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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 John Darrington <jmd@gnu.org>
;;; Copyright © 2014, 2016 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2020 Boris A. Dekshteyn <boris.dekshteyn@gmail.com>
;;; Copyright © 2020 Ekaitz Zarraga <ekaitz@elenq.tech>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages inkscape)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system cmake)
  #:use-module (gnu packages)
  #:use-module (gnu packages aspell)
  #:use-module (gnu packages bdw-gc)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages check)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages gnome)
  #:use-module (gnu packages graphics)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages imagemagick)
  #:use-module (gnu packages libreoffice)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pdf)
  #:use-module (gnu packages popt)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages ghostscript)
  #:use-module (gnu packages fontutils)
  #:use-module (gnu packages image)
  #:use-module (gnu packages pkg-config))

(define-public inkscape
  (package
    (name "inkscape")
    (version "0.92.4")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://media.inkscape.org/dl/"
                                  "resources/file/"
                                  "inkscape-" version ".tar.bz2"))
              (patches (search-patches "inkscape-poppler-0.76.patch"))
              (sha256
               (base32
                "0pjinhjibfsz1aywdpgpj3k23xrsszpj4a1ya5562dkv2yl2vv2p"))))
    (build-system cmake-build-system)
    (inputs
     `(("aspell" ,aspell)
       ("gtkmm" ,gtkmm-2)
       ("gtk" ,gtk+-2)
       ("gsl" ,gsl)
       ("poppler" ,poppler)
       ("libpng" ,libpng)
       ("libxml2" ,libxml2)
       ("libxslt" ,libxslt)
       ("libgc" ,libgc)
       ("freetype" ,freetype)
       ("popt" ,popt)
       ("potrace" ,potrace)
       ("python" ,python-wrapper)
       ("lcms" ,lcms)
       ("boost" ,boost)))
    (native-inputs
     `(("intltool" ,intltool)
       ("glib" ,glib "bin")
       ("perl" ,perl)
       ("pkg-config" ,pkg-config)))
    ;; FIXME: tests require gmock
    (arguments
     `(#:tests? #f
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-icon-cache-generator
           (lambda _
             (substitute* "share/icons/application/CMakeLists.txt"
              (("gtk-update-icon-cache") "true"))
             #t))
         (add-after 'unpack 'adjust-for-new-poppler
           (lambda _
             (substitute* (find-files "src/extension/internal/pdfinput")
               ;; Needed for Poppler 0.82.
               (("Unicode \\*u") "Unicode const *u")
               ;; Needed for Poppler 0.83.
               (("\\(GfxPath") "(const GfxPath")
               (("GfxSubpath") "const GfxSubpath")
               (("new GlobalParams\\(\\)")
                "std::unique_ptr<GlobalParams>(new GlobalParams())")
               (("new GlobalParams\\(poppler_datadir\\)")
                "std::unique_ptr<GlobalParams>(new GlobalParams(poppler_datadir))"))
             #t)))))
    (home-page "https://inkscape.org/")
    (synopsis "Vector graphics editor")
    (description "Inkscape is a vector graphics editor.  What sets Inkscape
apart is its use of Scalable Vector Graphics (SVG), an XML-based W3C standard,
as the native format.")
    (license license:gpl2+)))

(define-public inkscape-1.1
  (package
    (name "inkscape")
    (version "1.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://media.inkscape.org/dl/"
                           "resources/file/"
                           "inkscape-" version ".tar.xz"))
       (patches (search-patches "inkscape-1.1-fix-build-witch-gcc7.5.patch"))
       (sha256
        (base32
         "1rlm2wqg8bgdxkdvnadh49wfp0mrbrk7d8n4vdcjyw6z7z7firki"))
       (modules '((guix build utils)
                  (ice-9 format)))
       (snippet
        '(begin
           (let-syntax
               ;; XXX: The build system doesn't currently support using
               ;; system libraries over bundled ones (see:
               ;; https://gitlab.com/inkscape/inkscape/issues/876).
               ((unbundle
                 (syntax-rules ()
                   ((_ (name source-dir use-pkg-config?) ...)
                    (begin
                      ;; Delete bundled source directories.
                      (delete-file-recursively source-dir) ...
                      (substitute* '("src/CMakeLists.txt"
                                     "src/3rdparty/CMakeLists.txt")
                        (((string-append ".*add_subdirectory\\("
                                         (basename source-dir) "\\).*"))
                         "") ...)
                      ;; Remove bundled entries from INKSCAPE_TARGET_LIBS.
                      (substitute* "src/CMakeLists.txt"
                        (((string-append name "_LIB.*")) "") ...)
                      ;; Register the external libraries, so that their
                      ;; headers are added to INKSCAPE_INCS_SYS and their
                      ;; shared libraries added to INKSCAPE_LIBS.
                      (if use-pkg-config?
                          (let* ((width (string-length "pkg_check_modules("))
                                 (indent (string-join (make-list width " ") "")))
                            (substitute* "CMakeScripts/DefineDependsandFlags.cmake"
                              (("^pkg_check_modules\\(INKSCAPE_DEP REQUIRED.*" start)
                               (string-append start
                                              (format #f "~a~a~%" indent name)))))
                          (substitute* "CMakeScripts/DefineDependsandFlags.cmake"
                            (("^find_package\\(Iconv REQUIRED\\).*" start)
                             (string-append (format #f "
find_path(~a_INCLUDE_DIR NAMES ~:*~a/~:*~a.h ~:*~a.h)
if(NOT ~:*~a_INCLUDE_DIR)
  message(FATAL_ERROR \"~:*~a headers not found\")
else()
  list(APPEND INKSCAPE_INCS_SYS ${~:*~a_INCLUDE_DIR})
endif()

find_library(~:*~a_LIB NAMES ~:*~a)
if(NOT ~:*~a_LIB)
  message(FATAL_ERROR \"~:*~a library not found\")
else()
  list(APPEND INKSCAPE_LIBS ~:*~a_LIB)
endif()~%~%"
                                                    name)
                                            start)))) ...
                      ;; Fix the references to the headers of the
                      ;; unbundled libraries.
                      (substitute* (find-files "." "\\.h$|\\.cpp$")
                        (((string-append "#include (\"|<)3rdparty/"
                                         (basename source-dir)) _ quote)
                         (string-append "#include " quote
                                        (basename source-dir)))
                        ...))))))
             (unbundle ("2geom" "src/3rdparty/2geom" #t)
                       ;; libcroco cannot be unbundled as it is heavily
                       ;; modified (see:
                       ;; https://gitlab.com/inkscape/inkscape/issues/876#note_276114904).
                       ;; ("croco" "src/3rdparty/libcroco" #t)
                       ;; FIXME: Unbundle the following libraries once they
                       ;; have been packaged.
                       ;; ("cola" "src/3rdparty/adaptagrams/libcola")
                       ;; ("avoid" "src/3rdparty/adaptagrams/libavoid")
                       ;; ("vpsc" "src/3rdparty/adaptagrams/libvpsc")
                       ;; libuemf cannot be unbundled as it slightly modified
                       ;; from upstream (see:
                       ;; https://gitlab.com/inkscape/inkscape/issues/973).
                       ;; ("uemf" "src/3rdparty/libuemf" #f)
                       ;; FIXME: libdepixelize upstream is ancient and doesn't
                       ;; build with a recent lib2geom
                       ;; (see: https://bugs.launchpad.net/libdepixelize/+bug/1862458).
                       ;;("depixelize" "src/3rdparty/libdepixelize")
                       ("autotrace" "src/3rdparty/autotrace" #t)))
           ;; Lift the requirement on the double-conversion library, as
           ;; it is only needed by lib2geom, which is now unbundled.
           (substitute* "CMakeScripts/DefineDependsandFlags.cmake"
             ((".*find_package\\(DoubleConversion.*") ""))
           #t))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #t
       #:test-target "check"            ;otherwise some test binaries are missing
       #:imported-modules (,@%cmake-build-system-modules
                           (guix build glib-or-gtk-build-system))
       #:modules ((guix build cmake-build-system)
                  ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
                  (guix build utils))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-icon-cache-generator
           (lambda _
             (substitute* "share/icons/application/CMakeLists.txt"
               (("gtk-update-icon-cache") "true"))
             #t))
         (add-after 'unpack 'disable-latex-export-tests
           ;; FIXME: For some reason the test.pdf_tex file generated by the
           ;; "--export-latex" lacks "some text" in its content when run in
           ;; the build environment.  Skip the related tests.
           (lambda _
             (substitute* "testfiles/cli_tests/CMakeLists.txt"
               (("add_cli_test\\(export-latex")
                "message(TEST_DISABLED: export-latex"))
             #t))
         (add-after 'unpack 'set-home
           ;; Mute Inkscape warnings during tests.
           (lambda _
             (setenv "HOME" (getcwd))
             (format #t "ARGS is set to: ~a" (getenv "ARGS"))
             #t))
         ;; Move the check phase after the install phase, as when run in the
         ;; tests, Inkscape relies on files that are not yet installed, such
         ;; as the "share/inkscape/ui/units.xml" file.
         (delete 'check)
         (add-after 'install 'check
           (assoc-ref %standard-phases 'check))
         (add-after 'install 'glib-or-gtk-compile-schemas
           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-compile-schemas))
         (add-after 'glib-or-gtk-compile-schemas 'glib-or-gtk-wrap
           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))
         (add-after 'install 'wrap-program
           ;; Ensure Python is available at runtime.
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out")))
               (wrap-program (string-append out "/bin/inkscape")
                 `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH")))))
             #t)))))
    (inputs
     `(("aspell" ,aspell)
       ("autotrace" ,autotrace)
       ("gdl" ,gdl-minimal)
       ("gtkmm" ,gtkmm)
       ("gtk" ,gtk+)
       ("gtkspell3" ,gtkspell3)
       ("gsl" ,gsl)
       ("poppler" ,poppler)
       ("lib2geom" ,lib2geom)
       ("libjpeg" ,libjpeg-turbo)
       ("libpng" ,libpng)
       ("libxml2" ,libxml2)
       ("libxslt" ,libxslt)
       ("libgc" ,libgc)
       ("libsoup" ,libsoup-minimal)
       ("libcdr" ,libcdr)
       ("libvisio" ,libvisio)
       ("libwpd" ,libwpd)
       ("libwpg" ,libwpg)
       ("freetype" ,freetype)
       ("popt" ,popt)
       ("potrace" ,potrace)
       ("lcms" ,lcms)
       ("boost" ,boost)
       ("python" ,python-wrapper)
       ("python-scour" ,python-scour)
       ("python-pyserial" ,python-pyserial)
       ("python-numpy" ,python-numpy)
       ("python-lxml" ,python-lxml)))
    (native-inputs
     `(("imagemagick" ,imagemagick)     ;for tests
       ("intltool" ,intltool)
       ("glib" ,glib "bin")
       ("googletest" ,googletest)
       ("perl" ,perl)
       ("pkg-config" ,pkg-config)))
    (home-page "https://inkscape.org/")
    (synopsis "Vector graphics editor")
    (description "Inkscape is a vector graphics editor.  What sets Inkscape
apart is its use of Scalable Vector Graphics (SVG), an XML-based W3C standard,
as the native format.")
    (license license:gpl3+)))           ;see the file COPYING
6575'>gnu/packages/debug.scm14
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-rw-r--r--gnu/packages/gnome-xyz.scm16
-rw-r--r--gnu/packages/gnome.scm263
-rw-r--r--gnu/packages/gnunet.scm23
-rw-r--r--gnu/packages/gnustep.scm36
-rw-r--r--gnu/packages/gnuzilla.scm28
-rw-r--r--gnu/packages/golang.scm127
-rw-r--r--gnu/packages/gpodder.scm2
-rw-r--r--gnu/packages/gps.scm85
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-rw-r--r--gnu/packages/groff.scm2
-rw-r--r--gnu/packages/groovy.scm2
-rw-r--r--gnu/packages/gtk.scm4
-rw-r--r--gnu/packages/guile-xyz.scm64
-rw-r--r--gnu/packages/guile.scm2
-rw-r--r--gnu/packages/hardware.scm4
-rw-r--r--gnu/packages/haskell-apps.scm36
-rw-r--r--gnu/packages/haskell-check.scm2
-rw-r--r--gnu/packages/haskell-web.scm12
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-rw-r--r--gnu/packages/hexedit.scm2
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-rw-r--r--gnu/packages/icu4c.scm59
-rw-r--r--gnu/packages/image-processing.scm8
-rw-r--r--gnu/packages/image-viewers.scm133
-rw-r--r--gnu/packages/image.scm99
-rw-r--r--gnu/packages/ipfs.scm6
-rw-r--r--gnu/packages/irc.scm9
-rw-r--r--gnu/packages/jami.scm20
-rw-r--r--gnu/packages/java-compression.scm32
-rw-r--r--gnu/packages/java-graphics.scm2
-rw-r--r--gnu/packages/java-maths.scm2
-rw-r--r--gnu/packages/java.scm1606
-rw-r--r--gnu/packages/javascript.scm4
-rw-r--r--gnu/packages/jrnl.scm2
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-rw-r--r--gnu/packages/kde.scm6
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-rw-r--r--gnu/packages/language.scm2
-rw-r--r--gnu/packages/lean.scm12
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-rw-r--r--gnu/packages/patches/ganeti-shepherd-master-failover.patch18
-rw-r--r--gnu/packages/patches/ganeti-shepherd-support.patch87
-rw-r--r--gnu/packages/patches/gash-utils-ls-test.patch25
-rw-r--r--gnu/packages/patches/grub-cross-system-i686.patch31
-rw-r--r--gnu/packages/patches/icecat-makeicecat.patch4
-rw-r--r--gnu/packages/patches/ilmbase-fix-test-arm.patch60
-rw-r--r--gnu/packages/patches/intel-xed-fix-nondeterminism.patch113
-rw-r--r--gnu/packages/patches/libreoffice-poppler-compat.patch19
-rw-r--r--gnu/packages/patches/libvnc-CVE-2018-20750.patch44
-rw-r--r--gnu/packages/patches/libvnc-CVE-2019-15681.patch23
-rw-r--r--gnu/packages/patches/linbox-fix-pkgconfig.patch23
-rw-r--r--gnu/packages/patches/llvm-9-fix-bitcast-miscompilation.patch192
-rw-r--r--gnu/packages/patches/llvm-9-fix-lpad-miscompilation.patch97
-rw-r--r--gnu/packages/patches/llvm-9-fix-scev-miscompilation.patch113
-rw-r--r--gnu/packages/patches/luminance-hdr-qt-printer.patch28
-rw-r--r--gnu/packages/patches/maven-enforcer-api-fix-old-dependencies.patch177
-rw-r--r--gnu/packages/patches/opendht-fix-jami.patch33
-rw-r--r--gnu/packages/patches/ppsspp-disable-upgrade-and-gold.patch358
-rw-r--r--gnu/packages/patches/python-aionotify-0.2.0-py3.8.patch48
-rw-r--r--gnu/packages/patches/python-tinycss2-flake8-compat.patch36
-rw-r--r--gnu/packages/patches/qtbase-absolute-runpath.patch17
-rw-r--r--gnu/packages/patches/qtbase-fix-krita-deadlock.patch110
-rw-r--r--gnu/packages/patches/ruby-rubocop-break-dependency-cycle.patch101
-rw-r--r--gnu/packages/patches/rust-1.45-linker-locale.patch14
-rw-r--r--gnu/packages/patches/sqlite-hurd.patch58
-rw-r--r--gnu/packages/patches/tao-add-missing-headers.patch102
-rw-r--r--gnu/packages/patches/tao-fix-parser-types.patch26
-rw-r--r--gnu/packages/patches/transmission-CVE-2018-10756.patch71
-rw-r--r--gnu/packages/patches/u-boot-DT-for-Pinebook-Pro.patch1132
-rw-r--r--gnu/packages/patches/u-boot-add-boe-nv140fhmn49-display.patch29
-rw-r--r--gnu/packages/patches/u-boot-gpio-keys-binding-cons.patch37
-rw-r--r--gnu/packages/patches/u-boot-leds-common-binding-con.patch115
-rw-r--r--gnu/packages/patches/u-boot-riscv64-fix-extlinux.patch14
-rw-r--r--gnu/packages/patches/u-boot-support-Pinebook-Pro-laptop.patch367
-rw-r--r--gnu/packages/patches/u-boot-video-rockchip-fix-build.patch48
-rw-r--r--gnu/packages/patches/ungoogled-chromium-system-jsoncpp.patch65
-rw-r--r--gnu/packages/patches/ungoogled-chromium-system-nspr.patch120
-rw-r--r--gnu/packages/patches/ungoogled-chromium-system-zlib.patch47
-rw-r--r--gnu/packages/patches/widelands-system-wide_minizip.patch153
-rw-r--r--gnu/packages/patches/x265-arm-flags.patch38
-rw-r--r--gnu/packages/patches/xpra-4.0.1-systemd-run.patch34
-rw-r--r--gnu/packages/patchutils.scm2
-rw-r--r--gnu/packages/pdf.scm10
-rw-r--r--gnu/packages/perl6.scm22
-rw-r--r--gnu/packages/phabricator.scm4
-rw-r--r--gnu/packages/photo.scm20
-rw-r--r--gnu/packages/php.scm4
-rw-r--r--gnu/packages/plotutils.scm4
-rw-r--r--gnu/packages/popt.scm2
-rw-r--r--gnu/packages/presentation.scm90
-rw-r--r--gnu/packages/pretty-print.scm12
-rw-r--r--gnu/packages/printers.scm4
-rw-r--r--gnu/packages/prolog.scm24
-rw-r--r--gnu/packages/protobuf.scm111
-rw-r--r--gnu/packages/pulseaudio.scm6
-rw-r--r--gnu/packages/python-check.scm145
-rw-r--r--gnu/packages/python-compression.scm22
-rw-r--r--gnu/packages/python-crypto.scm41
-rw-r--r--gnu/packages/python-science.scm36
-rw-r--r--gnu/packages/python-web.scm418
-rw-r--r--gnu/packages/python-xyz.scm933
-rw-r--r--gnu/packages/python.scm23
-rw-r--r--gnu/packages/qt.scm36
-rw-r--r--gnu/packages/radio.scm32
-rw-r--r--gnu/packages/rails.scm4
-rw-r--r--gnu/packages/rdf.scm2
-rw-r--r--gnu/packages/rednotebook.scm2
-rw-r--r--gnu/packages/regex.scm13
-rw-r--r--gnu/packages/rpc.scm6
-rw-r--r--gnu/packages/rsync.scm2
-rw-r--r--gnu/packages/ruby.scm2456
-rw-r--r--gnu/packages/rust-apps.scm12
-rw-r--r--gnu/packages/rust.scm171
-rw-r--r--gnu/packages/sagemath.scm80
-rw-r--r--gnu/packages/scheme.scm4
-rw-r--r--gnu/packages/screen.scm2
-rw-r--r--gnu/packages/security-token.scm17
-rw-r--r--gnu/packages/selinux.scm4
-rw-r--r--gnu/packages/serialization.scm10
-rw-r--r--gnu/packages/shells.scm60
-rw-r--r--gnu/packages/shellutils.scm12
-rw-r--r--gnu/packages/simh.scm2
-rw-r--r--gnu/packages/skarnet.scm4
-rw-r--r--gnu/packages/sml.scm8
-rw-r--r--gnu/packages/sqlite.scm19
-rw-r--r--gnu/packages/ssh.scm90
-rw-r--r--gnu/packages/statistics.scm72
-rw-r--r--gnu/packages/stenography.scm65
-rw-r--r--gnu/packages/storage.scm9
-rw-r--r--gnu/packages/suckless.scm4
-rw-r--r--gnu/packages/sync.scm8
-rw-r--r--gnu/packages/syncthing.scm24
-rw-r--r--gnu/packages/synergy.scm19
-rw-r--r--gnu/packages/telephony.scm18
-rw-r--r--gnu/packages/terminals.scm22
-rw-r--r--gnu/packages/tex.scm41
-rw-r--r--gnu/packages/texinfo.scm2
-rw-r--r--gnu/packages/text-editors.scm8
-rw-r--r--gnu/packages/textutils.scm16
-rw-r--r--gnu/packages/time.scm9
-rw-r--r--gnu/packages/tls.scm49
-rw-r--r--gnu/packages/tmux.scm10
-rw-r--r--gnu/packages/tor.scm38
-rw-r--r--gnu/packages/toys.scm2
-rw-r--r--gnu/packages/usb-modeswitch.scm9
-rw-r--r--gnu/packages/version-control.scm28
-rw-r--r--gnu/packages/video.scm227
-rw-r--r--gnu/packages/vim.scm53
-rw-r--r--gnu/packages/virtualization.scm545
-rw-r--r--gnu/packages/vlang.scm4
-rw-r--r--gnu/packages/vnc.scm19
-rw-r--r--gnu/packages/vpn.scm10
-rw-r--r--gnu/packages/vulkan.scm45
-rw-r--r--gnu/packages/web-browsers.scm411
-rw-r--r--gnu/packages/web.scm75
-rw-r--r--gnu/packages/webkit.scm4
-rw-r--r--gnu/packages/wine.scm35
-rw-r--r--gnu/packages/wireservice.scm10
-rw-r--r--gnu/packages/wm.scm38
-rw-r--r--gnu/packages/wxwidgets.scm2
-rw-r--r--gnu/packages/xdisorg.scm91
-rw-r--r--gnu/packages/xfce.scm4
-rw-r--r--gnu/packages/xiph.scm8
-rw-r--r--gnu/packages/xml.scm20
-rw-r--r--gnu/packages/xorg.scm221
-rw-r--r--gnu/services.scm58
-rw-r--r--gnu/services/base.scm4
-rw-r--r--gnu/services/ganeti.scm1109
-rw-r--r--gnu/services/networking.scm35
-rw-r--r--gnu/services/nix.scm91
-rw-r--r--gnu/services/science.scm57
-rw-r--r--gnu/services/virtualization.scm11
-rw-r--r--gnu/services/web.scm31
-rw-r--r--gnu/system.scm99
-rw-r--r--gnu/system/hurd.scm2
-rw-r--r--gnu/system/images/hurd.scm8
-rw-r--r--gnu/system/vm.scm1
-rw-r--r--gnu/tests/docker.scm6
-rw-r--r--gnu/tests/ganeti.scm270
-rw-r--r--gnu/tests/install.scm14
-rw-r--r--gnu/tests/monitoring.scm2
-rw-r--r--gnu/tests/networking.scm17
-rw-r--r--gnu/tests/package-management.scm130
-rw-r--r--gnu/tests/web.scm73
341 files changed, 26960 insertions, 8798 deletions
diff --git a/gnu/build/hurd-boot.scm b/gnu/build/hurd-boot.scm
index aea2ac3307..adc8b4ce16 100644
--- a/gnu/build/hurd-boot.scm
+++ b/gnu/build/hurd-boot.scm
@@ -191,7 +191,8 @@ set."
"10.0.2.15" ;the default QEMU guest IP
"--netmask" "255.255.255.0"
"--gateway" "10.0.2.2"
- "--ipv6" "/servers/socket/16"))))
+ "--ipv6" "/servers/socket/16"))
+ ("proc" ("/hurd/procfs" "--stat-mode=444"))))
(define devices
'(("dev/full" ("/hurd/null" "--full") #o666)
@@ -232,17 +233,22 @@ set."
#o666)))
(for-each scope-set-translator servers)
- (mkdir* (scope "dev/vcs/1"))
- (mkdir* (scope "dev/vcs/2"))
- (mkdir* (scope "dev/vcs/2"))
- (rename-file (scope "/dev/console") (scope "/dev/console-"))
+ (mkdir* "dev/vcs/1")
+ (mkdir* "dev/vcs/2")
+ (mkdir* "dev/vcs/2")
+ (rename-file (scope "dev/console") (scope "dev/console-"))
(for-each scope-set-translator devices)
(false-if-EEXIST (symlink "/dev/random" (scope "dev/urandom")))
- (mkdir* (scope "dev/fd"))
+ (mkdir* "dev/fd")
(false-if-EEXIST (symlink "/dev/fd/0" (scope "dev/stdin")))
(false-if-EEXIST (symlink "/dev/fd/1" (scope "dev/stdout")))
- (false-if-EEXIST (symlink "/dev/fd/2" (scope "dev/stderr"))))
+ (false-if-EEXIST (symlink "/dev/fd/2" (scope "dev/stderr")))
+
+ ;; Make sure /etc/mtab is a symlink to /proc/mounts.
+ (false-if-exception (delete-file (scope "etc/mtab")))
+ (mkdir* (scope "etc"))
+ (symlink "/proc/mounts" (scope "etc/mtab")))
(define* (boot-hurd-system #:key (on-error 'debug))
diff --git a/gnu/build/image.scm b/gnu/build/image.scm
index e7b0418182..d8efa73f16 100644
--- a/gnu/build/image.scm
+++ b/gnu/build/image.scm
@@ -131,20 +131,23 @@ given CONFIG file."
(define* (register-closure prefix closure
#:key
(deduplicate? #t) (reset-timestamps? #t)
- (schema (sql-schema)))
+ (schema (sql-schema))
+ (wal-mode? #t))
"Register CLOSURE in PREFIX, where PREFIX is the directory name of the
target store and CLOSURE is the name of a file containing a reference graph as
produced by #:references-graphs.. As a side effect, if RESET-TIMESTAMPS? is
true, reset timestamps on store files and, if DEDUPLICATE? is true,
-deduplicates files common to CLOSURE and the rest of PREFIX."
+deduplicates files common to CLOSURE and the rest of PREFIX. Pass WAL-MODE?
+to call-with-database."
(let ((items (call-with-input-file closure read-reference-graph)))
(parameterize ((sql-schema schema))
(with-database (store-database-file #:prefix prefix) db
- (register-items db items
- #:prefix prefix
- #:deduplicate? deduplicate?
- #:reset-timestamps? reset-timestamps?
- #:registration-time %epoch)))))
+ #:wal-mode? wal-mode?
+ (register-items db items
+ #:prefix prefix
+ #:deduplicate? deduplicate?
+ #:reset-timestamps? reset-timestamps?
+ #:registration-time %epoch)))))
(define* (initialize-efi-partition root
#:key
@@ -164,14 +167,16 @@ deduplicates files common to CLOSURE and the rest of PREFIX."
(register-closures? #t)
system-directory
make-device-nodes
+ (wal-mode? #t)
#:allow-other-keys)
"Initialize the given ROOT directory. Use BOOTCFG and BOOTCFG-LOCATION to
install the bootloader configuration.
If REGISTER-CLOSURES? is true, register REFERENCES-GRAPHS in the store. If
DEDUPLICATE? is true, then also deduplicate files common to CLOSURES and the
-rest of the store when registering the closures. SYSTEM-DIRECTORY is the name
-of the directory of the 'system' derivation."
+rest of the store when registering the closures. SYSTEM-DIRECTORY is the name
+of the directory of the 'system' derivation. Pass WAL-MODE? to
+register-closure."
(populate-root-file-system system-directory root)
(populate-store references-graphs root)
@@ -184,7 +189,8 @@ of the directory of the 'system' derivation."
(register-closure root
closure
#:reset-timestamps? #t
- #:deduplicate? deduplicate?))
+ #:deduplicate? deduplicate?
+ #:wal-mode? wal-mode?))
references-graphs))
(when bootloader-installer
diff --git a/gnu/ci.scm b/gnu/ci.scm
index 834e0f1260..af0bb66775 100644
--- a/gnu/ci.scm
+++ b/gnu/ci.scm
@@ -229,7 +229,6 @@ system.")
(build-image
(image
(inherit efi-disk-image)
- (size (* 1500 MiB))
(operating-system installation-os))))
,(->job 'iso9660-image
(build-image
diff --git a/gnu/local.mk b/gnu/local.mk
index 4f0d8fb537..7f9ad1f97b 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1,6 +1,6 @@
# GNU Guix --- Functional package management for GNU
# Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
-# Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Andreas Enge <andreas@enge.fr>
+# Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Andreas Enge <andreas@enge.fr>
# Copyright © 2016 Mathieu Lirzin <mthl@gnu.org>
# Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Mark H Weaver <mhw@netris.org>
# Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
@@ -24,7 +24,7 @@
# Copyright © 2019, 2020 John Soo <jsoo1@asu.edu>
# Copyright © 2019 Jonathan Brielmaier <jonathan.brielmaier@web.de>
# Copyright © 2019 Evan Straw <evan.straw99@gmail.com>
-# Copyright © 2019 Brett Gilio <brettg@gnu.org>
+# Copyright © 2019, 2020 Brett Gilio <brettg@gnu.org>
# Copyright © 2019 Amin Bandali <bandali@gnu.org>
# Copyright © 2020 Brendan Tildesley <mail@brendan.scot>
# Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
@@ -359,9 +359,11 @@ GNU_SYSTEM_MODULES = \
%D%/packages/maths.scm \
%D%/packages/matrix.scm \
%D%/packages/maven.scm \
+ %D%/packages/maven-parent-pom.scm \
%D%/packages/mc.scm \
%D%/packages/mcrypt.scm \
%D%/packages/medical.scm \
+ %D%/packages/mercury.scm \
%D%/packages/mes.scm \
%D%/packages/messaging.scm \
%D%/packages/mingw.scm \
@@ -403,6 +405,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/openbox.scm \
%D%/packages/opencog.scm \
%D%/packages/openldap.scm \
+ %D%/packages/openpgp.scm \
%D%/packages/openstack.scm \
%D%/packages/orpheus.scm \
%D%/packages/ots.scm \
@@ -435,6 +438,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/pth.scm \
%D%/packages/pulseaudio.scm \
%D%/packages/pumpio.scm \
+ %D%/packages/presentation.scm \
%D%/packages/pretty-print.scm \
%D%/packages/protobuf.scm \
%D%/packages/pure.scm \
@@ -504,6 +508,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/stalonetray.scm \
%D%/packages/statistics.scm \
%D%/packages/stb.scm \
+ %D%/packages/stenography.scm \
%D%/packages/storage.scm \
%D%/packages/suckless.scm \
%D%/packages/swig.scm \
@@ -584,6 +589,7 @@ GNU_SYSTEM_MODULES = \
%D%/services/docker.scm \
%D%/services/authentication.scm \
%D%/services/games.scm \
+ %D%/services/ganeti.scm \
%D%/services/getmail.scm \
%D%/services/guix.scm \
%D%/services/hurd.scm \
@@ -599,6 +605,7 @@ GNU_SYSTEM_MODULES = \
%D%/services/nix.scm \
%D%/services/nfs.scm \
%D%/services/pam-mount.scm \
+ %D%/services/science.scm \
%D%/services/security-token.scm \
%D%/services/shepherd.scm \
%D%/services/sound.scm \
@@ -635,8 +642,6 @@ GNU_SYSTEM_MODULES = \
%D%/system/images/hurd.scm \
\
%D%/machine.scm \
- %D%/machine/digital-ocean.scm \
- %D%/machine/ssh.scm \
\
%D%/build/accounts.scm \
%D%/build/activation.scm \
@@ -661,6 +666,7 @@ GNU_SYSTEM_MODULES = \
%D%/tests/desktop.scm \
%D%/tests/dict.scm \
%D%/tests/docker.scm \
+ %D%/tests/ganeti.scm \
%D%/tests/guix.scm \
%D%/tests/monitoring.scm \
%D%/tests/nfs.scm \
@@ -670,6 +676,7 @@ GNU_SYSTEM_MODULES = \
%D%/tests/mail.scm \
%D%/tests/messaging.scm \
%D%/tests/networking.scm \
+ %D%/tests/package-management.scm \
%D%/tests/reconfigure.scm \
%D%/tests/rsync.scm \
%D%/tests/security-token.scm \
@@ -714,6 +721,14 @@ INSTALLER_MODULES = \
%D%/installer/newt/welcome.scm \
%D%/installer/newt/wifi.scm
+if HAVE_GUILE_SSH
+
+GNU_SYSTEM_MODULES += \
+ %D%/machine/digital-ocean.scm \
+ %D%/machine/ssh.scm
+
+endif HAVE_GUILE_SSH
+
# Always ship the installer modules but compile them only when
# ENABLE_INSTALLER is true.
if ENABLE_INSTALLER
@@ -884,6 +899,9 @@ dist_patch_DATA = \
%D%/packages/patches/dstat-skip-devices-without-io.patch \
%D%/packages/patches/dune-istl-2.7-fix-non-mpi-tests.patch \
%D%/packages/patches/dvd+rw-tools-add-include.patch \
+ %D%/packages/patches/ecl-16-format-directive-limit.patch \
+ %D%/packages/patches/ecl-16-ignore-stderr-write-error.patch \
+ %D%/packages/patches/ecl-16-libffi.patch \
%D%/packages/patches/eigen-stabilise-sparseqr-test.patch \
%D%/packages/patches/einstein-build.patch \
%D%/packages/patches/elfutils-tests-ptrace.patch \
@@ -892,6 +910,7 @@ dist_patch_DATA = \
%D%/packages/patches/elm-compiler-fix-map-key.patch \
%D%/packages/patches/emacs27-exec-path.patch \
%D%/packages/patches/emacs-exec-path.patch \
+ %D%/packages/patches/emacs-exwm-fix-fullscreen-states.patch \
%D%/packages/patches/emacs-fix-scheme-indent-function.patch \
%D%/packages/patches/emacs-json-reformat-fix-tests.patch \
%D%/packages/patches/emacs-highlight-stages-add-gexp.patch \
@@ -899,6 +918,7 @@ dist_patch_DATA = \
%D%/packages/patches/emacs-libgit-use-system-libgit2.patch \
%D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch \
%D%/packages/patches/emacs-source-date-epoch.patch \
+ %D%/packages/patches/emacs-telega-patch-server-functions.patch \
%D%/packages/patches/emacs-telega-test-env.patch \
%D%/packages/patches/emacs-undohist-ignored.patch \
%D%/packages/patches/emacs-wordnut-require-adaptive-wrap.patch \
@@ -928,13 +948,21 @@ dist_patch_DATA = \
%D%/packages/patches/findutils-localstatedir.patch \
%D%/packages/patches/findutils-test-rwlock-threads.patch \
%D%/packages/patches/flann-cmake-3.11.patch \
- %D%/packages/patches/flint-ldconfig.patch \
%D%/packages/patches/foobillard++-pkg-config.patch \
%D%/packages/patches/foomatic-filters-CVE-2015-8327.patch \
%D%/packages/patches/foomatic-filters-CVE-2015-8560.patch \
%D%/packages/patches/fontconfig-hurd-path-max.patch \
%D%/packages/patches/freeimage-unbundle.patch \
%D%/packages/patches/fuse-overlapping-headers.patch \
+ %D%/packages/patches/ganeti-deterministic-manual.patch \
+ %D%/packages/patches/ganeti-disable-version-symlinks.patch \
+ %D%/packages/patches/ganeti-drbd-compat.patch \
+ %D%/packages/patches/ganeti-haskell-pythondir.patch \
+ %D%/packages/patches/ganeti-os-disk-size.patch \
+ %D%/packages/patches/ganeti-preserve-PYTHONPATH.patch \
+ %D%/packages/patches/ganeti-shepherd-master-failover.patch \
+ %D%/packages/patches/ganeti-shepherd-support.patch \
+ %D%/packages/patches/gash-utils-ls-test.patch \
%D%/packages/patches/gawk-shell.patch \
%D%/packages/patches/gcc-arm-bug-71399.patch \
%D%/packages/patches/gcc-arm-link-spec-fix.patch \
@@ -1106,9 +1134,9 @@ dist_patch_DATA = \
%D%/packages/patches/id3lib-CVE-2007-4460.patch \
%D%/packages/patches/id3lib-UTF16-writing-bug.patch \
%D%/packages/patches/ilmbase-fix-tests.patch \
- %D%/packages/patches/ilmbase-fix-test-arm.patch \
%D%/packages/patches/inetutils-hurd.patch \
%D%/packages/patches/inkscape-poppler-0.76.patch \
+ %D%/packages/patches/intel-xed-fix-nondeterminism.patch \
%D%/packages/patches/intltool-perl-compatibility.patch \
%D%/packages/patches/iputils-libcap-compat.patch \
%D%/packages/patches/irrlicht-use-system-libs.patch \
@@ -1202,7 +1230,6 @@ dist_patch_DATA = \
%D%/packages/patches/libmygpo-qt-fix-qt-5.11.patch \
%D%/packages/patches/libmygpo-qt-missing-qt5-modules.patch \
%D%/packages/patches/libqalculate-3.8.0-libcurl-ssl-fix.patch \
- %D%/packages/patches/libreoffice-poppler-compat.patch \
%D%/packages/patches/libsndfile-armhf-type-checks.patch \
%D%/packages/patches/libsndfile-CVE-2017-8361-8363-8365.patch \
%D%/packages/patches/libsndfile-CVE-2017-8362.patch \
@@ -1220,8 +1247,6 @@ dist_patch_DATA = \
%D%/packages/patches/libutils-add-includes.patch \
%D%/packages/patches/libutils-remove-damaging-includes.patch \
%D%/packages/patches/libvdpau-va-gl-unbundle.patch \
- %D%/packages/patches/libvnc-CVE-2018-20750.patch \
- %D%/packages/patches/libvnc-CVE-2019-15681.patch \
%D%/packages/patches/libvpx-CVE-2016-2818.patch \
%D%/packages/patches/libxslt-generated-ids.patch \
%D%/packages/patches/libxt-guix-search-paths.patch \
@@ -1230,6 +1255,7 @@ dist_patch_DATA = \
%D%/packages/patches/lierolibre-newer-libconfig.patch \
%D%/packages/patches/lierolibre-remove-arch-warning.patch \
%D%/packages/patches/lierolibre-try-building-other-arch.patch \
+ %D%/packages/patches/linbox-fix-pkgconfig.patch \
%D%/packages/patches/linkchecker-tests-require-network.patch \
%D%/packages/patches/linphoneqt-tabbutton.patch \
%D%/packages/patches/linux-libre-support-for-Pinebook-Pro.patch \
@@ -1237,6 +1263,9 @@ dist_patch_DATA = \
%D%/packages/patches/lirc-localstatedir.patch \
%D%/packages/patches/lirc-reproducible-build.patch \
%D%/packages/patches/llvm-3.5-fix-clang-build-with-gcc5.patch \
+ %D%/packages/patches/llvm-9-fix-bitcast-miscompilation.patch \
+ %D%/packages/patches/llvm-9-fix-lpad-miscompilation.patch \
+ %D%/packages/patches/llvm-9-fix-scev-miscompilation.patch \
%D%/packages/patches/lm-sensors-hwmon-attrs.patch \
%D%/packages/patches/lrcalc-includes.patch \
%D%/packages/patches/lrzip-CVE-2017-8842.patch \
@@ -1247,13 +1276,13 @@ dist_patch_DATA = \
%D%/packages/patches/lua-liblua-so.patch \
%D%/packages/patches/luajit-no_ldconfig.patch \
%D%/packages/patches/luit-posix.patch \
- %D%/packages/patches/luminance-hdr-qt-printer.patch \
%D%/packages/patches/lvm2-static-link.patch \
%D%/packages/patches/make-impure-dirs.patch \
%D%/packages/patches/mariadb-client-test-32bit.patch \
%D%/packages/patches/mars-install.patch \
%D%/packages/patches/mars-sfml-2.3.patch \
%D%/packages/patches/maxima-defsystem-mkdir.patch \
+ %D%/packages/patches/maven-enforcer-api-fix-old-dependencies.patch \
%D%/packages/patches/maven-generate-component-xml.patch \
%D%/packages/patches/maven-generate-javax-inject-named.patch \
%D%/packages/patches/mcrypt-CVE-2012-4409.patch \
@@ -1330,6 +1359,7 @@ dist_patch_DATA = \
%D%/packages/patches/openbabel-fix-crash-on-nwchem-output.patch \
%D%/packages/patches/opencascade-oce-glibc-2.26.patch \
%D%/packages/patches/opencv-rgbd-aarch64-test-fix.patch \
+ %D%/packages/patches/opendht-fix-jami.patch \
%D%/packages/patches/openfoam-4.1-cleanup.patch \
%D%/packages/patches/openjdk-10-idlj-reproducibility.patch \
%D%/packages/patches/openmpi-mtl-priorities.patch \
@@ -1353,12 +1383,14 @@ dist_patch_DATA = \
%D%/packages/patches/pam-mount-luks2-support.patch \
%D%/packages/patches/pango-skip-libthai-test.patch \
%D%/packages/patches/pciutils-hurd-configure.patch \
+ %D%/packages/patches/ppsspp-disable-upgrade-and-gold.patch \
%D%/packages/patches/sdl-pango-api_additions.patch \
%D%/packages/patches/sdl-pango-blit_overflow.patch \
%D%/packages/patches/sdl-pango-fillrect_crash.patch \
%D%/packages/patches/sdl-pango-header-guard.patch \
%D%/packages/patches/sdl-pango-matrix_declarations.patch \
%D%/packages/patches/sdl-pango-sans-serif.patch \
+ %D%/packages/patches/sqlite-hurd.patch \
%D%/packages/patches/patchutils-test-perms.patch \
%D%/packages/patches/patch-hurd-path-max.patch \
%D%/packages/patches/perl-autosplit-default-time.patch \
@@ -1421,6 +1453,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-3.8-fix-tests.patch \
%D%/packages/patches/python-CVE-2018-14647.patch \
%D%/packages/patches/python-aiohttp-3.6.2-no-warning-fail.patch \
+ %D%/packages/patches/python-aionotify-0.2.0-py3.8.patch \
%D%/packages/patches/python-alembic-exceptions-cause.patch \
%D%/packages/patches/python-argcomplete-1.11.1-fish31.patch \
%D%/packages/patches/python-axolotl-AES-fix.patch \
@@ -1450,6 +1483,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-shouldbe-0.1.2-cpy3.8.patch \
%D%/packages/patches/python-slugify-depend-on-unidecode.patch \
%D%/packages/patches/python2-subprocess32-disable-input-test.patch \
+ %D%/packages/patches/python-tinycss2-flake8-compat.patch \
%D%/packages/patches/python-unittest2-python3-compat.patch \
%D%/packages/patches/python-unittest2-remove-argparse.patch \
%D%/packages/patches/python-waitress-fix-tests.patch \
@@ -1457,6 +1491,8 @@ dist_patch_DATA = \
%D%/packages/patches/qemu-glibc-2.27.patch \
%D%/packages/patches/qrcodegen-cpp-make-install.patch \
%D%/packages/patches/qt4-ldflags.patch \
+ %D%/packages/patches/qtbase-absolute-runpath.patch \
+ %D%/packages/patches/qtbase-fix-krita-deadlock.patch \
%D%/packages/patches/qtbase-moc-ignore-gcc-macro.patch \
%D%/packages/patches/qtbase-use-TZDIR.patch \
%D%/packages/patches/qtscript-disable-tests.patch \
@@ -1482,11 +1518,13 @@ dist_patch_DATA = \
%D%/packages/patches/racket-store-checksum-override.patch \
%D%/packages/patches/retroarch-disable-online-updater.patch \
%D%/packages/patches/ruby-rack-ignore-failing-test.patch \
+ %D%/packages/patches/ruby-rubocop-break-dependency-cycle.patch\
%D%/packages/patches/ruby-sanitize-system-libxml.patch \
%D%/packages/patches/ruby-tzinfo-data-ignore-broken-test.patch\
%D%/packages/patches/runc-CVE-2019-5736.patch \
%D%/packages/patches/rust-1.19-mrustc.patch \
%D%/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch \
+ %D%/packages/patches/rust-1.45-linker-locale.patch \
%D%/packages/patches/rust-bootstrap-stage0-test.patch \
%D%/packages/patches/rust-coresimd-doctest.patch \
%D%/packages/patches/rust-nettle-disable-vendor.patch \
@@ -1530,6 +1568,8 @@ dist_patch_DATA = \
%D%/packages/patches/t1lib-CVE-2011-0764.patch \
%D%/packages/patches/t1lib-CVE-2011-1552+.patch \
%D%/packages/patches/t4k-common-libpng16.patch \
+ %D%/packages/patches/tao-add-missing-headers.patch \
+ %D%/packages/patches/tao-fix-parser-types.patch \
%D%/packages/patches/tar-remove-wholesparse-check.patch \
%D%/packages/patches/tar-skip-unreliable-tests.patch \
%D%/packages/patches/tcc-boot-0.9.27.patch \
@@ -1550,7 +1590,6 @@ dist_patch_DATA = \
%D%/packages/patches/tipp10-fix-compiling.patch \
%D%/packages/patches/tipp10-remove-license-code.patch \
%D%/packages/patches/tk-find-library.patch \
- %D%/packages/patches/transmission-CVE-2018-10756.patch \
%D%/packages/patches/ttf2eot-cstddef.patch \
%D%/packages/patches/ttfautohint-source-date-epoch.patch \
%D%/packages/patches/tomb-fix-errors-on-open.patch \
@@ -1558,16 +1597,9 @@ dist_patch_DATA = \
%D%/packages/patches/tuxpaint-stamps-path.patch \
%D%/packages/patches/twinkle-bcg729.patch \
%D%/packages/patches/u-boot-riscv64-fix-extlinux.patch \
- %D%/packages/patches/u-boot-DT-for-Pinebook-Pro.patch \
- %D%/packages/patches/u-boot-add-boe-nv140fhmn49-display.patch \
- %D%/packages/patches/u-boot-gpio-keys-binding-cons.patch \
- %D%/packages/patches/u-boot-leds-common-binding-con.patch \
- %D%/packages/patches/u-boot-support-Pinebook-Pro-laptop.patch \
- %D%/packages/patches/u-boot-video-rockchip-fix-build.patch \
%D%/packages/patches/ucx-tcp-iface-ioctl.patch \
%D%/packages/patches/udiskie-no-appindicator.patch \
- %D%/packages/patches/ungoogled-chromium-system-jsoncpp.patch \
- %D%/packages/patches/ungoogled-chromium-system-zlib.patch \
+ %D%/packages/patches/ungoogled-chromium-system-nspr.patch \
%D%/packages/patches/unzip-CVE-2014-8139.patch \
%D%/packages/patches/unzip-CVE-2014-8140.patch \
%D%/packages/patches/unzip-CVE-2014-8141.patch \
@@ -1606,6 +1638,7 @@ dist_patch_DATA = \
%D%/packages/patches/wicd-get-selected-profile-fix.patch \
%D%/packages/patches/wicd-urwid-1.3.patch \
%D%/packages/patches/wicd-wpa2-ttls.patch \
+ %D%/packages/patches/widelands-system-wide_minizip.patch \
%D%/packages/patches/wmctrl-64-fix.patch \
%D%/packages/patches/wmfire-update-for-new-gdk-versions.patch \
%D%/packages/patches/wordnet-CVE-2008-2149.patch \
@@ -1626,6 +1659,7 @@ dist_patch_DATA = \
%D%/packages/patches/xplanet-1.3.1-libdisplay_DisplayOutput.cpp.patch \
%D%/packages/patches/xplanet-1.3.1-libimage_gif.c.patch \
%D%/packages/patches/xplanet-1.3.1-xpUtil-Add2017LeapSecond.cpp.patch \
+ %D%/packages/patches/xpra-4.0.1-systemd-run.patch \
%D%/packages/patches/xsane-fix-memory-leak.patch \
%D%/packages/patches/xsane-fix-pdf-floats.patch \
%D%/packages/patches/xsane-fix-snprintf-buffer-length.patch \
diff --git a/gnu/machine/ssh.scm b/gnu/machine/ssh.scm
index 7194181681..4148639292 100644
--- a/gnu/machine/ssh.scm
+++ b/gnu/machine/ssh.scm
@@ -37,6 +37,7 @@
#:use-module (guix store)
#:use-module (guix utils)
#:use-module (gcrypt pk-crypto)
+ #:use-module (ice-9 format)
#:use-module (ice-9 match)
#:use-module (ice-9 textual-ports)
#:use-module (srfi srfi-1)
diff --git a/gnu/packages/ada.scm b/gnu/packages/ada.scm
index a8c2bdc9a9..e58b0d7754 100644
--- a/gnu/packages/ada.scm
+++ b/gnu/packages/ada.scm
@@ -38,7 +38,7 @@
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/AdaCore/langkit.git")
+ (url "https://github.com/AdaCore/langkit")
(commit commit)))
(sha256
(base32
@@ -70,7 +70,7 @@ Ada library with bindings for the C and Python programming languages.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/AdaCore/libadalang.git")
+ (url "https://github.com/AdaCore/libadalang")
(commit commit)))
(sha256
(base32
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 9d9fd2d95d..c0e7831d5b 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2,7 +2,7 @@
;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
;;; Copyright © 2014, 2015, 2016, 2018, 2019 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2020 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2015, 2016 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com>
;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
@@ -85,6 +85,7 @@
#:use-module (gnu packages elf)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
+ #:use-module (gnu packages gawk)
#:use-module (gnu packages gettext)
#:use-module (gnu packages gl)
#:use-module (gnu packages glib)
@@ -146,7 +147,7 @@
(method git-fetch)
(uri
(git-reference
- (url "https://github.com/nomius/ktsuss.git")
+ (url "https://github.com/nomius/ktsuss")
(commit version)))
(sha256
(base32 "0q9931f9hp47v1n8scli4bdg2rkjpf5jf8v7jj2gdn83aia1r2hz"))
@@ -219,7 +220,7 @@ usual file attributes can be checked for inconsistencies.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Xfennec/progress.git")
+ (url "https://github.com/Xfennec/progress")
(commit (string-append "v" version))))
(sha256
(base32 "1cnb4ixlhshn139mj5sr42k5m6gjjbyqvkn1324c47niwrgp7dqm"))
@@ -1365,7 +1366,7 @@ system administrator.")
(define-public sudo
(package
(name "sudo")
- (version "1.9.1")
+ (version "1.9.2")
(source (origin
(method url-fetch)
(uri
@@ -1375,7 +1376,7 @@ system administrator.")
version ".tar.gz")))
(sha256
(base32
- "1zxd6hxwhxqrm876wsn9bfajbfc4hc6l9ivzj5rjg80hzv71ch99"))
+ "05432672iilb7s52j9l9xzrlambb1wg3k7qvf5973i41y40x563w"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -1487,7 +1488,7 @@ commands and their arguments.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Duncaen/OpenDoas.git")
+ (url "https://github.com/Duncaen/OpenDoas")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -1864,13 +1865,13 @@ development, not the kernel implementation of ACPI.")
(define-public s-tui
(package
(name "s-tui")
- (version "1.0.0")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "s-tui" version))
(sha256
- (base32 "0r5yhlsi5xiy7ii1w4kqkaxz9069v5bbfwi3x3xnxhk51yjfgr8n"))))
+ (base32 "0xkfdaz5np21311ffdvhks58155qby8j8scbcixhvjd913pj66qx"))))
(build-system python-build-system)
(inputs
`(("python-psutil" ,python-psutil)
@@ -1915,7 +1916,7 @@ system is under heavy load.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dharple/detox.git")
+ (url "https://github.com/dharple/detox")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -2105,7 +2106,7 @@ degradation and failure.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/adrianlopezroche/fdupes.git")
+ (url "https://github.com/adrianlopezroche/fdupes")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -2164,13 +2165,13 @@ of supported upstream metrics systems simultaneously.")
(define-public ansible
(package
(name "ansible")
- (version "2.9.9")
+ (version "2.9.11")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ansible" version))
(sha256
- (base32 "1l99vwkl48iwr8ffd1ihqia995mz8h8hwk4akm4w0cgiifp88gg8"))))
+ (base32 "1c9ayh61qwasgncmlw7rjx5r4g5n2cpg1d5blgn53zg7xhrx1yc8"))))
(build-system python-build-system)
(native-inputs
`(("python-bcrypt" ,python-bcrypt)
@@ -2357,7 +2358,7 @@ lookup to YAML Mode. You could enable the mode with @code{(add-hook
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/opsengine/cpulimit.git")
+ (url "https://github.com/opsengine/cpulimit")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -2396,7 +2397,7 @@ limits.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/wting/autojump.git")
+ (url "https://github.com/wting/autojump")
(commit (string-append "release-v" version))))
(file-name (git-file-name name version))
(sha256
@@ -2442,7 +2443,7 @@ frequently used directories by typing only a small pattern.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/clvv/fasd.git")
+ (url "https://github.com/clvv/fasd")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -2674,7 +2675,7 @@ results (ndiff), and a packet generation and response analysis tool (nping).")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dagwieers/dstat.git")
+ (url "https://github.com/dagwieers/dstat")
(commit (string-append "v" version))))
(file-name (git-file-name "dstat" version))
(sha256
@@ -2726,7 +2727,7 @@ throughput (in the same interval).")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/nvbn/thefuck.git")
+ (url "https://github.com/nvbn/thefuck")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -2802,7 +2803,7 @@ produce uniform output across heterogeneous networks.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/valr/cbatticon.git")
+ (url "https://github.com/valr/cbatticon")
(commit version)))
(sha256
(base32 "0ivm2dzhsa9ir25ry418r2qg2llby9j7a6m3arbvq5c3kaj8m9jr"))
@@ -2838,7 +2839,7 @@ the status of your battery in the system tray.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/TrilbyWhite/interrobang.git")
+ (url "https://github.com/TrilbyWhite/interrobang")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -2914,7 +2915,7 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/linux-sunxi/sunxi-tools.git")
+ (url "https://github.com/linux-sunxi/sunxi-tools")
(commit (string-append "v" version))))
(sha256
(base32 "04f3jqg8ww4jxsf9c6ddcdgy2xbhkyp0b3l5f1hvvbv94p81rjxd"))
@@ -3019,7 +3020,7 @@ in order to be able to find it.
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/aureliojargas/sedsed.git")
+ (url "https://github.com/aureliojargas/sedsed")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3252,17 +3253,105 @@ generate those nifty terminal theme information and ASCII distribution logos in
everyone's screenshots nowadays.")
(license license:gpl3)))
+(define-public ufetch
+ (let ((commit "98b622023e03fe24dbc137e9a68104dfe1fbd04a")
+ (revision "1"))
+ (package
+ (name "ufetch")
+ (version (git-version "0.2" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/jschx/ufetch.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "09c4zmikza16xpydinnqbi3hmcibfrrn10wij7j0j1wv1pj2sl2l"))))
+ (build-system trivial-build-system)
+ (inputs
+ `(("bash" ,bash)
+ ("tput" ,ncurses)))
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ (let* ((source (assoc-ref %build-inputs "source"))
+ (output (assoc-ref %outputs "out"))
+ (bindir (string-append output "/bin"))
+ (docdir (string-append output "/share/doc/ufetch-" ,version))
+ (tput (string-append (assoc-ref %build-inputs "tput") "/bin/tput")))
+ (install-file (string-append source "/LICENSE") docdir)
+ (setenv "PATH" (string-append (assoc-ref %build-inputs "bash") "/bin"))
+ (mkdir-p bindir)
+ (for-each (lambda (src)
+ (let ((dst (string-append bindir "/" (basename src))))
+ (copy-file src dst)
+ (patch-shebang dst)
+ (substitute* dst (("tput") tput))))
+ (find-files source "ufetch-[[:alpha:]]*$"))
+ ;; Note: the `ufetch` we create below will only work if run under
+ ;; the Guix System. I.e. a user trying to run `ufetch` on a
+ ;; foreign distro will not get great results. The `screenfetch`
+ ;; program does actual runtime detection of the operating system,
+ ;; and would be a better choice in such a situation.
+ (symlink "ufetch-guix" (string-append bindir "/ufetch"))))))
+ (home-page "https://gitlab.com/jschx/ufetch")
+ (synopsis "Tiny system info")
+ (description "This package provides a tiny system info utility.")
+ (license license:isc))))
+
+(define-public pfetch
+ (let ((commit "e18a0959ab98b963744755ec4687e59dc11db3c5")
+ (revision "0"))
+ (package
+ (name "pfetch")
+ (version (git-version "0.7.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dylanaraps/pfetch")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1md40av6i3xvvwig5jzhy4kf3s5sgxxk35r0vcyrjd8qyndk927l"))))
+ (build-system trivial-build-system)
+ (inputs `(("bash" ,bash)))
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ (let* ((source (lambda (f)
+ (string-append (assoc-ref %build-inputs "source") "/" f)))
+ (output (assoc-ref %outputs "out"))
+ (docdir (string-append output "/share/doc/pfetch-" ,version)))
+ (install-file (source "LICENSE.md") docdir)
+ (install-file (source "README.md") docdir)
+ (install-file (source "pfetch") (string-append output "/bin"))
+ (patch-shebang
+ (string-append output "/bin/pfetch")
+ (list (string-append (assoc-ref %build-inputs "bash") "/bin")))
+ #t))))
+ (home-page "https://github.com/dylanaraps/pfetch")
+ (synopsis "System information tool")
+ (description "This package provides a simple, configurable system
+information tool.")
+ (license license:expat))))
+
(define-public nnn
(package
(name "nnn")
- (version "3.2")
+ (version "3.3")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/jarun/nnn/releases/download/v"
version "/nnn-v" version ".tar.gz"))
(sha256
- (base32 "1zflz7yj5wzdnl0728g8qrld2z6dqn7sblbmkjvyqlv1fwjd1fsf"))))
+ (base32 "1jiaygylwrlz6rlls1q69xw10j6ypr96yshsbzisg0adk37lbchn"))))
(build-system gnu-build-system)
(inputs
`(("ncurses" ,ncurses)
@@ -3334,7 +3423,7 @@ on systems running the Linux kernel.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/robertdavidgraham/masscan.git")
+ (url "https://github.com/robertdavidgraham/masscan")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -3445,7 +3534,7 @@ launch daemons into the relevant nodes.")
;; We use git checkout to avoid github auto-generated tarballs
(method git-fetch)
(uri (git-reference
- (url "https://github.com/hpc/Spindle.git")
+ (url "https://github.com/hpc/Spindle")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3473,7 +3562,7 @@ Python loading in HPC environments.")
(let ((real-name "inxi"))
(package
(name "inxi-minimal")
- (version "3.1.03-1")
+ (version "3.1.04-1")
(source
(origin
(method git-fetch)
@@ -3482,7 +3571,7 @@ Python loading in HPC environments.")
(commit version)))
(file-name (git-file-name real-name version))
(sha256
- (base32 "0539hvlq021wxhbwzdp7qliiq1jgw60mxlwrwx0z2x8qi1zqdzg6"))))
+ (base32 "1mirnrrqfjyl2r7fwnpjlk37i5hf8f7lxv2yxcbdfjf2b3dfbpvl"))))
(build-system trivial-build-system)
(inputs
`(("bash" ,bash-minimal)
@@ -3656,7 +3745,7 @@ support forum. It runs with the @code{/exec} command in most IRC clients.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/pwr/Solaar.git")
+ (url "https://github.com/pwr/Solaar")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -3672,10 +3761,7 @@ support forum. It runs with the @code{/exec} command in most IRC clients.")
(("'--prefix' in sys\\.argv")
"len([x.startswith('--prefix=') for x in sys.argv]) > 0"))
#t))
- (replace 'build
- (lambda _
- (invoke "python" "setup.py" "build")))
- (add-before 'check 'setenv-PATH
+ (add-before 'build 'setenv-PATH
(lambda _
(setenv "PYTHONPATH" (string-append "lib:" (getenv "PYTHONPATH")))
#t)))))
@@ -3872,7 +3958,7 @@ supplied by the user when logging in.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/kellyjonbrazil/jc.git")
+ (url "https://github.com/kellyjonbrazil/jc")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3896,7 +3982,7 @@ file-types for easier parsing in scripts.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/kellyjonbrazil/jtbl.git")
+ (url "https://github.com/kellyjonbrazil/jtbl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3910,3 +3996,78 @@ file-types for easier parsing in scripts.")
(description "@code{jtbl} accepts piped JSON data from stdin and outputs a
text table representation to stdout.")
(license license:expat)))
+
+(define-public hosts
+ (package
+ (name "hosts")
+ (version "3.6.3")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/xwmx/hosts")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1ni4z89kxzgwm26hhx908g04f2h0fypy7lgfa0rvsz8d0wslgcsn"))))
+ (build-system trivial-build-system)
+ (inputs
+ `(("bats" ,bats) ;for test
+ ("awk" ,gawk)
+ ("bash" ,bash)
+ ("coreutils" ,coreutils)
+ ("diffutils" ,diffutils)
+ ("grep" ,grep)
+ ("ncurses" ,ncurses) ;tput
+ ("sed" ,sed)))
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ ;; copy source
+ (copy-recursively (assoc-ref %build-inputs "source") ".")
+ ;; patch-shebang phase
+ (setenv "PATH"
+ (string-append (assoc-ref %build-inputs "bash") "/bin"
+ ":" (assoc-ref %build-inputs "awk") "/bin"
+ ":" (assoc-ref %build-inputs "coreutils") "/bin"
+ ":" (assoc-ref %build-inputs "diffutils") "/bin"
+ ":" (assoc-ref %build-inputs "grep") "/bin"
+ ":" (assoc-ref %build-inputs "ncurses") "/bin"
+ ":" (assoc-ref %build-inputs "sed") "/bin"
+ ":" "/run/setuid-programs"
+ ":" (getenv "PATH")))
+ (substitute* "hosts"
+ (("#!/usr/bin/env bash")
+ (string-append "#!" (which "bash")
+ "\nPATH=" (getenv "PATH"))))
+ ;; check phase
+ (setenv "TERM" "linux") ;set to tty for test
+ (invoke (string-append (assoc-ref %build-inputs "bats") "/bin/bats")
+ "test")
+ ;; install phase
+ (install-file "hosts" (string-append %output "/bin"))
+ (let ((bash-completion
+ (string-append %output "/etc/bash_completion.d")))
+ (mkdir-p bash-completion)
+ (copy-file "etc/hosts-completion.bash"
+ (string-append bash-completion "/hosts")))
+ (let ((zsh-completion
+ (string-append %output "/share/zsh/site-functions")))
+ (mkdir-p zsh-completion)
+ (copy-file "etc/hosts-completion.zsh"
+ (string-append zsh-completion "/_hosts")))
+ (let ((doc (string-append %output "/share/doc/" ,name "-" ,version)))
+ (mkdir-p doc)
+ (install-file "LICENSE" doc)
+ (install-file "README.md" doc))
+ #t)))
+ (home-page "https://github.com/xwmx/hosts/")
+ (synopsis "Script for editing a foreign distro's @file{/etc/hosts} file")
+ (description "Hosts is a command line program for managing
+@file{/etc/hosts} entries. On Guix System, @file{/etc/hosts} is managed from
+the system configuration; hosts only works when using the Guix package manager
+on a foreign distro. @command{hosts} works with existing hosts files and
+entries, providing commands to add, remove, comment, and search.")
+ (license license:expat)))
diff --git a/gnu/packages/aidc.scm b/gnu/packages/aidc.scm
index 5648f5a9ec..944ea048bf 100644
--- a/gnu/packages/aidc.scm
+++ b/gnu/packages/aidc.scm
@@ -91,7 +91,7 @@ characters, and is highly robust.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dmtx/libdmtx.git")
+ (url "https://github.com/dmtx/libdmtx")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -163,7 +163,7 @@ Python as well as GUI widgets for GTK and Qt.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/nayuki/QR-Code-generator.git")
+ (url "https://github.com/nayuki/QR-Code-generator")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(patches (search-patches "qrcodegen-cpp-make-install.patch"))
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 90af1453eb..0da33a0156 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -155,7 +155,7 @@ line applications.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fplll/fplll.git")
+ (url "https://github.com/fplll/fplll")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -205,7 +205,7 @@ the real span of the lattice.")
;; Github instead.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fplll/fpylll.git")
+ (url "https://github.com/fplll/fpylll")
(commit (string-append version "dev"))))
(file-name (git-file-name name version))
(sha256
@@ -273,7 +273,7 @@ PARI is also available as a C library to allow for faster computations.")
(define-public gp2c
(package
(name "gp2c")
- (version "0.0.11pl3")
+ (version "0.0.11pl4")
(source (origin
(method url-fetch)
(uri (string-append
@@ -281,7 +281,7 @@ PARI is also available as a C library to allow for faster computations.")
version ".tar.gz"))
(sha256
(base32
- "0yymbrgyjw500hqgmkj5m4nmscd7c9rs9w2c96lxgrcyab8krhrm"))))
+ "1cnnh7diqc97q76q5pyhpbljbhc0sz8mlrbqgiwi0sjkgh8iqsj0"))))
(build-system gnu-build-system)
(native-inputs `(("perl" ,perl)))
(inputs `(("pari-gp" ,pari-gp)))
@@ -351,7 +351,7 @@ precision.")
(define-public giac
(package
(name "giac")
- (version "1.5.0-87")
+ (version "1.6.0-7")
(source
(origin
(method url-fetch)
@@ -363,7 +363,7 @@ precision.")
"~parisse/debian/dists/stable/main/source/"
"giac_" version ".tar.gz"))
(sha256
- (base32 "1d0h1yb7qvh9x7wwv9yrzmcp712f49w1iljkxp4y6g9pzsmg1mmv"))))
+ (base32 "1pvgp137zcl0rbhdn1j41xxfml7fp771a7x4ph8qrhhlx0hxzn3p"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((ice-9 ftw)
@@ -403,7 +403,7 @@ precision.")
(delete-file (string-append out "/bin/xcasnew"))
#t))))))
(inputs
- ;;; TODO: Add libnauty.
+;;; TODO: Add libnauty.
`(("fltk" ,fltk)
("glpk" ,glpk)
("gmp" ,gmp)
@@ -440,16 +440,17 @@ or text interfaces) or as a C++ library.")
(define-public flint
(package
(name "flint")
- (version "2.5.2")
+ (version "2.6.0")
(source (origin
(method url-fetch)
(uri (string-append
"http://flintlib.org/flint-"
version ".tar.gz"))
(sha256 (base32
- "11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
- (patches (search-patches "flint-ldconfig.patch"))))
+ "0h08a71kn8347zsqjamqnmrxjpsnnzpmhvxb6d2xmfrcs6nyv2ch"))))
(build-system gnu-build-system)
+ (inputs
+ `(("ntl" ,ntl)))
(propagated-inputs
`(("gmp" ,gmp)
("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
@@ -457,17 +458,24 @@ or text interfaces) or as a C++ library.")
`(#:parallel-tests? #f ; seems to be necessary on arm
#:phases
(modify-phases %standard-phases
+ (add-before 'configure 'newer-c++
+ (lambda _
+ (substitute* "configure"
+ (("-ansi") ""))
+ #t))
(replace 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(gmp (assoc-ref inputs "gmp"))
- (mpfr (assoc-ref inputs "mpfr")))
+ (mpfr (assoc-ref inputs "mpfr"))
+ (ntl (assoc-ref inputs "ntl")))
;; do not pass "--enable-fast-install", which makes the
;; homebrew configure process fail
(invoke "./configure"
(string-append "--prefix=" out)
(string-append "--with-gmp=" gmp)
- (string-append "--with-mpfr=" mpfr))
+ (string-append "--with-mpfr=" mpfr)
+ (string-append "--with-ntl=" ntl))
#t))))))
(synopsis "Fast library for number theory")
(description
@@ -487,16 +495,16 @@ fast arithmetic.")
(define-public arb
(package
(name "arb")
- (version "2.17.0")
+ (version "2.18.1")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fredrik-johansson/arb.git")
+ (url "https://github.com/fredrik-johansson/arb")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
- "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1"))))
+ "15fx3dcbzgwddw9p1nysmx0dbh058afv5m8cj5pdjkcmcl7kw7z9"))))
(build-system gnu-build-system)
(propagated-inputs
`(("flint" ,flint))) ; flint.h is included by arf.h
@@ -535,7 +543,7 @@ real and complex numbers, with automatic, rigorous error control.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fredrik-johansson/python-flint.git")
+ (url "https://github.com/fredrik-johansson/python-flint")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -728,7 +736,7 @@ syntax is similar to that of C, so basic usage is familiar. It also includes
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/extemporelang/kiss_fft.git")
+ (url "https://github.com/extemporelang/kiss_fft")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -834,7 +842,7 @@ cosine/ sine transforms or DCT/DST).")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/vkostyukov/la4j.git")
+ (url "https://github.com/vkostyukov/la4j")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -956,7 +964,7 @@ algorithms from the FORTRAN library MINPACK.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/symengine/symengine.git")
+ (url "https://github.com/symengine/symengine")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -1075,7 +1083,7 @@ features, and more.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/QuantStack/xtensor.git")
+ (url "https://github.com/QuantStack/xtensor")
(commit version)))
(sha256
(base32
@@ -1356,14 +1364,15 @@ algebra, such as the row echelon form.")
(file-name (git-file-name name version))
(sha256
(base32
- "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
+ "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))
+ (patches (search-patches "linbox-fix-pkgconfig.patch"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)
("pkg-config" ,pkg-config)))
- (inputs
+ (propagated-inputs
`(("fflas-ffpack" ,fflas-ffpack)))
(synopsis "C++ library for linear algebra over exact rings")
(description
diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index 9ee7d28687..0fb4330d3e 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -65,7 +65,7 @@
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/daym/android-make-stub.git")
+ (url "https://github.com/daym/android-make-stub")
(commit (string-append "v" version))))
(file-name (string-append "android-make-stub-"
version "-checkout"))
@@ -99,7 +99,7 @@ use their packages mostly unmodified in our Android NDK build system.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/google/googletest.git")
+ (url "https://github.com/google/googletest")
(commit (string-append "release-" version))))
(file-name (git-file-name name version))
(sha256
diff --git a/gnu/packages/animation.scm b/gnu/packages/animation.scm
index 0357ac1190..e041592dbd 100644
--- a/gnu/packages/animation.scm
+++ b/gnu/packages/animation.scm
@@ -201,7 +201,7 @@ contains the graphical user interface for synfig.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/LostMoho/Papagayo.git")
+ (url "https://github.com/LostMoho/Papagayo")
(commit commit)))
(file-name (git-file-name name version))
(sha256
diff --git a/gnu/packages/antivirus.scm b/gnu/packages/antivirus.scm
index 367ebe70dd..c7bf911ae7 100644
--- a/gnu/packages/antivirus.scm
+++ b/gnu/packages/antivirus.scm
@@ -44,14 +44,14 @@
(define-public clamav
(package
(name "clamav")
- (version "0.102.3")
+ (version "0.102.4")
(source (origin
(method url-fetch)
(uri (string-append "https://www.clamav.net/downloads/production/"
"clamav-" version ".tar.gz"))
(sha256
(base32
- "14q6vi178ih60yz4ja33b6181va1dcj8fyscnmxfx2crav250c7d"))
+ "06rrzyrhnr0rswryijpbbzywr6387rv8qjq8sb8cl3h2d1m45ggf"))
(modules '((guix build utils)))
(snippet
'(begin
diff --git a/gnu/packages/arcan.scm b/gnu/packages/arcan.scm
index e3f8b60aea..a84bf0d8dd 100644
--- a/gnu/packages/arcan.scm
+++ b/gnu/packages/arcan.scm
@@ -59,7 +59,7 @@
(method git-fetch)
(file-name (git-file-name name version))
(uri (git-reference
- (url "https://github.com/letoram/arcan.git")
+ (url "https://github.com/letoram/arcan")
(commit commit)))
(sha256
(base32 "1pd0avlzc2rig1hd37zbhc7r2s6fjzdhshfg9l9cfzibl7caclyw"))))
@@ -145,7 +145,7 @@
(method git-fetch)
(file-name "arcan-openal-0.5.4")
(uri (git-reference
- (url "https://github.com/letoram/openal.git")
+ (url "https://github.com/letoram/openal")
(commit "1c7302c580964fee9ee9e1d89ff56d24f934bdef")))
(sha256
(base32
@@ -195,7 +195,7 @@ engine programmable using Lua.")
(method git-fetch)
(file-name (git-file-name name version))
(uri (git-reference
- (url "https://github.com/letoram/xarcan.git")
+ (url "https://github.com/letoram/xarcan")
(commit commit)))
(sha256
(base32 "0zng7cs6733mnf0p6g5wv02981f2sf567n56csax6cmzb8fpamym"))))
diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm
index c9582bc596..6587dc5aa2 100644
--- a/gnu/packages/assembly.scm
+++ b/gnu/packages/assembly.scm
@@ -8,6 +8,7 @@
;;; Copyright © 2019 Andy Tai <atai@atai.org>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2020 Christopher Lemmer Webber <cwebber@dustycloud.org>
+;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -47,6 +48,7 @@
#:use-module (gnu packages texinfo)
#:use-module (gnu packages python)
#:use-module (gnu packages sphinx)
+ #:use-module (gnu packages shells)
#:use-module (gnu packages xml)
#:use-module ((guix utils)
#:select (%current-system)))
@@ -259,16 +261,16 @@ runtime")
(define-public rgbds
(package
(name "rgbds")
- (version "0.4.0")
+ (version "0.4.1")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/rednex/rgbds.git")
+ (url "https://github.com/rednex/rgbds")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "15680964nlsa83nqgxk7knxajn98lddz2hg6jnn8ffmnms5wdam7"))))
+ "05djzl3h18zg2z5p2a881wjbmgikzkhf67cgk00frhw4v05sq0lf"))))
(build-system gnu-build-system)
(arguments
`(#:phases
@@ -306,21 +308,21 @@ package for the Game Boy and Game Boy Color. It consists of:
(define-public wla-dx
(package
(name "wla-dx")
- (version "9.10")
+ (version "9.11")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/vhelin/wla-dx.git")
+ (url "https://github.com/vhelin/wla-dx")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "022isf7s9q5i0j4xj69zpp0lgw8p9n37sn7ii25v68r15zaahk2w"))))
+ "0i8pxvyaih79pqnyvqyqd9rwdid91pna76cap0k1n5zhg8xswf2f"))))
(build-system cmake-build-system)
(native-inputs
`(("sphinx" ,python-sphinx))) ; to generate man pages
(arguments
- `(#:tests? #f)) ; no tests
+ `(#:tests? #f)) ; no tests
(home-page "https://github.com/vhelin/wla-dx")
(synopsis "Assemblers for various processors")
(description "WLA DX is a set of tools to assemble assembly files to
@@ -371,3 +373,129 @@ It understands mnemonics and generates code for NMOS 6502s (such
as 6502A, 6504, 6507, 6510, 7501, 8500, 8501, 8502 ...),
CMOS 6502s (65C02 and Rockwell R65C02) and the 65816.")
(license license:gpl2)))
+
+(define-public armips
+ (package
+ (name "armips")
+ (version "0.11.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Kingcom/armips")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1c4dhjkvynqn9xm2vcvwzymk7yg8h25alnawkz4z1dnn1z1k3r9g"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key inputs #:allow-other-keys)
+ (invoke "./armipstests" "../source/Tests")))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (install-file "armips" (string-append (assoc-ref outputs "out")
+ "/bin"))
+ #t)))))
+ (home-page "https://github.com/Kingcom/armips")
+ (synopsis "Assembler for various ARM and MIPS platforms")
+ (description
+ "armips is an assembler with full support for the MIPS R3000, MIPS R4000,
+Allegrex and RSP instruction sets, partial support for the EmotionEngine
+instruction set, as well as complete support for the ARM7 and ARM9 instruction
+sets, both THUMB and ARM mode.")
+ (license license:expat)))
+
+(define-public intel-xed
+ (package
+ (name "intel-xed")
+ (version "11.2.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/intelxed/xed")
+ (commit version)))
+ (sha256 (base32 "1jffayski2gpd54vaska7fmiwnnia8v3cka4nfyzjgl8xsky9v2s"))
+ (file-name (git-file-name name version))
+ (patches (search-patches "intel-xed-fix-nondeterminism.patch"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("python-wrapper" ,python-wrapper)
+ ("tcsh" ,tcsh)
+ ;; As of the time of writing this comment, mbuild does not exist in the
+ ;; Python Package Index and seems to only be used by intel-xed, so we
+ ;; opt to include it here instead of packaging separately. Note also
+ ;; that the git repository contains no version tags, so we directly
+ ;; reference the "version" variable from setup.py instead.
+ ("mbuild"
+ ,(let ((name "mbuild")
+ (version "0.2496"))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/intelxed/mbuild.git")
+ (commit "5304b94361fccd830c0e2417535a866b79c1c297")))
+ (sha256
+ (base32
+ "0r3avc3035aklqxcnc14rlmmwpj3jp09vbcbwynhvvmcp8srl7dl"))
+ (file-name (git-file-name name version)))))))
+ (outputs '("out" "lib"))
+ (arguments
+ `(#:phases
+ ;; Upstream uses the custom Python build tool `mbuild', so we munge
+ ;; gnu-build-system to fit. The build process for this package is
+ ;; documented at https://intelxed.github.io/build-manual/.
+ (let* ((build-dir "build")
+ (kit-dir "kit"))
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((mbuild (assoc-ref inputs "mbuild")))
+ (setenv "PYTHONPATH" (string-append
+ (getenv "PYTHONPATH") ":" mbuild))
+ (invoke "./mfile.py"
+ (string-append "--build-dir=" build-dir)
+ (string-append "--install-dir=" kit-dir)
+ "examples"
+ "doc"
+ "install"))))
+ (replace 'check
+ (lambda _
+ ;; Skip broken test group `tests/tests-avx512pf'.
+ (invoke "tests/run-cmd.py"
+ (string-append "--build-dir=" kit-dir "/bin")
+ "--tests" "tests/tests-base"
+ "--tests" "tests/tests-avx512"
+ "--tests" "tests/tests-cet"
+ "--tests" "tests/tests-via"
+ "--tests" "tests/tests-syntax"
+ "--tests" "tests/tests-xop")))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (lib (assoc-ref outputs "lib")))
+ (copy-recursively (string-append kit-dir "/bin")
+ (string-append out "/bin"))
+ (copy-recursively (string-append kit-dir "/include")
+ (string-append lib "/include"))
+ (copy-recursively (string-append kit-dir "/lib")
+ (string-append lib "/lib"))
+ #t)))))))
+ (home-page "https://intelxed.github.io/")
+ (synopsis "Encoder and decoder for x86 (IA32 and Intel64) instructions")
+ (description "The Intel X86 Encoder Decoder (XED) is a software library and
+for encoding and decoding X86 (IA32 and Intel64) instructions. The decoder
+takes sequences of 1-15 bytes along with machine mode information and produces
+a data structure describing the opcode, operands, and flags. The encoder takes
+a similar data structure and produces a sequence of 1 to 15 bytes. Disassembly
+is essentially a printing pass on the data structure.
+
+The library and development files are under the @code{lib} output, with a
+family of command line utility wrappers in the default output. Each of the cli
+tools is named like @code{xed*}. Documentation for the cli tools is sparse, so
+this is a case where ``the code is the documentation.''")
+ (license license:asl2.0)))
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 5b4590945d..72368f12f1 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -159,7 +159,7 @@ programs for the manipulation and analysis of astronomical data.")
(define-public stellarium
(package
(name "stellarium")
- (version "0.20.1")
+ (version "0.20.2")
(source
(origin
(method url-fetch)
@@ -167,7 +167,7 @@ programs for the manipulation and analysis of astronomical data.")
"/releases/download/v" version
"/stellarium-" version ".tar.gz"))
(sha256
- (base32 "034jkrdaaamvbrkfwi3qcl6h8hwfnw2nvf7a82faj55rskcpnkhm"))))
+ (base32 "16symz212vjvhfabh39a68qf7d0rm574c6djlibj2qd1q9jgj3j0"))))
(build-system cmake-build-system)
(inputs
`(("qtbase" ,qtbase)
@@ -178,7 +178,7 @@ programs for the manipulation and analysis of astronomical data.")
("zlib" ,zlib)))
(native-inputs
`(("gettext" ,gettext-minimal) ; xgettext is used at compile time
- ("perl" ,perl) ; For pod2man
+ ("perl" ,perl) ; for pod2man
("qtbase" ,qtbase) ; Qt MOC is needed at compile time
("qttools" ,qttools)))
(arguments
@@ -191,7 +191,7 @@ programs for the manipulation and analysis of astronomical data.")
#:phases (modify-phases %standard-phases
(add-before 'check 'set-offscreen-display
(lambda _
- ;; make Qt render "offscreen", required for tests
+ ;; Make Qt render "offscreen", required for tests.
(setenv "QT_QPA_PLATFORM" "offscreen")
(setenv "HOME" "/tmp")
#t)))))
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 74ef7111c3..924fdd7f63 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -70,6 +70,7 @@
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gettext)
+ #:use-module (gnu packages gl)
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
#:use-module (gnu packages gnunet) ; libmicrohttpd
@@ -395,17 +396,17 @@ engineers, musicians, soundtrack editors and composers.")
(define-public audacity
(package
(name "audacity")
- (version "2.3.3")
+ (version "2.4.1")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/audacity/audacity.git")
+ (url "https://github.com/audacity/audacity")
(commit (string-append "Audacity-" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "0707fsnrl4vjalsi21w4blwgz024qhd0w8rdd5j5vpxf5lyk2rbk"))
+ "1xk0piv72d2xd3p7igr916fhcbrm76fhjr418k1rlqdzzg1hfljn"))
(patches (search-patches "audacity-build-with-system-portaudio.patch"))
(modules '((guix build utils)))
(snippet
@@ -718,7 +719,7 @@ tools (analyzer, mono/stereo tools, crossovers).")
;; Actually https://github.com/moddevices/caps-lv2.git, but it's
;; missing fixes for newer glibc, so using the origin of a pull
;; request regarding this issue:
- (url "https://github.com/jujudusud/caps-lv2.git")
+ (url "https://github.com/jujudusud/caps-lv2")
(commit "9c9478b7fbd8f9714f552ebe2a6866398b0babfb")))
(file-name (git-file-name name version))
(sha256
@@ -754,7 +755,7 @@ generators of mostly elementary and occasionally exotic nature.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ssj71/infamousPlugins.git")
+ (url "https://github.com/ssj71/infamousPlugins")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -793,7 +794,7 @@ envelope follower, distortion effects, tape effects and more.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/swh/ladspa.git")
+ (url "https://github.com/swh/ladspa")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -823,7 +824,7 @@ envelope follower, distortion effects, tape effects and more.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/swh/lv2.git")
+ (url "https://github.com/swh/lv2")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -861,6 +862,76 @@ flanger), ringmodulator, distortion, filters, pitchshift, oscillators,
emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.")
(license license:gpl3+)))
+(define-public tao
+ (package
+ (name "tao")
+ (version "1.0-beta-10May2006")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/taopm/Tao/"
+ "tao-" version "/"
+ "tao-" version ".tar.gz"))
+ (sha256
+ (base32
+ "156py3g6mmglldfd0j76bn7n242hdwf49diaprjpj7crp8vgf2pz"))
+ (patches
+ (search-patches "tao-add-missing-headers.patch"
+ "tao-fix-parser-types.patch"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (substitute* "configure"
+ (("SHELL=/bin/sh") ""))
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:configure-flags '("TAO_RELEASE=-beta")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-references
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* "user-scripts/tao.in"
+ (("taoparse")
+ (string-append (assoc-ref outputs "out") "/bin/taoparse"))
+ (("grep") (which "grep"))
+ (("sed -f \\$distdir/user-scripts/")
+ (string-append (which "sed") " -f $distdir/"))
+ (("distdir=.*")
+ (string-append "distdir="
+ (assoc-ref outputs "out") "/share/tao")))
+ #t))
+ (add-after 'install 'install-extra-files
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (share (string-append out "/share/tao/"))
+ (inc (string-append out "/include/tao/")))
+ (mkdir-p share)
+ (mkdir-p inc)
+ (install-file "user-scripts/error.parse" share)
+ (copy-recursively "examples" (string-append share "examples"))
+ (for-each (lambda (file) (install-file file inc))
+ (find-files "include" "\\.h"))
+ #t))))))
+ (inputs
+ `(("audiofile" ,audiofile)
+ ("libxi" ,libxi)
+ ("libxmu" ,libxmu)
+ ("mesa" ,mesa)
+ ("glut" ,freeglut)
+ ("flex" ,flex)
+ ("bison" ,bison)
+ ("sed" ,sed)
+ ("grep" ,grep)))
+ (home-page "http://taopm.sourceforge.net/")
+ (synopsis "Sound Synthesis with Physical Models")
+ (description "Tao is a software package for sound synthesis using physical
+models. It provides a virtual acoustic material constructed from masses and
+springs which can be used as the basis for building quite complex virtual
+musical instruments. Tao comes with a synthesis language for creating and
+playing instruments and a C++ API for those who would like to use it as an
+object library.")
+ (license license:gpl2+)))
+
(define-public csound
(package
(name "csound")
@@ -869,7 +940,7 @@ emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/csound/csound.git")
+ (url "https://github.com/csound/csound")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -1255,16 +1326,16 @@ follower.")
(define-public fluidsynth
(package
(name "fluidsynth")
- (version "2.1.3")
+ (version "2.1.4")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/FluidSynth/fluidsynth.git")
+ (url "https://github.com/FluidSynth/fluidsynth")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "0dv6jprz2bzasvk91x2rv2pqyyvxkc72s4r6vsqw723a3kqa5bhc"))))
+ "1r3khwyw57ybg5m4x0rvdzq7hgw2484sd52k6bm19akbw8yicfna"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no check target
@@ -1339,7 +1410,7 @@ PS, and DAB+.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/grame-cncm/faust.git")
+ (url "https://github.com/grame-cncm/faust")
(commit (string-append "v"
(string-map (lambda (c)
(if (char=? c #\.) #\- c))
@@ -1619,15 +1690,16 @@ especially for creating reverb effects. It supports impulse responses with 1,
(package
(name "jack")
(version "0.125.0")
- (source (origin
- (method url-fetch)
- (uri (string-append
- "http://jackaudio.org/downloads/jack-audio-connection-kit-"
- version
- ".tar.gz"))
- (sha256
- (base32
- "0i6l25dmfk2ji2lrakqq9icnwjxklgcjzzk65dmsff91z2zva5rm"))))
+ (source
+ (origin
+ (method url-fetch)
+ ;; jackaudio.org/downloads/jack-audio-connection-kit-0.125.0.tar.gz
+ ;; no longer exists (404). Use an unofficial mirror.
+ (uri (string-append "https://crux.ster.zone/downloads/"
+ "jack-audio-connection-kit/"
+ "jack-audio-connection-kit-" version ".tar.gz"))
+ (sha256
+ (base32 "0i6l25dmfk2ji2lrakqq9icnwjxklgcjzzk65dmsff91z2zva5rm"))))
(build-system gnu-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
@@ -1647,7 +1719,7 @@ especially for creating reverb effects. It supports impulse responses with 1,
("bdb" ,bdb)))
(native-inputs
`(("pkg-config" ,pkg-config)))
- (home-page "http://jackaudio.org/")
+ (home-page "https://jackaudio.org/")
(synopsis "JACK audio connection kit")
(description
"JACK is a low-latency audio server. It can connect a number of
@@ -2023,21 +2095,21 @@ significantly faster and have minimal dependencies.")
(version "1.18.0")
(source (origin
(method url-fetch)
- (uri (string-append "http://lv2plug.in/spec/lv2-"
+ (uri (string-append "https://lv2plug.in/spec/lv2-"
version ".tar.bz2"))
(sha256
(base32
"0gs7401xz23q9vajqr31aa2db8dvssgyh5zrvr4ipa6wig7yb8wh"))))
(build-system waf-build-system)
(arguments
- `(#:tests? #f ; no check target
+ `(#:tests? #f ; no check target
#:configure-flags '("--no-plugins")))
(inputs
;; Leaving off cairo and gtk+-2.0 which are needed for example plugins
`(("libsndfile" ,libsndfile)))
(native-inputs
`(("pkg-config" ,pkg-config)))
- (home-page "http://lv2plug.in/")
+ (home-page "https://lv2plug.in/")
(synopsis "LV2 audio plugin specification")
(description
"LV2 is an open specification for audio plugins and host applications.
@@ -2100,7 +2172,7 @@ software.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lvtk/lvtk.git")
+ (url "https://github.com/lvtk/lvtk")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -2302,7 +2374,7 @@ into various outputs and to start, stop and configure jackd")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/orouits/qjackrcd.git")
+ (url "https://github.com/orouits/qjackrcd")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -2337,7 +2409,7 @@ background file post-processing.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/supercollider/supercollider.git")
+ (url "https://github.com/supercollider/supercollider")
(commit (string-append "Version-" version))
;; for nova-simd, nova-tt, hidapi, TLSF, oscpack
(recursive? #t)))
@@ -2786,17 +2858,31 @@ stretching and pitch scaling of audio. This package contains the library.")
(define-public wavpack
(package
(name "wavpack")
- (version "5.3.0")
- (source (origin
- (method url-fetch)
- (uri (string-append "http://www.wavpack.com/"
- "wavpack-" version ".tar.xz"))
- (sha256
- (base32
- "01r351ggha9pdfk7p601dlxac4ka1q89lgnb6zqk00zf1fd3fi5l"))))
+ (version "5.3.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dbry/WavPack")
+ (commit "e4e8d191e8dd74cbdbeaef3232c16a7ef517e68d")))
+ (sha256
+ (base32 "1zj8svk6giy1abq3940sz32ygz7zldppxl47852zgn5wfm3l2spx"))
+ (file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
- '(#:configure-flags '("--disable-static")))
+ '(#:configure-flags
+ (list "--disable-static")
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'bootstrap
+ ;; Running ./autogen.sh would cause premature configuration.
+ (lambda _
+ (invoke "autoreconf" "-vif")
+ #t)))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)))
(home-page "http://www.wavpack.com/")
(synopsis "Hybrid lossless audio codec")
(description
@@ -3084,7 +3170,7 @@ synthesizer written in C++.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Themaister/RSound.git")
+ (url "https://github.com/Themaister/RSound")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3123,7 +3209,7 @@ with a much different focus than most other audio daemons.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/johnhldavis/xjackfreak.git")
+ (url "https://github.com/johnhldavis/xjackfreak")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3203,7 +3289,7 @@ engine.")
(define-public zita-resampler
(package
(name "zita-resampler")
- (version "1.3.0")
+ (version "1.6.2")
(source (origin
(method url-fetch)
(uri (string-append
@@ -3213,26 +3299,28 @@ engine.")
(snippet
;; Don't optimize for a specific processor architecture.
'(begin
- (substitute* '("apps/Makefile" "libs/Makefile")
+ (substitute* '("apps/Makefile" "source/Makefile")
(("^CXXFLAGS \\+= -march=native") ""))
#t))
(modules '((guix build utils)))
(sha256
(base32
- "0r9ary5sc3y8vba5pad581ha7mgsrlyai83w7w4x2fmhfy64q0wq"))))
+ "1my5k2dh2dkvjp6xjnf9qy6i7s28z13kw1n9pwa4a2cpwbzawfr3"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
- #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+ #:make-flags
+ (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+ (string-append "SUFFIX="))
#:phases
(modify-phases %standard-phases
(add-after
'unpack 'patch-makefile-and-enter-directory
(lambda _
- (substitute* "libs/Makefile"
+ (substitute* "source/Makefile"
(("ldconfig") "true")
(("^LIBDIR =.*") "LIBDIR = lib\n"))
- (chdir "libs")
+ (chdir "source")
#t))
(add-after
'install 'install-symlink
@@ -3254,7 +3342,7 @@ provide high-quality sample rate conversion.")
(define-public zita-alsa-pcmi
(package
(name "zita-alsa-pcmi")
- (version "0.2.0")
+ (version "0.3.2")
(source (origin
(method url-fetch)
(uri (string-append
@@ -3263,19 +3351,21 @@ provide high-quality sample rate conversion.")
version ".tar.bz2"))
(sha256
(base32
- "1rgv332g82rrrlm4vdam6p2pyrisxbi7b3izfaa0pcjglafsy7j9"))))
+ "12d7vdg74yh21w69qi0wg57iz4876j94qbiq09bvscih6xz9y78s"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
- #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+ #:make-flags
+ (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+ (string-append "SUFFIX="))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-makefile-and-enter-directory
(lambda _
- (substitute* "libs/Makefile"
+ (substitute* "source/Makefile"
(("ldconfig") "true")
(("^LIBDIR =.*") "LIBDIR = lib\n"))
- (chdir "libs")
+ (chdir "source")
#t))
(add-after 'install 'install-symlink
(lambda _
@@ -3304,7 +3394,7 @@ point audio data.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/svend/cuetools.git")
+ (url "https://github.com/svend/cuetools")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -3354,7 +3444,7 @@ use them split WAVE data into multiple files.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/foo86/dcadec.git")
+ (url "https://github.com/foo86/dcadec")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3432,7 +3522,7 @@ loudness of audio and video files to the same level.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/irungentoo/filter_audio.git")
+ (url "https://github.com/irungentoo/filter_audio")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -3541,7 +3631,7 @@ mixers.")
;; bootstrapped build system.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Arkq/bluez-alsa.git")
+ (url "https://github.com/Arkq/bluez-alsa")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3586,14 +3676,14 @@ on the ALSA software PCM plugin.")
(define-public snd
(package
(name "snd")
- (version "20.4")
+ (version "20.5")
(source (origin
(method url-fetch)
(uri (string-append "ftp://ccrma-ftp.stanford.edu/pub/Lisp/"
"snd-" version ".tar.gz"))
(sha256
(base32
- "0irdizlng2s3akmxdbfxcbd93bbjz9543nh7fisszim6v0ks59d9"))))
+ "1frg64q2d8cia6v7jia7kahzx0apwdl0z252mzlbwqdz5960nv90"))))
(build-system glib-or-gtk-build-system)
(arguments
`(#:tests? #f ; no tests
@@ -3650,7 +3740,7 @@ the Snd sources), Ruby, or Forth.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lucianodato/noise-repellent.git")
+ (url "https://github.com/lucianodato/noise-repellent")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -3695,7 +3785,7 @@ the following features:
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dpayne/cli-visualizer.git")
+ (url "https://github.com/dpayne/cli-visualizer")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3740,7 +3830,7 @@ representations.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/karlstav/cava.git")
+ (url "https://github.com/karlstav/cava")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -3893,7 +3983,7 @@ library.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/FNA-XNA/FAudio.git")
+ (url "https://github.com/FNA-XNA/FAudio")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -3998,6 +4088,45 @@ stream to one or more IceCast and/or ShoutCast servers.")
(home-page "https://x42.github.io/libltc/")
(license license:lgpl3+)))
+(define-public ttaenc
+ (package
+ (name "ttaenc")
+ (version "3.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/tta/"
+ "tta/ttaenc-src"
+ "/ttaenc-" version "-src.tgz"))
+ (sha256
+ (base32
+ "1iixpr4b89g9g1hwn8ak8k8iflcww3r5f09a117qdidc2nqcijdj"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no tests
+ #:make-flags
+ (list (string-append "CC=" ,(cc-for-target))
+ (string-append "INSDIR=" (assoc-ref %outputs "out") "/bin"))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; no configure
+ (add-before 'install 'make-bindir
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out")))
+ (mkdir-p (string-append out "/bin"))
+ #t))))))
+ (synopsis "TTA lossless audio encoder")
+ (description
+ "TTA performs lossless compression on multichannel 8,16 and 24 bits
+data of the Wav audio files. Being lossless means that no data-
+quality is lost in the compression - when uncompressed, the data will
+be identical to the original. The compression ratios of TTA depend on
+the type of music file being compressed, but the compression size
+will generally range between 30% - 70% of the original. TTA format
+supports both of ID3v1/v2 and APEv2 tags.")
+ (home-page "http://tausoft.org/")
+ (license license:gpl2+)))
+
(define-public redkite
(package
(name "redkite")
@@ -4030,18 +4159,18 @@ as is the case with audio plugins.")
(define-public carla
(package
(name "carla")
- (version "2.0.0")
+ (version "2.1.1")
(source
(origin
(method git-fetch)
(uri
(git-reference
- (url "https://github.com/falkTX/Carla.git")
+ (url "https://github.com/falkTX/Carla")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "0fqgncqlr86n38yy7pa118mswfacmfczj7w9xx6c6k0jav3wk29k"))))
+ "0c3y4a6cgi4bv1mg57i3qn5ia6pqjqlaylvkapj6bmpsw71ig22g"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
@@ -4072,6 +4201,7 @@ as is the case with audio plugins.")
("file" ,file)
("liblo" ,liblo)
("libsndfile" ,libsndfile)
+ ("gtk2" ,gtk+-2) ;needed for bridging GTK2 plugins in GTK3 hosts
("gtk+" ,gtk+)
("python-pyliblo" ,python-pyliblo)
("python-pyqt" ,python-pyqt)
@@ -4143,7 +4273,7 @@ in the package.")
(define-public libaudec
(package
(name "libaudec")
- (version "0.2")
+ (version "0.2.2")
(source
(origin
(method git-fetch)
@@ -4153,7 +4283,7 @@ in the package.")
(file-name (git-file-name name version))
(sha256
(base32
- "0lfydvs92b0hr72z71ci3yi356rjzi162pgms8dphgg18bz8dazv"))))
+ "04mpmfmqc43asw0m3zxhb6jj4qms7x4jw7mx4xb1d3lh16xllniz"))))
(build-system meson-build-system)
(arguments
`(#:configure-flags `("-Denable_tests=true -Denable_ffmpeg=true")))
@@ -4287,7 +4417,7 @@ minimum.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/drowe67/codec2.git")
+ (url "https://github.com/drowe67/codec2")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -4320,7 +4450,7 @@ digital radio.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Ableton/link.git")
+ (url "https://github.com/Ableton/link")
(commit (string-append "Link-" version))))
(file-name (git-file-name name version))
(sha256
diff --git a/gnu/packages/authentication.scm b/gnu/packages/authentication.scm
index d995ef7e85..b3ff912c8f 100644
--- a/gnu/packages/authentication.scm
+++ b/gnu/packages/authentication.scm
@@ -101,7 +101,7 @@ and the time-based @dfn{TOTP} algorithm (RFC6238).")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Yubico/yubico-pam.git")
+ (url "https://github.com/Yubico/yubico-pam")
(commit commit)))
(file-name (git-file-name name version))
(sha256
diff --git a/gnu/packages/avr.scm b/gnu/packages/avr.scm
index f8884bb6cb..76af6fdef1 100644
--- a/gnu/packages/avr.scm
+++ b/gnu/packages/avr.scm
@@ -176,7 +176,7 @@ C++.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ryansuchocki/microscheme.git")
+ (url "https://github.com/ryansuchocki/microscheme")
(commit (string-append "v" version))))
(sha256
(base32 "1r3ng4pw1s9yy1h5rafra1rq19d3vmb5pzbpcz1913wz22qdd976"))
diff --git a/gnu/packages/axoloti.scm b/gnu/packages/axoloti.scm
index 94d3d818c5..ba49a9d0f0 100644
--- a/gnu/packages/axoloti.scm
+++ b/gnu/packages/axoloti.scm
@@ -71,7 +71,7 @@
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/axoloti/axoloti.git")
+ (url "https://github.com/axoloti/axoloti")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -367,7 +367,7 @@ patcher application.")))
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/axoloti/axoloti.git")
+ (url "https://github.com/axoloti/axoloti")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -607,7 +607,7 @@ patcher application.")))
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/JohannesTaelman/elfloader.git")
+ (url "https://github.com/JohannesTaelman/elfloader")
(commit commit)))
(file-name (git-file-name "elfloader" commit))
(sha256
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 74acd791ac..fb6d000170 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2015, 2020 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -55,6 +55,7 @@
#:use-module (gnu packages dbm)
#:use-module (gnu packages dejagnu)
#:use-module (gnu packages ftp)
+ #:use-module (gnu packages gettext)
#:use-module (gnu packages glib)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages golang)
@@ -80,7 +81,7 @@
(define-public duplicity
(package
(name "duplicity")
- (version "0.7.19")
+ (version "0.8.14")
(source
(origin
(method url-fetch)
@@ -89,32 +90,36 @@
"-series/" version "/+download/duplicity-"
version ".tar.gz"))
(sha256
- (base32 "0ag9dknslxlasslwfjhqgcqbkb1mvzzx93ry7lch2lfzcdd91am6"))))
+ (base32 "1af7rppsd8kj66xhbc04x1di3rpncrz0prxq1z7npg11c769vb1x"))))
(build-system python-build-system)
(native-inputs
- `(("util-linux" ,util-linux) ; setsid command, for the tests
+ `(("gettext" ,gnu-gettext) ; for msgfmt
+ ("util-linux" ,util-linux) ; setsid command, for the tests
("par2cmdline" ,par2cmdline)
- ("python-pexpect" ,python2-pexpect)
- ("python-fasteners" ,python2-fasteners)
+ ("python-fasteners" ,python-fasteners)
+ ("python-future" ,python-future) ; for tests
+ ("python-pexpect" ,python-pexpect)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-runner" ,python-pytest-runner)
+ ("python-setuptools-scm" ,python-setuptools-scm)
("tzdata" ,tzdata-for-tests)
- ("mock" ,python2-mock)))
+ ("mock" ,python-mock)))
(propagated-inputs
- `(("lockfile" ,python2-lockfile)
- ("urllib3" ,python2-urllib3)))
+ `(("lockfile" ,python-lockfile)
+ ("urllib3" ,python-urllib3)))
(inputs
- `(("librsync" ,librsync-0.9)
+ `(("librsync" ,librsync)
("lftp" ,lftp)
("gnupg" ,gnupg) ; gpg executable needed
("util-linux" ,util-linux))) ; for setsid
(arguments
- `(#:python ,python-2 ; setup assumes Python 2
- #:test-target "test"
+ `(#:test-target "test"
#:phases
(modify-phases %standard-phases
(add-before 'build 'use-store-file-names
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "duplicity/gpginterface.py"
- (("self.call = 'gpg'")
+ (("self.call = u'gpg'")
(string-append "self.call = '" (assoc-ref inputs "gnupg") "/bin/gpg'")))
(substitute* '("testing/functional/__init__.py"
@@ -146,7 +151,7 @@ spying and/or modification by the server.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Parchive/par2cmdline.git")
+ (url "https://github.com/Parchive/par2cmdline")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -310,7 +315,7 @@ random access nor for in-place modification.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/miekg/rdup.git")
+ (url "https://github.com/miekg/rdup")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -404,23 +409,24 @@ errors.")
(define-public rdiff-backup
(package
(name "rdiff-backup")
- (version "1.2.8")
+ (version "2.0.3")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://savannah/rdiff-backup/rdiff-backup-"
- version ".tar.gz"))
+ (uri (string-append "https://github.com/rdiff-backup/rdiff-backup/releases/"
+ "download/v" version "/rdiff-backup-" version ".tar.gz"))
(sha256
(base32
- "1nwmmh816f96h0ff1jxk95ad38ilbhbdl5dgibx1d4cl81dsi48d"))))
+ "1qfmvwwb942srhg6gw77ncy4z5z54b4wfz8bpd5bpml8hp1d5qh4"))))
(build-system python-build-system)
+ (native-inputs
+ `(("python-setuptools-scm" ,python-setuptools-scm)))
(inputs
- `(("python" ,python-2)
- ("librsync" ,librsync-0.9)))
+ `(("python" ,python)
+ ("librsync" ,librsync)))
(arguments
- `(#:python ,python-2
- #:tests? #f))
- (home-page "https://www.nongnu.org/rdiff-backup/")
+ `(#:tests? #f)) ; Tests require root/sudo
+ (home-page "https://rdiff-backup.net/")
(synopsis "Local/remote mirroring+incremental backup")
(description
"Rdiff-backup backs up one directory to another, possibly over a network.
@@ -999,7 +1005,7 @@ precious backup space.
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/zbackup/zbackup.git")
+ (url "https://github.com/zbackup/zbackup")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -1053,12 +1059,12 @@ is format-agnostic, so you can feed virtually any files to it.")
("util-linux" ,util-linux "lib")
("e2fsprogs" ,e2fsprogs)))
(home-page "https://dump.sourceforge.io/")
- (synopsis "Ext2/3/4 filesystem dump/restore utilities")
- (description "Dump examines files in a filesystem, determines which ones
+ (synopsis "Ext2/3/4 file system dump/restore utilities")
+ (description "Dump examines files in a file system, determines which ones
need to be backed up, and copies those files to a specified disk, tape or
other storage medium. Subsequent incremental backups can then be layered on
top of the full backup. The restore command performs the inverse function of
-dump; it can restore a full backup of a filesystem. Single files and
+dump; it can restore a full backup of a file system. Single files and
directory subtrees may also be restored from full or partial backups in
interractive mode.")
(license license:bsd-3)))
@@ -1066,14 +1072,16 @@ interractive mode.")
(define-public burp
(package
(name "burp")
- (version "2.3.28")
- (source (origin
- (method url-fetch)
- (uri (string-append "mirror://sourceforge/burp/burp-" version
- "/burp-" version ".tar.bz2"))
- (sha256
- (base32
- "18f8cjsb87skabvz4cl5pdln35qmim7x686js1xzpld6wyl9kv2k"))))
+ (version "2.3.30")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/grke/burp")
+ (commit version)))
+ (sha256
+ (base32 "1f9i5d415psbr03fqd47p162qy25sypra1w8w16ym6jk1pvdjsgx"))
+ (file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
`(#:phases
@@ -1086,12 +1094,15 @@ interractive mode.")
(string-append prefix " 3600" suffix "\n")))
#t)))))
(inputs
- `(("librsync" ,librsync)
+ `(("acl" ,acl)
+ ("librsync" ,librsync)
("openssl" ,openssl)
("uthash" ,uthash)
("zlib" ,zlib)))
(native-inputs
- `(("check" ,check)
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("check" ,check)
("pkg-config" ,pkg-config)))
(home-page "https://burp.grke.org")
(synopsis "Differential backup and restore")
diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index 71888976e6..7116708743 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -342,6 +342,7 @@ used to apply commands with arbitrarily long arguments.")
(list (string-append "XFAIL_TESTS=tests/misc/env-S.pl"
" tests/misc/kill.sh"
" tests/misc/nice.sh"
+ " tests/misc/pwd-long.sh"
" tests/split/fail.sh"
" test-fdutimensat"
" test-futimens"
diff --git a/gnu/packages/bash.scm b/gnu/packages/bash.scm
index 3ba8a13e40..47ca625d9a 100644
--- a/gnu/packages/bash.scm
+++ b/gnu/packages/bash.scm
@@ -3,7 +3,7 @@
;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;;
;;; This file is part of GNU Guix.
@@ -24,11 +24,13 @@
(define-module (gnu packages bash)
#:use-module (guix licenses)
#:use-module (gnu packages)
+ #:use-module (gnu packages base)
#:use-module (gnu packages bootstrap)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages readline)
#:use-module (gnu packages bison)
#:use-module (gnu packages linux)
+ #:use-module (gnu packages guile)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
@@ -37,6 +39,7 @@
#:use-module (guix monads)
#:use-module (guix store)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system trivial)
#:autoload (guix gnupg) (gnupg-verify*)
#:autoload (guix base32) (bytevector->nix-base32-string)
@@ -327,7 +330,7 @@ completion for many common commands.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/illusori/bash-tap.git")
+ (url "https://github.com/illusori/bash-tap")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -362,3 +365,53 @@ for Bash shell scripts and functions. Along with the Test::More-style testing
helpers it provides helper functions for mocking commands and in-process output
capturing.")
(license expat)))
+
+(define-public bats
+ (package
+ (name "bats")
+ (version "1.2.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/bats-core/bats-core")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0f59zh4d4pa1a7ybs5zl6h0csbqqv11lbnq0jl1dgwm1s6p49bsq"))))
+ (inputs
+ `(("bash" ,bash)
+ ("coreutils" ,coreutils)
+ ("guile" ,guile-3.0) ;for wrap-script
+ ("grep" ,grep)))
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ (copy-recursively (assoc-ref %build-inputs "source") ".")
+ (setenv "PATH"
+ (string-append (assoc-ref %build-inputs "bash") "/bin"
+ ":" (assoc-ref %build-inputs "coreutils") "/bin"
+ ":" (assoc-ref %build-inputs "grep") "/bin"
+ ":" (assoc-ref %build-inputs "guile") "/bin"
+ ":" (getenv "PATH")))
+ (for-each (lambda (file) (patch-shebang file)) (find-files "."))
+ (substitute* "bin/bats"
+ (("export BATS_ROOT" line)
+ (string-append "BATS_ROOT=\"${BATS_ROOT:-" %output "/libexec/bats-core}\"\n"
+ line)))
+ ;; Install phase
+ (invoke "./install.sh" %output)
+ (wrap-script (string-append %output "/bin/bats")
+ (list "PATH" 'prefix (string-split (getenv "PATH")
+ #\:))))))
+ (build-system trivial-build-system)
+ (home-page "https://github.com/bats-core/bats-core/")
+ (synopsis "Bash Automated Testing System")
+ (description
+ "Bats is a @acronym{TAP, Test Anything Protocol}-compliant testing
+framework for Bash. It provides a simple way to verify that the UNIX programs
+you write behave as expected. Bats is most useful when testing software written
+in Bash, but you can use it to test any UNIX program.")
+ (license expat)))
diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index 0ac1833487..5bd16ad7be 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -46,14 +46,14 @@
(define-public fio
(package
(name "fio")
- (version "3.20")
+ (version "3.21")
(source (origin
(method url-fetch)
(uri (string-append "https://brick.kernel.dk/snaps/"
"fio-" version ".tar.bz2"))
(sha256
(base32
- "1mwqafn81a9pxy2kw9rl4p3r2brhg2ckwrcwzy0q4gffxgn3k9c7"))))
+ "0np1scxqfpd6fcnnnfyn8xdsh6lc5pyq3vk1jm1zk7sa58fvccd4"))))
(build-system gnu-build-system)
(arguments
'(#:test-target "test"
@@ -131,7 +131,7 @@ is to write a job file matching the I/O load one wants to simulate.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/intel/mpi-benchmarks.git")
+ (url "https://github.com/intel/mpi-benchmarks")
(commit (string-append "IMB-v" version))))
(file-name (git-file-name name version))
(sha256
@@ -217,7 +217,7 @@ This can give a much better understanding of the command's performance.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/google/benchmark.git")
+ (url "https://github.com/google/benchmark")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 002f4a0edb..b191c8b4ae 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1587,7 +1587,7 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
("r-reshape2" ,r-reshape2)))
(native-inputs
`(("r-knitr" ,r-knitr)))
- (home-page "http://github.com/jdstorey/qvalue")
+ (home-page "https://github.com/StoreyLab/qvalue")
(synopsis "Q-value estimation for false discovery rate control")
(description
"This package takes a list of p-values resulting from the simultaneous
@@ -2934,7 +2934,7 @@ qPCR data, but could be used with other types as well.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/cole-trapnell-lab/monocle3.git")
+ (url "https://github.com/cole-trapnell-lab/monocle3")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -5781,14 +5781,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "2.2.2")
+ (version "2.2.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "1wgilpaw70dwg0zilx5i1pmi4j8wri6wi2ha1d3bapfhlwc6igml"))))
+ "0yznfqgp5cbz68n3rrfvm752267da16kl538zdrb1g1aw9zdfqc6"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -6374,14 +6374,14 @@ delete entire rows with missing data.")
(define-public r-depecher
(package
(name "r-depecher")
- (version "1.4.0")
+ (version "1.4.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DepecheR" version))
(sha256
(base32
- "0nmx04qybzf6nhfngmdxwpbbz9x32v34mbnpg8jq7a2cgchzsj9s"))))
+ "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v"))))
(properties `((upstream-name . "DepecheR")))
(build-system r-build-system)
(propagated-inputs
@@ -6509,7 +6509,7 @@ accessibility data.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/cole-trapnell-lab/cicero-release.git")
+ (url "https://github.com/cole-trapnell-lab/cicero-release")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -6530,7 +6530,7 @@ accessibility data.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/aertslab/cisTopic.git")
+ (url "https://github.com/aertslab/cisTopic")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -7048,14 +7048,14 @@ arrays based on fast wavelet-based functional models.")
(define-public r-variancepartition
(package
(name "r-variancepartition")
- (version "1.18.0")
+ (version "1.18.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "variancePartition" version))
(sha256
(base32
- "1rn655qq7dshbk1dd41n7y2hfz8498jxd2j4rk7p8hrikd3s32dm"))))
+ "19bhkb8vd44m3nkznw075fx3y2p3a1bsazbhcfiqw9n4190k9bgv"))))
(properties
`((upstream-name . "variancePartition")))
(build-system r-build-system)
@@ -7187,21 +7187,20 @@ using whole genome sequencing data.")
(define-public r-activepathways
(package
(name "r-activepathways")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ActivePathways" version))
(sha256
(base32
- "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20"))))
+ "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
(properties
`((upstream-name . "ActivePathways")))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
- ("r-ggplot2" ,r-ggplot2)
- ("r-metap" ,r-metap)))
+ ("r-ggplot2" ,r-ggplot2)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/ActivePathways/")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 957c88d0c6..681919df3d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -189,7 +189,7 @@ structure of the predicted RNA.")
(method git-fetch)
;; BamM is not available on pypi.
(uri (git-reference
- (url "https://github.com/Ecogenomics/BamM.git")
+ (url "https://github.com/Ecogenomics/BamM")
(commit version)
(recursive? #t)))
(file-name (git-file-name name version))
@@ -283,7 +283,7 @@ instance, it implements several methods to assess contig-wise read coverage.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/pezmaster31/bamtools.git")
+ (url "https://github.com/pezmaster31/bamtools")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -361,7 +361,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/bedops/bedops.git")
+ (url "https://github.com/bedops/bedops")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -484,7 +484,7 @@ BED, GFF/GTF, VCF.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/PacificBiosciences/pbbam.git")
+ (url "https://github.com/PacificBiosciences/pbbam")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -540,7 +540,7 @@ Non-PacBio BAMs will cause exceptions to be thrown.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/PacificBiosciences/blasr_libcpp.git")
+ (url "https://github.com/PacificBiosciences/blasr_libcpp")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -602,7 +602,7 @@ hdf and alignment.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/PacificBiosciences/blasr.git")
+ (url "https://github.com/PacificBiosciences/blasr")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -693,7 +693,7 @@ provides the Ribotaper pipeline.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ratschlab/RiboDiff.git")
+ (url "https://github.com/ratschlab/RiboDiff")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -737,7 +737,7 @@ independently with transcriptional regulation.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lh3/bioawk.git")
+ (url "https://github.com/lh3/bioawk")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -900,7 +900,7 @@ Python.")
;; Use GitHub as source because PyPI distribution does not contain
;; test data: https://github.com/biocore/biom-format/issues/693
(uri (git-reference
- (url "https://github.com/biocore/biom-format.git")
+ (url "https://github.com/biocore/biom-format")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -1327,15 +1327,15 @@ package provides command line tools using the Bio++ library.")
(define-public blast+
(package
(name "blast+")
- (version "2.7.1")
+ (version "2.10.1")
(source (origin
(method url-fetch)
(uri (string-append
- "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
+ "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
version "/ncbi-blast-" version "+-src.tar.gz"))
(sha256
(base32
- "1jlq0afxxgczpp35k6mxh8mn4jzq7vqcnaixk166sfj10wq8v9qh"))
+ "11kvrrl0mcwww6530r55hccpg3x3msmhr3051fwnjbq8rzg2j1qi"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -1567,7 +1567,7 @@ errors at the end of reads.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/BenLangmead/bowtie2.git")
+ (url "https://github.com/BenLangmead/bowtie2")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -1783,7 +1783,7 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/pkerpedjiev/bwa-pssm.git")
+ (url "https://github.com/pkerpedjiev/bwa-pssm")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -1813,7 +1813,7 @@ well as many of the command line options.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/brentp/bwa-meth.git")
+ (url "https://github.com/brentp/bwa-meth")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -1887,7 +1887,7 @@ multiple sequence alignments.")
(method git-fetch)
;; Test data is missing on PyPi.
(uri (git-reference
- (url "https://github.com/pysam-developers/pysam.git")
+ (url "https://github.com/pysam-developers/pysam")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -2036,7 +2036,7 @@ high-throughput sequencing data – with an emphasis on simplicity.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/mhammell-laboratory/tetoolkit.git")
+ (url "https://github.com/mhammell-laboratory/tetoolkit")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -2153,7 +2153,7 @@ databases.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/YeoLab/clipper.git")
+ (url "https://github.com/YeoLab/clipper")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -2412,7 +2412,7 @@ interval trees with associated meta-data. It is primarily used by the
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/deeptools/deepTools.git")
+ (url "https://github.com/deeptools/deepTools")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -2480,7 +2480,7 @@ other types of unwanted sequence from high-throughput sequencing reads.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dpryan79/libBigWig.git")
+ (url "https://github.com/dpryan79/libBigWig")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -2560,7 +2560,7 @@ accessing bigWig files.")
(method git-fetch)
;; Source from GitHub so that tests are included.
(uri (git-reference
- (url "https://github.com/jeetsukumaran/DendroPy.git")
+ (url "https://github.com/jeetsukumaran/DendroPy")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -2618,7 +2618,7 @@ with Python.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dellytools/delly.git")
+ (url "https://github.com/dellytools/delly")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -2665,7 +2665,7 @@ accurately delineate genomic rearrangements throughout the genome.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/bbuchfink/diamond.git")
+ (url "https://github.com/bbuchfink/diamond")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -2700,7 +2700,7 @@ data and settings.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/maaskola/discrover.git")
+ (url "https://github.com/maaskola/discrover")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -2773,7 +2773,7 @@ of nucleic acid binding proteins.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/DReichLab/EIG.git")
+ (url "https://github.com/DReichLab/EIG")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3021,7 +3021,7 @@ dynamic programming or a variety of heuristics.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/adarob/eXpress.git")
+ (url "https://github.com/adarob/eXpress")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -3072,7 +3072,7 @@ ChIP-Seq, and analysis of metagenomic data.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dparks1134/ExpressBetaDiversity.git")
+ (url "https://github.com/dparks1134/ExpressBetaDiversity")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3199,7 +3199,7 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/seqan/flexbar.git")
+ (url "https://github.com/seqan/flexbar")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3342,7 +3342,7 @@ genes in incomplete assemblies or complete genomes.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ctSkennerton/fxtract.git")
+ (url "https://github.com/ctSkennerton/fxtract")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -3378,7 +3378,7 @@ genes in incomplete assemblies or complete genomes.")
,(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ctSkennerton/util.git")
+ (url "https://github.com/ctSkennerton/util")
(commit util-commit)))
(file-name (string-append
"ctstennerton-util-" util-commit "-checkout"))
@@ -3405,7 +3405,7 @@ comment or quality sections.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/xiangzhou/GEMMA.git")
+ (url "https://github.com/xiangzhou/GEMMA")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -3465,7 +3465,7 @@ association studies (GWAS).")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/nboley/grit.git")
+ (url "https://github.com/nboley/grit")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -3690,7 +3690,7 @@ from high-throughput sequencing assays.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/samtools/htsjdk.git")
+ (url "https://github.com/samtools/htsjdk")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -3740,7 +3740,7 @@ manipulating HTS data.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/samtools/htsjdk.git")
+ (url "https://github.com/samtools/htsjdk")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -3784,7 +3784,7 @@ manipulating HTS data.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/samtools/htsjdk.git")
+ (url "https://github.com/samtools/htsjdk")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -3812,7 +3812,7 @@ manipulating HTS data.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/broadinstitute/picard.git")
+ (url "https://github.com/broadinstitute/picard")
(commit version)))
(file-name (string-append "java-picard-" version "-checkout"))
(sha256
@@ -3891,7 +3891,7 @@ VCF.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/broadinstitute/picard.git")
+ (url "https://github.com/broadinstitute/picard")
(commit version)))
(file-name (string-append "java-picard-" version "-checkout"))
(sha256
@@ -3981,7 +3981,7 @@ VCF.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/broadinstitute/picard.git")
+ (url "https://github.com/broadinstitute/picard")
(commit version)))
(file-name (string-append "java-picard-" version "-checkout"))
(sha256
@@ -4178,7 +4178,7 @@ The main functions of FastQC are:
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/OpenGene/fastp.git")
+ (url "https://github.com/OpenGene/fastp")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -4258,7 +4258,7 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/nboley/idr.git")
+ (url "https://github.com/nboley/idr")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -4349,7 +4349,7 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dib-lab/khmer.git")
+ (url "https://github.com/dib-lab/khmer")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -4457,7 +4457,7 @@ experiments.")
;; The PyPi tarball does not contain tests.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/taoliu/MACS.git")
+ (url "https://github.com/taoliu/MACS")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -4580,7 +4580,7 @@ sequences).")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/marbl/mash.git")
+ (url "https://github.com/marbl/mash")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -4719,7 +4719,7 @@ probabilistic distances of genome abundance and tetranucleotide frequency.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ctSkennerton/minced.git")
+ (url "https://github.com/ctSkennerton/minced")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -4861,7 +4861,7 @@ program for nucleotide and protein sequences.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/tjunier/newick_utils.git")
+ (url "https://github.com/tjunier/newick_utils")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -4999,7 +4999,7 @@ the phenotype as it models the data.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/PacificBiosciences/cDNA_primer.git")
+ (url "https://github.com/PacificBiosciences/cDNA_primer")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -5220,7 +5220,7 @@ different command-line tools:
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/hyattpd/Prodigal.git")
+ (url "https://github.com/hyattpd/Prodigal")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -5369,7 +5369,7 @@ extremely diverse sets of genomes.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/stamatak/standard-RAxML.git")
+ (url "https://github.com/stamatak/standard-RAxML")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -5410,7 +5410,7 @@ phylogenies.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/deweylab/RSEM.git")
+ (url "https://github.com/deweylab/RSEM")
(commit (string-append "v" version))))
(sha256
(base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
@@ -5699,7 +5699,7 @@ viewer.")
;; There are no release tarballs nor tags.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/wanpinglee/MOSAIK.git")
+ (url "https://github.com/wanpinglee/MOSAIK")
(commit commit)))
(file-name (string-append name "-" version))
(sha256
@@ -5745,7 +5745,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ncbi/ngs.git")
+ (url "https://github.com/ncbi/ngs")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -5811,7 +5811,7 @@ simultaneously.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ncbi/ncbi-vdb.git")
+ (url "https://github.com/ncbi/ncbi-vdb")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -5983,7 +5983,7 @@ subsequent visualization, annotation and storage of results.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/chrchang/plink-ng.git")
+ (url "https://github.com/chrchang/plink-ng")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -6022,7 +6022,7 @@ subsequent visualization, annotation and storage of results.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/smithlabcode/smithlab_cpp.git")
+ (url "https://github.com/smithlabcode/smithlab_cpp")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -6171,7 +6171,7 @@ sequence itself can be retrieved from these databases.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ncbi/sra-tools.git")
+ (url "https://github.com/ncbi/sra-tools")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -6381,7 +6381,7 @@ is one that takes arguments.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lh3/seqtk.git")
+ (url "https://github.com/lh3/seqtk")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -6417,7 +6417,7 @@ optionally compressed by gzip.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/amplab/snap.git")
+ (url "https://github.com/amplab/snap")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -6459,7 +6459,7 @@ of these reads to align data quickly through a hash-based indexing scheme.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/biocore/sortmerna.git")
+ (url "https://github.com/biocore/sortmerna")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -6505,7 +6505,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/alexdobin/STAR.git")
+ (url "https://github.com/alexdobin/STAR")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -6733,7 +6733,7 @@ Cuffdiff or Ballgown programs.")
;; The Pypi version does not include tests.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fhcrc/taxtastic.git")
+ (url "https://github.com/fhcrc/taxtastic")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -6858,7 +6858,7 @@ sequence.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/hms-dbmi/scde.git")
+ (url "https://github.com/hms-dbmi/scde")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -6986,14 +6986,14 @@ distribution.")
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.34.0")
+ (version "1.34.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "1inyxb89hd5bn0sl7a9qbv9d1g40z4v1s9qwxkcsx5c79fl04n1h"))))
+ "1m03awaw06mfv5gszq23k5apsqqzjqa5rcwp20y4xbpl7bywpsyl"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -7304,7 +7304,7 @@ annotation infrastructure.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/torognes/vsearch.git")
+ (url "https://github.com/torognes/vsearch")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -7505,13 +7505,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.")
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.56.0")
+ (version "1.56.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "1h4cmfbff79v9xrh271dp3rv0877ris06lmkvc39kqzj7yjsh7c2"))))
+ "0zcx8gha3x3jc0ra6ii6wwq2vfsmffrrnilknbq8h5xjrl55m6ci"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
@@ -7894,13 +7894,13 @@ on Bioconductor or which replace R functions.")
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.50.0")
+ (version "1.50.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "10gplxal0qphcn29azv0i6hiim9q45lmhzvhhhsnwfhwpgja7p05"))))
+ "00pd8lsdppxlmx0l65phw0jhsm0qkwjc4wsdxpvgc31iiz9yslbj"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
@@ -8092,13 +8092,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.18.1")
+ (version "1.18.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "07rc79k5dp0dnf4dvsxif995aa9cgfkf13yf84qnwl64k9pf3c2c"))))
+ "1raw5ycigr6gjgzn3kx3jls5hzww10fhnwd8c17c20hmhirf13rw"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
@@ -8205,13 +8205,13 @@ as well as query and modify the browser state, such as the current viewport.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.40.0")
+ (version "1.40.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "09ffsflk2yhhj9ivm028y3qdkvv8idgxpm4il3y9rym7shc8b3f8"))))
+ "0zm7q957g952qyfqmvf27sldsnq6sqd0wlgnqzvmxayg9pxh0l0z"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -8415,7 +8415,7 @@ reference point and sorted by a user defined feature.")
("r-seqpattern" ,r-seqpattern)))
(native-inputs
`(("r-knitr" ,r-knitr)))
- (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
(synopsis "Summary, annotation and visualization of genomic data")
(description
"This package provides a package for summary and annotation of genomic
@@ -8448,7 +8448,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
(arguments `(#:substitutable? #f))
(native-inputs
`(("r-knitr" ,r-knitr)))
- (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
(synopsis "Experimental data for use with the genomation package")
(description
"This package contains experimental genetic data for use with the
@@ -8532,16 +8532,12 @@ two-dimensional genome scans.")
(define-public r-qtl2
(package
(name "r-qtl2")
- (version "0.20")
+ (version "0.22-11")
(source (origin
- (method git-fetch)
- ;; Not yet available in cran.
- (uri (git-reference
- (url "https://github.com/rqtl/qtl2.git")
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0l1asr28q25jzbwrbg5490962sg3y4sjrd0qf09p78ws1aq8vfs0"))))
+ (method url-fetch)
+ (uri (cran-uri "qtl2" version))
+ (sha256
+ (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
@@ -8551,11 +8547,12 @@ two-dimensional genome scans.")
("r-rsqlite" ,r-rsqlite)
("r-yaml" ,r-yaml)))
(home-page "https://kbroman.org/qtl2/")
- (synopsis
- "QTL analysis software for high-dimensional data and complex cross designs")
+ (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
(description
- "R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software
-R/qtl, to better handle high-dimensional data and complex cross designs.")
+ "This package provides a set of tools to perform @dfn{Quantitative Trait
+Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
+@code{R/qtl} package to better handle high-dimensional data and complex cross
+designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
(license license:gpl3)))
(define-public r-zlibbioc
@@ -8812,7 +8809,7 @@ in SNV base substitution data.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ManuSetty/ChIPKernels.git")
+ (url "https://github.com/ManuSetty/ChIPKernels")
(commit commit)))
(file-name (string-append name "-" version))
(sha256
@@ -8846,7 +8843,7 @@ Sequences.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ManuSetty/SeqGL.git")
+ (url "https://github.com/ManuSetty/SeqGL")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -8896,13 +8893,13 @@ of gene-level counts.")
(define-public r-rhdf5
(package
(name "r-rhdf5")
- (version "2.32.1")
+ (version "2.32.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rhdf5" version))
(sha256
(base32
- "102zam2j43jwgaz9ch6y2jjbc3qf56ngmggikf99s8l3w9ggbskm"))))
+ "1v6ygi0avh3gmaj2ld2nr7vww4ipw39b5kqci9w27i3ja985lb8j"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rhdf5lib" ,r-rhdf5lib)))
@@ -9022,7 +9019,7 @@ tools for sequence analysis into a seamless whole.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/arq5x/bits.git")
+ (url "https://github.com/arq5x/bits")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -9068,7 +9065,7 @@ intervals (e.g. genes, sequence alignments).")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/smithlabcode/piranha.git")
+ (url "https://github.com/smithlabcode/piranha")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -9107,7 +9104,7 @@ intervals (e.g. genes, sequence alignments).")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/smithlabcode/smithlab_cpp.git")
+ (url "https://github.com/smithlabcode/smithlab_cpp")
(commit commit)))
(file-name (string-append "smithlab_cpp-" commit "-checkout"))
(sha256
@@ -9160,7 +9157,7 @@ group or two ChIP groups run under different conditions.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ekg/filevercmp.git")
+ (url "https://github.com/ekg/filevercmp")
(commit commit)))
(file-name (git-file-name name commit))
(sha256
@@ -9237,7 +9234,7 @@ common bioinformatics tools.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/vatlab/varianttools.git")
+ (url "https://github.com/vatlab/varianttools")
;; There is no tag corresponding to version 3.1.2
(commit "813ae4a90d25b69abc8a40f4f70441fe09015249")))
(file-name (git-file-name name version))
@@ -10843,14 +10840,14 @@ block processing.")
(define-public r-rhdf5lib
(package
(name "r-rhdf5lib")
- (version "1.10.0")
+ (version "1.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhdf5lib" version))
(sha256
(base32
- "09ylwyk6a8sdrmi1mx7vpycpykqlqylmwa973g6jrcmk0h0qfa4w"))
+ "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -10870,14 +10867,7 @@ block processing.")
(for-each delete-file '("configure" "configure.ac"))
;; Do not make other packages link with the proprietary libsz.
(substitute* "R/zzz.R"
- (("'\"%s/libhdf5.a\" \"%s/libsz.a\" -lz'")
- "'\"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'")
- (("'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libsz.a\" -lz'")
- "'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'")
- (("'%s/libhdf5_hl.a %s/libhdf5.a %s/libsz.a -lz'")
- "'%s/libhdf5_hl.a %s/libhdf5.a %s/libhdf5.a -lz'")
- (("'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'")
- "'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'"))
+ ((" \"%s/libsz.a\"") ""))
(with-directory-excursion "src"
(invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
(rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
@@ -10986,13 +10976,13 @@ libraries.")
(define-public r-scater
(package
(name "r-scater")
- (version "1.16.1")
+ (version "1.16.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "scater" version))
(sha256
(base32
- "0pi4mpc3lvskj5biyhc9cskcnz9q2wjmfrz7xdnx8qqd8vpy84g3"))))
+ "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
@@ -11066,14 +11056,14 @@ variable and significantly correlated genes.")
(define-public r-delayedmatrixstats
(package
(name "r-delayedmatrixstats")
- (version "1.10.0")
+ (version "1.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DelayedMatrixStats" version))
(sha256
(base32
- "0i6gw8058gw9yajya3w9qq6l3p634fq9sv8dh8ifigxz0k9b98r6"))))
+ "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
(properties
`((upstream-name . "DelayedMatrixStats")))
(build-system r-build-system)
@@ -11137,7 +11127,7 @@ Maximum Parsimony, distance methods and Hadamard conjugation.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/rajewsky-lab/dropbead.git")
+ (url "https://github.com/rajewsky-lab/dropbead")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -11167,7 +11157,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lomereiter/htslib.git")
+ (url "https://github.com/lomereiter/htslib")
(commit commit)))
(file-name (string-append "htslib-" version "-checkout"))
(sha256
@@ -11186,7 +11176,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lomereiter/sambamba.git")
+ (url "https://github.com/lomereiter/sambamba")
(commit (string-append "v" version))))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -11235,7 +11225,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/biod/BioD.git")
+ (url "https://github.com/biod/BioD")
(commit commit)))
(file-name (string-append "biod-"
(string-take commit 9)
@@ -11262,7 +11252,7 @@ sort, markdup, and depth.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/KlugerLab/Ritornello.git")
+ (url "https://github.com/KlugerLab/Ritornello")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -11308,7 +11298,7 @@ with narrow binding events such as transcription factor ChIP-seq.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/FelixKrueger/TrimGalore.git")
+ (url "https://github.com/FelixKrueger/TrimGalore")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -11523,7 +11513,7 @@ applications for tackling some common problems in a user-friendly way.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/3DGenomes/TADbit.git")
+ (url "https://github.com/3DGenomes/TADbit")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -11585,7 +11575,7 @@ models. TADbit is complemented by TADkit for visualizing 3D models.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ENCODE-DCC/kentUtils.git")
+ (url "https://github.com/ENCODE-DCC/kentUtils")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -11701,7 +11691,7 @@ browser.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/aboyle/F-seq.git")
+ (url "https://github.com/aboyle/F-seq")
(commit commit)))
(file-name (string-append name "-" version))
(sha256
@@ -11759,7 +11749,7 @@ Browser.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/FelixKrueger/Bismark.git")
+ (url "https://github.com/FelixKrueger/Bismark")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -11911,7 +11901,7 @@ using nucleotide or amino-acid sequence data.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/pachterlab/kallisto.git")
+ (url "https://github.com/pachterlab/kallisto")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -11960,7 +11950,7 @@ accurate as existing quantification tools.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Kingsford-Group/libgff.git")
+ (url "https://github.com/Kingsford-Group/libgff")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -11983,7 +11973,7 @@ dependency like SeqAn.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/kingsfordgroup/sailfish.git")
+ (url "https://github.com/kingsfordgroup/sailfish")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -12098,7 +12088,7 @@ dependency like SeqAn.")
("rapmap" ,(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/COMBINE-lab/RapMap.git")
+ (url "https://github.com/COMBINE-lab/RapMap")
(commit (string-append "sf-v" version))))
(file-name (string-append "rapmap-sf-v" version "-checkout"))
(sha256
@@ -12133,7 +12123,7 @@ file(s) containing your reads.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/COMBINE-lab/staden-io_lib.git")
+ (url "https://github.com/COMBINE-lab/staden-io_lib")
(commit (string-append "v" version))))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -12174,7 +12164,7 @@ The following file formats are supported:
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/COMBINE-lab/salmon.git")
+ (url "https://github.com/COMBINE-lab/salmon")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -12287,7 +12277,7 @@ The following file formats are supported:
("rapmap" ,(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/COMBINE-lab/RapMap.git")
+ (url "https://github.com/COMBINE-lab/RapMap")
(commit (string-append "salmon-v" version))))
(file-name (string-append "rapmap-salmon-v" version "-checkout"))
(sha256
@@ -12320,7 +12310,7 @@ variational inference.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/linnarsson-lab/loompy.git")
+ (url "https://github.com/linnarsson-lab/loompy")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -12363,7 +12353,7 @@ single-cell RNA-seq data.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/cmzmasek/forester.git")
+ (url "https://github.com/cmzmasek/forester")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -12569,7 +12559,7 @@ reading, writing, and exporting phylogenetic trees.")
(native-inputs
`(("java-junit" ,java-junit)
("java-hamcrest-core" ,java-hamcrest-core)))
- (home-page "http://biojava.org")
+ (home-page "https://biojava.org")
(synopsis "Core libraries of Java framework for processing biological data")
(description "BioJava is a project dedicated to providing a Java framework
for processing biological data. It provides analytical and statistical
@@ -12612,7 +12602,7 @@ This package provides the core libraries.")
(native-inputs
`(("java-junit" ,java-junit)
("java-hamcrest-core" ,java-hamcrest-core)))
- (home-page "http://biojava.org")
+ (home-page "https://biojava.org")
(synopsis "Biojava interface to the forester phylogenomics library")
(description "The phylo module provides a biojava interface layer to the
forester phylogenomics library for constructing phylogenetic trees.")))
@@ -12649,7 +12639,7 @@ forester phylogenomics library for constructing phylogenetic trees.")))
(native-inputs
`(("java-junit" ,java-junit)
("java-hamcrest-core" ,java-hamcrest-core)))
- (home-page "http://biojava.org")
+ (home-page "https://biojava.org")
(synopsis "Biojava API for genetic sequence alignment")
(description "The alignment module of BioJava provides an API that
contains
@@ -12706,7 +12696,7 @@ contains
(native-inputs
`(("java-junit" ,java-junit)
("java-hamcrest-core" ,java-hamcrest-core)))
- (home-page "http://biojava.org")
+ (home-page "https://biojava.org")
(synopsis "Biojava interface to the forester phylogenomics library")
(description "The phylo module provides a biojava interface layer to the
forester phylogenomics library for constructing phylogenetic trees.")))
@@ -12743,7 +12733,7 @@ forester phylogenomics library for constructing phylogenetic trees.")))
(native-inputs
`(("java-junit" ,java-junit)
("java-hamcrest-core" ,java-hamcrest-core)))
- (home-page "http://biojava.org")
+ (home-page "https://biojava.org")
(synopsis "Biojava API for genetic sequence alignment")
(description "The alignment module of BioJava provides an API that
contains
@@ -12955,7 +12945,7 @@ once. This package provides tools to perform Drop-seq analyses.")
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for RNA sequencing experiments")
(description "PiGX RNAseq is an analysis pipeline for preprocessing and
reporting for RNA sequencing experiments. It is easy to use and produces high
@@ -13024,7 +13014,7 @@ expression report comparing samples in an easily configurable manner.")
("kentutils" ,kentutils)))
(native-inputs
`(("python-pytest" ,python-pytest)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for ChIP sequencing experiments")
(description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
calling and reporting for ChIP sequencing experiments. It is easy to use and
@@ -13086,7 +13076,7 @@ in an easily configurable manner.")
("trim-galore" ,trim-galore)
("cutadapt" ,cutadapt)
("samtools" ,samtools)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
(description "PiGx BSseq is a data processing pipeline for raw fastq read
data of bisulfite experiments; it produces reports on aggregate methylation
@@ -13150,7 +13140,7 @@ methylation and segmentation.")
("r-singlecellexperiment" ,r-singlecellexperiment)
("r-stringr" ,r-stringr)
("r-yaml" ,r-yaml)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
(description "PiGX scRNAseq is an analysis pipeline for preprocessing and
quality control for single cell RNA sequencing experiments. The inputs are
@@ -13179,7 +13169,7 @@ based methods.")
("pigx-chipseq" ,pigx-chipseq)
("pigx-rnaseq" ,pigx-rnaseq)
("pigx-scrnaseq" ,pigx-scrnaseq)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipelines for genomics")
(description "PiGx is a collection of genomics pipelines. It includes the
following pipelines:
@@ -13203,7 +13193,7 @@ HTML reports with interesting findings about your samples.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/jsh58/Genrich.git")
+ (url "https://github.com/jsh58/Genrich")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -13238,7 +13228,7 @@ enrichment.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/splatlab/mantis.git")
+ (url "https://github.com/splatlab/mantis")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -13305,7 +13295,7 @@ rate speciation and extinction.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/pervouchine/sjcount-full.git")
+ (url "https://github.com/pervouchine/sjcount-full")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
@@ -13450,7 +13440,7 @@ Thus the per-base error rate is similar to the raw input reads.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/BIMSBbioinfo/ciRcus.git")
+ (url "https://github.com/BIMSBbioinfo/ciRcus")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -13496,7 +13486,7 @@ can be calculated, and a number of descriptive plots easily generated.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/gpertea/gffread.git")
+ (url "https://github.com/gpertea/gffread")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -13530,7 +13520,7 @@ can be calculated, and a number of descriptive plots easily generated.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/gpertea/gclib.git")
+ (url "https://github.com/gpertea/gclib")
(commit commit)))
(file-name (git-file-name "gclib" version))
(sha256
@@ -13557,7 +13547,7 @@ conversions, region filtering, FASTA sequence extraction and more.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/marvin-jens/find_circ.git")
+ (url "https://github.com/marvin-jens/find_circ")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -13837,7 +13827,7 @@ bound.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/4dn-dcic/pairix.git")
+ (url "https://github.com/4dn-dcic/pairix")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -13936,7 +13926,7 @@ such as Hi-C contact matrices.")
;; Version 12 is not available on pypi.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/deeptools/HiCMatrix.git")
+ (url "https://github.com/deeptools/HiCMatrix")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -13976,7 +13966,7 @@ the HiCExplorer and pyGenomeTracks packages.")
;; The latest version is not available on Pypi.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/deeptools/HiCExplorer.git")
+ (url "https://github.com/deeptools/HiCExplorer")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -14125,7 +14115,7 @@ sequencing data.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/renozao/xbioc.git")
+ (url "https://github.com/renozao/xbioc")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -14158,7 +14148,7 @@ provided by Bioconductor packages.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/shenorrLab/csSAM.git")
+ (url "https://github.com/shenorrLab/csSAM")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -14189,7 +14179,7 @@ SAM.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/shenorrLab/bseqsc.git")
+ (url "https://github.com/shenorrLab/bseqsc")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -14237,7 +14227,7 @@ and intra-cell population structure.\" Baron et al. Cell Systems (2016)
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/rrwick/Porechop.git")
+ (url "https://github.com/rrwick/Porechop")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -14268,7 +14258,7 @@ Barcoding Kit or Rapid Barcoding Kit.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/arq5x/poretools.git")
+ (url "https://github.com/arq5x/poretools")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -14329,7 +14319,7 @@ absolute GSEA.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/mahmoudibrahim/JAMM.git")
+ (url "https://github.com/mahmoudibrahim/JAMM")
(commit (string-append "JAMMv" version))))
(file-name (git-file-name name version))
(sha256
@@ -14529,7 +14519,7 @@ datasets.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/rrwick/Filtlong.git")
+ (url "https://github.com/rrwick/Filtlong")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -14590,7 +14580,7 @@ choosing which reads pass the filter.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/jts/nanopolish.git")
+ (url "https://github.com/jts/nanopolish")
(commit commit)
(recursive? #t)))
(file-name (git-file-name name version))
@@ -14664,7 +14654,7 @@ polymorphisms) and indels with respect to a reference genome and more.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/etal/cnvkit.git")
+ (url "https://github.com/etal/cnvkit")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -14700,7 +14690,7 @@ Torrent.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/KlugerLab/pyFIt-SNE.git")
+ (url "https://github.com/KlugerLab/pyFIt-SNE")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -14963,7 +14953,7 @@ tools which build on STAR, Arriba does not require to reduce the
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/MikkelSchubert/adapterremoval.git")
+ (url "https://github.com/MikkelSchubert/adapterremoval")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -15002,7 +14992,7 @@ sequence for paired-ended data, for which this information is not available.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/matsen/pplacer.git")
+ (url "https://github.com/matsen/pplacer")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -15224,7 +15214,7 @@ on the needs of the user.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ParkerLab/ataqv.git")
+ (url "https://github.com/ParkerLab/ataqv")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -15265,7 +15255,7 @@ might be caused by ATAC-seq library prep or sequencing. The main program,
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/kcha/psiplot.git")
+ (url "https://github.com/kcha/psiplot")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -15296,7 +15286,7 @@ are generated using @code{ggplot2}.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/nanoporetech/ont_fast5_api.git")
+ (url "https://github.com/nanoporetech/ont_fast5_api")
(commit (string-append "release_" version))))
(file-name (git-file-name name version))
(sha256
@@ -15327,7 +15317,7 @@ and reflect the fast5 file schema, and tools to convert between
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/phoenixding/tbsp.git")
+ (url "https://github.com/phoenixding/tbsp")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -15639,7 +15629,7 @@ manipulations on VCF files.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ekg/freebayes.git")
+ (url "https://github.com/ekg/freebayes")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -15757,7 +15747,7 @@ length of a short-read sequencing alignment.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/GregoryFaust/samblaster.git")
+ (url "https://github.com/GregoryFaust/samblaster")
(commit (string-append "v." version))))
(file-name (git-file-name name version))
(sha256
@@ -15794,7 +15784,7 @@ pairs.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/velocyto-team/velocyto.R.git")
+ (url "https://github.com/velocyto-team/velocyto.R")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -15835,7 +15825,7 @@ patterns.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dpryan79/MethylDackel.git")
+ (url "https://github.com/dpryan79/MethylDackel")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -15883,7 +15873,7 @@ containing the reference genome as well.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/daler/gffutils.git")
+ (url "https://github.com/daler/gffutils")
(commit commit)))
(file-name (git-file-name name version))
(sha256
diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm
index 52160b9025..9cf8e2eb40 100644
--- a/gnu/packages/bittorrent.scm
+++ b/gnu/packages/bittorrent.scm
@@ -1,7 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017, 2018, 2019 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Tomáš Čech <sleep_walker@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -9,7 +9,7 @@
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
;;; Copyright © 2018 Nam Nguyen <namn@berkeley.edu>
;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
+;;; Copyright © 2019, 2020 Brett Gilio <brettg@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -65,16 +65,15 @@
(define-public transmission
(package
(name "transmission")
- (version "2.94")
+ (version "3.00")
(source (origin
(method url-fetch)
- (uri (string-append
- "https://github.com/transmission/transmission-releases/raw/"
- "master/transmission-" version ".tar.xz"))
- (patches (search-patches "transmission-CVE-2018-10756.patch"))
+ (uri (string-append "https://github.com/transmission/transmission"
+ "/releases/download/" version "/transmission-"
+ version ".tar.xz"))
(sha256
(base32
- "0zbbj7rlm6m7vb64x68a64cwmijhsrwx9l63hbwqs7zr9742qi1m"))))
+ "1wjmn96zrvmk8j1yz2ysmqd7a2x6ilvnwwapcvfzgxs2wwpnai4i"))))
(build-system glib-or-gtk-build-system)
(outputs '("out" ; library and command-line interface
"gui")) ; graphical user interface
@@ -90,8 +89,7 @@
(gui (assoc-ref outputs "gui")))
(mkdir-p (string-append gui "/bin"))
(rename-file (string-append out "/bin/transmission-gtk")
- (string-append gui
- "/bin/transmission-gtk"))
+ (string-append gui "/bin/transmission-gtk"))
;; Move the '.desktop' and icon files as well.
(mkdir (string-append gui "/share"))
@@ -183,38 +181,36 @@ XML-RPC over SCGI.")
(license l:gpl2+)))
(define-public tremc
- (let ((commit "4d50dab7376601daca13f7be6eabc0eaa057c1b0")
- (revision "0"))
- (package
- (name "tremc")
- (version (git-version "0.9.1" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/tremc/tremc.git")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0qpi65n8rv7l9mg8qyqx70z83inkl8v5r5nks65c99lhscdki0w7"))))
- (build-system gnu-build-system)
- (arguments
- `(#:tests? #f ; no test suite
- #:make-flags
- (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
- #:phases
- (modify-phases %standard-phases
- ;; The software is just a Python script that must be copied into place.
- (delete 'configure)
- (delete 'build))))
- (inputs
- `(("python" ,python)))
- (synopsis "Console client for the Transmission BitTorrent daemon")
- (description "Tremc is a console client, with a curses interface, for the
+ (package
+ (name "tremc")
+ (version "0.9.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/tremc/tremc")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1fqspp2ckafplahgba54xmx0sjidx1pdzyjaqjhz0ivh98dkx2n5"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no test suite
+ #:make-flags
+ (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+ #:phases
+ (modify-phases %standard-phases
+ ;; The software is just a Python script that must be copied into place.
+ (delete 'configure)
+ (delete 'build))))
+ (inputs
+ `(("python" ,python)))
+ (synopsis "Console client for the Transmission BitTorrent daemon")
+ (description "Tremc is a console client, with a curses interface, for the
Transmission BitTorrent daemon.")
- (home-page "https://github.com/tremc/tremc")
- (license l:gpl3+))))
+ (home-page "https://github.com/tremc/tremc")
+ (license l:gpl3+)))
(define-public transmission-remote-cli
(package
@@ -223,7 +219,7 @@ Transmission BitTorrent daemon.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fagga/transmission-remote-cli.git")
+ (url "https://github.com/fagga/transmission-remote-cli")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -347,7 +343,7 @@ downloads, download scheduling, download rate limiting.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Rudde/mktorrent.git")
+ (url "https://github.com/Rudde/mktorrent")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
@@ -379,17 +375,17 @@ and will take advantage of multiple processor cores where possible.")
(define-public libtorrent-rasterbar
(package
(name "libtorrent-rasterbar")
- (version "1.1.14")
+ (version "1.2.7")
(source (origin
(method url-fetch)
(uri
(string-append
- "https://github.com/arvidn/libtorrent/releases/download/libtorrent-"
+ "https://github.com/arvidn/libtorrent/releases/download/libtorrent_"
(string-join (string-split version #\.) "_")
"/libtorrent-rasterbar-" version ".tar.gz"))
(sha256
(base32
- "0sn3ingmk1lk9p56f9ifgdwhjg0qizcfgv15wyc9s71nm5fya7sc"))))
+ "001g35janbxi20c7jzsf3ii9mkagz4kdsp7f3sz5r0n0cng0c05w"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@@ -416,16 +412,16 @@ desktops.")
(define-public qbittorrent
(package
(name "qbittorrent")
- (version "4.2.1")
+ (version "4.2.5")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/qbittorrent/qBittorrent.git")
+ (url "https://github.com/qbittorrent/qBittorrent")
(commit (string-append "release-" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0bz4l7awkx4qf3gh9c8gj8fab989439zj8qy4x9r36wxdjg5cxil"))))
+ (base32 "1n613ylg6i9gisgk0dbr2kpfasyizrkdjff1r8smd4vri2qrdksn"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm
index 9e7c40cd99..6a08b0d6c7 100644
--- a/gnu/packages/boost.scm
+++ b/gnu/packages/boost.scm
@@ -288,7 +288,7 @@ across a broad spectrum of applications.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/boostorg/sync.git")
+ (url "https://github.com/boostorg/sync")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -317,7 +317,7 @@ Boost.Thread.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/boostorg/signals2.git")
+ (url "https://github.com/boostorg/signals2")
(commit (string-append "boost-" version))))
(file-name (git-file-name name version))
(sha256
diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 07b406b42a..769238203c 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -446,7 +446,7 @@ tree binary files. These are board description files used by Linux and BSD.")
(define u-boot
(package
(name "u-boot")
- (version "2020.04")
+ (version "2020.07")
(source (origin
(method url-fetch)
(uri (string-append
@@ -454,7 +454,7 @@ tree binary files. These are board description files used by Linux and BSD.")
"u-boot-" version ".tar.bz2"))
(sha256
(base32
- "0wjkasnz87q86hx93inspdjfjsinmxi87bcvj30c773x0fpjlwzy"))))
+ "0sjzy262x93aaqd6z24ziaq19xjjjk5f577ivf768vmvwsgbzxf1"))))
(native-inputs
`(("bc" ,bc)
("bison" ,bison)
@@ -885,15 +885,6 @@ to Novena upstream, does not load u-boot.img from the first partition.")
(let ((base (make-u-boot-package "pinebook-pro-rk3399" "aarch64-linux-gnu")))
(package
(inherit base)
- (source (origin
- (inherit (package-source u-boot))
- (patches
- (search-patches "u-boot-add-boe-nv140fhmn49-display.patch"
- "u-boot-gpio-keys-binding-cons.patch"
- "u-boot-leds-common-binding-con.patch"
- "u-boot-DT-for-Pinebook-Pro.patch"
- "u-boot-support-Pinebook-Pro-laptop.patch"
- "u-boot-video-rockchip-fix-build.patch"))))
(arguments
(substitute-keyword-arguments (package-arguments base)
((#:phases phases)
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm