExecX86int10(pSmi->pInt10);
+ 
+ 	/* Enable linear mode. */
+-	outb(pSmi->PIOBase + VGA_SEQ_INDEX, 0x18);
+-	tmp = inb(pSmi->PIOBase + VGA_SEQ_DATA);
+-	outb(pSmi->PIOBase + VGA_SEQ_DATA, tmp | 0x01);
++	tmp = VGAIN8_INDEX(pSmi, VGA_SEQ_INDEX, VGA_SEQ_DATA, 0x18);
++	VGAOUT8_INDEX(pSmi, VGA_SEQ_INDEX, VGA_SEQ_DATA, 0x18, tmp | 0x01);
+ 
+ 	/* Enable DPR/VPR registers. */
+ 	tmp = VGAIN8_INDEX(pSmi, VGA_SEQ_INDEX, VGA_SEQ_DATA, 0x21);
+-- 
+2.7.4
+

gnu/packages/python.scm

@@ -3611,15 +3611,14 @@ (define-public python2-rq
 (define-public python-cython
   (package
     (name "python-cython")
-    (version "0.25.2")
+    (version "0.26")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Cython" version))
-       (patches (search-patches "python-cython-fix-tests-32bit.patch"))
        (sha256
         (base32
-         "01h3lrf6d98j07iakifi81qjszh6faa37ibx7ylva1vsqbwx2hgi"))))
+         "0riciynnr0r68cvg6r3gbhi9x7h44pdwb7926m6n5vfs5p1f492c"))))
     (build-system python-build-system)
     ;; we need the full python package and not just the python-wrapper
     ;; because we need libpython3.3m.so
@@ -3630,7 +3629,7 @@ (define-public python-cython
        (modify-phases %standard-phases
          (add-before 'check 'set-HOME
            ;; some tests require access to "$HOME/.cython"
-           (lambda _ (setenv "HOME" "/tmp")))
+           (lambda _ (setenv "HOME" "/tmp") #t))
          (replace 'check
            (lambda _ (zero? (system* "python" "runtests.py" "-vv")))))))
     (home-page "http://cython.org/")
@@ -3915,14 +3914,14 @@ (define-public python2-numpy-documentation
 (define-public python-pygit2
   (package
     (name "python-pygit2")
-    (version "0.25.0")
+    (version "0.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pygit2" version))
        (sha256
         (base32
-         "0wf5rp0fvrw7j3j18dvwjq6xqlbm611wd55aphrfpps0v1gxh3ny"))
+         "1cbc488ra3kg7r3qky17ms0szi3cda2d96qfkv1l9djsy9hnvw57"))
        (patches
         (search-patches "python-pygit2-disable-network-tests.patch"))))
     (build-system python-build-system)
@@ -7296,7 +7295,7 @@ (define-public python2-msgpack
 (define-public python-netaddr
   (package
     (name "python-netaddr")
-    (version "0.7.18")
+    (version "0.7.19")
     (source
      (origin
        (method url-fetch)
@@ -7306,7 +7305,7 @@ (define-public python-netaddr
              ".tar.gz"))
        (sha256
          (base32
-          "06dxjlbcicq7q3vqy8agq11ra01kvvd47j4mk6dmghjsyzyckxd1"))))
+          "1zdfadvpq4lmcqzr383gywxn4xyn355kj1n3lk9q2l03vmyfrbiq"))))
     (build-system python-build-system)
     (arguments `(#:tests? #f)) ;; No tests.
     (home-page "https://github.com/drkjam/netaddr/")
@@ -7691,14 +7690,14 @@ (define-public python2-pretend
 (define-public python-cryptography-vectors
   (package
     (name "python-cryptography-vectors")
-    (version "2.0.2")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cryptography_vectors" version))
        (sha256
         (base32
-         "0yvi2cp23rg20bq3hd47ixbvjh0zgxnxrriqx5v17d7vkmliwbsi"))))
+         "1qa117fs1yd50zn2cfxh7d9l999ds0z4h83m9m7j4fk6ffm33f5y"))))
     (build-system python-build-system)
     (home-page "https://github.com/pyca/cryptography")
     (synopsis "Test vectors for the cryptography package")
@@ -7713,14 +7712,14 @@ (define-public python2-cryptography-vectors
 (define-public python-cryptography
   (package
     (name "python-cryptography")
-    (version "2.0.2")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cryptography" version))
        (sha256
         (base32
-         "1aq6ilnf2zdqshwqai4w8gmb5y6p7ip34qrjp1yb7sz77rkb501p"))))
+         "0fnck37zyvbzmccbp7w3jy27jgmij1992j5wyy3gxhw6a11b4jyh"))))
     (build-system python-build-system)
     (inputs
      `(("openssl" ,openssl)))

gnu/packages/rdesktop.scm

@@ -26,7 +26,9 @@ (define-module (gnu packages rdesktop)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cups)
+  #:use-module (gnu packages docbook)
   #:use-module (gnu packages gstreamer)
+  #:use-module (gnu packages image)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
@@ -70,51 +72,65 @@ (define-public rdesktop
     (license license:gpl3+)))
 
 (define-public freerdp
-  (package
+  (let ((commit "03ab68318966c3a22935a02838daaea7b7fbe96c"))
-    (name "freerdp")
+    (package
-    (version "2.0.0-rc0")
+      (name "freerdp")
-    (source (origin
+      (version (git-version "1.1" "1" commit))
-              (method url-fetch)
+      (source (origin
-              (uri (string-append "https://github.com/FreeRDP/FreeRDP/archive/"
+                (method git-fetch)
-                                  version ".tar.gz"))
+                (uri (git-reference
-              (file-name (string-append name "-" version ".tar.gz"))
+                      ;; We need the 1.1 branch for RDP support in vinagre.
-              (sha256
+                      (url "git://github.com/FreeRDP/FreeRDP.git")
-               (base32 "0r36zwhl7fhmdng5pvl2a106gqbcqq184g2i2klz6ilna8pxjcml"))))
+                      (commit commit)))
-    (build-system cmake-build-system)
+                (file-name (git-file-name name version))
-    (native-inputs
+                (sha256
-     `(("pkg-config" ,pkg-config)
+                 (base32 "07ish8rmvbk2zd99k91qybmmh5h4afly75l5kbvslhq1r6k8pbmp"))))
-       ("xmlto" ,xmlto)))
+      (build-system cmake-build-system)
-    (inputs
+      (native-inputs
-     `(("libx11" ,libx11)
+       `(("pkg-config" ,pkg-config)
-       ("libxkbfile" ,libxkbfile)
+         ("libxslt" ,libxslt)
-       ("libxcursor" ,libxcursor)
+         ("libxml2" ,libxml2)
-       ("libxext" ,libxext)
+         ("docbook-xsl" ,docbook-xsl)
-       ("libxi" ,libxi)
+         ("xmlto" ,xmlto)))
-       ("libxv" ,libxv)
+      (inputs
-       ("libxrandr" ,libxrandr)
+       `(("libx11" ,libx11)
-       ("libxrender" ,libxrender)
+         ("libxkbfile" ,libxkbfile)
-       ("libxinerama" ,libxinerama)
+         ("libxcursor" ,libxcursor)
-       ("libxshmfence" ,libxshmfence)
+         ("libxext" ,libxext)
-       ("libxml2" ,libxml2)
+         ("libxi" ,libxi)
-       ("libxslt" ,libxslt)
+         ("libxv" ,libxv)
-       ("cups" ,cups)
+         ("libxrandr" ,libxrandr)
-       ("ffmpeg" ,ffmpeg)
+         ("libxrender" ,libxrender)
-       ("pulseaudio" ,pulseaudio)
+         ("libxinerama" ,libxinerama)
-       ("alsa-lib" ,alsa-lib)
+         ("libxshmfence" ,libxshmfence)
-       ("gstreamer" ,gstreamer)
+         ("cups" ,cups)
-       ("gst-plugins-base" ,gst-plugins-base)
+         ("ffmpeg" ,ffmpeg-2.8)
-       ("zlib" ,zlib)
+         ("libjpeg" ,libjpeg)
-       ("openssl" ,openssl)))
+         ("pulseaudio" ,pulseaudio)
-    (arguments
+         ("alsa-lib" ,alsa-lib)
-     `(#:configure-flags
+         ("zlib" ,zlib)
-       '("-DCMAKE_INSTALL_LIBDIR=lib"
+         ("openssl" ,openssl)))
-         "-DWITH_PULSE=ON"
+      (arguments
-         "-DWITH_CUPS=ON")
+       `(#:configure-flags
-       #:tests? #f))                              ; no 'test' target
+         (list "-DCMAKE_INSTALL_LIBDIR=lib"
-    (home-page "https://www.freerdp.com")
+               "-DCMAKE_BUILD_TYPE=RELEASE"
-    (synopsis "Remote Desktop Protocol implementation")
+               "-DWITH_JPEG=ON"
-    (description "FreeRDP implements Microsoft's Remote Desktop Protocol.  It
+               ,@(if (string-prefix? "x86_64"
-consists of the @code{xfreerdp} client, libraries for client and server
+                                     (or (%current-target-system)
+                                         (%current-system)))
+                     '("-DWITH_SSE2=ON")
+                     '())
+               (string-append "-DDOCBOOKXSL_DIR="
+                              (assoc-ref %build-inputs "docbook-xsl")
+                              "/xml/xsl/docbook-xsl-"
+                              ,(package-version docbook-xsl))
+               "-DWITH_PULSE=ON"
+               "-DWITH_CUPS=ON")
+         #:tests? #f))                              ; no 'test' target
+      (home-page "https://www.freerdp.com")
+      (synopsis "Remote Desktop Protocol implementation")
+      (description "FreeRDP implements Microsoft's Remote Desktop Protocol.
+It consists of the @code{xfreerdp} client, libraries for client and server
 functionality, and Windows Portable Runtime (WinPR), a portable implementation
 of parts of the Windows API.")
-    (license license:asl2.0)))
+    (license license:asl2.0))))

gnu/packages/ruby.scm

@@ -464,13 +464,13 @@ (define-public ruby-rspec-2
 (define-public bundler
   (package
     (name "bundler")
-    (version "1.15.3")
+    (version "1.15.4")
     (source (origin
               (method url-fetch)
               (uri (rubygems-uri "bundler" version))
               (sha256
                (base32
-                "125amldnpzzrfw76mmr7mlx002k1k6xdyrqf5bdnzl5hajvn0s5f"))))
+                "0wl4r7wbwdq68xidfv4hhzfb1spb6lmhbspwlzrg4pf1l6ipxlgs"))))
     (build-system ruby-build-system)
     (arguments
      '(#:tests? #f)) ; avoid dependency cycles

gnu/packages/shells.scm

@@ -148,7 +148,7 @@ (define-public fish-guix
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://dist.pragmatique.xyz/fish-guix/"
+       (uri (string-append "https://dist.infotropique.org/fish-guix/"
                            name "-" version ".tar.xz"))
        (sha256
         (base32

gnu/packages/statistics.scm

@@ -65,7 +65,7 @@ (define-module (gnu packages statistics)
 (define-public pspp
   (package
     (name "pspp")
-    (version "0.10.2")
+    (version "1.0.0")
     (source
      (origin
       (method url-fetch)
@@ -73,7 +73,7 @@ (define-public pspp
                           version ".tar.gz"))
       (sha256
        (base32
-        "1afsq0a3iij64qacczvwhk81qg0q5rfqm055y5h9ls28d6paqz7p"))))
+        "10yb8nknh33c1y2ji3gww5dcnx9n3nqgsj6yfb4wibdjypa1m68v"))))
     (build-system gnu-build-system)
     (inputs
      `(("cairo" ,cairo)
@@ -126,6 +126,12 @@ (define-public r-minimal
              "PKG_BUILT_STAMP=1970-01-01")
        #:phases
        (modify-phases %standard-phases
+         ;; FIXME: see bug #28157.
+         (add-before 'configure 'patch-which
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "src/library/base/R/unix/system.unix.R"
+               (("@WHICH@") "which"))
+             #t))
          (add-before 'configure 'patch-uname
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
@@ -227,7 +233,6 @@ (define-public r-minimal
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("texinfo" ,texinfo) ; for building HTML manuals
-       ("which" ,which) ; for tests/Examples/base-Ex.R
        ("tzdata" ,tzdata-2017a)
        ("xz" ,xz)))
     (inputs
@@ -246,6 +251,9 @@ (define-public r-minimal
        ("pcre" ,pcre)
        ("readline" ,readline)
        ("zlib" ,zlib)))
+    ;; FIXME: By default Sys.which embeds a reference to "which", but this
+    ;; reference is not detected by Guix (see bug #28157).
+    (propagated-inputs `(("which" ,which)))
     (native-search-paths
      (list (search-path-specification
             (variable "R_LIBS_SITE")
@@ -4724,7 +4732,8 @@ (define-public r-trimcluster
      "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
 Matran (1997).  This optimizes the k-means criterion under trimming a portion
 of the points.")
-    (license license:gpl2+)))
+    ;; Any GPL version
+    (license (list license:gpl2+ license:gpl3+))))
 
 (define-public r-fpc
   (package

gnu/packages/syndication.scm

@@ -18,6 +18,7 @@ (define-module (gnu packages syndication)
   #:use-module (guix download)
   #:use-module (guix packages)
   #:use-module (guix build-system gnu)
+  #:use-module (gnu packages)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages gettext)
@@ -37,6 +38,7 @@ (define-public newsbeuter
         (method url-fetch)
         (uri (string-append "https://newsbeuter.org/downloads/newsbeuter-"
                             version ".tar.gz"))
+        (patches (search-patches "newsbeuter-CVE-2017-12904.patch"))
         (sha256
          (base32
           "1j1x0hgwxz11dckk81ncalgylj5y5fgw5bcmp9qb5hq9kc0vza3l"))))

gnu/packages/tls.scm

@@ -112,7 +112,7 @@ (define-public asn1c
 (define-public p11-kit
   (package
     (name "p11-kit")
-    (version "0.23.7")
+    (version "0.23.8")
     (source
      (origin
       (method url-fetch)
@@ -120,7 +120,7 @@ (define-public p11-kit
                           "download/" version "/p11-kit-" version ".tar.gz"))
       (sha256
        (base32
-        "0hdy4h8byvcvd4av504xqfqyd1h6xy914j034mq3c6v4ya37r3lq"))))
+        "0gqk1d09yyin75lvlywpbf3kxlnrcwbq8ridgapvqqjbzvjk98ab"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -667,7 +667,7 @@ (define perl-crypt-arguments
 (define-public perl-crypt-openssl-bignum
  (package
   (name "perl-crypt-openssl-bignum")
-  (version "0.06")
+  (version "0.08")
   (source
     (origin
       (method url-fetch)
@@ -677,7 +677,7 @@ (define-public perl-crypt-openssl-bignum
              ".tar.gz"))
       (sha256
         (base32
-          "05yzrdglrrzp191krf77zrwfkmzrfwrsrx1vyskbj94522lszk67"))))
+          "0gamn4dff1bz77nswacy1dlpn9fkwahzw7yvvik4nbwwy2s63hc8"))))
   (build-system perl-build-system)
   (inputs `(("openssl" ,openssl)))
   (arguments perl-crypt-arguments)

gnu/packages/version-control.scm

@@ -9,7 +9,7 @@
 ;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Kyle Meyer <kyle@kyleam.com>
 ;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017 ng0 <contact.ng0@cryptolab.net>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Vasile Dumitrascu <va511e@yahoo.com>
@@ -121,6 +121,8 @@ (define-public bazaar
 (define-public git
   (package
    (name "git")
+   ;; XXX When updating Git, check if the special 'git:src' input to cgit needs
+   ;; to be updated as well.
    (version "2.14.1")
    (source (origin
             (method url-fetch)
@@ -349,23 +351,6 @@ (define-public git
    (license license:gpl2)
    (home-page "https://git-scm.com/")))
 
-;; Some dependent packages directly access internal interfaces which
-;; have changed in 2.12. TODO: Remove this for cgit > 1.1.
-(define-public git@2.10
-  (package
-    (inherit git)
-    (version "2.10.4")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://kernel.org/software/scm/git/git-"
-                                  version ".tar.xz"))
-              (sha256
-               (base32
-                "1pni4mgih5w42813dxljl61s7xmcpdnar34d9m4548hzpljjyd4l"))))
-    (arguments
-     `(#:tests? #f
-       ,@(package-arguments git)))))
-
 (define-public libgit2
   (package
     (name "libgit2")
@@ -502,6 +487,8 @@ (define-public git-remote-gcrypt
 (define-public cgit
   (package
     (name "cgit")
+    ;; XXX When updating cgit, try removing the special 'git:src' input and
+    ;; using the source of the git package.
     (version "1.1")
     (source (origin
               (method url-fetch)
@@ -546,7 +533,16 @@ (define-public cgit
      ;; For building manpage.
      `(("asciidoc" ,asciidoc)))
     (inputs
-     `(("git:src" ,(package-source git@2.10))
+     `(;; Cgit directly accesses some internal Git interfaces that changed in
+       ;; Git 2.12.  Try removing this special input and using the source of the
+       ;; Git package for cgit > 1.1.
+       ("git:src"
+        ,(origin
+           (method url-fetch)
+           (uri "mirror://kernel.org/software/scm/git/git-2.10.4.tar.xz")
+           (sha256
+            (base32
+             "1pni4mgih5w42813dxljl61s7xmcpdnar34d9m4548hzpljjyd4l"))))
        ("openssl" ,openssl)
        ("zlib" ,zlib)))
     (home-page "https://git.zx2c4.com/cgit/")
@@ -1341,16 +1337,21 @@ (define-public git-annex-remote-hubic
 (define-public fossil
   (package
     (name "fossil")
-    (version "1.35")
+    (version "2.2")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
+       ;; Older downloads are moved to another URL.
-             "https://www.fossil-scm.org/index.html/uv/download/"
+       (uri (list
-             "fossil-src-" version ".tar.gz"))
+             (string-append
+              "https://www.fossil-scm.org/index.html/uv/download/"
+              "fossil-src-" version ".tar.gz")
+             (string-append
+              "https://www.fossil-scm.org/index.html/uv/"
+              "fossil-src-" version ".tar.gz")))
        (sha256
         (base32
-         "07ds6rhq69bhydpm9a01mgdhxf88p9b6y5hdnhn8gjc7ba92zyf1"))))
+         "0wfgacfg29dkl0c3l1rp5ji0kraa64gcbg5lh8p4m7mqdqcq53wv"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("tcl" ,tcl)                     ;for configuration only
@@ -1379,9 +1380,6 @@ (define-public fossil
                     (lambda _
                       (setenv "USER" "guix")
                       (setenv "TZ" "UTC")
-                      ;; Fixing the th1 test would require many backports, so
-                      ;; just disable for now.
-                      (delete-file "test/th1.test")
                       #t)))))
     (home-page "https://fossil-scm.org")
     (synopsis "Software configuration management system")

gnu/packages/video.scm

@@ -1121,7 +1121,7 @@ (define-public libvpx
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2017.08.13")
+    (version "2017.08.18")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1129,7 +1129,7 @@ (define-public youtube-dl
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1parn0xda7mp1phcj19axldifgh6mcwia6wdi3m20kidc9m4wb11"))))
+                "1mn3wi31k62c6drpplzp2irygjhiwprj5k7w4m0g8m4bgfdjgx57"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion

gnu/packages/vim.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 ng0 <ng0@no-reply.pragmatique.xyz>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
@@ -648,24 +648,46 @@ (define-public neovim
 (define-public vifm
   (package
     (name "vifm")
-    (version "0.8.2")
+    (version "0.9")
     (source
       (origin
         (method url-fetch)
-        (uri (string-append "mirror://sourceforge/vifm/vifm/vifm-"
+        (uri (list
-                            version ".tar.bz2"))
+               (string-append "https://github.com/vifm/vifm/releases/download/v"
+                              version "/vifm-" version ".tar.bz2")
+               (string-append "https://sourceforge.net/projects/vifm/files/vifm/"
+                              "vifm-" version ".tar.bz2")))
         (sha256
          (base32
-          "07r15kq7kjl3a41sd11ncpsii866xxps4f90zh3lv8jqcrv6silb"))))
+          "1zd72vcgir3g9rhs2iyca13qf5fc0b1f22y20f5gy92c3sfwj45b"))))
     (build-system gnu-build-system)
     (arguments
-    '(#:phases
+    '(#:configure-flags '("--disable-build-timestamp")
+      #:phases
       (modify-phases %standard-phases
         (add-after 'patch-source-shebangs 'patch-test-shebangs
           (lambda _
-            (substitute* (find-files "tests" "\\.c$")
+            (substitute* (cons* "src/background.c"
-              (("/bin/sh") (which "sh")))
+                                "src/cfg/config.c"
-            #t)))))
+                                (find-files "tests" "\\.c$"))
+              (("/bin/sh") (which "sh"))
+              (("/bin/bash") (which "bash")))
+            ;; This test segfaults
+            (substitute* "tests/Makefile"
+              (("misc") ""))
+            #t))
+         (add-after 'install 'install-vim-plugin-files
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (vifm (string-append out "/share/vifm"))
+                    (vimfiles (string-append out "/share/vim/vimfiles")))
+               (copy-recursively (string-append vifm "/colors")
+                                 (string-append vimfiles "/colors"))
+               (copy-recursively (string-append vifm "/vim")
+                                 vimfiles)
+               (delete-file-recursively (string-append vifm "/colors"))
+               (delete-file-recursively (string-append vifm "/vim")))
+             #t)))))
     (native-inputs
      `(("groff" ,groff) ; for the documentation
        ("perl" ,perl)))

gnu/packages/web.scm

@@ -933,7 +933,7 @@ (define-public serf
 (define-public sassc
   ;; libsass must be statically linked and it isn't included in the sassc
   ;; release tarballs, hence this odd package recipe.
-  (let* ((version "3.2.5")
+  (let* ((version "3.4.5")
          (libsass
           (origin
             (method url-fetch)
@@ -943,7 +943,7 @@ (define-public sassc
             (file-name (string-append "libsass-" version ".tar.gz"))
             (sha256
              (base32
-              "1x25k6p1s1yzsdpzb7bzh8japilmi1mk3z96q66pycbinj9z9is4")))))
+              "1j22138l5ymqjfj5zan9d2hipa3ahjmifgpjahqy1smlg5sb837x")))))
     (package
       (name "sassc")
       (version version)
@@ -954,11 +954,16 @@ (define-public sassc
                 (file-name (string-append "sassc-" version ".tar.gz"))
                 (sha256
                  (base32
-                  "1xf3w75w840rj0nx375rxi7mcv1ngqqq8p3zrzjlyx8jfpnldmv5"))))
+                  "1xk4kmmvziz9sal3swpqa10q0s289xjpcz8aggmly8mvxvmngsi9"))))
       (build-system gnu-build-system)
       (arguments
-       `(#:make-flags '("CC=gcc")
+       `(#:make-flags
+         (list "CC=gcc"
+               (string-append "PREFIX=" (assoc-ref %outputs "out")))
          #:test-target "test"
+         ;; FIXME: "make test" rebuilds the application and gets lost in a
+         ;; non-existing directory.
+         #:tests? #f
          #:phases
          (modify-phases %standard-phases
            (delete 'configure)
@@ -968,13 +973,7 @@ (define-public sassc
                     (begin
                       (setenv "SASS_LIBSASS_PATH"
                               (string-append (getcwd) "/libsass-" ,version))
-                      #t))))
+                      #t)))))))
-           (replace 'install ; no install target
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (mkdir-p bin)
-                 (copy-file "bin/sassc" (string-append bin "/sassc"))
-                 #t))))))
       (inputs
        `(("libsass" ,libsass)))
       (synopsis "CSS pre-processor")
@@ -4920,3 +4919,67 @@ (define-public r-crosstalk
 communicate with each other, with Shiny or without (i.e.  static @code{.html}
 files).  It currently supports linked brushing and filtering.")
     (license l:expat)))
+
+(define-public r-rook
+  (package
+    (name "r-rook")
+    (version "1.1-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Rook" version))
+       (sha256
+        (base32
+         "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
+    (properties `((upstream-name . "Rook")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-brew" ,r-brew)))
+    (home-page "http://cran.r-project.org/web/packages/Rook")
+    (synopsis "Web server interface for R")
+    (description
+     "This package contains the Rook specification and convenience software
+for building and running Rook applications.  A Rook application is an R
+reference class object that implements a @code{call} method or an R closure
+that takes exactly one argument, an environment, and returns a list with three
+named elements: the @code{status}, the @code{headers}, and the @code{body}.")
+    (license l:gpl2)))
+
+(define-public rss-bridge
+  (package
+    (name "rss-bridge")
+    (version "2017-08-03")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/RSS-Bridge/rss-bridge/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "05s16y552hbyj91s7bnlkx1bi64s6aw0fjy29az8via3i3b21yhl"))))
+    (build-system trivial-build-system)
+    (native-inputs
+     `(("gzip" ,gzip)
+       ("tar" ,tar)))
+    (arguments
+     '(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils)
+                      (ice-9 match))
+         (let* ((out (assoc-ref %outputs "out"))
+                (share-rss-bridge (string-append out "/share/rss-bridge")))
+           (set-path-environment-variable
+            "PATH" '("bin") (map (match-lambda ((_ . input) input))
+                                 %build-inputs))
+           (mkdir-p share-rss-bridge)
+           (system* "tar" "xvf" (assoc-ref %build-inputs "source")
+                    "--strip-components" "1" "-C" share-rss-bridge)
+           #t))))
+    (home-page "https://github.com/RSS-Bridge/rss-bridge")
+    (synopsis "Generate Atom feeds for social networking websites")
+    (description "rss-bridge generates Atom feeds for social networking
+websites lacking feeds.  Supported websites include Facebook, Twitter,
+Instagram and YouTube.")
+    (license (list l:public-domain
+                   l:expat)))) ;; vendor/simplehtmldom/simple_html_dom.php

gnu/packages/wm.scm

@@ -73,7 +73,7 @@ (define-module (gnu packages wm)
 (define-public libconfuse
   (package
     (name "libconfuse")
-    (version "3.2")
+    (version "3.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/martinh/libconfuse/"
@@ -81,7 +81,7 @@ (define-public libconfuse
                                   "/confuse-" version ".tar.xz"))
               (sha256
                (base32
-                "0j2fg93w22apjfqnkak8k8m395n2l7hhm9xnjx0k2v82js3bnsm4"))))
+                "0pnjmlj9i0alp407qd7c0vq83sz7gpsjrbdgpcn4xvzjp9r35ii3"))))
     (build-system gnu-build-system)
     (home-page "https://github.com/martinh/libconfuse")
     (synopsis "Configuration file parser library")

gnu/packages/xorg.scm

@@ -3220,7 +3220,8 @@ (define-public xf86-video-siliconmotion
                ".tar.bz2"))
         (sha256
           (base32
-           "1g2r6gxqrmjdff95d42msxdw6vmkg2zn5sqv0rxd420iwy8wdwyh"))))
+           "1g2r6gxqrmjdff95d42msxdw6vmkg2zn5sqv0rxd420iwy8wdwyh"))
+        (patches (search-patches "xf86-video-siliconmotion-fix-ftbfs.patch"))))
     (build-system gnu-build-system)
     (inputs `(("xorg-server" ,xorg-server)))
     (native-inputs `(("pkg-config" ,pkg-config)))

gnu/services/databases.scm

@@ -216,6 +216,14 @@ (define %memcached-accounts
          (home-directory "/var/empty")
          (shell (file-append shadow "/sbin/nologin")))))
 
+(define memcached-activation
+  #~(begin
+      (use-modules (guix build utils))
+      (let ((user (getpwnam "memcached")))
+        (mkdir-p "/var/run/memcached")
+        (chown "/var/run/memcached"
+               (passwd:uid user) (passwd:gid user)))))
+
 (define memcached-shepherd-service
   (match-lambda
     (($ <memcached-configuration> memcached interfaces tcp-port udp-port
@@ -233,11 +241,14 @@ (define memcached-shepherd-service
                           "-p" #$(number->string tcp-port)
                           "-U" #$(number->string udp-port)
                           "--daemon"
-                          "-P" "/var/run/memcached.pid"
+                          ;; Memcached changes to the memcached user prior to
+                          ;; writing the pid file, so write it to a directory
+                          ;; that memcached owns.
+                          "-P" "/var/run/memcached/pid"
                           "-u" "memcached"
                           ,#$@additional-options)
                         #:log-file "/var/log/memcached"
-                        #:pid-file "/var/run/memcached.pid"))
+                        #:pid-file "/var/run/memcached/pid"))
               (stop #~(make-kill-destructor))))))))
 
 (define memcached-service-type
@@ -245,6 +256,8 @@ (define memcached-service-type
                 (extensions
                  (list (service-extension shepherd-root-service-type
                                           memcached-shepherd-service)
+                       (service-extension activation-service-type
+                                          (const memcached-activation))
                        (service-extension account-service-type
                                           (const %memcached-accounts))))
                 (default-value (memcached-configuration))))

gnu/services/web.scm

@@ -114,105 +114,109 @@ (define-record-type* <nginx-configuration>
 (define (config-domain-strings names)
  "Return a string denoting the nginx config representation of NAMES, a list
 of domain names."
- (string-join
+ (map (match-lambda
-  (map (match-lambda
         ('default "_ ")
-        ((? string? str) (string-append str " ")))
+        ((? string? str) (list str " ")))
-       names)))
+      names))
 
 (define (config-index-strings names)
  "Return a string denoting the nginx config representation of NAMES, a list
 of index files."
- (string-join
+ (map (match-lambda
-  (map (match-lambda
+        ((? string? str) (list str " ")))
-        ((? string? str) (string-append str " ")))
+      names))
-       names)))
 
-(define nginx-location-config
+(define emit-nginx-location-config
   (match-lambda
     (($ <nginx-location-configuration> uri body)
-     (string-append
+     (list
       "      location " uri " {\n"
-      "        " (string-join body "\n    ") "\n"
+      (map (lambda (x) (list "        " x "\n")) body)
       "      }\n"))
     (($ <nginx-named-location-configuration> name body)
-     (string-append
+     (list
       "      location @" name " {\n"
-      "        " (string-join body "\n    ") "\n"
+      (map (lambda (x) (list "        " x "\n")) body)
       "      }\n"))))
 
-(define (default-nginx-server-config server)
+(define (emit-nginx-server-config server)
-  (string-append
+  (let ((http-port (nginx-server-configuration-http-port server))
-   "    server {\n"
+        (https-port (nginx-server-configuration-https-port server))
-   (if (nginx-server-configuration-http-port server)
+        (server-name (nginx-server-configuration-server-name server))
-       (string-append "      listen "
+        (ssl-certificate (nginx-server-configuration-ssl-certificate server))
-                      (number->string (nginx-server-configuration-http-port server))
+        (ssl-certificate-key
-                      ";\n")
+         (nginx-server-configuration-ssl-certificate-key server))
-       "")
+        (root (nginx-server-configuration-root server))
-   (if (nginx-server-configuration-https-port server)
+        (index (nginx-server-configuration-index server))
-       (string-append "      listen "
+        (server-tokens? (nginx-server-configuration-server-tokens? server))
-                      (number->string (nginx-server-configuration-https-port server))
+        (locations (nginx-server-configuration-locations server)))
-                      " ssl;\n")
+    (define-syntax-parameter <> (syntax-rules ()))
-       "")
+    (define-syntax-rule (and/l x tail ...)
-   "      server_name " (config-domain-strings
+      (let ((x* x))
-                         (nginx-server-configuration-server-name server))
+        (if x*
-                        ";\n"
+            (syntax-parameterize ((<> (identifier-syntax x*)))
-   (if (nginx-server-configuration-ssl-certificate server)
+              (list tail ...))
-       (let ((certificate (nginx-server-configuration-ssl-certificate server)))
+            '())))
-         ;; lstat fails when the certificate file does not exist: it aborts
+    (for-each
-         ;; and lets the user fix their configuration.
+     (match-lambda
-         (lstat certificate)
+      ((record-key . file)
-         (string-append "      ssl_certificate " certificate ";\n"))
+       (if (and file (not (file-exists? file)))
-       "")
+           (error
-   (if (nginx-server-configuration-ssl-certificate-key server)
+            (simple-format
-       (let ((key (nginx-server-configuration-ssl-certificate-key server)))
+             #f
-         (lstat key)
+             "~A in the nginx configuration for the server with name \"~A\" does not exist" record-key server-name)))))
-         (string-append "      ssl_certificate_key " key ";\n"))
+     `(("ssl-certificate"     . ,ssl-certificate)
-       "")
+       ("ssl-certificate-key" . ,ssl-certificate-key)))
-   "      root " (nginx-server-configuration-root server) ";\n"
+    (list
-   "      index " (config-index-strings (nginx-server-configuration-index server)) ";\n"
+     "    server {\n"
-   "      server_tokens " (if (nginx-server-configuration-server-tokens? server)
+     (and/l http-port  "      listen " (number->string <>) ";\n")
-                              "on" "off") ";\n"
+     (and/l https-port "      listen " (number->string <>) " ssl;\n")
-   "\n"
+     "      server_name " (config-domain-strings server-name) ";\n"
-   (string-join
+     (and/l ssl-certificate     "      ssl_certificate " <> ";\n")
-    (map nginx-location-config (nginx-server-configuration-locations server))
+     (and/l ssl-certificate-key "      ssl_certificate_key " <> ";\n")
-    "\n")
+     "      root " root ";\n"
+     "      index " (config-index-strings index) ";\n"
+     "      server_tokens " (if server-tokens? "on" "off") ";\n"
+     "\n"
+     (map emit-nginx-location-config locations)
+     "\n"
+     "    }\n")))
+
+(define (emit-nginx-upstream-config upstream)
+  (list
+   "    upstream " (nginx-upstream-configuration-name upstream) " {\n"
+   (map (lambda (server)
+          (simple-format #f "      server ~A;\n" server))
+        (nginx-upstream-configuration-servers upstream))
    "    }\n"))
 
-(define (nginx-upstream-config upstream)
+(define (flatten . lst)
-  (string-append
+  "Return a list that recursively concatenates all sub-lists of LST."
-   "    upstream " (nginx-upstream-configuration-name upstream) " {\n"
+  (define (flatten1 head out)
-   (string-concatenate
+    (if (list? head)
-    (map (lambda (server)
+        (fold-right flatten1 out head)
-           (simple-format #f "      server ~A;\n" server))
+        (cons head out)))
-         (nginx-upstream-configuration-servers upstream)))
+  (fold-right flatten1 '() lst))
-   "    }\n"))
 
 (define (default-nginx-config nginx log-directory run-directory server-list upstream-list)
-  (mixed-text-file "nginx.conf"
+  (apply mixed-text-file "nginx.conf"
-               "user nginx nginx;\n"
+         (flatten
-               "pid " run-directory "/pid;\n"
+          "user nginx nginx;\n"
-               "error_log " log-directory "/error.log info;\n"
+          "pid " run-directory "/pid;\n"
-               "http {\n"
+          "error_log " log-directory "/error.log info;\n"
-               "    client_body_temp_path " run-directory "/client_body_temp;\n"
+          "http {\n"
-               "    proxy_temp_path " run-directory "/proxy_temp;\n"
+          "    client_body_temp_path " run-directory "/client_body_temp;\n"
-               "    fastcgi_temp_path " run-directory "/fastcgi_temp;\n"
+          "    proxy_temp_path " run-directory "/proxy_temp;\n"
-               "    uwsgi_temp_path " run-directory "/uwsgi_temp;\n"
+          "    fastcgi_temp_path " run-directory "/fastcgi_temp;\n"
-               "    scgi_temp_path " run-directory "/scgi_temp;\n"
+          "    uwsgi_temp_path " run-directory "/uwsgi_temp;\n"
-               "    access_log " log-directory "/access.log;\n"
+          "    scgi_temp_path " run-directory "/scgi_temp;\n"
-               "    include " nginx "/share/nginx/conf/mime.types;\n"
+          "    access_log " log-directory "/access.log;\n"
-               "\n"
+          "    include " nginx "/share/nginx/conf/mime.types;\n"
-               (string-join
+          "\n"
-                (filter (lambda (section) (not (null? section)))
+          (map emit-nginx-upstream-config upstream-list)
-                        (map nginx-upstream-config upstream-list))
+          (map emit-nginx-server-config server-list)
-                "\n")
+          "}\n"
-               "\n"
+          "events {}\n")))
-               (let ((http (map default-nginx-server-config server-list)))
-                 (do ((http http (cdr http))
-                      (block "" (string-append (car http) "\n" block )))
-                     ((null? http) block)))
-               "}\n"
-               "events {}\n"))
 
 (define %nginx-accounts
   (list (user-group (name "nginx") (system? #t))

gnu/system/examples/bare-bones.tmpl

@@ -12,7 +12,9 @@
 
   ;; Assuming /dev/sdX is the target hard disk, and "my-root" is
   ;; the label of the target root file system.
-  (bootloader (grub-configuration (device "/dev/sdX")))
+  (bootloader (bootloader-configuration
+                (bootloader grub-bootloader)
+                (device "/dev/sdX")))
   (file-systems (cons (file-system
                         (device "my-root")
                         (title 'label)

gnu/system/examples/desktop.tmpl

@@ -13,19 +13,20 @@
 
   ;; Assuming /dev/sdX is the target hard disk, and "my-root"
   ;; is the label of the target root file system.
-  (bootloader (grub-configuration (device "/dev/sdX")))
+  (bootloader (bootloader-configuration
+                (bootloader grub-bootloader)
+                (device "/dev/sdX")))
 
   ;; Specify a mapped device for the encrypted root partition.
   ;; The UUID is that returned by 'cryptsetup luksUUID'.
   (mapped-devices
    (list (mapped-device
           (source (uuid "12345678-1234-1234-1234-123456789abc"))
-          (target "the-root-device")
+          (target "my-root")
           (type luks-device-mapping))))
 
   (file-systems (cons (file-system
                         (device "my-root")
-                        (title 'label)
                         (mount-point "/")
                         (type "ext4")
                         (dependencies mapped-devices))

gnu/system/examples/lightweight-desktop.tmpl

@@ -12,9 +12,10 @@
   (locale "en_US.utf8")
 
   ;; Use the UEFI variant of GRUB with the EFI System
-  ;; Partition on /dev/sda1.
+  ;; Partition mounted on /boot/efi.
-  (bootloader (grub-configuration (grub grub-efi)
+  (bootloader (bootloader-configuration
-                                  (device "/dev/sda1")))
+                (bootloader grub-efi-bootloader)
+                (device "/boot/efi")))
 
   ;; Assume the target root file system is labelled "my-root".
   (file-systems (cons* (file-system

gnu/tests/databases.scm

@@ -63,13 +63,15 @@ (define marionette
           (test-begin "memcached")
 
           ;; Wait for memcached to be up and running.
-          (test-eq "service running"
+          (test-assert "service running"
-            'running!
             (marionette-eval
              '(begin
                 (use-modules (gnu services herd))
-                (start-service 'memcached)
+                (match (start-service 'memcached)
-                'running!)
+                  (#f #f)
+                  (('service response-parts ...)
+                   (match (assq-ref response-parts 'running)
+                     ((pid) (number? pid))))))
              marionette))
 
           (let* ((ai (car (getaddrinfo "localhost"

guix/scripts/download.scm

@@ -143,12 +143,15 @@ (define (parse-options)
            (arg   (or (assq-ref opts 'argument)
                       (leave (G_ "no download URI was specified~%"))))
            (uri   (or (string->uri arg)
+                      (false-if-exception
+                       (string->uri
+                        (string-append "file://" (canonicalize-path arg))))
                       (leave (G_ "~a: failed to parse URI~%")
                              arg)))
            (fetch (assq-ref opts 'download-proc))
            (path  (parameterize ((current-terminal-columns
                                   (terminal-columns)))
-                    (fetch arg
+                    (fetch (uri->string uri)
                            #:verify-certificate?
                            (assq-ref opts 'verify-certificate?))))
            (hash  (call-with-input-file

guix/scripts/pack.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -50,19 +51,20 @@ (define-record-type <compressor>
   (compressor name extension command)
   compressor?
   (name       compressor-name)      ;string (e.g., "gzip")
-  (extension  compressor-extension) ;string (e.g., "lz")
+  (extension  compressor-extension) ;string (e.g., ".lz")
   (command    compressor-command))  ;gexp (e.g., #~("/gnu/store/…/gzip" "-9n"))
 
 (define %compressors
   ;; Available compression tools.
-  (list (compressor "gzip"  "gz"
+  (list (compressor "gzip"  ".gz"
                     #~(#+(file-append gzip "/bin/gzip") "-9n"))
-        (compressor "lzip"  "lz"
+        (compressor "lzip"  ".lz"
                     #~(#+(file-append lzip "/bin/lzip") "-9"))
-        (compressor "xz"    "xz"
+        (compressor "xz"    ".xz"
                     #~(#+(file-append xz "/bin/xz") "-e -T0"))
-        (compressor "bzip2" "bz2"
+        (compressor "bzip2" ".bz2"
-                    #~(#+(file-append bzip2 "/bin/bzip2") "-9"))))
+                    #~(#+(file-append bzip2 "/bin/bzip2") "-9"))
+        (compressor "none" "" #f)))
 
 (define (lookup-compressor name)
   "Return the compressor object called NAME.  Error out if it could not be
@@ -180,7 +182,7 @@ (define tar-supports-sort?
                                           (_ #f))
                                         directives)))))))))
 
-  (gexp->derivation (string-append name ".tar."
+  (gexp->derivation (string-append name ".tar"
                                    (compressor-extension compressor))
                     build
                     #:references-graphs `(("profile" ,profile))))
@@ -245,7 +247,7 @@ (define build
                               #:compressor '#$(compressor-command compressor)
                               #:creation-time (make-time time-utc 0 1)))))
 
-  (gexp->derivation (string-append name ".tar."
+  (gexp->derivation (string-append name ".tar"
                                    (compressor-extension compressor))
                     build
                     #:references-graphs `(("profile" ,profile))))

nix/libstore/build.cc

@@ -2086,12 +2086,8 @@ void DerivationGoal::runChild()
                outside of the namespace.  Making a subtree private is
                local to the namespace, though, so setting MS_PRIVATE
                does not affect the outside world. */
-            Strings mounts = tokenizeString<Strings>(readFile("/proc/self/mountinfo", true), "\n");
+            if (mount(0, "/", 0, MS_REC|MS_PRIVATE, 0) == -1) {
-            foreach (Strings::iterator, i, mounts) {
+                throw SysError("unable to make ‘/’ private mount");
-                vector<string> fields = tokenizeString<vector<string> >(*i, " ");
-                string fs = decodeOctalEscaped(fields.at(4));
-                if (mount(0, fs.c_str(), 0, MS_PRIVATE, 0) == -1)
-                    throw SysError(format("unable to make filesystem `%1%' private") % fs);
             }
 
             /* Bind-mount chroot directory to itself, to treat it as a

nix/libutil/util.cc

@@ -1106,21 +1106,6 @@ bool endOfList(std::istream & str)
 }
 
 
-string decodeOctalEscaped(const string & s)
-{
-    string r;
-    for (string::const_iterator i = s.begin(); i != s.end(); ) {
-        if (*i != '\\') { r += *i++; continue; }
-        unsigned char c = 0;
-        ++i;
-        while (i != s.end() && *i >= '0' && *i < '8')
-            c = c * 8 + (*i++ - '0');
-        r += c;
-    }
-    return r;
-}
-
-
 void ignoreException()
 {
     try {

nix/libutil/util.hh

@@ -356,12 +356,6 @@ string parseString(std::istream & str);
 bool endOfList(std::istream & str);
 
 
-/* Escape a string that contains octal-encoded escape codes such as
-   used in /etc/fstab and /proc/mounts (e.g. "foo\040bar" decodes to
-   "foo bar"). */
-string decodeOctalEscaped(const string & s);
-
-
 /* Exception handling in destructors: print an error message, then
    ignore the exception. */
 void ignoreException();

tests/guix-download.sh

@@ -29,12 +29,15 @@ then false; else true; fi
 if guix download unknown://some/where;
 then false; else true; fi
 
-if guix download not/a/uri;
+if guix download /does-not-exist
 then false; else true; fi
 
 # This one should succeed.
 guix download "file://$abs_top_srcdir/README"
 
+# And this one, without the URI scheme.
+guix download "$abs_top_srcdir/README"
+
 # This one too, even if it cannot talk to the daemon.
 output="t-download-$$"
 trap 'rm -f "$output"' EXIT