gnu: gd: Fix CVE-2016-8670.

* gnu/packages/patches/gd-CVE-2016-8670.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Use it.

gnu: services sddm  Fix typo.

* gnu/services/sddm.scm: sddm-confiugration? --> sddm-configuration?

gnu: guitarix: Update to 0.35.2.

* gnu/packages/audio.scm (guitarix): Update to 0.35.2.

gnu: gx-switchless-wah-lv2: Fix SSE detection.

* gnu/packages/music.scm (gx-switchless-wah-lv2)[arguments]: Add phase
"escape-shell-commands".

gnu: gx-slow-gear-lv2: Fix SSE detection.

* gnu/packages/music.scm (gx-slow-gear-lv2)[arguments]: Add phase
"escape-shell-commands".

gnu: gx-vintage-fuzz-master-lv2: Fix SSE detection.

* gnu/packages/music.scm (gx-vintage-fuzz-master-lv2)[arguments]: Add
phase "escape-shell-commands".

gnu: gx-super-fuzz-lv2: Fix SSE detection.

* gnu/packages/music.scm (gx-super-fuzz-lv2)[arguments]: Add phase
"escape-shell-commands".

gnu: gx-voodoo-fuzz-lv2: Fix SSE detection.

* gnu/packages/music.scm (gx-voodoo-fuzz-lv2)[arguments]: Add phase
"escape-shell-commands".

gnu: gx-hyperion-lv2: Fix SSE detection.

* gnu/packages/music.scm (gx-hyperion-lv2)[arguments]: Add phase
"escape-shell-commands".

gnu: gx-saturator-lv2: Fix SSE detection.

* gnu/packages/music.scm (gx-saturator-lv2)[arguments]: Add phase
"escape-shell-commands".

grafts: 'graft-derivation' does now introduce grafts that shadow other grafts.

Partly fixes <http://bugs.gnu.org/24418>.

* guix/grafts.scm (cumulative-grafts)[graft-origin?]: New procedure.
[dependency-grafts]: Use it in new 'if' around recursive call.
* tests/grafts.scm ("graft-derivation, grafts are not shadowed"): New test.

packages: 'package-grafts' applies grafts on replacement.

Partly fixes <http://bugs.gnu.org/24418>.

* guix/packages.scm (input-graft): Compute 'new' with #:graft? #t.
(input-cross-graft): Likewise.
* tests/packages.scm ("package-grafts, indirect grafts, cross"): Comment
out.
("replacement also grafted"): New test.

gnu: libraw: Update to 0.17.2 [fixes CVE-2015-{8366,8367}].

* gnu/packages/photo.scm (libraw): Update to 0.17.2.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: freeimage: Use 'modify-phases' syntax.

* gnu/packages/image.scm (freeimage)[arguments]: Use 'modify-phases'
syntax.

gnu: freeimage: Fix CVE-2016-5684.

* gnu/packages/image.scm (freeimage)[source]: Add patch.
* gnu/packages/patches/freeimage-CVE-2016-5684.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

gnu: mail: Add notifymuch.

* gnu/packages/mail.scm (notifymuch): New variable.

gnu: dbus: Replace with 1.10.12 [security fix].

Fixes <https://bugs.freedesktop.org/show_bug.cgi?id=98157>
"format string vulnerability processing ActivationFailure messages"

* gnu/packages/glib.scm (dbus)[replacement]: New field.
(dbus-1.10.12): New variable.

gnu: Add jack-keyboard.

* gnu/packages/music.scm (jack-keyboard): New variable.

gnu: Add gx-switchless-wah-lv2.

* gnu/packages/music.scm (gx-switchless-wah-lv2): New variable.

gnu: Add gx-slow-gear-lv2.

* gnu/packages/music.scm (gx-slow-gear-lv2): New variable.

gnu: Add gx-vintage-fuzz-master-lv2.

* gnu/packages/music.scm (gx-vintage-fuzz-master-lv2): New variable.

gnu: Add gx-super-fuzz-lv2.

* gnu/packages/music.scm (gx-super-fuzz-lv2): New variable.

gnu: Add gx-voodoo-fuzz-lv2.

* gnu/packages/music.scm (gx-voodoo-fuzz-lv2): New variable.

gnu: Add gx-hyperion-lv2.

* gnu/packages/music.scm (gx-hyperion-lv2): New variable.

gnu: Add gx-saturator-lv2.

* gnu/packages/music.scm (gx-saturator-lv2): New variable.

gnu: Add gx-suppa-tone-bender-lv2.

* gnu/packages/music.scm (gx-suppa-tone-bender-lv2): New variable.

gnu: Add gx-push-pull-lv2.

* gnu/packages/music.scm (gx-push-pull-lv2): New variable.

gnu: Add gx-tone-mender-lv2.

* gnu/packages/music.scm (gx-tone-mender-lv2): New variable.

gnu: Add gx-overdriver-lv2.

* gnu/packages/music.scm (gx-overdriver-lv2): New variable.

gnu: Add gx-vbass-preamp-lv2.

* gnu/packages/music.scm (gx-vbass-preamp-lv2): New variable.

gnu: Add gx-guvnor-lv2.

* gnu/packages/music.scm (gx-guvnor-lv2): New variable.

gnu: Add emacs-nginx-mode.

* gnu/packages/emacs.scm (emacs-nginx-mode): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>

gnu: Add emacs-evil.

* gnu/packages/emacs.scm (emacs-evil): New variable.

Co-authored-by: Alex Kost <alezost@gmail.com>

gnu: Add emacs-goto-chg.

* gnu/packages/emacs.scm (emacs-goto-chg): New variable.

Co-authored-by: Alex Kost <alezost@gmail.com>

Revert "guix: python-build-system: Fix an outdated comment."

This reverts commit 635a7af45d6e2105ad65d1a9531126cc232a2a50.

guix: python-build-system: Fix an outdated comment.

The python-build-system uses phases the build and install, but not
configure. So the old comment was plain wrong since Sept. 2013, when the build
phase has been added.

gnu: python-pathlib: Update description.

* gnu/packages/python.scm (python-pathlib, python2-pathlib): Update
  description.

gnu: python-keyring: Update home-page url.

* gnu/packages/python.scm (python-keyring, python2-keyring): Update home-page
  url.

gnu: python-pylockfile: Update home-page url.

* gnu/packages/python.scm (python-pylockfile, python2-pylockfile): Update
  home-page url.

gnu: python-zope-testing: Strip byte-code and backup-files from source.

* gnu/package/python.scm (python-zope-testing, python2-zope-testing)[source]:
  Add snippet to strip byte-code and backup-files.

gnu: python-pytest-xdist: Remove python byte-code files from source.

* gnu/packages/python.scm (python-pytest-xdist,
  python2-pytest-xdist)[source]: Add snippet.

gnu: python2-pytest-runner, python2-msgpack: Remove duplicate definitions.

* gnu/packages/python.scm (python2-pytest-runner): Was defined twice, remove
  duplicate definition. (python2-msgpack): Was defined twice, but differently,
  remove the obviously wrong second definition.

git: webkitgtk: Update to 2.14.1.

* gnu/packages/webkit.scm (webkitgtk): Update to 2.14.1.

gnu: linux-libre@4.1: Update to 4.1.34.

* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.34.

gnu: graphicsmagick: Update to 1.3.25-1-56c8cae [security fixes].

Fixes CVE-2016-7800, CVE-2016-7996, CVE-2016-7997, and several other flaws.

* gnu/packages/imagemagick.scm (graphicsmagick): Update to 1.3.25-1-56c8cae.
[source]: Change method from 'url-fetch' to 'hg-fetch'.  Add 'file-name'.

gnu: imagemagick: Disable tests.

* gnu/packages/imagemagick.scm (imagemagick)[arguments]: Disable tests.

gnu: imagemagick: Update to 6.9.6-2 [Fixes CVE-2016-{7799,7906}].

* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.6-2.

gnu: ghostscript-with-x: Avoid inheriting replacement field.

This is a followup to commit 1de17a648fa631f0074d315bfff0716220ce4880.

* gnu/packages/ghostscript.scm (ghostscript/fixed)[replacement]:
Override inherited value.

gnu: ghostscript: Fix CVE-2013-5653 and CVE-2016-{7976,7978,7979,8602}.

* gnu/packages/patches/ghostscript-CVE-2013-5653.patch,
gnu/packages/patches/ghostscript-CVE-2016-7976.patch,
gnu/packages/patches/ghostscript-CVE-2016-7978.patch,
gnu/packages/patches/ghostscript-CVE-2016-7979.patch,
gnu/packages/patches/ghostscript-CVE-2016-8602.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/ghostscript.scm (ghostscript)[replacement]: New field.
(ghostscript/fixed): New variable.
(ghostscript/x): Inherit 'ghostscript/fixed'.

doc: Add guide on how to specify dependencies for Python packages.

* doc/guix.texi (Python Modules): New sub-subsection "Specifying
Dependencies".

Co-authored-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add hdf4

* gnu/packages/maths.scm (hdf4, hdf4-alt): New variables.
* gnu/packages/patches/hdf4-reproducibility.patch: New file.
* gnu/packages/patches/hdf4-shared-fortran.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add patches.

Co-Authored-By: Jeremy Robst <jpro@bas.ac.uk>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

build: Make 'assert-no-store-file-names' effective.

Lack of '-E' made it useless.

* Makefile.am (assert-no-store-file-names): Pass '-E' to grep.  Add
'--exclude' and '--exclude-dir' flags.

build: Arrange so temporary .go files are deleted upon SIGINT.

* build-aux/compile-all.scm: Install SIGINT handler.

gnu: Add NFS related services.

* gnu/services/nfs.scm (pipefs-service-type): New variable,
(gss-service-type): New variable, (idmap-service-type) New variable.

* doc/guix.texi (Network File System): New node.

gnu: mcelog: Update to 142.

* gnu/packages/linux.scm (mcelog): Update to 142.

gnu: btrfs-progs: Update to 4.8.1.

* gnu/packages/linux.scm (btrfs-progs): Update to 4.8.1.

gnu: icecat: Update to 45.3.0-gnu1-beta. Add fixes from Firefox ESR 45.4.0.

Includes fixes for CVE-2016-5250, CVE-2016-5257, CVE-2016-5261, CVE-2016-5270,
CVE-2016-5272, CVE-2016-5274, CVE-2016-5276, CVE-2016-5277, CVE-2016-5278,
CVE-2016-5280, CVE-2016-5281, and CVE-2016-5284.

* gnu/packages/gnuzilla.scm (mozilla-patch): New procedure.
(icecat): Update to 45.3.0-gnu1.
[source]: Add alternate source URI for the beta release.  Update patches.
[inputs]: Replace 'sqlite' input with a customized sqlite with
SQLITE_ENABLE_DBSTAT_VTAB support.
[native-inputs]: Add 'which'.
* gnu/packages/patches/icecat-avoid-bundled-includes.patch: Rename to...
* gnu/packages/patches/icecat-avoid-bundled-libraries.patch: ... and adapt
to version 45.
* gnu/packages/patches/icecat-CVE-2016-2818-pt1.patch,
gnu/packages/patches/icecat-CVE-2016-2818-pt2.patch,
gnu/packages/patches/icecat-CVE-2016-2818-pt3.patch,
gnu/packages/patches/icecat-CVE-2016-2818-pt4.patch,
gnu/packages/patches/icecat-CVE-2016-2818-pt5.patch,
gnu/packages/patches/icecat-CVE-2016-2818-pt6.patch,
gnu/packages/patches/icecat-CVE-2016-2818-pt7.patch,
gnu/packages/patches/icecat-CVE-2016-2818-pt8.patch,
gnu/packages/patches/icecat-CVE-2016-2818-pt9.patch,
gnu/packages/patches/icecat-CVE-2016-2819.patch,
gnu/packages/patches/icecat-CVE-2016-2821.patch,
gnu/packages/patches/icecat-CVE-2016-2824.patch,
gnu/packages/patches/icecat-CVE-2016-2828.patch,
gnu/packages/patches/icecat-CVE-2016-2831.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Update accordingly.

gnu: redis: Update to 3.2.4.

* gnu/packages/databases.scm (redis): Update to 3.2.4.
[arguments]: Add LDFLAGS to #:make-flags to work around missing linker
flag.

gnu: newt: Update source and home-page URLs.

* gnu/packages/slang.scm (newt)[source]: Update URL.
[home-page]: Update URL.

gnu: vsearch: Update to 2.3.0.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.0.

gnu: diamond: Update to 0.8.23.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.23.

Update e-mail address for ng0.

* .mailmap: Update entries for ng0.

gnu: qemu: Patch CVE-2016-857{6,7,8}.

* gnu/packages/qemu.scm (qemu)[source]: Add patches.
* gnu/packages/patches/qemu-CVE-2016-8576.patch,
gnu/packages/patches/qemu-CVE-2016-8577.patch,
gnu/packages/patches/qemu-CVE-2016-8578.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register them.

gnu: Add infamous-plugins.

* gnu/packages/audio.scm (infamous-plugins): New variable.

grafts: Always make directories #o755.

Fixes <http://bugs.gnu.org/22954>.
Reported by Albin <albin@fripost.org>
and Jeffrey Serio <serio.jeffrey@gmail.com>.

* guix/build/graft.scm (mkdir-p*): New procedure.
(rewrite-directory): Use it instead of 'mkdir-p'.

bournish: Add 'reboot' command.

Suggested by Ricardo Wurmus.

* guix/build/bournish.scm (reboot-command): New procedure.
(%commands): Add it.

substitute: Make download messages more concise.

'guix substitute' now displays 2 lines per download instead of 4.
Suggested by Ricardo Wurmus.

* guix/scripts/substitute.scm (assert-valid-narinfo): Have #:verbose?
default to #f.  Remove leading newline in message.
(process-substitution): Display the URI rather than the store file name.
Display two newlines after the substitution.

gnu: font-un: Update source uri.

Fixes <http://bugs.gnu.org/22908>.

* gnu/packages/fonts.scm (font-un)[source]: Update source uri.

gnu: man-pages: Update to 4.08.

* gnu/packages/man.scm (man-pages): Update to 4.08.

gnu: cmocka: Update to 1.1.0.

* gnu/packages/check.scm (cmocka): Update to 1.1.0.

gnu: cppcheck: Update to 1.76.

* gnu/packages/check.scm (cppcheck): Update to 1.76.

gnu: libuninameslist: Use 'modify-phases' syntax.

* gnu/packages/fontutils.scm (libuninameslist)[arguments]: Use
'modify-phases' syntax.

gnu: libuninameslist: Update to 20160701.

* gnu/packages/fontutils.scm (libuninameslist): Update to 20160701.

gnu: bash-completion: Update to 2.4.

* gnu/packages/bash.scm (bash-completion): Update to 2.4.
[home-page]: Update to redirected home-page.

import: github: Add .love extension.

* guix/import/github.scm (find-extension): Add '.love' extension to the
list of extensions checked.

gnu: obs: Update to 0.16.2.

* gnu/packages/video.scm (obs): Update to 0.16.2.

gnu: laby: Update source uri.

* gnu/packages/games.scm (laby)[source]: Use the publicly visible
download uri.

gnu: Add gxtuner.

* gnu/packages/music.scm (gxtuner): New variable.

gnu: gnome: Add pinentry-gnome3 to gnome

* gnu/packages/gnome.scm (gnome)[propagated-inputs]: Add
pinentry-gnome3.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add pinentry-gnome3.

* gnu/packages/gnupg.scm (pinentry-gnome3): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: pinentry: Remove 'gpg2' from description.

* gnu/package/gnupg.scm (pinentry-tty, pinentry-gtk2, pinentry-qt)
[description]: The default in Guix is gpg, so only use this.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: sane-backends: Update to 1.0.25.

* gnu/packages/scanner.scm (sane-backends): Update to 1.0.25.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: wpa-supplicant: Update to 2.6.

* gnu/packages/admin.scm (wpa-supplicant-minimal)[source]: Update to
  2.6. Remove 'patches' field.
* gnu/packages/patches/wpa-supplicant-CVE-2015-5310.patch,
  gnu/packages/patches/wpa-supplicant-CVE-2015-5314.patch,
  gnu/packages/patches/wpa-supplicant-CVE-2015-5315.patch,
  gnu/packages/patches/wpa-supplicant-CVE-2015-5316.patch,
  gnu/packages/patches/wpa-supplicant-CVE-2016-4476.patch,
  gnu/packages/patches/wpa-supplicant-CVE-2016-4477-pt1.patch,
  gnu/packages/patches/wpa-supplicant-CVE-2016-4477-pt2.patch,
  gnu/packages/patches/wpa-supplicant-CVE-2016-4477-pt3.patch,
  gnu/packages/patches/wpa-supplicant-CVE-2016-4477-pt4.patch: Delete
  files.
* gnu/local.mk (dist_patch_DATA): Remove them.

Signed-off-by: Leo Famulari <leo@famulari.name>

gnu: guile-ssh: Update to 0.10.1.

* gnu/packages/ssh.scm (libssh-0.6): Remove.
(guile-ssh): Update to 0.10.1.
[inputs]: Use LIBSSH instead of LIBSSH-0.7.3.
[arguments]: Remove #:configure-flags.

gnu: guile-ssh: Compile .scm files after patching them.

Before this commit, the .go files were obtained by compiling the
unpatched .scm files, so they would refer to libguile-ssh without its
absolute file name.

* gnu/packages/ssh.scm (guile-ssh)[arguments]: Move
'fix-libguile-ssh-file-name' before 'build'.  Have it run "make install
-C libguile-ssh" first.

gnu: guile-ssh: Use 'modify-phases'.

* gnu/packages/ssh.scm (guile-ssh)[arguments]: Use 'modify-phases'.

gnu: gcj: Switch dejagnu test command.

* gnu/packages/gcc.scm (gcj)[arguments]: Switch the depreciated dejagnu
command 'absolute' for the new testing command 'file normalize'.

gnu: lynx: Update to 2.8.9dev.9 and fix GnuTLS support.

* gnu/packages/lynx.scm (lynx): Update to 2.8.9dev.9.
[arguments]: Append the path to the GnuTLS to "--with-gnutls=".

gnu: hexchat: Update to 2.12.2.

* gnu/packages/messaging.scm (hexchat): Update to 2.12.2.

gnu: vdirsyncer: Update to 0.13.1.

* gnu/packages/dav.scm (vdirsyncer): Update to 0.13.1.

gnu: libupnp: Fix CVE-2016-6255.

* gnu/packages/patches/libupnp-CVE-2016-6255.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/libupnp.scm (libupnp): Use it.

gnu: ardour: Update to 5.4.

* gnu/packages/audio.scm (ardour): Update to 5.4.
[inputs]: Add libarchive.

gnu: Add gtkwave.

* gnu/packages/fpga.scm (gtkwave): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add arachne-pnr.

* gnu/packages/fpga.scm (arachne-pnr): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add icestorm.

* gnu/packages/fpga.scm (icestorm): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add yosys.

* gnu/packages/fpga.scm (yosys): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add iverilog.

* gnu/packages/fpga.scm (iverilog): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add abc.

* gnu/packages/fpga.scm (abc): New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: guile-next: Increase timeout.

* gnu/packages/guile.scm (guile-next)[properties]: Set timeout to
20 hours.

gnu: Add newlib-nano-arm-none-eabi.

* gnu/packages/embedded.scm (newlib-nano-arm-none-eabi): New variable.