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authorMark H Weaver <mhw@netris.org>2018-04-30 04:03:54 -0400
committerMark H Weaver <mhw@netris.org>2018-04-30 04:03:54 -0400
commit3d5ad159b336a9903b31d0be7ae052dbc8d5bfcc (patch)
treeee7dce4e436490a1db5f18e4bfad55511d2fff32 /gnu
parentc77835db04ee20c0afe20600dc8f91a67bc2421e (diff)
parent8c21c64e59d3f4d223d8aeef91f06fdde7de1ab7 (diff)
downloadpatches-3d5ad159b336a9903b31d0be7ae052dbc8d5bfcc.tar
patches-3d5ad159b336a9903b31d0be7ae052dbc8d5bfcc.tar.gz
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu')
-rw-r--r--gnu/local.mk15
-rw-r--r--gnu/packages/admin.scm81
-rw-r--r--gnu/packages/android.scm4
-rw-r--r--gnu/packages/audio.scm15
-rw-r--r--gnu/packages/benchmark.scm9
-rw-r--r--gnu/packages/bioconductor.scm259
-rw-r--r--gnu/packages/bioinformatics.scm102
-rw-r--r--gnu/packages/bittorrent.scm2
-rw-r--r--gnu/packages/bootloaders.scm25
-rw-r--r--gnu/packages/cdrom.scm2
-rw-r--r--gnu/packages/commencement.scm8
-rw-r--r--gnu/packages/cran.scm353
-rw-r--r--gnu/packages/cups.scm10
-rw-r--r--gnu/packages/databases.scm4
-rw-r--r--gnu/packages/debug.scm3
-rw-r--r--gnu/packages/dictionaries.scm17
-rw-r--r--gnu/packages/disk.scm28
-rw-r--r--gnu/packages/education.scm43
-rw-r--r--gnu/packages/emacs.scm115
-rw-r--r--gnu/packages/emulators.scm6
-rw-r--r--gnu/packages/engineering.scm6
-rw-r--r--gnu/packages/enlightenment.scm24
-rw-r--r--gnu/packages/freedesktop.scm4
-rw-r--r--gnu/packages/game-development.scm27
-rw-r--r--gnu/packages/games.scm3
-rw-r--r--gnu/packages/geo.scm8
-rw-r--r--gnu/packages/gnome.scm48
-rw-r--r--gnu/packages/gnunet.scm2
-rw-r--r--gnu/packages/gnupg.scm4
-rw-r--r--gnu/packages/golang.scm12
-rw-r--r--gnu/packages/graph.scm11
-rw-r--r--gnu/packages/gstreamer.scm2
-rw-r--r--gnu/packages/guile.scm2
-rw-r--r--gnu/packages/image-viewers.scm4
-rw-r--r--gnu/packages/image.scm32
-rw-r--r--gnu/packages/irc.scm9
-rw-r--r--gnu/packages/java.scm303
-rw-r--r--gnu/packages/julia.scm2
-rw-r--r--gnu/packages/libreoffice.scm8
-rw-r--r--gnu/packages/linux.scm127
-rw-r--r--gnu/packages/lxde.scm13
-rw-r--r--gnu/packages/machine-learning.scm44
-rw-r--r--gnu/packages/mail.scm4
-rw-r--r--gnu/packages/maths.scm16
-rw-r--r--gnu/packages/mes.scm9
-rw-r--r--gnu/packages/messaging.scm36
-rw-r--r--gnu/packages/mpd.scm4
-rw-r--r--gnu/packages/music.scm35
-rw-r--r--gnu/packages/node.scm4
-rw-r--r--gnu/packages/package-management.scm11
-rw-r--r--gnu/packages/parallel.scm6
-rw-r--r--gnu/packages/patches/bcftools-regidx-unsigned-char.patch16
-rw-r--r--gnu/packages/patches/ceph-skip-collect-sys-info-test.patch11
-rw-r--r--gnu/packages/patches/freeimage-unbundle.patch18
-rw-r--r--gnu/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch81
-rw-r--r--gnu/packages/patches/pcmanfm-CVE-2017-8934.patch56
-rw-r--r--gnu/packages/patches/pt-scotch-build-parallelism.patch13
-rw-r--r--gnu/packages/patches/qemu-CVE-2018-7550.patch66
-rw-r--r--gnu/packages/patches/quassel-fix-tls-check.patch25
-rw-r--r--gnu/packages/patches/scotch-build-parallelism.patch39
-rw-r--r--gnu/packages/patches/scotch-graph-diam-64.patch27
-rw-r--r--gnu/packages/patches/scotch-graph-induce-type-64.patch19
-rw-r--r--gnu/packages/patches/zsh-CVE-2018-7548.patch48
-rw-r--r--gnu/packages/patches/zsh-CVE-2018-7549.patch56
-rw-r--r--gnu/packages/perl-check.scm24
-rw-r--r--gnu/packages/perl.scm84
-rw-r--r--gnu/packages/photo.scm8
-rw-r--r--gnu/packages/python-crypto.scm13
-rw-r--r--gnu/packages/python-web.scm13
-rw-r--r--gnu/packages/python.scm62
-rw-r--r--gnu/packages/ruby.scm8
-rw-r--r--gnu/packages/scheme.scm4
-rw-r--r--gnu/packages/sdl.scm2
-rw-r--r--gnu/packages/shells.scm10
-rw-r--r--gnu/packages/spice.scm4
-rw-r--r--gnu/packages/ssh.scm16
-rw-r--r--gnu/packages/statistics.scm105
-rw-r--r--gnu/packages/storage.scm4
-rw-r--r--gnu/packages/syncthing.scm2
-rw-r--r--gnu/packages/text-editors.scm19
-rw-r--r--gnu/packages/textutils.scm8
-rw-r--r--gnu/packages/version-control.scm50
-rw-r--r--gnu/packages/video.scm91
-rw-r--r--gnu/packages/virtualization.scm111
-rw-r--r--gnu/packages/vpn.scm40
-rw-r--r--gnu/packages/vulkan.scm5
-rw-r--r--gnu/packages/web.scm16
-rw-r--r--gnu/packages/xdisorg.scm8
-rw-r--r--gnu/services/base.scm160
-rw-r--r--gnu/services/networking.scm275
-rw-r--r--gnu/system/file-systems.scm9
-rw-r--r--gnu/tests/networking.scm98
92 files changed, 2529 insertions, 1116 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index 114dfcad8b..e2dc64b7e9 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -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
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index d1af6d9474..a6abe86403 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -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 @@
#: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 @@
#: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 @@ services.")
(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 @@ This package provides the 'wpa_supplicant' daemon and the 'wpa_cli' command.")
(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 @@ of supported upstream metrics systems simultaneously.")
(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 @@ throughput (in the same interval).")
(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 @@ throughput (in the same interval).")
(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 @@ throughput (in the same interval).")
(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 @@ Intel DRM Driver.")
(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 @@ you are running, what theme or icon set you are using, etc.")
(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 @@ you are running, what theme or icon set you are using, etc.")
(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 @@ launch daemons into the relevant nodes.")
"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)))
diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index 96fc34eb6e..105e3d1775 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -341,7 +341,7 @@ Images.")
(define-public android-udev-rules
(package
(name "android-udev-rules")
- (version "20171113")
+ (version "20180112")
(source
(origin
(method git-fetch)
@@ -350,7 +350,7 @@ Images.")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
- (base32 "11gcnk6wjc2sw05hwi4xphvx9ksmkpvsdziaczymqxkaads3f1dy"))))
+ (base32 "13gj79nnd04szqlrrzzkdr6wi1fky08pi7x8xfbg0jj3d3v0giah"))))
(build-system trivial-build-system)
(native-inputs `(("source" ,source)))
(arguments
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index df1202087c..83fde34325 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -285,14 +285,15 @@ engineers, musicians, soundtrack editors and composers.")
(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 @@ based on human speech recordings.")
(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 @@ based on human speech recordings.")
(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 @@ based on human speech recordings.")
"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 @@ based on human speech recordings.")
("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
diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index 77dcd78331..ebc8bdb5f2 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -34,7 +34,7 @@
(define-public fio
(package
(name "fio")
- (version "3.5")
+ (version "3.6")
(source (origin
(method url-fetch)
(uri (string-append
@@ -42,7 +42,7 @@
"fio-" version ".tar.bz2"))
(sha256
(base32
- "1rrzcrn07db4pffvi2q0d0k884bwcapx6r1rfv4yx9066snvx240"))))
+ "1d2jibp1b2dq97f22wj6pcjl7gbd2kmhfggj2c7q3j8v9axjqsh2"))))
(build-system gnu-build-system)
(arguments
'(#:test-target "test"
@@ -67,8 +67,9 @@
;; 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.
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 09581d9fde..76ff773ef1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -23,6 +23,8 @@
#: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 @@ the Human Protein Atlas project.")
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+)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5af4947b68..61e5d8bc34 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -252,7 +252,7 @@ instance, it implements several methods to assess contig-wise read coverage.")
(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 @@ instance, it implements several methods to assess contig-wise read coverage.")
(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 @@ BAM files.")
(define-public bcftools
(package
(name "bcftools")
- (version "1.5")
+ (version "1.8")
(source (origin
(method url-fetch)
(uri (string-append
@@ -293,12 +293,11 @@ BAM files.")
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 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
(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 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
+ "0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
@@ -2089,7 +2088,7 @@ accurately delineate genomic rearrangements throughout the genome.")
(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 @@ accurately delineate genomic rearrangements throughout the genome.")
(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 @@ dynamic programming or a variety of heuristics.")
(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 @@ The main functions of FastQC are:
(define-public htslib
(package
(name "htslib")
- (version "1.7")
+ (version "1.8")
(source (origin
(method url-fetch)
(uri (string-append
@@ -3470,7 +3470,7 @@ The main functions of FastQC are:
version "/htslib-" version ".tar.bz2"))
(sha256
(base32
- "1il6i2p84b0y9c93dhvzzki1ifw9bvapm2mvpr0xvb2nq8jlwgdy"))))
+ "18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0"))))
(build-system gnu-build-system)
(inputs
`(("openssl" ,openssl)
@@ -4587,7 +4587,7 @@ partial genes, and identifies translation initiation sites.")
(define-public roary
(package
(name "roary")
- (version "3.11.0")
+ (version "3.12.0")
(source
(origin
(method url-fetch)
@@ -4596,7 +4596,7 @@ partial genes, and identifies translation initiation sites.")
version ".tar.gz"))
(sha256
(base32
- "10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i"))))
+ "0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff"))))
(build-system perl-build-system)
(arguments
`(#:phases
@@ -4934,7 +4934,7 @@ to the user's query of interest.")
(define-public samtools
(package
(name "samtools")
- (version "1.7")
+ (version "1.8")
(source
(origin
(method url-fetch)
@@ -4943,7 +4943,7 @@ to the user's query of interest.")
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
- "18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77"))))
+ "05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((ice-9 ftw)
@@ -5784,7 +5784,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
(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 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a"))
+ "0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -5979,13 +5979,13 @@ Cuffdiff or Ballgown programs.")
(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 @@ information as possible.")
(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 @@ distribution.")
(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 @@ SELECT or UPDATE queries to an end-point.")
(define-public vsearch
(package
(name "vsearch")
- (version "2.7.1")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
@@ -6629,7 +6630,7 @@ SELECT or UPDATE queries to an end-point.")
(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 @@ samples.")
(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 @@ replacement for strverscmp.")
(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 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(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 @@ Main-Class: ModularityOptimizer\n")))
(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 @@ Main-Class: ModularityOptimizer\n")))
("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 @@ effort and encourages consistency.")
(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 @@ interval to data view, mismatch pileup, and several splicing summaries.")
(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 @@ several related annotation packages.")
(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 @@ by Ernst and Kellis.")
(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 @@ assays such as Hi-C.")
(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 @@ quality control.")
(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 @@ expression report comparing samples in an easily configurable manner.")
(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 @@ expression report comparing samples in an easily configurable manner.")
"/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
diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm
index ae9b3bc62d..9df4f097ac 100644
--- a/gnu/packages/bittorrent.scm
+++ b/gnu/packages/bittorrent.scm
@@ -315,8 +315,6 @@ Aria2 can be manipulated via built-in JSON-RPC and XML-RPC interfaces.")
(base32
"0919cf7lfk1djdl003cahqjvafdliv7v2l8r5wg95n4isqggdk75"))))
(build-system gnu-build-system)
- (native-inputs
- `(("intltool" ,intltool)))
(inputs
`(("curl" ,curl)
("gtk+" ,gtk+)
diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 5be77e550b..0db6ad3f6a 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -72,23 +72,6 @@
(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 @@ also initializes the boards (RAM etc).")
(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 @@ also initializes the boards (RAM etc).")
(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")
diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm
index e26a1bbf63..5d45d07288 100644
--- a/gnu/packages/cdrom.scm
+++ b/gnu/packages/cdrom.scm
@@ -394,7 +394,7 @@ capacity is user-selectable.")
("fontconfig" ,fontconfig)
("libexif" ,libexif)
("libjpeg" ,libjpeg)
- ("ffmpeg" ,ffmpeg)))
+ ("ffmpeg" ,ffmpeg-3.4)))
(native-inputs
`(("pkg-config" ,pkg-config)
("flex" ,flex)
diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index 057ee169dd..9f85781db2 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -1024,6 +1024,9 @@ COREUTILS-FINAL vs. COREUTILS, etc."
(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 @@ COREUTILS-FINAL vs. COREUTILS, etc."
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 @@ and binaries, plus debugging symbols in the 'debug' output), and Binutils.")
("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))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0ac35a909b..bc95fd2aa4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -35,6 +35,7 @@
#: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 @@ scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
(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 @@ that.")
(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 @@ initiative to bring PASSTEC 2000 functionalities to R.")
(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 @@ error stream.")
(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 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
(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 @@ where the bound function accepts additional arguments.")
(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 @@ ellipses, circles, cylinders, arrows, ...")
(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 @@ matrices.")
(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 @@ available in a vignette.")
(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 @@ regression using Kernel Ridge Regression.")
(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 @@ Engineering and Computational Finance\" and for managing chronological and
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 @@ color labels, layout, etc.")
(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 @@ training models for classification or ranking.")
(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 @@ plotting. a three dimensional point cloud.")
(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 @@ display.")
(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 @@ terminals.")
(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 @@ automatically.")
(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 @@ Cambridge University Press, 1993.")
(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 @@ It also includes interpolation functions.")
(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 @@ serve as a useful front end for structural equation modeling.")
(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 @@ selection, and goodness-of-fit. Cross-validation tools are also available for
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+))))
diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index d3246ab36f..a9cc3acba0 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -616,7 +616,7 @@ HP@tie{}LaserJet, and possibly other printers. See @file{README} for details.")
(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 @@ HP@tie{}LaserJet, and possibly other printers. See @file{README} for details.")
(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
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 01b897da22..441a6977f6 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -846,7 +846,7 @@ types are supported, as is encryption.")
(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 @@ types are supported, as is encryption.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0hp7jxr99vyc57n708hiqk4lks9a9zmjgfjc21mx6v1rmabj2944"))
+ "1jcwgsjhk4hdfr2wf549blkgb89vwcdb5i2ahhqs6zf3mm20i3bf"))
(modules '((guix build utils)))
(snippet
'(begin
diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index 1f238637a4..2ff26aebae 100644
--- a/gnu/packages/debug.scm
+++ b/gnu/packages/debug.scm
@@ -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 @@ tools that process C/C++ code.")
(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)
diff --git a/gnu/packages/dictionaries.scm b/gnu/packages/dictionaries.scm
index d09280a3d4..ec85831d64 100644
--- a/gnu/packages/dictionaries.scm
+++ b/gnu/packages/dictionaries.scm
@@ -211,7 +211,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
(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 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
"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
diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index 595000bf88..d7bf726830 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -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 @@
#: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 @@ your data as it changes, without having to re-checksum unchanged data.
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)))
diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm
index e8fb1e64d6..58f06c3106 100644
--- a/gnu/packages/education.scm
+++ b/gnu/packages/education.scm
@@ -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 @@ of categories with some of the activities available in that category.
(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
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index bc98284686..3bd15989ad 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -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 @@ editor (without an X toolkit)" )
(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 @@ configuration files, such as .gitattributes, .gitignore, and .git/config.")
(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 @@ configuration files, such as .gitattributes, .gitignore, and .git/config.")
(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 @@ support for Git-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 @@ support for Git-SVN.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1dnk611f7lww6rb03hk8ijg2jwxx9f26pjfff4bwjmnjz7hnd6vz"))))
+ "1kz6vj67awkwf9y2wj6m3l2him3znm08z6bkdvnmfr6rwd96dr39"))))
(build-system emacs-build-system)
(arguments
`(#:phases
@@ -4536,6 +4536,31 @@ main features of Vim, and provides facilities for writing custom
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 @@ passive voice.")
(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 @@ reproducible research.")
(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 @@ To make YASnippet aware of these snippets, add the above directory to
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 @@ well as Github-style emojis like @code{:smile:}. It provides a minor mode
(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 @@ want to use it.")
(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 @@ want to use it.")
(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 @@ name and password. To skip it press a @key{Return} key.
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+)))
diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index a502af9c09..7943d51cf4 100644
--- a/gnu/packages/emulators.scm
+++ b/gnu/packages/emulators.scm
@@ -186,7 +186,7 @@
("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 @@ emulation community. It provides highly accurate emulation.")
(define-public retroarch
(package
(name "retroarch")
- (version "1.7.1")
+ (version "1.7.2")
(source
(origin
(method url-fetch)
@@ -1054,7 +1054,7 @@ emulation community. It provides highly accurate emulation.")
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
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index e6a29554f1..ed0239a613 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -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 @@ as well as pick-place files.")
(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"
diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index ae5deeccb5..ef2be9ad41 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -49,6 +49,7 @@
#: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 @@ removable devices or support for multimedia.")
(define-public terminology
(package
(name "terminology")
- (version "1.1.1")
+ (version "1.2.0")
(source (origin
(method url-fetch)
(uri
@@ -184,25 +185,17 @@ removable devices or support for multimedia.")
"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 @@ removable devices or support for multimedia.")
(lambda _ (setenv "HOME" "/tmp") #t)))))
(native-inputs
`(("gettext" ,gettext-minimal)
+ ("perl" ,perl)
("pkg-config" ,pkg-config)))
(inputs
`(("efl" ,efl)))
@@ -257,7 +251,7 @@ Libraries with some extra bells and whistles.")
(define-public enlightenment
(package
(name "enlightenment")
- (version "0.22.2")
+ (version "0.22.3")
(source (origin
(method url-fetch)
(uri
@@ -265,7 +259,7 @@ Libraries with some extra bells and whistles.")
name "/" name "-" version ".tar.xz"))
(sha256
(base32
- "0b33w75s4w7xmz9cv8dyp8vy2gcffnrvjys20fhcpw26abw1wn2d"))))
+ "16zydv7z94aw3rywmb9gr8ya85k7b75h22wng95lfx1x0y1yb0ad"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("--enable-mount-eeze")
diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index 2dad010587..49e391f9db 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -348,7 +348,7 @@ of a the system to know what users are logged in, and where.")
(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 @@ of a the system to know what users are logged in, and where.")
"PackageKit-" version ".tar.xz"))
(sha256
(base32
- "035pqxgkyki813hyw2frrbpfllq113zfk5qcp9wvsq5lsp74ix2h"))))
+ "1msfmb22cm4s3l6vsbr86b8s0v897sy6gcga3qg87z7640a0di2b"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f
diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 3b7db9caef..3ff27b4a1b 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -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 @@ games.")
(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 @@ games.")
"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 @@ games.")
("glu" ,glu)
("libtheora" ,libtheora)
("libvorbis" ,libvorbis)
+ ("libvpx" ,libvpx)
("libwebp" ,libwebp)
("libx11" ,libx11)
("libxcursor" ,libxcursor)
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index f1f76258f9..b62d679a91 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -4913,7 +4913,8 @@ Strife, Chex Quest, and fan-created games like Harmony, Hacx and Freedoom.")
,(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/")
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 9f31d90619..75ed83f8a4 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -500,14 +500,14 @@ development.")
(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 @@ Projection code and larger maps are in separate packages ('mapproj' and
(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")
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 4c9cdef7cf..319c2e6fd0 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -533,7 +533,7 @@ and keep up to date translations of documentation.")
(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 @@ and keep up to date translations of documentation.")
name "-" version ".tar.xz"))
(sha256
(base32
- "1wjnw9hpjqyhrr116491rfzd0837g6jqvzq2z1ndx2sdqv19caxa"))))
+ "09dmknfas8iifv6k5jb4a9ag57s8awrn0f26fd1qlg0mbfjlnfd6"))))
(build-system meson-build-system)
(native-inputs
`(("glib:bin" ,glib "bin")
@@ -725,7 +725,7 @@ forgotten when the session ends.")
(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 @@ forgotten when the session ends.")
name "-" version ".tar.xz"))
(sha256
(base32
- "1a3kcls18dcz1lj8hrx8skcli9xxfyi71c17xjwayh71cm5jc8zs"))))
+ "1qbk1x2c7iacmmfwjzh136v2sdacrkqn9d6bnqid7xn9hlnx4m89"))))
(build-system glib-or-gtk-build-system)
(arguments
`(#:configure-flags '("--disable-nautilus")
@@ -2062,7 +2062,7 @@ libraries written in C.")
(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 @@ libraries written in C.")
name "-" version ".tar.xz"))
(sha256
(base32
- "1kq9bxf7waap190zx5k78d21y3l31npblrnhfkxz4j7zz9mk3pbr"))))
+ "1lva70inb5y8p42rg95fb88z2ybwcz0lybla3ixbgp2sj0s4rzdh"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
@@ -2730,7 +2730,7 @@ more fun.")
(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 @@ more fun.")
name "-" version ".tar.xz"))
(sha256
(base32
- "1c05f2lrlm8jfx2394k6nabg4ml07lqasxaja5v98mhlm0aa96rs"))))
+ "1hqwh12hiy73mazqgvyrq8jk4c669x2fb4nh8mwby3qbk8ca19pp"))))
(build-system glib-or-gtk-build-system)
(arguments
'(#:configure-flags
@@ -6302,7 +6302,7 @@ existing databases over the internet.")
(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 @@ existing databases over the internet.")
(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 @@ existing databases over the internet.")
#: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 @@ existing databases over the internet.")
(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
diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm
index 939bdf9148..c74ccc9229 100644
--- a/gnu/packages/gnunet.scm
+++ b/gnu/packages/gnunet.scm
@@ -88,7 +88,7 @@
`(("exiv2" ,exiv2)
("bzip2" ,bzip2)
("flac" ,flac)
- ("ffmpeg" ,ffmpeg)
+ ("ffmpeg" ,ffmpeg-3.4)
("file" ,file) ;libmagic, for the MIME plug-in
("glib" ,glib)
("gstreamer" ,gstreamer)
diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index 80bae77ca3..17207e2173 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -797,7 +797,7 @@ passphrase when @code{gpg} is run and needs it.")))
(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 @@ passphrase when @code{gpg} is run and needs it.")))
version ".tar.gz"))
(sha256
(base32
- "1yybj8bj68v4lxwpn596b6ismh2fyixw5vlqqg26byrn4d9dfmsv"))))
+ "1prd2jaf4zjad3xhv160hmi5n408ssljfg7iz90jxs9w111pjwy4"))))
(build-system gnu-build-system)
(arguments
`(#:phases
diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 485aa02c46..c6fc68468f 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -195,7 +195,7 @@
;; 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 @@ in the style of communicating sequential processes (@dfn{CSP}).")
(package
(inherit go-1.4)
(name "go")
- (version "1.9.4")
+ (version "1.9.5")
(source
(origin
(method url-fetch)
@@ -222,7 +222,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
name version ".src.tar.gz"))
(sha256
(base32
- "01nw8rfvf10naja0wq0kabsm012sbqq76hd4b8c7g28n6ggshwq5"))))
+ "1g4zqhbh1yw3gnb400szzwrdz0k5s3h0h5nc35xgmn5v69zvphpi"))))
(arguments
(substitute-keyword-arguments (package-arguments go-1.4)
((#:phases phases)
@@ -292,6 +292,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
("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 @@ in the style of communicating sequential processes (@dfn{CSP}).")
(package
(inherit go-1.9)
(name "go")
- (version "1.10")
+ (version "1.10.1")
(source
(origin
(method url-fetch)
@@ -390,7 +391,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
name version ".src.tar.gz"))
(sha256
(base32
- "093z1h0gmi458kv7smpx0ph6jm7ss9mzxa432kysbz85jhl4kppk"))))
+ "1p1xyyxicp752n9wj10sljjl6mjxpfsplkhx74fzzjrwdkzlk52q"))))
(arguments
(substitute-keyword-arguments (package-arguments go-1.9)
((#:phases phases)
@@ -460,6 +461,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
("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.+)")
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 74fbe9e84e..a9ee949855 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -98,23 +98,24 @@ more.")
(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")
diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm
index 58b0abcecf..cb72d25921 100644
--- a/gnu/packages/gstreamer.scm
+++ b/gnu/packages/gstreamer.scm
@@ -404,7 +404,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.")
("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/")
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index d9379b3bec..c9497225a9 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -1501,7 +1501,7 @@ users and in some situations.")
(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
diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm
index ae7ae0f519..1f0a9e46e1 100644
--- a/gnu/packages/image-viewers.scm
+++ b/gnu/packages/image-viewers.scm
@@ -59,7 +59,7 @@
(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 @@
name "-" version ".tar.bz2"))
(sha256
(base32
- "197sm78bm33dvahr5nxqkbmpmdn4b13ahc9mrgn1l7n104bg4phc"))))
+ "11kckzwk3b734l0n4j41k40liq1v2lbbj1gzir5qc386g7fvzmmi"))))
(build-system gnu-build-system)
(arguments
'(#:phases (modify-phases %standard-phases (delete 'configure))
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index d312fb79de..a6d8b320da 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -716,7 +716,8 @@ supplies a generic doubly-linked list and some string functions.")
(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 @@ supplies a generic doubly-linked list and some string functions.")
;; 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 @@ multi-dimensional image processing.")
(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 @@ multi-dimensional image processing.")
("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
diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm
index e1c49d1385..2b266748ae 100644
--- a/gnu/packages/irc.scm
+++ b/gnu/packages/irc.scm
@@ -65,18 +65,17 @@
(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 @@
("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
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 4f882c3e6f..7000e5a475 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -8150,70 +8150,50 @@ by technical operatives or consultants working with enterprise platforms.")
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)))))
+ (invoke "ant" "-f" "ant/jdk15+.xml" "test")))
+ (replace 'install
+ (install-jars "build/artifacts/jdk1.5/jars")))))
+ (inputs
+ `(("java-javax-mail" ,java-javax-mail)))
(native-inputs
`(("unzip" ,unzip)
- ("junit" ,java-junit)))
- (inputs
- `(("bcprov" ,java-bouncycastle-bcprov)))
+ ("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 @@ protocol-independent framework to build mail and messaging applications.")
("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 @@ Java method invocation.")
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)))
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index 7a44abdec2..6fb1eee6cc 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -384,7 +384,7 @@
;; 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
diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index 50f44b5d65..65119e85df 100644
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -359,14 +359,14 @@ CorelDRAW documents of all versions.")
(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 @@ spreadsheet documents.")
(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)
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index a3b3ab262e..b92b146f3b 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -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 @@ It has been modified to remove all non-free binary blobs.")
;; supports qemu "virt" machine and possibly a large number of ARM boards.
;; See : https://wiki.debian.org/DebianKernel/ARMMP.
-(define %linux-libre-version "4.16.3")
-(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 @@ It has been modified to remove all non-free binary blobs.")
%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 @@ It has been modified to remove all non-free binary blobs.")
#:configuration-file kernel-config))
(define-public linux-libre-4.9
- (make-linux-libre "4.9.95"
- "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 @@ arrays when needed.")
(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 @@ arrays when needed.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "02lk453wa2gfxkl8zmdws15nkcibln2yw76zm779pkngkhggl6w8"))
+ "0zkcayi3mmp43ji2zid1gprgsvqhjjapsw7jjd60sf75prf50h2r"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -3306,7 +3307,8 @@ disks and SD cards. This package provides the userland utilities.")
(("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 @@ available in the kernel Linux.")
(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 @@ the @code{coretemp} module and sets the fan speed using the @code{applesmc}
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)))
diff --git a/gnu/packages/lxde.scm b/gnu/packages/lxde.scm
index 8166fb8d71..af576c44f7 100644
--- a/gnu/packages/lxde.scm
+++ b/gnu/packages/lxde.scm
@@ -48,7 +48,7 @@
(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 @@
"%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 @@ speed up the access to freedesktop.org defined application menus.")
(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.")
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index d9b54d692f..fb511b4949 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -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 @@ mining and data analysis.")
(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))
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index fb13ec1fdb..8980b3df74 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -747,14 +747,14 @@ invoking @command{notifymuch} from the post-new hook.")
(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)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2f6c6d6277..a2bf14ea84 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1779,7 +1779,7 @@ arising after the discretization of partial differential equations.")
(define-public mumps
(package
(name "mumps")
- (version "5.0.2")
+ (version "5.1.2")
(source
(origin
(method url-fetch)
@@ -1787,7 +1787,7 @@ arising after the discretization of partial differential equations.")
version ".tar.gz"))
(sha256
(base32
- "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
+ "1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
(patches (search-patches "mumps-build-parallelism.patch"))))
(build-system gnu-build-system)
(inputs
@@ -2208,16 +2208,18 @@ implemented in ANSI C, and MPI for communications.")
(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 @@ analysed.")
(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)))
diff --git a/gnu/packages/mes.scm b/gnu/packages/mes.scm
index 5c832f9d13..d2ce394a03 100644
--- a/gnu/packages/mes.scm
+++ b/gnu/packages/mes.scm
@@ -60,16 +60,15 @@ extensive examples, including parsers for the Javascript and C99 languages.")
(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
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index b3205c7ae2..c31e3604c8 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -802,7 +802,7 @@ protocols.")
(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 @@ protocols.")
(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 @@ messenger protocol.")
(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 @@ instant messenger with audio and video chat capabilities.")
(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 @@ instant messenger with audio and video chat capabilities.")
,(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 @@ building the IRC clients and bots.")
(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
diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm
index 0e2acedf7f..a9d317eb7b 100644
--- a/gnu/packages/mpd.scm
+++ b/gnu/packages/mpd.scm
@@ -88,7 +88,7 @@ interfacing MPD in the C, C++ & Objective C languages.")
(define-public mpd
(package
(name "mpd")
- (version "0.20.18")
+ (version "0.20.19")
(source (origin
(method url-fetch)
(uri
@@ -97,7 +97,7 @@ interfacing MPD in the C, C++ & Objective C languages.")
"/mpd-" version ".tar.xz"))
(sha256
(base32
- "0d6lz8ykyvxkl0fwnd9c5vzbbhmjh1yzv7rzhprlzfchmv12sn3a"))))
+ "1hsng4mnaz1jr2s3fy3q78vf2f6102lwphjdls7qln0pj8dyzk81"))))
(build-system gnu-build-system)
(arguments
`(#:phases
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index c8f2fd84b4..6f17fa799e 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1601,7 +1601,7 @@ is subjective.")
(define-public tuxguitar
(package
(name "tuxguitar")
- (version "1.4")
+ (version "1.5")
(source (origin
(method url-fetch)
(uri (string-append
@@ -1609,7 +1609,7 @@ is subjective.")
version "/tuxguitar-" version "-src.tar.gz"))
(sha256
(base32
- "041275vwfr82kass7wiq9g2y82w9qrbzfinzcvfij2f2q45njwmc"))
+ "1yd5wv17sh6i8pkndxayfd6r2k1ccgnc4w3nda3lpniv8cpjzz3k"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -1691,7 +1691,7 @@ is subjective.")
#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 @@ browser.")
(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 @@ browser.")
(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 @@ computer's keyboard.")
(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 @@ tune-in sender list from @url{http://opml.radiotime.com}.")
("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 @@ available memory.")
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)
diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm
index 848399a8a1..1a79066eac 100644
--- a/gnu/packages/node.scm
+++ b/gnu/packages/node.scm
@@ -43,14 +43,14 @@
(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
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 7e35af5dfd..ea90e78547 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -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 @@
;; 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 @@
(commit commit)))
(sha256
(base32
- "12ghbby83w335g7vbg7h52hjaal5l6mc6qmldlx8029340br8h1w"))
+ "1c00yr2vgsdl3kmlbjppyws47ssahamdx88y0wg26x73px71rd19"))
(file-name (string-append "guix-" version "-checkout"))))
(build-system gnu-build-system)
(arguments
@@ -534,13 +535,13 @@ transactions from C or Python.")
(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
diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 66d9e933e7..1dfafac4e7 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -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-public parallel
(package
(name "parallel")
- (version "20180322")
+ (version "20180422")
(source
(origin
(method url-fetch)
@@ -55,7 +55,7 @@
version ".tar.bz2"))
(sha256
(base32
- "15v46pv4z98xm3fkwy7335faw4r7pilrxp4xis5a4zi4319sv2b3"))))
+ "0xsfpbxwgd4197gra981iv0nmjfk58c0d88dxx6dh6yrqz523klx"))))
(build-system gnu-build-system)
(arguments
`(#:phases
diff --git a/gnu/packages/patches/bcftools-regidx-unsigned-char.patch b/gnu/packages/patches/bcftools-regidx-unsigned-char.patch
deleted file mode 100644
index af5bc160f5..0000000000
--- a/gnu/packages/patches/bcftools-regidx-unsigned-char.patch
+++ /dev/null
@@ -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)
- {
diff --git a/gnu/packages/patches/ceph-skip-collect-sys-info-test.patch b/gnu/packages/patches/ceph-skip-collect-sys-info-test.patch
index f210799254..429087c661 100644
--- a/gnu/packages/patches/ceph-skip-collect-sys-info-test.patch
+++ b/gnu/packages/patches/ceph-skip-collect-sys-info-test.patch
@@ -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
-
diff --git a/gnu/packages/patches/freeimage-unbundle.patch b/gnu/packages/patches/freeimage-unbundle.patch
index 2727d9fbda..ca907d3276 100644
--- a/gnu/packages/patches/freeimage-unbundle.patch
+++ b/gnu/packages/patches/freeimage-unbundle.patch
@@ -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
diff --git a/gnu/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch b/gnu/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch
new file mode 100644
index 0000000000..506de833dd
--- /dev/null
+++ b/gnu/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch
@@ -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
diff --git a/gnu/packages/patches/pcmanfm-CVE-2017-8934.patch b/gnu/packages/patches/pcmanfm-CVE-2017-8934.patch
deleted file mode 100644
index 489d22c83b..0000000000
--- a/gnu/packages/patches/pcmanfm-CVE-2017-8934.patch
+++ /dev/null
@@ -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
-
diff --git a/gnu/packages/patches/pt-scotch-build-parallelism.patch b/gnu/packages/patches/pt-scotch-build-parallelism.patch
deleted file mode 100644
index 2ac5f27f52..0000000000
--- a/gnu/packages/patches/pt-scotch-build-parallelism.patch
+++ /dev/null
@@ -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)
diff --git a/gnu/packages/patches/qemu-CVE-2018-7550.patch b/gnu/packages/patches/qemu-CVE-2018-7550.patch
deleted file mode 100644
index 43f111e206..0000000000
--- a/gnu/packages/patches/qemu-CVE-2018-7550.patch
+++ /dev/null
@@ -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
-
diff --git a/gnu/packages/patches/quassel-fix-tls-check.patch b/gnu/packages/patches/quassel-fix-tls-check.patch
deleted file mode 100644
index 057bc02a14..0000000000
--- a/gnu/packages/patches/quassel-fix-tls-check.patch
+++ /dev/null
@@ -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} ${Qt5Core_EXECUTABLE_COMPILE_FLAGS}")
-+
-+if (USE_QT5 AND Qt5_POSITION_INDEPENDENT_CODE)
-+ set(CMAKE_REQUIRED_FLAGS "-fPIC -DQT_NO_VERSION_TAGGING")
-+endif()
-+
- check_cxx_source_compiles("
- #include \"qglobal.h\"
- #if defined QT_NO_SSL
-
diff --git a/gnu/packages/patches/scotch-build-parallelism.patch b/gnu/packages/patches/scotch-build-parallelism.patch
new file mode 100644
index 0000000000..a669f1dbeb
--- /dev/null
+++ b/gnu/packages/patches/scotch-build-parallelism.patch
@@ -0,0 +1,39 @@
+Fixes make with -j, otherwise scotch.h may not be generated by the time make
+tries to compile library_graph_diam.o et al.
+
+Reported upstream at
+https://gforge.inria.fr/tracker/index.php?func=detail&aid=21651&group_id=248&atid=1081
+
+diff --git a/src/libscotch/Makefile b/src/libscotch/Makefile
+index 9898894..b0ee14c 100644
+--- a/src/libscotch/Makefile
++++ b/src/libscotch/Makefile
+@@ -2229,6 +2229,28 @@ library_graph_color_f$(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 \
diff --git a/gnu/packages/patches/scotch-graph-diam-64.patch b/gnu/packages/patches/scotch-graph-diam-64.patch
new file mode 100644
index 0000000000..2ae31e3c3b
--- /dev/null
+++ b/gnu/packages/patches/scotch-graph-diam-64.patch
@@ -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));
+ }
diff --git a/gnu/packages/patches/scotch-graph-induce-type-64.patch b/gnu/packages/patches/scotch-graph-induce-type-64.patch
new file mode 100644
index 0000000000..d2eee52a7b
--- /dev/null
+++ b/gnu/packages/patches/scotch-graph-induce-type-64.patch
@@ -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);
diff --git a/gnu/packages/patches/zsh-CVE-2018-7548.patch b/gnu/packages/patches/zsh-CVE-2018-7548.patch
deleted file mode 100644
index 1ee15fad73..0000000000
--- a/gnu/packages/patches/zsh-CVE-2018-7548.patch
+++ /dev/null
@@ -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
-
diff --git a/gnu/packages/patches/zsh-CVE-2018-7549.patch b/gnu/packages/patches/zsh-CVE-2018-7549.patch
deleted file mode 100644
index abefcdf2f9..0000000000
--- a/gnu/packages/patches/zsh-CVE-2018-7549.patch
+++ /dev/null
@@ -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
-
diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm
index 832efc2b78..9c17733d4c 100644
--- a/gnu/packages/perl-check.scm
+++ b/gnu/packages/perl-check.scm
@@ -96,7 +96,7 @@ warning content is outputted via diag.")
(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 @@ warning content is outputted via diag.")
"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 @@ structures without getting caught in an infinite loop.")
(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 @@ structures without getting caught in an infinite loop.")
"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 @@ If used in a subtest, the remainder of the subtest will be skipped.")
(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 @@ If used in a subtest, the remainder of the subtest will be skipped.")
".tar.gz"))
(sha256
(base32
- "127kpl1va267qar2ia4c22xb96jby2jqnda3sj5pjgmxg8si26cg"))))
+ "0c306p9qdpa2ycii3c50hml23mwy6bjxpry126g1dw11hyiwcxgv"))))
(build-system perl-build-system)
(home-page
"http://search.cpan.org/dist/Test-NoTabs/")
@@ -869,14 +869,14 @@ usually called epsilon. This module provides such a function for use with
(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 @@ as flexible as possible to the tester.")
(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 @@ as flexible as possible to the tester.")
"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 @@ makes fork(2) safe to use in test cases.")
(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
diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index c3609dfd58..c4228e4e05 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -162,7 +162,7 @@
;; 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 @@ error when it would have happened.")
(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 @@ error when it would have happened.")
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 @@ all known commands are checked.")
(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 @@ all known commands are checked.")
"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 @@ Agency.")
(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 @@ Agency.")
"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 @@ algorithm to keep the most used entries in the cache.")
(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 @@ algorithm to keep the most used entries in the cache.")
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 @@ to the calling program.")
(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 @@ to the calling program.")
"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 @@ arrays for their internal representation.")
(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 @@ variable in a subroutines scope to one of your choosing.")
(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 @@ variable in a subroutines scope to one of your choosing.")
"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 @@ separator.")
(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 @@ type.")
(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 @@ type.")
"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 @@ distributions. It is a companion module to File::ShareDir.")
(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 @@ distributions. It is a companion module to File::ShareDir.")
"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 @@ logging mechanism.")
(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 @@ messages.")
(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 @@ messages.")
"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 @@ debug options.
(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 @@ debug options.
"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 @@ and libraries based on OpenSSL.")
(define-public perl-multidimensional
(package
(name "perl-multidimensional")
- (version "0.013")
+ (version "0.014")
(source
(origin
(method url-fetch)
@@ -6267,7 +6267,7 @@ and libraries based on OpenSSL.")
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 @@ and @code{deserialize_regexp}.")
(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 @@ and @code{deserialize_regexp}.")
"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 @@ run from within a source-controlled directory.")
(define-public perl-strictures-2
(package
(inherit perl-strictures)
- (version "2.000003")
+ (version "2.000004")
(source
(origin
(method url-fetch)
@@ -7460,7 +7460,7 @@ run from within a source-controlled directory.")
"strictures-" version ".tar.gz"))
(sha256
(base32
- "08mgvf1d2651gsg3jgjfs13878ndqa4ji8vfsda9f7jjd84ymy17"))))))
+ "0lzp0q6kwk6vgf7zdlvy9zz28fj6n1b776irm556c7gylcq29113"))))))
(define-public perl-string-camelcase
(package
@@ -7691,7 +7691,7 @@ return value is the sub.")
(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 @@ return value is the sub.")
version ".tar.gz"))
(sha256
(base32
- "1zv45cvj4ifkbr61ydcpphnj6lvib37gfxwfh40h0yzf3c8lbca4"))))
+ "01xsvfdpxzimsbrp9mqipsr93y83nhj21q05g8v1bw6yfl3lzayn"))))
(build-system perl-build-system)
(native-inputs
`(("perl-test-fatal" ,perl-test-fatal)))
@@ -7873,7 +7873,7 @@ of a system.")
(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 @@ of a system.")
"Task-Weaken-" version ".tar.gz"))
(sha256
(base32
- "0p5ryr3421p5rqj6dk5dcvxsml5gl9skbn7gv4szk50fimrvzww5"))))
+ "1gk6rmnp4x50lzr0vfng41khf0f8yzxlm0pad1j69vxskpdzx0r3"))))
(build-system perl-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
@@ -8261,7 +8261,7 @@ to tabs.")
(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 @@ to tabs.")
"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 @@ variable conform.")
(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 @@ variable conform.")
"Type-Tiny-" version ".tar.gz"))
(sha256
(base32
- "1p8krim8kvw123nady96fagi8sk2pj1z8jkr4r8n45ihyamfxjck"))))
+ "0b48v28rvl20969gyr62yg6gr6a2nj9qik0bixavbjdmk67hqnx8"))))
(build-system perl-build-system)
(native-inputs
`(("perl-test-warnings" ,perl-test-warnings)))
diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm
index 437acd305d..2c0c2313f4 100644
--- a/gnu/packages/photo.scm
+++ b/gnu/packages/photo.scm
@@ -69,14 +69,14 @@
(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 @@ photographic equipment.")
(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 @@ photographic equipment.")
version "/darktable-" version ".tar.xz"))
(sha256
(base32
- "10asz918kv2248px3w9bn5k8cfrad5xrci58x9y61l0yf5hcpk0r"))))
+ "1lq3xp7hhfhfwqrz0f2mrp3xywnpvb0nlw6lbm5cgx22s5xzri8x"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; There are no tests.
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index 69b6ffd3f4..48e84521c5 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -620,6 +620,9 @@ Networking and Cryptography library. These libraries have a stated goal
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 @@ Python.")
(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)))
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index d15ad92a56..6e8d9ab954 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -44,6 +44,7 @@
#: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 @@ and written in Python.")
(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 @@ facilities for defining, registering and looking up components.")
(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 @@ of the SSL peer.")
(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)))))
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index e342d62a03..37434c4758 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1290,14 +1290,14 @@ after Andy Lester’s Perl module WWW::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 @@ sources.")
(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 @@ and several other projects.")
(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 @@ multivalue dictionary that retains the order of insertions and deletions.")
(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 @@ anymore.")
(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 @@ a file-like object from which an arbitrarly-sized key can be read.")
(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 @@ and works only with Python 2 and NumPy < 1.9.")
(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 @@ in Python. You can simply type pybtex instead of bibtex.")
(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
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 98bb5bd110..c15e677438 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -4079,14 +4079,14 @@ support to both Ruby and JRuby. It uses @code{unf_ext} on CRuby and
(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 @@ files and use the data therein.")
(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)))
diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm
index 50b5368a3b..dba5067e9e 100644
--- a/gnu/packages/scheme.scm
+++ b/gnu/packages/scheme.scm
@@ -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 @@ Scheme and C programs and between Scheme and Java programs.")
version ".tar.gz"))
(sha256
(base32
- "09m7pahjsp7wxzd20cdph9j3mgf2nq5dyckcjljcd40m25v85kks"))))
+ "0bvq79vxcpgwydwi923cxb5w9isx2x8r3d0xndbdhacmmsw1m811"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm
index 72abfbf699..43cf2795dd 100644
--- a/gnu/packages/sdl.scm
+++ b/gnu/packages/sdl.scm
@@ -505,7 +505,7 @@ sound and device input (keyboards, joysticks, mice, etc.).")
(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)
diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm
index 5527e8ab79..8b41c8d613 100644
--- a/gnu/packages/shells.scm
+++ b/gnu/packages/shells.scm
@@ -292,20 +292,18 @@ history mechanism, job control and a C-like syntax.")
(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
diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm
index 521be54c49..38d4a3a6bd 100644
--- a/gnu/packages/spice.scm
+++ b/gnu/packages/spice.scm
@@ -302,7 +302,7 @@ resolution scaling on graphical console window resize.")
(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 @@ resolution scaling on graphical console window resize.")
"virt-viewer-" version ".tar.gz"))
(sha256
(base32
- "0blbp1wkw8ahss9va0bmcz2yx18j0mvm6fzrzhh2ly3sja5ysb8b"))))
+ "1chqrf658niivzfh85cbwkbv9vyg8sv1mv3i31vawkfsfdvvsdwh"))))
(build-system gnu-build-system)
(inputs
`(("gtk+" ,gtk+)
diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm
index d712e06431..112ccb3280 100644
--- a/gnu/packages/ssh.scm
+++ b/gnu/packages/ssh.scm
@@ -258,8 +258,20 @@ Additionally, various channel-specific options can be negotiated.")
(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)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 5069ef7c5d..51f5ad91b1 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -361,14 +361,14 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
(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 @@ code for possible problems.")
(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 @@ and operations on them using LAPACK and SuiteSparse.")
(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 @@ analysis.")
(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 @@ a column in data frame.")
(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 @@ ldap, and also supports cookies, redirects, authentication, etc.")
(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 @@ plotted and compared with the asymptotic curve.")
(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 @@ safety.")
(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 @@ want to migrate to S4.")
(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 @@ series of numeric vectors/matrices and factors.")
(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 @@ closely-packed, non-overlapping points.")
(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 @@ can be efficiently implemented directly in the R language.")
(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 @@ algorithms.")
(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 @@ modification of F-tests for linear mixed effects models and a parametric
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 @@ first and second order derivatives.")
(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)
diff --git a/gnu/packages/storage.scm b/gnu/packages/storage.scm
index 9882a4ec34..11f6f9d7e8 100644
--- a/gnu/packages/storage.scm
+++ b/gnu/packages/storage.scm
@@ -51,14 +51,14 @@
(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"
diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 93390df946..0a90610ecb 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -860,8 +860,6 @@ implements arithmetic over the Galois Field GF(256).")
`(#: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,
diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm
index 06e8e47323..2536754eb7 100644
--- a/gnu/packages/text-editors.scm
+++ b/gnu/packages/text-editors.scm
@@ -239,14 +239,16 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings. e3 can be used on
(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 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings. e3 can be used on
;; 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 @@ team.")
(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 @@ team.")
(file-name (git-file-name name version))
(sha256
(base32
- "1ihdr4xk0j83q83xknbikxb7yf9qhlkgvc89w33lhj090cv376gd"))))
+ "0251563zy0q69fzfacvalpx43y15cshb0bhshyd4w37061gh1c12"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 78532ec268..5734bf62d6 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -135,7 +135,7 @@ libenca and several charset conversion libraries and tools.")
(define-public utf8proc
(package
(name "utf8proc")
- (version "2.1.0")
+ (version "2.1.1")
(source
(origin
(method url-fetch)
@@ -144,9 +144,9 @@ libenca and several charset conversion libraries and tools.")
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 @@ libenca and several charset conversion libraries and tools.")
(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
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index ef891a8b17..0c84c29fe8 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -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 @@ repository is the centre, directories are branches and files are leaves.
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)))
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index ad7e12079a..85efda65ec 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -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 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).")
(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 @@ convert and stream audio and video. It includes the libavcodec
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 @@ audio/video codec library.")
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 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.")
(inputs
`(("alsa-lib" ,alsa-lib)
("enca" ,enca)
- ("ffmpeg" ,ffmpeg-git)
+ ("ffmpeg" ,ffmpeg)
("jack" ,jack-1)
("ladspa" ,ladspa)
("lcms" ,lcms)
@@ -1162,7 +1155,7 @@ access to mpv's powerful playback capabilities.")
(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 @@ access to mpv's powerful playback capabilities.")
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 @@ audio, images) from the Web. It can use either mpv or vlc for playback.")
(define-public youtube-viewer
(package
(name "youtube-viewer")
- (version "3.3.3")
+ (version "3.3.4")
(source (origin
(method url-fetch)
(uri (string-append
@@ -1328,7 +1321,7 @@ audio, images) from the Web. It can use either mpv or vlc for playback.")
(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 @@ from sites like Twitch.tv and pipes them into a video player of choice.")
#t)))))
(inputs
`(("alsa-lib" ,alsa-lib)
- ("ffmpeg" ,ffmpeg)
+ ("ffmpeg" ,ffmpeg-3.4)
("fftw" ,fftw)
("libxml2" ,libxml2)
("jack" ,jack-1)
@@ -2093,7 +2086,7 @@ making @dfn{screencasts}.")
;; 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 @@ It counts more than 100 plugins.")
("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 @@ the results, download the highest-rated result in the requested language and
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)))
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index 0b373b1407..9dd8bb8971 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -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 @@
#: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 @@
#: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-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 @@ exec smbd $@")))
`(("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 @@ exec smbd $@")))
;; ("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 @@ server and embedded PowerPC, and S390 guests.")
''("--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 @@ virtualization library.")
(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 @@ virtualization library.")
version ".tar.gz"))
(sha256
(base32
- "093azs8p4p7y4nf5j25xpsvdxww7gky1g0hs8mkcvmpxl2wjd0jj"))))
+ "1ardmd4sxdmd57y7qpka44gf09c1yq2g0xs074d3k1h925crv27f"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
@@ -777,3 +807,60 @@ monitor/GPU.")
;; 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)))
diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 2fc930aa9e..fb06196ec4 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -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 @@
#: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 @@ example for writing your own. For example, @command{vpnc-script-sshd} contains
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 @@ and probably others.")
(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 @@ and probably others.")
version ".tar.xz"))
(sha256
(base32
- "17njq59hsraqyxrbhkrxr7dvx0p066s3pn8w1mi0yd9jldis7h23"))))
+ "09lck4wmkas3iyrzaspin9gn3wiclqb1m9sf8diy7j8wakx38r2g"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags '("--enable-iproute2=yes")))
diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm
index 12b1f93015..ac9f6f2f25 100644
--- a/gnu/packages/vulkan.scm
+++ b/gnu/packages/vulkan.scm
@@ -160,7 +160,7 @@ interpretation of the specifications for these languages.")
(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 @@ interpretation of the specifications for these languages.")
"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 @@ interpretation of the specifications for these languages.")
#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)
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 88c3b4aa1c..a8f28040b0 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3784,15 +3784,19 @@ CDF, Atom 0.3, and Atom 1.0 feeds.")
(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 @@ directory.")
(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 @@ responsive, and powerful applications with minimal effort.")
(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.
diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index 7486d8f29d..dc74c9f59e 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -496,7 +496,7 @@ of the screen selected by mouse.")
(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 @@ of the screen selected by mouse.")
(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 @@ selection's dimensions to stdout.")
(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 @@ selection's dimensions to stdout.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0f54s7csrxjd5r9anqqa92diwmzdplpws3llmbr6g3c0l6bp8815"))))
+ "02blbimjdckbcb04crhv0k2vxnp3rcgskyq66sk0v13l2h52849v"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f)) ; no "check" target
diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index be1bfce578..694aab882e 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -26,7 +26,6 @@
#: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 @@
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 @@ This service is not part of @var{%base-services}."
(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.
diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm
index 6ac440fd26..67674e895e 100644
--- a/gnu/services/networking.scm
+++ b/gnu/services/networking.scm
@@ -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 @@
#:use-module (srfi srfi-26)
#:use-module (ice-9 match)
#:export (%facebook-host-aliases
- static-networking
+ dhcp-client-service
- static-networking?
- static-networking-interface
- static-networking-ip
- static-networking-netmask
- static-networking-gateway
- static-networking-requirement
+ 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
- static-networking-service
- static-networking-service-type
- dhcp-client-service
%ntp-servers
ntp-configuration
@@ -90,6 +93,9 @@
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 @@ fe80::1%lo0 connect.facebook.net
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 @@ to handle."
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
@@ -891,6 +815,17 @@ and @command{wicd-curses} user interfaces."
;;;
+;;; 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
;;;
@@ -1028,6 +963,30 @@ 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
;;;
diff --git a/gnu/system/file-systems.scm b/gnu/system/file-systems.scm
index 7f5afb00fe..d2acd705de 100644
--- a/gnu/system/file-systems.scm
+++ b/gnu/system/file-systems.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -47,6 +47,7 @@
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 @@ TARGET in the other system."
;;; 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
diff --git a/gnu/tests/networking.scm b/gnu/tests/networking.scm
index d7d9166fa7..323679e7fc 100644
--- a/gnu/tests/networking.scm
+++ b/gnu/tests/networking.scm
@@ -22,6 +22,7 @@
#: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 @@
#: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 @@ port 7, and a dict service on port 2628."
(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))))