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Merge branch 'master' into core-updates

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Mark H Weaver 2018-04-30 04:03:54 -04:00
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105 changed files with 29149 additions and 23582 deletions
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5
Makefile.am
View file

@ -740,6 +740,7 @@ assert-no-store-file-names: $(distdir)/ChangeLog
$(AM_V_at)if grep -r --exclude=*.texi --exclude=*.info \
--exclude=*.info-[0-9] --exclude=*.dot \
--exclude=*.eps --exclude-dir=bootstrap \
--exclude=guix-manual.pot --exclude=guix-manual.*.po \
--exclude=guix-prettify.el \
--exclude=ChangeLog \
-E "$(storedir)/[a-z0-9]{32}-" $(distdir) ; \
@ -800,3 +801,7 @@ AM_V_HELP2MAN_0 = @echo " HELP2MAN" $@;
AM_V_PO4A = $(AM_V_PO4A_$(V))
AM_V_PO4A_ = $(AM_V_PO4A_$(AM_DEFAULT_VERBOSITY))
AM_V_PO4A_0 = @echo " PO4A" $@;
AM_V_POXREF = $(AM_V_POXREF_$(V))
AM_V_POXREF_ = $(AM_V_POXREF_$(AM_DEFAULT_VERBOSITY))
AM_V_POXREF_0 = @echo " POXREF" $@;

14
build-aux/test-env.in
View file

@ -1,7 +1,7 @@
#!/bin/sh
# GNU Guix --- Functional package management for GNU
# Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
# Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
#
# This file is part of GNU Guix.
#
@ -118,6 +118,18 @@ then
bootstrap_directory="@abs_top_builddir@/gnu/packages/bootstrap/@guix_system@"
if [ -d "$bootstrap_directory" ]
then
# Make sure 'guix-daemon' is listening before invoking 'guix
# download'.
"@abs_top_builddir@/pre-inst-env" "@GUILE@" -c \
'(use-modules (guix))
(let loop ((i 10))
(catch #t
(lambda () (open-connection))
(lambda (key . args)
(if (zero? i)
(apply throw key args)
(begin (usleep 500000) (loop (- i 1)))))))'
for file in "$bootstrap_directory"/guile-*
do
"@abs_top_builddir@/pre-inst-env" \

7
doc/contributing.texi
View file

@ -308,6 +308,13 @@ indent a whole file, omit the second argument:
./etc/indent-code.el gnu/services/@var{file}.scm
@end example
@cindex Vim, Scheme code editing
If you are editing code with Vim, we recommend that you run @code{:set
autoindent} so that your code is automatically indented as you type.
Additionally,
@uref{https://www.vim.org/scripts/script.php?script_id=3998,
@code{paredit.vim}} may help you deal with all these parentheses.
We require all top-level procedures to carry a docstring. This
requirement can be relaxed for simple private procedures in the
@code{(guix build @dots{})} name space, though.

67
doc/guix.texi
View file

@ -10694,6 +10694,51 @@ Return a service that runs @var{dhcp}, a Dynamic Host Configuration
Protocol (DHCP) client, on all the non-loopback network interfaces.
@end deffn
@deffn {Scheme Procedure} dhcpd-service-type
This type defines a service that runs a DHCP daemon. To create a
service of this type, you must supply a @code{<dhcpd-configuration>}.
For example:
@example
(service dhcpd-service-type
(dhcpd-configuration
(config-file (local-file "my-dhcpd.conf"))
(interfaces '("enp0s25"))))
@end example
@end deffn
@deftp {Data Type} dhcpd-configuration
@table @asis
@item @code{package} (default: @code{isc-dhcp})
The package that provides the DHCP daemon. This package is expected to
provide the daemon at @file{sbin/dhcpd} relative to its output
directory. The default package is the
@uref{http://www.isc.org/products/DHCP, ISC's DHCP server}.
@item @code{config-file} (default: @code{#f})
The configuration file to use. This is required. It will be passed to
@code{dhcpd} via its @code{-cf} option. This may be any ``file-like''
object (@pxref{G-Expressions, file-like objects}). See @code{man
dhcpd.conf} for details on the configuration file syntax.
@item @code{version} (default: @code{"4"})
The DHCP version to use. The ISC DHCP server supports the values ``4'',
``6'', and ``4o6''. These correspond to the @code{dhcpd} program
options @code{-4}, @code{-6}, and @code{-4o6}. See @code{man dhcpd} for
details.
@item @code{run-directory} (default: @code{"/run/dhcpd"})
The run directory to use. At service activation time, this directory
will be created if it does not exist.
@item @code{pid-file} (default: @code{"/run/dhcpd/dhcpd.pid"})
The PID file to use. This corresponds to the @code{-pf} option of
@code{dhcpd}. See @code{man dhcpd} for details.
@item @code{interfaces} (default: @code{'()})
The names of the network interfaces on which dhcpd should listen for
broadcasts. If this list is not empty, then its elements (which must be
strings) will be appended to the @code{dhcpd} invocation when starting
the daemon. It may not be necessary to explicitly specify any
interfaces here; see @code{man dhcpd} for details.
@end table
@end deftp
@defvr {Scheme Variable} static-networking-service-type
This is the type for statically-configured network interfaces.
@c TODO Document <static-networking> data structures.
@ -10728,6 +10773,28 @@ several commands to interact with the daemon and configure networking:
and @command{wicd-curses} user interfaces.
@end deffn
@cindex ModemManager
@defvr {Scheme Variable} modem-manager-service-type
This is the service type for the
@uref{https://wiki.gnome.org/Projects/ModemManager, ModemManager}
service. The value for this service type is a
@code{modem-manager-configuration} record.
This service is part of @code{%desktop-services} (@pxref{Desktop
Services}).
@end defvr
@deftp {Data Type} modem-manager-configuration
Data type representing the configuration of ModemManager.
@table @asis
@item @code{modem-manager} (default: @code{modem-manager})
The ModemManager package to use.
@end table
@end deftp
@cindex NetworkManager
@defvr {Scheme Variable} network-manager-service-type

12
doc/local.mk
View file

@ -1,6 +1,6 @@
# GNU Guix --- Functional package management for GNU
# Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
# Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
# Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
# Copyright © 2013 Andreas Enge <andreas@enge.fr>
# Copyright © 2016 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
# Copyright © 2016, 2018 Mathieu Lirzin <mthl@gnu.org>
@ -90,15 +90,15 @@ cat "$@.tmp" | egrep '@p?x?ref' -A1 | sed 'N;s|--\n||g;P;D' | sed 's|^| |g' | \
done
endef
$(srcdir)/%D%/guix.%.texi: po/doc/guix.%.po $(srcdir)/%D%/contributing.%.texi
$(srcdir)/%D%/guix.%.texi: po/doc/guix-manual.%.po $(srcdir)/%D%/contributing.%.texi
-$(AM_V_PO4A)$(PO4A_TRANSLATE) $(PO4A_PARAMS) -m "%D%/guix.texi" -p "$<" -l "$@.tmp"
-sed -i "s|guix\.info|$$(basename "$@" | sed 's|texi$$|info|')|" "$@.tmp"
-$(xref_command)
-$(AM_V_POXREF)$(xref_command)
-mv "$@.tmp" "$@"
$(srcdir)/%D%/contributing.%.texi: po/doc/guix.%.po po/doc/contributing.%.po
-$(AM_V_PO4A)$(PO4A_TRANSLATE) $(PO4A_PARAMS) -m "%D%/contributing.texi" -p "$(word 2,$^)" -l "$@.tmp"
-$(xref_command)
$(srcdir)/%D%/contributing.%.texi: po/doc/guix-manual.%.po
-$(AM_V_PO4A)$(PO4A_TRANSLATE) $(PO4A_PARAMS) -m "%D%/contributing.texi" -p "$<" -l "$@.tmp"
-$(AM_V_POXREF)$(xref_command)
-mv "$@.tmp" "$@"
%D%/os-config-%.texi: gnu/system/examples/%.tmpl

15
gnu/local.mk
View file

@ -575,7 +575,6 @@ dist_patch_DATA = \
%D%/packages/patches/azr3.patch \
%D%/packages/patches/bash-completion-directories.patch \
%D%/packages/patches/bazaar-CVE-2017-14176.patch \
%D%/packages/patches/bcftools-regidx-unsigned-char.patch \
%D%/packages/patches/binutils-loongson-workaround.patch \
%D%/packages/patches/blast+-fix-makefile.patch \
%D%/packages/patches/boost-fix-icu-build.patch \
@ -795,6 +794,7 @@ dist_patch_DATA = \
%D%/packages/patches/intltool-perl-compatibility.patch \
%D%/packages/patches/isl-0.11.1-aarch64-support.patch \
%D%/packages/patches/jacal-fix-texinfo.patch \
%D%/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch \
%D%/packages/patches/java-jeromq-fix-tests.patch \
%D%/packages/patches/java-powermock-fix-java-files.patch \
%D%/packages/patches/java-simple-xml-fix-tests.patch \
@ -976,7 +976,6 @@ dist_patch_DATA = \
%D%/packages/patches/patchelf-rework-for-arm.patch \
%D%/packages/patches/patchutils-xfail-gendiff-tests.patch \
%D%/packages/patches/patch-hurd-path-max.patch \
%D%/packages/patches/pcmanfm-CVE-2017-8934.patch \
%D%/packages/patches/perl-file-path-CVE-2017-6512.patch \
%D%/packages/patches/perl-autosplit-default-time.patch \
%D%/packages/patches/perl-dbd-mysql-CVE-2017-10788.patch \
@ -1012,9 +1011,8 @@ dist_patch_DATA = \
%D%/packages/patches/psm-arch.patch \
%D%/packages/patches/psm-ldflags.patch \
%D%/packages/patches/psm-repro.patch \
%D%/packages/patches/pt-scotch-build-parallelism.patch \
%D%/packages/patches/pulseaudio-glibc-2.27.patch \
%D%/packages/patches/pulseaudio-fix-mult-test.patch \
%D%/packages/patches/pulseaudio-glibc-2.27.patch \
%D%/packages/patches/pulseaudio-longer-test-timeout.patch \
%D%/packages/patches/pybugz-encode-error.patch \
%D%/packages/patches/pybugz-stty.patch \
@ -1057,13 +1055,11 @@ dist_patch_DATA = \
%D%/packages/patches/python-unittest2-python3-compat.patch \
%D%/packages/patches/python-unittest2-remove-argparse.patch \
%D%/packages/patches/python-waitress-fix-tests.patch \
%D%/packages/patches/qemu-CVE-2018-7550.patch \
%D%/packages/patches/qemu-glibc-2.27.patch \
%D%/packages/patches/qt4-ldflags.patch \
%D%/packages/patches/qtbase-use-TZDIR.patch \
%D%/packages/patches/qtscript-disable-tests.patch \
%D%/packages/patches/quagga-reproducible-build.patch \
%D%/packages/patches/quassel-fix-tls-check.patch \
%D%/packages/patches/quickswitch-fix-dmenu-check.patch \
%D%/packages/patches/rapicorn-isnan.patch \
%D%/packages/patches/raptor2-heap-overflow.patch \
@ -1087,6 +1083,9 @@ dist_patch_DATA = \
%D%/packages/patches/rxvt-unicode-escape-sequences.patch \
%D%/packages/patches/scheme48-tests.patch \
%D%/packages/patches/scotch-test-threading.patch \
%D%/packages/patches/scotch-build-parallelism.patch \
%D%/packages/patches/scotch-graph-diam-64.patch \
%D%/packages/patches/scotch-graph-induce-type-64.patch \
%D%/packages/patches/sdl-libx11-1.6.patch \
%D%/packages/patches/seq24-rename-mutex.patch \
%D%/packages/patches/shadow-CVE-2018-7169.patch \
@ -1191,9 +1190,7 @@ dist_patch_DATA = \
%D%/packages/patches/xinetd-CVE-2013-4342.patch \
%D%/packages/patches/xmodmap-asprintf.patch \
%D%/packages/patches/libyaml-CVE-2014-9130.patch \
%D%/packages/patches/zathura-plugindir-environment-variable.patch \
%D%/packages/patches/zsh-CVE-2018-7548.patch \
%D%/packages/patches/zsh-CVE-2018-7549.patch
%D%/packages/patches/zathura-plugindir-environment-variable.patch
MISC_DISTRO_FILES = \
%D%/packages/ld-wrapper.in

81
gnu/packages/admin.scm
View file

@ -18,7 +18,7 @@
;;; Copyright © 2017 Ben Sturmfels <ben@sturm.com.au>
;;; Copyright © 2017 Ethan R. Jones <doubleplusgood23@gmail.com>
;;; Copyright © 2017 Christopher Allan Webber <cwebber@dustycloud.org>
;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
;;;
@ -58,6 +58,8 @@ (define-module (gnu packages admin)
#:use-module (gnu packages lua)
#:use-module (gnu packages guile)
#:use-module (gnu packages gettext)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages inkscape)
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages perl-check)
@ -76,6 +78,7 @@ (define-module (gnu packages admin)
#:use-module (gnu packages python)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages qt)
#:use-module (gnu packages terminals)
#:use-module (gnu packages texinfo)
#:use-module (gnu packages groff)
@ -242,16 +245,16 @@ (define-public daemontools
(define-public dfc
(package
(name "dfc")
(version "3.0.4")
(version "3.1.1")
(source
(origin
(method url-fetch)
(uri (string-append
"http://projects.gw-computing.net/attachments/download/79/dfc-"
"http://projects.gw-computing.net/attachments/download/615/dfc-"
version ".tar.gz"))
(sha256
(base32
"0zk1ppx93ijimf4sbgqilxxikpsa2gmpbynknyh41xy7jbdjxp0b"))))
"0m1fd7l85ckb7bq4c5c3g257bkjglm8gq7x42pkmpp87fkknc94n"))))
(build-system cmake-build-system)
(arguments '(#:tests? #f)) ; There are no tests.
(native-inputs `(("gettext" ,gettext-minimal)))
@ -1142,6 +1145,51 @@ (define-public wpa-supplicant
(string-append dir "/wpa_supplicant.conf")))
#t))))))))
(define-public wpa-supplicant-gui
(package
(inherit wpa-supplicant)
(name "wpa-supplicant-gui")
(inputs `(("qtbase" ,qtbase)
("qtsvg" ,qtsvg)
,@(package-inputs wpa-supplicant)))
(native-inputs
;; For icons.
`(("imagemagick" ,imagemagick)
("inkscape" ,inkscape)
,@(package-native-inputs wpa-supplicant)))
(arguments
`(#:phases (modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "wpa_supplicant/wpa_gui-qt4")
#t))
(delete 'configure)
(replace 'build
(lambda _
(invoke "qmake" "wpa_gui.pro")
(invoke "make" "-j" (number->string (parallel-job-count)))
(invoke "make" "-C" "icons")))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(qt '("qtbase" "qtsvg")))
(substitute* "wpa_gui.desktop"
(("Exec=wpa_gui")
(string-append "Exec=" out "/bin/wpa_gui")))
(install-file "wpa_gui" (string-append out "/bin"))
(install-file "wpa_gui.desktop"
(string-append out "/share/applications"))
(copy-recursively "icons/hicolor"
(string-append out "/share/icons/hicolor"))
(wrap-program (string-append out "/bin/wpa_gui")
`("QT_PLUGIN_PATH" ":" prefix
,(map (lambda (label)
(string-append (assoc-ref inputs label)
"/lib/qt5/plugins/"))
qt)))
#t))))))
(synopsis "Graphical user interface for WPA supplicant")))
(define-public wakelan
(package
(name "wakelan")
@ -1534,7 +1582,9 @@ (define-public ansible
(patches (search-patches "ansible-wrap-program-hack.patch"))))
(build-system python-build-system)
(native-inputs
`(("python2-pycrypto" ,python2-pycrypto)
`(("python2-bcrypt" ,python2-bcrypt)
("python2-pycrypto" ,python2-pycrypto)
("python2-pynacl" ,python2-pynacl)
("python2-httplib2" ,python2-httplib2)
("python2-passlib" ,python2-passlib)
("python2-nose" ,python2-nose)
@ -1899,7 +1949,7 @@ (define-public dstat
(define-public thefuck
(package
(name "thefuck")
(version "3.25")
(version "3.26")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/nvbn/thefuck/archive/"
@ -1907,7 +1957,7 @@ (define-public thefuck
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"088bn2l1376qlndbpnjya4q1x3913nj3yj3wc7s2w3bz66d23skk"))
"0ddlf25ik97z34bcpc52xyfhlfm6a3hdi43l6cz4ggwcawdwvn1p"))
(patches (search-patches "thefuck-test-environ.patch"))))
(build-system python-build-system)
(arguments
@ -1920,7 +1970,8 @@ (define-public thefuck
(add-installed-pythonpath inputs outputs)
;; Some tests need write access to $HOME.
(setenv "HOME" "/tmp")
(zero? (system* "py.test" "-v")))))))
(invoke "py.test" "-v")
#t)))))
(propagated-inputs
`(("python-colorama" ,python-colorama)
("python-decorator" ,python-decorator)
@ -2294,21 +2345,23 @@ (define-public intel-gpu-tools
(define-public fabric
(package
(name "fabric")
(version "1.13.2")
(version "1.14.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Fabric" version))
(sha256
(base32
"0k944dxr41whw7ib6380q9x15wyskx7fqni656icdn8rzshn9bwq"))))
"13r0b0hllgf8j9rh6x1knmbgvingbdmx046aazv6vck2ll120mw1"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2)) ; Python 2 only
(native-inputs
`(("python2-fudge" ,python2-fudge)
("python2-jinja2" ,python2-jinja2)
("python2-nose" ,python2-nose)))
("python2-nose" ,python2-nose)
("python2-pynacl" ,python2-pynacl)
("python2-bcrypt" ,python2-bcrypt)))
(propagated-inputs
`(("python2-paramiko" ,python2-paramiko)))
(home-page "http://fabfile.org")
@ -2375,7 +2428,7 @@ (define-public neofetch
(define-public nnn
(package
(name "nnn")
(version "1.5")
(version "1.7")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/jarun/nnn/"
@ -2383,7 +2436,7 @@ (define-public nnn
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0zswf8lb29zr1z642i1d0zi1y2mxal8qjqdrpdiqjh197jamj3zm"))))
"0z3lqbfx3y1caxvn7yq90b7whwyq2y32zf8kyd976ilbxpxnxqpv"))))
(build-system gnu-build-system)
(inputs `(("ncurses" ,ncurses)
("readline" ,readline)))
@ -2606,4 +2659,6 @@ (define-public spindle
"Spindle is a tool for improving the performance of dynamic library and
Python loading in HPC environments.")
(home-page "https://github.com/hpc/Spindle")
;; This package supports x86_64 and PowerPC64
(supported-systems '("x86_64-linux"))
(license license:lgpl2.1)))

4
gnu/packages/android.scm
View file

@ -341,7 +341,7 @@ (define-public mkbootimg
(define-public android-udev-rules
(package
(name "android-udev-rules")
(version "20171113")
(version "20180112")
(source
(origin
(method git-fetch)
@ -350,7 +350,7 @@ (define-public android-udev-rules
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32 "11gcnk6wjc2sw05hwi4xphvx9ksmkpvsdziaczymqxkaads3f1dy"))))
(base32 "13gj79nnd04szqlrrzzkdr6wi1fky08pi7x8xfbg0jj3d3v0giah"))))
(build-system trivial-build-system)
(native-inputs `(("source" ,source)))
(arguments

15
gnu/packages/audio.scm
View file

@ -285,14 +285,15 @@ (define-public ardour
(define-public audacity
(package
(name "audacity")
(version "2.2.1")
(version "2.2.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/audacity/audacity/archive"
"/Audacity-" version ".tar.gz"))
(sha256
(base32 "1n05r8b4rnf9fas0py0is8cm97s3h65dgvqkk040aym5d1x6wd7z"))
(base32
"18q7i77ynihx7xp45lz2lv0k0wrh6736pcrivlpwrxjgbvyqx7km"))
(patches (search-patches "audacity-build-with-system-portaudio.patch"))
(modules '((guix build utils)))
(snippet
@ -555,7 +556,7 @@ (define-public espeak
(define-public infamous-plugins
(package
(name "infamous-plugins")
(version "0.2.02")
(version "0.2.04")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/ssj71/infamousPlugins/"
@ -563,10 +564,10 @@ (define-public infamous-plugins
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0qm3ak07vc1l3f5c3c2lq9gkfknlxwn8ks03cysw1pk8hj7dwnv6"))))
"1n6rhqsmvad7692w2h01niw5gqg5yk7a09wxl5ivs77zyp93vf7z"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; There are no tests
`(#:tests? #f ; there are no tests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'remove-compiler-flags
@ -581,7 +582,7 @@ (define-public infamous-plugins
"src/powercut/CMakeLists.txt"
"src/powerup/CMakeLists.txt"
"src/stuck/CMakeLists.txt")
(("-msse2 -mfpmath=sse") ""))
(("-msse2 -mfpmath=sse") ""))
#t)))))
(inputs
`(("cairo" ,cairo)
@ -591,7 +592,7 @@ (define-public infamous-plugins
("zita-resampler" ,zita-resampler)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://ssj71.github.io/infamousPlugins")
(home-page "https://ssj71.github.io/infamousPlugins")
(synopsis "LV2 plugins for live use")
(description
"The infamous plugins are a collection of LV2 audio plugins for live

9
gnu/packages/benchmark.scm
View file

@ -34,7 +34,7 @@ (define-module (gnu packages benchmark)
(define-public fio
(package
(name "fio")
(version "3.5")
(version "3.6")
(source (origin
(method url-fetch)
(uri (string-append
@ -42,7 +42,7 @@ (define-public fio
"fio-" version ".tar.bz2"))
(sha256
(base32
"1rrzcrn07db4pffvi2q0d0k884bwcapx6r1rfv4yx9066snvx240"))))
"1d2jibp1b2dq97f22wj6pcjl7gbd2kmhfggj2c7q3j8v9axjqsh2"))))
(build-system gnu-build-system)
(arguments
'(#:test-target "test"
@ -67,8 +67,9 @@ (define-public fio
;; The configure script doesn't understand some of the
;; GNU options, so we can't use #:configure-flags.
(let ((out (assoc-ref outputs "out")))
(zero? (system* "./configure"
(string-append "--prefix=" out))))))
(invoke "./configure"
(string-append "--prefix=" out))
#t)))
;; The main `fio` executable is fairly small and self contained.
;; Moving the auxiliary python and gnuplot scripts to a separate
;; output saves almost 400 MiB on the closure.

259
gnu/packages/bioconductor.scm
View file

@ -23,6 +23,8 @@ (define-module (gnu packages bioconductor)
#:use-module (guix download)
#:use-module (guix build-system r)
#:use-module (gnu packages)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
#:use-module (gnu packages statistics)
#:use-module (gnu packages bioinformatics))
@ -70,3 +72,260 @@ (define-public r-regioner
customizable permutation tests to assess the association between genomic
region sets and other genomic features.")
(license license:artistic2.0)))
(define-public r-diffbind
(package
(name "r-diffbind")
(version "2.6.6")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
"1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-amap" ,r-amap)
("r-biocparallel" ,r-biocparallel)
("r-deseq2" ,r-deseq2)
("r-dplyr" ,r-dplyr)
("r-edger" ,r-edger)
("r-genomicalignments" ,r-genomicalignments)
("r-ggrepel" ,r-ggrepel)
("r-gplots" ,r-gplots)
("r-iranges" ,r-iranges)
("r-lattice" ,r-lattice)
("r-limma" ,r-limma)
("r-locfit" ,r-locfit)
("r-rcolorbrewer" , r-rcolorbrewer)
("r-rcpp" ,r-rcpp)
("r-rsamtools" ,r-rsamtools)
("r-s4vectors" ,r-s4vectors)
("r-systempiper" ,r-systempiper)
("r-zlibbioc" ,r-zlibbioc)))
(home-page "http://bioconductor.org/packages/DiffBind")
(synopsis "Differential binding analysis of ChIP-Seq peak data")
(description
"This package computes differentially bound sites from multiple
ChIP-seq experiments using affinity (quantitative) data. Also enables
occupancy (overlap) analysis and plotting functions.")
(license license:artistic2.0)))
(define-public r-ripseeker
(package
(name "r-ripseeker")
(version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RIPSeeker" version))
(sha256
(base32
"0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y"))))
(properties `((upstream-name . "RIPSeeker")))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-genomicranges" ,r-genomicranges)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-rsamtools" ,r-rsamtools)
("r-genomicalignments" ,r-genomicalignments)
("r-rtracklayer" ,r-rtracklayer)))
(home-page "http://bioconductor.org/packages/RIPSeeker")
(synopsis
"Identifying protein-associated transcripts from RIP-seq experiments")
(description
"This package infers and discriminates RIP peaks from RIP-seq alignments
using two-state HMM with negative binomial emission probability. While
RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
a suite of bioinformatics tools integrated within this self-contained software
package comprehensively addressing issues ranging from post-alignments
processing to visualization and annotation.")
(license license:gpl2)))
(define-public r-multtest
(package
(name "r-multtest")
(version "2.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "multtest" version))
(sha256
(base32
"0n11rd49xl2vn3ldmfips7d3yb70l8npjcqsxyswr9ypjhgzkv9j"))))
(build-system r-build-system)
(propagated-inputs
`(("r-survival" ,r-survival)
("r-biocgenerics" ,r-biocgenerics)
("r-biobase" ,r-biobase)
("r-mass" ,r-mass)))
(home-page "http://bioconductor.org/packages/multtest")
(synopsis "Resampling-based multiple hypothesis testing")
(description
"This package can do non-parametric bootstrap and permutation
resampling-based multiple testing procedures (including empirical Bayes
methods) for controlling the family-wise error rate (FWER), generalized
family-wise error rate (gFWER), tail probability of the proportion of
false positives (TPPFP), and false discovery rate (FDR). Several choices
of bootstrap-based null distribution are implemented (centered, centered
and scaled, quantile-transformed). Single-step and step-wise methods are
available. Tests based on a variety of T- and F-statistics (including
T-statistics based on regression parameters from linear and survival models
as well as those based on correlation parameters) are included. When probing
hypotheses with T-statistics, users may also select a potentially faster null
distribution which is multivariate normal with mean zero and variance
covariance matrix derived from the vector influence function. Results are
reported in terms of adjusted P-values, confidence regions and test statistic
cutoffs. The procedures are directly applicable to identifying differentially
expressed genes in DNA microarray experiments.")
(license license:lgpl3)))
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
(version "3.12.7")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
"1zab489d7a6bh6ylc68x6yn47gdkmr7p3677grx9l2qafrryjr04"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-go-db" ,r-go-db)
("r-biomart" ,r-biomart)
("r-bsgenome" ,r-bsgenome)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomeinfodb" ,r-genomeinfodb)
("r-matrixstats" ,r-matrixstats)
("r-annotationdbi" ,r-annotationdbi)
("r-limma" ,r-limma)
("r-multtest" ,r-multtest)
("r-rbgl" ,r-rbgl)
("r-graph" ,r-graph)
("r-biocinstaller" ,r-biocinstaller)
("r-regioner" ,r-regioner)
("r-dbi" ,r-dbi)
("r-ensembldb" ,r-ensembldb)
("r-biobase" ,r-biobase)
("r-seqinr" ,r-seqinr)
("r-idr" ,r-idr)
("r-genomicalignments" ,r-genomicalignments)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-rsamtools" ,r-rsamtools)
("r-venndiagram" ,r-venndiagram)))
(home-page "http://bioconductor.org/packages/ChIPpeakAnno")
(synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
(description
"The package includes functions to retrieve the sequences around the peak,
obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
custom features such as most conserved elements and other transcription factor
binding sites supplied by users. Starting 2.0.5, new functions have been added
for finding the peaks with bi-directional promoters with summary statistics
(peaksNearBDP), for summarizing the occurrence of motifs in peaks
(summarizePatternInPeaks) and for adding other IDs to annotated peaks or
enrichedGO (addGeneIDs).")
(license license:gpl2+)))
(define-public r-marray
(package
(name "r-marray")
(version "1.56.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "marray" version))
(sha256
(base32 "14c93i86yc7jn4ax8p4l0z6v9xisw1bv7gzb4a0gbxhxn7mddaic"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-limma" ,r-limma)))
(home-page "http://bioconductor.org/packages/marray")
(synopsis "Exploratory analysis for two-color spotted microarray data")
(description "This package contains class definitions for two-color spotted
microarray data. It also includes fuctions for data input, diagnostic plots,
normalization and quality checking.")
(license license:lgpl2.0+)))
(define-public r-cghbase
(package
(name "r-cghbase")
(version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHbase" version))
(sha256
(base32 "0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm"))))
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-marray" ,r-marray)))
(home-page "http://bioconductor.org/packages/CGHbase")
(synopsis "Base functions and classes for arrayCGH data analysis")
(description "This package contains functions and classes that are needed by
the @code{arrayCGH} packages.")
(license license:gpl2+)))
(define-public r-cghcall
(package
(name "r-cghcall")
(version "2.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHcall" version))
(sha256
(base32 "11pi6awz3858yb4s0z3qf3kcmsdgp6d4aj41g4lfix1sv5amllch"))))
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-cghbase" ,r-cghbase)
("r-impute" ,r-impute)
("r-dnacopy" ,r-dnacopy)
("r-snowfall" ,r-snowfall)))
(home-page "http://bioconductor.org/packages/CGHcall")
(synopsis "Base functions and classes for arrayCGH data analysis")
(description "This package contains functions and classes that are needed by
@code{arrayCGH} packages.")
(license license:gpl2+)))
(define-public r-qdnaseq
(package
(name "r-qdnaseq")
(version "1.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QDNAseq" version))
(sha256
(base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy"))))
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-cghbase" ,r-cghbase)
("r-cghcall" ,r-cghcall)
("r-dnacopy" ,r-dnacopy)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-matrixstats" ,r-matrixstats)
("r-r-utils" ,r-r-utils)
("r-rsamtools" ,r-rsamtools)))
(home-page "http://bioconductor.org/packages/QDNAseq")
(synopsis "Quantitative DNA sequencing for chromosomal aberrations")
(description "The genome is divided into non-overlapping fixed-sized bins,
number of sequence reads in each counted, adjusted with a simultaneous
two-dimensional loess correction for sequence mappability and GC content, and
filtered to remove spurious regions in the genome. Downstream steps of
segmentation and calling are also implemented via packages DNAcopy and CGHcall,
respectively.")
(license license:gpl2+)))

102
gnu/packages/bioinformatics.scm
View file

@ -252,7 +252,7 @@ (define-public bamm
(define-public bamtools
(package
(name "bamtools")
(version "2.4.1")
(version "2.5.1")
(source (origin
(method url-fetch)
(uri (string-append
@ -261,7 +261,7 @@ (define-public bamtools
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk"))))
"1z3kg24qrwq13a88n9d86izngrar4fll7gr6phddb2faw75pdgaa"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;no "check" target
@ -285,7 +285,7 @@ (define-public bamtools
(define-public bcftools
(package
(name "bcftools")
(version "1.5")
(version "1.8")
(source (origin
(method url-fetch)
(uri (string-append
@ -293,12 +293,11 @@ (define-public bcftools
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
"0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
(patches (search-patches "bcftools-regidx-unsigned-char.patch"))
"1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
(delete-file-recursively "htslib-1.5")
(delete-file-recursively "htslib-1.8")
#t))))
(build-system gnu-build-system)
(arguments
@ -339,7 +338,7 @@ (define-public bcftools
(define-public bedops
(package
(name "bedops")
(version "2.4.14")
(version "2.4.33")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/bedops/bedops/archive/v"
@ -347,7 +346,7 @@ (define-public bedops
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
"0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
@ -2089,7 +2088,7 @@ (define-public delly
(define-public diamond
(package
(name "diamond")
(version "0.9.19")
(version "0.9.21")
(source (origin
(method url-fetch)
(uri (string-append
@ -2098,7 +2097,7 @@ (define-public diamond
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0c4y8l90vdxmglb0w37y0413v11qzcwg8sdmy9k0c0gr3bsq7dzs"))))
"1cf98vcsiwcv3c4apg50w1240v1mpw0zln1sdw3g692dqa4y041z"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
@ -2349,7 +2348,8 @@ (define-public express
(string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
(substitute* "src/CMakeLists.txt"
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
(string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
(string-append (assoc-ref inputs "bamtools") "/lib"))
(("libprotobuf.a") "libprotobuf.so"))
#t)))))
(inputs
`(("boost" ,boost)
@ -3462,7 +3462,7 @@ (define-public fastqc
(define-public htslib
(package
(name "htslib")
(version "1.7")
(version "1.8")
(source (origin
(method url-fetch)
(uri (string-append
@ -3470,7 +3470,7 @@ (define-public htslib
version "/htslib-" version ".tar.bz2"))
(sha256
(base32
"1il6i2p84b0y9c93dhvzzki1ifw9bvapm2mvpr0xvb2nq8jlwgdy"))))
"18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0"))))
(build-system gnu-build-system)
(inputs
`(("openssl" ,openssl)
@ -4587,7 +4587,7 @@ (define-public prodigal
(define-public roary
(package
(name "roary")
(version "3.11.0")
(version "3.12.0")
(source
(origin
(method url-fetch)
@ -4596,7 +4596,7 @@ (define-public roary
version ".tar.gz"))
(sha256
(base32
"10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i"))))
"0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff"))))
(build-system perl-build-system)
(arguments
`(#:phases
@ -4934,7 +4934,7 @@ (define-public seek
(define-public samtools
(package
(name "samtools")
(version "1.7")
(version "1.8")
(source
(origin
(method url-fetch)
@ -4943,7 +4943,7 @@ (define-public samtools
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
"18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77"))))
"05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((ice-9 ftw)
@ -5784,7 +5784,7 @@ (define-public sortmerna
(define-public star
(package
(name "star")
(version "2.5.3a")
(version "2.6.0a")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/alexdobin/STAR/archive/"
@ -5792,7 +5792,7 @@ (define-public star
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a"))
"0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56"))
(modules '((guix build utils)))
(snippet
'(begin
@ -5979,13 +5979,13 @@ (define-public stringtie
(define-public taxtastic
(package
(name "taxtastic")
(version "0.6.4")
(version "0.8.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "taxtastic" version))
(sha256
(base32
"0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929"))))
"03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
@ -6098,19 +6098,20 @@ (define-public r-centipede
(define-public r-vegan
(package
(name "r-vegan")
(version "2.4-6")
(version "2.5-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "vegan" version))
(sha256
(base32
"175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w"))))
"0pynr02d1xngda6c3va8fc4nxpgfkawhzcnz1ws4dnarp9b1w90r"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(propagated-inputs
`(("r-cluster" ,r-cluster)
("r-knitr" ,r-knitr)
("r-lattice" ,r-lattice)
("r-mass" ,r-mass)
("r-mgcv" ,r-mgcv)
@ -6266,14 +6267,14 @@ (define-public r-deseq2
(define-public r-dexseq
(package
(name "r-dexseq")
(version "1.24.3")
(version "1.24.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
"0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084"))))
"1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
@ -6619,7 +6620,7 @@ (define-public r-sparql
(define-public vsearch
(package
(name "vsearch")
(version "2.7.1")
(version "2.8.0")
(source
(origin
(method url-fetch)
@ -6629,7 +6630,7 @@ (define-public vsearch
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0jlzfgh79fzmb4g7sngzdjjsjyc37icvs1k7vmc2ksxglj6x5i7f"))
"15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3"))
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet
'(begin
@ -7604,13 +7605,13 @@ (define-public r-summarizedexperiment
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
(version "1.14.1")
(version "1.14.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
"033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39"))))
"1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
@ -9077,14 +9078,14 @@ (define-public filevercmp
(define-public multiqc
(package
(name "multiqc")
(version "1.4")
(version "1.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "multiqc" version))
(sha256
(base32
"0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8"))))
"02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy"))))
(build-system python-build-system)
(propagated-inputs
`(("python-jinja2" ,python-jinja2)
@ -9652,13 +9653,13 @@ (define-public r-msnid
(define-public r-seurat
(package
(name "r-seurat")
(version "2.2.1")
(version "2.3.0")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
"1sr82nf38hq07avrfn8vlrzjq7dfm4pcr8l1nh6mnglcql2bk9z2"))
"0kp3lw1s896zkjd6x2wp8qcg7wnm5b40g8vihps13f1m7j4nx7r0"))
;; Delete pre-built jar.
(snippet
'(begin (delete-file "inst/java/ModularityOptimizer.jar")
@ -9688,11 +9689,15 @@ (define-public r-seurat
(propagated-inputs
`(("r-ape" ,r-ape)
("r-caret" ,r-caret)
("r-cluster" ,r-cluster)
("r-cowplot" ,r-cowplot)
("r-diffusionmap" ,r-diffusionmap)
("r-dosnow" ,r-dosnow)
("r-dplyr" ,r-dplyr)
("r-dtw" ,r-dtw)
("r-fitdistrplus" ,r-fitdistrplus)
("r-fnn" ,r-fnn)
("r-foreach" ,r-foreach)
("r-fpc" ,r-fpc)
("r-gdata" ,r-gdata)
("r-ggplot2" ,r-ggplot2)
@ -9704,13 +9709,16 @@ (define-public r-seurat
("r-igraph" ,r-igraph)
("r-irlba" ,r-irlba)
("r-lars" ,r-lars)
("r-lmtest" ,r-lmtest)
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
("r-metap" ,r-metap)
("r-mixtools" ,r-mixtools)
("r-pbapply" ,r-pbapply)
("r-plotly" ,r-plotly)
("r-png" ,r-png)
("r-ranger" ,r-ranger)
("r-rann" ,r-rann)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rcpp" ,r-rcpp)
("r-rcppeigen" ,r-rcppeigen)
@ -10185,14 +10193,14 @@ (define-public r-biovizbase
(define-public r-ggbio
(package
(name "r-ggbio")
(version "1.26.0")
(version "1.26.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggbio" version))
(sha256
(base32
"1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9"))))
"1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@ -10237,14 +10245,14 @@ (define-public r-ggbio
(define-public r-gprofiler
(package
(name "r-gprofiler")
(version "0.6.4")
(version "0.6.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "gProfileR" version))
(sha256
(base32
"1cka02zbz1rbppm782qpxk1xn9qxbrv2gp5rgf970j906hxm2y0b"))))
"1n6cj12j102b4x9vhyl4dljp1i0r43p23cnhqbx4als2xfxdlqgi"))))
(properties `((upstream-name . "gProfileR")))
(build-system r-build-system)
(propagated-inputs
@ -10355,14 +10363,14 @@ (define-public r-homo-sapiens
(define-public r-erma
(package
(name "r-erma")
(version "0.10.0")
(version "0.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "erma" version))
(sha256
(base32
"0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g"))))
"1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@ -10391,14 +10399,14 @@ (define-public r-erma
(define-public r-ldblock
(package
(name "r-ldblock")
(version "1.8.0")
(version "1.8.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ldblock" version))
(sha256
(base32
"18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba"))))
"1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-erma" ,r-erma)
@ -10608,13 +10616,13 @@ (define-public r-fithic
(define-public r-hitc
(package
(name "r-hitc")
(version "1.22.0")
(version "1.22.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "HiTC" version))
(sha256
(base32
"0288xa1jy6nzvz2ha07csmp6dirjw5r7p9vy69q2wsbyzr02ymkp"))))
"0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl"))))
(properties `((upstream-name . "HiTC")))
(build-system r-build-system)
(propagated-inputs
@ -10856,14 +10864,14 @@ (define-public r-scater
(define-public r-scran
(package
(name "r-scran")
(version "1.6.8")
(version "1.6.9")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
"07wniyrh2fhhkz28v0bfgpvpi1hkkn2cvhacrvvvck142j79944x"))))
"0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
@ -12826,7 +12834,7 @@ (define-public pigx-rnaseq
(define-public pigx-chipseq
(package
(name "pigx-chipseq")
(version "0.0.10")
(version "0.0.15")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
@ -12834,7 +12842,7 @@ (define-public pigx-chipseq
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
"13w99bkr0w4j28ms0yzpl1x6fkpdqay0vh495q3x20bcilsjwnf1"))))
"11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; parts of the tests rely on access to the network

2
gnu/packages/bittorrent.scm
View file

@ -315,8 +315,6 @@ (define-public uget
(base32
"0919cf7lfk1djdl003cahqjvafdliv7v2l8r5wg95n4isqggdk75"))))
(build-system gnu-build-system)
(native-inputs
`(("intltool" ,intltool)))
(inputs
`(("curl" ,curl)
("gtk+" ,gtk+)

25
gnu/packages/bootloaders.scm
View file

@ -72,23 +72,6 @@ (define unifont
(base32
"0p2vhnc18cnbmb39vq4m7hzv4mhnm2l0a2s7gx3ar277fwng3hys"))))
;; The GRUB test suite fails with later versions of Qemu, so we
;; keep it at 2.10 for now. See
;; <https://lists.gnu.org/archive/html/bug-grub/2018-02/msg00004.html>.
;; TODO: When grub no longer needs this version, move to gnu/packages/debug.scm.
(define qemu-minimal-2.10
(package
(inherit qemu-minimal)
(version "2.10.2")
(source (origin
(method url-fetch)
(uri (string-append "https://download.qemu.org/qemu-"
version ".tar.xz"))
(sha256
(base32
"17w21spvaxaidi2am5lpsln8yjpyp2zi3s3gc6nsxj5arlgamzgw"))
(patches (search-patches "qemu-glibc-2.27.patch"))))))
(define-public grub
(package
(name "grub")
@ -425,7 +408,7 @@ (define (make-u-boot-package board triplet)
(libexec (string-append out "/libexec"))
(uboot-files (append
(find-files "." ".*\\.(bin|efi|img|spl|itb|dtb)$")
(find-files "." "^MLO$"))))
(find-files "." "^(MLO|SPL)$"))))
(mkdir-p libexec)
(install-file ".config" libexec)
(for-each
@ -480,6 +463,12 @@ (define-public u-boot-a20-olinuxino-micro
(define-public u-boot-nintendo-nes-classic-edition
(make-u-boot-package "Nintendo_NES_Classic_Edition" "arm-linux-gnueabihf"))
(define-public u-boot-wandboard
(make-u-boot-package "wandboard" "arm-linux-gnueabihf"))
(define-public u-boot-mx6cuboxi
(make-u-boot-package "mx6cuboxi" "arm-linux-gnueabihf"))
(define-public vboot-utils
(package
(name "vboot-utils")

2
gnu/packages/cdrom.scm
View file

@ -394,7 +394,7 @@ (define-public dvdstyler
("fontconfig" ,fontconfig)
("libexif" ,libexif)
("libjpeg" ,libjpeg)
("ffmpeg" ,ffmpeg)))
("ffmpeg" ,ffmpeg-3.4)))
(native-inputs
`(("pkg-config" ,pkg-config)
("flex" ,flex)

8
gnu/packages/commencement.scm
View file

@ -1024,6 +1024,9 @@ (define (make-gcc-toolchain gcc)
(union-build (assoc-ref %outputs "debug")
(list (assoc-ref %build-inputs
"libc-debug")))
(union-build (assoc-ref %outputs "static")
(list (assoc-ref %build-inputs
"libc-static")))
#t))))
(native-search-paths (package-native-search-paths gcc))
@ -1036,7 +1039,7 @@ (define (make-gcc-toolchain gcc)
be installed in user profiles. This includes GCC, as well as libc (headers
and binaries, plus debugging symbols in the 'debug' output), and Binutils.")
(home-page "https://gcc.gnu.org/")
(outputs '("out" "debug"))
(outputs '("out" "debug" "static"))
;; The main raison d'être of this "meta-package" is (1) to conveniently
;; install everything that we need, and (2) to make sure ld-wrapper comes
@ -1045,7 +1048,8 @@ (define (make-gcc-toolchain gcc)
("ld-wrapper" ,(car (assoc-ref %final-inputs "ld-wrapper")))
("binutils" ,binutils-final)
("libc" ,glibc-final)
("libc-debug" ,glibc-final "debug")))))
("libc-debug" ,glibc-final "debug")
("libc-static" ,glibc-final "static")))))
(define-public gcc-toolchain-4.8
(make-gcc-toolchain gcc-4.8))

353
gnu/packages/cran.scm
View file

@ -35,6 +35,7 @@ (define-module (gnu packages cran)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages statistics)
#:use-module (gnu packages web))
@ -113,16 +114,18 @@ (define-public r-rvest
(define-public r-selectr
(package
(name "r-selectr")
(version "0.3-2")
(version "0.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "selectr" version))
(sha256
(base32
"0kdrj64rqg4z6hg92y9r2h602a2i73r5rnlpg23ys33d5d32n8jy"))))
"1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b"))))
(build-system r-build-system)
(propagated-inputs `(("r-stringr" ,r-stringr)))
(propagated-inputs
`(("r-stringr" ,r-stringr)
("r-r6" ,r-r6)))
(home-page "https://sjp.co.nz/projects/selectr/")
(synopsis "Translate CSS selectors to XPath expressions")
(description
@ -190,14 +193,14 @@ (define-public r-callr
(define-public r-readxl
(package
(name "r-readxl")
(version "1.0.0")
(version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "readxl" version))
(sha256
(base32
"1bf7gxw9r11m4llyymplxiaa4gzgyj4bwmwad5in756pzq3jzmpv"))))
"05ii8knrg4jji6h7bv6bfpn279b6x52yrskdx5rv7b0hcpy22gdn"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cellranger" ,r-cellranger)
@ -404,14 +407,14 @@ (define-public r-pastecs
(define-public r-plogr
(package
(name "r-plogr")
(version "0.1-1")
(version "0.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "plogr" version))
(sha256
(base32
"13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92"))))
"0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
(build-system r-build-system)
(home-page "https://github.com/krlmlr/plogr")
(synopsis "R bindings for the plog C++ logging library")
@ -424,13 +427,13 @@ (define-public r-plogr
(define-public r-rcpp
(package
(name "r-rcpp")
(version "0.12.15")
(version "0.12.16")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rcpp" version))
(sha256
(base32 "1pnv6sl4vdn69ygmgrb1b3gsigfdcfb56wnzikic93l8gkvdsvxv"))))
(base32 "1rm8hcy72p1jvxikvmkwg20pjqmvmfvqb45lfghmddp2adp67qfl"))))
(build-system r-build-system)
(home-page "http://www.rcpp.org")
(synopsis "Seamless R and C++ integration")
@ -448,14 +451,14 @@ (define-public r-rcpp
(define-public r-bindr
(package
(name "r-bindr")
(version "0.1")
(version "0.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "bindr" version))
(sha256
(base32
"0d95ifm0x4mrfzi20xf39f5pzd7rfzqsld0vjqf6xzga5rhnd8fc"))))
"1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
(build-system r-build-system)
(home-page "https://github.com/krlmlr/bindr")
(synopsis "Parametrized active bindings")
@ -467,14 +470,14 @@ (define-public r-bindr
(define-public r-bindrcpp
(package
(name "r-bindrcpp")
(version "0.2")
(version "0.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "bindrcpp" version))
(sha256
(base32
"0l1l22zl87wiyl79m3gj2vlxmkhxvrkl4alhyy08h55q7hqs3vyh"))))
"0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bindr" ,r-bindr)
@ -554,14 +557,14 @@ (define-public r-shape
(define-public r-globaloptions
(package
(name "r-globaloptions")
(version "0.0.12")
(version "0.0.13")
(source
(origin
(method url-fetch)
(uri (cran-uri "GlobalOptions" version))
(sha256
(base32
"1abpc03cfvazbwj2sx6qgngs5pgpzysvxkana20hyvb4n7ws77f0"))))
"04jvha0mafslqz5nr99xjylg9n2x31gj9v4mgyg7qcmfwpqyw3ch"))))
(properties `((upstream-name . "GlobalOptions")))
(build-system r-build-system)
(home-page "https://github.com/jokergoo/GlobalOptions")
@ -936,19 +939,21 @@ (define-public r-rmtstat
(define-public r-rmpi
(package
(name "r-rmpi")
(version "0.6-6")
(version "0.6-7")
(source (origin
(method url-fetch)
(uri (cran-uri "Rmpi" version))
(sha256
(base32
"0fm6z049aaq2c9xagm8n64d9560hg9d8hyb0m359fii672nhkz6q"))))
"1b62gs7w1xqadqd7ir41jnxlcf14gcqfxd0915kn9ckdlsdrh0sw"))))
(properties `((upstream-name . "Rmpi")))
(build-system r-build-system)
(arguments
`(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")))
(inputs
`(("openmpi" ,openmpi)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
(synopsis "R interface to message-passing interface (MPI)")
(description
@ -1364,14 +1369,14 @@ (define-public r-squarem
(define-public r-lava
(package
(name "r-lava")
(version "1.6")
(version "1.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "lava" version))
(sha256
(base32
"02xf5d968raz9gnq5ywy04wz29xpdyca1hm79vbbg1mcxvzdl1dz"))))
"11k9npmzp3nk2qx0h1dwwfc37j4ddd9y54bppxby0ffnb8qlpw1k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-numderiv" ,r-numderiv)
@ -1411,14 +1416,14 @@ (define-public r-drr
(define-public r-prodlim
(package
(name "r-prodlim")
(version "1.6.1")
(version "2018.04.18")
(source
(origin
(method url-fetch)
(uri (cran-uri "prodlim" version))
(sha256
(base32
"0m51rkivx1zr6whdqwj66jpnkmp4385m06kkha3dp8qqf4jna9iz"))))
"1aslq87sqwikh8chxc378r38146y7kv79zz0kcq3j93ivx7va8jb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-kernsmooth" ,r-kernsmooth)
@ -1476,21 +1481,75 @@ (define-public r-timedate
calendar objects.")
(license license:gpl2+)))
(define-public r-magic
(package
(name "r-magic")
(version "1.5-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "magic" version))
(sha256
(base32
"083cgpp3v03li0h8597b3g21pd9lkbmn9pyssblnhc800mpc52vz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-abind" ,r-abind)))
(home-page "https://github.com/RobinHankin/magic.git")
(synopsis "Create and investigate magic squares")
(description
"This package provides a collection of efficient, vectorized algorithms
for the creation and investigation of magic squares and hypercubes, including
a variety of functions for the manipulation and analysis of arbitrarily
dimensioned arrays.")
(license license:gpl2)))
(define-public r-geometry
(package
(name "r-geometry")
(version "0.3-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "geometry" version))
(sha256
(base32
"0s09vi0rr0smys3an83mz6fk41bplxyz4myrbiinf4qpk6n33qib"))))
(build-system r-build-system)
(propagated-inputs `(("r-magic" ,r-magic)))
(home-page "http://geometry.r-forge.r-project.org/")
(synopsis "Mesh generation and surface tesselation")
(description
"This package makes the qhull library available in R, in a similar manner
as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
intersections about a point, Voronoi diagrams, furthest-site Delaunay
triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
and higher dimensions. It implements the Quickhull algorithm for computing
the convex hull. Qhull does not support constrained Delaunay triangulations,
or mesh generation of non-convex objects, but the package does include some R
functions that allow for this. Currently the package only gives access to
Delaunay triangulation and convex hull computation.")
;; The Qhull sources are included and are distributed under a custom
;; non-copyleft license. The R sources are released under GPL version 2.
(license (list license:gpl2
(license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
(define-public r-ddalpha
(package
(name "r-ddalpha")
(version "1.3.1.1")
(version "1.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ddalpha" version))
(sha256
(base32
"13w8ir5rd80rka4mq343zd4wn93vfw870lzfqrd3cxgwb1bwcw7y"))))
"1i2zcz20zy9xd42kdz09njbkq07mj2pp6f07z6dnwi5hrmvhbh9r"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
("r-class" ,r-class)
("r-geometry" ,r-geometry)
("r-mass" ,r-mass)
("r-rcpp" ,r-rcpp)
("r-robustbase" ,r-robustbase)
@ -1761,14 +1820,14 @@ (define-public r-corrplot
(define-public r-stringdist
(package
(name "r-stringdist")
(version "0.9.4.6")
(version "0.9.4.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringdist" version))
(sha256
(base32
"0j5b7hr53nr9xq44famkpwzi4khix93ffani5pwldqkf8bpdvhci"))))
"1qg80wmcrpkba9njvgjdg15bgw7ddks40kkfh5x61as9lhchy4i4"))))
(build-system r-build-system)
(home-page "https://github.com/markvanderloo/stringdist")
(synopsis "Approximate string matching and string distance functions")
@ -1986,14 +2045,14 @@ (define-public r-rsofia
(define-public r-xts
(package
(name "r-xts")
(version "0.10-1")
(version "0.10-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "xts" version))
(sha256
(base32
"1j9ddh9v9081zrqlpylsk13fldilhjdyaw6r6pa726fhgnrsf8a2"))))
"1i11fczks4lh8rpi6xbm9bm7f3jpcp6xw03kv178g3n3361qhmc1"))))
(build-system r-build-system)
(propagated-inputs `(("r-zoo" ,r-zoo)))
(native-inputs `(("gfortran" ,gfortran)))
@ -2172,19 +2231,20 @@ (define-public r-scatterplot3d
(define-public r-ggridges
(package
(name "r-ggridges")
(version "0.4.1")
(version "0.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggridges" version))
(sha256
(base32
"0kfa3icqdalqdg1klxjrhfl7if35d3wnsiyl86bprw5dyqyh3lh3"))))
"1znvsbl3px8dddpjgdrygnpz4s685wizi0jnjvx2hrz58i0chjqj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
("r-plyr" ,r-plyr)
("r-scales" ,r-scales)))
("r-scales" ,r-scales)
("r-withr" ,r-withr)))
(home-page "https://github.com/clauswilke/ggridges")
(synopsis "Ridgeline plots in ggplot2")
(description
@ -2511,14 +2571,14 @@ (define-public r-utf8
(define-public r-pillar
(package
(name "r-pillar")
(version "1.2.1")
(version "1.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "pillar" version))
(sha256
(base32
"1ryd7m570y6q3w71wd5dz042b3d0dv24g2rbkw1kdx0n6jj9gsbd"))))
"1kmqvny3rw4p5kgxz6mhqfpp7j3nnpp22dfai4kjrr2cfmj6wvb7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@ -2555,14 +2615,14 @@ (define-public r-uuid
(define-public r-tinytex
(package
(name "r-tinytex")
(version "0.3")
(version "0.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
"0mhxlr4709mca9jshnah5i7yjyy6k12s933619p7p9c8nbqj39cn"))))
"1pg4jfyvandjwz3lmr38pbqi9d045iwkk3xklhsfhhxq6aviq9p7"))))
(build-system r-build-system)
(home-page "https://github.com/yihui/tinytex")
(synopsis "Helper functions for TeX Live and compiling LaTeX documents")
@ -2577,14 +2637,14 @@ (define-public r-tinytex
(define-public r-metap
(package
(name "r-metap")
(version "0.8")
(version "0.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "metap" version))
(sha256
(base32
"06ny9zkilawdy0s8yiwhnygs3yppw89bbyf76zgdavykbzscz5lh"))))
"03vg0mb6q7j2z0pkxykbak0hcp6dcak7zxs1lw9hswz9kqrq5jhz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
@ -2775,14 +2835,14 @@ (define-public r-sapa
(define-public r-quantmod
(package
(name "r-quantmod")
(version "0.4-12")
(version "0.4-13")
(source
(origin
(method url-fetch)
(uri (cran-uri "quantmod" version))
(sha256
(base32
"0y7gh0k1s10vdsfch8777avbhf99mc9crikvx7ahqrw0j631vmhq"))))
"16aldg96z7amp5mr90nb8127yy04gxsihfr26km5p3cx3j117yv0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
@ -3323,14 +3383,14 @@ (define-public r-signal
(define-public r-psych
(package
(name "r-psych")
(version "1.7.8")
(version "1.8.3.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "psych" version))
(sha256
(base32
"0daismb8pdk392vdy304hqx0m3jx62gx3a0hygjygc125rhfla7k"))))
"1zhp8j81nkzd65168zdw9ylypb9n07ajan21x0wqcn8jdbg970sg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-foreign" ,r-foreign)
@ -3354,14 +3414,14 @@ (define-public r-psych
(define-public r-gsubfn
(package
(name "r-gsubfn")
(version "0.6-6")
(version "0.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "gsubfn" version))
(sha256
(base32
"196x4c3ihf4q3i0v7b1xa6jm8jjld2rsx00qz03n90wfnjdx5idv"))))
"00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
(build-system r-build-system)
(propagated-inputs `(("r-proto" ,r-proto)))
(home-page "http://gsubfn.googlecode.com")
@ -3704,3 +3764,212 @@ (define-public r-abc
measuring the accuracy of ABC estimates, and to calculate the
misclassification probabilities of different models.")
(license license:gpl3+)))
(define-public r-openxlsx
(package
(name "r-openxlsx")
(version "4.0.17")
(source
(origin
(method url-fetch)
(uri (cran-uri "openxlsx" version))
(sha256
(base32
"1mq4lasp12kc30sxcsmz9gskd114l8s7z7wd6svv2nm8qllrhsqi"))))
(build-system r-build-system)
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
(home-page "https://github.com/awalker89/openxlsx")
(synopsis "Read, write and edit XLSX files")
(description
"This package simplifies the creation of Excel @code{.xlsx} files by
providing a high level interface to writing, styling and editing worksheets.
Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
and @code{XLConnect} packages with the added benefit of removing the
dependency on Java.")
(license license:gpl3)))
(define-public r-rio
(package
(name "r-rio")
(version "0.5.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "rio" version))
(sha256
(base32
"158xg3vj0glk3fslwi6fywwmfym2b6kn3fdmjligdfy5lf68khix"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
("r-data-table" ,r-data-table)
("r-foreign" ,r-foreign)
("r-haven" ,r-haven)
("r-openxlsx" ,r-openxlsx)
("r-readxl" ,r-readxl)
("r-tibble" ,r-tibble)))
(home-page "https://github.com/leeper/rio")
(synopsis "Swiss-army knife for data I/O")
(description
"This package provides streamlined data import and export infrastructure
by making assumptions that the user is probably willing to make: @code{import}
and @code{export} determine the data structure from the file extension,
reasonable defaults are used for data import and export (e.g.,
@code{stringsAsFactors=FALSE}), web-based import is natively
supported (including from SSL/HTTPS), compressed files can be read directly
without explicit decompression, and fast import packages are used where
appropriate. An additional convenience function, @code{convert}, provides a
simple method for converting between file types.")
(license license:gpl2)))
(define-public r-maptools
(package
(name "r-maptools")
(version "0.9-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "maptools" version))
(sha256
(base32
"075lmb3b62171cw2dg8fv1vwmvfzg39r1ji7jwb8s5k9dz88ry1v"))))
(build-system r-build-system)
(propagated-inputs
`(("r-foreign" ,r-foreign)
("r-lattice" ,r-lattice)
("r-sp" ,r-sp)))
(home-page "http://r-forge.r-project.org/projects/maptools/")
(synopsis "Tools for reading and handling spatial objects")
(description
"This package provides a set of tools for manipulating and reading
geographic data, in particular ESRI Shapefiles. It includes binary access to
GSHHG shoreline files. The package also provides interface wrappers for
exchanging spatial objects with other R packages.")
;; The C source files from shapelib are released under the Expat license.
;; The R code is released under GPL version 2 or later.
(license (list license:gpl2+
license:expat))))
(define-public r-later
(package
(name "r-later")
(version "0.7.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "later" version))
(sha256
(base32
"0z9jymmclkq9zcg1fd8p6gsnm5z1sn3n9pfz3bs03qjrkbizgrvz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
("r-rcpp" ,r-rcpp)
("r-rlang" ,r-rlang)))
(home-page "https://github.com/r-lib/later")
(synopsis "Utilities for delaying function execution")
(description
"This package provides tools to execute arbitrary R or C functions some
time after the current time, after the R execution stack has emptied.")
(license license:gpl2+)))
(define-public r-promises
(package
(name "r-promises")
(version "1.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "promises" version))
(sha256
(base32
"0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-later" ,r-later)
("r-magrittr" ,r-magrittr)
("r-r6" ,r-r6)
("r-rcpp" ,r-rcpp)
("r-rlang" ,r-rlang)))
(home-page "https://rstudio.github.io/promises")
(synopsis "Abstractions for promise-based asynchronous programming")
(description
"This package provides fundamental abstractions for doing asynchronous
programming in R using promises. Asynchronous programming is useful for
allowing a single R process to orchestrate multiple tasks in the background
while also attending to something else. Semantics are similar to JavaScript
promises, but with a syntax that is idiomatic R.")
(license license:expat)))
(define-public r-dosnow
(package
(name "r-dosnow")
(version "1.0.16")
(source
(origin
(method url-fetch)
(uri (cran-uri "doSNOW" version))
(sha256
(base32
"13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n"))))
(properties `((upstream-name . "doSNOW")))
(build-system r-build-system)
(propagated-inputs
`(("r-foreach" ,r-foreach)
("r-iterators" ,r-iterators)
("r-snow" ,r-snow)))
(home-page "https://cran.r-project.org/web/packages/doSNOW")
(synopsis "Foreach parallel adaptor for the snow package")
(description
"This package provides a parallel backend for the @code{%dopar%} function
using the @code{snow} package.")
(license license:gpl2)))
(define-public r-snowfall
(package
(name "r-snowfall")
(version "1.84-6.1")
(source (origin
(method url-fetch)
(uri (cran-uri "snowfall" version))
(sha256
(base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
(build-system r-build-system)
(propagated-inputs
`(("r-snow" ,r-snow)))
(home-page "http://cran.r-project.org/web/packages/snowfall/")
(synopsis "Easier cluster computing")
(description "This package is a usability wrapper around snow for easier
development of parallel R programs. This package offers e.g. extended error
checks, and additional functions. All functions work in sequential mode, too,
if no cluster is present or wished. The package is also designed as connector
to the cluster management tool @code{sfCluster}, but can also used without
it.")
(license license:gpl2+)))
(define-public r-codedepends
(package
(name "r-codedepends")
(version "0.5-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "CodeDepends" version))
(sha256
(base32
"03p82s0abca2jimzqvxdzykfzca7c7fhm5xsjxybcksr4gggr5sc"))))
(properties `((upstream-name . "CodeDepends")))
(build-system r-build-system)
(propagated-inputs
`(("r-codetools" ,r-codetools)
("r-xml" ,r-xml)))
(home-page "http://cran.r-project.org/web/packages/CodeDepends")
(synopsis "Analysis of R code for reproducible research and code comprehension")
(description
"This package provides tools for analyzing R expressions or blocks of
code and determining the dependencies between them. It focuses on R scripts,
but can be used on the bodies of functions. There are many facilities
including the ability to summarize or get a high-level view of code,
determining dependencies between variables, code improvement suggestions.")
;; Any version of the GPL
(license (list license:gpl2+ license:gpl3+))))

10
gnu/packages/cups.scm
View file

@ -616,7 +616,7 @@ (define-public foo2zjs
(define-public escpr
(package
(name "escpr")
(version "1.6.18")
(version "1.6.20")
;; XXX: This currently works. But it will break as soon as a newer
;; version is available since the URLs for older versions are not
;; preserved. An alternative source will be added as soon as
@ -624,12 +624,12 @@ (define-public escpr
(source (origin
(method url-fetch)
;; The uri has to be chopped up in order to satisfy guix lint.
(uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/06/86/80/"
"9955e43f3aead20366851d24cea65de779cf5aa7/"
"epson-inkjet-printer-escpr-1.6.18-1lsb3.2.tar.gz"))
(uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/07/16/23/"
"804253d188a31ae6a0f2722648248ef952afedfb/"
"epson-inkjet-printer-escpr-1.6.20-1lsb3.2.tar.gz"))
(sha256
(base32
"137jf52dhi5v2rkmlw4b73f7r7f98m61dpgsb7yvqs2f0yhsjsb3"))))
"19800pl7kbbgdzbsy9ijmd7dm3ly4kr2h1dxypqpd075g6n0i770"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags

4
gnu/packages/databases.scm
View file

@ -846,7 +846,7 @@ (define-public recutils
(define-public rocksdb
(package
(name "rocksdb")
(version "5.10.4")
(version "5.12.4")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/facebook/rocksdb"
@ -854,7 +854,7 @@ (define-public rocksdb
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0hp7jxr99vyc57n708hiqk4lks9a9zmjgfjc21mx6v1rmabj2944"))
"1jcwgsjhk4hdfr2wf549blkgb89vwcdb5i2ahhqs6zf3mm20i3bf"))
(modules '((guix build utils)))
(snippet
'(begin

3
gnu/packages/debug.scm
View file

@ -2,6 +2,7 @@
;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -169,7 +170,7 @@ (define-public american-fuzzy-lop
(inputs
`(("custom-qemu"
;; The afl-qemu tool builds qemu 2.10.0 with a few patches applied.
,(package (inherit (@@ (gnu packages bootloaders) qemu-minimal-2.10))
,(package (inherit qemu-minimal-2.10)
(name "afl-qemu")
(inputs
`(("afl-src" ,source)

17
gnu/packages/dictionaries.scm
View file

@ -211,7 +211,7 @@ (define-public ding
(define-public grammalecte
(package
(name "grammalecte")
(version "0.6.3.1")
(version "0.6.4")
(source
(origin
(method url-fetch/zipbomb)
@ -219,21 +219,8 @@ (define-public grammalecte
"Grammalecte-fr-v" version ".zip"))
(sha256
(base32
"0jlzrhpx9qvjdq679w188p86x09yfjf3l0h4scjl9w26yyp53gr8"))))
"13var1gi3gb2bwi7k21bn2pla0rs17cd7kc3mc5a2nsyqgsrzxfw"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-setup
;; Fix typos in "setup.py". In particular, add the new
;; "graphspell" module introduced in 0.6.2. Reported upstream:
;; <https://www.dicollecte.org/thread.php?prj=fr&t=709>
(lambda _
(substitute* "setup.py"
(("packages=\\['grammalecte', 'grammalecte.fr'\\],")
"packages=['grammalecte', 'grammalecte.fr', 'grammalecte.graphspell'],")
(("_dictionaries/French.bdic") "graphspell/_dictionaries/fr.bdic"))
#t)))))
(home-page "https://www.dicollecte.org")
(synopsis "French spelling and grammar checker")
(description "Grammalecte is a grammar checker dedicated to the French

28
gnu/packages/disk.scm
View file

@ -10,6 +10,7 @@
;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
;;; Copyright © 2018 Vasile Dumitrascu <va511e@yahoo.com>
;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -35,6 +36,7 @@ (define-module (gnu packages disk)
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages check)
#:use-module (gnu packages databases)
#:use-module (gnu packages docbook)
#:use-module (gnu packages gettext)
@ -502,3 +504,29 @@ (define-public duperemove
Duperemove can also take input from the @command{fdupes} program.")
(license license:gpl2)))
(define-public ranger
(package
(name "ranger")
(version "1.9.1")
(source (origin
(method url-fetch)
(uri (string-append "https://ranger.github.io/"
"ranger-" version ".tar.gz"))
(sha256
(base32
"1lnzkrxcnlwnyi3z0v8ybyp8d5rm26qm35rr68kbs2lbs06inha0"))))
(build-system python-build-system)
(native-inputs ;for tests
`(("python-pytest" ,python-pytest)
("python-pylint" ,python-pylint)
("python-flake8" ,python-flake8)
("which" ,which)))
(arguments '(#:test-target "test"))
(home-page "https://ranger.github.io/")
(synopsis "Console file manager")
(description "ranger is a console file manager with Vi key bindings. It
provides a minimalistic and nice curses interface with a view on the directory
hierarchy. It ships with @code{rifle}, a file launcher that is good at
automatically finding out which program to use for what file type.")
(license license:gpl3)))

43
gnu/packages/education.scm
View file

@ -2,7 +2,7 @@
;;; Copyright © 2016 Danny Milosavljevic <dannym@scratchpost.org>
;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -107,29 +107,54 @@ (define-public gcompris
(define-public gcompris-qt
(package
(name "gcompris-qt")
(version "0.70")
(version "0.90")
(source
(origin
(method url-fetch)
(uri (string-append
"http://gcompris.net/download/qt/src/gcompris-qt-"
"https://gcompris.net/download/qt/src/gcompris-qt-"
version ".tar.xz"))
(sha256
(base32
"01r7i8dmwb2nlfyp0y0mzs8yydmvn5gq7xn1w7g21lysak1mliwa"))))
"1i5adxnhig849qxwi3c4v7r84q6agx1zxkd69fh4y7lcmq2qiaza"))))
(build-system cmake-build-system)
(arguments
;; Qml_box2d is unmaintained and not actually required for building
'(#:configure-flags (list "-DQML_BOX2D_MODULE=disabled")
`(#:phases
(modify-phases %standard-phases
(add-after 'install 'wrap-executable
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(wrap-program (string-append out "/bin/gcompris-qt")
`("QT_PLUGIN_PATH" ":" prefix
,(map (lambda (label)
(string-append (assoc-ref inputs label)
"/lib/qt5/plugins"))
'("qtbase" "qtdeclarative" "qtmultimedia" "qtsvg")))
`("QML2_IMPORT_PATH" ":" prefix
,(map (lambda (label)
(string-append (assoc-ref inputs label)
"/lib/qt5/qml"))
'("qtdeclarative" "qtgraphicaleffects"
"qtmultimedia" "qtquickcontrols"))))
#t))))
#:configure-flags (list "-DQML_BOX2D_MODULE=disabled")
#:tests? #f)) ; no test target
(native-inputs
`(("extra-cmake-modules" ,extra-cmake-modules)
("gettext" ,gettext-minimal)
("perl" ,perl)))
("perl" ,perl)
("qttools" ,qttools)))
(inputs
`(("python-2" ,python-2)
("qt" ,qt))) ; Cannot find qtquick at runtime with modular qt.
(home-page "http://gcompris.net/index-en.html")
("qtbase" ,qtbase)
("qtdeclarative" ,qtdeclarative)
("qtgraphicaleffects" ,qtgraphicaleffects)
("qtmultimedia" ,qtmultimedia)
("qtquickcontrols" ,qtquickcontrols)
("qtsensors" ,qtsensors)
("qtsvg" ,qtsvg)
("qtxmlpatterns" ,qtxmlpatterns)))
(home-page "https://gcompris.net/index-en.html")
(synopsis "Educational games for small children")
(description
"Gcompris offers a large collection of educational games for small

115
gnu/packages/emacs.scm
View file

@ -2,7 +2,7 @@
;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014, 2015, 2016, 2017, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014, 2015, 2016, 2017 Alex Kost <alezost@gmail.com>
;;; Copyright © 2014, 2015, 2016, 2017, 2018 Alex Kost <alezost@gmail.com>
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017 Chris Marusich <cmmarusich@gmail.com>
@ -321,14 +321,14 @@ (define-public guile-emacs
(define-public geiser
(package
(name "geiser")
(version "0.9")
(version "0.10")
(source (origin
(method url-fetch)
(uri (string-append "mirror://savannah/geiser/" version
"/geiser-" version ".tar.gz"))
(sha256
(base32
"0phz9d8wjk4p13vqannv0003fwh8qqrp0gfzcs2hgq1mrmv1srss"))))
"0pj3l7p8d60c9b4vfprnv6g5l61d74pls4b5dvd84cn4ky9mzwjv"))))
(build-system gnu-build-system)
(arguments
'(#:phases
@ -412,7 +412,7 @@ (define-public git-modes/old-name
(define-public emacs-with-editor
(package
(name "emacs-with-editor")
(version "2.7.0")
(version "2.7.2")
(source (origin
(method url-fetch)
(uri (string-append
@ -421,7 +421,7 @@ (define-public emacs-with-editor
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0kah7pv211zx9fsb5g4hd51bqcq2bxd1chdykd488ihvfz1l5y14"))))
"1jqi3axcs0cb1pcv1jxxc2a09v6psrm33wwl6hmyshzl8kbxs2mv"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-dash" ,emacs-dash)))
@ -561,7 +561,7 @@ (define-public magit-svn
(define-public emacs-magit-popup
(package
(name "emacs-magit-popup")
(version "2.12.0")
(version "2.12.3")
(source (origin
(method url-fetch)
(uri (string-append
@ -570,7 +570,7 @@ (define-public emacs-magit-popup
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1dnk611f7lww6rb03hk8ijg2jwxx9f26pjfff4bwjmnjz7hnd6vz"))))
"1kz6vj67awkwf9y2wj6m3l2him3znm08z6bkdvnmfr6rwd96dr39"))))
(build-system emacs-build-system)
(arguments
`(#:phases
@ -4536,6 +4536,31 @@ (define-public emacs-evil
extensions.")
(license license:gpl3+)))
(define-public emacs-evil-collection
(let ((commit "f40704a57fd33b4bfad64147a2b771fc8961fdfc")
(revision "1"))
(package
(name "emacs-evil-collection")
(version (git-version "20180425" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/emacs-evil/evil-collection")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0qn19k0f3isnbi1hkmcf3qjxbyvp23m5ak5ny7623qgwb2nwz1l5"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-evil" ,emacs-evil)))
(home-page "https://github.com/emacs-evil/evil-collection")
(synopsis "Collection of Evil bindings for many major and minor modes")
(description "This is a collection of Evil bindings for the parts of
Emacs that Evil does not cover properly by default, such as @code{help-mode},
@code{M-x calendar}, Eshell and more.")
(license license:gpl3+))))
(define-public emacs-goto-chg
(package
(name "emacs-goto-chg")
@ -4627,14 +4652,14 @@ (define-public emacs-org
(name "emacs-org")
;; emacs-org-contrib inherits from this package. Please update its sha256
;; checksum as well.
(version "9.1.10")
(version "9.1.11")
(source (origin
(method url-fetch)
(uri (string-append "http://elpa.gnu.org/packages/org-"
version ".tar"))
(sha256
(base32
"01vvq6m7r2ifyflvq5ga241qvl4j62smz0zr6jljk56b6nqi20lm"))))
"0i27g5qbkfqbxhgiz917pjwkxg3rwid99d0ickwx43bzq0zi7c1m"))))
(build-system emacs-build-system)
(home-page "https://orgmode.org/")
(synopsis "Outline-based notes management and organizer")
@ -4648,14 +4673,14 @@ (define-public emacs-org-contrib
(package
(inherit emacs-org)
(name "emacs-org-contrib")
(version "20180416")
(version "20180423")
(source (origin
(method url-fetch)
(uri (string-append "https://orgmode.org/elpa/org-plus-contrib-"
version ".tar"))
(sha256
(base32
"1f5zdfsa1fcf66hk3w57wh5385069yg0b86h57jgkcbmxkcmj6ij"))))
"1aggvdy74q8p79xyc19zring5gjvlzp6lbsq8ar319zkmcjrapqd"))))
(arguments
`(#:modules ((guix build emacs-build-system)
(guix build utils)
@ -5201,6 +5226,34 @@ (define-public emacs-helm-c-yasnippet
Yasnippet.")
(license license:gpl2+))))
(define-public emacs-helm-system-packages
(let ((commit "986b7bd360a705053500c4ce2c9bea03dd7b24a6")
(revision "1"))
(package
(name "emacs-helm-system-packages")
(version (git-version "1.9.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/emacs-helm/helm-system-packages")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"19iklhpxgh5xx6h4dysf58nd46lmyb46xj601lf7kbwl6yq0y61f"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-helm" ,emacs-helm)))
(home-page "https://github.com/emacs-helm/helm-system-packages")
(synopsis "Helm System Packages is an interface to your package manager")
(description "List all available packages in Helm (with installed
packages displayed in their own respective face). Fuzzy-search, mark and
execute the desired action over any selections of packages: Install,
uninstall, display packages details (in Org Mode) or insert details at point,
find files owned by packages... And much more, including performing all the
above over the network.")
(license license:gpl3+))))
(define-public emacs-memoize
(package
(name "emacs-memoize")
@ -6834,15 +6887,17 @@ (define-public emacs-emojify
(define-public emacs-websocket
(package
(name "emacs-websocket")
(version "1.8")
(version "1.10")
(source
(origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/websocket-"
version ".tar"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/ahyatt/emacs-websocket.git")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0dcxmnnm8z7cvsc7nkb822a1g6w03klp7cijjnfq0pz84p3w9cd9"))))
"1dgrf7na6r6mmkknphzshlbd5fnzisg0qn0j7vfpa38wgsymaq52"))))
(build-system emacs-build-system)
(home-page "http://elpa.gnu.org/packages/websocket.html")
(synopsis "Emacs WebSocket client and server")
@ -6906,8 +6961,8 @@ (define-public emacs-circe
(license license:gpl3+)))
(define-public emacs-slack
(let ((commit "92724604879149cf331fa8778d089813a9d4ce1a")
(revision "3"))
(let ((commit "d90395482d26175ce38fd935e978c428be8af9a0")
(revision "4"))
(package
(name "emacs-slack")
(version (string-append "0-" revision "." (string-take commit 7)))
@ -6919,7 +6974,7 @@ (define-public emacs-slack
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1fdf8s3ca356k7m7f5kqzfamfl2nrqjj2pynjv3kkrr0ad15nxmw"))))
"14f6wjcbl09cfd3yngr6m1k1d4nr764im666mbnqbk9nmqf50nib"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-alert" ,emacs-alert)
@ -7943,3 +7998,25 @@ (define-public emacs-epkg
You could get a Epkg package list by invoking @code{epkg-list-packages} in
Emacs.")
(license license:gpl3+))))
(define-public emacs-elisp-slime-nav
(package
(name "emacs-elisp-slime-nav")
(version "0.9")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/purcell/elisp-slime-nav/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1vq7ym1q47p97gxrv45c9gm96d23xbp237vkmakikj6grngxjfb2"))))
(build-system emacs-build-system)
(home-page "https://github.com/purcell/elisp-slime-nav")
(synopsis "Make @code{M-.} and @code{M-,} work for elisp like they do in SLIME")
(description
"This package provides SLIME's convenient @code{M-.}and @code{M-,} navigation
in @code{emacs-lisp-mode}, together with an elisp equivalent of
@code{slime-describe-symbol}.")
(license license:gpl3+)))

6
gnu/packages/emulators.scm
View file

@ -186,7 +186,7 @@ (define-public dolphin-emu
("bluez" ,bluez)
("curl" ,curl)
("eudev" ,eudev)
("ffmpeg" ,ffmpeg)
("ffmpeg" ,ffmpeg-3.4)
("font-wqy-microhei" ,font-wqy-microhei)
("freetype" ,freetype)
("glew" ,glew)
@ -1046,7 +1046,7 @@ (define-public nestopia-ue
(define-public retroarch
(package
(name "retroarch")
(version "1.7.1")
(version "1.7.2")
(source
(origin
(method url-fetch)
@ -1054,7 +1054,7 @@ (define-public retroarch
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "1wykv0w0kdlh7lh0k1ig0lpk5vh4c7r19jlfa9103jmjlryrq679"))))
(base32 "1y9fakr41h6xpddpkj12mcw1kgldvy76nzvxm5jk5v7iyiks4c6k"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ; no tests

6
gnu/packages/engineering.scm
View file

@ -3,7 +3,7 @@
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 David Thompson <davet@gnu.org>
;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017 Theodoros Foradis <theodoros@foradis.org>
;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@ -585,7 +585,9 @@ (define-public libfive
(file-name (git-file-name name version))
(snippet
;; Remove bundled catch since we provide our own.
'(delete-file "libfive/test/catch.hpp"))))
'(begin
(delete-file "libfive/test/catch.hpp")
#t))))
(build-system cmake-build-system)
(arguments
`(#:test-target "libfive-test"

24
gnu/packages/enlightenment.scm
View file

@ -49,6 +49,7 @@ (define-module (gnu packages enlightenment)
#:use-module (gnu packages llvm)
#:use-module (gnu packages lua)
#:use-module (gnu packages pdf)
#:use-module (gnu packages perl)
#:use-module (gnu packages photo)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages pulseaudio)
@ -176,7 +177,7 @@ (define-public efl
(define-public terminology
(package
(name "terminology")
(version "1.1.1")
(version "1.2.0")
(source (origin
(method url-fetch)
(uri
@ -184,25 +185,17 @@ (define-public terminology
"terminology/terminology-" version ".tar.xz"))
(sha256
(base32
"05ncxvzb9rzkyjvd95hzn8lswqdwr8cix6rd54nqn9559jibh4ns"))
"0kw34l5lahn1qaks3ah6x8k41d6hfywpqfak2p7qq1z87zj506mx"))
(modules '((guix build utils)))
;; Remove the bundled fonts.
;; TODO: Remove bundled lz4.
(snippet
'(begin
(delete-file-recursively "data/fonts")
(substitute* '("data/Makefile.in" "data/Makefile.am")
(("fonts") ""))
(substitute* "configure"
(("data/fonts/Makefile") "")
(("\\\"data/fonts/Makefile") "# \"data/fonts/Makefile"))
(substitute* '("data/themes/Makefile.in"
"data/themes/Makefile.am"
"data/themes/nyanology/Makefile.in"
"data/themes/nyanology/Makefile.am")
(("-fd \\$\\(top_srcdir\\)/data/fonts") ""))
(substitute* "data/meson.build"
(("subdir\\('fonts'\\)") ""))
#t))))
(build-system gnu-build-system)
(build-system meson-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
@ -211,6 +204,7 @@ (define-public terminology
(lambda _ (setenv "HOME" "/tmp") #t)))))
(native-inputs
`(("gettext" ,gettext-minimal)
("perl" ,perl)
("pkg-config" ,pkg-config)))
(inputs
`(("efl" ,efl)))
@ -257,7 +251,7 @@ (define-public rage
(define-public enlightenment
(package
(name "enlightenment")
(version "0.22.2")
(version "0.22.3")
(source (origin
(method url-fetch)
(uri
@ -265,7 +259,7 @@ (define-public enlightenment
name "/" name "-" version ".tar.xz"))
(sha256
(base32
"0b33w75s4w7xmz9cv8dyp8vy2gcffnrvjys20fhcpw26abw1wn2d"))))
"16zydv7z94aw3rywmb9gr8ya85k7b75h22wng95lfx1x0y1yb0ad"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("--enable-mount-eeze")

4
gnu/packages/freedesktop.scm
View file

@ -348,7 +348,7 @@ (define-public elogind
(define-public packagekit
(package
(name "packagekit")
(version "1.1.5")
(version "1.1.10")
(source (origin
(method url-fetch)
(uri (string-append
@ -357,7 +357,7 @@ (define-public packagekit
"PackageKit-" version ".tar.xz"))
(sha256
(base32
"035pqxgkyki813hyw2frrbpfllq113zfk5qcp9wvsq5lsp74ix2h"))))
"1msfmb22cm4s3l6vsbr86b8s0v897sy6gcga3qg87z7640a0di2b"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f

27
gnu/packages/game-development.scm
View file

@ -13,6 +13,7 @@
;;; Copyright © 2017 Peter Mikkelsen <petermikkelsen10@gmail.com>
;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -1059,16 +1060,34 @@ (define-public openmw
(define-public godot
(package
(name "godot")
(version "3.0.1")
(version "3.0.2")
(source (origin
(method url-fetch)
(uri
(string-append "https://github.com/godotengine/godot/archive/"
version "-stable.tar.gz"))
(file-name (string-append name "-" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0k8c12nzhl98i9il9s3awbwdamkrwxk0s47jr7n8a3z93rpszd2p"))))
"0ldnk3j4w2kh454mzclmq8nk7zqrn758yrqq85i4kzljpkf93g0m"))
(modules '((guix build utils)))
(snippet
'(begin
;; Drop libraries that we take from Guix. Note that some
;; of these may be modified; see "thirdparty/README.md".
(with-directory-excursion "thirdparty"
(for-each delete-file-recursively
'("freetype"
"libogg"
"libpng"
"libtheora"
"libvorbis"
"libvpx"
"libwebp"
"openssl"
"opus"
"zlib"))
#t)))))
(build-system scons-build-system)
(arguments
`(#:scons ,scons-python2
@ -1086,6 +1105,7 @@ (define-public godot
"builtin_libpng=no"
"builtin_libtheora=no"
"builtin_libvorbis=no"
"builtin_libvpx=no"
"builtin_libwebp=no"
"builtin_openssl=no"
"builtin_opus=no"
@ -1141,6 +1161,7 @@ (define-public godot
("glu" ,glu)
("libtheora" ,libtheora)
("libvorbis" ,libvorbis)
("libvpx" ,libvpx)
("libwebp" ,libwebp)
("libx11" ,libx11)
("libxcursor" ,libxcursor)

3
gnu/packages/games.scm
View file

@ -4913,7 +4913,8 @@ (define-public fortune-mod
,(origin
(method url-fetch)
(uri (string-append "https://bitbucket.org/shlomif/shlomif-cmake-modules/"
"raw/default/shlomif-cmake-modules/Shlomif_Common.cmake"))
"raw/c505713d7a7cda608f97f01577e5868a711b883e/"
"shlomif-cmake-modules/Shlomif_Common.cmake"))
(sha256
(base32 "0kx9s1qqhhzprp1w3b67xmsns0n0v506bg5hgrshxaxpy6lqiwb2"))))))
(home-page "http://www.shlomifish.org/open-source/projects/fortune-mod/")

8
gnu/packages/geo.scm
View file

@ -500,14 +500,14 @@ (define-public spatialite-gui
(define-public r-maps
(package
(name "r-maps")
(version "3.2.0")
(version "3.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "maps" version))
(sha256
(base32
"0577f3b5d3a7djl7r0miy9mzr6xq6jb32p8nyrma7m2azasbwyj3"))))
"05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/maps")
(synopsis "Draw geographical maps")
@ -519,14 +519,14 @@ (define-public r-maps
(define-public r-mapproj
(package
(name "r-mapproj")
(version "1.2-5")
(version "1.2.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "mapproj" version))
(sha256
(base32
"0rjz37r4rizk2c6jaf54f0kfb60dqv6b262cnhiwjl55d4x6l0pk"))))
"1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
(build-system r-build-system)
(propagated-inputs `(("r-maps" ,r-maps)))
(home-page "https://cran.r-project.org/web/packages/mapproj")

48
gnu/packages/gnome.scm
View file

@ -533,7 +533,7 @@ (define-public gnome-doc-utils
(define-public gnome-disk-utility
(package
(name "gnome-disk-utility")
(version "3.26.2")
(version "3.28.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
@ -541,7 +541,7 @@ (define-public gnome-disk-utility
name "-" version ".tar.xz"))
(sha256
(base32
"1wjnw9hpjqyhrr116491rfzd0837g6jqvzq2z1ndx2sdqv19caxa"))))
"09dmknfas8iifv6k5jb4a9ag57s8awrn0f26fd1qlg0mbfjlnfd6"))))
(build-system meson-build-system)
(native-inputs
`(("glib:bin" ,glib "bin")
@ -725,7 +725,7 @@ (define-public gnome-keyring
(define-public evince
(package
(name "evince")
(version "3.28.0")
(version "3.28.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
@ -733,7 +733,7 @@ (define-public evince
name "-" version ".tar.xz"))
(sha256
(base32
"1a3kcls18dcz1lj8hrx8skcli9xxfyi71c17xjwayh71cm5jc8zs"))))
"1qbk1x2c7iacmmfwjzh136v2sdacrkqn9d6bnqid7xn9hlnx4m89"))))
(build-system glib-or-gtk-build-system)
(arguments
`(#:configure-flags '("--disable-nautilus")
@ -2062,7 +2062,7 @@ (define-public vala
(define-public vte
(package
(name "vte")
(version "0.50.2")
(version "0.52.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
@ -2070,7 +2070,7 @@ (define-public vte
name "-" version ".tar.xz"))
(sha256
(base32
"1kq9bxf7waap190zx5k78d21y3l31npblrnhfkxz4j7zz9mk3pbr"))))
"1lva70inb5y8p42rg95fb88z2ybwcz0lybla3ixbgp2sj0s4rzdh"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
@ -2730,7 +2730,7 @@ (define-public gnome-sudoku
(define-public gnome-terminal
(package
(name "gnome-terminal")
(version "3.26.2")
(version "3.28.1")
(source
(origin
(method url-fetch)
@ -2739,7 +2739,7 @@ (define-public gnome-terminal
name "-" version ".tar.xz"))
(sha256
(base32
"1c05f2lrlm8jfx2394k6nabg4ml07lqasxaja5v98mhlm0aa96rs"))))
"1hqwh12hiy73mazqgvyrq8jk4c669x2fb4nh8mwby3qbk8ca19pp"))))
(build-system glib-or-gtk-build-system)
(arguments
'(#:configure-flags
@ -6302,7 +6302,7 @@ (define-public gnome-dictionary
(define-public gnome-tweak-tool
(package
(name "gnome-tweak-tool")
(version "3.24.1")
(version "3.26.4")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/gnome-tweak-tool/"
@ -6312,7 +6312,7 @@ (define-public gnome-tweak-tool
(search-patch "gnome-tweak-tool-search-paths.patch")))
(sha256
(base32
"0rgmm7n6jwc5hz64sprm4jxnky62hw839a7r18rn1mj884vnn8hr"))))
"1pq5a0kzh1sz7s7ax5c7p6212k9d51nk5bfvjfyqn99cs928187x"))))
(build-system glib-or-gtk-build-system)
(arguments
`(#:configure-flags '("--localstatedir=/tmp"
@ -6320,6 +6320,16 @@ (define-public gnome-tweak-tool
#:imported-modules ((guix build python-build-system)
,@%glib-or-gtk-build-system-modules)
#:phases (modify-phases %standard-phases
(delete 'configure)
(replace 'build
(lambda* (#:key outputs #:allow-other-keys)
(invoke "meson" "build"
"--prefix" (assoc-ref outputs "out"))))
(replace 'check
(lambda _ (invoke "ninja" "-C" "build" "test")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(invoke "ninja" "-C" "build" "install")))
(add-after 'install 'wrap-program
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
@ -6330,17 +6340,21 @@ (define-public gnome-tweak-tool
(add-after 'install 'wrap
(@@ (guix build python-build-system) wrap)))))
(native-inputs
`(("intltool" ,intltool)
`(("gtk+:bin" ,gtk+ "bin") ; For gtk-update-icon-cache
("intltool" ,intltool)
("meson" ,meson-for-build)
("ninja" ,ninja)
("pkg-config" ,pkg-config)))
(inputs
`(("python" ,python-2)
("python2-pygobject" ,python2-pygobject)
("gnome-desktop" ,gnome-desktop)
("libsoup" ,libsoup)
("libnotify" ,libnotify)
`(("gnome-desktop" ,gnome-desktop)
("gtk+" ,gtk+)
("gobject-introspection" ,gobject-introspection)
("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
("gtk+" ,gtk+)))
("libnotify" ,libnotify)
("libsoup" ,libsoup)
("nautilus" ,nautilus)
("python" ,python)
("python-pygobject" ,python-pygobject)))
(synopsis "Customize advanced GNOME 3 options")
(home-page "https://wiki.gnome.org/action/show/Apps/GnomeTweakTool")
(description

2
gnu/packages/gnunet.scm
View file

@ -88,7 +88,7 @@ (define-public libextractor
`(("exiv2" ,exiv2)
("bzip2" ,bzip2)
("flac" ,flac)
("ffmpeg" ,ffmpeg)
("ffmpeg" ,ffmpeg-3.4)
("file" ,file) ;libmagic, for the MIME plug-in
("glib" ,glib)
("gstreamer" ,gstreamer)

4
gnu/packages/gnupg.scm
View file

@ -797,7 +797,7 @@ (define-public pinentry
(define-public paperkey
(package
(name "paperkey")
(version "1.3")
(version "1.5")
(source (origin
(method url-fetch)
(uri (string-append "http://www.jabberwocky.com/"
@ -805,7 +805,7 @@ (define-public paperkey
version ".tar.gz"))
(sha256
(base32
"1yybj8bj68v4lxwpn596b6ismh2fyixw5vlqqg26byrn4d9dfmsv"))))
"1prd2jaf4zjad3xhv160hmi5n408ssljfg7iz90jxs9w111pjwy4"))))
(build-system gnu-build-system)
(arguments
`(#:phases

12
gnu/packages/golang.scm
View file

@ -195,7 +195,7 @@ (define-public go-1.4
;; https://github.com/golang/go/issues/24046
("gcc:lib" ,gcc-6 "lib")))
(native-inputs
`(("pkg-config" ,%pkg-config)
`(("pkg-config" ,pkg-config)
("which" ,which)
("net-base" ,net-base)
("perl" ,perl)))
@ -214,7 +214,7 @@ (define-public go-1.9
(package
(inherit go-1.4)
(name "go")
(version "1.9.4")
(version "1.9.5")
(source
(origin
(method url-fetch)
@ -222,7 +222,7 @@ (define-public go-1.9
name version ".src.tar.gz"))
(sha256
(base32
"01nw8rfvf10naja0wq0kabsm012sbqq76hd4b8c7g28n6ggshwq5"))))
"1g4zqhbh1yw3gnb400szzwrdz0k5s3h0h5nc35xgmn5v69zvphpi"))))
(arguments
(substitute-keyword-arguments (package-arguments go-1.4)
((#:phases phases)
@ -292,6 +292,7 @@ (define-public go-1.9
("syscall/syscall_unix_test.go" "(.+)(TestPassFD\\(.+)")
("os/exec/exec_test.go" "(.+)(TestExtraFiles/areturn.+)")
("cmd/go/go_test.go" "(.+)(TestCoverageWithCgo.+)")
("cmd/go/go_test.go" "(.+)(TestTwoPkgConfigs.+)")
("os/exec/exec_test.go" "(.+)(TestOutputStderrCapture.+)")
("os/exec/exec_test.go" "(.+)(TestExtraFiles.+)")
("os/exec/exec_test.go" "(.+)(TestExtraFilesRace.+)")
@ -382,7 +383,7 @@ (define-public go-1.10
(package
(inherit go-1.9)
(name "go")
(version "1.10")
(version "1.10.1")
(source
(origin
(method url-fetch)
@ -390,7 +391,7 @@ (define-public go-1.10
name version ".src.tar.gz"))
(sha256
(base32
"093z1h0gmi458kv7smpx0ph6jm7ss9mzxa432kysbz85jhl4kppk"))))
"1p1xyyxicp752n9wj10sljjl6mjxpfsplkhx74fzzjrwdkzlk52q"))))
(arguments
(substitute-keyword-arguments (package-arguments go-1.9)
((#:phases phases)
@ -460,6 +461,7 @@ (define-public go-1.10
("syscall/syscall_unix_test.go" "(.+)(TestPassFD\\(.+)")
("os/exec/exec_test.go" "(.+)(TestExtraFiles/areturn.+)")
("cmd/go/go_test.go" "(.+)(TestCoverageWithCgo.+)")
("cmd/go/go_test.go" "(.+)(TestTwoPkgConfigs.+)")
("os/exec/exec_test.go" "(.+)(TestOutputStderrCapture.+)")
("os/exec/exec_test.go" "(.+)(TestExtraFiles.+)")
("os/exec/exec_test.go" "(.+)(TestExtraFilesRace.+)")

11
gnu/packages/graph.scm
View file

@ -98,23 +98,24 @@ (define-public python-igraph
(define-public r-igraph
(package
(name "r-igraph")
(version "1.1.2")
(version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "igraph" version))
(sha256
(base32
"1v26wyk52snh8z6m5p7yqwcd9dbqifhm57j112i9x53ppi0npcc9"))))
"1hcr6b1lz030lgay1bz8y8sxaf2j93ds8n8gsqr6qhssz141hd2m"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(inputs
`(("gmp" ,gmp)
("libxml2" ,libxml2)))
("glpk" ,glpk)
("libxml2" ,libxml2)
("zlib" ,zlib)))
(propagated-inputs
`(("r-irlba" ,r-irlba)
("r-magrittr" ,r-magrittr)
`(("r-magrittr" ,r-magrittr)
("r-matrix" ,r-matrix)
("r-pkgconfig" ,r-pkgconfig)))
(home-page "http://igraph.org")

2
gnu/packages/gstreamer.scm
View file

@ -404,7 +404,7 @@ (define-public gst-libav
("python" ,python)))
(inputs
`(("gst-plugins-base" ,gst-plugins-base)
("ffmpeg" ,ffmpeg)
("ffmpeg" ,ffmpeg-3.4)
("orc" ,orc)
("zlib" ,zlib)))
(home-page "https://gstreamer.freedesktop.org/")

2
gnu/packages/guile.scm
View file

@ -1501,7 +1501,7 @@ (define-public guile-sly
(description "Sly is a 2D/3D game engine written in Guile Scheme. Sly
features a functional reactive programming interface and live coding
capabilities.")
(home-page "http://dthompson.us/pages/software/sly.html")
(home-page "https://dthompson.us/projects/sly.html")
(license license:gpl3+)))
(define-public g-wrap

4
gnu/packages/image-viewers.scm
View file

@ -59,7 +59,7 @@ (define-module (gnu packages image-viewers)
(define-public feh
(package
(name "feh")
(version "2.25.1")
(version "2.26")
(home-page "https://feh.finalrewind.org/")
(source (origin
(method url-fetch)
@ -67,7 +67,7 @@ (define-public feh
name "-" version ".tar.bz2"))
(sha256
(base32
"197sm78bm33dvahr5nxqkbmpmdn4b13ahc9mrgn1l7n104bg4phc"))))
"11kckzwk3b734l0n4j41k40liq1v2lbbj1gzir5qc386g7fvzmmi"))))
(build-system gnu-build-system)
(arguments
'(#:phases (modify-phases %standard-phases (delete 'configure))

32
gnu/packages/image.scm
View file

@ -716,7 +716,8 @@ (define-public freeimage
(for-each
(lambda (dir)
(delete-file-recursively (string-append "Source/" dir)))
'("LibJPEG" "LibJXR" "LibOpenJPEG" "LibPNG" "LibRawLite"
'("LibJPEG" "LibOpenJPEG" "LibPNG" "LibRawLite"
;; "LibJXR"
"LibWebP" "OpenEXR" "ZLib"))))
(patches (search-patches "freeimage-unbundle.patch"
"freeimage-CVE-2015-0852.patch"
@ -752,14 +753,15 @@ (define-public freeimage
;; We need '-fpermissive' for Source/FreeImage.h.
;; libjxr doesn't have a pkg-config file.
(string-append "CFLAGS+=-O2 -fPIC -fvisibility=hidden -fpermissive "
"-I" (assoc-ref %build-inputs "libjxr") "/include/jxrlib"))
;"-I" (assoc-ref %build-inputs "libjxr") "/include/jxrlib"
))
#:tests? #f)) ; no check target
(native-inputs
`(("pkg-config" ,pkg-config)
("unzip" ,unzip)))
(inputs
`(("libjpeg" ,libjpeg)
("libjxr" ,libjxr)
;("libjxr" ,libjxr)
("libpng" ,libpng)
("libraw" ,libraw)
("libtiff" ,libtiff)
@ -836,16 +838,18 @@ (define-public vigra
(define-public libwebp
(package
(name "libwebp")
(version "0.6.1")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (string-append
"http://downloads.webmproject.org/releases/webp/libwebp-" version
".tar.gz"))
;; No tarballs are provided for >0.6.1.
(method git-fetch)
(uri (git-reference
(url "https://chromium.googlesource.com/webm/libwebp")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1ayq2zq0zbgf5yizbm32zh7p1vb8kibw74am6am1n5cz5mw3ql06"))))
"1w8jzdbr1s4238ygyrlxryycss3f2z6d9amxdq8m82nl3l6skar4"))))
(build-system gnu-build-system)
(inputs
`(("freeglut" ,freeglut)
@ -853,10 +857,18 @@ (define-public libwebp
("libjpeg" ,libjpeg)
("libpng" ,libpng)
("libtiff" ,libtiff)))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)))
(arguments
'(#:configure-flags '("--enable-libwebpmux"
"--enable-libwebpdemux"
"--enable-libwebpdecoder")))
"--enable-libwebpdecoder")
#:phases (modify-phases %standard-phases
(add-after 'unpack 'bootstrap
(lambda _
(invoke "autoreconf" "-vif"))))))
(home-page "https://developers.google.com/speed/webp/")
(synopsis "Lossless and lossy image compression")
(description

9
gnu/packages/irc.scm
View file

@ -65,18 +65,17 @@ (define-module (gnu packages irc)
(define-public quassel
(package
(name "quassel")
(version "0.12.4")
(version "0.12.5")
(source
(origin
(method url-fetch)
(uri (string-append "http://quassel-irc.org/pub/quassel-"
version ".tar.bz2"))
(patches (search-patches "quassel-fix-tls-check.patch"))
(sha256
(base32
"0ka456fb8ha3w7g74xlzfg6w4azxjjxgrhl4aqpbwg3lnd6fbr4k"))
"1qkl3sb4ijx4k17m0c42j2p5bc4jymypwhmplm942rbrzm6mg50q"))
(modules '((guix build utils)))
;; We don't want to install the bundles scripts
;; We don't want to install the bundled scripts.
(snippet
'(begin
(delete-file-recursively "data/scripts")
@ -105,7 +104,7 @@ (define-public quassel
("qtscript" ,qtscript)
("snorenotify" ,snorenotify)
("zlib" ,zlib)))
(home-page "http://quassel-irc.org/")
(home-page "https://quassel-irc.org/")
(synopsis "Distributed IRC client")
(description "Quassel is a distributed IRC client, meaning that one or more
clients can attach to and detach from the central core. It resembles the

305
gnu/packages/java.scm
View file

@ -8150,70 +8150,50 @@ (define-public java-lz4
algorithms and xxHash hashing algorithm.")
(license license:asl2.0)))
(define-public java-bouncycastle-bcprov
(define-public java-bouncycastle
(package
(name "java-bouncycastle-bcprov")
(version "1.58")
(name "java-bouncycastle")
(version "1.59")
(source (origin
(method url-fetch)
(uri "https://bouncycastle.org/download/bcprov-jdk15on-158.tar.gz")
(uri (string-append "https://github.com/bcgit/bc-java/archive/r"
(substring version 0 1) "rv"
(substring version 2 4) ".tar.gz"))
(sha256
(base32
"1hgkg96llbvgs8i0krwz2n0j7wlg6jfnq8w8kg0cc899j0wfmf3n"))))
"1bwl499whlbq896w18idqw2dkp8v0wp0npv9g71i5fgf8xjh0k3q"))
(modules '((guix build utils)))
(snippet
'(begin
(for-each delete-file
(find-files "." "\\.jar$"))
#t))))
(build-system ant-build-system)
(arguments
`(#:jar-name "bouncycastle-bcprov.jar"
#:tests? #f; no tests
#:source-dir "src"
`(#:jdk ,icedtea-8
#:phases
(modify-phases %standard-phases
(add-before 'configure 'unzip-src
(replace 'build
(lambda _
(mkdir-p "src")
(with-directory-excursion "src"
(invoke "unzip" "../src.zip"))
#t)))))
(native-inputs
`(("unzip" ,unzip)
("junit" ,java-junit)))
(home-page "https://www.bouncycastle.org")
(synopsis "Cryptographic library")
(description "Bouncy Castle Provider (bcprov) is a cryptographic library
for the Java programming language.")
(license license:expat)))
(define-public java-bouncycastle-bcpkix
(package
(name "java-bouncycastle-bcpkix")
(version "1.58")
(source (origin
(method url-fetch)
(uri "https://bouncycastle.org/download/bcpkix-jdk15on-158.tar.gz")
(sha256
(base32
"0is7qay02803s9f7lhnfcjlz61ni3hq5d7apg0iil7nbqkbfbcq2"))))
(build-system ant-build-system)
(arguments
`(#:jar-name "bouncycastle-bcpkix.jar"
#:tests? #f; no tests
#:source-dir "src"
#:phases
(modify-phases %standard-phases
(add-before 'configure 'unzip-src
(invoke "ant" "-f" "ant/jdk15+.xml" "build-provider")
(invoke "ant" "-f" "ant/jdk15+.xml" "build")
#t))
(replace 'check
(lambda _
(mkdir-p "src")
(with-directory-excursion "src"
(invoke "unzip" "../src.zip"))
#t)))))
(native-inputs
`(("unzip" ,unzip)
("junit" ,java-junit)))
(invoke "ant" "-f" "ant/jdk15+.xml" "test")))
(replace 'install
(install-jars "build/artifacts/jdk1.5/jars")))))
(inputs
`(("bcprov" ,java-bouncycastle-bcprov)))
`(("java-javax-mail" ,java-javax-mail)))
(native-inputs
`(("unzip" ,unzip)
("junit" ,java-junit)
("java-native-access" ,java-native-access)
("java-native-access-platform" ,java-native-access-platform)))
(home-page "https://www.bouncycastle.org")
(synopsis "Cryptographic library")
(description "Bouncy Castle Java API for PKIX, CMS, EAC, TSP, PKCS, OCSP,
CMP, and CRMF.")
(description "Bouncy Castle is a cryptographic library for the Java
programming language.")
(license license:expat)))
(define-public java-lmax-disruptor
@ -8636,8 +8616,7 @@ (define-public java-kafka-clients
("powermock-junit4-common" ,java-powermock-modules-junit4-common)
("powermock-junit4" ,java-powermock-modules-junit4)
("powermock-support" ,java-powermock-api-support)
("bouncycastle" ,java-bouncycastle-bcprov)
("bouncycastle-bcpkix" ,java-bouncycastle-bcpkix)))
("java-bouncycastle" ,java-bouncycastle)))
(home-page "https://kafka.apache.org")
(synopsis "Distributed streaming platform")
(description "Kafka is a distributed streaming platform, which means:
@ -9610,3 +9589,225 @@ (define-public java-native-access-platform
and mappings for a number of commonly used platform functions, including a
large number of Win32 mappings as well as a set of utility classes that
simplify native access.")))
(define-public java-jsch-agentproxy-core
(package
(name "java-jsch-agentproxy-core")
(version "0.0.8")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/ymnk/jsch-agent-proxy/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"02iqg6jbc1kxvfzqcg6wy9ygqxfm82bw5rf6vnswqy4y572niz4q"))))
(build-system ant-build-system)
(arguments
`(#:jar-name "jsch-agentproxy-core.jar"
#:source-dir "jsch-agent-proxy-core/src/main/java"
#:tests? #f)); no tests
(home-page "https://github.com/ymnk/jsch-agent-proxy")
(synopsis "Core component of the proxy to ssh-agent and Pageant in Java")
(description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent
and Pageant included Putty. It will be easily integrated into JSch, and users
will be allowed to use these programs for authentication.")
(license license:bsd-3)))
(define-public java-jsch-agentproxy-sshagent
(package
(inherit java-jsch-agentproxy-core)
(name "java-jsch-agentproxy-sshagent")
(arguments
`(#:jar-name "jsch-agentproxy-sshagent.jar"
#:source-dir "jsch-agent-proxy-sshagent/src/main/java"
#:tests? #f)); no tests
(inputs
`(("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core)))
(synopsis "Proxy to ssh-agent")
(description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent
and Pageant included in Putty. This component contains the code for a proxy to
ssh-agent.")))
(define-public java-jsch-agentproxy-usocket-jna
(package
(inherit java-jsch-agentproxy-core)
(name "java-jsch-agentproxy-usocket-jna")
(arguments
`(#:jar-name "jsch-agentproxy-usocket-jna.jar"
#:source-dir "jsch-agent-proxy-usocket-jna/src/main/java"
#:tests? #f)); no tests
(inputs
`(("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core)
("java-native-access" ,java-native-access)))
(synopsis "USocketFactory implementation using JNA")
(description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent
and Pageant included in Putty. This component contains an implementation of
USocketFactory using @dfn{JNA} (Java Native Access).")))
(define-public java-jsch-agentproxy-pageant
(package
(inherit java-jsch-agentproxy-core)
(name "java-jsch-agentproxy-pageant")
(arguments
`(#:jar-name "jsch-agentproxy-pageant.jar"
#:source-dir "jsch-agent-proxy-pageant/src/main/java"
#:tests? #f)); no tests
(inputs
`(("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core)
("java-native-access" ,java-native-access)
("java-native-access-platform" ,java-native-access-platform)))
(synopsis "Proxy to pageant")
(description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent
and Pageant included in Putty. This component contains the code for a proxy to
pageant.")))
(define-public java-jsch-agentproxy-usocket-nc
(package
(inherit java-jsch-agentproxy-core)
(name "java-jsch-agentproxy-usocket-nc")
(arguments
`(#:jar-name "jsch-agentproxy-usocket-nc.jar"
#:source-dir "jsch-agent-proxy-usocket-nc/src/main/java"
#:tests? #f)); no tests
(inputs
`(("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core)))
(synopsis "USocketFactory implementation using netcat")
(description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent
and Pageant included in Putty. This component contains an implementation of
USocketFactory using netcat.")))
(define-public java-jsch-agentproxy-connector-factory
(package
(inherit java-jsch-agentproxy-core)
(name "java-jsch-agentproxy-connector-factory")
(arguments
`(#:jar-name "jsch-agentproxy-connector-factory.jar"
#:source-dir "jsch-agent-proxy-connector-factory/src/main/java"
#:tests? #f)); no tests
(inputs
`(("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core)
("java-jsch-agentproxy-sshagent" ,java-jsch-agentproxy-sshagent)
("java-jsch-agentproxy-usocket-jna" ,java-jsch-agentproxy-usocket-jna)
("java-jsch-agentproxy-pageant" ,java-jsch-agentproxy-pageant)
("java-jsch-agentproxy-usocket-nc" ,java-jsch-agentproxy-usocket-nc)))
(synopsis "Connector factory for jsch agent proxy")
(description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent
and Pageant included in Putty. This component contains a connector factory.")))
(define-public java-jsch-agentproxy-jsch
(package
(inherit java-jsch-agentproxy-core)
(name "java-jsch-agentproxy-jsch")
(arguments
`(#:jar-name "jsch-agentproxy-jsch.jar"
#:source-dir "jsch-agent-proxy-jsch/src/main/java"
#:tests? #f)); no tests
(inputs
`(("java-jsch" ,java-jsch)
("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core)))
(synopsis "JSch integration library for agentproxy")
(description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent
and Pageant included in Putty. This component contains a library to use
jsch-agent-proxy with JSch.")))
(define-public java-apache-ivy
(package
(name "java-apache-ivy")
(version "2.4.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://apache//ant/ivy/" version
"/apache-ivy-" version "-src.tar.gz"))
(sha256
(base32
"1xkfn57g2m7l6y0xdq75x5rnrgk52m9jx2xah70g3ggl8750hbr0"))
(patches
(search-patches
"java-apache-ivy-port-to-latest-bouncycastle.patch"))))
(build-system ant-build-system)
(arguments
`(#:jar-name "ivy.jar"
#:tests? #f
#:phases
(modify-phases %standard-phases
(add-before 'build 'remove-example
(lambda _
(delete-file-recursively "src/example")
#t))
(add-before 'build 'copy-resources
(lambda _
(with-directory-excursion "src/java"
(for-each (lambda (file)
(install-file file (string-append "../../build/classes/" (dirname file))))
(append
(find-files "." ".*.css")
(find-files "." ".*.ent")
(find-files "." ".*.html")
(find-files "." ".*.properties")
(find-files "." ".*.xsd")
(find-files "." ".*.xsl")
(find-files "." ".*.xml"))))))
(add-before 'build 'fix-vfs
(lambda _
(substitute*
'("src/java/org/apache/ivy/plugins/repository/vfs/VfsRepository.java"
"src/java/org/apache/ivy/plugins/repository/vfs/VfsResource.java")
(("import org.apache.commons.vfs") "import org.apache.commons.vfs2"))
#t))
(add-before 'install 'copy-manifest
(lambda _
(install-file "META-INF/MANIFEST.MF" "build/classes/META-INF")
#t))
(add-before 'install 'repack
(lambda _
(invoke "jar" "-cmf" "build/classes/META-INF/MANIFEST.MF" "build/jar/ivy.jar"
"-C" "build/classes" ".")
#t))
(add-after 'install 'install-bin
(lambda* (#:key outputs #:allow-other-keys)
(let* ((bin (string-append (assoc-ref outputs "out") "/bin"))
(ivy (string-append bin "/ivy"))
(jar (string-append (assoc-ref outputs "out") "/share/java/ivy.jar")))
(mkdir-p bin)
(with-output-to-file ivy
(lambda _
(display (string-append
"#!" (which "sh") "\n"
"if [[ -z $CLASSPATH ]]; then\n"
" cp=\"" (getenv "CLASSPATH") ":" jar "\"\n"
"else\n"
" cp=\"" (getenv "CLASSPATH") ":" jar ":$CLASSPATH\"\n"
"fi\n"
(which "java") " -cp $cp org.apache.ivy.Main $@\n"))))
(chmod ivy #o755)
#t))))))
(inputs
`(("java-bouncycastle" ,java-bouncycastle)
("java-commons-cli" ,java-commons-cli)
("java-commons-collections" ,java-commons-collections)
("java-commons-httpclient" ,java-commons-httpclient)
("java-commons-lang" ,java-commons-lang)
("java-commons-vfs" ,java-commons-vfs)
("java-jakarta-oro" ,java-jakarta-oro)
("java-jsch" ,java-jsch)
("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core)
("java-jsch-agentproxy-connector-factory" ,java-jsch-agentproxy-connector-factory)
("java-jsch-agentproxy-jsch" ,java-jsch-agentproxy-jsch)
("java-junit" ,java-junit)))
(home-page "https://ant.apache.org/ivy")
(synopsis "Dependency manager for the Java programming language")
(description "Ivy is a tool for managing (recording, tracking, resolving
and reporting) project dependencies. It is characterized by the following:
@itemize
@item flexibility and configurability - Ivy is essentially process agnostic
and is not tied to any methodology or structure. Instead it provides the
necessary flexibility and configurability to be adapted to a broad range
of dependency management and build processes.
@item tight integration with Apache Ant - while available as a standalone tool,
Ivy works particularly well with Apache Ant providing a number of
powerful Ant tasks ranging from dependency resolution to dependency
reporting and publication.
@end itemize")
(license license:asl2.0)))

2
gnu/packages/julia.scm
View file

@ -384,7 +384,7 @@ (define-public julia
;; Julia is not officially released for ARM and MIPS.
;; See https://github.com/JuliaLang/julia/issues/10639
(supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))
(home-page "http://julialang.org/")
(home-page "https://julialang.org/")
(synopsis "High-performance dynamic language for technical computing")
(description
"Julia is a high-level, high-performance dynamic programming language for

8
gnu/packages/libreoffice.scm
View file

@ -359,14 +359,14 @@ (define-public libcdr
(define-public libetonyek
(package
(name "libetonyek")
(version "0.1.7")
(version "0.1.8")
(source
(origin
(method url-fetch)
(uri (string-append "http://dev-www.libreoffice.org/src/" name "/"
name "-" version ".tar.xz"))
(sha256 (base32
"1b1lqy6g7flximlv0bp8jbsivyhdp679yj0d0q4jzm968h6y3nv9"))))
"0bfq9rwm040xhh7b3v0gsdavwvnrz4hkwnhpggarxk70mr3j7jcx"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("--with-mdds=1.2")))
@ -611,14 +611,14 @@ (define-public libmwaw
(define-public libstaroffice
(package
(name "libstaroffice")
(version "0.0.5")
(version "0.0.6")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/fosnola/libstaroffice/releases/download/"
version "/libstaroffice-" version ".tar.xz"))
(sha256 (base32
"10m9imcgqf7kdhn1a5ara62fdayidwm7qzj3binsls40snnhfm9i"))))
"1i0ykl0c94lc1qzb5mbyf9jr7qw8p38ja424whmhgrllh7ny203b"))))
(build-system gnu-build-system)
(inputs
`(("librevenge" ,librevenge)

127
gnu/packages/linux.scm
View file

@ -27,6 +27,7 @@
;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2017 nee <nee-git@hidamari.blue>
;;; Copyright © 2017 Dave Love <fx@gnu.org>
;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -391,8 +392,8 @@ (define %linux-compatible-systems '("x86_64-linux" "i686-linux" "armhf-linux"))
;; supports qemu "virt" machine and possibly a large number of ARM boards.
;; See : https://wiki.debian.org/DebianKernel/ARMMP.
(define %linux-libre-version "4.16.3")
(define %linux-libre-hash "1wmx0ph8nbwidlx1dh8bi4p97b84nif9ymv00mafnn6iykdfdin0")
(define %linux-libre-version "4.16.6")
(define %linux-libre-hash "069bxqx27xib1gz4aayy8ar2hfp68cpdi8h51g6453k0w14pkchn")
(define-public linux-libre
(make-linux-libre %linux-libre-version
@ -400,8 +401,8 @@ (define-public linux-libre
%linux-compatible-systems
#:configuration-file kernel-config))
(define %linux-libre-4.14-version "4.14.35")
(define %linux-libre-4.14-hash "0dfzc2290zks1a63zld8ac0xarc8gxwwh4wsr71y8mas7gfmyqzj")
(define %linux-libre-4.14-version "4.14.38")
(define %linux-libre-4.14-hash "09lmz8zbd3c1qf8z3d2lkhcqcwawajh76s85zdhgqdmd2idpwach")
(define-public linux-libre-4.14
(make-linux-libre %linux-libre-4.14-version
@ -410,14 +411,14 @@ (define-public linux-libre-4.14
#:configuration-file kernel-config))
(define-public linux-libre-4.9
(make-linux-libre "4.9.95"
"06i756gbglxa2m4lib4p0fff5m2fm4s6f9aqc58i8lihnjqpkldk"
(make-linux-libre "4.9.97"
"1xc3mj1qi51n1kr5bxmdf1rlpyj78x9imhfc7gihn8qjc6zsf1sp"
%intel-compatible-systems
#:configuration-file kernel-config))
(define-public linux-libre-4.4
(make-linux-libre "4.4.128"
"1aqz5skyz534bcpnn6w9madg6kadgyjjypah9dhmqf841rygb6rk"
(make-linux-libre "4.4.130"
"15cayafj7d9y5fs9flg115kzrcrjycbvax9hgfzz6yym94v9k8lk"
%intel-compatible-systems
#:configuration-file kernel-config))
@ -2898,7 +2899,7 @@ (define-public mdadm-static
(define-public multipath-tools
(package
(name "multipath-tools")
(version "0.7.4")
(version "0.7.6")
(source (origin
(method url-fetch)
(uri (string-append "https://git.opensvc.com/?p=multipath-tools/"
@ -2906,7 +2907,7 @@ (define-public multipath-tools
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"02lk453wa2gfxkl8zmdws15nkcibln2yw76zm779pkngkhggl6w8"))
"0zkcayi3mmp43ji2zid1gprgsvqhjjapsw7jjd60sf75prf50h2r"))
(modules '((guix build utils)))
(snippet
'(begin
@ -3306,7 +3307,8 @@ (define-public freefall
(("alarm\\(2\\)") "alarm(5)"))
#t)))
#:make-flags (list (string-append "PREFIX="
(assoc-ref %outputs "out")))
(assoc-ref %outputs "out"))
"CC=gcc")
#:tests? #f)) ;no tests
(home-page (package-home-page linux-libre))
(synopsis "Free-fall protection for spinning laptop hard drives")
@ -4301,20 +4303,20 @@ (define-public proot-static
(define-public cpuid
(package
(name "cpuid")
(version "20170122")
(version "20180419")
(source (origin
(method url-fetch)
(uri (string-append "http://www.etallen.com/cpuid/cpuid-"
version ".src.tar.gz"))
(sha256
(base32
"0ra8ph9m1dckqaikfnbsh408fp2w9k49fkl423fl2hvhwsm14xk6"))))
"0cnxj72pjalsszhn862r6shw64zbrkw0k3mm36fn93bivswjnj12"))))
(build-system gnu-build-system)
(arguments
'(#:make-flags '("CC=gcc")
#:tests? #f ; no tests
#:tests? #f ; no tests
#:phases (modify-phases %standard-phases
(delete 'configure)
(delete 'configure) ; no configure script
(add-before 'install 'fix-makefile
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "Makefile"
@ -4628,3 +4630,98 @@ (define-public mbpfan
module. It can be executed as a daemon or in the foreground with root
privileges.")
(license license:gpl3+)))
(define-public psm2
(package
(name "psm2")
(version "10.3-46")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/intel/opa-psm2.git")
(commit (string-append "PSM2_" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0wadphv4rl5p38x6a3dgpbijlzqdvcn02cfafnp72nh9faz0zvlx"))))
(build-system gnu-build-system)
(arguments
'(#:make-flags
`(,(string-append "LDFLAGS=-Wl,-rpath=" %output "/lib"))
#:tests? #f
#:phases (modify-phases %standard-phases
(delete 'configure)
(add-after 'unpack 'patch-Makefiles
(lambda _
(substitute* "Makefile"
(("/lib64") "/lib")
(("/usr") ""))
(substitute* "compat/Makefile"
(("/lib64") "/lib")
(("/usr") ""))
#t))
(replace 'install
(lambda _
(setenv "DESTDIR" %output)
(invoke "make" "install")
#t)))))
(inputs
`(("rdma-core" ,rdma-core)
("numactl" ,numactl)))
(synopsis "Intel Performance Scaled Messaging 2 (PSM2) library")
(description
"This package is low-level user-level Intel's communications interface.
The PSM2 API is a high-performance vendor-specific protocol that provides a
low-level communications interface for the Intel Omni-Path family of
high-speed networking devices.")
(home-page "https://github.com/intel/opa-psm2")
;; Only the x86_64 architecure is supported.
(supported-systems '("x86_64-linux"))
(license (list license:bsd-3 license:gpl2)))) ; dual
(define-public libpfm4
(package
(name "libpfm4")
(version "4.9.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/perfmon2/"
name "/libpfm-" version ".tar.gz"))
(sha256
(base32
"1qp4g4n6dw42p2w5rkwzdb7ynk8h7g5vg01ybpmvxncgwa7bw3yv"))))
(build-system gnu-build-system)
(arguments
'(#:modules ((guix build utils)
(guix build gnu-build-system))
#:phases (modify-phases %standard-phases
(delete 'configure)
(delete 'check)
(replace 'build
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")))
(setenv "CC" "gcc")
(invoke "make")
#t)))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")))
(invoke "make"
(string-append "PREFIX=" out)
"install")
#t))))))
(synopsis "Performance event monitoring library")
(description
"This package provides a library called libpfm4, which is used to develop
monitoring tools exploiting the performance monitoring events such as those
provided by the Performance Monitoring Unit (PMU) of modern processors.
Libpfm4 helps convert from an event name, expressed as a string, to the event
encoding that is either the raw event as documented by the hardware vendor or
the OS-specific encoding. In the latter case, the library is able to prepare
the OS-specific data structures needed by the kernel to setup the event.
libpfm4 provides support for the @code{perf_events} interface, which was
introduced in Linux 2.6.31.")
(home-page "http://perfmon2.sourceforge.net/")
(license license:expat)))

13
gnu/packages/lxde.scm
View file

@ -48,7 +48,7 @@ (define-module (gnu packages lxde)
(define-public libfm
(package
(name "libfm")
(version "1.2.5")
(version "1.3.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/pcmanfm/"
@ -56,7 +56,7 @@ (define-public libfm
"%29/LibFM/" name "-" version ".tar.xz"))
(sha256
(base32
"0nlvfwh09gbq8bkbvwnw6iqr918rrs9gc9ljb9pjspyg408bn1n7"))))
"151jyy8ipmp2h829gd9s4s429qafv1zxl7j6zaj1k1gzm9s5rmnb"))))
(build-system gnu-build-system)
(inputs `(("glib" ,glib)
("gtk+" ,gtk+-2)))
@ -205,26 +205,25 @@ (define-public menu-cache
(define-public pcmanfm
(package
(name "pcmanfm")
(version "1.2.5")
(version "1.3.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/" name "/"
"PCManFM%20%2B%20Libfm%20%28tarball%20release"
"%29/PCManFM/" name "-" version ".tar.xz"))
(patches (search-patches "pcmanfm-CVE-2017-8934.patch"))
(sha256
(base32
"0rxdh0dfzc84l85c54blq42gczygq8adhr3l9hqzy1dp530cm1hc"))))
"1ywgfyklms5hqkapsbjps4kyx20ac0d1qk16ww74yagkyfdkwsas"))))
(build-system gnu-build-system)
(inputs `(("gtk+" ,gtk+-2)
("gvfs" ,gvfs) ;for trash and mount support
("gvfs" ,gvfs) ; for trash and mount support
("libfm" ,libfm)
("libx11" ,libx11)))
(native-inputs `(("intltool" ,intltool)
("libtool" ,libtool)
("pkg-config" ,pkg-config)))
(propagated-inputs
`(("lxmenu-data" ,lxmenu-data))) ;for "Open With..." application list
`(("lxmenu-data" ,lxmenu-data))) ; for "Open With..." application list
(synopsis "LXDE file manager")
(description "PCMan is a lightweight GTK+ based file manager, compliant
with freedesktop.org standard.")

44
gnu/packages/machine-learning.scm
View file

@ -6,6 +6,7 @@
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -689,3 +690,46 @@ (define-public python-scikit-learn
(define-public python2-scikit-learn
(package-with-python2 python-scikit-learn))
(define-public python-autograd
(let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
(revision "0")
(version (git-version "0.0.0" revision commit)))
(package
(name "python-autograd")
(home-page "https://github.com/HIPS/autograd")
(source (origin
(method git-fetch)
(uri (git-reference
(url home-page)
(commit commit)))
(sha256
(base32
"189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
(file-name (git-file-name name version))))
(version version)
(build-system python-build-system)
(native-inputs
`(("python-nose" ,python-nose)
("python-pytest" ,python-pytest)))
(propagated-inputs
`(("python-future" ,python-future)
("python-numpy" ,python-numpy)))
(arguments
`(#:phases (modify-phases %standard-phases
(replace 'check
(lambda _
(invoke "py.test" "-v"))))))
(synopsis "Efficiently computes derivatives of NumPy code")
(description "Autograd can automatically differentiate native Python and
NumPy code. It can handle a large subset of Python's features, including loops,
ifs, recursion and closures, and it can even take derivatives of derivatives
of derivatives. It supports reverse-mode differentiation
(a.k.a. backpropagation), which means it can efficiently take gradients of
scalar-valued functions with respect to array-valued arguments, as well as
forward-mode differentiation, and the two can be composed arbitrarily. The
main intended application of Autograd is gradient-based optimization.")
(license license:expat))))
(define-public python2-autograd
(package-with-python2 python-autograd))

4
gnu/packages/mail.scm
View file

@ -747,14 +747,14 @@ (define-public notifymuch
(define-public notmuch
(package
(name "notmuch")
(version "0.26.1")
(version "0.26.2")
(source (origin
(method url-fetch)
(uri (string-append "https://notmuchmail.org/releases/notmuch-"
version ".tar.gz"))
(sha256
(base32
"0dx8nhdmkaqabxcgxfa757m99fi395y76h9ynx8539yh9m7y9xyk"))))
"0fqf6wwvqlccq9qdnd0mky7fx0kbkczd28blf045s0vsvdjii70h"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build gnu-build-system)

16
gnu/packages/maths.scm
View file

@ -1779,7 +1779,7 @@ (define-public slepc-complex-openmpi
(define-public mumps
(package
(name "mumps")
(version "5.0.2")
(version "5.1.2")
(source
(origin
(method url-fetch)
@ -1787,7 +1787,7 @@ (define-public mumps
version ".tar.gz"))
(sha256
(base32
"0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
"1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
(patches (search-patches "mumps-build-parallelism.patch"))))
(build-system gnu-build-system)
(inputs
@ -2208,16 +2208,18 @@ (define-public superlu-dist
(define-public scotch
(package
(name "scotch")
(version "6.0.4")
(version "6.0.5a")
(source
(origin
(method url-fetch)
(uri (string-append "https://gforge.inria.fr/frs/download.php/"
"latestfile/298/scotch_" version ".tar.gz"))
(sha256
(base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
(base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av"))
(patches (search-patches "scotch-test-threading.patch"
"pt-scotch-build-parallelism.patch"))))
"scotch-build-parallelism.patch"
"scotch-graph-induce-type-64.patch"
"scotch-graph-diam-64.patch"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)
@ -3845,14 +3847,14 @@ (define-public mcrl2
(define-public r-subplex
(package
(name "r-subplex")
(version "1.5-2")
(version "1.5-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "subplex" version))
(sha256
(base32
"1v9xrnkapnq7v1jbhlg32ignklzf2vn8rqpayc8pzk8wvz53r33g"))))
"10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))

9
gnu/packages/mes.scm
View file

@ -60,16 +60,15 @@ (define-public mes
(let ((triplet "i686-unknown-linux-gnu"))
(package
(name "mes")
(version "0.12")
(version "0.13")
(source (origin
(method url-fetch)
(uri (string-append "https://gitlab.com/janneke/mes"
"/repository/archive.tar.gz?ref=v"
version))
(file-name (string-append name "-" version ".tar.gz"))
"/-/archive/v" version
"/mes-" version ".tar.gz"))
(sha256
(base32
"0lbwmyl5262z28kpac6kmxxx8aglzy8n6bsicp5lyzkmzkzvjnh2"))))
"0db4f32rak839ff3n7ywkkng9672457pd2pvvgvcsyndqmmdsqw0"))))
(build-system gnu-build-system)
(supported-systems '("i686-linux" "x86_64-linux"))
(propagated-inputs

36
gnu/packages/messaging.scm
View file

@ -802,7 +802,7 @@ (define-public libtoxcore
(define-public c-toxcore
(package
(name "c-toxcore")
(version "0.1.11")
(version "0.2.2")
(source
(origin
(method url-fetch)
@ -811,7 +811,10 @@ (define-public c-toxcore
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"040vwihl1r5159vzimmnff75iqfg53vhnfi5wcb3cd0c2r51idl5"))))
"18bfqx0ylbas9gs91rkspf04l5fjjcl0mxm1gfs2d59bv65mvcm3"))))
(arguments
`(#:tests? #f)) ; FIXME: Testsuite seems to stay stuck on test 3. Disable
; for now.
(build-system cmake-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
@ -829,23 +832,26 @@ (define-public c-toxcore
(define-public utox
(package
(name "utox")
(version "0.16.1")
(version "0.17.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/uTox/uTox/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/uTox/uTox.git")
(commit "v0.17.0")
(recursive? #t))) ;; Needed for 'minini' git submodule.
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"14xl72y4w1x2kk0cvkcr9pmywllm0r9w2grjqiknwn95pw6yxz6q"))))
"12wbq883il7ikldayh8hm0cjfrkp45vn05xx9s1jbfz6gmkidyar"))))
(build-system cmake-build-system)
(arguments
`(#:phases
`(#:configure-flags '("-DENABLE_TESTS=on")
#:phases
(modify-phases %standard-phases
(add-before 'build 'patch-absolute-filename-libgtk-3
(lambda* (#:key inputs outputs #:allow-other-keys)
(substitute* "../uTox-0.16.1/src/xlib/gtk.c"
(substitute* "../source/src/xlib/gtk.c"
(("libgtk-3.so")
(string-append (assoc-ref inputs "gtk+")
"/lib/libgtk-3.so")))))
@ -884,14 +890,14 @@ (define-public utox
(define-public qtox
(package
(name "qtox")
(version "1.13.0")
(version "1.15.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/qTox/qTox/archive/v"
version ".tar.gz"))
(sha256
(base32
"0dyplmlqhg4zbg7hdzp3iqppn9xgp7pds5k6w6byjcqhb9zv91ca"))
"0bmnx6m33qn9nx40yy268x4wnvv2y7bvm41hzrlbhsiaph7kg583"))
(file-name (string-append name "-" version ".tar.gz"))))
(build-system cmake-build-system)
(arguments
@ -913,7 +919,7 @@ (define-public qtox
,(list (string-append (assoc-ref inputs "qtsvg")
"/lib/qt5/plugins/"))))))))))
(inputs
`(("ffmpeg" ,ffmpeg)
`(("ffmpeg" ,ffmpeg-3.4)
("filteraudio" ,filteraudio)
("glib" ,glib)
("gtk+" ,gtk+-2)
@ -1520,14 +1526,14 @@ (define-public libircclient
(define-public toxic
(package
(name "toxic")
(version "0.8.0")
(version "0.8.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/JFreegman/toxic/archive/v"
version ".tar.gz"))
(sha256
(base32
"0166lqb47f4kj34mhi57aqmnk9mh4hsicmbdsj6ag54sy1zicy20"))
"1dx6z7k0zpsd7dpysdy23f0hnm49qlikb0mq8fg0y01dsz9vxgak"))
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments

4
gnu/packages/mpd.scm
View file

@ -88,7 +88,7 @@ (define-public libmpdclient
(define-public mpd
(package
(name "mpd")
(version "0.20.18")
(version "0.20.19")
(source (origin
(method url-fetch)
(uri
@ -97,7 +97,7 @@ (define-public mpd
"/mpd-" version ".tar.xz"))
(sha256
(base32
"0d6lz8ykyvxkl0fwnd9c5vzbbhmjh1yzv7rzhprlzfchmv12sn3a"))))
"1hsng4mnaz1jr2s3fy3q78vf2f6102lwphjdls7qln0pj8dyzk81"))))
(build-system gnu-build-system)
(arguments
`(#:phases

35
gnu/packages/music.scm
View file

@ -1601,7 +1601,7 @@ (define-public bristol
(define-public tuxguitar
(package
(name "tuxguitar")
(version "1.4")
(version "1.5")
(source (origin
(method url-fetch)
(uri (string-append
@ -1609,7 +1609,7 @@ (define-public tuxguitar
version "/tuxguitar-" version "-src.tar.gz"))
(sha256
(base32
"041275vwfr82kass7wiq9g2y82w9qrbzfinzcvfij2f2q45njwmc"))
"1yd5wv17sh6i8pkndxayfd6r2k1ccgnc4w3nda3lpniv8cpjzz3k"))
(modules '((guix build utils)))
(snippet
'(begin
@ -1691,7 +1691,7 @@ (define-public tuxguitar
#t))))))
(inputs
`(("java-swt" ,java-swt)))
(home-page "http://tuxguitar.pw")
(home-page "http://tuxguitar.com.ar/")
(synopsis "Multitrack tablature editor and player")
(description
"TuxGuitar is a guitar tablature editor with player support through midi.
@ -1883,17 +1883,17 @@ (define-public frescobaldi
(define-public drumstick
(package
(name "drumstick")
(version "1.1.0")
(version "1.1.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/drumstick/"
version "/drumstick-" version ".tar.bz2"))
(sha256
(base32
"13pkfqrav30bbcddgf1imd7jk6lpqbxkz1qv31718pdl446jq7df"))))
"0avwxr6n9ra7narxc5lmkhdqi8ix10gmif8rpd06wp4g9iv46xrn"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; no test target
`(#:tests? #f ; no test target
#:configure-flags '("-DLIB_SUFFIX=")
#:phases
(modify-phases %standard-phases
@ -1909,11 +1909,10 @@ (define-public drumstick
(inputs
`(("qtbase" ,qtbase)
("qtsvg" ,qtsvg)
("alsa-lib" ,alsa-lib)
("fluidsynth" ,fluidsynth)))
("alsa-lib" ,alsa-lib)))
(native-inputs
`(("pkg-config" ,pkg-config)
("libxslt" ,libxslt) ;for xsltproc
("libxslt" ,libxslt) ; for xsltproc
("docbook-xsl" ,docbook-xsl)
("doxygen" ,doxygen)))
(home-page "http://drumstick.sourceforge.net/")
@ -2150,14 +2149,14 @@ (define-public cursynth
(define-public aj-snapshot
(package
(name "aj-snapshot")
(version "0.9.7")
(version "0.9.8")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/aj-snapshot/"
"aj-snapshot-" version ".tar.bz2"))
(sha256
(base32
"0yxccgp9qw2cyqv719wlbq8wfsr5ga8czvwa7bmb8dh5s11n3rn8"))))
"0wilky1g2mb88v2z0520s7sw1dsn10iwanc8id5p6z1xsnhg7b6p"))))
(build-system gnu-build-system)
(inputs
`(("minixml" ,minixml)
@ -2393,7 +2392,7 @@ (define-public pianobar
("curl" ,curl)
("libgcrypt" ,libgcrypt)
("json-c" ,json-c)
("ffmpeg" ,ffmpeg)))
("ffmpeg" ,ffmpeg-3.4)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://6xq.net/projects/pianobar/")
@ -2785,21 +2784,13 @@ (define-public moc
name "-" version ".tar.bz2"))
(sha256
(base32
"026v977kwb0wbmlmf6mnik328plxg8wykfx9ryvqhirac0aq39pk"))
(modules '((guix build utils)))
(snippet
;; Remove use of __DATE__ and __TIME__ for reproducibility.
'(begin
(substitute* "main.c"
(("printf \\(\" Built : %s\", __DATE__\\);") "")
(("printf \\(\" %s\", __TIME__\\);") ""))
#t))))
"026v977kwb0wbmlmf6mnik328plxg8wykfx9ryvqhirac0aq39pk"))))
(build-system gnu-build-system)
(inputs
`(("alsa-lib" ,alsa-lib)
("curl" ,curl)
("faad2" ,faad2)
("ffmpeg" ,ffmpeg)
("ffmpeg" ,ffmpeg-3.4)
("file" ,file)
("jack" ,jack-1)
("libid3tag" ,libid3tag)

4
gnu/packages/node.scm
View file

@ -43,14 +43,14 @@ (define-module (gnu packages node)
(define-public node
(package
(name "node")
(version "9.10.0")
(version "9.11.1")
(source (origin
(method url-fetch)
(uri (string-append "http://nodejs.org/dist/v" version
"/node-v" version ".tar.gz"))
(sha256
(base32
"0xld7jh3fx85az7s5zbbsbccnfjwp99xxfn5w0gh2zfc5dalwrg5"))
"1vjh9zvw7wkdz6b0l99ya7mqjk0l8lbg9isr1q8rxwp400dhkk32"))
(modules '((guix build utils)))
(snippet
`(begin

11
gnu/packages/package-management.scm
View file

@ -6,6 +6,7 @@
;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -93,8 +94,8 @@ (define-public guix
;; Note: the 'update-guix-package.scm' script expects this definition to
;; start precisely like this.
(let ((version "0.14.0")
(commit "486de7377f25438b0f44fd93f97e9ef822d558b8")
(revision 10))
(commit "ab85cf7185da366da56314c53d8e43276e1cccc4")
(revision 11))
(package
(name "guix")
@ -110,7 +111,7 @@ (define-public guix
(commit commit)))
(sha256
(base32
"12ghbby83w335g7vbg7h52hjaal5l6mc6qmldlx8029340br8h1w"))
"1c00yr2vgsdl3kmlbjppyws47ssahamdx88y0wg26x73px71rd19"))
(file-name (string-append "guix-" version "-checkout"))))
(build-system gnu-build-system)
(arguments
@ -534,13 +535,13 @@ (define-public rpm
(define-public diffoscope
(package
(name "diffoscope")
(version "90")
(version "93")
(source (origin
(method url-fetch)
(uri (pypi-uri name version))
(sha256
(base32
"0hhg26vi0z2q4gwklwq4k16hibc4kq16jvyzp6zhr4kspi07wl6i"))))
"0g90nf7817jk03hzk36l3hymky4xqs50iynfld3r0in7hffly5nj"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases

6
gnu/packages/parallel.scm
View file

@ -6,7 +6,7 @@
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
@ -47,7 +47,7 @@ (define-module (gnu packages parallel)
(define-public parallel
(package
(name "parallel")
(version "20180322")
(version "20180422")
(source
(origin
(method url-fetch)
@ -55,7 +55,7 @@ (define-public parallel
version ".tar.bz2"))
(sha256
(base32
"15v46pv4z98xm3fkwy7335faw4r7pilrxp4xis5a4zi4319sv2b3"))))
"0xsfpbxwgd4197gra981iv0nmjfk58c0d88dxx6dh6yrqz523klx"))))
(build-system gnu-build-system)
(arguments
`(#:phases

16
gnu/packages/patches/bcftools-regidx-unsigned-char.patch
View file

@ -1,16 +0,0 @@
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)
{

11
gnu/packages/patches/ceph-skip-collect-sys-info-test.patch
View file

@ -1,14 +1,13 @@
This test fails because /etc/os-release is not available.
diff --git a/src/test/common/test_util.cc b/src/test/common/test_util.cc
index 288dd37db1..95b6cd4b30 100644
index 64eace923c..6daf4aa514 100644
--- a/src/test/common/test_util.cc
+++ b/src/test/common/test_util.cc
@@ -31,19 +31,3 @@ TEST(util, unit_to_bytesize)
@@ -32,17 +32,3 @@ TEST(util, unit_to_bytesize)
ASSERT_EQ(65536ll, unit_to_bytesize(" 64K", &cerr));
}
-
-#if defined(__linux__)
-TEST(util, collect_sys_info)
-{
@ -18,12 +17,8 @@ index 288dd37db1..95b6cd4b30 100644
- collect_sys_info(&sys_info, cct);
-
- ASSERT_TRUE(sys_info.find("distro") != sys_info.end());
- ASSERT_TRUE(sys_info.find("distro_version") != sys_info.end());
- ASSERT_TRUE(sys_info.find("distro_description") != sys_info.end());
-
- cct->put();
-}
-#endif
--
2.11.1

18
gnu/packages/patches/freeimage-unbundle.patch
View file

@ -25,7 +25,7 @@ diff -rupN FreeImage/gensrclist.sh FreeImage-new/gensrclist.sh
#!/bin/sh
-DIRLIST=". Source Source/Metadata Source/FreeImageToolkit Source/LibJPEG Source/LibPNG Source/LibTIFF4 Source/ZLib Source/LibOpenJPEG Source/OpenEXR Source/OpenEXR/Half Source/OpenEXR/Iex Source/OpenEXR/IlmImf Source/OpenEXR/IlmThread Source/OpenEXR/Imath Source/OpenEXR/IexMath Source/LibRawLite Source/LibRawLite/dcraw Source/LibRawLite/internal Source/LibRawLite/libraw Source/LibRawLite/src Source/LibWebP Source/LibJXR Source/LibJXR/common/include Source/LibJXR/image/sys Source/LibJXR/jxrgluelib"
+DIRLIST=". Source Source/Metadata Source/FreeImageToolkit"
+DIRLIST=". Source Source/Metadata Source/FreeImageToolkit Source/LibJXR Source/LibJXR/common/include Source/LibJXR/image/sys Source/LibJXR/jxrgluelib"
echo "VER_MAJOR = 3" > Makefile.srcs
echo "VER_MINOR = 17.0" >> Makefile.srcs
@ -90,8 +90,8 @@ diff -rupN FreeImage/Makefile.gnu FreeImage-new/Makefile.gnu
-# LibJXR
-CXXFLAGS += -D__ANSI__
-CXXFLAGS += $(INCLUDE)
+override CFLAGS += $(INCLUDE) -D__ANSI__ -I/usr/include/jxrlib $(shell pkg-config --cflags OpenEXR libopenjp2 libraw libpng libtiff-4 libwebp libwebpmux zlib)
+override LDFLAGS += -ljpeg -ljpegxr -ljxrglue $(shell pkg-config --libs OpenEXR libopenjp2 libraw libpng libtiff-4 libwebp libwebpmux zlib)
+override CFLAGS += $(INCLUDE) -D__ANSI__ $(shell pkg-config --cflags OpenEXR libopenjp2 libraw libpng libtiff-4 libwebp libwebpmux zlib)
+override LDFLAGS += -ljpeg $(shell pkg-config --libs OpenEXR libopenjp2 libraw libpng libtiff-4 libwebp libwebpmux zlib)
ifeq ($(shell sh -c 'uname -m 2>/dev/null || echo not'),x86_64)
- CFLAGS += -fPIC
@ -215,18 +215,6 @@ diff -rupN FreeImage/Source/FreeImage/PluginJPEG.cpp FreeImage-new/Source/FreeIm
}
#include "FreeImage.h"
diff -rupN FreeImage/Source/FreeImage/PluginJXR.cpp FreeImage-new/Source/FreeImage/PluginJXR.cpp
--- FreeImage/Source/FreeImage/PluginJXR.cpp 2015-03-02 02:07:08.000000000 +0100
+++ FreeImage-new/Source/FreeImage/PluginJXR.cpp 2015-09-05 02:13:52.043353343 +0200
@@ -23,7 +23,7 @@
#include "Utilities.h"
#include "../Metadata/FreeImageTag.h"
-#include "../LibJXR/jxrgluelib/JXRGlue.h"
+#include <JXRGlue.h>
// ==========================================================
// Plugin Interface
diff -rupN FreeImage/Source/FreeImage/PluginPNG.cpp FreeImage-new/Source/FreeImage/PluginPNG.cpp
--- FreeImage/Source/FreeImage/PluginPNG.cpp 2015-03-10 20:16:12.000000000 +0100
+++ FreeImage-new/Source/FreeImage/PluginPNG.cpp 2015-09-05 02:13:52.044353363 +0200

81
gnu/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch Normal file
View file

@ -0,0 +1,81 @@
From 29055a825af5405e44ffcd59a776f8952bdc7203 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Fri, 15 Dec 2017 16:03:23 +0100
Subject: [PATCH] Port to latest bouncycastle.
---
.../bouncycastle/OpenPGPSignatureGenerator.java | 34 ++++++++++------------
1 file changed, 16 insertions(+), 18 deletions(-)
diff --git a/src/java/org/apache/ivy/plugins/signer/bouncycastle/OpenPGPSignatureGenerator.java b/src/java/org/apache/ivy/plugins/signer/bouncycastle/OpenPGPSignatureGenerator.java
index af7beae..34c204f 100644
--- a/src/java/org/apache/ivy/plugins/signer/bouncycastle/OpenPGPSignatureGenerator.java
+++ b/src/java/org/apache/ivy/plugins/signer/bouncycastle/OpenPGPSignatureGenerator.java
@@ -41,6 +41,11 @@ import org.bouncycastle.openpgp.PGPSecretKeyRingCollection;
import org.bouncycastle.openpgp.PGPSignature;
import org.bouncycastle.openpgp.PGPSignatureGenerator;
import org.bouncycastle.openpgp.PGPUtil;
+import org.bouncycastle.openpgp.operator.PBESecretKeyDecryptor;
+import org.bouncycastle.openpgp.operator.bc.BcPBESecretKeyDecryptorBuilder;
+import org.bouncycastle.openpgp.operator.bc.BcPGPDigestCalculatorProvider;
+import org.bouncycastle.openpgp.operator.bc.BcPGPContentSignerBuilder;
+import org.bouncycastle.openpgp.operator.bc.BcKeyFingerprintCalculator;
public class OpenPGPSignatureGenerator implements SignatureGenerator {
@@ -101,11 +106,15 @@ public class OpenPGPSignatureGenerator implements SignatureGenerator {
pgpSec = readSecretKey(keyIn);
}
- PGPPrivateKey pgpPrivKey = pgpSec.extractPrivateKey(password.toCharArray(),
- BouncyCastleProvider.PROVIDER_NAME);
- PGPSignatureGenerator sGen = new PGPSignatureGenerator(pgpSec.getPublicKey()
- .getAlgorithm(), PGPUtil.SHA1, BouncyCastleProvider.PROVIDER_NAME);
- sGen.initSign(PGPSignature.BINARY_DOCUMENT, pgpPrivKey);
+ PBESecretKeyDecryptor decryptor =
+ new BcPBESecretKeyDecryptorBuilder(new BcPGPDigestCalculatorProvider())
+ .build(password.toCharArray());
+ PGPPrivateKey pgpPrivKey = pgpSec.extractPrivateKey(decryptor);
+ BcPGPContentSignerBuilder builder = new BcPGPContentSignerBuilder(
+ pgpSec.getPublicKey().getAlgorithm(), PGPUtil.SHA1);
+
+ PGPSignatureGenerator sGen = new PGPSignatureGenerator(builder);
+ sGen.init(PGPSignature.BINARY_DOCUMENT, pgpPrivKey);
in = new FileInputStream(src);
out = new BCPGOutputStream(new ArmoredOutputStream(new FileOutputStream(dest)));
@@ -116,22 +125,10 @@ public class OpenPGPSignatureGenerator implements SignatureGenerator {
}
sGen.generate().encode(out);
- } catch (SignatureException e) {
- IOException ioexc = new IOException();
- ioexc.initCause(e);
- throw ioexc;
} catch (PGPException e) {
IOException ioexc = new IOException();
ioexc.initCause(e);
throw ioexc;
- } catch (NoSuchAlgorithmException e) {
- IOException ioexc = new IOException();
- ioexc.initCause(e);
- throw ioexc;
- } catch (NoSuchProviderException e) {
- IOException ioexc = new IOException();
- ioexc.initCause(e);
- throw ioexc;
} finally {
if (out != null) {
try {
@@ -156,7 +153,8 @@ public class OpenPGPSignatureGenerator implements SignatureGenerator {
private PGPSecretKey readSecretKey(InputStream in) throws IOException, PGPException {
in = PGPUtil.getDecoderStream(in);
- PGPSecretKeyRingCollection pgpSec = new PGPSecretKeyRingCollection(in);
+ PGPSecretKeyRingCollection pgpSec = new PGPSecretKeyRingCollection(in,
+ new BcKeyFingerprintCalculator());
PGPSecretKey key = null;
for (Iterator it = pgpSec.getKeyRings(); key == null && it.hasNext();) {
--
2.15.1

56
gnu/packages/patches/pcmanfm-CVE-2017-8934.patch
View file

@ -1,56 +0,0 @@
From bc8c3d871e9ecc67c47ff002b68cf049793faf08 Mon Sep 17 00:00:00 2001
From: Andriy Grytsenko <andrej@rep.kiev.ua>
Date: Sun, 14 May 2017 21:35:40 +0300
Subject: [PATCH] Fix potential access violation, use runtime user dir instead
of tmp dir.
---
NEWS | 4 ++++
src/single-inst.c | 7 ++++++-
2 files changed, 10 insertions(+), 1 deletion(-)
diff --git a/NEWS b/NEWS
index 8c2049a..876f7f3 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,7 @@
+* Fixed potential access violation, use runtime user dir instead of tmp dir
+ for single instance socket.
+
+
Changes on 1.2.5 since 1.2.4:
* Removed options to Cut, Remove and Rename from context menu on mounted
diff --git a/src/single-inst.c b/src/single-inst.c
index 62c37b3..aaf84ab 100644
--- a/src/single-inst.c
+++ b/src/single-inst.c
@@ -2,7 +2,7 @@
* single-inst.c: simple IPC mechanism for single instance app
*
* Copyright 2010 Hong Jen Yee (PCMan) <pcman.tw@gmail.com>
- * Copyright 2012 Andriy Grytsenko (LStranger) <andrej@rep.kiev.ua>
+ * Copyright 2012-2017 Andriy Grytsenko (LStranger) <andrej@rep.kiev.ua>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -404,11 +404,16 @@ static void get_socket_name(SingleInstData* data, char* buf, int len)
}
else
dpynum = 0;
+#if GLIB_CHECK_VERSION(2, 28, 0)
+ g_snprintf(buf, len, "%s/%s-socket-%s-%d", g_get_user_runtime_dir(),
+ data->prog_name, host ? host : "", dpynum);
+#else
g_snprintf(buf, len, "%s/.%s-socket-%s-%d-%s",
g_get_tmp_dir(),
data->prog_name,
host ? host : "",
dpynum,
g_get_user_name());
+#endif
}
--
2.1.4

13
gnu/packages/patches/pt-scotch-build-parallelism.patch
View file

@ -1,13 +0,0 @@
Building with -j may cause the esmumps_main target to fail with a "no rule for
dependency libptesmumps.a" error. Fix the dependency name.
--- scotch_6.0.4/src/esmumps/Makefile 2012-12-01 08:29:29.000000000 -0600
+++ scotch_6.0.4/src/esmumps/Makefile 2015-06-15 17:29:23.279605734 -0500
@@ -160,6 +160,6 @@
order.h \
symbol.h \
esmumps.h \
- lib$(ESMUMPSLIB)$(LIB) \
+ libesmumps$(LIB) \
$(libdir)/lib$(SCOTCHLIB)$(LIB) \
$(libdir)/lib$(SCOTCHLIB)errexit$(LIB)

66
gnu/packages/patches/qemu-CVE-2018-7550.patch
View file

@ -1,66 +0,0 @@
Fix CVE-2018-7550:
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7550
Patch copied from upstream source repository:
https://git.qemu.org/?p=qemu.git;a=patch;h=2a8fcd119eb7c6bb3837fc3669eb1b2dfb31daf8
From 2a8fcd119eb7c6bb3837fc3669eb1b2dfb31daf8 Mon Sep 17 00:00:00 2001
From: Jack Schwartz <jack.schwartz@oracle.com>
Date: Thu, 21 Dec 2017 09:25:15 -0800
Subject: [PATCH] multiboot: bss_end_addr can be zero
The multiboot spec (https://www.gnu.org/software/grub/manual/multiboot/),
section 3.1.3, allows for bss_end_addr to be zero.
A zero bss_end_addr signifies there is no .bss section.
Suggested-by: Daniel Kiper <daniel.kiper@oracle.com>
Signed-off-by: Jack Schwartz <jack.schwartz@oracle.com>
Reviewed-by: Daniel Kiper <daniel.kiper@oracle.com>
Reviewed-by: Prasad J Pandit <pjp@fedoraproject.org>
Signed-off-by: Kevin Wolf <kwolf@redhat.com>
---
hw/i386/multiboot.c | 18 ++++++++++--------
1 file changed, 10 insertions(+), 8 deletions(-)
diff --git a/hw/i386/multiboot.c b/hw/i386/multiboot.c
index 46d9c68bf5..bb8d8e4629 100644
--- a/hw/i386/multiboot.c
+++ b/hw/i386/multiboot.c
@@ -233,12 +233,6 @@ int load_multiboot(FWCfgState *fw_cfg,
mh_entry_addr = ldl_p(header+i+28);
if (mh_load_end_addr) {
- if (mh_bss_end_addr < mh_load_addr) {
- fprintf(stderr, "invalid mh_bss_end_addr address\n");
- exit(1);
- }
- mb_kernel_size = mh_bss_end_addr - mh_load_addr;
-
if (mh_load_end_addr < mh_load_addr) {
fprintf(stderr, "invalid mh_load_end_addr address\n");
exit(1);
@@ -249,8 +243,16 @@ int load_multiboot(FWCfgState *fw_cfg,
fprintf(stderr, "invalid kernel_file_size\n");
exit(1);
}
- mb_kernel_size = kernel_file_size - mb_kernel_text_offset;
- mb_load_size = mb_kernel_size;
+ mb_load_size = kernel_file_size - mb_kernel_text_offset;
+ }
+ if (mh_bss_end_addr) {
+ if (mh_bss_end_addr < (mh_load_addr + mb_load_size)) {
+ fprintf(stderr, "invalid mh_bss_end_addr address\n");
+ exit(1);
+ }
+ mb_kernel_size = mh_bss_end_addr - mh_load_addr;
+ } else {
+ mb_kernel_size = mb_load_size;
}
/* Valid if mh_flags sets MULTIBOOT_HEADER_HAS_VBE.
--
2.17.0

25
gnu/packages/patches/quassel-fix-tls-check.patch
View file

@ -1,25 +0,0 @@
This allows quasselclient to connect to SSL-enabled quasselcore instances.
The check in qglobal.h requires -fPIC (not -fPIE as it is now). When this check
fails SSL / TLS is disabled.
This patch comes from the upstream source repository [0] and can be
removed when the next version is packaged.
[0] https://github.com/quassel/quassel/commit/4768c9e99f99b581d4e32e797db91d0182391696
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -428,6 +428,11 @@ endif()
cmake_push_check_state(RESET)
set(CMAKE_REQUIRED_INCLUDES ${QT_INCLUDES} ${Qt5Core_INCLUDE_DIRS})
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Core_EXECUTABLE_COMPILE_FLAGS}")
+
+if (USE_QT5 AND Qt5_POSITION_INDEPENDENT_CODE)
+ set(CMAKE_REQUIRED_FLAGS "-fPIC -DQT_NO_VERSION_TAGGING")
+endif()
+
check_cxx_source_compiles("
#include \"qglobal.h\"
#if defined QT_NO_SSL

39
gnu/packages/patches/scotch-build-parallelism.patch Normal file
View file

@ -0,0 +1,39 @@
Fixes make with -j, otherwise scotch.h may not be generated by the time make
tries to compile library_graph_diam.o et al.
Reported upstream at
https://gforge.inria.fr/tracker/index.php?func=detail&aid=21651&group_id=248&atid=1081
diff --git a/src/libscotch/Makefile b/src/libscotch/Makefile
index 9898894..b0ee14c 100644
--- a/src/libscotch/Makefile
+++ b/src/libscotch/Makefile
@@ -2229,6 +2229,28 @@ library_graph_color_f$(OBJ) : library_graph_color_f.c \
common.h \
scotch.h
+library_graph_diam$(OBJ) : library_graph_diam.c \
+ module.h \
+ common.h \
+ graph.h \
+ scotch.h
+
+library_graph_diam_f$(OBJ) : library_graph_diam.c \
+ module.h \
+ common.h \
+ scotch.h
+
+library_graph_induce$(OBJ) : library_graph_diam.c \
+ module.h \
+ common.h \
+ graph.h \
+ scotch.h
+
+library_graph_induce_f$(OBJ) : library_graph_diam.c \
+ module.h \
+ common.h \
+ scotch.h
+
library_graph_io_chac$(OBJ) : library_graph_io_chac.c \
module.h \
common.h \

27
gnu/packages/patches/scotch-graph-diam-64.patch Normal file
View file

@ -0,0 +1,27 @@
Fixes test_scotch_graph_diam test with -DINTSIZE64.
Reported upstream at
https://gforge.inria.fr/tracker/index.php?func=detail&aid=21650&group_id=248&atid=1081
--- scotch-6.0.5a/src/libscotch/library.h
+++ scotch-6.0.5a/src/libscotch/library.h
@@ -187,6 +187,7 @@ SCOTCH_Num SCOTCH_graphBase (SCOTCH_Graph * const, const SCO
int SCOTCH_graphCheck (const SCOTCH_Graph * const);
void SCOTCH_graphSize (const SCOTCH_Graph * const, SCOTCH_Num * const, SCOTCH_Num * const);
void SCOTCH_graphData (const SCOTCH_Graph * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num ** const, SCOTCH_Num ** const, SCOTCH_Num ** const, SCOTCH_Num ** const, SCOTCH_Num * const, SCOTCH_Num ** const, SCOTCH_Num ** const);
+SCOTCH_Num SCOTCH_graphDiamPV (SCOTCH_Graph * const);
void SCOTCH_graphStat (const SCOTCH_Graph * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, double * const, double * const, SCOTCH_Num * const, SCOTCH_Num * const, double * const, double * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, double * const, double * const);
int SCOTCH_graphCoarsen (const SCOTCH_Graph * const, const SCOTCH_Num, const double, const SCOTCH_Num, SCOTCH_Graph * const, SCOTCH_Num * const);
int SCOTCH_graphCoarsenMatch (const SCOTCH_Graph * const, SCOTCH_Num * const, const double, const SCOTCH_Num, SCOTCH_Num * const);
--- scotch-6.0.5a/src/libscotch/library_graph_diam.c
+++ scotch-6.0.5a/src/libscotch/library_graph_diam.c
@@ -72,8 +72,7 @@
SCOTCH_Num
SCOTCH_graphDiamPV (
-SCOTCH_Graph * const grafptr,
-const SCOTCH_Num baseval)
+SCOTCH_Graph * const grafptr)
{
return ((SCOTCH_Num) graphDiamPV ((Graph * const) grafptr));
}

19
gnu/packages/patches/scotch-graph-induce-type-64.patch Normal file
View file

@ -0,0 +1,19 @@
Fixes return type of SCOTCH_graphInduceList and SCOTCH_graphInducePart
so that the definition matches with -DINTSIZE64.
Reported upstream at
https://gforge.inria.fr/tracker/index.php?func=detail&aid=21608&group_id=248&atid=1081
--- scotch_6.0.5a/src/libscotch/library.h.orig 2018-02-11 10:52:38.000000000 -0600
+++ scotch_6.0.5a/src/libscotch/library.h 2018-02-23 16:56:41.000000000 -0600
@@ -199,8 +199,8 @@
int SCOTCH_graphGeomSaveChac (const SCOTCH_Graph * const, const SCOTCH_Geom * const, FILE * const, FILE * const, const char * const);
int SCOTCH_graphGeomSaveMmkt (const SCOTCH_Graph * const, const SCOTCH_Geom * const, FILE * const, FILE * const, const char * const);
int SCOTCH_graphGeomSaveScot (const SCOTCH_Graph * const, const SCOTCH_Geom * const, FILE * const, FILE * const, const char * const);
-int SCOTCH_graphInduceList (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_Num * const, SCOTCH_Graph * const);
-int SCOTCH_graphInducePart (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_GraphPart2 * const, const SCOTCH_GraphPart2, SCOTCH_Graph * const);
+SCOTCH_Num SCOTCH_graphInduceList (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_Num * const, SCOTCH_Graph * const);
+SCOTCH_Num SCOTCH_graphInducePart (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_GraphPart2 * const, const SCOTCH_GraphPart2, SCOTCH_Graph * const);
int SCOTCH_graphMapInit (const SCOTCH_Graph * const, SCOTCH_Mapping * const, const SCOTCH_Arch * const, SCOTCH_Num * const);
void SCOTCH_graphMapExit (const SCOTCH_Graph * const, SCOTCH_Mapping * const);

48
gnu/packages/patches/zsh-CVE-2018-7548.patch
View file

@ -1,48 +0,0 @@
Fix CVE-2018-7548:
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7548
Patch copied from upstream source repository:
https://sourceforge.net/p/zsh/code/ci/110b13e1090bc31ac1352b28adc2d02b6d25a102
From 110b13e1090bc31ac1352b28adc2d02b6d25a102 Mon Sep 17 00:00:00 2001
From: Joey Pabalinas <joeypabalinas@gmail.com>
Date: Tue, 23 Jan 2018 22:28:08 -0800
Subject: [PATCH] 42313: avoid null-pointer deref when using ${(PA)...} on an
empty array result
---
ChangeLog | 5 +++++
Src/subst.c | 2 +-
2 files changed, 6 insertions(+), 1 deletion(-)
#diff --git a/ChangeLog b/ChangeLog
#index d2ba94afc..3037edda4 100644
#--- a/ChangeLog
#+++ b/ChangeLog
#@@ -1,3 +1,8 @@
#+2018-01-23 Barton E. Schaefer <schaefer@zsh.org>
#+
#+ * Joey Pabalinas: 42313: Src/subst.c: avoid null-pointer deref
#+ when using ${(PA)...} on an empty array result
#+
# 2018-01-23 Oliver Kiddle <okiddle@yahoo.co.uk>
#
# * 42317: Completion/Linux/Command/_cryptsetup,
diff --git a/Src/subst.c b/Src/subst.c
index d027e3d83..a265a187e 100644
--- a/Src/subst.c
+++ b/Src/subst.c
@@ -2430,7 +2430,7 @@ paramsubst(LinkList l, LinkNode n, char **str, int qt, int pf_flags,
val = aval[0];
isarr = 0;
}
- s = dyncat(val, s);
+ s = val ? dyncat(val, s) : dupstring(s);
/* Now behave po-faced as if it was always like that... */
subexp = 0;
/*
--
2.16.2

56
gnu/packages/patches/zsh-CVE-2018-7549.patch
View file

@ -1,56 +0,0 @@
Fix CVE-2018-7549:
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7549
Patch copied from upstream source repository:
https://sourceforge.net/p/zsh/code/ci/c2cc8b0fbefc9868fa83537f5b6d90fc1ec438dd
From c2cc8b0fbefc9868fa83537f5b6d90fc1ec438dd Mon Sep 17 00:00:00 2001
From: Stephane Chazelas <stephane.chazelas@gmail.com>
Date: Fri, 22 Dec 2017 22:17:09 +0000
Subject: [PATCH] Avoid crash copying empty hash table.
Visible with typeset -p.
---
ChangeLog | 2 ++
Src/params.c | 11 +++++++----
2 files changed, 9 insertions(+), 4 deletions(-)
#diff --git a/ChangeLog b/ChangeLog
#index f74c26b88..e3628cfa7 100644
#--- a/ChangeLog
#+++ b/ChangeLog
#@@ -1,5 +1,7 @@
# 2018-01-04 Peter Stephenson <p.stephenson@samsung.com>
#
#+ * Stephane: 42159: Src/params.c: avoid crash copying empty hash table.
#+
# * Sebastian: 42188: Src/Modules/system.c: It is necessary to
# close the lock descriptor in some failure cases.
#
diff --git a/Src/params.c b/Src/params.c
index 31ff0445b..de7730ae7 100644
--- a/Src/params.c
+++ b/Src/params.c
@@ -549,10 +549,13 @@ scancopyparams(HashNode hn, UNUSED(int flags))
HashTable
copyparamtable(HashTable ht, char *name)
{
- HashTable nht = newparamtable(ht->hsize, name);
- outtable = nht;
- scanhashtable(ht, 0, 0, 0, scancopyparams, 0);
- outtable = NULL;
+ HashTable nht = 0;
+ if (ht) {
+ nht = newparamtable(ht->hsize, name);
+ outtable = nht;
+ scanhashtable(ht, 0, 0, 0, scancopyparams, 0);
+ outtable = NULL;
+ }
return nht;
}
--
2.16.2

24
gnu/packages/perl-check.scm
View file

@ -96,7 +96,7 @@ (define-public perl-test2-plugin-nowarnings
(define-public perl-test-base
(package
(name "perl-test-base")
(version "0.88")
(version "0.89")
(source
(origin
(method url-fetch)
@ -104,7 +104,7 @@ (define-public perl-test-base
"Test-Base-" version ".tar.gz"))
(sha256
(base32
"0fch1cvivnszbnwhpfmwv1rin04j5xkj1n1ylfmlxg6bm72qqdjj"))))
"056hibgg3i2b89mwr76vyxi6ayb3hqjqcwicvn3s5lximsma3517"))))
(build-system perl-build-system)
(native-inputs
`(("perl-algorithm-diff" ,perl-algorithm-diff)
@ -317,7 +317,7 @@ (define-public perl-test-deep
(define-public perl-test-differences
(package
(name "perl-test-differences")
(version "0.63")
(version "0.64")
(source
(origin
(method url-fetch)
@ -325,7 +325,7 @@ (define-public perl-test-differences
"Test-Differences-" version ".tar.gz"))
(sha256
(base32
"0rhs4q6qn64ji06ns7lwl6iiiw3mggvd9xk9nkiqvx1jihbplrbw"))))
"0xmj5vgklq4yqvi7l63ky1k6g7fhww68llpmw9rhlaihqbcrsicz"))))
(build-system perl-build-system)
(native-inputs
`(("perl-module-build" ,perl-module-build)))
@ -798,7 +798,7 @@ (define-public perl-test-needs
(define-public perl-test-notabs
(package
(name "perl-test-notabs")
(version "2.00")
(version "2.02")
(source
(origin
(method url-fetch)
@ -808,7 +808,7 @@ (define-public perl-test-notabs
".tar.gz"))
(sha256
(base32
"127kpl1va267qar2ia4c22xb96jby2jqnda3sj5pjgmxg8si26cg"))))
"0c306p9qdpa2ycii3c50hml23mwy6bjxpry126g1dw11hyiwcxgv"))))
(build-system perl-build-system)
(home-page
"http://search.cpan.org/dist/Test-NoTabs/")
@ -869,14 +869,14 @@ (define-public perl-test-number-delta
(define-public perl-test-output
(package
(name "perl-test-output")
(version "1.03")
(version "1.031")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cpan/authors/id/B/BD/BDFOY/"
"Test-Output-" version ".tar.gz"))
(sha256
(base32
"12991jnzj4cbw9whhprmqvnzd1ayii84g2mh8vxbjngwqrjsy41i"))))
"193y1xjvgc1p9pdgdwps2127knvpz9wc1xh6gmr74y3ihmqz7f7q"))))
(build-system perl-build-system)
(propagated-inputs
`(("perl-capture-tiny" ,perl-capture-tiny)
@ -894,7 +894,7 @@ (define-public perl-test-output
(define-public perl-test-pod
(package
(name "perl-test-pod")
(version "1.51")
(version "1.52")
(source
(origin
(method url-fetch)
@ -902,7 +902,7 @@ (define-public perl-test-pod
"Test-Pod-" version ".tar.gz"))
(sha256
(base32
"1yvy5mc4j3s2h4aizryvark2nm58g2c6zhw9mlx9wmsavz7d78f1"))))
"1z75x1pxwp8ajwq9iazlg2c3wd7rdlim08yclpdg32qnc36dpa30"))))
(build-system perl-build-system)
(native-inputs `(("perl-module-build" ,perl-module-build)))
(home-page "http://search.cpan.org/dist/Test-Pod/")
@ -1077,14 +1077,14 @@ (define-public perl-test-sharedfork
(define-public perl-test-simple
(package
(name "perl-test-simple")
(version "1.302122")
(version "1.302136")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cpan/authors/id/E/EX/EXODIST/"
"Test-Simple-" version ".tar.gz"))
(sha256
(base32
"117m707cbvrh01s3w6g371i9xvpnklifiqpcmky4f49jgck8izgm"))))
"0inlv8f4rbhsw6qnqhf1w6ay153xbw27fldmb2pmg4ihn19mr6ld"))))
(build-system perl-build-system)
(synopsis "Basic utilities for writing tests")
(description

84
gnu/packages/perl.scm
View file

@ -162,7 +162,7 @@ (define-public perl
;; Fixes CVE-2018-6797, CVE-2018-6798, and CVE-2018-6913.
;; See <https://metacpan.org/changes/release/SHAY/perl-5.26.2>.
(define-public perl-5.26.2
(define perl-5.26.2
(package
(inherit perl)
(version "5.26.2")
@ -386,7 +386,7 @@ (define-public perl-autovivification
(define-public perl-bareword-filehandles
(package
(name "perl-bareword-filehandles")
(version "0.005")
(version "0.006")
(source
(origin
(method url-fetch)
@ -395,7 +395,7 @@ (define-public perl-bareword-filehandles
version ".tar.gz"))
(sha256
(base32
"0fdirls2pg7d6ymvlzzz59q3dy6hgh08k0qpr2mw51w127s8rav6"))))
"1yxz6likpfshpyfrgwyi7dw6ig1wjhh0vnvbcs6ypr62pv00fv5d"))))
(build-system perl-build-system)
(native-inputs
`(("perl-b-hooks-op-check" ,perl-b-hooks-op-check)
@ -453,7 +453,7 @@ (define-public perl-browser-open
(define-public perl-b-hooks-endofscope
(package
(name "perl-b-hooks-endofscope")
(version "0.21")
(version "0.24")
(source
(origin
(method url-fetch)
@ -461,7 +461,7 @@ (define-public perl-b-hooks-endofscope
"B-Hooks-EndOfScope-" version ".tar.gz"))
(sha256
(base32
"0b70vbpabsy9ia366k330cz1zbdyb1pwhb0l7j28pmpih045iwwh"))))
"1imcqxp23yc80a7p0h56sja9glbrh4qyhgzljqd4g9habpz3vah3"))))
(build-system perl-build-system)
(propagated-inputs
`(("perl-module-runtime" ,perl-module-runtime)
@ -611,7 +611,7 @@ (define-public perl-business-isbn-data
(define-public perl-business-isbn
(package
(name "perl-business-isbn")
(version "3.003")
(version "3.004")
(source
(origin
(method url-fetch)
@ -619,7 +619,7 @@ (define-public perl-business-isbn
"Business-ISBN-" version ".tar.gz"))
(sha256
(base32
"1i2bxzqkki257rqbswa4ryj1grmwa5s47wrxln2ff5mha1ry31gm"))))
"07l3zfv8hagv37i3clvj5a1zc2jarr5phg80c93ks35zaz6llx9i"))))
(build-system perl-build-system)
(propagated-inputs
`(("perl-business-isbn-data" ,perl-business-isbn-data)
@ -721,7 +721,7 @@ (define-public perl-cache-fastmmap
(define-public perl-capture-tiny
(package
(name "perl-capture-tiny")
(version "0.46")
(version "0.48")
(source
(origin
(method url-fetch)
@ -730,7 +730,7 @@ (define-public perl-capture-tiny
version ".tar.gz"))
(sha256
(base32
"05bhlx6d4nzamhkkh0pkckg7wlvaq6mazf7q1fbb5wpp1j1nlyjx"))))
"069yrikrrb4vqzc3hrkkfj96apsh7q0hg8lhihq97lxshwz128vc"))))
(build-system perl-build-system)
(home-page "http://search.cpan.org/dist/Capture-Tiny/")
(synopsis "Capture STDOUT and STDERR from Perl, XS or external programs")
@ -1121,7 +1121,7 @@ (define-public perl-class-factory-util
(define-public perl-class-inspector
(package
(name "perl-class-inspector")
(version "1.31")
(version "1.32")
(source
(origin
(method url-fetch)
@ -1129,7 +1129,7 @@ (define-public perl-class-inspector
"Class-Inspector-" version ".tar.gz"))
(sha256
(base32
"1sqfjgzxx1f951fykc6vgfvys4j8rxaw2zf3jq26yrvs3ygn8pq6"))))
"0d85rihxahdvhj8cysqrgg0kbmcqghz5hgy41dbkxr1qaf5xrynf"))))
(build-system perl-build-system)
(home-page "http://search.cpan.org/dist/Class-Inspector/")
(synopsis "Get information about a class and its structure")
@ -1321,14 +1321,14 @@ (define-public perl-class-xsaccessor
(define-public perl-clone
(package
(name "perl-clone")
(version "0.38")
(version "0.39")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cpan/authors/id/G/GA/GARU/"
"Clone-" version ".tar.gz"))
(sha256
(base32
"1s5xrv9zlckqqzyhxi0l9lwj9m6na2bz5hqxrkva2v7gnx5m7c4z"))))
"0bgsidb96gxzf3zhy6v1ksj1c200vxbwykk32fqm1mj97rl4dc5c"))))
(build-system perl-build-system)
(synopsis "Recursively copy Perl datatypes")
(description
@ -2713,7 +2713,7 @@ (define-public perl-devel-lexalias
(define-public perl-devel-overloadinfo
(package
(name "perl-devel-overloadinfo")
(version "0.004")
(version "0.005")
(source
(origin
(method url-fetch)
@ -2721,7 +2721,7 @@ (define-public perl-devel-overloadinfo
"Devel-OverloadInfo-" version ".tar.gz"))
(sha256
(base32
"0zckjhzdqa6smpp98y15mqafsyzwjxwrvk10snzhn2sb0r889s43"))))
"1rx6g8pyhi7lx6z130b7vlf8syzrq92w9ky8mpw4d6bwlkzy5zcb"))))
(build-system perl-build-system)
(native-inputs
`(("perl-test-fatal" ,perl-test-fatal)))
@ -3026,14 +3026,14 @@ (define-public perl-env-path
(define-public perl-error
(package
(name "perl-error")
(version "0.17023")
(version "0.17025")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cpan/authors/id/S/SH/SHLOMIF/"
"Error-" version ".tar.gz"))
(sha256
(base32
"0dsxic78mxy30qvbbdzfyp501hbkwhnbmafqfxipr0yqfy8f2j5g"))))
"1bzgzmf1v4md02vadm46b4j4ilqxrcrfasvbzymhrznlsd54g7vc"))))
(build-system perl-build-system)
(native-inputs `(("perl-module-build" ,perl-module-build)))
(home-page "http://search.cpan.org/dist/Error/")
@ -3371,7 +3371,7 @@ (define-public perl-file-copy-recursive
(define-public perl-file-find-rule
(package
(name "perl-file-find-rule")
(version "0.33")
(version "0.34")
(source
(origin
(method url-fetch)
@ -3379,7 +3379,7 @@ (define-public perl-file-find-rule
"File-Find-Rule-" version ".tar.gz"))
(sha256
(base32
"0w73b4jr2fcrd74a1w3b2jryq3mqzc8z5mk7ia9p85xn3qmpa5r4"))))
"1znachnhmi1w5pdqx8dzgfa892jb7x8ivrdy4pzjj7zb6g61cvvy"))))
(build-system perl-build-system)
(propagated-inputs
`(("perl-text-glob" ,perl-text-glob)
@ -3636,7 +3636,7 @@ (define-public perl-file-sharedir-dist
(define-public perl-file-sharedir-install
(package
(name "perl-file-sharedir-install")
(version "0.11")
(version "0.13")
(source
(origin
(method url-fetch)
@ -3644,7 +3644,7 @@ (define-public perl-file-sharedir-install
"File-ShareDir-Install-" version ".tar.gz"))
(sha256
(base32
"1j0cw1aq9fdv9kl1a6fnfa4zihsvmcqzy9sb0xk0i9pyx5r8ggrj"))))
"1yc0wlkav2l2wr36a53n4mnhsy2zv29z5nm14mygxgjwv7qgvgj5"))))
(build-system perl-build-system)
(native-inputs
`(("perl-module-build" ,perl-module-build)))
@ -4522,17 +4522,17 @@ (define-public perl-log-any
(define-public perl-log-any-adapter-log4perl
(package
(name "perl-log-any-adapter-log4perl")
(version "0.08")
(version "0.09")
(source
(origin
(method url-fetch)
(uri (string-append
"mirror://cpan/authors/id/D/DA/DAGOLDEN/Log-Any-Adapter-Log4perl-"
"mirror://cpan/authors/id/P/PR/PREACTION/Log-Any-Adapter-Log4perl-"
version
".tar.gz"))
(sha256
(base32
"0xf4fnrsznvg0hf36q481124ja1hp3lybki1xjgnk82z9990jmxn"))))
"19f1drqnzr6g4xwjm6jk4iaa3zmiax8bzxqch04f4jr12bjd75qi"))))
(build-system perl-build-system)
(propagated-inputs
`(("perl-log-any" ,perl-log-any)
@ -4981,7 +4981,7 @@ (define-public perl-mime-tools
(define-public perl-mime-types
(package
(name "perl-mime-types")
(version "2.16")
(version "2.17")
(source
(origin
(method url-fetch)
@ -4989,7 +4989,7 @@ (define-public perl-mime-types
"MIME-Types-" version ".tar.gz"))
(sha256
(base32
"0nkv99yd8bxa6h8c52nd07142f0mdzjnhcdw66s3wljmzsi9z8hk"))))
"1xlg7q6h8zyb8534sy0iqn90py18kilg419q6051bwqz5zadfkp0"))))
(build-system perl-build-system)
(home-page "http://search.cpan.org/dist/MIME-Types/")
(synopsis "Definition of MIME types")
@ -5127,7 +5127,7 @@ (define-public perl-module-build-xsutil
(define-public perl-module-find
(package
(name "perl-module-find")
(version "0.12")
(version "0.13")
(source
(origin
(method url-fetch)
@ -5135,7 +5135,7 @@ (define-public perl-module-find
"Module-Find-" version ".tar.gz"))
(sha256
(base32
"1lc33jdv4pgmm7nkr9bff0lhwjhhw91kaf6iiy2n7i7mw8dfv47l"))))
"0s45y5lvd9k89g7lds83c0bn1p29c13hfsbrd7x64jfaf8h8cisa"))))
(build-system perl-build-system)
(home-page "http://search.cpan.org/dist/Module-Find/")
(synopsis "Find and use installed modules in a (sub)category")
@ -6258,7 +6258,7 @@ (define-public perl-mozilla-ca
(define-public perl-multidimensional
(package
(name "perl-multidimensional")
(version "0.013")
(version "0.014")
(source
(origin
(method url-fetch)
@ -6267,7 +6267,7 @@ (define-public perl-multidimensional
version ".tar.gz"))
(sha256
(base32
"02p5zv68i39hnkmzzxsk1fi7xy56pfcsslrd7yqwzhq74czcw81x"))))
"0prchsg547ziysjl8ghiid6ph3m2xnwpsrwrjymibga7fhqi9sqj"))))
(build-system perl-build-system)
(native-inputs
`(("perl-b-hooks-op-check" ,perl-b-hooks-op-check)
@ -7172,7 +7172,7 @@ (define-public perl-role-tiny-2
(define-public perl-safe-isa
(package
(name "perl-safe-isa")
(version "1.000008")
(version "1.000010")
(source
(origin
(method url-fetch)
@ -7180,7 +7180,7 @@ (define-public perl-safe-isa
"Safe-Isa-" version ".tar.gz"))
(sha256
(base32
"08r74hwxq5b3bibnbwjr9anybg15l3zqdgcirpw1xm2qpvcxgdkx"))))
"0sm6p1kw98s7j6n92vvxjqf818xggnmjwci34xjmw7gzl2519x47"))))
(build-system perl-build-system)
(home-page "http://search.cpan.org/dist/Safe-Isa/")
(synopsis "Call isa, can, does, and DOES safely")
@ -7452,7 +7452,7 @@ (define-public perl-strictures
(define-public perl-strictures-2
(package
(inherit perl-strictures)
(version "2.000003")
(version "2.000004")
(source
(origin
(method url-fetch)
@ -7460,7 +7460,7 @@ (define-public perl-strictures-2
"strictures-" version ".tar.gz"))
(sha256
(base32
"08mgvf1d2651gsg3jgjfs13878ndqa4ji8vfsda9f7jjd84ymy17"))))))
"0lzp0q6kwk6vgf7zdlvy9zz28fj6n1b776irm556c7gylcq29113"))))))
(define-public perl-string-camelcase
(package
@ -7691,7 +7691,7 @@ (define-public perl-sub-name
(define-public perl-sub-quote
(package
(name "perl-sub-quote")
(version "2.005000")
(version "2.005001")
(source
(origin
(method url-fetch)
@ -7700,7 +7700,7 @@ (define-public perl-sub-quote
version ".tar.gz"))
(sha256
(base32
"1zv45cvj4ifkbr61ydcpphnj6lvib37gfxwfh40h0yzf3c8lbca4"))))
"01xsvfdpxzimsbrp9mqipsr93y83nhj21q05g8v1bw6yfl3lzayn"))))
(build-system perl-build-system)
(native-inputs
`(("perl-test-fatal" ,perl-test-fatal)))
@ -7873,7 +7873,7 @@ (define-public perl-sys-hostname-long
(define-public perl-task-weaken
(package
(name "perl-task-weaken")
(version "1.05")
(version "1.06")
(source
(origin
(method url-fetch)
@ -7881,7 +7881,7 @@ (define-public perl-task-weaken
"Task-Weaken-" version ".tar.gz"))
(sha256
(base32
"0p5ryr3421p5rqj6dk5dcvxsml5gl9skbn7gv4szk50fimrvzww5"))))
"1gk6rmnp4x50lzr0vfng41khf0f8yzxlm0pad1j69vxskpdzx0r3"))))
(build-system perl-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
@ -8261,7 +8261,7 @@ (define-public perl-text-format
(define-public perl-text-glob
(package
(name "perl-text-glob")
(version "0.09")
(version "0.11")
(source
(origin
(method url-fetch)
@ -8269,7 +8269,7 @@ (define-public perl-text-glob
"Text-Glob-" version ".tar.gz"))
(sha256
(base32
"0lr76wrsj8wcxrq4wi8z1640w4dmdbkznp06q744rg3g0bd238d5"))))
"11sj62fynfgwrlgkv5a051cq6yn0pagxqjsz27dxx8phsd4wv706"))))
(build-system perl-build-system)
(native-inputs `(("perl-module-build" ,perl-module-build)))
(home-page "http://search.cpan.org/dist/Text-Glob/")
@ -8791,7 +8791,7 @@ (define-public perl-type-tie
(define-public perl-type-tiny
(package
(name "perl-type-tiny")
(version "1.002001")
(version "1.002002")
(source
(origin
(method url-fetch)
@ -8799,7 +8799,7 @@ (define-public perl-type-tiny
"Type-Tiny-" version ".tar.gz"))
(sha256
(base32
"1p8krim8kvw123nady96fagi8sk2pj1z8jkr4r8n45ihyamfxjck"))))
"0b48v28rvl20969gyr62yg6gr6a2nj9qik0bixavbjdmk67hqnx8"))))
(build-system perl-build-system)
(native-inputs
`(("perl-test-warnings" ,perl-test-warnings)))

8
gnu/packages/photo.scm
View file

@ -69,14 +69,14 @@ (define-module (gnu packages photo)
(define-public libraw
(package
(name "libraw")
(version "0.18.8")
(version "0.18.9")
(source (origin
(method url-fetch)
(uri (string-append "https://www.libraw.org/data/LibRaw-"
version ".tar.gz"))
(sha256
(base32
"1qi0fkw2zmd0yplrf79z7lgpz0hxl45dj5rdgpaj7283jzys9b2n"))))
"0kmjfdr409k9q9n17k9ywims5z4kqc16s81ba7y09n7669q1gvyj"))))
(build-system gnu-build-system)
(home-page "https://www.libraw.org")
(synopsis "Raw image decoder")
@ -330,7 +330,7 @@ (define-public lensfun
(define-public darktable
(package
(name "darktable")
(version "2.4.2")
(version "2.4.3")
(source (origin
(method url-fetch)
(uri (string-append
@ -339,7 +339,7 @@ (define-public darktable
version "/darktable-" version ".tar.xz"))
(sha256
(base32
"10asz918kv2248px3w9bn5k8cfrad5xrci58x9y61l0yf5hcpk0r"))))
"1lq3xp7hhfhfwqrz0f2mrp3xywnpvb0nlw6lbm5cgx22s5xzri8x"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; There are no tests.

13
gnu/packages/python-crypto.scm
View file

@ -620,6 +620,9 @@ (define-public python-pynacl
of improving usability, security and speed.")
(license license:asl2.0)))
(define-public python2-pynacl
(package-with-python2 python-pynacl))
(define-public python2-pgpdump
(package
(name "python2-pgpdump")
@ -715,28 +718,28 @@ (define-public python2-ecpy
(define-public python-josepy
(package
(name "python-josepy")
(version "1.0.1")
(version "1.1.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "josepy" version))
(sha256
(base32
"1k0ahzzaq2rrjiifwbhbp7vm8z4zk0ipgiqwicil80kzlf6bhj4z"))))
"11khz8malzrv375b27jjkv66z6z6khdx1v5mkkr4vq16gp3n4p7v"))))
(build-system python-build-system)
(arguments
;; The tests require pytest >= 3.2, which is not yet packaged.
;; The tests require flake8 >= 3.5, which is not yet packaged.
'(#:tests? #f))
(propagated-inputs
`(("python-cryptography" ,python-cryptography)
("python-pyopenssl" ,python-pyopenssl)
("python-six" ,python-six)))
;; TODO Enable when we have pytest >= 3.2.
;; TODO Enable when we have flake8 >= 3.5.
; (native-inputs
; `(("python-coverage" ,python-coverage)
; ("python-flake8" ,python-flake8)
; ("python-isort" ,python-isort)
; ("python-mock" ,python-mock)
; ("python-pytest" ,python-pytest-3.0)
; ("python-pytest" ,python-pytest)
; ("python-pytest-cov" ,python-pytest-cov)
; ("python-pytest-cache" ,python-pytest-cache)
; ("python-pytest-flake8" ,python-pytest-flake8)))

13
gnu/packages/python-web.scm
View file

@ -44,6 +44,7 @@ (define-module (gnu packages python-web)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system python)
#:use-module (guix utils)
#:use-module (gnu packages)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
@ -214,13 +215,13 @@ (define-public python2-html5lib-0.9
(define-public python-html5-parser
(package
(name "python-html5-parser")
(version "0.4.4")
(version "0.4.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "html5-parser" version))
(sha256
(base32
"1d8sxhl41ffh7qlk7wlsy17xw6slzx5v1yna9s72wx5qrpaa3wxr"))))
"01mx33sx4dhl4kj6wc48nj6jz7ry60rkhjv0s6k8h5xmjf5yy0x9"))))
(build-system python-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
@ -998,13 +999,13 @@ (define-public python2-zope-component
(define-public python-ndg-httpsclient
(package
(name "python-ndg-httpsclient")
(version "0.4.4")
(version "0.5.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "ndg_httpsclient" version))
(sha256
(base32
"0sl5ak1r1xil9ms0a9fh9fm6ncml65kgnjpjfic9dhnaimwx997v"))))
"12q8rjvsvjphj6lvvcka2izdjr36a5lgkygajwx6p4wh0x1za2f0"))))
(build-system python-build-system)
(arguments
'(;; The tests appear to require networking.
@ -1024,7 +1025,9 @@ (define-public python-ndg-httpsclient
(define-public python2-ndg-httpsclient
(package (inherit python-ndg-httpsclient)
(name "python2-ndg-httpsclient")
(arguments `(#:python ,python-2))
(arguments
(substitute-keyword-arguments (package-arguments python-ndg-httpsclient)
((#:python _) python-2)))
(propagated-inputs
`(("python2-pyopenssl" ,python2-pyopenssl)))))

62
gnu/packages/python.scm
View file

@ -1290,14 +1290,14 @@ (define-public python2-mechanize
(define-public python-simplejson
(package
(name "python-simplejson")
(version "3.13.2")
(version "3.14.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "simplejson" version))
(sha256
(base32
"02jg5nixffqyicfqdl4dil82fh1z9p2as758wp0nqwalw0hcykjc"))))
"1lkv3xlf7ryzi69zqfdbkvpxdfy1rg1rq2yzcnxgf4km5m6difqy"))))
(build-system python-build-system)
(home-page "http://simplejson.readthedocs.org/en/latest/")
(synopsis
@ -2525,13 +2525,13 @@ (define-public python-sphinx
(define-public python-sphinx-1.6
(package (inherit python-sphinx)
(name "python-sphinx")
(version "1.6.3")
(version "1.6.4")
(source (origin
(method url-fetch)
(uri (pypi-uri "Sphinx" version))
(sha256
(base32
"1rj6f3i8hmrx2qlkshi5kp5xcy98dlynwlyl05yvflj5f66dp2xg"))))
"0gjakw9fv5pwqb5yyclxycs36sapxizk1vx6mkcdizmzgzcfy0gi"))))
(arguments
`(#:phases
(modify-phases %standard-phases
@ -2638,14 +2638,14 @@ (define-public python2-guzzle-sphinx-theme
(define-public python-rst.linker
(package
(name "python-rst.linker")
(version "1.7")
(version "1.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "rst.linker" version))
(sha256
(base32
"0bh4lnj2p1nh0wf5pgxgfbrp27xhb1rinahkb5j7s3qprq6qn0sr"))))
"16crgnai6020vdmnpwdimw1vm3jb74ysfyb3kmcidb0lgma5xq2d"))))
(build-system python-build-system)
(propagated-inputs
`(("python-dateutil" ,python-dateutil)
@ -3876,28 +3876,28 @@ (define-public python2-orderedmultidict
(define-public python-autopep8
(package
(name "python-autopep8")
(version "1.3.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "autopep8" version))
(sha256
(base32
"1p9pa1ffg4iy96l918808jggg9a69iaka5awmj8xid36yc5mk0ky"))))
(build-system python-build-system)
(propagated-inputs
`(("python-pycodestyle" ,python-pycodestyle)))
(home-page "https://github.com/hhatto/autopep8")
(synopsis "Format Python code according to the PEP 8 style guide")
(description
"@code{autopep8} automatically formats Python code to conform to
(name "python-autopep8")
(version "1.3.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "autopep8" version))
(sha256
(base32
"192bvhzi4d0claqxgzymvv7k3qnj627742bc8sgxpzjj42pd9112"))))
(build-system python-build-system)
(propagated-inputs
`(("python-pycodestyle" ,python-pycodestyle)))
(home-page "https://github.com/hhatto/autopep8")
(synopsis "Format Python code according to the PEP 8 style guide")
(description
"@code{autopep8} automatically formats Python code to conform to
the PEP 8 style guide. It uses the pycodestyle utility to determine
what parts of the code needs to be formatted. @code{autopep8} is
capable of fixing most of the formatting issues that can be reported
by pycodestyle.")
(license (license:non-copyleft
"https://github.com/hhatto/autopep8/blob/master/LICENSE"))))
(license (license:non-copyleft
"https://github.com/hhatto/autopep8/blob/master/LICENSE"))))
(define-public python2-autopep8
(package-with-python2 python-autopep8))
@ -8264,13 +8264,13 @@ (define-public python2-pathlib
(define-public python2-pathlib2
(package
(name "python2-pathlib2")
(version "2.3.0")
(version "2.3.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "pathlib2" version))
(sha256
(base32
"1cx5gs2v9j2vnzmcrbq5l8fq2mwrr1h6pyf1sjdji2w1bavm09fk"))))
"10yb0iv5x2hs631rcppkhbddx799d3h8pcwmkbh2a66ns3w71ccf"))))
(build-system python-build-system)
;; We only need the the Python 2 variant, since for Python 3 our minimum
;; version is 3.4 which already includes this package as part of the
@ -10482,14 +10482,14 @@ (define-public python2-pbkdf2
(define-public python-qrcode
(package
(name "python-qrcode")
(version "5.3")
(version "6.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "qrcode" version))
(sha256
(base32
"0kljfrfq0c2rmxf8am57333ia41kd0snbm2rnqbdy816hgpcq5a1"))))
"1gz1g2n9kqwqkak78aavr354z1v3yyiksk7q6xp5hi1zr6s0syq3"))))
(build-system python-build-system)
(arguments
;; FIXME: Tests require packaging 'pymaging'.
@ -12788,14 +12788,14 @@ (define-public python2-phonenumbers
(define-public python-yapf
(package
(name "python-yapf")
(version "0.20.1")
(version "0.21.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "yapf" version))
(sha256
(base32
"0s7l6afzxvpx39kzd0lwshlaxw8m4fwh4iy0rlmav4vipr3g46dx"))))
"144gc7d6b1415vh02409rnb8qd5kxi6mxlr7y64d5cizgxbf72kx"))))
(build-system python-build-system)
(home-page "https://github.com/google/yapf")
(synopsis "Formatter for Python code")
@ -13263,7 +13263,7 @@ (define-public python-onetimepass
(sha256
(base32 "09vagxgbq78wvq4xbikmn2hpqqsa2i96kqsmphf7dqynfv0dlsd5"))))
(build-system python-build-system)
(inputs `(("python-six" ,python-six)))
(propagated-inputs `(("python-six" ,python-six)))
(home-page "https://github.com/tadeck/onetimepass/")
(synopsis "One-time password library")
(description "Python one-time password library for HMAC-based (HOTP) and

8
gnu/packages/ruby.scm
View file

@ -4079,14 +4079,14 @@ (define-public ruby-unf
(define-public ruby-domain-name
(package
(name "ruby-domain-name")
(version "0.5.20170404")
(version "0.5.20180417")
(source
(origin
(method url-fetch)
(uri (rubygems-uri "domain_name" version))
(sha256
(base32
"12hs8yijhak7p2hf1xkh98g0mnp5phq3mrrhywzaxpwz1gw5r3kf"))))
"0abdlwb64ns7ssmiqhdwgl27ly40x2l27l8hs8hn0z4kb3zd2x3v"))))
(build-system ruby-build-system)
(arguments
`(#:phases
@ -4585,14 +4585,14 @@ (define-public ruby-afm
(define-public ruby-ascii85
(package
(name "ruby-ascii85")
(version "1.0.2")
(version "1.0.3")
(source
(origin
(method url-fetch)
(uri (rubygems-uri "Ascii85" version))
(sha256
(base32
"0j95sbxd18kc8rhcnvl1w37kflqpax1r12h1x47gh4xxn3mz4m7q"))))
"0658m37jjjn6drzqg1gk4p6c205mgp7g1jh2d00n4ngghgmz5qvs"))))
(build-system ruby-build-system)
(native-inputs
`(("bundler" ,bundler)))

4
gnu/packages/scheme.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015, 2016 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
@ -302,7 +302,7 @@ (define-public hop
version ".tar.gz"))
(sha256
(base32
"09m7pahjsp7wxzd20cdph9j3mgf2nq5dyckcjljcd40m25v85kks"))))
"0bvq79vxcpgwydwi923cxb5w9isx2x8r3d0xndbdhacmmsw1m811"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"

2
gnu/packages/sdl.scm
View file

@ -505,7 +505,7 @@ (define-public guile-sdl2
(string-append "--with-libsdl2-mixer-prefix="
(assoc-ref %build-inputs "sdl2-mixer")))))
(native-inputs
`(("guile" ,guile-2.0)
`(("guile" ,guile-2.2)
("pkg-config" ,pkg-config)))
(inputs
`(("sdl2" ,sdl2)

10
gnu/packages/shells.scm
View file

@ -292,20 +292,18 @@ (define-public tcsh
(define-public zsh
(package
(name "zsh")
(version "5.4.2")
(version "5.5.1")
(source (origin
(method url-fetch)
(uri (list (string-append
"http://www.zsh.org/pub/zsh-" version
".tar.gz")
".tar.xz")
(string-append
"http://www.zsh.org/pub/old/zsh-" version
".tar.gz")))
(patches (search-patches "zsh-CVE-2018-7548.patch"
"zsh-CVE-2018-7549.patch"))
".tar.xz")))
(sha256
(base32
"1jdcfinzmki2w963msvsanv29vqqfmdfm4rncwpw0r3zqnrcsywm"))))
"105aqkdfsdxc4531anrj2zis2ywz6icagjam9lsc235yzh48ihz1"))))
(build-system gnu-build-system)
(arguments `(#:configure-flags '("--with-tcsetpgrp" "--enable-pcre")
#:phases

4
gnu/packages/spice.scm
View file

@ -302,7 +302,7 @@ (define-public spice-vdagent
(define-public virt-viewer
(package
(name "virt-viewer")
(version "5.0")
(version "6.0")
(source (origin
(method url-fetch)
(uri (string-append
@ -310,7 +310,7 @@ (define-public virt-viewer
"virt-viewer-" version ".tar.gz"))
(sha256
(base32
"0blbp1wkw8ahss9va0bmcz2yx18j0mvm6fzrzhh2ly3sja5ysb8b"))))
"1chqrf658niivzfh85cbwkbv9vyg8sv1mv3i31vawkfsfdvvsdwh"))))
(build-system gnu-build-system)
(inputs
`(("gtk+" ,gtk+)

16
gnu/packages/ssh.scm
View file

@ -258,8 +258,20 @@ (define-public guile-ssh
(substitute* (find-files "." "\\.scm$")
(("\"libguile-ssh\"")
(string-append "\"" libdir "/libguile-ssh\"")))
#t)))))
#t))))
(add-after 'install 'remove-bin-directory
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(examples (string-append
out "/share/guile-ssh/examples")))
(mkdir-p examples)
(rename-file (string-append bin "/ssshd.scm")
(string-append examples "/ssshd.scm"))
(rename-file (string-append bin "/sssh.scm")
(string-append examples "/sssh.scm"))
(delete-file-recursively bin)
#t))))
;; Tests are not parallel-safe.
#:parallel-tests? #f))
(native-inputs `(("autoconf" ,autoconf)

105
gnu/packages/statistics.scm
View file

@ -361,14 +361,14 @@ (define-public r-class
(define-public r-cluster
(package
(name "r-cluster")
(version "2.0.7")
(version "2.0.7-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "cluster" version))
(sha256
(base32
"0nf2hnsv5rhw6399b4gk1rj5c8hfc6ajfnkh3qbwfx3cz4asrg45"))))
"1grxbifbc4nwig25dmjgkympnbzb4al0w6k1c0ibdhpk1h4l20di"))))
(build-system r-build-system)
(inputs
`(("gfortran" ,gfortran)))
@ -402,14 +402,14 @@ (define-public r-codetools
(define-public r-foreign
(package
(name "r-foreign")
(version "0.8-69")
(version "0.8-70")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreign" version))
(sha256
(base32
"0s1lxmd85dd0kxx8hwk02w9l7pmpk4bpy7787fbyh2dbq5g9ys0k"))))
"11mql8q3i1q593dvd351fhvkvfab25li80d1ahl4xjjzy52qdkc6"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/foreign")
(synopsis "Read data stored by other statistics software")
@ -488,14 +488,14 @@ (define-public r-matrix
(define-public r-nlme
(package
(name "r-nlme")
(version "3.1-131.1")
(version "3.1-137")
(source
(origin
(method url-fetch)
(uri (cran-uri "nlme" version))
(sha256
(base32
"1xafi670a9jzb52kqxkacxfmy0viac3aql5byfq86kgkgla2sg0y"))))
"11vyxxc0n36vb8d8g02zr0402ymicvbifwdsqm7gy9iqqnwrn101"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
@ -593,14 +593,14 @@ (define-public r-spatial
(define-public r-survival
(package
(name "r-survival")
(version "2.41-3")
(version "2.42-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "survival" version))
(sha256
(base32
"07cnr0hnki6ybbjll54l4s5lllhk19vni5f8m0mvsfp99ls7qygk"))))
"15pasbfzmg2r5bfpsadp9ia4cpybqz6n1kwm7ma02ykzf7bk4xx0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)))
@ -2694,13 +2694,13 @@ (define-public r-blob
(define-public r-rsqlite
(package
(name "r-rsqlite")
(version "2.0")
(version "2.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RSQLite" version))
(sha256
(base32
"1xpg1i1jkzkzv44k512k90c2vvl960pl2d4a3spwcha6yclyc3vz"))))
"0hknfqcgijdapx1ryy20zy68qmm8wsb1hjx4n4hmkgl552z82q5d"))))
(properties `((upstream-name . "RSQLite")))
(build-system r-build-system)
(propagated-inputs
@ -2766,13 +2766,13 @@ (define-public r-rcurl
(define-public r-xml
(package
(name "r-xml")
(version "3.98-1.10")
(version "3.98-1.11")
(source (origin
(method url-fetch)
(uri (cran-uri "XML" version))
(sha256
(base32
"1faza9bbllp67lf1yv1sllxc3iv8llz52m9diazhq322iqbh97m1"))))
"18izvlg2x9mzr6yb3yf02ghwbyn00frki3av4lpc44r22m4djnsh"))))
(properties
`((upstream-name . "XML")))
(build-system r-build-system)
@ -2820,28 +2820,17 @@ (define-public r-xnomial
(define-public r-lambda-r
(package
(name "r-lambda-r")
(version "1.2")
(version "1.2.2")
(source (origin
(method url-fetch)
(uri (cran-uri "lambda.r" version))
(sha256
(base32
"0vql32np716dpd0kjn7s7wgawd02ysgp2a5il4kb19nlw661ii3x"))))
"05cfaq9dbgdnmmj3d6ggmsw300qgiw8k7f6h6k0ylv63cf3v6pkq"))))
(properties `((upstream-name . "lambda.r")))
(build-system r-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'check 'delete-test-log
;; The test report contains time stamps and is not important for
;; the installed package.
(lambda* (#:key outputs #:allow-other-keys)
(delete-file-recursively
(string-append (assoc-ref outputs "out")
"/site-library/lambda.r/unitTests"))
#t)))))
(native-inputs
`(("r-runit" ,r-runit)))
(propagated-inputs
`(("r-formatr" ,r-formatr)))
(home-page "https://cran.r-project.org/web/packages/lambda.r")
(synopsis "Functional programming extension for R")
(description
@ -2854,13 +2843,13 @@ (define-public r-lambda-r
(define-public r-futile-options
(package
(name "r-futile-options")
(version "1.0.0")
(version "1.0.1")
(source (origin
(method url-fetch)
(uri (cran-uri "futile.options" version))
(sha256
(base32
"1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f"))))
"0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
(properties
`((upstream-name . "futile.options")))
(build-system r-build-system)
@ -3410,13 +3399,13 @@ (define-public r-r-methodss3
(define-public r-r-oo
(package
(name "r-r-oo")
(version "1.21.0")
(version "1.22.0")
(source (origin
(method url-fetch)
(uri (cran-uri "R.oo" version))
(sha256
(base32
"0723gxjazgqq7v3lwnl7axw3brzcnizvhbd71ijkkv8mz31fwp34"))))
"0k6xwy93fpb2p7bs76lzk52br9rv5xnd9524xj8qyazv1132x1n0"))))
(properties `((upstream-name . "R.oo")))
(build-system r-build-system)
(propagated-inputs
@ -4222,13 +4211,13 @@ (define-public r-zoo
(define-public r-ztable
(package
(name "r-ztable")
(version "0.1.5")
(version "0.1.8")
(source (origin
(method url-fetch)
(uri (cran-uri "ztable" version))
(sha256
(base32
"1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r"))))
"1hk5k9614n52dpfrhdws06w4gvwhnz8q47x4cwxx88qmrzm8z2m3"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/ztable")
(synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
@ -4281,14 +4270,14 @@ (define-public r-beeswarm
(define-public r-sourcetools
(package
(name "r-sourcetools")
(version "0.1.6")
(version "0.1.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "sourcetools" version))
(sha256
(base32
"0l8c6fql82cb246qh7hfgxb4s35qn0qfgy6dzvkx0zkz1cpqvx69"))))
"1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/sourcetools")
(synopsis "Tools for reading, tokenizing and parsing R code")
@ -4697,14 +4686,14 @@ (define-public r-deoptimr
(define-public r-robustbase
(package
(name "r-robustbase")
(version "0.92-8")
(version "0.93-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "robustbase" version))
(sha256
(base32
"080ynchq8pvhnmbivj4fp74n0x9lyr9923sg0s9gq5irgm68kgxw"))))
"130pzibn5cb8mycv8byc6npzcpddghz8m7jqwk15qmx4g3cj8zgy"))))
(build-system r-build-system)
(inputs
`(("gfortran" ,gfortran)))
@ -5071,14 +5060,14 @@ (define-public r-nloptr
(define-public r-lme4
(package
(name "r-lme4")
(version "1.1-16")
(version "1.1-17")
(source
(origin
(method url-fetch)
(uri (cran-uri "lme4" version))
(sha256
(base32
"0p5x9ki4dq8058mc7k9wdnlh60z1xa3wk2nmf71wl7w59m4szh92"))))
"0czwdy1s8h3slaw73pz0h8qmqczf5135fz6i46i2dv1ql2pbq49x"))))
(build-system r-build-system)
(native-inputs
`(("r-rcpp" ,r-rcpp)
@ -5123,24 +5112,50 @@ (define-public r-pbkrtest
bootstrap test for generalized linear mixed models.")
(license license:gpl2+)))
(define-public r-cardata
(package
(name "r-cardata")
(version "3.0-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "carData" version))
(sha256
(base32
"193pdwgw6gk19v7swk1kwphg3vqdmpsgi555g9nyz93sa39j7r8j"))))
(properties `((upstream-name . "carData")))
(build-system r-build-system)
(home-page "https://r-forge.r-project.org/projects/car/")
(synopsis "Data Sets for the book Companion to Applied Regression")
(description
"This package provides datasets to accompany J. Fox and S. Weisberg, An R
Companion to Applied Regression, Third Edition, Sage.")
(license license:gpl2+)))
(define-public r-car
(package
(name "r-car")
(version "2.1-6")
(version "3.0-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "car" version))
(sha256
(base32
"14l4d9j87xnb0bz2wgqqbxnlnbcdfb5vx2fw6kdxj91kyrk6lhnj"))))
"1ks2jaav8lbxhzw56vpbnysjk3pvpmqh6avd574k0bha1226k81h"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
`(("r-abind" ,r-abind)
("r-cardata" ,r-cardata)
("r-lme4" ,r-lme4)
("r-maptools" ,r-maptools)
("r-mass" ,r-mass)
("r-mgcv" ,r-mgcv)
("r-nlme" ,r-nlme)
("r-nnet" ,r-nnet)
("r-pbkrtest" ,r-pbkrtest)
("r-quantreg" ,r-quantreg)))
("r-quantreg" ,r-quantreg)
("r-rio" ,r-rio)))
(home-page "https://r-forge.r-project.org/projects/car/")
(synopsis "Companion to applied regression")
(description
@ -5247,14 +5262,14 @@ (define-public r-numderiv
(define-public r-sn
(package
(name "r-sn")
(version "1.5-1")
(version "1.5-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sn" version))
(sha256
(base32
"0l7qlah6dwkp8jswnr2mn3phlm15naba5zkmv0g5pcqy5ix0gz7w"))))
"16gwr68zzj5v83bqfmzxnzwig3dnjrkxdhs6clri1caqkvrq6aig"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mnormt" ,r-mnormt)

4
gnu/packages/storage.scm
View file

@ -51,14 +51,14 @@ (define-module (gnu packages storage)
(define-public ceph
(package
(name "ceph")
(version "12.2.4")
(version "12.2.5")
(source (origin
(method url-fetch)
(uri (string-append "https://download.ceph.com/tarballs/ceph-"
version ".tar.gz"))
(sha256
(base32
"13hv8scaxc1gdvrhzbfnsk4yy3pla6n1i4j4j4zf7schmbf0j8mp"))
"1ydc3mfvc0vpnpfnfmissvsrsj4jyxgzc2pcl1a4vdr3bwkcglp3"))
(patches
(search-patches "ceph-skip-unittest_blockdev.patch"
"ceph-skip-collect-sys-info-test.patch"

2
gnu/packages/syncthing.scm
View file

@ -860,8 +860,6 @@ (define-public go-github-com-vitrun-qart-qr
`(#:import-path "github.com/vitrun/qart/qr"
#:unpack-path "github.com/vitrun/qart"))
(synopsis "Qart component for generating QR codes")
(description "This package, a component of @code{qart}, provides
@code{qr}, for QR code generation.")
(description "This package provides a library for embedding
human-meaningful graphics in QR codes. However, instead of scribbling on
redundant pieces and relying on error correction to preserve the meaning,

19
gnu/packages/text-editors.scm
View file

@ -239,14 +239,16 @@ (define-public e3
(define-public mg
(package
(name "mg")
(version "20171014")
(version "20180408")
(source (origin
(method url-fetch)
(uri (string-append "https://homepage.boetes.org/software/mg/mg-"
version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/hboetes/mg")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0hakfikzsml7z0hja8m8mcahrmfy2piy81bq9nccsjplyfc9clai"))
"06w86xk7sjl2x2h3z6msn8kpmwj05qdimcym77wzhz5s94dzh1bl"))
(modules '((guix build utils)))
(snippet '(begin
(substitute* "GNUmakefile"
@ -262,10 +264,9 @@ (define-public mg
;; No test suite available.
'(#:tests? #f
#:make-flags (list (string-append "prefix=" %output)
"CURSES_LIBS=-lncurses"
"CC=gcc")
#:phases (modify-phases %standard-phases
(delete 'configure)
(delete 'configure) ; no configure script
(add-before 'build 'correct-location-of-difftool
(lambda _
(substitute* "buffer.c"
@ -294,7 +295,7 @@ (define-public mg
(define-public ghostwriter
(package
(name "ghostwriter")
(version "1.6.1")
(version "1.6.2")
(source (origin
(method git-fetch)
(uri (git-reference
@ -303,7 +304,7 @@ (define-public ghostwriter
(file-name (git-file-name name version))
(sha256
(base32
"1ihdr4xk0j83q83xknbikxb7yf9qhlkgvc89w33lhj090cv376gd"))))
"0251563zy0q69fzfacvalpx43y15cshb0bhshyd4w37061gh1c12"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)

8
gnu/packages/textutils.scm
View file

@ -135,7 +135,7 @@ (define-public enca
(define-public utf8proc
(package
(name "utf8proc")
(version "2.1.0")
(version "2.1.1")
(source
(origin
(method url-fetch)
@ -144,9 +144,9 @@ (define-public utf8proc
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "0q1jhdkk4f9b0zb8s2ql3sba3br5nvjsmbsaybmgj064k9hwbk15"))))
(base32 "1cnpigrazhslw65s4j1a56j7p6d7d61wsxxjf1218i9mkwv2yw17"))))
(build-system gnu-build-system)
(inputs ;test data that is otherwise downloaded with curl
(inputs ; test data that is otherwise downloaded with curl
`(("NormalizationTest.txt"
,(origin
(method url-fetch)
@ -176,7 +176,7 @@ (define-public utf8proc
(substitute* "data/GraphemeBreakTest.txt"
(("÷") "/")
(("×") "+")))))))
(home-page "http://julialang.org/utf8proc/")
(home-page "https://julialang.org/utf8proc/")
(synopsis "C library for processing UTF-8 Unicode data")
(description "utf8proc is a small C library that provides Unicode
normalization, case-folding, and other operations for data in the UTF-8

50
gnu/packages/version-control.scm
View file

@ -18,6 +18,7 @@
;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -1910,3 +1911,52 @@ (define-public gource
Contributors to the source code appear and disappear as they contribute to
specific files and directories.")
(license license:gpl3+)))
(define-public src
(package
(name "src")
(version "1.18")
(source (origin
(method url-fetch)
(uri (string-append
"http://www.catb.org/~esr/src/src-" version ".tar.gz"))
(sha256
(base32
"0n0skhvya8w2az45h2gsafxy8m2mvqas64nrgxifcmrzfv0rf26c"))))
(build-system gnu-build-system)
(arguments
'(#:make-flags
(list (string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
(delete 'configure) ; no 'configure' script
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(prog (string-append out "/bin/src"))
(rcs (assoc-ref inputs "rcs")))
(wrap-program prog
`("PATH" ":" prefix (,(string-append rcs "/bin"))))
#t)))
(replace 'check
(lambda _
(setenv "HOME" (getenv "TMPDIR"))
(invoke "git" "config" "--global" "user.name" "guix")
(invoke "git" "config" "--global" "user.email" "guix")
(invoke "./srctest"))))))
(native-inputs
;; For testing.
`(("git" ,git)
("perl" ,perl)))
(inputs
`(("python" ,python-wrapper)
("rcs" ,rcs)))
(synopsis "Simple revision control")
(home-page "http://www.catb.org/~esr/src/")
(description
"SRC (or src) is simple revision control, a version-control system for
single-file projects by solo developers and authors. It modernizes the
venerable RCS, hence the anagrammatic acronym. The design is tuned for use
cases like all those little scripts in your @file{~/bin} directory, or a
directory full of HOWTOs.")
(license license:bsd-2)))

91
gnu/packages/video.scm
View file

@ -19,7 +19,7 @@
;;; Copyright © 2017 Chris Marusich <cmmarusich@gmail.com>
;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017 Ethan R. Jones <doubleplusgood23@gmail.com>
;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2017 Gregor Giesen <giesen@zaehlwerk.net>
;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
@ -598,14 +598,14 @@ (define-public libva
(define-public ffmpeg
(package
(name "ffmpeg")
(version "3.4.2")
(version "4.0")
(source (origin
(method url-fetch)
(uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
version ".tar.xz"))
(sha256
(base32
"0h6prjn1ijkzzhkyj8mazp0wpx7m0n9ycadjxagf9czqirbyk4ib"))))
"0gx4ngnhi5glmxh38603qy5n6vq8bl1cr4sqd1xff95i82pmv57d"))))
(build-system gnu-build-system)
(inputs
`(("fontconfig" ,fontconfig)
@ -771,6 +771,18 @@ (define-public ffmpeg
audio/video codec library.")
(license license:gpl2+)))
(define-public ffmpeg-3.4
(package
(inherit ffmpeg)
(version "3.4.2")
(source (origin
(method url-fetch)
(uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
version ".tar.xz"))
(sha256
(base32
"0h6prjn1ijkzzhkyj8mazp0wpx7m0n9ycadjxagf9czqirbyk4ib"))))))
(define-public ffmpeg-2.8
(package
(inherit ffmpeg)
@ -791,25 +803,6 @@ (define-public ffmpeg-2.8
flag))
,flags))))))
;; Annoyingly enough, the latest mpv release does not build with the stable
;; release of ffmpeg. Use a git commit until the situation is fixed.
(define-public ffmpeg-git
(let ((commit "3f887440677328c9cfed97ad81d14051ffa32aae")
(revision "1"))
(package
(inherit ffmpeg)
(name "ffmpeg-git")
(version (string-append "3.4-" revision "." (string-take commit 9)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/FFmpeg/FFmpeg.git")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1b7n3g4m2rbvrwsgbfl8wl91z42g1ld42clwxs8qpl9ny5rwz6sq")))))))
(define-public vlc
(package
(name "vlc")
@ -1033,7 +1026,7 @@ (define-public mpv
(inputs
`(("alsa-lib" ,alsa-lib)
("enca" ,enca)
("ffmpeg" ,ffmpeg-git)
("ffmpeg" ,ffmpeg)
("jack" ,jack-1)
("ladspa" ,ladspa)
("lcms" ,lcms)
@ -1162,7 +1155,7 @@ (define-public libvpx
(define-public youtube-dl
(package
(name "youtube-dl")
(version "2018.04.16")
(version "2018.04.25")
(source (origin
(method url-fetch)
(uri (string-append "https://yt-dl.org/downloads/"
@ -1170,7 +1163,7 @@ (define-public youtube-dl
version ".tar.gz"))
(sha256
(base32
"046zg8pww2xg1yibh7c1a8jcg8f1znr4hsz1l1da03djcp6na99d"))))
"17zxgwfcy7c6gdyxdgh02f5zi52gvmy0zpccfj6zjkhw5iqj1vbw"))))
(build-system python-build-system)
(arguments
;; The problem here is that the directory for the man page and completion
@ -1319,7 +1312,7 @@ (define-public you-get
(define-public youtube-viewer
(package
(name "youtube-viewer")
(version "3.3.3")
(version "3.3.4")
(source (origin
(method url-fetch)
(uri (string-append
@ -1328,7 +1321,7 @@ (define-public youtube-viewer
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1j572his6qmazlmyrbnfq62s9bqml875ay7wy26byy9hfc7m0vgk"))))
"1dqaxkz5svv0lmxds6lppcpzhkq6gar2raw9gx6imrd7yz02fpgn"))))
(build-system perl-build-system)
(native-inputs
`(("perl-module-build" ,perl-module-build)))
@ -1857,7 +1850,7 @@ (define-public mlt
#t)))))
(inputs
`(("alsa-lib" ,alsa-lib)
("ffmpeg" ,ffmpeg)
("ffmpeg" ,ffmpeg-3.4)
("fftw" ,fftw)
("libxml2" ,libxml2)
("jack" ,jack-1)
@ -2093,7 +2086,7 @@ (define-public simplescreenrecorder
;; As a result, they are omitted. Please add them back if problems appear.
(inputs
`(("alsa-lib" ,alsa-lib)
("ffmpeg" ,ffmpeg)
("ffmpeg" ,ffmpeg-3.4)
("glu" ,glu)
("jack" ,jack-1)
("libxi" ,libxi)
@ -2806,7 +2799,7 @@ (define-public motion
("pkg-config" ,pkg-config)))
(inputs
`(("libjpeg" ,libjpeg)
("ffmpeg" ,ffmpeg)
("ffmpeg" ,ffmpeg-3.4)
("sqlite" ,sqlite)))
(arguments
'(#:phases (modify-phases %standard-phases
@ -2864,3 +2857,41 @@ (define-public subdl
save it to the appropriate filename.")
(license license:gpl3+)
(home-page "https://github.com/alexanderwink/subdl"))))
(define-public l-smash
(package
(name "l-smash")
(version "2.14.5")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/" name "/" name "/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0dary0h65kq6sv93iabv25djlvzr5ckdcp3ywagbix44wqfw7xz6"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no tests
#:make-flags
(list (string-append "LDFLAGS=-Wl,-L.,-rpath="
(assoc-ref %outputs "out") "/lib"))
#:phases
(modify-phases %standard-phases
;; configure fails if it is followed by CONFIG_SHELL
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(invoke "./configure" (string-append "--prefix=" out)
"--disable-static")))))))
(native-inputs
`(("which" ,which)))
(home-page "https://l-smash.github.io/l-smash/")
(synopsis "MP4 multiplexer and demultiplexer library")
(description
"L-SMASH is a cross-platform library that handles the ISO base media file
format and some of its derived file formats, including MP4. It operates as a
multiplexer and demultiplexer, and can mux video and audio in several formats
using standalone executable files.")
(license license:isc)))

111
gnu/packages/virtualization.scm
View file

@ -5,9 +5,10 @@
;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2017 Andy Patterson <ajpatter@uwaterloo.ca>
;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Danny Milosavljevic <dannym@scratchpost.org>
;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -40,9 +41,11 @@ (define-module (gnu packages virtualization)
#:use-module (gnu packages documentation)
#:use-module (gnu packages flex)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gettext)
#:use-module (gnu packages gl)
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
#:use-module (gnu packages golang)
#:use-module (gnu packages gtk)
#:use-module (gnu packages image)
#:use-module (gnu packages libusb)
@ -65,9 +68,11 @@ (define-module (gnu packages virtualization)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages xml)
#:use-module (guix build-system gnu)
#:use-module (guix build-system go)
#:use-module (guix build-system python)
#:use-module (guix download)
#:use-module ((guix licenses) #:select (gpl2 gpl2+ gpl3+ lgpl2.1 lgpl2.1+))
#:use-module ((guix licenses) #:select (gpl2 gpl2+ gpl3+ lgpl2.1 lgpl2.1+
asl2.0))
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (srfi srfi-1))
@ -85,16 +90,14 @@ (define (qemu-patch commit file-name sha256)
(define-public qemu
(package
(name "qemu")
(version "2.11.1")
(version "2.12.0")
(source (origin
(method url-fetch)
(uri (string-append "https://download.qemu.org/qemu-"
version ".tar.xz"))
(sha256
(base32
"11l6cs6mib16rgdrnqrhkqs033fjik316gkgfz3asbmxz38lalca"))
(patches (search-patches "qemu-glibc-2.27.patch"
"qemu-CVE-2018-7550.patch"))))
"1z66spkm1prvhbq7h5mfnp0i6mmamsb938fqmdfvyrgzc7rh34z6"))))
(build-system gnu-build-system)
(arguments
'(;; Running tests in parallel can occasionally lead to failures, like:
@ -173,6 +176,7 @@ (define-public qemu
`(("alsa-lib" ,alsa-lib)
("attr" ,attr)
("glib" ,glib)
("gtk+" ,gtk+)
("libaio" ,libaio)
("libattr" ,attr)
("libcap" ,libcap) ; virtfs support requires libcap & libattr
@ -187,19 +191,20 @@ (define-public qemu
;; ("pciutils" ,pciutils)
("pixman" ,pixman)
("pulseaudio" ,pulseaudio)
("sdl" ,sdl)
("sdl2" ,sdl2)
("spice" ,spice)
("usbredir" ,usbredir)
("util-linux" ,util-linux)
;; ("vde2" ,vde2)
("virglrenderer" ,virglrenderer)
("zlib" ,zlib)))
(native-inputs `(("glib:bin" ,glib "bin") ; gtester, etc.
(native-inputs `(("gettext" ,gettext-minimal)
("glib:bin" ,glib "bin") ; gtester, etc.
("perl" ,perl)
("flex" ,flex)
("bison" ,bison)
("pkg-config" ,pkg-config)
("python" ,python-2) ; incompatible with Python 3 according to error message
("python-wrapper" ,python-wrapper)
("texinfo" ,texinfo)))
(home-page "https://www.qemu.org")
(synopsis "Machine emulator and virtualizer")
@ -234,10 +239,35 @@ (define-public qemu-minimal
''("--target-list=i386-softmmu,x86_64-softmmu,mips64el-softmmu,arm-softmmu,aarch64-softmmu"))))
;; Remove dependencies on optional libraries, notably GUI libraries.
(native-inputs (fold alist-delete (package-native-inputs qemu)
'("gettext")))
(inputs (fold alist-delete (package-inputs qemu)
'("libusb" "mesa" "sdl" "spice" "virglrenderer"
'("libusb" "mesa" "sdl2" "spice" "virglrenderer" "gtk+"
"usbredir" "libdrm" "libepoxy" "pulseaudio")))))
;; The GRUB test suite fails with later versions of Qemu, so we
;; keep it at 2.10 for now. See
;; <https://lists.gnu.org/archive/html/bug-grub/2018-02/msg00004.html>.
;; This package is hidden since we do not backport updates to it.
(define-public qemu-minimal-2.10
(hidden-package
(package
(inherit qemu-minimal)
(version "2.10.2")
(source (origin
(method url-fetch)
(uri (string-append "https://download.qemu.org/qemu-"
version ".tar.xz"))
(sha256
(base32
"17w21spvaxaidi2am5lpsln8yjpyp2zi3s3gc6nsxj5arlgamzgw"))
(patches
(search-patches "qemu-glibc-2.27.patch"))))
;; qemu-minimal-2.10 needs Python 2. Remove below once no longer necessary.
(native-inputs `(("python-2" ,python-2)
,@(fold alist-delete (package-native-inputs qemu)
'("python-wrapper")))))))
(define-public libosinfo
(package
(name "libosinfo")
@ -524,7 +554,7 @@ (define-public python2-libvirt
(define-public virt-manager
(package
(name "virt-manager")
(version "1.4.3")
(version "1.5.1")
(source (origin
(method url-fetch)
(uri (string-append "https://virt-manager.org/download/sources"
@ -532,7 +562,7 @@ (define-public virt-manager
version ".tar.gz"))
(sha256
(base32
"093azs8p4p7y4nf5j25xpsvdxww7gky1g0hs8mkcvmpxl2wjd0jj"))))
"1ardmd4sxdmd57y7qpka44gf09c1yq2g0xs074d3k1h925crv27f"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
@ -777,3 +807,60 @@ (define-public lookingglass
;; This package requires SSE instructions.
(supported-systems '("i686-linux" "x86_64-linux"))
(license gpl2+)))
(define-public runc
(package
(name "runc")
(version "1.0.0-rc5")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/opencontainers/runc/releases/"
"download/v" version "/runc.tar.xz"))
(sha256
(base32
"081avdzwnqpk368wbaihlzsypaxpj42d7699h7jgp0fks14x4103"))))
(build-system go-build-system)
(arguments
'(#:import-path "github.com/opencontainers/runc"
#:install-source? #f
;; XXX: 20/139 tests fail due to missing /var, cgroups and apparmor in
;; the build environment.
#:tests? #f
#:phases
(modify-phases %standard-phases
(replace 'unpack
(lambda* (#:key source import-path #:allow-other-keys)
;; Unpack the tarball into 'runc' instead of 'runc-1.0.0-rc5'.
(let ((dest (string-append "src/" import-path)))
(mkdir-p dest)
(invoke "tar" "-C" (string-append "src/" import-path)
"--strip-components=1"
"-xvf" source))))
(replace 'build
(lambda* (#:key import-path #:allow-other-keys)
(chdir (string-append "src/" import-path))
;; XXX: requires 'go-md2man'.
;; (invoke "make" "man")
(invoke "make")))
;; (replace 'check
;; (lambda _
;; (invoke "make" "localunittest")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(invoke "make" "install" "install-bash"
(string-append "PREFIX=" out))))))))
(native-inputs
`(("pkg-config" ,pkg-config)))
(inputs
`(("libseccomp" ,libseccomp)))
(synopsis "Open container initiative runtime")
(home-page "https://www.opencontainers.org/")
(description
"@command{runc} is a command line client for running applications
packaged according to the
@uref{https://github.com/opencontainers/runtime-spec/blob/master/spec.md, Open
Container Initiative (OCI) format} and is a compliant implementation of the
Open Container Initiative specification.")
(license asl2.0)))

40
gnu/packages/vpn.scm
View file

@ -6,6 +6,7 @@
;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -32,9 +33,11 @@ (define-module (gnu packages vpn)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages check)
#:use-module (gnu packages autotools)
#:use-module (gnu packages compression)
#:use-module (gnu packages gettext)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages libevent)
#:use-module (gnu packages linux)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
@ -207,6 +210,39 @@ (define-public vpnc-scripts
the entire VPN in a network namespace accessible only through SSH.")
(license license:gpl2+))))
(define-public ocproxy
(package
(name "ocproxy")
(version "1.60")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/cernekee/ocproxy/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1b4rg3xq5jnrp2l14sw0msan8kqhdxmsd7gpw9lkiwvxy13pcdm7"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)))
(inputs
`(("libevent" ,libevent)))
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _ (invoke "sh" "autogen.sh"))))))
(home-page "https://github.com/cernekee/ocproxy")
(synopsis "OpenConnect proxy")
(description
"User-level @dfn{SOCKS} and port forwarding proxy for OpenConnect based
on LwIP. When using ocproxy, OpenConnect only handles network activity that
the user specifically asks to proxy, so the @dfn{VPN} interface no longer
\"hijacks\" all network traffic on the host.")
(license license:bsd-3)))
(define-public openconnect
(package
(name "openconnect")
@ -243,7 +279,7 @@ (define-public openconnect
(define-public openvpn
(package
(name "openvpn")
(version "2.4.5")
(version "2.4.6")
(source (origin
(method url-fetch)
(uri (string-append
@ -251,7 +287,7 @@ (define-public openvpn
version ".tar.xz"))
(sha256
(base32
"17njq59hsraqyxrbhkrxr7dvx0p066s3pn8w1mi0yd9jldis7h23"))))
"09lck4wmkas3iyrzaspin9gn3wiclqb1m9sf8diy7j8wakx38r2g"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags '("--enable-iproute2=yes")))

5
gnu/packages/vulkan.scm
View file

@ -160,7 +160,7 @@ (define-public glslang
(define-public vulkan-icd-loader
(package
(name "vulkan-icd-loader")
(version "1.1.70.0")
(version "1.1.73.0")
(source
(origin
(method url-fetch)
@ -169,7 +169,7 @@ (define-public vulkan-icd-loader
"archive/sdk-" version ".tar.gz"))
(sha256
(base32
"15qkh77596v3xivnbb3l0q9zbmmsdglnaza2m1g7f8q7bbigyc5x"))))
"1qb34j2zrc04fgs96m3k76vi4nx3sygbdcyg7pbwasr45cbdhsxb"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;FIXME: 23/39 tests fail. Try "tests/run_all_tests.sh".
@ -182,6 +182,7 @@ (define-public vulkan-icd-loader
#t)))
#:configure-flags (list
"-DBUILD_LAYERS=OFF" ; FIXME: Fails to build.
"-DBUILD_TESTS=OFF" ; FIXME: Needs 'googletest' submodule.
(string-append "-DCMAKE_INSTALL_LIBDIR="
(assoc-ref %outputs "out") "/lib"))))
(inputs `(("glslang" ,glslang)

16
gnu/packages/web.scm
View file

@ -3784,15 +3784,19 @@ (define-public python2-feedparser
(define-public r-httpuv
(package
(name "r-httpuv")
(version "1.3.6.2")
(version "1.4.1")
(source (origin
(method url-fetch)
(uri (cran-uri "httpuv" version))
(sha256
(base32
"0h3hkw575b211bxma23inbq1565wkhiapgasd539h219apqs534f"))))
"1pndv0h870ygibk0bmg9ayzkls60jqscrsyk39k29gy2pvm9ha5y"))))
(build-system r-build-system)
(native-inputs `(("r-rcpp" ,r-rcpp)))
(propagated-inputs
`(("r-bh" ,r-bh)
("r-later" ,r-later)
("r-promises" ,r-promises)))
(home-page "https://github.com/rstudio/httpuv")
(synopsis "HTTP and WebSocket server library for R")
(description
@ -3892,13 +3896,13 @@ (define-public r-htmltools
(define-public r-htmlwidgets
(package
(name "r-htmlwidgets")
(version "1.0")
(version "1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "htmlwidgets" version))
(sha256
(base32
"09lkmzh35l1420sg0dyh4vgyishqx3g8xmgs2y9z7lbi09xgwwwr"))))
"04c4d0mfcy3dkdlbxnaccpdgxvyxfdwfmmh5djim6v9hyg0j2z8s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
@ -5432,13 +5436,13 @@ (define-public r-shiny
(define-public r-shinydashboard
(package
(name "r-shinydashboard")
(version "0.6.1")
(version "0.7.0")
(source (origin
(method url-fetch)
(uri (cran-uri "shinydashboard" version))
(sha256
(base32
"14zi7g5wrngy6lwi9xpvaid7727m6rfdijbb89al9likfhjqzqqy"))))
"10yqcqqcxgfqwkmscqwvvgr710im583qsqnsqkfpisjvkqp10yqb"))))
(build-system r-build-system)
;; The directory inst/AdminLTE/ contains a minified JavaScript file.
;; Regenerate it from the included sources.

8
gnu/packages/xdisorg.scm
View file

@ -496,7 +496,7 @@ (define-public scrot
(define-public slop
(package
(name "slop")
(version "7.3.49")
(version "7.4")
(source (origin
(method url-fetch)
(uri (string-append
@ -505,7 +505,7 @@ (define-public slop
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0gxi174vi13ldjaf776s2jcdyy379lnwwml29nk1bkzj5d5gpghm"))))
"1kpdrikgpjb4fpxalb6pjcih5njv1w9cnrjj5612ywdv1q5mjs48"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f)) ; no "check" target
@ -529,7 +529,7 @@ (define-public slop
(define-public maim
(package
(name "maim")
(version "5.4.68")
(version "5.5")
(source (origin
(method url-fetch)
(uri (string-append
@ -538,7 +538,7 @@ (define-public maim
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0f54s7csrxjd5r9anqqa92diwmzdplpws3llmbr6g3c0l6bp8815"))))
"02blbimjdckbcb04crhv0k2vxnp3rcgskyq66sk0v13l2h52849v"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f)) ; no "check" target

160
gnu/services/base.scm
View file

@ -26,7 +26,6 @@ (define-module (gnu services base)
#:use-module (guix store)
#:use-module (gnu services)
#:use-module (gnu services shepherd)
#:use-module (gnu services networking)
#:use-module (gnu system pam)
#:use-module (gnu system shadow) ; 'user-account', etc.
#:use-module (gnu system uuid)
@ -64,6 +63,18 @@ (define-module (gnu services base)
console-font-service
virtual-terminal-service-type
static-networking
static-networking?
static-networking-interface
static-networking-ip
static-networking-netmask
static-networking-gateway
static-networking-requirement
static-networking-service
static-networking-service-type
udev-configuration
udev-configuration?
udev-configuration-rules
@ -2045,6 +2056,153 @@ (define kmscon-command
(start #~(make-forkexec-constructor #$kmscon-command))
(stop #~(make-kill-destructor)))))))
(define-record-type* <static-networking>
static-networking make-static-networking
static-networking?
(interface static-networking-interface)
(ip static-networking-ip)
(netmask static-networking-netmask
(default #f))
(gateway static-networking-gateway ;FIXME: doesn't belong here
(default #f))
(provision static-networking-provision
(default #f))
(requirement static-networking-requirement
(default '()))
(name-servers static-networking-name-servers ;FIXME: doesn't belong here
(default '())))
(define static-networking-shepherd-service
(match-lambda
(($ <static-networking> interface ip netmask gateway provision
requirement name-servers)
(let ((loopback? (and provision (memq 'loopback provision))))
(shepherd-service
(documentation
"Bring up the networking interface using a static IP address.")
(requirement requirement)
(provision (or provision
(list (symbol-append 'networking-
(string->symbol interface)))))
(start #~(lambda _
;; Return #t if successfully started.
(let* ((addr (inet-pton AF_INET #$ip))
(sockaddr (make-socket-address AF_INET addr 0))
(mask (and #$netmask
(inet-pton AF_INET #$netmask)))
(maskaddr (and mask
(make-socket-address AF_INET
mask 0)))
(gateway (and #$gateway
(inet-pton AF_INET #$gateway)))
(gatewayaddr (and gateway
(make-socket-address AF_INET
gateway 0))))
(configure-network-interface #$interface sockaddr
(logior IFF_UP
#$(if loopback?
#~IFF_LOOPBACK
0))
#:netmask maskaddr)
(when gateway
(let ((sock (socket AF_INET SOCK_DGRAM 0)))
(add-network-route/gateway sock gatewayaddr)
(close-port sock))))))
(stop #~(lambda _
;; Return #f is successfully stopped.
(let ((sock (socket AF_INET SOCK_STREAM 0)))
(when #$gateway
(delete-network-route sock
(make-socket-address
AF_INET INADDR_ANY 0)))
(set-network-interface-flags sock #$interface 0)
(close-port sock)
: #f)))
(respawn? #f))))))
(define (static-networking-etc-files interfaces)
"Return a /etc/resolv.conf entry for INTERFACES or the empty list."
(match (delete-duplicates
(append-map static-networking-name-servers
interfaces))
(()
'())
((name-servers ...)
(let ((content (string-join
(map (cut string-append "nameserver " <>)
name-servers)
"\n" 'suffix)))
`(("resolv.conf"
,(plain-file "resolv.conf"
(string-append "\
# Generated by 'static-networking-service'.\n"
content))))))))
(define (static-networking-shepherd-services interfaces)
"Return the list of Shepherd services to bring up INTERFACES, a list of
<static-networking> objects."
(define (loopback? service)
(memq 'loopback (shepherd-service-provision service)))
(let ((services (map static-networking-shepherd-service interfaces)))
(match (remove loopback? services)
(()
;; There's no interface other than 'loopback', so we assume that the
;; 'networking' service will be provided by dhclient or similar.
services)
((non-loopback ...)
;; Assume we're providing all the interfaces, and thus, provide a
;; 'networking' service.
(cons (shepherd-service
(provision '(networking))
(requirement (append-map shepherd-service-provision
services))
(start #~(const #t))
(stop #~(const #f))
(documentation "Bring up all the networking interfaces."))
services)))))
(define static-networking-service-type
;; The service type for statically-defined network interfaces.
(service-type (name 'static-networking)
(extensions
(list
(service-extension shepherd-root-service-type
static-networking-shepherd-services)
(service-extension etc-service-type
static-networking-etc-files)))
(compose concatenate)
(extend append)
(description
"Turn up the specified network interfaces upon startup,
with the given IP address, gateway, netmask, and so on. The value for
services of this type is a list of @code{static-networking} objects, one per
network interface.")))
(define* (static-networking-service interface ip
#:key
netmask gateway provision
;; Most interfaces require udev to be usable.
(requirement '(udev))
(name-servers '()))
"Return a service that starts @var{interface} with address @var{ip}. If
@var{netmask} is true, use it as the network mask. If @var{gateway} is true,
it must be a string specifying the default network gateway.
This procedure can be called several times, one for each network
interface of interest. Behind the scenes what it does is extend
@code{static-networking-service-type} with additional network interfaces
to handle."
(simple-service 'static-network-interface
static-networking-service-type
(list (static-networking (interface interface) (ip ip)
(netmask netmask) (gateway gateway)
(provision provision)
(requirement requirement)
(name-servers name-servers)))))
(define %base-services
;; Convenience variable holding the basic services.

277
gnu/services/networking.scm
View file

@ -24,12 +24,14 @@
(define-module (gnu services networking)
#:use-module (gnu services)
#:use-module (gnu services base)
#:use-module (gnu services shepherd)
#:use-module (gnu services dbus)
#:use-module (gnu system shadow)
#:use-module (gnu system pam)
#:use-module (gnu packages admin)
#:use-module (gnu packages connman)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages linux)
#:use-module (gnu packages tor)
#:use-module (gnu packages messaging)
@ -45,18 +47,19 @@ (define-module (gnu services networking)
#:use-module (srfi srfi-26)
#:use-module (ice-9 match)
#:export (%facebook-host-aliases
static-networking
static-networking?
static-networking-interface
static-networking-ip
static-networking-netmask
static-networking-gateway
static-networking-requirement
static-networking-service
static-networking-service-type
dhcp-client-service
dhcpd-service-type
dhcpd-configuration
dhcpd-configuration?
dhcpd-configuration-package
dhcpd-configuration-config-file
dhcpd-configuration-version
dhcpd-configuration-run-directory
dhcpd-configuration-lease-file
dhcpd-configuration-pid-file
dhcpd-configuration-interfaces
%ntp-servers
ntp-configuration
@ -90,6 +93,9 @@ (define-module (gnu services networking)
connman-configuration?
connman-service-type
modem-manager-configuration
modem-manager-configuration?
modem-manager-service-type
wpa-supplicant-service-type
openvswitch-service-type
@ -134,154 +140,6 @@ (define %facebook-host-aliases
fe80::1%lo0 www.connect.facebook.net
fe80::1%lo0 apps.facebook.com\n")
(define-record-type* <static-networking>
static-networking make-static-networking
static-networking?
(interface static-networking-interface)
(ip static-networking-ip)
(netmask static-networking-netmask
(default #f))
(gateway static-networking-gateway ;FIXME: doesn't belong here
(default #f))
(provision static-networking-provision
(default #f))
(requirement static-networking-requirement
(default '()))
(name-servers static-networking-name-servers ;FIXME: doesn't belong here
(default '())))
(define static-networking-shepherd-service
(match-lambda
(($ <static-networking> interface ip netmask gateway provision
requirement name-servers)
(let ((loopback? (and provision (memq 'loopback provision))))
(shepherd-service
(documentation
"Bring up the networking interface using a static IP address.")
(requirement requirement)
(provision (or provision
(list (symbol-append 'networking-
(string->symbol interface)))))
(start #~(lambda _
;; Return #t if successfully started.
(let* ((addr (inet-pton AF_INET #$ip))
(sockaddr (make-socket-address AF_INET addr 0))
(mask (and #$netmask
(inet-pton AF_INET #$netmask)))
(maskaddr (and mask
(make-socket-address AF_INET
mask 0)))
(gateway (and #$gateway
(inet-pton AF_INET #$gateway)))
(gatewayaddr (and gateway
(make-socket-address AF_INET
gateway 0))))
(configure-network-interface #$interface sockaddr
(logior IFF_UP
#$(if loopback?
#~IFF_LOOPBACK
0))
#:netmask maskaddr)
(when gateway
(let ((sock (socket AF_INET SOCK_DGRAM 0)))
(add-network-route/gateway sock gatewayaddr)
(close-port sock))))))
(stop #~(lambda _
;; Return #f is successfully stopped.
(let ((sock (socket AF_INET SOCK_STREAM 0)))
(when #$gateway
(delete-network-route sock
(make-socket-address
AF_INET INADDR_ANY 0)))
(set-network-interface-flags sock #$interface 0)
(close-port sock)
#f)))
(respawn? #f))))))
(define (static-networking-etc-files interfaces)
"Return a /etc/resolv.conf entry for INTERFACES or the empty list."
(match (delete-duplicates
(append-map static-networking-name-servers
interfaces))
(()
'())
((name-servers ...)
(let ((content (string-join
(map (cut string-append "nameserver " <>)
name-servers)
"\n" 'suffix)))
`(("resolv.conf"
,(plain-file "resolv.conf"
(string-append "\
# Generated by 'static-networking-service'.\n"
content))))))))
(define (static-networking-shepherd-services interfaces)
"Return the list of Shepherd services to bring up INTERFACES, a list of
<static-networking> objects."
(define (loopback? service)
(memq 'loopback (shepherd-service-provision service)))
(let ((services (map static-networking-shepherd-service interfaces)))
(match (remove loopback? services)
(()
;; There's no interface other than 'loopback', so we assume that the
;; 'networking' service will be provided by dhclient or similar.
services)
((non-loopback ...)
;; Assume we're providing all the interfaces, and thus, provide a
;; 'networking' service.
(cons (shepherd-service
(provision '(networking))
(requirement (append-map shepherd-service-provision
services))
(start #~(const #t))
(stop #~(const #f))
(documentation "Bring up all the networking interfaces."))
services)))))
(define static-networking-service-type
;; The service type for statically-defined network interfaces.
(service-type (name 'static-networking)
(extensions
(list
(service-extension shepherd-root-service-type
static-networking-shepherd-services)
(service-extension etc-service-type
static-networking-etc-files)))
(compose concatenate)
(extend append)
(description
"Turn up the specified network interfaces upon startup,
with the given IP address, gateway, netmask, and so on. The value for
services of this type is a list of @code{static-networking} objects, one per
network interface.")))
(define* (static-networking-service interface ip
#:key
netmask gateway provision
;; Most interfaces require udev to be usable.
(requirement '(udev))
(name-servers '()))
"Return a service that starts @var{interface} with address @var{ip}. If
@var{netmask} is true, use it as the network mask. If @var{gateway} is true,
it must be a string specifying the default network gateway.
This procedure can be called several times, one for each network
interface of interest. Behind the scenes what it does is extend
@code{static-networking-service-type} with additional network interfaces
to handle."
(simple-service 'static-network-interface
static-networking-service-type
(list (static-networking (interface interface) (ip ip)
(netmask netmask) (gateway gateway)
(provision provision)
(requirement requirement)
(name-servers name-servers)))))
(define dhcp-client-service-type
(shepherd-service-type
'dhcp-client
@ -341,6 +199,72 @@ (define* (dhcp-client-service #:key (dhcp isc-dhcp))
Protocol (DHCP) client, on all the non-loopback network interfaces."
(service dhcp-client-service-type dhcp))
(define-record-type* <dhcpd-configuration>
dhcpd-configuration make-dhcpd-configuration
dhcpd-configuration?
(package dhcpd-configuration-package ;<package>
(default isc-dhcp))
(config-file dhcpd-configuration-config-file ;file-like
(default #f))
(version dhcpd-configuration-version ;"4", "6", or "4o6"
(default "4"))
(run-directory dhcpd-configuration-run-directory
(default "/run/dhcpd"))
(lease-file dhcpd-configuration-lease-file
(default "/var/db/dhcpd.leases"))
(pid-file dhcpd-configuration-pid-file
(default "/run/dhcpd/dhcpd.pid"))
;; list of strings, e.g. (list "enp0s25")
(interfaces dhcpd-configuration-interfaces
(default '())))
(define dhcpd-shepherd-service
(match-lambda
(($ <dhcpd-configuration> package config-file version run-directory
lease-file pid-file interfaces)
(unless config-file
(error "Must supply a config-file"))
(list (shepherd-service
;; Allow users to easily run multiple versions simultaneously.
(provision (list (string->symbol
(string-append "dhcpv" version "-daemon"))))
(documentation (string-append "Run the DHCPv" version " daemon"))
(requirement '(networking))
(start #~(make-forkexec-constructor
'(#$(file-append package "/sbin/dhcpd")
#$(string-append "-" version)
"-lf" #$lease-file
"-pf" #$pid-file
"-cf" #$config-file
#$@interfaces)
#:pid-file #$pid-file))
(stop #~(make-kill-destructor)))))))
(define dhcpd-activation
(match-lambda
(($ <dhcpd-configuration> package config-file version run-directory
lease-file pid-file interfaces)
(with-imported-modules '((guix build utils))
#~(begin
(unless (file-exists? #$run-directory)
(mkdir #$run-directory))
;; According to the DHCP manual (man dhcpd.leases), the lease
;; database must be present for dhcpd to start successfully.
(unless (file-exists? #$lease-file)
(with-output-to-file #$lease-file
(lambda _ (display ""))))
;; Validate the config.
(invoke
#$(file-append package "/sbin/dhcpd") "-t" "-cf"
#$config-file))))))
(define dhcpd-service-type
(service-type
(name 'dhcpd)
(extensions
(list (service-extension shepherd-root-service-type dhcpd-shepherd-service)
(service-extension activation-service-type dhcpd-activation)))))
(define %ntp-servers
;; Default set of NTP servers. These URLs are managed by the NTP Pool project.
;; Within Guix, Leo Famulari <leo@famulari.name> is the administrative contact
@ -889,6 +813,17 @@ (define* (wicd-service #:key (wicd wicd))
and @command{wicd-curses} user interfaces."
(service wicd-service-type wicd))
;;;
;;; ModemManager
;;;
(define-record-type* <modem-manager-configuration>
modem-manager-configuration make-modem-manager-configuration
modem-manager-configuration?
(modem-manager modem-manager-configuration-modem-manager
(default modem-manager)))
;;;
;;; NetworkManager
@ -1026,6 +961,30 @@ (define connman-service-type
"Run @url{https://01.org/connman,Connman},
a network connection manager."))))
;;;
;;; Modem manager
;;;
(define modem-manager-service-type
(let ((config->package
(match-lambda
(($ <modem-manager-configuration> modem-manager)
(list modem-manager)))))
(service-type (name 'modem-manager)
(extensions
(list (service-extension dbus-root-service-type
config->package)
(service-extension udev-service-type
config->package)
(service-extension polkit-service-type
config->package)))
(default-value (modem-manager-configuration))
(description
"Run @uref{https://wiki.gnome.org/Projects/ModemManager,
ModemManager}, a modem management daemon that aims to simplify dialup
networking."))))
;;;
;;; WPA supplicant

9
gnu/system/file-systems.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -47,6 +47,7 @@ (define-module (gnu system file-systems)
spec->file-system
specification->file-system-mapping
%pseudo-file-system-types
%fuse-control-file-system
%binary-format-file-system
%shared-memory-file-system
@ -203,6 +204,12 @@ (define (specification->file-system-mapping spec writable?)
;;; Common file systems.
;;;
(define %pseudo-file-system-types
;; List of know pseudo file system types. This is used when validating file
;; system definitions.
'("binfmt_misc" "cgroup" "debugfs" "devpts" "devtmpfs" "efivarfs" "fusectl"
"hugetlbfs" "overlay" "proc" "securityfs" "sysfs" "tmpfs"))
(define %fuse-control-file-system
;; Control file system for Linux' file systems in user-space (FUSE).
(file-system

98
gnu/tests/networking.scm
View file

@ -22,6 +22,7 @@ (define-module (gnu tests networking)
#:use-module (gnu system)
#:use-module (gnu system vm)
#:use-module (gnu services)
#:use-module (gnu services base)
#:use-module (gnu services networking)
#:use-module (guix gexp)
#:use-module (guix store)
@ -29,7 +30,7 @@ (define-module (gnu tests networking)
#:use-module (gnu packages bash)
#:use-module (gnu packages networking)
#:use-module (gnu services shepherd)
#:export (%test-inetd %test-openvswitch))
#:export (%test-inetd %test-openvswitch %test-dhcpd))
(define %inetd-os
;; Operating system with 2 inetd services.
@ -243,3 +244,98 @@ (define %test-openvswitch
(name "openvswitch")
(description "Test a running OpenvSwitch configuration.")
(value (run-openvswitch-test))))
;;;
;;; DHCP Daemon
;;;
(define minimal-dhcpd-v4-config-file
(plain-file "dhcpd.conf"
"\
default-lease-time 600;
max-lease-time 7200;
subnet 192.168.1.0 netmask 255.255.255.0 {
range 192.168.1.100 192.168.1.200;
option routers 192.168.1.1;
option domain-name-servers 192.168.1.2, 192.168.1.3;
option domain-name \"dummy.domain.name.abc123xyz\";
}
"))
(define dhcpd-v4-configuration
(dhcpd-configuration
(config-file minimal-dhcpd-v4-config-file)
(version "4")
(interfaces '("eth0"))))
(define %dhcpd-os
(simple-operating-system
(static-networking-service "eth0" "192.168.1.4"
#:netmask "255.255.255.0"
#:gateway "192.168.1.1"
#:name-servers '("192.168.1.2" "192.168.1.3"))
(service dhcpd-service-type dhcpd-v4-configuration)))
(define (run-dhcpd-test)
(define os
(marionette-operating-system %dhcpd-os
#:imported-modules '((gnu services herd))))
(define test
(with-imported-modules '((gnu build marionette))
#~(begin
(use-modules (gnu build marionette)
(ice-9 popen)
(ice-9 rdelim)
(srfi srfi-64))
(define marionette
(make-marionette (list #$(virtual-machine os))))
(mkdir #$output)
(chdir #$output)
(test-begin "dhcpd")
(test-assert "pid file exists"
(marionette-eval
'(file-exists?
#$(dhcpd-configuration-pid-file dhcpd-v4-configuration))
marionette))
(test-assert "lease file exists"
(marionette-eval
'(file-exists?
#$(dhcpd-configuration-lease-file dhcpd-v4-configuration))
marionette))
(test-assert "run directory exists"
(marionette-eval
'(file-exists?
#$(dhcpd-configuration-run-directory dhcpd-v4-configuration))
marionette))
(test-assert "dhcpd is alive"
(marionette-eval
'(begin
(use-modules (gnu services herd)
(srfi srfi-1))
(live-service-running
(find (lambda (live)
(memq 'dhcpv4-daemon
(live-service-provision live)))
(current-services))))
marionette))
(test-end)
(exit (= (test-runner-fail-count (test-runner-current)) 0)))))
(gexp->derivation "dhcpd-test" test))
(define %test-dhcpd
(system-test
(name "dhcpd")
(description "Test a running DHCP daemon configuration.")
(value (run-dhcpd-test))))

8
guix/download.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
@ -509,6 +509,8 @@ (define tar
#:system system
#:guile guile)))
;; Take the tar bomb, and simply unpack it as a directory.
;; Use ungrafted tar/gzip so that the resulting tarball doesn't depend on
;; whether grafts are enabled.
(gexp->derivation (or name file-name)
(with-imported-modules '((guix build utils))
#~(begin
@ -518,6 +520,7 @@ (define tar
(chdir #$output)
(invoke (string-append #$tar "/bin/tar")
"xf" #$drv)))
#:graft? #f
#:local-build? #t)))
(define* (url-fetch/zipbomb url hash-algo hash
@ -541,6 +544,8 @@ (define unzip
#:system system
#:guile guile)))
;; Take the zip bomb, and simply unpack it as a directory.
;; Use ungrafted unzip so that the resulting tarball doesn't depend on
;; whether grafts are enabled.
(gexp->derivation (or name file-name)
(with-imported-modules '((guix build utils))
#~(begin
@ -549,6 +554,7 @@ (define unzip
(chdir #$output)
(invoke (string-append #$unzip "/bin/unzip")
#$drv)))
#:graft? #f
#:local-build? #t)))
(define* (download-to-store store url #:optional (name (basename url))

24
guix/scripts/system.scm
View file

@ -583,7 +583,8 @@ (define (check-file-system-availability file-systems)
(define relevant
(filter (lambda (fs)
(and (file-system-mount? fs)
(not (string=? "tmpfs" (file-system-type fs)))
(not (member (file-system-type fs)
%pseudo-file-system-types))
(not (memq 'bind-mount (file-system-flags fs)))))
file-systems))
@ -592,6 +593,11 @@ (define labeled
(eq? (file-system-title fs) 'label))
relevant))
(define literal
(filter (lambda (fs)
(eq? (file-system-title fs) 'device))
relevant))
(define uuid
(filter (lambda (fs)
(eq? (file-system-title fs) 'uuid))
@ -610,6 +616,22 @@ (define (file-system-location* fs)
(set! fail? #t)
(format (current-error-port)
args ...))))))
(for-each (lambda (fs)
(catch 'system-error
(lambda ()
(stat (file-system-device fs)))
(lambda args
(let ((errno (system-error-errno args))
(device (file-system-device fs)))
(error (G_ "~a: error: device '~a' not found: ~a~%")
(file-system-location* fs) device
(strerror errno))
(unless (string-prefix? "/" device)
(display-hint (format #f (G_ "If '~a' is a file system
label, you need to add @code{(title 'label)} to your @code{file-system}
definition.")
device)))))))
literal)
(for-each (lambda (fs)
(unless (find-partition-by-label (file-system-device fs))
(error (G_ "~a: error: file system with label '~a' not found~%")

1
guix/ui.scm
View file

@ -66,6 +66,7 @@ (define-module (guix ui)
#:use-module (texinfo string-utils)
#:re-export (G_ N_ P_) ;backward compatibility
#:export (report-error
display-hint
leave
make-user-module
load*

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