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01/01: Merge branch 'master' into core-updates
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From: |
guix-commits |
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Subject: |
01/01: Merge branch 'master' into core-updates |
|
Date: |
Tue, 17 Sep 2019 10:28:20 -0400 (EDT) |
civodul pushed a commit to branch core-updates
in repository guix.
commit 9ff87bb99614923fa3336ab4bbf22e3444709b48
Merge: ae71bef 9e8e252
Author: Ludovic Courtès <address@hidden>
Date: Tue Sep 17 16:17:20 2019 +0200
Merge branch 'master' into core-updates
Makefile.am | 2 +
build-aux/pre-inst-env.in | 14 +-
config-daemon.ac | 11 -
doc/build.scm | 32 +-
doc/contributing.texi | 16 +-
doc/guix.texi | 713 +++++++++++----------
etc/guix-daemon.cil.in | 4 -
gnu/build/linux-container.scm | 7 +-
gnu/build/shepherd.scm | 8 +-
gnu/local.mk | 2 +-
gnu/packages/admin.scm | 4 +-
gnu/packages/algebra.scm | 4 +-
gnu/packages/audio.scm | 20 +-
gnu/packages/authentication.scm | 41 ++
gnu/packages/bioconductor.scm | 615 +++++++++++++++++-
gnu/packages/bioinformatics.scm | 32 +-
gnu/packages/check.scm | 12 +-
gnu/packages/cluster.scm | 35 +
gnu/packages/cmake.scm | 12 +
gnu/packages/cran.scm | 476 ++++++++++++--
gnu/packages/crates-io.scm | 4 +-
gnu/packages/cups.scm | 4 +-
gnu/packages/dictionaries.scm | 6 +-
gnu/packages/education.scm | 102 ++-
gnu/packages/emacs-xyz.scm | 170 +++--
gnu/packages/emulators.scm | 8 +-
gnu/packages/engineering.scm | 69 ++
gnu/packages/finance.scm | 31 +-
gnu/packages/freedesktop.scm | 8 +-
gnu/packages/game-development.scm | 10 +
gnu/packages/games.scm | 19 +-
gnu/packages/gnome.scm | 72 ++-
gnu/packages/gnupg.scm | 32 +-
gnu/packages/graph.scm | 4 +-
gnu/packages/graphics.scm | 41 ++
gnu/packages/guile-xyz.scm | 28 +-
gnu/packages/guile.scm | 12 +-
gnu/packages/haskell-apps.scm | 18 +-
gnu/packages/haskell-xyz.scm | 37 +-
gnu/packages/haskell.scm | 8 +-
gnu/packages/image.scm | 73 +++
gnu/packages/irc.scm | 20 +-
gnu/packages/javascript.scm | 139 ++--
gnu/packages/kde.scm | 32 +-
gnu/packages/language.scm | 481 +++++++++++++-
gnu/packages/linux.scm | 40 +-
gnu/packages/lisp.scm | 73 +++
gnu/packages/lua.scm | 66 +-
gnu/packages/lxqt.scm | 3 +-
gnu/packages/maths.scm | 43 +-
gnu/packages/mes.scm | 31 +-
gnu/packages/music.scm | 69 +-
gnu/packages/networking.scm | 8 +-
gnu/packages/ntp.scm | 8 +-
gnu/packages/ocr.scm | 75 +++
gnu/packages/package-management.scm | 102 ++-
gnu/packages/patches/cmake-curl-certificates.patch | 40 ++
gnu/packages/patches/tipp10-fix-compiling.patch | 3 +-
gnu/packages/patches/weechat-python.patch | 40 --
gnu/packages/perl-compression.scm | 5 +-
gnu/packages/python-check.scm | 23 +-
gnu/packages/python-xyz.scm | 213 ++++--
gnu/packages/python.scm | 6 +-
gnu/packages/ruby.scm | 30 +
gnu/packages/shellutils.scm | 103 ++-
gnu/packages/sphinx.scm | 21 +-
gnu/packages/statistics.scm | 36 +-
gnu/packages/suckless.scm | 28 +
gnu/packages/sync.scm | 4 +-
gnu/packages/terminals.scm | 7 +-
gnu/packages/tex.scm | 9 +-
gnu/packages/textutils.scm | 51 +-
gnu/packages/tls.scm | 19 +
gnu/packages/video.scm | 4 +-
gnu/packages/vim.scm | 13 +-
gnu/packages/virtualization.scm | 17 +-
gnu/packages/vpn.scm | 8 +-
gnu/packages/vulkan.scm | 4 +-
gnu/packages/web-browsers.scm | 4 +-
gnu/packages/web.scm | 6 +-
gnu/packages/wget.scm | 68 +-
gnu/packages/wine.scm | 6 +-
gnu/packages/wm.scm | 135 +++-
gnu/packages/xfce.scm | 38 +-
gnu/services/base.scm | 9 +-
gnu/services/certbot.scm | 1 +
gnu/services/networking.scm | 203 ++++--
gnu/services/virtualization.scm | 11 +-
gnu/system/file-systems.scm | 2 +-
gnu/system/linux-container.scm | 61 +-
guix/build/cargo-build-system.scm | 5 +-
guix/docker.scm | 43 +-
guix/gnu-maintenance.scm | 44 +-
guix/import/cran.scm | 1 +
guix/import/crate.scm | 29 +-
guix/import/github.scm | 2 +-
guix/import/kde.scm | 190 ++++++
guix/import/utils.scm | 17 +-
guix/packages.scm | 2 +-
guix/scripts/environment.scm | 13 +-
guix/scripts/gc.scm | 15 +
guix/scripts/import/crate.scm | 13 +-
guix/scripts/pack.scm | 16 +-
guix/scripts/refresh.scm | 12 +-
guix/store/roots.scm | 129 +++-
guix/upstream.scm | 12 +-
guix/utils.scm | 7 +
nix/libstore/build.cc | 63 +-
nix/libstore/builtins.cc | 4 +-
nix/libstore/gc.cc | 11 +-
nix/libstore/globals.cc | 2 +-
nix/libstore/globals.hh | 11 +-
nix/libstore/local-store.cc | 102 +--
nix/libstore/local-store.hh | 12 +-
nix/local.mk | 16 -
nix/nix-daemon/guix-daemon.cc | 20 +-
nix/nix-daemon/nix-daemon.cc | 17 +-
nix/scripts/authenticate.in | 11 -
nix/scripts/download.in | 11 -
nix/scripts/list-runtime-roots.in | 147 -----
nix/scripts/offload.in | 11 -
nix/scripts/substitute.in | 11 -
tests/networking.scm | 113 ++++
tests/opam.scm | 2 +-
124 files changed, 4794 insertions(+), 1554 deletions(-)
diff --cc gnu/packages/cmake.scm
index 1d8d829,95f884b..64349be
--- a/gnu/packages/cmake.scm
+++ b/gnu/packages/cmake.scm
@@@ -166,47 -158,24 +166,59 @@@
CMake is used to control the software compilation process using simple
platform
and compiler independent configuration files. CMake generates native
makefiles
and workspaces that can be used in the compiler environment of your choice.")
- (license (list license:bsd-3 ; cmake
- license:bsd-4 ; cmcompress
- license:bsd-2 ; cmlibarchive
- license:expat ; cmjsoncpp is dual MIT/public
domain
+ (properties '((hidden? . #t)))
+ (license (list license:bsd-3 ; cmake
+ license:bsd-4 ; cmcompress
+ license:bsd-2 ; cmlibarchive
+ license:expat ; cmjsoncpp is dual MIT/public domain
license:public-domain)))) ; cmlibarchive/archive_getdate.c
+(define-public cmake
+ (package
+ (inherit cmake-minimal)
+ (name "cmake")
+ (arguments
+ (substitute-keyword-arguments (package-arguments cmake-minimal)
+ ((#:configure-flags configure-flags ''())
+ `(append ,configure-flags
+ ;; Extra configure flags used to generate the documentation.
+ '("--sphinx-info"
+ "--sphinx-man"
+ "--sphinx-html")))
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-after 'install 'move-html-doc
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (doc (assoc-ref outputs "doc"))
+ (html (string-append "/share/doc/cmake-"
+ ,(version-major+minor
+ (package-version cmake-minimal))
+ "/html")))
+ (copy-recursively (string-append out html)
+ (string-append doc html))
+ (delete-file-recursively (string-append out html))
+ #t)))))))
+ ;; Extra inputs required to build the documentation.
+ (native-inputs
+ `(,@(package-native-inputs cmake-minimal)
+ ("python-sphinx" ,python-sphinx)
+ ("texinfo" ,texinfo)))
+ (outputs '("out" "doc"))
+ (properties (alist-delete 'hidden? (package-properties cmake-minimal)))))
+
+ (define-public cmake/fixed
+ ;; This is a variant of CMake that fixes X.509 certificate lookup:
+ ;; <https://issues.guix.gnu.org/issue/37371>.
+ (package
+ (inherit cmake)
+ (version (string-append (package-version cmake) "-1"))
+ (source (origin
+ (inherit (package-source cmake))
+ (patches
+ (append (search-patches "cmake-curl-certificates.patch")
+ (origin-patches (package-source cmake))))))))
+
(define-public emacs-cmake-mode
(package
(inherit cmake)
diff --cc gnu/packages/gnome.scm
index a2a5f98,31ff2ab..520d04d
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@@ -2626,13 -2632,21 +2629,13 @@@ library."
(method url-fetch)
(uri (string-append "mirror://gnome/sources/glib-networking/"
(version-major+minor version) "/"
- name "-" version ".tar.xz"))
+ "glib-networking-" version ".tar.xz"))
(sha256
(base32
- "0s006gs9nsq6mg31spqha1jffzmp6qjh10y27h0fxf1iw1ah5ymx"))
- (patches (search-patches "glib-networking-connection.patch"))))
+ "1mfw44qpmwvz6yzj8c6spx6z357wrmkk15byrkc5byagd82860fm"))))
(build-system meson-build-system)
(arguments
- `(#:configure-flags '("-Dlibproxy_support=false")
- #:phases (modify-phases %standard-phases
- (add-before 'check 'disable-TLSv1.3
- (lambda _
- ;; XXX: One test fails when TLS 1.3 is enabled, fixed
in 2.60.0:
- ;; <https://gitlab.com/gnutls/gnutls/issues/615>.
- (setenv "G_TLS_GNUTLS_PRIORITY" "NORMAL:-VERS-TLS1.3")
- #t)))))
+ `(#:configure-flags '("-Dlibproxy_support=false")))
(native-inputs
`(("pkg-config" ,pkg-config)
("intltool" ,intltool)))
@@@ -4201,28 -4182,29 +4204,28 @@@ part of udev-extras, then udev, then sy
(define-public gvfs
(package
(name "gvfs")
- (version "1.36.2")
+ (version "1.40.1")
(source (origin
(method url-fetch)
- (uri (string-append "mirror://gnome/sources/" name "/"
+ (uri (string-append "mirror://gnome/sources/gvfs/"
(version-major+minor version) "/"
- name "-" version ".tar.xz"))
+ "gvfs-" version ".tar.xz"))
(sha256
(base32
- "1xq105596sk9yram5a143b369wpaiiwc9gz86n0j1kfr7nipkqn4"))))
- (build-system gnu-build-system)
+ "1cfnzamr4mvgpf6yhm28lh9cafy9z6842s8jpbqnfizfxybg8ylj"))))
+ (build-system meson-build-system)
(arguments
- '(#:tests? #f ; XXX: requiring `pidof'
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'remove-broken-autogen-script
- (lambda _ (delete-file "autogen.sh") #t)))))
+ '(#:glib-or-gtk? #t
+ #:configure-flags
+ (list "-Dsystemduserunitdir=no"
+ "-Dtmpfilesdir=no"
+ ;; Otherwise, the RUNPATH will lack the final path component.
+ (string-append "-Dc_link_args=-Wl,-rpath="
+ (assoc-ref %outputs "out") "/lib/gvfs"))))
(native-inputs
`(("glib:bin" ,glib "bin") ; for glib-genmarshal, etc.
- ("autoconf" ,autoconf)
- ("automake" ,automake)
("gettext" ,gettext-minimal)
("gtk-doc" ,gtk-doc)
- ("libtool" ,libtool)
("pkg-config" ,pkg-config)
("xsltproc" ,libxslt)))
(inputs
@@@ -8118,36 -8119,25 +8121,36 @@@ generic enough to work for everyone."
"evolution-" version ".tar.xz"))
(sha256
(base32
- "0sdv5lg2vlz5f4raymz9d8a5jq4j18vbqyigaip6508p3bjnfj8l"))))
+ "1hhxj3rh921pp3l3c5k33bdypcas1p66krzs65k1qn82c5fpgl2h"))))
(build-system cmake-build-system)
(arguments
- `(#:configure-flags
- (list "-DENABLE_PST_IMPORT=OFF" ; libpst is not packaged
- "-DENABLE_LIBCRYPTUI=OFF") ; libcryptui hasn't seen a release
- ; in four years and cannot be built
+ `(#: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))
+ #:configure-flags
+ (list "-DENABLE_PST_IMPORT=OFF" ; libpst is not packaged
+ "-DENABLE_LIBCRYPTUI=OFF") ; libcryptui hasn't seen a release
+ ; in four years and cannot be built.
#:phases
(modify-phases %standard-phases
- (add-after 'install 'wrap-program
+ ;; The build system attempts to install user interface modules to the
+ ;; output directory of the "evolution-data-server" package. This
+ ;; change redirects that change.
+ (add-after 'unpack 'patch-ui-module-dir
(lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (wrap-program (string-append out "/bin/evolution")
- `("XDG_DATA_DIRS" ":" prefix (,(getenv "XDG_DATA_DIRS")))
- `("GSETTINGS_SCHEMA_DIR" =
- (,(string-append out "/share/glib-2.0/schemas")))))
- #t)))))
+ (substitute* "src/modules/alarm-notify/CMakeLists.txt"
+ (("\\$\\{edsuimoduledir\\}")
+ (string-append (assoc-ref outputs "out")
+ "/lib/evolution-data-server/ui-modules")))
+ #t))
+ (add-after 'install 'glib-or-gtk-compile-schemas
+ (assoc-ref glib-or-gtk:%standard-phases
'glib-or-gtk-compile-schemas))
+ (add-after 'install 'glib-or-gtk-wrap
+ (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
(native-inputs
- `(("glib" ,glib "bin") ; glib-mkenums
+ `(("glib" ,glib "bin") ; glib-mkenums
("pkg-config" ,pkg-config)
("intltool" ,intltool)
("itstool" ,itstool)))
diff --cc gnu/packages/maths.scm
index 16d3af3,5380b4a..e44ec66
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@@ -3100,8 -3096,12 +3105,12 @@@ parts of it."
(define-public openblas
(package
+ ;; TODO: Incorporate 'openblas/fixed-num-threads' changes on the next
+ ;; rebuild cycle.
+ (replacement openblas/fixed-num-threads)
+
(name "openblas")
- (version "0.3.5")
+ (version "0.3.6")
(source
(origin
(method url-fetch)
diff --cc gnu/packages/mes.scm
index 7bdd122,49224a7..e1cb736
--- a/gnu/packages/mes.scm
+++ b/gnu/packages/mes.scm
@@@ -138,33 -136,32 +135,49 @@@ Guile."
(license gpl3+)))
(define-public mescc-tools
+ (let ((commit "bb062b0da7bf2724ca40f9002b121579898d4ef7")
+ (revision "0")
+ (version "0.5.2"))
+ (package
+ (name "mescc-tools")
+ (version (string-append version "-" revision "." (string-take commit
7)))
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+
"https://git.savannah.nongnu.org/cgit/mescc-tools.git/snapshot/";
+ name "-" commit
+ ".tar.gz"))
+ (sha256
+ (base32
+ "1h6j57wyf91i42b26f8msbv6451cw3nm4nmpl1fckp9c7vi8mwkh"))))
+ (build-system gnu-build-system)
+ (supported-systems '("i686-linux" "x86_64-linux"))
+ (arguments
+ `(#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs
"out")))
+ #:test-target "test"
+ #:phases (modify-phases %standard-phases
+ (delete 'configure))))
+ (synopsis "Tools for the full source bootstrapping process")
+ (description
+ "Mescc-tools is a collection of tools for use in a full source
+bootstrapping process. It consists of the M1 macro assembler, the hex2
+linker, the blood-elf symbol table generator, the kaem shell, exec_enable and
+get_machine.")
+ (home-page "https://savannah.nongnu.org/projects/mescc-tools";)
+ (license gpl3+))))
++
++(define-public mescc-tools-0.6.1
+ (package
++ (inherit mescc-tools)
+ (name "mescc-tools")
+ (version "0.6.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+
"http://git.savannah.nongnu.org/cgit/mescc-tools.git/snapshot/";
+ name "-Release_" version
+ ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
- "06jpvq6xfjzn2al6b4rdwd3zv3h4cvilc4n9gqcnjr9cr6wjpw2n"))))
- (build-system gnu-build-system)
- (supported-systems '("i686-linux" "x86_64-linux"))
- (arguments
- `(#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
- "CC=gcc")
- #:test-target "test"
- #:phases (modify-phases %standard-phases
- (delete 'configure))))
- (synopsis "Tools for the full source bootstrapping process")
- (description
- "Mescc-tools is a collection of tools for use in a full source
-bootstrapping process. It consists of the M1 macro assembler, the hex2
-linker, the blood-elf symbol table generator, the kaem shell, exec_enable and
-get_machine.")
- (home-page "https://savannah.nongnu.org/projects/mescc-tools";)
- (license gpl3+)))
++ "06jpvq6xfjzn2al6b4rdwd3zv3h4cvilc4n9gqcnjr9cr6wjpw2n"))))))
diff --cc gnu/packages/networking.scm
index ee7d65f,6bdf7f9..bfa901a
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@@ -276,15 -276,15 +276,15 @@@ transparently check connection attempt
(package
(name "zeromq")
(version "4.3.2")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "https://github.com/zeromq/libzmq/releases/";
- "download/v" version "/zeromq-" version ".tar.gz"))
- (sha256
- (base32 "0qzp80ky4y2k7k1ya09v9gkivvfbz2km813snrb8jhnn634bbmzb"))))
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/zeromq/libzmq/releases";
+ "/download/v" version "/zeromq-" version
".tar.gz"))
+ (sha256
+ (base32
+ "0qzp80ky4y2k7k1ya09v9gkivvfbz2km813snrb8jhnn634bbmzb"))))
(build-system gnu-build-system)
- (home-page "http://zeromq.org";)
+ (home-page "https://zeromq.org";)
(synopsis "Library for message-based applications")
(description
"The 0MQ lightweight messaging kernel is a library which extends the
diff --cc gnu/packages/tls.scm
index d896908,45ec4f7..6689375
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@@ -270,7 -270,8 +270,8 @@@ required structures."
(define-public openssl
(package
(name "openssl")
- (replacement openssl/fixed)
- (version "1.0.2p")
+ (version "1.1.1c")
++ (replacement openssl-1.1.1d)
(source (origin
(method url-fetch)
(uri (list (string-append
"https://www.openssl.org/source/openssl-";
@@@ -372,28 -399,36 +373,46 @@@
(license license:openssl)
(home-page "https://www.openssl.org/";)))
-(define-public openssl/fixed
- (hidden-package
- (package
- (inherit openssl)
- (source (origin
- (inherit (package-source openssl))
- (patches (append (origin-patches (package-source openssl))
- (search-patches
"openssl-CVE-2019-1559.patch"))))))))
-
-(define-public openssl-next
- (package
- (inherit openssl)
- (name "openssl")
- (version "1.1.1d")
- (source (origin
++(define openssl-1.1.1d
++ (package/inherit
++ openssl
++ (version "1.1.1d")
++ (source (origin
+ (method url-fetch)
+ (uri (list (string-append
"https://www.openssl.org/source/openssl-";
+ version ".tar.gz")
+ (string-append "ftp://ftp.openssl.org/source/";
+ "openssl-" version ".tar.gz")
+ (string-append "ftp://ftp.openssl.org/source/old/";
+ (string-trim-right version
char-set:letter)
+ "/openssl-" version ".tar.gz")))
- (patches (search-patches "openssl-1.1-c-rehash-in.patch"))
++ (patches (search-patches "openssl-1.1-c-rehash-in.patch"))
++ (sha256
++ (base32
++ "1whinyw402z3b9xlb3qaxv4b9sk4w1bgh9k0y8df1z4x3yy92fhy"))))))
++
+(define-public openssl-1.0
+ (package
+ (inherit openssl)
+ (name "openssl")
+ (version "1.0.2s")
+ (source (origin
+ (method url-fetch)
+ (uri (list (string-append
"https://www.openssl.org/source/openssl-";
+ version ".tar.gz")
+ (string-append "ftp://ftp.openssl.org/source/";
+ "openssl-" version ".tar.gz")
+ (string-append "ftp://ftp.openssl.org/source/old/";
+ (string-trim-right version
char-set:letter)
+ "/openssl-" version ".tar.gz")))
(sha256
(base32
- "1whinyw402z3b9xlb3qaxv4b9sk4w1bgh9k0y8df1z4x3yy92fhy"))))
+ "15mbmg8hf7s12vr3v2bdc0pi9y4pdbnsxhzk4fyyap42jaa5rgfa"))
+ (patches (search-patches "openssl-runpath.patch"
+ "openssl-c-rehash-in.patch"))))
(outputs '("out"
- "doc" ; 6.8 MiB of man3 pages and full HTML
documentation
- "static")) ; 6.4 MiB of .a files
+ "doc" ;1.5MiB of man3 pages
+ "static")) ;6MiB of .a files
(arguments
(substitute-keyword-arguments (package-arguments openssl)
((#:phases phases)
diff --cc gnu/packages/virtualization.scm
index 2e5b1ce,f46c31d..e1ac218
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@@ -466,12 -441,10 +460,11 @@@ manage system or application containers
("libpciaccess" ,libpciaccess)
("gnutls" ,gnutls)
("dbus" ,dbus)
- ("qemu" ,qemu)
("libpcap" ,libpcap)
("libnl" ,libnl)
+ ("libtirpc" ,libtirpc) ;for <rpc/rpc.h>
("libuuid" ,util-linux)
- ("lvm2" ,lvm2) ; for libdevmapper
+ ("lvm2" ,lvm2) ;for libdevmapper
("curl" ,curl)
("openssl" ,openssl)
("cyrus-sasl" ,cyrus-sasl)
diff --cc gnu/packages/web.scm
index 591ae2c,39475bd..f7730f3
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@@ -6389,10 -6386,10 +6389,10 @@@ derivation by David Revoy from the orig
(method url-fetch)
(uri (string-append "https://github.com/nghttp2/nghttp2/";
"releases/download/v" version "/"
- name "-" version ".tar.xz"))
+ "nghttp2-" version ".tar.xz"))
(sha256
(base32
- "0fi6qg2w82636wixwkqy7bclpgxslmvg82r431hs8h6aqc4mnzwv"))))
+ "0j0lk37k8k3f61r9nw647hg4b22z1753l36n3xrp9x01civ614b7"))))
(build-system gnu-build-system)
(outputs (list "out"
"lib")) ; only libnghttp2