From 9d541e97e99793d0c75f01bc52de61473632e0ec Mon Sep 17 00:00:00 2001 From: Greg Hogan Date: Tue, 19 Jan 2021 12:43:48 +0000 Subject: gnu: aws-c-common: Update to 0.5.2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/c.scm (aws-c-common): Update to 0.5.2. [arguments]: Build as shared library. Signed-off-by: Ludovic Courtès --- gnu/packages/c.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'gnu/packages/c.scm') diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm index 7d8d41d266..75fa6460be 100644 --- a/gnu/packages/c.scm +++ b/gnu/packages/c.scm @@ -10,7 +10,7 @@ ;;; Copyright © 2020 Marius Bakke ;;; Copyright © 2020 Katherine Cox-Buday ;;; Copyright © 2020 Maxim Cournoyer -;;; Copyright © 2020 Greg Hogan +;;; Copyright © 2020, 2021 Greg Hogan ;;; ;;; This file is part of GNU Guix. ;;; @@ -545,7 +545,7 @@ portability.") (define-public aws-c-common (package (name "aws-c-common") - (version "0.4.63") + (version "0.5.2") (source (origin (method git-fetch) (uri (git-reference @@ -554,8 +554,11 @@ portability.") (file-name (git-file-name name version)) (sha256 (base32 - "16bc6fn1gq3nqcrzgpi2kjphq7xkkr73aljakrg89ysm6hyzyim9")))) + "0rd2qzaa9mmn5f6f2bl1wgv54f17pqx3vwyy9f8ylh59qfnilpmg")))) (build-system cmake-build-system) + (arguments + '(#:configure-flags + '("-DBUILD_SHARED_LIBS=ON"))) (synopsis "Amazon Web Services core C library") (description "This library provides common C99 primitives, configuration, data -- cgit v1.2.3 range
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authorMarius Bakke <mbakke@fastmail.com>2019-08-13 20:42:06 +0200
committerMarius Bakke <mbakke@fastmail.com>2019-08-13 20:42:06 +0200
commit462ad9f56b9665b8d22960acee73ad91f1052c9c (patch)
tree814be463d6d0517e7db9b9e6f15dbc7516955674
parent7f5f61ae99321a7a6e08b0100cd428e11ce6a837 (diff)
parent1b1b006afd31c5526f34d157baef492c7dde2e9c (diff)
downloadguix-462ad9f56b9665b8d22960acee73ad91f1052c9c.tar.gz
guix-462ad9f56b9665b8d22960acee73ad91f1052c9c.zip
Merge branch 'master' into core-updates
Diffstat
-rw-r--r--doc/guix.texi27
-rw-r--r--gnu/local.mk14
-rw-r--r--gnu/machine.scm12
-rw-r--r--gnu/machine/ssh.scm174
-rw-r--r--gnu/packages/admin.scm46
-rw-r--r--gnu/packages/algebra.scm7
-rw-r--r--gnu/packages/audio.scm4
-rw-r--r--gnu/packages/bioconductor.scm45
-rw-r--r--gnu/packages/bioinformatics.scm455
-rw-r--r--gnu/packages/bittorrent.scm61
-rw-r--r--gnu/packages/certs.scm4
-rw-r--r--gnu/packages/chromium.scm98
-rw-r--r--gnu/packages/cran.scm337
-rw-r--r--gnu/packages/crates-io.scm890
-rw-r--r--gnu/packages/cups.scm4
-rw-r--r--gnu/packages/databases.scm39
-rw-r--r--gnu/packages/docbook.scm3
-rw-r--r--gnu/packages/docker.scm16
-rw-r--r--gnu/packages/education.scm4
-rw-r--r--gnu/packages/emacs-xyz.scm555
-rw-r--r--gnu/packages/emulators.scm20
-rw-r--r--gnu/packages/enchant.scm4
-rw-r--r--gnu/packages/engineering.scm47
-rw-r--r--gnu/packages/finance.scm43
-rw-r--r--gnu/packages/fonts.scm4
-rw-r--r--gnu/packages/fontutils.scm2
-rw-r--r--gnu/packages/freedesktop.scm6
-rw-r--r--gnu/packages/games.scm4
-rw-r--r--gnu/packages/gl.scm15
-rw-r--r--gnu/packages/gnome.scm115
-rw-r--r--gnu/packages/golang.scm10
-rw-r--r--gnu/packages/graphics.scm4
-rw-r--r--gnu/packages/gtk.scm6
-rw-r--r--gnu/packages/guile-xyz.scm21
-rw-r--r--gnu/packages/guile.scm44
-rw-r--r--gnu/packages/haskell-apps.scm18
-rw-r--r--gnu/packages/haskell-check.scm2
-rw-r--r--gnu/packages/haskell-crypto.scm63
-rw-r--r--gnu/packages/haskell-web.scm169
-rw-r--r--gnu/packages/haskell-xyz.scm276
-rw-r--r--gnu/packages/haskell.scm172
-rw-r--r--gnu/packages/image.scm17
-rw-r--r--gnu/packages/imagemagick.scm4
-rw-r--r--gnu/packages/kde.scm4
-rw-r--r--gnu/packages/libevent.scm4
-rw-r--r--gnu/packages/linux.scm46
-rw-r--r--gnu/packages/lisp.scm54
-rw-r--r--gnu/packages/machine-learning.scm17
-rw-r--r--gnu/packages/mail.scm16
-rw-r--r--gnu/packages/man.scm4
-rw-r--r--gnu/packages/maths.scm8
-rw-r--r--gnu/packages/mp3.scm3
-rw-r--r--gnu/packages/mpd.scm4
-rw-r--r--gnu/packages/multiprecision.scm25
-rw-r--r--gnu/packages/networking.scm4
-rw-r--r--gnu/packages/nss.scm5
-rw-r--r--gnu/packages/package-management.scm11
-rw-r--r--gnu/packages/patches/emacs-dired-toggle-sudo-emacs-26.patch49
-rw-r--r--gnu/packages/patches/flac-CVE-2017-6888.patch29
-rw-r--r--gnu/packages/patches/isc-dhcp-4.4.1-fixes-for-newer-bind.patch100
-rw-r--r--gnu/packages/patches/libmad-frame-length.patch199
-rw-r--r--gnu/packages/patches/libmad-length-check.patch819
-rw-r--r--gnu/packages/patches/libmad-md_size.patch60
-rw-r--r--gnu/packages/patches/libvirt-remove-ATTRIBUTE_UNUSED.patch34
-rw-r--r--gnu/packages/patches/mame-rapidjson-fix.patch37
-rw-r--r--gnu/packages/patches/nss-freebl-stubs.patch20
-rw-r--r--gnu/packages/patches/pcre2-fix-jit_match-crash.patch25
-rw-r--r--gnu/packages/patches/scribus-poppler.patch72
-rw-r--r--gnu/packages/patches/strace-ipc-tests.patch30
-rw-r--r--gnu/packages/pcre.scm2
-rw-r--r--gnu/packages/pdf.scm8
-rw-r--r--gnu/packages/perl.scm8
-rw-r--r--gnu/packages/photo.scm4
-rw-r--r--gnu/packages/php.scm10
-rw-r--r--gnu/packages/plotutils.scm3
-rw-r--r--gnu/packages/python-xyz.scm25
-rw-r--r--gnu/packages/regex.scm4
-rw-r--r--gnu/packages/ruby.scm6
-rw-r--r--gnu/packages/samba.scm4
-rw-r--r--gnu/packages/scanner.scm12
-rw-r--r--gnu/packages/scribus.scm106
-rw-r--r--gnu/packages/search.scm6
-rw-r--r--gnu/packages/security-token.scm4
-rw-r--r--gnu/packages/shells.scm9
-rw-r--r--gnu/packages/statistics.scm163
-rw-r--r--gnu/packages/syncthing.scm14
-rw-r--r--gnu/packages/terminals.scm6
-rw-r--r--gnu/packages/tex.scm4437
-rw-r--r--gnu/packages/text-editors.scm7
-rw-r--r--gnu/packages/version-control.scm10
-rw-r--r--gnu/packages/video.scm60
-rw-r--r--gnu/packages/vim.scm56
-rw-r--r--gnu/packages/virtualization.scm12
-rw-r--r--gnu/packages/vpn.scm18
-rw-r--r--gnu/packages/vulkan.scm8
-rw-r--r--gnu/packages/web.scm8
-rw-r--r--gnu/packages/wine.scm43
-rw-r--r--gnu/packages/wm.scm22
-rw-r--r--gnu/packages/xiph.scm5
-rw-r--r--gnu/packages/xorg.scm10
-rw-r--r--gnu/tests/reconfigure.scm32
-rw-r--r--guix/build-system/texlive.scm15
-rw-r--r--guix/build/ant-build-system.scm10
-rw-r--r--guix/build/cargo-build-system.scm48
-rw-r--r--guix/build/svn.scm9
-rw-r--r--guix/scripts/deploy.scm6
-rw-r--r--guix/scripts/system/reconfigure.scm27
-rw-r--r--guix/svn-download.scm59
108 files changed, 7408 insertions, 3428 deletions
diff --git a/doc/guix.texi b/doc/guix.texi
index 4034948b2f..42acc3c7f3 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -5854,8 +5854,11 @@ should be added to the package definition via the
In its @code{configure} phase, this build system will make any source inputs
specified in the @code{#:cargo-inputs} and @code{#:cargo-development-inputs}
-parameters available to cargo. The @code{install} phase installs any crate
-the binaries if they are defined by the crate.
+parameters available to cargo. The @code{update-cargo-lock} phase will,
+when there is a @code{Cargo.lock} file, update the @code{Cargo.lock} file
+with the inputs and their versions available at build time. The
+@code{install} phase installs any crate the binaries if they are defined by
+the crate.
@end defvr
@cindex Clojure (programming language)
@@ -25507,7 +25510,7 @@ evaluates to. As an example, @var{file} might contain a definition like this:
%base-services))))
(list (machine
- (system %system)
+ (operating-system %system)
(environment managed-host-environment-type)
(configuration (machine-ssh-configuration
(host-name "localhost")
@@ -25527,12 +25530,28 @@ complex deployment may involve, for example, starting virtual machines through
a Virtual Private Server (VPS) provider. In such a case, a different
@var{environment} type would be used.
+Do note that you first need to generate a key pair on the coordinator machine
+to allow the daemon to export signed archives of files from the store
+(@pxref{Invoking guix archive}).
+
+@example
+# guix archive --generate-key
+@end example
+
+@noindent
+Each target machine must authorize the key of the master machine so that it
+accepts store items it receives from the coordinator:
+
+@example
+# guix archive --authorize < coordinator-public-key.txt
+@end example
+
@deftp {Data Type} machine
This is the data type representing a single machine in a heterogeneous Guix
deployment.
@table @asis
-@item @code{system}
+@item @code{operating-system}
The object of the operating system configuration to deploy.
@item @code{environment}
diff --git a/gnu/local.mk b/gnu/local.mk
index 41f4e4eec2..c6962aebd1 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -238,6 +238,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/haskell-check.scm \
%D%/packages/haskell-crypto.scm \
%D%/packages/haskell-web.scm \
+ %D%/packages/haskell-xyz.scm \
%D%/packages/ham-radio.scm \
%D%/packages/hexedit.scm \
%D%/packages/hugs.scm \
@@ -771,6 +772,7 @@ dist_patch_DATA = \
%D%/packages/patches/elfutils-tests-ptrace.patch \
%D%/packages/patches/elixir-path-length.patch \
%D%/packages/patches/einstein-build.patch \
+ %D%/packages/patches/emacs-dired-toggle-sudo-emacs-26.patch \
%D%/packages/patches/emacs-exec-path.patch \
%D%/packages/patches/emacs-fix-scheme-indent-function.patch \
%D%/packages/patches/emacs-json-reformat-fix-tests.patch \
@@ -806,7 +808,6 @@ dist_patch_DATA = \
%D%/packages/patches/findutils-localstatedir.patch \
%D%/packages/patches/findutils-makedev.patch \
%D%/packages/patches/findutils-test-xargs.patch \
- %D%/packages/patches/flac-CVE-2017-6888.patch \
%D%/packages/patches/flann-cmake-3.11.patch \
%D%/packages/patches/flint-ldconfig.patch \
%D%/packages/patches/foomatic-filters-CVE-2015-8327.patch \
@@ -961,6 +962,7 @@ dist_patch_DATA = \
%D%/packages/patches/inkscape-poppler-0.76.patch \
%D%/packages/patches/intltool-perl-compatibility.patch \
%D%/packages/patches/irrlicht-use-system-libs.patch \
+ %D%/packages/patches/isc-dhcp-4.4.1-fixes-for-newer-bind.patch \
%D%/packages/patches/isl-0.11.1-aarch64-support.patch \
%D%/packages/patches/jacal-fix-texinfo.patch \
%D%/packages/patches/jamvm-arm.patch \
@@ -1026,7 +1028,8 @@ dist_patch_DATA = \
%D%/packages/patches/libotr-test-auth-fix.patch \
%D%/packages/patches/libmad-armv7-thumb-pt1.patch \
%D%/packages/patches/libmad-armv7-thumb-pt2.patch \
- %D%/packages/patches/libmad-frame-length.patch \
+ %D%/packages/patches/libmad-length-check.patch \
+ %D%/packages/patches/libmad-md_size.patch \
%D%/packages/patches/libmad-mips-newgcc.patch \
%D%/packages/patches/libmp4v2-c++11.patch \
%D%/packages/patches/libmygpo-qt-fix-qt-5.11.patch \
@@ -1047,7 +1050,6 @@ 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/libvirt-remove-ATTRIBUTE_UNUSED.patch \
%D%/packages/patches/libvpx-CVE-2016-2818.patch \
%D%/packages/patches/libvpx-use-after-free-in-postproc.patch \
%D%/packages/patches/libxslt-generated-ids.patch \
@@ -1078,6 +1080,7 @@ dist_patch_DATA = \
%D%/packages/patches/lxsession-use-gapplication.patch \
%D%/packages/patches/make-glibc-compat.patch \
%D%/packages/patches/make-impure-dirs.patch \
+ %D%/packages/patches/mame-rapidjson-fix.patch \
%D%/packages/patches/mariadb-client-test-32bit.patch \
%D%/packages/patches/mars-install.patch \
%D%/packages/patches/mars-sfml-2.3.patch \
@@ -1124,6 +1127,7 @@ dist_patch_DATA = \
%D%/packages/patches/nfs-utils-missing-headers.patch \
%D%/packages/patches/ngircd-handle-zombies.patch \
%D%/packages/patches/nm-plugin-path.patch \
+ %D%/packages/patches/nss-freebl-stubs.patch \
%D%/packages/patches/nss-increase-test-timeout.patch \
%D%/packages/patches/nss-pkgconfig.patch \
%D%/packages/patches/ntfs-3g-CVE-2019-9755.patch \
@@ -1169,6 +1173,7 @@ dist_patch_DATA = \
%D%/packages/patches/patchelf-rework-for-arm.patch \
%D%/packages/patches/patchutils-test-perms.patch \
%D%/packages/patches/patch-hurd-path-max.patch \
+ %D%/packages/patches/pcre2-fix-jit_match-crash.patch \
%D%/packages/patches/perl-autosplit-default-time.patch \
%D%/packages/patches/perl-deterministic-ordering.patch \
%D%/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch \
@@ -1291,8 +1296,6 @@ dist_patch_DATA = \
%D%/packages/patches/scheme48-tests.patch \
%D%/packages/patches/scotch-build-parallelism.patch \
%D%/packages/patches/scotch-integer-declarations.patch \
- %D%/packages/patches/scribus-poppler.patch \
- %D%/packages/patches/scribus-poppler-0.73.patch \
%D%/packages/patches/sdl-libx11-1.6.patch \
%D%/packages/patches/seq24-rename-mutex.patch \
%D%/packages/patches/sharutils-CVE-2018-1000097.patch \
@@ -1308,6 +1311,7 @@ dist_patch_DATA = \
%D%/packages/patches/soundconverter-remove-gconf-dependency.patch \
%D%/packages/patches/sssd-curl-compat.patch \
%D%/packages/patches/steghide-fixes.patch \
+ %D%/packages/patches/strace-ipc-tests.patch \
%D%/packages/patches/streamlink-update-test.patch \
%D%/packages/patches/stumpwm-fix-broken-read-one-line.patch \
%D%/packages/patches/superlu-dist-awpm-grid.patch \
diff --git a/gnu/machine.scm b/gnu/machine.scm
index 0b79402b0a..30ae97f6ec 100644
--- a/gnu/machine.scm
+++ b/gnu/machine.scm
@@ -34,7 +34,7 @@
machine?
this-machine
- machine-system
+ machine-operating-system
machine-environment
machine-configuration
machine-display-name
@@ -85,14 +85,14 @@
make-machine
machine?
this-machine
- (system machine-system) ; <operating-system>
- (environment machine-environment) ; symbol
- (configuration machine-configuration ; configuration object
- (default #f))) ; specific to environment
+ (operating-system machine-operating-system) ; <operating-system>
+ (environment machine-environment) ; symbol
+ (configuration machine-configuration ; configuration object
+ (default #f))) ; specific to environment
(define (machine-display-name machine)
"Return the host-name identifying MACHINE."
- (operating-system-host-name (machine-system machine)))
+ (operating-system-host-name (machine-operating-system machine)))
(define (machine-remote-eval machine exp)
"Evaluate EXP, a gexp, on MACHINE. Ensure that all the elements EXP refers to
diff --git a/gnu/machine/ssh.scm b/gnu/machine/ssh.scm
index 552eafa9de..ba3e33c922 100644
--- a/gnu/machine/ssh.scm
+++ b/gnu/machine/ssh.scm
@@ -20,6 +20,9 @@
#:use-module (gnu machine)
#:autoload (gnu packages gnupg) (guile-gcrypt)
#:use-module (gnu system)
+ #:use-module (gnu system file-systems)
+ #:use-module (gnu system uuid)
+ #:use-module (guix diagnostics)
#:use-module (guix gexp)
#:use-module (guix i18n)
#:use-module (guix modules)
@@ -29,6 +32,7 @@
#:use-module (guix scripts system reconfigure)
#:use-module (guix ssh)
#:use-module (guix store)
+ #:use-module (guix utils)
#:use-module (ice-9 match)
#:use-module (srfi srfi-19)
#:use-module (srfi srfi-26)
@@ -40,6 +44,7 @@
machine-ssh-configuration
machine-ssh-configuration-host-name
+ machine-ssh-configuration-build-locally?
machine-ssh-configuration-port
machine-ssh-configuration-user
machine-ssh-configuration-session))
@@ -62,15 +67,17 @@
make-machine-ssh-configuration
machine-ssh-configuration?
this-machine-ssh-configuration
- (host-name machine-ssh-configuration-host-name) ; string
- (port machine-ssh-configuration-port ; integer
- (default 22))
- (user machine-ssh-configuration-user ; string
- (default "root"))
- (identity machine-ssh-configuration-identity ; path to a private key
- (default #f))
- (session machine-ssh-configuration-session ; session
- (default #f)))
+ (host-name machine-ssh-configuration-host-name) ; string
+ (build-locally? machine-ssh-configuration-build-locally?
+ (default #t))
+ (port machine-ssh-configuration-port ; integer
+ (default 22))
+ (user machine-ssh-configuration-user ; string
+ (default "root"))
+ (identity machine-ssh-configuration-identity ; path to a private key
+ (default #f))
+ (session machine-ssh-configuration-session ; session
+ (default #f)))
(define (machine-ssh-session machine)
"Return the SSH session that was given in MACHINE's configuration, or create
@@ -96,7 +103,149 @@ one from the configuration's parameters if one was not provided."
"Internal implementation of 'machine-remote-eval' for MACHINE instances with
an environment type of 'managed-host."
(maybe-raise-unsupported-configuration-error machine)
- (remote-eval exp (machine-ssh-session machine)))
+ (remote-eval exp (machine-ssh-session machine)
+ #:build-locally?
+ (machine-ssh-configuration-build-locally?
+ (machine-configuration machine))))
+
+
+;;;
+;;; Safety checks.
+;;;
+
+(define (machine-check-file-system-availability machine)
+ "Raise a '&message' error condition if any of the file-systems specified in
+MACHINE's 'system' declaration do not exist on the machine."
+ (define file-systems
+ (filter (lambda (fs)
+ (and (file-system-mount? fs)
+ (not (member (file-system-type fs)
+ %pseudo-file-system-types))
+ (not (memq 'bind-mount (file-system-flags fs)))))
+ (operating-system-file-systems (machine-operating-system machine))))
+
+ (define (check-literal-file-system fs)
+ (define remote-exp
+ #~(catch 'system-error
+ (lambda ()
+ (stat #$(file-system-device fs))
+ #t)
+ (lambda args
+ (system-error-errno args))))
+
+ (mlet %store-monad ((errno (machine-remote-eval machine remote-exp)))
+ (when (number? errno)
+ (raise (condition
+ (&message
+ (message (format #f (G_ "device '~a' not found: ~a")
+ (file-system-device fs)
+ (strerror errno)))))))
+ (return #t)))
+
+ (define (check-labeled-file-system fs)
+ (define remote-exp
+ (with-imported-modules '((gnu build file-systems))
+ #~(begin
+ (use-modules (gnu build file-systems))
+ (find-partition-by-label #$(file-system-label->string
+ (file-system-device fs))))))
+
+ (mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
+ (unless result
+ (raise (condition
+ (&message
+ (message (format #f (G_ "no file system with label '~a'")
+ (file-system-label->string
+ (file-system-device fs))))))))
+ (return #t)))
+
+ (define (check-uuid-file-system fs)
+ (define remote-exp
+ (with-imported-modules (source-module-closure
+ '((gnu build file-systems)
+ (gnu system uuid)))
+ #~(begin
+ (use-modules (gnu build file-systems)
+ (gnu system uuid))
+
+ (define uuid
+ (string->uuid #$(uuid->string (file-system-device fs))))
+
+ (find-partition-by-uuid uuid))))
+
+ (mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
+ (unless result
+ (raise (condition
+ (&message
+ (message (format #f (G_ "no file system with UUID '~a'")
+ (uuid->string (file-system-device fs))))))))
+ (return #t)))
+
+ (mbegin %store-monad
+ (mapm %store-monad check-literal-file-system
+ (filter (lambda (fs)
+ (string? (file-system-device fs)))
+ file-systems))
+ (mapm %store-monad check-labeled-file-system
+ (filter (lambda (fs)
+ (file-system-label? (file-system-device fs)))
+ file-systems))
+ (mapm %store-monad check-uuid-file-system
+ (filter (lambda (fs)
+ (uuid? (file-system-device fs)))
+ file-systems))))
+
+(define (machine-check-initrd-modules machine)
+ "Raise a '&message' error condition if any of the modules needed by
+'needed-for-boot' file systems in MACHINE are not available in the initrd."
+ (define file-systems
+ (filter file-system-needed-for-boot?
+ (operating-system-file-systems (machine-operating-system machine))))
+
+ (define (missing-modules fs)
+ (define remote-exp
+ (let ((device (file-system-device fs)))
+ (with-imported-modules (source-module-closure
+ '((gnu build file-systems)
+ (gnu build linux-modules)
+ (gnu system uuid)))
+ #~(begin
+ (use-modules (gnu build file-systems)
+ (gnu build linux-modules)
+ (gnu system uuid))
+
+ (define dev
+ #$(cond ((string? device) device)
+ ((uuid? device) #~(find-partition-by-uuid
+ (string->uuid
+ #$(uuid->string device))))
+ ((file-system-label? device)
+ #~(find-partition-by-label
+ (file-system-label->string #$device)))))
+
+ (missing-modules dev '#$(operating-system-initrd-modules
+ (machine-operating-system machine)))))))
+ (mlet %store-monad ((missing (machine-remote-eval machine remote-exp)))
+ (return (list fs missing))))
+
+ (mlet %store-monad ((device (mapm %store-monad missing-modules file-systems)))
+ (for-each (match-lambda
+ ((fs missing)
+ (unless (null? missing)
+ (raise (condition
+ (&message
+ (message (format #f (G_ "~a missing modules ~{ ~a~}~%")
+ (file-system-device fs)
+ missing))))))))
+ device)
+ (return #t)))
+
+(define (check-deployment-sanity machine)
+ "Raise a '&message' error condition if it is clear that deploying MACHINE's
+'system' declaration would fail."
+ (mbegin %store-monad
+ (machine-check-file-system-availability machine)
+ (machine-check-initrd-modules machine)))
;;;
@@ -165,8 +314,9 @@ of MACHINE's system profile, ordered from most recent to oldest."
"Internal implementation of 'deploy-machine' for MACHINE instances with an
environment type of 'managed-host."
(maybe-raise-unsupported-configuration-error machine)
- (mlet %store-monad ((boot-parameters (machine-boot-parameters machine)))
- (let* ((os (machine-system machine))
+ (mlet %store-monad ((_ (check-deployment-sanity machine))
+ (boot-parameters (machine-boot-parameters machine)))
+ (let* ((os (machine-operating-system machine))
(eval (cut machine-remote-eval machine <>))
(menu-entries (map boot-parameters->menu-entry boot-parameters))
(bootloader-configuration (operating-system-bootloader os))
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index c3b1e04901..bd3c14033e 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -1,7 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
-;;; Copyright © 2014, 2015, 2016, 2018 Mark H Weaver <mhw@netris.org>
+;;; 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 © 2015, 2016 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com>
@@ -684,9 +684,9 @@ connection alive.")
(define-public isc-dhcp
(let* ((bind-major-version "9")
(bind-minor-version "11")
- (bind-patch-version "4")
- (bind-release-type "-P") ; for patch release, use "-P"
- (bind-release-version "2") ; for patch release, e.g. "6"
+ (bind-patch-version "9")
+ (bind-release-type "") ; for patch release, use "-P"
+ (bind-release-version "") ; for patch release, e.g. "6"
(bind-version (string-append bind-major-version
"."
bind-minor-version
@@ -710,7 +710,18 @@ connection alive.")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'replace-bundled-bind
- (lambda* (#:key inputs #:allow-other-keys)
+ (lambda* (#:key inputs native-inputs #:allow-other-keys)
+ ;; XXX TODO: Remove the following invocation of 'patch' when
+ ;; isc-dhcp is updated. It should be needed only for 4.4.1.
+ (let ((patch (string-append (assoc-ref (or native-inputs inputs)
+ "patch")
+ "/bin/patch"))
+ (the-patch (assoc-ref (or native-inputs inputs)
+ "fixes-for-newer-bind.patch")))
+ (format #t "applying '~a'...~%" the-patch)
+ (invoke patch "--force" "--no-backup-if-mismatch"
+ "-p1" "--input" the-patch))
+
(delete-file "bind/bind.tar.gz")
(copy-file (assoc-ref inputs "bind-source-tarball")
"bind/bind.tar.gz")
@@ -743,15 +754,18 @@ connection alive.")
;; shell is used.
(with-directory-excursion "bind"
(substitute* "Makefile"
- (("\\./configure")
+ (("\\./configure ")
(let ((sh (which "sh")))
(string-append "./configure CONFIG_SHELL="
- sh " SHELL=" sh))))
+ sh " SHELL=" sh " "))))
(let ((bind-directory (string-append "bind-" ,bind-version)))
(invoke "tar" "xf" "bind.tar.gz")
(for-each patch-shebang
(find-files bind-directory ".*"))
+ (substitute* (string-append bind-directory "/configure")
+ (("/usr/bin/file")
+ (which "file")))
(invoke "tar" "cf" "bind.tar.gz"
bind-directory
;; avoid non-determinism in the archive
@@ -787,7 +801,15 @@ connection alive.")
(list inetutils net-tools coreutils sed))))
#t))))))
- (native-inputs `(("perl" ,perl)))
+ (native-inputs
+ `(("perl" ,perl)
+ ("file" ,file)
+
+ ;; XXX TODO: Remove the following patch, and also the 'patch'
+ ;; program, when isc-dhcp is updated.
+ ("fixes-for-newer-bind.patch"
+ ,(search-patch "isc-dhcp-4.4.1-fixes-for-newer-bind.patch"))
+ ("patch" ,patch)))
(inputs `(("inetutils" ,inetutils)
("net-tools" ,net-tools)
@@ -803,7 +825,7 @@ connection alive.")
"/bind-" bind-version ".tar.gz"))
(sha256
(base32
- "04fq17zksd2b3w6w6padps5n7b6s2lasxpksbhl4378h56vgfnm8"))))
+ "03n57as73ygw6g3lqsmq2idkykajpbskzgixixdvi5a76m4g0fwn"))))
;; When cross-compiling, we need the cross Coreutils and sed.
;; Otherwise just use those from %FINAL-INPUTS.
@@ -1181,7 +1203,7 @@ commands and their arguments.")
(define-public wpa-supplicant-minimal
(package
(name "wpa-supplicant-minimal")
- (version "2.8")
+ (version "2.9")
(source (origin
(method url-fetch)
(uri (string-append
@@ -1189,7 +1211,7 @@ commands and their arguments.")
version ".tar.gz"))
(sha256
(base32
- "15ixzm347n8w6gdvi3j3yks3i15qmp6by9ayvswm34d929m372d6"))
+ "05qzak1mssnxcgdrafifxh9w86a4ha69qabkg4bsigk499xyxggw"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -2606,7 +2628,7 @@ buffers.")
`(#:tests? #f ; many of the tests try to load kernel modules
#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'autogen
+ (replace 'bootstrap
(lambda _
;; Don't run configure in this phase.
(setenv "NOCONFIGURE" "1")
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 1e21562e91..fb9e78bf92 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -236,8 +236,7 @@ the real span of the lattice.")
(build-system gnu-build-system)
(native-inputs
`(("texlive" ,(texlive-union
- (list texlive-fonts-amsfonts
- texlive-latex-amsfonts)))))
+ (list texlive-amsfonts)))))
(inputs `(("gmp" ,gmp)
("libx11" ,libx11)
("perl" ,perl)
@@ -345,7 +344,7 @@ precision.")
(define-public giac
(package
(name "giac")
- (version "1.5.0-61")
+ (version "1.5.0-63")
(source (origin
(method url-fetch)
;; "~parisse/giac" is not used because the maintainer regularly
@@ -357,7 +356,7 @@ precision.")
"source/giac_" version ".tar.gz"))
(sha256
(base32
- "050vzpqq77fhky32sbisc0ysimgp60xjv39q7y45jkaabdkmclwh"))))
+ "1jp7awyp8j8w6fhn802z8ddbq1fxhkyk9xdf0mq0mm0chpkylwqk"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((ice-9 ftw)
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 43c1bc6c8b..c3bcecf349 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -3692,7 +3692,7 @@ library.")
(define-public faudio
(package
(name "faudio")
- (version "19.07")
+ (version "19.08")
(source
(origin
(method git-fetch)
@@ -3701,7 +3701,7 @@ library.")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
- (base32 "1wf6skc5agaikc9qgwk8bx56sad31fafs53lqqn4jmx8i76pl0lw"))))
+ (base32 "1v13kfhyr46241vb6a4dcb4gw5f149525sprwa9cj4rv6wlcqgm5"))))
(arguments
'(#:tests? #f ; No tests.
#:configure-flags '("-DFFMPEG=ON")))
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1adf47b08f..74620a2cbe 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -38,7 +38,8 @@
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages statistics)
- #:use-module (gnu packages web))
+ #:use-module (gnu packages web)
+ #:use-module (srfi srfi-1))
;;; Annotations
@@ -1211,14 +1212,14 @@ determining dependencies between variables, code improvement suggestions.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.18.1")
+ (version "3.18.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji"))))
+ "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
@@ -1520,14 +1521,14 @@ experiments.")
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
- "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
+ "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
@@ -3528,14 +3529,14 @@ position-specific scores within R and Bioconductor.")
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
- (version "1.8.1")
+ (version "1.8.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
- "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69"))))
+ "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
@@ -3620,14 +3621,14 @@ annotations and ontologies.")
(define-public r-abaenrichment
(package
(name "r-abaenrichment")
- (version "1.14.0")
+ (version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ABAEnrichment" version))
(sha256
(base32
- "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
+ "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
(properties `((upstream-name . "ABAEnrichment")))
(build-system r-build-system)
(propagated-inputs
@@ -4840,14 +4841,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "1.34.4")
+ (version "1.34.6")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "1230p8nsakifmpsqfiaj8rpm7npa8ab903mfjmayfa71n6yzvcbs"))))
+ "0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -5128,3 +5129,25 @@ data, to only emphasize the data that actually matters.")
accessibility data. It also extends the monocle package for use in chromatin
accessibility data.")
(license license:expat)))
+
+;; This is the latest commit on the "monocle3" branch.
+(define-public r-cicero-monocle3
+ (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
+ (revision "1"))
+ (package (inherit r-cicero)
+ (name "r-cicero-monocle3")
+ (version (git-version "1.3.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/cole-trapnell-lab/cicero-release.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
+ (propagated-inputs
+ `(("r-monocle3" ,r-monocle3)
+ ,@(alist-delete "r-monocle"
+ (package-propagated-inputs r-cicero)))))))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b1cf294177..898b8d200e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13,6 +13,7 @@
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -4195,8 +4196,15 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
(modify-phases %standard-phases
(add-after 'unpack 'set-cc
(lambda _ (setenv "CC" "gcc") #t))
- ;; FIXME: This fails with "permission denied".
- (delete 'reset-gzip-timestamps))))
+
+ (add-before 'reset-gzip-timestamps 'make-files-writable
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Make sure .gz files are writable so that the
+ ;; 'reset-gzip-timestamps' phase can do its work.
+ (let ((out (assoc-ref outputs "out")))
+ (for-each make-file-writable
+ (find-files out "\\.gz$"))
+ #t))))))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
@@ -7439,13 +7447,13 @@ names in their natural, rather than lexicographic, order.")
(define-public r-edger
(package
(name "r-edger")
- (version "3.26.5")
+ (version "3.26.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "0iba4krz30dx5b0s89n5cfkwn64867s7vmvvfqms9lbcr4kj439m"))))
+ "17vadhamjv4x0l4qqq2p2fi6j2bkllz5zd8dq761vgd5ic23zizm"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
@@ -7506,13 +7514,13 @@ coding changes and predict coding outcomes.")
(define-public r-limma
(package
(name "r-limma")
- (version "3.40.2")
+ (version "3.40.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "1d4ig2b7fa9mwja52isxrwmprfdjdk1mlcf2skhdp51l24z6wbk7"))))
+ "166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7639,13 +7647,13 @@ annotation data packages using SQLite data storage.")
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.40.1")
+ (version "2.40.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "1abl0c4qbhfqf9ixdp74183phm7s8rszrr5ldczm59b8vyng8rhx"))))
+ "022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
@@ -7672,13 +7680,13 @@ powerful online queries from gene annotation to database mining.")
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.18.0")
+ (version "1.18.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "0v8rhf3hbgb3v32h2pmsv1y6q2x4airmpp50fk7z6ardcn4aza7x"))))
+ "1j6wbls4qgvi5gj99c51r00jhxrzxk3x3258wg7dcjzbfqypvyw3"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
@@ -7800,13 +7808,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.14.0")
+ (version "1.14.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci"))))
+ "0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
@@ -7864,13 +7872,13 @@ alignments.")
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.44.0")
+ (version "1.44.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "161gcks9b12993g9k27gf7wfh8lgd8m8rr7x2slgfqqssk0yrmpd"))))
+ "03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -7911,13 +7919,13 @@ as well as query and modify the browser state, such as the current viewport.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.36.3")
+ (version "1.36.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "0zkd57i5qjxsravv0gbyckc0wrnqzgxd61ibh3jmhmrccrr9ihn3"))))
+ "0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -8335,13 +8343,13 @@ paired-end data.")
(define-public r-rcas
(package
(name "r-rcas")
- (version "1.10.0")
+ (version "1.10.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "RCAS" version))
(sha256
(base32
- "1h4vf5gzilqbdrd8m9l3zc2m4sca8cir8366a7njgd558k7ld5kl"))))
+ "06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz"))))
(properties `((upstream-name . "RCAS")))
(build-system r-build-system)
(propagated-inputs
@@ -9399,14 +9407,14 @@ of mass spectrometry based proteomics data.")
(define-public r-msnid
(package
(name "r-msnid")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
- "18mp8zacawhfapfwpq8czbswxix2ykvqhwjga54v0a99zg3k87h3"))))
+ "1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(propagated-inputs
@@ -10406,14 +10414,14 @@ provided.")
(define-public r-hdf5array
(package
(name "r-hdf5array")
- (version "1.12.1")
+ (version "1.12.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
- "0n8zc1x582vwb0zfhrjmnqbnpqky9zbhjc2j836i0a4yisklwdcp"))))
+ "0afradisrr5gn0lf2kxjw55vdm3lm9mlgx53qlr9r40c1hrydpf5"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(inputs
@@ -14804,3 +14812,406 @@ trees by inserting random mutations. The tbsp package implements an
alternative method to detect significant, cell type specific sequence
mutations from scRNA-Seq data.")
(license license:expat))))
+
+(define-public tabixpp
+ (package
+ (name "tabixpp")
+ (version "1.0.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/tabixpp")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "08vx6nsipk971cyr8z53rnzwkvlld63kcn1fw0pwddynz91xfny8"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("htslib" ,htslib)
+ ("zlib" ,zlib)))
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ ;; The build phase needs overriding the location of htslib.
+ (replace 'build
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((htslib-ref (assoc-ref inputs "htslib")))
+ (invoke "make"
+ (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
+ "HTS_HEADERS=" ; No need to check for headers here.
+ (string-append "LIBPATH=-L. -L" htslib-ref "/include")))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "tabix++" bin))
+ #t)))))
+ (home-page "https://github.com/ekg/tabixpp")
+ (synopsis "C++ wrapper around tabix project")
+ (description "This is a C++ wrapper around the Tabix project which abstracts
+some of the details of opening and jumping in tabix-indexed files.")
+ (license license:expat)))
+
+(define tabixpp-freebayes
+ ;; This version works with FreeBayes while the released
+ ;; version doesn't. The released creates a variable with the name \"vcf\"
+ ;; somewhere, which is also the name of a namespace in vcflib.
+ (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7"))
+ (package
+ (inherit tabixpp)
+ (name "tabixpp-freebayes")
+ (version (git-version "0.0.0" "1" commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/tabixpp/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g")))))))
+
+(define-public smithwaterman
+ ;; TODO: Upgrading smithwaterman breaks FreeBayes.
+ (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
+ (package
+ (name "smithwaterman")
+ (version (string-append "0-1." (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/smithwaterman/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "smithwaterman" bin))
+ #t)))))
+ (home-page "https://github.com/ekg/smithwaterman")
+ (synopsis "Implementation of the Smith-Waterman algorithm")
+ (description "Implementation of the Smith-Waterman algorithm.")
+ ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9.
+ (license (list license:gpl2 license:expat)))))
+
+(define-public multichoose
+ (package
+ (name "multichoose")
+ (version "1.0.3")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/multichoose/")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; Tests require node.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ ;; TODO: There are Python modules for these programs too.
+ (install-file "multichoose" bin)
+ (install-file "multipermute" bin))
+ #t)))))
+ (home-page "https://github.com/ekg/multichoose")
+ (synopsis "Efficient loopless multiset combination generation algorithm")
+ (description "This library implements an efficient loopless multiset
+combination generation algorithm which is (approximately) described in
+\"Loopless algorithms for generating permutations, combinations, and other
+combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM),
+1973. (Algorithm 7.)")
+ (license license:expat)))
+
+(define-public fsom
+ (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3"))
+ (package
+ (name "fsom")
+ (version (git-version "0.0.0" "1" commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/fsom/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "fsom" bin))
+ #t)))))
+ (home-page "https://github.com/ekg/fsom")
+ (synopsis "Manage SOM (Self-Organizing Maps) neural networks")
+ (description "A tiny C library for managing SOM (Self-Organizing Maps)
+neural networks.")
+ (license license:gpl3))))
+
+(define-public fastahack
+ (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd"))
+ (package
+ (name "fastahack")
+ (version (git-version "0.0.0" "1" commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/fastahack/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0hfdv67l9g611i2ck4l92pd6ygmsp9g1ph4zx1ni7qkpsikf0l19"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "fastahack" bin))
+ #t)))))
+ (home-page "https://github.com/ekg/fastahack")
+ (synopsis "Indexing and sequence extraction from FASTA files")
+ (description "Fastahack is a small application for indexing and
+extracting sequences and subsequences from FASTA files. The included library
+provides a FASTA reader and indexer that can be embedded into applications
+which would benefit from directly reading subsequences from FASTA files. The
+library automatically handles index file generation and use.")
+ (license (list license:expat license:gpl2)))))
+
+(define-public vcflib
+ (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92")
+ (revision "1"))
+ (package
+ (name "vcflib")
+ (version (git-version "0.0.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vcflib/vcflib/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (native-inputs
+ `(("perl" ,perl)
+ ("python" ,python-2)
+ ;; Submodules.
+ ;; This package builds against the .o files so we need to extract the source.
+ ("tabixpp-src" ,(package-source tabixpp-freebayes))
+ ("smithwaterman-src" ,(package-source smithwaterman))
+ ("multichoose-src" ,(package-source multichoose))
+ ("fsom-src" ,(package-source fsom))
+ ("filevercmp-src" ,(package-source filevercmp))
+ ("fastahack-src" ,(package-source fastahack))
+ ("intervaltree-src"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/intervaltree/")
+ (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
+ (file-name "intervaltree-src-checkout")
+ (sha256
+ (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))))
+ (arguments
+ `(#:tests? #f ; no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'check)
+ (add-after 'unpack 'unpack-submodule-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((unpack (lambda (source target)
+ (with-directory-excursion target
+ (if (file-is-directory? (assoc-ref inputs source))
+ (copy-recursively (assoc-ref inputs source) ".")
+ (invoke "tar" "xvf"
+ (assoc-ref inputs source)
+ "--strip-components=1"))))))
+ (and
+ (unpack "intervaltree-src" "intervaltree")
+ (unpack "fastahack-src" "fastahack")
+ (unpack "filevercmp-src" "filevercmp")
+ (unpack "fsom-src" "fsom")
+ (unpack "multichoose-src" "multichoose")
+ (unpack "smithwaterman-src" "smithwaterman")
+ (unpack "tabixpp-src" "tabixpp")))))
+ (replace 'build
+ (lambda* (#:key inputs make-flags #:allow-other-keys)
+ (with-directory-excursion "tabixpp"
+ (invoke "make"))
+ (invoke "make" "CC=gcc"
+ (string-append "CFLAGS=\"" "-Itabixpp " "\"")
+ "all")))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+ (lib (string-append (assoc-ref outputs "out") "/lib")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "bin" ".*"))
+ ;; The header files in src/ do not interface libvcflib,
+ ;; therefore they are left out.
+ (install-file "libvcflib.a" lib))
+ #t)))))
+ (home-page "https://github.com/vcflib/vcflib/")
+ (synopsis "Library for parsing and manipulating VCF files")
+ (description "Vcflib provides methods to manipulate and interpret
+sequence variation as it can be described by VCF. It is both an API for parsing
+and operating on records of genomic variation as it can be described by the VCF
+format, and a collection of command-line utilities for executing complex
+manipulations on VCF files.")
+ (license license:expat))))
+
+(define-public freebayes
+ (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
+ (revision "1")
+ (version "1.0.2"))
+ (package
+ (name "freebayes")
+ (version (git-version version revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/freebayes.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("bamtools" ,bamtools)
+ ("htslib" ,htslib)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("bc" ,bc) ; Needed for running tests.
+ ("samtools" ,samtools) ; Needed for running tests.
+ ("parallel" ,parallel) ; Needed for running tests.
+ ("perl" ,perl) ; Needed for running tests.
+ ("procps" ,procps) ; Needed for running tests.
+ ("python" ,python-2) ; Needed for running tests.
+ ("vcflib-src" ,(package-source vcflib))
+ ;; These are submodules for the vcflib version used in freebayes.
+ ;; This package builds against the .o files so we need to extract the source.
+ ("tabixpp-src" ,(package-source tabixpp-freebayes))
+ ("smithwaterman-src" ,(package-source smithwaterman))
+ ("multichoose-src" ,(package-source multichoose))
+ ("fsom-src" ,(package-source fsom))
+ ("filevercmp-src" ,(package-source filevercmp))
+ ("fastahack-src" ,(package-source fastahack))
+ ("intervaltree-src"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/intervaltree/")
+ (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
+ (file-name "intervaltree-src-checkout")
+ (sha256
+ (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))
+ ;; These submodules are needed to run the tests.
+ ("bash-tap-src" ,(package-source bash-tap))
+ ("test-simple-bash-src"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ingydotnet/test-simple-bash/")
+ (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
+ (file-name "test-simple-bash-src-checkout")
+ (sha256
+ (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
+ (arguments
+ `(#:make-flags
+ (list "CC=gcc"
+ (string-append "BAMTOOLS_ROOT="
+ (assoc-ref %build-inputs "bamtools")))
+ #:test-target "test"
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'fix-tests
+ (lambda _
+ (substitute* "test/t/01_call_variants.t"
+ (("grep -P \"\\(\\\\t500\\$\\|\\\\t11000\\$\\|\\\\t1000\\$\\)\"")
+ "grep -E ' (500|11000|1000)$'"))
+ #t))
+ (add-after 'unpack 'unpack-submodule-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((unpack (lambda (source target)
+ (with-directory-excursion target
+ (if (file-is-directory? (assoc-ref inputs source))
+ (copy-recursively (assoc-ref inputs source) ".")
+ (invoke "tar" "xvf"
+ (assoc-ref inputs source)
+ "--strip-components=1"))))))
+ (and
+ (unpack "vcflib-src" "vcflib")
+ (unpack "fastahack-src" "vcflib/fastahack")
+ (unpack "filevercmp-src" "vcflib/filevercmp")
+ (unpack "fsom-src" "vcflib/fsom")
+ (unpack "intervaltree-src" "vcflib/intervaltree")
+ (unpack "multichoose-src" "vcflib/multichoose")
+ (unpack "smithwaterman-src" "vcflib/smithwaterman")
+ (unpack "tabixpp-src" "vcflib/tabixpp")
+ (unpack "test-simple-bash-src" "test/test-simple-bash")
+ (unpack "bash-tap-src" "test/bash-tap")))))
+ (add-after 'unpack-submodule-sources 'fix-makefiles
+ (lambda _
+ ;; We don't have the .git folder to get the version tag from.
+ (substitute* "vcflib/Makefile"
+ (("^GIT_VERSION.*")
+ (string-append "GIT_VERSION = v" ,version)))
+ (substitute* "src/Makefile"
+ (("-I\\$\\(BAMTOOLS_ROOT\\)/src")
+ "-I$(BAMTOOLS_ROOT)/include/bamtools"))
+ #t))
+ (add-before 'build 'build-tabixpp-and-vcflib
+ (lambda* (#:key inputs make-flags #:allow-other-keys)
+ (with-directory-excursion "vcflib"
+ (with-directory-excursion "tabixpp"
+ (apply invoke "make"
+ (string-append "HTS_LIB="
+ (assoc-ref inputs "htslib")
+ "/lib/libhts.a")
+ make-flags))
+ (apply invoke "make"
+ (string-append "CFLAGS=-Itabixpp")
+ "all"
+ make-flags))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "bin/freebayes" bin)
+ (install-file "bin/bamleftalign" bin))
+ #t)))))
+ (home-page "https://github.com/ekg/freebayes")
+ (synopsis "Haplotype-based variant detector")
+ (description "FreeBayes is a Bayesian genetic variant detector designed to
+find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
+indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
+complex events (composite insertion and substitution events) smaller than the
+length of a short-read sequencing alignment.")
+ (license license:expat))))
diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm
index e622170815..b0893d9410 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 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016, 2017, 2018, 2019 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Tomáš Čech <sleep_walker@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -183,35 +183,38 @@ XML-RPC over SCGI.")
(license l:gpl2+)))
(define-public tremc
- (package
- (name "tremc")
- (version "0.9.1")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/tremc/tremc.git")
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1yhwvlcyv1s830p5a7q5x3mkb3mbvr5cn5nh7y62l5b6iyyynlvm"))))
- (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
+ (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
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
diff --git a/gnu/packages/certs.scm b/gnu/packages/certs.scm
index c41870332c..7e0071ecf9 100644
--- a/gnu/packages/certs.scm
+++ b/gnu/packages/certs.scm
@@ -76,7 +76,7 @@
(define-public nss-certs
(package
(name "nss-certs")
- (version "3.44.1")
+ (version "3.45")
(source (origin
(method url-fetch)
(uri (let ((version-with-underscores
@@ -87,7 +87,7 @@
"nss-" version ".tar.gz")))
(sha256
(base32
- "1y0jvva4s3j7cjz22kqw2lsml0an1295bgpc2raf7kc9r60cpr7w"))))
+ "12sfq9xvpwpc22qnjsg1if1lmchiy33byrh92wn91phz7li0abqi"))))
(build-system gnu-build-system)
(outputs '("out"))
(native-inputs
diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm
index 3dccecba88..3b45c430ca 100644
--- a/gnu/packages/chromium.scm
+++ b/gnu/packages/chromium.scm
@@ -73,7 +73,8 @@
#:use-module (srfi srfi-1))
(define %preserved-third-party-files
- '("base/third_party/dmg_fp" ;X11-style
+ '("base/third_party/cityhash" ;Expat
+ "base/third_party/dmg_fp" ;X11-style
"base/third_party/dynamic_annotations" ;BSD-2
"base/third_party/icu" ;Unicode, X11-style
"base/third_party/superfasthash" ;BSD-3
@@ -85,7 +86,7 @@
"courgette/third_party/divsufsort" ;Expat
"net/third_party/mozilla_security_manager" ;MPL-1.1/GPL2+/LGPL2.1+
"net/third_party/nss" ;MPL-2.0
- "net/third_party/quic" ;BSD-3
+ "net/third_party/quiche" ;BSD-3
"net/third_party/uri_template" ;ASL2.0
"third_party/abseil-cpp" ;ASL2.0
"third_party/adobe/flash/flapper_version.h" ;no license, trivial
@@ -105,6 +106,10 @@
"third_party/blink" ;BSD-3, LGPL2+
"third_party/boringssl" ;OpenSSL/ISC (Google additions are ISC)
"third_party/boringssl/src/third_party/fiat" ;Expat
+ "third_party/boringssl/src/third_party/sike" ;Expat
+ ;; XXX: these files are generated by fp-$arch.pl in the above directory.
+ "third_party/boringssl/linux-aarch64/crypto/third_party/sike/asm/fp-armv8.S"
+ "third_party/boringssl/linux-x86_64/crypto/third_party/sike/asm/fp-x86_64.S"
"third_party/breakpad" ;BSD-3
"third_party/brotli" ;Expat
"third_party/cacheinvalidation" ;ASL2.0
@@ -164,6 +169,7 @@
"third_party/nasm" ;BSD-2
"third_party/node" ;Expat
"third_party/node/node_modules/polymer-bundler/lib/third_party/UglifyJS2" ;BSD-2
+ "third_party/openscreen" ;BSD-3
"third_party/ots" ;BSD-3
"third_party/pdfium" ;BSD-3
"third_party/pdfium/third_party/agg23" ;Expat
@@ -182,9 +188,10 @@
"third_party/s2cellid" ;ASL2.0
"third_party/sfntly" ;ASL2.0
"third_party/skia" ;BSD-3
+ "third_party/skia/include/third_party/skcms" ;BSD-3
"third_party/skia/third_party/gif" ;MPL1.1/GPL2+/LGPL2.1+
"third_party/skia/third_party/skcms" ;BSD-3
- "third_party/skia/third_party/vulkan" ;BSD-3
+ "third_party/skia/third_party/vulkanmemoryallocator" ;BSD-3, Expat
"third_party/smhasher" ;Expat, public domain
"third_party/speech-dispatcher" ;GPL2+
"third_party/spirv-headers" ;ASL2.0
@@ -231,9 +238,9 @@ from forcing GEXP-PROMISE."
#:system system
#:guile-for-build guile)))
-(define %chromium-version "75.0.3770.142")
-(define %ungoogled-revision "5d8abc38b43a62f379615a0dc972b29d9aebb4b4")
-(define %debian-revision "debian/75.0.3770.90-1")
+(define %chromium-version "76.0.3809.100")
+(define %ungoogled-revision "8eba5c0df1a318012e3deab39a9add252a0d56a3")
+(define %debian-revision "debian/76.0.3809.87-2")
(define package-revision "0")
(define %package-version (string-append %chromium-version "-"
package-revision "."
@@ -247,7 +254,7 @@ from forcing GEXP-PROMISE."
%chromium-version ".tar.xz"))
(sha256
(base32
- "1b550hc9sav0qdnh4hiin2bb3jmfyrb3dhbmnc0v8662rjknq3ji"))))
+ "0vfjfxsqf8jrmd7y08ln1lpbilwi150875zn2bawwdq87vd3mncc"))))
(define %ungoogled-origin
(origin
@@ -258,7 +265,7 @@ from forcing GEXP-PROMISE."
(string-take %ungoogled-revision 7)))
(sha256
(base32
- "1vk8jzzsn20ysn4nlz84mwwhfa9nnywzd1lrahlhcky9pf6xzpwa"))))
+ "08fd9whfc1qky44xqxbypr7jz1rg6cma017wj4b5c5b14grxz6k6"))))
(define %debian-origin
(origin
@@ -272,7 +279,29 @@ from forcing GEXP-PROMISE."
(string-take %debian-revision 7))))
(sha256
(base32
- "0sh6z2lx44zb31qrpa29vm0sw09dxi7i9h6fsq3ivfxjs7v98bbx"))))
+ "1fjhpzrxmgjr7i31li1vsfmp0qkbi0cpyc7p1zjwvf2x4da0v907"))))
+
+(define (gentoo-patch name hash revision)
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://gitweb.gentoo.org/repo/gentoo.git/plain"
+ "/www-client/chromium/files/" name "?id=" revision))
+ (file-name name)
+ (sha256 (base32 hash))))
+
+(define-syntax-rule (gentoo-patches (name hash) ...)
+ (list (gentoo-patch name hash "9fd80e7d75aa63843ec33c9d44fee32596ae8f25")
+ ...))
+
+(define %auxiliary-patches
+ ;; XXX: Debians "gcc/wrong-namespace.patch" and "fixes/inspector.patch" does
+ ;; not work for us, so we take these upstream fixes via Gentoo instead.
+ (gentoo-patches
+ ("chromium-76-quiche.patch" "1cs0y16jn7r1nxh0j36vqcsdvigl902kdcqfmyivnxgblrx66l2i")
+ ("chromium-76-gcc-blink-namespace1.patch"
+ "0k7nrn0dhvqxj4sg2gndzxih0l1f77h6pv7jhcdz7h69sm4xci2z")
+ ("chromium-76-gcc-blink-namespace2.patch"
+ "014y2d8ii9sr340sjbv1fhsjd5s3dl0vbmq5wzlkdjsp91dcn9ch")))
;; This is a "computed" origin that does the following:
;; *) Runs the Ungoogled scripts on a pristine Chromium tarball.
@@ -314,6 +343,12 @@ from forcing GEXP-PROMISE."
(force-output)
(invoke "tar" "xf" #+chromium-source)
+ ;; Ungoogled-Chromium contains a forked subset of the Debian
+ ;; patches. Disable those, as we apply newer versions later.
+ (substitute* "patches/series"
+ ((".*/debian_buster/.*")
+ ""))
+
(format #t "Ungooglifying...~%")
(force-output)
(invoke "python3" "utils/prune_binaries.py" chromium-dir
@@ -330,16 +365,7 @@ from forcing GEXP-PROMISE."
(force-output)
(let* ((debian #+debian-source)
(patches (string-append debian "/debian/patches"))
- (series (string-append patches "/series"))
- (grep-q (lambda (query file)
- (with-input-from-file file
- (lambda ()
- (let loop ((line (read-line))
- (match #f))
- (if (or match (eof-object? line))
- (if match #t #f)
- (loop (read-line)
- (string-contains line query)))))))))
+ (series (string-append patches "/series")))
(with-input-from-file series
(lambda ()
(let loop ((line (read-line)))
@@ -347,19 +373,35 @@ from forcing GEXP-PROMISE."
(when (and (> (string-length line) 1)
;; Skip the Debian-specific ones.
(not (string-prefix? "debianization/" line))
+ (not (string-prefix? "buster/" line))
;; And those that conflict with Ungoogled.
(not (any (cute string-suffix? <> line)
'("widevine-buildflag.patch"
"signin.patch"
- "third-party-cookies.patch")))
- ;; Ungoogled includes a subset of the Debian
- ;; patches. Exclude those already present.
- (not (grep-q line "../patches/series")))
+ "third-party-cookies.patch"
+
+ ;; XXX: 'fixes/inspector.patch'
+ ;; makes v8 reuse the top-level
+ ;; third_party/inspector_protocol
+ ;; instead of its own bundled copy,
+ ;; but that does not work here for
+ ;; some reason. Ignore that patch
+ ;; and those that depend on it.
+ "wrong-namespace.patch"
+ "explicit-specialization.patch"
+ "inspector.patch"))))
(invoke "patch" "--force" "-p1" "--input"
(string-append patches "/" line)
"--no-backup-if-mismatch"))
(loop (read-line)))))))
+ (format #t "Applying Guix-specific patches...~%")
+ (force-output)
+ (for-each (lambda (patch)
+ (invoke "patch" "--force" "-p1" "--input"
+ patch "--no-backup-if-mismatch"))
+ '#+%auxiliary-patches)
+
(format #t "Pruning third party files...~%")
(force-output)
(apply invoke "python"
@@ -458,7 +500,6 @@ from forcing GEXP-PROMISE."
"is_clang=false"
;; Disable debugging features to save space. These are normally
;; pulled in by "is_official_build", but that requires "is_clang".
- "blink_symbol_level=0"
"enable_iterator_debugging=false"
"exclude_unwind_tables=true"
;; Optimize for building everything at once, as opposed to
@@ -488,7 +529,7 @@ from forcing GEXP-PROMISE."
'("use_vaapi=true")
'())
- ;; Don't arbitrarily restrict formats supported by system ffmpeg.
+ ;; Do not artifically restrict formats supported by system ffmpeg.
"proprietary_codecs=true"
"ffmpeg_branding=\"Chrome\""
@@ -561,12 +602,12 @@ from forcing GEXP-PROMISE."
(substitute* "third_party/webrtc/rtc_base/strings/json.h"
(("#include \"third_party/jsoncpp/") "#include \"json/"))
- (substitute* '("ui/gfx/skia_util.h"
+ (substitute* '("components/viz/common/gpu/vulkan_context_provider.h"
"components/viz/common/resources/resource_format_utils.h")
(("third_party/vulkan/include/") ""))
(substitute* "third_party/skia/include/gpu/vk/GrVkVulkan.h"
- (("\\.\\./\\.\\./include/third_party/vulkan/") ""))
+ (("include/third_party/vulkan/") ""))
;; Building chromedriver embeds some files using the ZIP
;; format which doesn't support timestamps before
@@ -587,6 +628,9 @@ from forcing GEXP-PROMISE."
(setenv "AR" "ar") (setenv "NM" "nm")
(setenv "CC" "gcc") (setenv "CXX" "g++")
+ ;; Prevent GCC from optimizing away null pointer safety checks.
+ (setenv "CXXFLAGS" "-fno-delete-null-pointer-checks")
+
;; Work around <https://bugs.gnu.org/30756>.
(unsetenv "C_INCLUDE_PATH")
(unsetenv "CPLUS_INCLUDE_PATH")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3bd0d664da..17c85fe512 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -78,14 +78,14 @@
(define-public r-clipr
(package
(name "r-clipr")
- (version "0.6.0")
+ (version "0.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "clipr" version))
(sha256
(base32
- "0k9kimkmmj9k7290sxiqn4kd1vvm4w7q9a44wp0w30b7yjpavx2m"))))
+ "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
(build-system r-build-system)
(home-page "https://github.com/mdlincoln/clipr")
(synopsis "Read and write from the system clipboard")
@@ -97,14 +97,14 @@ the system clipboards.")
(define-public r-ellipsis
(package
(name "r-ellipsis")
- (version "0.2.0")
+ (version "0.2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ellipsis" version))
(sha256
(base32
- "0hdk79q4wn5nq52p8qd65kqz81l0b8gfzsbzyvmfais0p24qclib"))))
+ "0hx9l043433bwm1np9sypph77c7y9dddpz0wrhbkcv01x32jhr8f"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rlang" ,r-rlang)))
@@ -370,14 +370,14 @@ such as copy/paste from an R session.")
(define-public r-callr
(package
(name "r-callr")
- (version "3.2.0")
+ (version "3.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "callr" version))
(sha256
(base32
- "1s5h2k7c1vgbry90xczin66q89cbkc6mvh4679l5rsz83087pd2b"))))
+ "0rvrlg86fxr5nadvqa0dr1iifqjs4d1rc32v76m3ccvx6m3xlq5z"))))
(build-system r-build-system)
(propagated-inputs
`(("r-r6" ,r-r6)
@@ -420,21 +420,21 @@ the embedded @code{RapidXML} C++ library.")
(define-public r-modelr
(package
(name "r-modelr")
- (version "0.1.4")
+ (version "0.1.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "modelr" version))
(sha256
(base32
- "1ngxphbjkv7yl1rg30sj36mfwhc76g452drjrq9abgab4k0pgnml"))))
+ "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
("r-dplyr" ,r-dplyr)
- ("r-lazyeval" ,r-lazyeval)
("r-magrittr" ,r-magrittr)
("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)))
(home-page "https://github.com/tidyverse/modelr")
@@ -500,13 +500,13 @@ in systems and applications.")
(define-public r-servr
(package
(name "r-servr")
- (version "0.14")
+ (version "0.15")
(source (origin
(method url-fetch)
(uri (cran-uri "servr" version))
(sha256
(base32
- "0zjjnfgas9d16fihksyk24kgkkqswb4sd0rz51id2ni1ymdyasjk"))))
+ "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-httpuv" ,r-httpuv)
@@ -614,13 +614,13 @@ LaTeX.")
(define-public r-curl
(package
(name "r-curl")
- (version "3.3")
+ (version "4.0")
(source (origin
(method url-fetch)
(uri (cran-uri "curl" version))
(sha256
(base32
- "1gd5i25anzi28lg1f8p7g63z9d46xi0qaw4lxpml5p0f52lvkc0c"))))
+ "0wb1j87fa2nd4a9x1w2nmc453nzvx6qiq8dviwc4jr36hsf9ra89"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -1205,14 +1205,14 @@ including functions for geolocation and routing.")
(define-public r-haven
(package
(name "r-haven")
- (version "2.1.0")
+ (version "2.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "haven" version))
(sha256
(base32
- "0x5fwc4q2gdxwwp5sxdd6q17jhpisd769y9kv0xgnjcm0cdwz8f0"))))
+ "12h64r2v2451igyl7v4w2kg0hzw9rnanph0m7smffq29ybkv9g4h"))))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
@@ -1441,14 +1441,14 @@ processes. Most of its code is based on the @code{psutil} Python package.")
(define-public r-pkgbuild
(package
(name "r-pkgbuild")
- (version "1.0.3")
+ (version "1.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "pkgbuild" version))
(sha256
(base32
- "0k8zwa66rm1ncx19ld5mbaxcjxkswiczpdqyssy44vl8k6scwfn9"))))
+ "0prvx91dha5pvd0k4jca2arkngvi6vnfs2indmiy3kwwzyjyyd19"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
@@ -1497,13 +1497,13 @@ you to rapidly iterate while developing a package.")
(define-public r-rcpp
(package
(name "r-rcpp")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rcpp" version))
(sha256
- (base32 "015rmxns8mhmnd9wnz9bmma4iwx2sf4bcwkkp9hcgvdmblzf0vg7"))))
+ (base32 "170jlmjrs92z5qdv58badhxycjvfjpqwwpic7rm13pc9zkb3i4xd"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr))) ; for vignettes
@@ -2230,14 +2230,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).")
(define-public r-lpsolve
(package
(name "r-lpsolve")
- (version "5.6.13.1")
+ (version "5.6.13.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "lpSolve" version))
(sha256
(base32
- "1f10ywlaaldgjj84vs108ly0nsbkrdgbn5d6qj7nk93j1x1xrn3a"))))
+ "0fc5m259ayc880f5hvnq59ih6nb2rlp394n756n1khmxbjpw1w3m"))))
(properties `((upstream-name . "lpSolve")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/lpSolve")
@@ -2315,14 +2315,14 @@ data). Weighted versions of MLE, MME and QME are available.")
(define-public r-energy
(package
(name "r-energy")
- (version "1.7-5")
+ (version "1.7-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "energy" version))
(sha256
(base32
- "15k9dg0a82cs9ypm0wpcsff3il1hzhnnv86dv5ngby1r144czhi4"))))
+ "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-boot" ,r-boot)
@@ -2450,14 +2450,14 @@ available in a vignette.")
(define-public r-lava
(package
(name "r-lava")
- (version "1.6.5")
+ (version "1.6.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "lava" version))
(sha256
(base32
- "13rlqdg42ylnz4hc932bl50xismrcr4d9ykcd9zs19cw5mckjx0f"))))
+ "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-numderiv" ,r-numderiv)
@@ -2640,20 +2640,41 @@ to access PostgreSQL database systems.")
;; under the PostgreSQL license.
(license license:gpl2)))
+(define-public r-linprog
+ (package
+ (name "r-linprog")
+ (version "0.9-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "linprog" version))
+ (sha256
+ (base32
+ "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
+ (home-page "http://linprog.r-forge.r-project.org/")
+ (synopsis "Linear programming and optimization")
+ (description
+ "This package can be used to solve Linear Programming / Linear
+Optimization problems by using the simplex algorithm.")
+ (license license:gpl2+)))
+
(define-public r-geometry
(package
(name "r-geometry")
- (version "0.4.1")
+ (version "0.4.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "geometry" version))
(sha256
(base32
- "0v3ivaw8vbjyxg08dd573qk3kqfyknj5hli9503dza6p6xz0dzmm"))))
+ "0vq334115qi039vy198ggv1dsp6n1s6jwcm9ivipf5r8lbm287zz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-magic" ,r-magic)
+ ("r-linprog" ,r-linprog)
("r-lpsolve" ,r-lpsolve)
("r-rcpp" ,r-rcpp)
("r-rcppprogress" ,r-rcppprogress)))
@@ -2871,14 +2892,14 @@ provides a one-row summary of model-level statistics.")
(define-public r-recipes
(package
(name "r-recipes")
- (version "0.1.5")
+ (version "0.1.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "recipes" version))
(sha256
(base32
- "056zv4vhayyy8q9izcdknbb9hff2gxivg21g5mkssia78vw8g3mg"))))
+ "1ndz9h0zvdj141r63l8047wbhaj0x8fwzzyq7b8mh78pvrrdpq2i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -2890,7 +2911,6 @@ provides a one-row summary of model-level statistics.")
("r-magrittr" ,r-magrittr)
("r-matrix" ,r-matrix)
("r-purrr" ,r-purrr)
- ("r-rcpproll" ,r-rcpproll)
("r-rlang" ,r-rlang)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)
@@ -3056,14 +3076,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.")
(define-public r-jomo
(package
(name "r-jomo")
- (version "2.6-8")
+ (version "2.6-9")
(source
(origin
(method url-fetch)
(uri (cran-uri "jomo" version))
(sha256
(base32
- "097zfdcqc3a45ay8xxbraqh8xsfyivskkdmc2b4ca4n979lx8vyb"))))
+ "16ychdhhv8cii8zrdfdf5gzgnvmfaq573bmi00xqdf323q3lf3xr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lme4" ,r-lme4)
@@ -3129,14 +3149,14 @@ analysis of multiply imputed data sets.")
(define-public r-mice
(package
(name "r-mice")
- (version "3.5.0")
+ (version "3.6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mice" version))
(sha256
(base32
- "0icydc312sbvzbp0r0mhs2r77a2ly2xvz5w5amirz3wdkvgyrk2g"))))
+ "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
@@ -3212,14 +3232,14 @@ programming} (SQP) based solver).")
(define-public r-hardyweinberg
(package
(name "r-hardyweinberg")
- (version "1.6.2")
+ (version "1.6.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "HardyWeinberg" version))
(sha256
(base32
- "15i7b444hikkfgqmx2ki827998xwra38k9v7a7kavwz6zmq5mmv9"))))
+ "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
(properties `((upstream-name . "HardyWeinberg")))
(build-system r-build-system)
(propagated-inputs
@@ -3289,14 +3309,14 @@ structure.")
(define-public r-vioplot
(package
(name "r-vioplot")
- (version "0.3.0")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "vioplot" version))
(sha256
(base32
- "1ddmmqq7qrnvr5q518afnysrl7ccr8am9njknv3dpwaqzcdr9akn"))))
+ "13kfjp747bnzksai8j39y2hyl3ljc6n53c2cfhaw78q3d63x0lbv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-sm" ,r-sm)
@@ -3631,14 +3651,14 @@ constants, and control debugging of packages via environment variables.")
(define-public r-processx
(package
(name "r-processx")
- (version "3.3.1")
+ (version "3.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "processx" version))
(sha256
(base32
- "1bhbfacx2z2d97pz5bch45nvbvywhx2zp049czlfbdivkzgxn8v1"))))
+ "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ps" ,r-ps)
@@ -3839,18 +3859,19 @@ to variables on the left-hand side of the assignment.")
(define-public r-vctrs
(package
(name "r-vctrs")
- (version "0.1.0")
+ (version "0.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "vctrs" version))
(sha256
(base32
- "13w1r8zpalirpfaz5sykpn0mj4jmhxi2qkdcfq081ixlfjyzwa6c"))))
+ "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
("r-digest" ,r-digest)
+ ("r-ellipsis" ,r-ellipsis)
("r-glue" ,r-glue)
("r-rlang" ,r-rlang)
("r-zeallot" ,r-zeallot)))
@@ -3877,14 +3898,14 @@ to variables on the left-hand side of the assignment.")
(define-public r-pillar
(package
(name "r-pillar")
- (version "1.4.1")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "pillar" version))
(sha256
(base32
- "0mcc09caxm69pghhz6b8vawj9ni63aijv5qba53pg4ph7rxclwgm"))))
+ "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@@ -3923,14 +3944,14 @@ terminals.")
(define-public r-tinytex
(package
(name "r-tinytex")
- (version "0.14")
+ (version "0.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
- "0aab7ybc6kkxxk3lzdmbla8zcpp6nmlahchc33miv28cmnqw363w"))))
+ "145dmgq7h55mmqqlnnj153j484x2a9s1fbvjbjkdyqzpnz9qh2ax"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
@@ -4628,14 +4649,14 @@ files.")
(define-public r-shinyace
(package
(name "r-shinyace")
- (version "0.3.3")
+ (version "0.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinyAce" version))
(sha256
(base32
- "02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j"))))
+ "0hvih5g0pswlnz5rf3blx5yqw11ssxvm8w4klxddp1ap20ncbgl1"))))
(properties `((upstream-name . "shinyAce")))
(build-system r-build-system)
(propagated-inputs
@@ -4678,14 +4699,14 @@ systems.")
(define-public r-radiant-data
(package
(name "r-radiant-data")
- (version "0.9.9")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "radiant.data" version))
(sha256
(base32
- "17mgm0sggh4f7ihqmj9m3996p3pqc7h2cwx6ll1ha3kg5mx0znyn"))
+ "0b35jn4mcj10hqra18l8pi6s4pvj6fxipslbn6hkr4zza1z27gzw"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -5140,14 +5161,14 @@ misclassification probabilities of different models.")
(define-public r-zip
(package
(name "r-zip")
- (version "2.0.2")
+ (version "2.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "zip" version))
(sha256
(base32
- "1xvgs7mhxi0sdp5ix4nisqm9lf8f75b7ip7b1hqpq9bzh0x6z8ix"))))
+ "0zii05jg9v9ljd0wd67g9x4bhlmpmsy5dzd093sbnc5n3vjbi32a"))))
(build-system r-build-system)
(home-page "https://github.com/gaborcsardi/zip")
(synopsis "Cross-platform Zip compression")
@@ -5298,14 +5319,14 @@ promises, but with a syntax that is idiomatic R.")
(define-public r-dosnow
(package
(name "r-dosnow")
- (version "1.0.16")
+ (version "1.0.18")
(source
(origin
(method url-fetch)
(uri (cran-uri "doSNOW" version))
(sha256
(base32
- "13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n"))))
+ "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
(properties `((upstream-name . "doSNOW")))
(build-system r-build-system)
(propagated-inputs
@@ -5431,14 +5452,14 @@ obtain a better initial configuration in non-metric MDS.")
(define-public r-reticulate
(package
(name "r-reticulate")
- (version "1.12")
+ (version "1.13")
(source
(origin
(method url-fetch)
(uri (cran-uri "reticulate" version))
(sha256
(base32
- "0pqr1rcs8yg9nlh729mvlws93cqhpmv49j9bcgarh7vxzkwyv0kb"))))
+ "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
(build-system r-build-system)
(inputs `(("python" ,python)))
(propagated-inputs
@@ -5523,14 +5544,14 @@ movies, and TV shows.")
(define-public r-ggsignif
(package
(name "r-ggsignif")
- (version "0.5.0")
+ (version "0.6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggsignif" version))
(sha256
(base32
- "0z04g5kqdj66fyfxb5d2m7njkqd7idbiy4xgsnxdh5pbh3cr643x"))))
+ "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)))
@@ -5548,14 +5569,14 @@ and adds the annotation to the plot.")
(define-public r-ggpubr
(package
(name "r-ggpubr")
- (version "0.2.1")
+ (version "0.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggpubr" version))
(sha256
(base32
- "0a4dv6a752hwvc7l31xs7bgqhfzfdy94xp6wgwaxf5dxm46na7k1"))))
+ "0r5knv3707pmpngmj60zn761y3bh8lj89dhh1b80ss083xnxr4qw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cowplot" ,r-cowplot)
@@ -5569,6 +5590,7 @@ and adds the annotation to the plot.")
("r-magrittr" ,r-magrittr)
("r-polynom" ,r-polynom)
("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
("r-scales" ,r-scales)
("r-tidyr" ,r-tidyr)))
(home-page "http://www.sthda.com/english/rpkgs/ggpubr")
@@ -5628,14 +5650,14 @@ clustering.")
(define-public r-factominer
(package
(name "r-factominer")
- (version "1.41")
+ (version "1.42")
(source
(origin
(method url-fetch)
(uri (cran-uri "FactoMineR" version))
(sha256
(base32
- "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259"))))
+ "1yl16inb2m89l1czgaf0pgy9655dpr751hyx92yw6rqpd2ryznac"))))
(properties `((upstream-name . "FactoMineR")))
(build-system r-build-system)
(propagated-inputs
@@ -5918,20 +5940,19 @@ to help insert or delete content at a specific location in the document.")
(define-public r-abn
(package
(name "r-abn")
- (version "1.3")
+ (version "2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "abn" version))
(sha256
(base32
- "1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm"))))
+ "08jlvb6i5f7ry2dwm0jgrnn2w95vr0l67dpx13n9878lz9ld131b"))))
(build-system r-build-system)
(inputs
`(("gsl" ,gsl)))
(propagated-inputs
- `(("r-cairo" ,r-cairo)
- ("r-lme4" ,r-lme4)
+ `(("r-lme4" ,r-lme4)
("r-mass" ,r-mass)
("r-nnet" ,r-nnet)
("r-rcpp" ,r-rcpp)
@@ -6070,14 +6091,14 @@ other add-on packages.")
(define-public r-insight
(package
(name "r-insight")
- (version "0.3.0")
+ (version "0.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "insight" version))
(sha256
(base32
- "1r288hc01cpyrk3nias30fw783z2vw20qr1k67vr65anh7mwm7vb"))))
+ "1lw1r3mb97z5p9z25jfzlhs0sbnwp6v8kzysf0am01x4m7l3iz82"))))
(build-system r-build-system)
(home-page "https://easystats.github.io/insight/")
(synopsis "Easy access to model information for various model objects")
@@ -6527,14 +6548,14 @@ containing one or more SNPs that evolved under directional selection.")
(define-public r-proc
(package
(name "r-proc")
- (version "1.15.0")
+ (version "1.15.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "pROC" version))
(sha256
(base32
- "1dxxkwdhxfnj2znq4c5ggrr9m5klh5pmfxg17rz59vr2hfb73m24"))))
+ "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
(properties `((upstream-name . "pROC")))
(build-system r-build-system)
(propagated-inputs
@@ -6900,14 +6921,14 @@ used to teach mathematics, statistics, computation and modeling.")
(define-public r-raster
(package
(name "r-raster")
- (version "2.9-5")
+ (version "2.9-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "raster" version))
(sha256
(base32
- "0ljrymsp4zzaxdj1l0mw0a6hi88m5h0h920ixfzrg0szbyxqd0yk"))))
+ "1brqigic8ygr223bp2hgk5qjz3q03r4sfglrv4an0ghy7fgfralh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
@@ -7468,14 +7489,14 @@ multiple-imputation datasets.")
(define-public r-magick
(package
(name "r-magick")
- (version "2.0")
+ (version "2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "magick" version))
(sha256
(base32
- "18y465325mhf48x2jn3jz9khwq1z2aj13wfbdkv8k3hln1sd572m"))))
+ "1pz71maz05gx4ds1wfw0alggc8nn2w75lj12dg1zr72s3kybhkzg"))))
(build-system r-build-system)
(inputs
`(("imagemagick" ,imagemagick)
@@ -7857,14 +7878,14 @@ Hothorn, Westfall, 2010, CRC Press).")
(define-public r-emmeans
(package
(name "r-emmeans")
- (version "1.3.5.1")
+ (version "1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "emmeans" version))
(sha256
(base32
- "0rgzjvmp3yqhwgfg96v17wi8gbafzbrmz134shj2jsf5bsmw6vbj"))))
+ "1ynf9hhbch83k63lwps69ijfch30fk5v0sc418ck264c5vih26dh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-estimability" ,r-estimability)
@@ -8089,14 +8110,14 @@ differentiation.")
(define-public r-bayestestr
(package
(name "r-bayestestr")
- (version "0.2.2")
+ (version "0.2.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayestestR" version))
(sha256
(base32
- "09r654lrhwwnshn5h2s2fbx3c8wigv3j4sva5hmfnkwjg8cclhd9"))))
+ "08d3bsb6li59n17bx1zrqnlnvniyb3vls9kl856km4chx3b2ff82"))))
(properties `((upstream-name . "bayestestR")))
(build-system r-build-system)
(propagated-inputs
@@ -8114,14 +8135,14 @@ ROPE percentage and pd).")
(define-public r-performance
(package
(name "r-performance")
- (version "0.2.0")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "performance" version))
(sha256
(base32
- "1pzd6z7i1jxr2xi1shg3d0bxlbpmjl7kpmwgjnfys6syv57znd1z"))))
+ "13j74ffhx950kacs86ixx84nviq9qlwzr7hjnhkmzw2hspjxq99w"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
@@ -8141,14 +8162,14 @@ effects models and Bayesian models.")
(define-public r-ggeffects
(package
(name "r-ggeffects")
- (version "0.10.0")
+ (version "0.11.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggeffects" version))
(sha256
(base32
- "0gmqzjk8k8q6j4q6asv9f3b1fv4qrw5w8xa48ha3y98shzm5np9k"))))
+ "1b0lxa8bljdh6h4lk7pql1lrhjlvh7p5c8qlgb8ac6ay8hb79vmi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -8175,14 +8196,14 @@ results using @code{ggplot2}.")
(define-public r-sjplot
(package
(name "r-sjplot")
- (version "2.6.3")
+ (version "2.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjPlot" version))
(sha256
(base32
- "0h1mkmp5mrkbf7y3zh6m4cnm737cpg1m5si0lrmal7j2ixqicwjy"))))
+ "1m0gy991fmxvqry91kkzdkdapyalhrwql25d0hg2a2naxgfw4zpk"))))
(properties `((upstream-name . "sjPlot")))
(build-system r-build-system)
(propagated-inputs
@@ -8192,6 +8213,7 @@ results using @code{ggplot2}.")
("r-forcats" ,r-forcats)
("r-ggeffects" ,r-ggeffects)
("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
("r-glmmtmb" ,r-glmmtmb)
("r-insight" ,r-insight)
("r-knitr" ,r-knitr)
@@ -8311,14 +8333,14 @@ terminals that do not support Unicode.")
(define-public r-usethis
(package
(name "r-usethis")
- (version "1.5.0")
+ (version "1.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "usethis" version))
(sha256
(base32
- "0pn6ka3726psaqlx573g6nxi90apf0rn5m4k2lz1jr66xdc19sag"))))
+ "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-clipr" ,r-clipr)
@@ -8674,14 +8696,14 @@ analysing multivariate abundance data in community ecology.")
(define-public r-afex
(package
(name "r-afex")
- (version "0.23-0")
+ (version "0.24-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "afex" version))
(sha256
(base32
- "0yv4s7461swn0116y4wq9v139p1br5rr6hhnq1cmkbvybmwj2vp7"))))
+ "14w7kcwr5hxmjcjmdm5ia9ka3bw1nl18pxlm1vpw62nmvicn3455"))))
(build-system r-build-system)
(propagated-inputs
`(("r-car" ,r-car)
@@ -8908,14 +8930,14 @@ Bioconductor packages.")
(define-public r-rgl
(package
(name "r-rgl")
- (version "0.100.24")
+ (version "0.100.26")
(source
(origin
(method url-fetch)
(uri (cran-uri "rgl" version))
(sha256
(base32
- "0nm3iyvhhmh0zlywkfmrq3vyh8z1l296xxfmcky0ifd2qnysfcqj"))))
+ "0h77akviwjd86j2qyx326xynbmwhypd6ydprzlwqnidd4ckrr271"))))
(build-system r-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
@@ -9374,14 +9396,14 @@ maps.")
(define-public r-tidytree
(package
(name "r-tidytree")
- (version "0.2.4")
+ (version "0.2.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidytree" version))
(sha256
(base32
- "04bznlfs617plv258nmsyq2pywnijcnzy2pbn5b2fgjk2xqkp29w"))))
+ "13mhizbsawmfqjpnzb73yw6kn1f1wlz0vhyzj3g0rj6ry880rw89"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ape" ,r-ape)
@@ -9442,14 +9464,14 @@ giving it a description in the specific format.")
(define-public r-sparsesvd
(package
(name "r-sparsesvd")
- (version "0.1-4")
+ (version "0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sparsesvd" version))
(sha256
(base32
- "1yf373552wvdnd65r7hfcqa3v29dqn7jd4cn431mqd2acnqjrsam"))))
+ "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
(build-system r-build-system)
(propagated-inputs `(("r-matrix" ,r-matrix)))
(home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
@@ -9664,14 +9686,14 @@ diagnostics for controlling type-1 errors are also provided.")
(define-public r-flare
(package
(name "r-flare")
- (version "1.6.0")
+ (version "1.6.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "flare" version))
(sha256
(base32
- "0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1"))))
+ "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-igraph" ,r-igraph)
@@ -9764,14 +9786,14 @@ Touzet and Varre (2007).")
(define-public r-rnifti
(package
(name "r-rnifti")
- (version "0.11.0")
+ (version "0.11.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "RNifti" version))
(sha256
(base32
- "0zs8ffa6gpi9cygxk7xjin6k3vpvfgb540a506zlk50bf6kc5nlf"))))
+ "0jcgdg5k2swmi57aqj347kfi1fc4nvag7pxdfz61kc0vqqamm0wg"))))
(properties `((upstream-name . "RNifti")))
(build-system r-build-system)
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -9787,14 +9809,14 @@ used by other packages.")
(define-public r-shades
(package
(name "r-shades")
- (version "1.3.1")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "shades" version))
(sha256
(base32
- "0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv"))))
+ "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
(build-system r-build-system)
(home-page "https://github.com/jonclayden/shades")
(synopsis "Simple color manipulation")
@@ -10143,23 +10165,51 @@ library.")
and manipulating sets of ontological terms.")
(license license:gpl2+)))
+(define-public r-gargle
+ (package
+ (name "r-gargle")
+ (version "0.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gargle" version))
+ (sha256
+ (base32
+ "0vqgp4w03sdyj0q96gxkybqflzzbaw84zifsbi7pxk5y08fimj2v"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-fs" ,r-fs)
+ ("r-glue" ,r-glue)
+ ("r-httr" ,r-httr)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-rlang" ,r-rlang)
+ ("r-withr" ,r-withr)))
+ (home-page "https://gargle.r-lib.org")
+ (synopsis "Utilities for working with Google APIs")
+ (description
+ "This package provides utilities for working with Google APIs. This
+includes functions and classes for handling common credential types and for
+preparing, executing, and processing HTTP requests.")
+ (license license:expat)))
+
(define-public r-bigrquery
(package
(name "r-bigrquery")
- (version "1.1.1")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "bigrquery" version))
(sha256
(base32
- "1if39xkr231xmjq10fx2g7bgg4jgfd3wzx1p9g3pq4hbf2s6x0is"))))
+ "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
("r-bit64" ,r-bit64)
("r-curl" ,r-curl)
("r-dbi" ,r-dbi)
+ ("r-gargle" ,r-gargle)
("r-glue" ,r-glue)
("r-httr" ,r-httr)
("r-jsonlite" ,r-jsonlite)
@@ -10167,6 +10217,7 @@ and manipulating sets of ontological terms.")
("r-progress" ,r-progress)
("r-rapidjsonr" ,r-rapidjsonr)
("r-rcpp" ,r-rcpp)
+ ("r-rlang" ,r-rlang)
("r-tibble" ,r-tibble)))
(home-page "https://github.com/rstats-db/bigrquery")
(synopsis "R interface to Google's BigQuery API")
@@ -10724,14 +10775,14 @@ covariance functions for large data sets.")
(define-public r-spatialextremes
(package
(name "r-spatialextremes")
- (version "2.0-7")
+ (version "2.0-7.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "SpatialExtremes" version))
(sha256
(base32
- "1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050"))))
+ "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
(properties
`((upstream-name . "SpatialExtremes")))
(build-system r-build-system)
@@ -10994,14 +11045,14 @@ model with finite state space using the Aalen-Johansen estimator.")
(define-public r-epi
(package
(name "r-epi")
- (version "2.37")
+ (version "2.38")
(source
(origin
(method url-fetch)
(uri (cran-uri "Epi" version))
(sha256
(base32
- "1lanr9x0c6w22406p56j7cwk6wck8njq6pscb4gzc613d68zj1lk"))))
+ "0ald9fjynrlyah8nzwfs49a08j4myd3c5bm56zn61gg5pyyhi8hd"))))
(properties `((upstream-name . "Epi")))
(build-system r-build-system)
(propagated-inputs
@@ -11177,14 +11228,14 @@ them in distributed compute environments.")
(define-public r-future
(package
(name "r-future")
- (version "1.13.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "future" version))
(sha256
(base32
- "0h8ng2a6vg4axd5f75xcb3ip9d95zi22fa048dq2bzlnncwlznjz"))))
+ "1jyv2wlmpfqbk3hw269h4xg36na3wh1kd1lxmwdb40bsv4850lqa"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
@@ -11237,14 +11288,14 @@ machine or distributed on a compute cluster.")
(define-public r-rsvd
(package
(name "r-rsvd")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "rsvd" version))
(sha256
(base32
- "1faskhf5j2bj9f971qljsmh182g3rnyilj1wwijz530a6skxidzz"))))
+ "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)))
@@ -11445,14 +11496,14 @@ identifying outliers.")
(define-public r-bayesm
(package
(name "r-bayesm")
- (version "3.1-1")
+ (version "3.1-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayesm" version))
(sha256
(base32
- "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28"))))
+ "041ach2f2vrqzd5kz17v7wmkjz6z8cjjihpk4qvczm4cr9z85r2i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
@@ -11849,14 +11900,14 @@ probabilities from a standard bivariate normal CDF.")
(define-public r-lavaan
(package
(name "r-lavaan")
- (version "0.6-3")
+ (version "0.6-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "lavaan" version))
(sha256
(base32
- "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz"))))
+ "1zf0sxpms35rhq2syb7r3sshhc8kjvc3pv97dk9x0gf4xl7pck4g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
@@ -12073,14 +12124,14 @@ running IRkernel session.")
(define-public r-irkernel
(package
(name "r-irkernel")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "IRkernel" version))
(sha256
(base32
- "1gij59b068qp7sbn9d0b9ghmnhfks15a9anj7bp26acv0yvdsg3s"))))
+ "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp"))))
(properties `((upstream-name . "IRkernel")))
(build-system r-build-system)
(arguments
@@ -12192,14 +12243,14 @@ R, enabling interactive analysis and visualization of genome-scale data.")
(define-public r-rematch2
(package
(name "r-rematch2")
- (version "2.0.1")
+ (version "2.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "rematch2" version))
(sha256
(base32
- "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6"))))
+ "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-tibble" ,r-tibble)))
@@ -12541,14 +12592,14 @@ classes.")
(define-public r-classint
(package
(name "r-classint")
- (version "0.3-3")
+ (version "0.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "classInt" version))
(sha256
(base32
- "0c2z6shlxa928xa20yl956r06lx20mji3mwipdvmj3f4z5g6hgm9"))))
+ "00q1bpgblrldckn1rk166q1b0hgap2sjjyfmfcyh6ydk6y73ziir"))))
(properties `((upstream-name . "classInt")))
(build-system r-build-system)
(propagated-inputs
@@ -12616,14 +12667,14 @@ sampling.")
(define-public r-deldir
(package
(name "r-deldir")
- (version "0.1-21")
+ (version "0.1-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "deldir" version))
(sha256
(base32
- "03392pl6j8rm3n32xrfkyfx866k1vm5sj87pva70yyiwh70vrnmr"))))
+ "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/deldir")
@@ -12640,14 +12691,14 @@ tessellation.")
(define-public r-sf
(package
(name "r-sf")
- (version "0.7-4")
+ (version "0.7-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "sf" version))
(sha256
(base32
- "0vnyr7xyfcl928kbrb1k8l4fkd0cjrfq486g6gxpvy5j0cc2h4i1"))))
+ "192hw52x1qlif8zyai1kff1wiyr3yl5f7jj1rk3k0nr8das0qy6i"))))
(build-system r-build-system)
(inputs
`(("gdal" ,gdal)
@@ -13022,18 +13073,19 @@ inbred lines, F2 intercrosses, and association mapping populations.")
(define-public r-ldheatmap
(package
(name "r-ldheatmap")
- (version "0.99-5")
+ (version "0.99-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "LDheatmap" version))
(sha256
(base32
- "0il3g3n3bzv74lz7dlhyiwc2x2417v6yhx2g47pahxdzqa09kf4s"))))
+ "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
(properties `((upstream-name . "LDheatmap")))
(build-system r-build-system)
(propagated-inputs
`(("r-genetics" ,r-genetics)
+ ("r-rcpp" ,r-rcpp)
("r-snpstats" ,r-snpstats)))
(home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
(synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
@@ -13112,13 +13164,13 @@ SELECT or UPDATE queries to an end-point.")
(define-public r-bookdown
(package
(name "r-bookdown")
- (version "0.11")
+ (version "0.12")
(source (origin
(method url-fetch)
(uri (cran-uri "bookdown" version))
(sha256
(base32
- "0w4fkv5fqiaqgkx44p0s161imf29zir9742126xkz1pl1j25jn1r"))))
+ "1c2v0rpa1rrpbx8yb66sfvrf4gf57f6a8x7ydjqqbkbwhxdlrsrq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
@@ -13585,14 +13637,14 @@ package.")
(define-public r-ggplotify
(package
(name "r-ggplotify")
- (version "0.0.3")
+ (version "0.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggplotify" version))
(sha256
(base32
- "14hqlpvnaq5psz1ljcpw9isa06827rg3fm5c1dx159rsjfi56yby"))))
+ "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -13712,14 +13764,14 @@ sets of URLs.")
(define-public r-ggforce
(package
(name "r-ggforce")
- (version "0.2.2")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggforce" version))
(sha256
(base32
- "0snxx9zhcccxa7pz9pf3bjqmcmv9mz4m47v81hklnhm25jj40xg2"))))
+ "118qyzy8h9kkkdpjd09667gxgw7xy1kbc8r87pswh54ixn8hymwk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -13730,7 +13782,9 @@ sets of URLs.")
("r-rcppeigen" ,r-rcppeigen)
("r-rlang" ,r-rlang)
("r-scales" ,r-scales)
- ("r-tweenr" ,r-tweenr)))
+ ("r-tidyselect" ,r-tidyselect)
+ ("r-tweenr" ,r-tweenr)
+ ("r-withr" ,r-withr)))
(home-page "https://ggforce.data-imaginist.com")
(synopsis "Accelerating ggplot2")
(description
@@ -14562,14 +14616,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
(define-public r-dalex
(package
(name "r-dalex")
- (version "0.4")
+ (version "0.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "DALEX" version))
(sha256
(base32
- "1mr8lqq8s4aacmh7xdhmkmv8vsjqjczlqlaw27xnsljgj2kgq87a"))))
+ "04i17ni8g595jj8dxdfwr9vsxmdn2kkam90ab68vlwws3ywqjl6r"))))
(properties `((upstream-name . "DALEX")))
(build-system r-build-system)
(propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
@@ -14588,14 +14642,14 @@ and model output.")
(define-public r-enrichr
(package
(name "r-enrichr")
- (version "1.0")
+ (version "2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "enrichR" version))
(sha256
(base32
- "0lfdr45sdyqhvgz8q4qdbk12mpv86d6id665kq6aaslgr8jggfmn"))))
+ "056m6hksfss29fj7zvlk7pbh8g3gq84kjh3240isrsnhp9m1h9iz"))))
(properties `((upstream-name . "enrichR")))
(build-system r-build-system)
(propagated-inputs
@@ -14698,18 +14752,17 @@ into R and converted to @code{BibEntry} objects.")
(define-public r-citr
(package
(name "r-citr")
- (version "0.3.0")
+ (version "0.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "citr" version))
(sha256
(base32
- "0pik6s6xk5768s3kkppw2192dj455py53gsn6k2b7xgg96ircy0g"))))
+ "0p2sg0fl7cppxxmr20qyqzs2469kglmgpsvykynw4qx501as57rc"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
- ("r-bibtex" ,r-bibtex)
("r-curl" ,r-curl)
("r-httr" ,r-httr)
("r-miniui" ,r-miniui)
@@ -14729,14 +14782,14 @@ the current document.")
(define-public r-xgboost
(package
(name "r-xgboost")
- (version "0.82.1")
+ (version "0.90.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "xgboost" version))
(sha256
(base32
- "0plhx63wcm4syslzmjfv6bdgaqn96fnav048hrj0vxk4dzgfp8sq"))))
+ "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index db9665d1aa..6500adb215 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Ivan Petkov <ivanppetkov@gmail.com>
+;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -22,27 +23,473 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages))
-(define-public rust-unicode-xid
+;;;
+;;; Please: Try to add new module packages in alphabetic order.
+;;;
+
+(define-public rust-autocfg
(package
- (name "rust-unicode-xid")
- (version "0.1.0")
+ (name "rust-autocfg")
+ (version "0.1.5")
(source
(origin
(method url-fetch)
- (uri (crate-uri "unicode-xid" version))
- (file-name
- (string-append name "-" version ".tar.gz"))
+ (uri (crate-uri "autocfg" version))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32
- "1z57lqh4s18rr4x0j4fw4fmp9hf9346h0kmdgqsqx0fhjr3k0wpw"))))
+ (base32
+ "0asl6fnc35yk5l2rxwhp25v128jgm45dp754h9z8x51b6n90w4r2"))))
(build-system cargo-build-system)
- (home-page
- "https://github.com/unicode-rs/unicode-xid")
- (synopsis "Determine Unicode XID related properties")
- (description "Determine whether characters have the XID_Start
-or XID_Continue properties according to Unicode Standard Annex #31.")
- ;; Dual licensed.
- (license (list license:asl2.0 license:expat))))
+ (home-page "https://github.com/cuviper/autocfg")
+ (synopsis "Automatic cfg for Rust compiler features")
+ (description "Rust library for build scripts to automatically configure
+code based on compiler support. Code snippets are dynamically tested to see
+if the @code{rustc} will accept them, rather than hard-coding specific version
+support.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-bencher
+ (package
+ (name "rust-bencher")
+ (version "0.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "bencher" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1x8p2xblgqssay8cdykp5pkfc0np0jk5bs5cx4f5av097aav9zbx"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/bluss/bencher/")
+ (synopsis "Port of the libtest benchmark runner to Rust stable")
+ (description "This package provides a port of the libtest (unstable Rust)
+benchmark runner to Rust stable releases. Supports running benchmarks and
+filtering based on the name. Benchmark execution works exactly the same way
+and no more (caveat: black_box is still missing!).")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-bitflags
+ (package
+ (name "rust-bitflags")
+ (version "1.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "bitflags" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1zc1qb1hwsnl2d8rhzicsv9kqd5b2hwbrscrcfw5as4sfr35659x"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/bitflags/bitflags")
+ (synopsis "Macro to generate structures which behave like bitflags")
+ (description "This package provides a macro to generate structures which
+behave like a set of bitflags.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-cfg-if
+ (package
+ (name "rust-cfg-if")
+ (version "0.1.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "cfg-if" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0csygklgz3ybpr0670rkip49zh76m43ar3k7xgypkzbzrwycx1ml"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/alexcrichton/cfg-if")
+ (synopsis "Define an item depending on parameters")
+ (description "This package provides a macro to ergonomically define an item
+depending on a large number of #[cfg] parameters. Structured like an
+@code{if-else} chain, the first matching branch is the item that gets emitted.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-discard
+ (package
+ (name "rust-discard")
+ (version "1.0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "discard" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1h67ni5bxvg95s91wgicily4ix7lcw7cq0a5gy9njrybaibhyb91"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/Pauan/rust-discard")
+ (synopsis "Allow for intentionally leaking memory")
+ (description "There are situations where you need to intentionally leak some
+memory but not other memory. This package provides a discard trait which allows
+for intentionally leaking memory")
+ (license license:expat)))
+
+(define-public rust-doc-comment
+ (package
+ (name "rust-doc-comment")
+ (version "0.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "doc-comment" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "15rsqxgarfpb1yim9sbp9yfgj7p2dq6v51c6bq1a62paii9ylgcj"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/GuillaumeGomez/doc-comment")
+ (synopsis "Macro to generate doc comments")
+ (description "This package provides a way to generate doc comments
+from macros.")
+ (license license:expat)))
+
+(define-public rust-dtoa
+ (package
+ (name "rust-dtoa")
+ (version "0.4.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "dtoa" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0phbm7i0dpn44gzi07683zxaicjap5064w62pidci4fhhciv8mza"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/dtolnay/dtoa")
+ (synopsis "Fast functions for printing floating-point primitives")
+ (description "This crate provides fast functions for printing
+floating-point primitives to an @code{io::Write}.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-fallible-iterator
+ (package
+ (name "rust-fallible-iterator")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "fallible-iterator" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1xq759lsr8gqss7hva42azn3whgrbrs2sd9xpn92c5ickxm1fhs4"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/sfackler/rust-fallible-iterator")
+ (synopsis "Fallible iterator traits")
+ (description "If the @code{std} or @code{alloc} features are enabled, this
+crate provides implementations for @code{Box}, @code{Vec}, @code{BTreeMap}, and
+@code{BTreeSet}. If the @code{std} feature is enabled, this crate additionally
+provides implementations for @code{HashMap} and @code{HashSet}.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-fnv
+ (package
+ (name "rust-fnv")
+ (version "1.0.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "fnv" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1ww56bi1r5b8id3ns9j3qxbi7w5h005rzhiryy0zi9h97raqbb9g"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/servo/rust-fnv")
+ (synopsis "implementation of the Fowler-Noll-Vo hash function")
+ (description "The @code{fnv} hash function is a custom @code{Hasher}
+implementation that is more efficient for smaller hash keys.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-fs-extra
+ (package
+ (name "rust-fs-extra")
+ (version "1.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "fs_extra" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0x6675wdhsx277k1k1235jwcv38naf20d8kwrk948ds26hh4lajz"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/webdesus/fs_extra")
+ (synopsis "Extra filesystem methods")
+ (description "Expanding opportunities standard library @code{std::fs} and
+@code{std::io}. Recursively copy folders with recept information about
+process and much more.")
+ (license license:expat)))
+
+(define-public rust-futures
+ (package
+ (name "rust-futures")
+ (version "0.1.28")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "futures" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0saq8ffjw1pwf1pzhw3kq1z7dfq6wpd8x93dnni6vbkc799kkp25"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/rust-lang-nursery/futures-rs")
+ (synopsis "Implementation of zero-cost futures in Rust")
+ (description "An implementation of @code{futures} and @code{streams}
+featuring zero allocations, composability, and iterator-like interfaces.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-hex
+ (package
+ (name "rust-hex")
+ (version "0.3.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "hex" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0xsdcjiik5j750j67zk42qdnmm4ahirk3gmkmcqgq7qls2jjcl40"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/KokaKiwi/rust-hex")
+ (synopsis "Encode and decode data to/from hexadecimals")
+ (description "This crate allows for encoding and decoding data into/from
+hexadecimal representation.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-itoa
+ (package
+ (name "rust-itoa")
+ (version "0.4.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "itoa" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0zvg2d9qv3avhf3d8ggglh6fdyw8kkwqg3r4622ly5yhxnvnc4jh"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/dtolnay/itoa")
+ (synopsis "Fast functions for printing integer primitives")
+ (description "This crate provides fast functions for printing integer
+primitives to an @code{io::Write}.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-json
+ (package
+ (name "rust-json")
+ (version "0.11.14")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "json" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1hj8c6xj5c2aqqszi8naaflmcdbya1i9byyjrq4iybxjb4q91mq1"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/maciejhirsz/json-rust")
+ (synopsis "JSON implementation in Rust")
+ (description "This crate provides a JSON implementation in Rust, reducing
+friction with idiomatic Rust structs to ease interopability.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-maplit
+ (package
+ (name "rust-maplit")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "maplit" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0hsczmvd6zkqgzqdjp5hfyg7f339n68w83n4pxvnsszrzssbdjq8"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/bluss/maplit")
+ (synopsis "Collection of Map macros")
+ (description "This crate provides a collection of @code{literal} macros for
+@code{HashMap}, @code{HashSet}, @code{BTreeMap}, and @code{BTreeSet.}")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-matches
+ (package
+ (name "rust-matches")
+ (version "0.1.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "matches" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "020axl4q7rk9vz90phs7f8jas4imxal9y9kxl4z4v7a6719mrz3z"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/SimonSapin/rust-std-candidates")
+ (synopsis "Macro to evaluate whether an expression matches a pattern.")
+ (description "This package provides a macro to evaluate, as a boolean,
+whether an expression matches a pattern.")
+ (license license:expat)))
+
+(define-public rust-md5
+ (package
+ (name "rust-md5")
+ (version "0.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "md5" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "17b2xm4h4cvxsdjsf3kdrzqv2za60kak961xzi5kmw6g6djcssvy"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/stainless-steel/md5")
+ (synopsis "MD5 hash function in Rust")
+ (description "The package provides the MD5 hash function.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-peeking-take-while
+ (package
+ (name "rust-peeking-take-while")
+ (version "0.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "peeking_take_while" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "16bhqr6rdyrp12zv381cxaaqqd0pwysvm1q8h2ygihvypvfprc8r"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/fitzgen/peeking_take_while")
+ (synopsis "Provides the peeking_take_while iterator adaptor method")
+ (description
+ "Like @code{Iterator::take_while}, but calls the predicate on a peeked
+value. This allows you to use @code{Iterator::by_ref} and
+@code{Iterator::take_while} together, and still get the first value for which
+the @code{take_while} predicate returned false after dropping the @code{by_ref}.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-percent-encoding
+ (package
+ (name "rust-percent-encoding")
+ (version "2.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "percent-encoding" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0m6rkp3iy11la04p6z3492rns6n693pvmx585dvfmzzlzak2hkxs"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/servo/rust-url/")
+ (synopsis "Percent encoding and decoding")
+ (description "This crate provides percent encoding and decoding.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-pin-utils
+ (package
+ (name "rust-pin-utils")
+ (version "0.1.0-alpha.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "pin-utils" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "11xmyx00n4m37d546by2rxb8ryxs12v55cc172i3yak1rqccd52q"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/rust-lang-nursery/pin-utils")
+ (synopsis "Utilities for pinning")
+ (description "This crate provides utilities for pinning values on the stack.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-plain
+ (package
+ (name "rust-plain")
+ (version "0.2.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "plain" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "19n1xbxb4wa7w891268bzf6cbwq4qvdb86bik1z129qb0xnnnndl"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/randomites/plain")
+ (synopsis "Rust library that allows reinterpreting data safely")
+ (description "This package provides a small Rust library that allows users
+ to reinterpret data of certain types safely.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-pocket-resources
+ (package
+ (name "rust-pocket-resources")
+ (version "0.3.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "pocket-resources" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1n2i5vmi8fdbw89wm5nz1ws1z9f1qax911p6ksg4scmdg23z6df1"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/tomaka/pocket-resources")
+ (synopsis "Include resources in your applications")
+ (description "This crate allows you to include resources in your
+applications.")
+ (license license:expat)))
+
+(define-public rust-ppv-lite86
+ (package
+ (name "rust-ppv-lite86")
+ (version "0.2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "ppv-lite86" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "06snnv338w341nicfqba2jgln5dsla72ndkgrw7h1dfdb3vgkjz3"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/cryptocorrosion/cryptocorrosion")
+ (synopsis "Implementation of the crypto-simd API for x86")
+ (description "This crate provides an implementation of the crypto-simd API
+for x86.")
+ (license (list license:asl2.0
+ license:expat))))
(define-public rust-proc-macro2
(package
@@ -69,6 +516,26 @@ in terms of the upstream unstable API.")
;; Dual licensed.
(license (list license:asl2.0 license:expat))))
+(define-public rust-quick-error
+ (package
+ (name "rust-quick-error")
+ (version "1.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "quick-error" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1w6kgwwv7p7zr0yyg5rb315lkk24bimywklwx7fsvsbwi10bjx4j"))))
+ (build-system cargo-build-system)
+ (home-page "http://github.com/tailhook/quick-error")
+ (synopsis "Macro which makes error types pleasant to write")
+ (description "This crate provides a macro which makes error types pleasant
+to write.")
+ (license (list license:asl2.0
+ license:expat))))
+
(define-public rust-quote
(package
(name "rust-quote")
@@ -90,3 +557,396 @@ in terms of the upstream unstable API.")
(description "Quasi-quoting macro quote!(...)")
;; Dual licensed.
(license (list license:asl2.0 license:expat))))
+
+(define-public rust-rustc-std-workspace-core
+ (package
+ (name "rust-rustc-std-workspace-core")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "rustc-std-workspace-core" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1309xhwyai9xpz128xrfjqkmnkvgjwddznmj7brbd8i8f58zamhr"))))
+ (build-system cargo-build-system)
+ (home-page "https://crates.io/crates/rustc-std-workspace-core")
+ (synopsis "Explicitly empty crate for rust-lang/rust integration")
+ (description "This crate provides an explicitly empty crate for
+rust-lang/rust integration.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-scoped-tls
+ (package
+ (name "rust-scoped-tls")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "scoped-tls" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1hj8lifzvivdb1z02lfnzkshpvk85nkgzxsy2hc0zky9wf894spa"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/alexcrichton/scoped-tls")
+ (synopsis "Rust library providing the old standard library's scoped_thread_local")
+ (description "This crate provides a library implementation of the standard
+library's old @code{scoped_thread_local!} macro for providing scoped access to
+@dfn{thread local storage} (TLS) so any type can be stored into TLS.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-scopeguard
+ (package
+ (name "rust-scopeguard")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "scopeguard" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "03aay84r1f6w87ckbpj6cc4rnsxkxcfs13n5ynxjia0qkgjiabml"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/bluss/scopeguard")
+ (synopsis "Scope guard which will run a closure even out of scope")
+ (description "This package provides a RAII scope guard that will run a
+given closure when it goes out of scope, even if the code between panics
+(assuming unwinding panic). Defines the macros @code{defer!},
+@code{defer_on_unwind!}, @code{defer_on_success!} as shorthands for guards
+with one of the implemented strategies.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-semver-parser
+ (package
+ (name "rust-semver-parser")
+ (version "0.9.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "semver-parser" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1ahqhvgpzhcsd28id7xnrjv4419i9yyalhm7d7zi430qx0hi2vml"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/steveklabnik/semver-parser")
+ (synopsis "Parsing of the semver spec")
+ (description "This package provides for parsing of the semver spec.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-shlex
+ (package
+ (name "rust-shlex")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "shlex" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1lmv6san7g8dv6jdfp14m7bdczq9ss7j7bgsfqyqjc3jnjfippvz"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/comex/rust-shlex")
+ (synopsis "Split a string into shell words, like Python's shlex")
+ (description "This crate provides a method to split a string into shell
+words, like Python's shlex.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-slab
+ (package
+ (name "rust-slab")
+ (version "0.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "slab" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1y59xsa27jk84sxzswjk60xcjf8b4fm5960jwpznrrcmasyva4f1"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/carllerche/slab")
+ (synopsis "Pre-allocated storage for a uniform data type")
+ (description "This create provides a pre-allocated storage for a uniform
+data type.")
+ (license license:expat)))
+
+(define-public rust-spin
+ (package
+ (name "rust-spin")
+ (version "0.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "spin" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0m9clchsj0rf13bggsgvbv9haiy0f6rhvnvkpvkk8720a5pkydj4"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/mvdnes/spin-rs.git")
+ (synopsis "Synchronization primitives based on spinning")
+ (description "This crate provides synchronization primitives based on
+spinning. They may contain data, are usable without @code{std},and static
+initializers are available.")
+ (license license:expat)))
+
+(define-public rust-stdweb-internal-runtime
+ (package
+ (name "rust-stdweb-internal-runtime")
+ (version "0.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "stdweb-internal-runtime" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1nhpyra7glbwcpakhpj5a3d7h7kx1ynif473nzshmk226m91f8ym"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/koute/stdweb")
+ (synopsis "Internal runtime for the @code{stdweb} crate")
+ (description "This crate provides internal runtime for the @code{stdweb}
+crate.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-strsim
+ (package
+ (name "rust-strsim")
+ (version "0.9.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "strsim" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1xphwhf86yxxmcpvm4mikj8ls41f6nf7gqyjm98b74mfk81h6b03"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/dguo/strsim-rs")
+ (synopsis "Rust implementations of string similarity metrics")
+ (description "This crate includes implementations of string similarity
+metrics. It includes Hamming, Levenshtein, OSA, Damerau-Levenshtein, Jaro,
+and Jaro-Winkler.")
+ (license license:expat)))
+
+(define-public rust-synstructure-test-traits
+ (package
+ (name "rust-synstructure-test-traits")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "synstructure_test_traits" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1b3fs2b9kc1gy9dilaxqjbdl4z0mlrbbxjzkprdx953rif1c3q66"))))
+ (build-system cargo-build-system)
+ (home-page "https://crates.io/crates/synstructure_test_traits")
+ (synopsis "Helper test traits for synstructure doctests")
+ (description
+ "This package provides helper test traits for synstructure doctests.")
+ (license license:expat)))
+
+(define-public rust-typenum
+ (package
+ (name "rust-typenum")
+ (version "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "typenum" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0sc1jirllfhdi52z1xv9yqzxzpk6v7vadd13n7wvs1wnjipn6bb1"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/paholg/typenum")
+ (synopsis "Rust library for type-level numbers evaluated at compile time")
+ (description "Typenum is a Rust library for type-level numbers evaluated at
+compile time. It currently supports bits, unsigned integers, and signed
+integers. It also provides a type-level array of type-level numbers, but its
+implementation is incomplete.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-ucd-util
+ (package
+ (name "rust-ucd-util")
+ (version "0.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "ucd-util" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0x088q5z0m09a2jqcfgsnq955y8syn1mgn35cl78qinkxm4kp6zs"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/BurntSushi/ucd-generate")
+ (synopsis "library for working with the Unicode character database")
+ (description "This package provides a small utility library for working
+with the Unicode character database.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-unicode-width
+ (package
+ (name "rust-unicode-width")
+ (version "0.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "unicode-width" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "09k5lipygardwy0660jhls08fsgknrazzivmn804gps53hiqc8w8"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/unicode-rs/unicode-width")
+ (synopsis "Determine displayed width according to Unicode rules")
+ (description "This crate allows you to determine displayed width of
+@code{char} and @code{str} types according to Unicode Standard Annex #11 rules.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-unicode-xid
+ (package
+ (name "rust-unicode-xid")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "unicode-xid" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1z57lqh4s18rr4x0j4fw4fmp9hf9346h0kmdgqsqx0fhjr3k0wpw"))))
+ (build-system cargo-build-system)
+ (home-page
+ "https://github.com/unicode-rs/unicode-xid")
+ (synopsis "Determine Unicode XID related properties")
+ (description "Determine whether characters have the XID_Start
+or XID_Continue properties according to Unicode Standard Annex #31.")
+ ;; Dual licensed.
+ (license (list license:asl2.0 license:expat))))
+
+(define-public rust-unindent
+ (package
+ (name "rust-unindent")
+ (version "0.1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "unindent" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1x21ilf78aqcq9xzb9b7i628wm10rhk0jp0chlv06rkc690l8jw3"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/dtolnay/indoc")
+ (synopsis "Remove a column of leading whitespace from a string")
+ (description "This crate allows you to remove a column of leading
+whitespace from a string.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-wasm-bindgen-shared
+ (package
+ (name "rust-wasm-bindgen-shared")
+ (version "0.2.48")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "wasm-bindgen-shared" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "08rnfhjyk0f6liv8n4rdsvhx7r02glkhcbj2lp9lcbkbfpad9hnr"))))
+ (build-system cargo-build-system)
+ (home-page "https://rustwasm.github.io/wasm-bindgen/")
+ (synopsis "Shared support between wasm-bindgen and wasm-bindgen cli")
+ (description "This package provides shared support between
+@code{wasm-bindgen} and @code{wasm-bindgen} cli, an internal dependency.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-winapi
+ (package
+ (name "rust-winapi")
+ (version "0.3.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "winapi" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0w7pbhcl087lkggxdflfp2i92rq89ahsfdkjkv44fgmiy9m3h3pi"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-winapi-i686-pc-windows-gnu"
+ ,rust-winapi-i686-pc-windows-gnu)
+ ("rust-winapi-x86-64-pc-windows-gnu"
+ ,rust-winapi-x86-64-pc-windows-gnu))))
+ (home-page "https://github.com/retep998/winapi-rs")
+ (synopsis "Raw FFI bindings for all of Windows API.")
+ (description
+ "Raw FFI bindings for all of Windows API.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-winapi-i686-pc-windows-gnu
+ (package
+ (name "rust-winapi-i686-pc-windows-gnu")
+ (version "0.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "winapi-i686-pc-windows-gnu" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1dmpa6mvcvzz16zg6d5vrfy4bxgg541wxrcip7cnshi06v38ffxc"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/retep998/winapi-rs")
+ (synopsis "Import libraries for the i686-pc-windows-gnu target")
+ (description "This crate provides import libraries for the
+i686-pc-windows-gnu target. Please don't use this crate directly, depend on
+@code{winapi} instead.")
+ (license (list license:asl2.0
+ license:expat))))
+
+(define-public rust-winapi-x86-64-pc-windows-gnu
+ (package
+ (name "rust-winapi-x86-64-pc-windows-gnu")
+ (version "0.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "winapi-x86_64-pc-windows-gnu" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0gqq64czqb64kskjryj8isp62m2sgvx25yyj3kpc2myh85w24bki"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/retep998/winapi-rs")
+ (synopsis "Import libraries for the x86_64-pc-windows-gnu target")
+ (description "This package provides import libraries for the
+x86_64-pc-windows-gnu target. Please don't use this crate directly, depend on
+@code{winapi} instead.")
+ (license (list license:asl2.0
+ license:expat))))
diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index b87203cab6..467aa5d84c 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -57,7 +57,7 @@
(define-public cups-filters
(package
(name "cups-filters")
- (version "1.25.0")
+ (version "1.25.1")
(source(origin
(method url-fetch)
(uri
@@ -65,7 +65,7 @@
"cups-filters-" version ".tar.xz"))
(sha256
(base32
- "1laiscq8yvynw862calkgbz9irrdkmd5l821q6a6wik1ifd186c1"))
+ "0nlq44jnjcnrbdv0dv5myg5kaycmk6a4klynpvj65xvn3l9cq28s"))
(modules '((guix build utils)))
(snippet
;; install backends, banners and filters to cups-filters output
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 26f7bb8f73..771981fb19 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -132,12 +132,13 @@
(name "4store")
(version "1.1.6")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/4store/4store/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/4store/4store.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "004fmcf1w75zhc1x3zc6kc97j4jqn2v5nhk6yb3z3cpfrhzi9j50"))
+ (base32 "1kzdfmwpzy64cgqlkcz5v4klwx99w0jk7afckyf7yqbqb4rydmpk"))
(patches (search-patches "4store-unset-preprocessor-directive.patch"
"4store-fix-buildsystem.patch"))))
(build-system gnu-build-system)
@@ -160,12 +161,6 @@
("cyrus-sasl" ,cyrus-sasl)
("openssl" ,openssl)
("util-linux" ,util-linux)))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'generate-configure
- (lambda _
- (invoke "sh" "autogen.sh"))))))
;; http://www.4store.org has been down for a while now.
(home-page "https://github.com/4store/4store")
(synopsis "Clustered RDF storage and query engine")
@@ -616,15 +611,15 @@ Language.")
(define-public mariadb
(package
(name "mariadb")
- (version "10.1.40")
+ (version "10.1.41")
(source (origin
(method url-fetch)
- (uri (string-append "https://downloads.mariadb.org/f/"
- name "-" version "/source/"
- name "-" version ".tar.gz"))
+ (uri (string-append "https://downloads.mariadb.com/MariaDB"
+ "/mariadb-" version "/source/mariadb-"
+ version ".tar.gz"))
(sha256
(base32
- "19375bnq0yg52kqh6cy00s5rglcxdrs5bb2hy7dqv2xqa9z7lxci"))
+ "1wh0073lqw3d9xs150bf2q3qvjwa6886mfi9khmsn7p8vapw6irb"))
(patches (search-patches "mariadb-client-test-32bit.patch"))
(modules '((guix build utils)))
(snippet
@@ -806,14 +801,14 @@ as a drop-in replacement of MySQL.")
(define-public postgresql
(package
(name "postgresql")
- (version "10.9")
+ (version "10.10")
(source (origin
(method url-fetch)
(uri (string-append "https://ftp.postgresql.org/pub/source/v"
version "/postgresql-" version ".tar.bz2"))
(sha256
(base32
- "0m0gbf7nwgag6a1z5f9xszwzgf2xhx0ncakyxwxlzs87n1zk32wm"))
+ "0lzj46dwd9cw94gnqm36bxd7jlhfdyqjrfzr3c4xd3prfn2rnkxd"))
(patches (search-patches "postgresql-disable-resolve_symlinks.patch"))))
(build-system gnu-build-system)
(arguments
@@ -853,27 +848,27 @@ pictures, sounds, or video.")
(package
(inherit postgresql)
(name "postgresql")
- (version "11.4")
+ (version "11.5")
(source (origin
(method url-fetch)
(uri (string-append "https://ftp.postgresql.org/pub/source/v"
version "/postgresql-" version ".tar.bz2"))
(sha256
(base32
- "12ycjlqncijgmd5z078ybwda8ilas96lc7nxxmdq140mzpgjv002"))))))
+ "106ikalvrilihlvhq7xj7snq98hgbgq6qsgjrd252wgw1c327pvz"))))))
(define-public postgresql-9.6
(package
(inherit postgresql)
(name "postgresql")
- (version "9.6.14")
+ (version "9.6.15")
(source (origin
(method url-fetch)
(uri (string-append "https://ftp.postgresql.org/pub/source/v"
version "/postgresql-" version ".tar.bz2"))
(sha256
(base32
- "08hsqczy1ixkjyf2vr3s9x69agfz9yr8lh31fir4z0dfr5jw421z"))))))
+ "02hp69h2p02asfblkaahblzdz2zmawd2r11h6237y5j7yadgxn9w"))))))
(define-public python-pymysql
(package
diff --git a/gnu/packages/docbook.scm b/gnu/packages/docbook.scm
index 1e5379b020..d114e24ee7 100644
--- a/gnu/packages/docbook.scm
+++ b/gnu/packages/docbook.scm
@@ -195,7 +195,7 @@ by no means limited to these applications.) This package provides XML DTDs.")
(build-system python-build-system)
;; TODO: Add xfig/transfig for fig2dev utility
(inputs
- `(("texlive" ,(texlive-union (list texlive-latex-amsfonts
+ `(("texlive" ,(texlive-union (list texlive-amsfonts
texlive-latex-anysize
texlive-latex-appendix
texlive-latex-changebar
@@ -219,7 +219,6 @@ by no means limited to these applications.) This package provides XML DTDs.")
texlive-latex-url
texlive-latex-wasysym
- texlive-fonts-amsfonts
texlive-fonts-ec
texlive-fonts-rsfs
texlive-fonts-stmaryrd
diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm
index 18e7bea724..94cfa2bdb7 100644
--- a/gnu/packages/docker.scm
+++ b/gnu/packages/docker.scm
@@ -63,12 +63,13 @@
(arguments '(#:tests? #f))
(inputs
`(("python-requests" ,python-requests-2.20)
- ("python-docker-pycreds" ,python-docker-pycreds)
("python-ipaddress" ,python-ipaddress)
- ("python-paramiko" ,python-paramiko)
("python-six" ,python-six)
("python-urllib3" ,python-urllib3-1.24)
("python-websocket-client" ,python-websocket-client)))
+ (propagated-inputs
+ `(("python-docker-pycreds" ,python-docker-pycreds)
+ ("python-paramiko" ,python-paramiko))) ; adds SSH support
(home-page "https://github.com/docker/docker-py/")
(synopsis "Python client for Docker")
(description "Docker-Py is a Python client for the Docker container
@@ -113,17 +114,11 @@ client.")
;; TODO: Tests require running Docker daemon.
(arguments '(#:tests? #f))
(inputs
- `(("python2-backport-ssl-match-hostname"
- ,python2-backport-ssl-match-hostname)
- ("python-cached-property"
+ `(("python-cached-property"
,python-cached-property)
- ("python-colorama" ,python-colorama)
("python-docker-py" ,python-docker-py)
- ("python-docker-pycreds" ,python-docker-pycreds)
("python-dockerpty" ,python-dockerpty)
("python-docopt" ,python-docopt)
- ("python-ipaddress" ,python-ipaddress)
- ("python-paramiko" ,python-paramiko)
("python-jsonschema" ,python-jsonschema-2.6)
("python-pyyaml" ,python-pyyaml)
("python-requests" ,python-requests-2.20)
@@ -586,6 +581,9 @@ provisioning etc.")
;; information, and the DWARF symbol table.
(setenv "LDFLAGS" "-s -w")
+ ;; Make sure "docker -v" prints a usable version string.
+ (setenv "VERSION" ,%docker-version)
+
;; Make build reproducible.
(setenv "BUILDTIME" "1970-01-01 00:00:01.000000000+00:00")
(symlink "src/github.com/docker/cli/scripts" "./scripts")
diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm
index 4b1563efb6..70e7c8331b 100644
--- a/gnu/packages/education.scm
+++ b/gnu/packages/education.scm
@@ -251,7 +251,7 @@ easy.")
(define-public snap
(package
(name "snap")
- (version "5.0.4")
+ (version "5.0.8")
(source
(origin
(method git-fetch)
@@ -261,7 +261,7 @@ easy.")
(file-name (git-file-name name version))
(sha256
(base32
- "1zdypxifvxjkzhi4n9mkck8l419wc0pg103339yzhsbb9kkd3jlr"))))
+ "0fwfssdgv3mfzyv8hw1a1z5ky1yn0p59kyl6l9fxsm4w2ckgyizd"))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 303a807e69..886307d02b 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -51,6 +51,7 @@
;;; Copyright © 2019 Baptiste Strazzulla <bstrazzull@hotmail.fr>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autitici.org>
;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
+;;; Copyright © 2019 Amin Bandali <bandali@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -876,7 +877,7 @@ in certain cases. It also enables recursion for anonymous functions.")
(define-public emacs-xr
(package
(name "emacs-xr")
- (version "1.12")
+ (version "1.13")
(source
(origin
(method url-fetch)
@@ -884,7 +885,7 @@ in certain cases. It also enables recursion for anonymous functions.")
"https://elpa.gnu.org/packages/xr-" version ".tar"))
(sha256
(base32
- "1vv87h0h8ldc1mbsn45w5z1m6jq8j2js4xz23a9ixdby06g60y3g"))))
+ "1km4x92pii8c4bcimks4xzhmwpypdf183z0zh7raj062jz4jb74r"))))
(build-system emacs-build-system)
(home-page "http://elpa.gnu.org/packages/xr.html")
(synopsis "Convert string regexp to rx notation")
@@ -929,7 +930,7 @@ optional minor mode which can apply this command automatically on save.")
(define-public emacs-relint
(package
(name "emacs-relint")
- (version "1.8")
+ (version "1.10")
(source
(origin
(method url-fetch)
@@ -937,7 +938,7 @@ optional minor mode which can apply this command automatically on save.")
"https://elpa.gnu.org/packages/relint-" version ".el"))
(sha256
(base32
- "1bl6m2h7131acbmr0kqfnjjpv2syiv2mxfnm61g874ynnvkmmkm3"))))
+ "1l0lh4pkksw7brmhhbaikwzs4zkgd2962ks1zy7m262dvkhxjfv8"))))
(build-system emacs-build-system)
(propagated-inputs `(("emacs-xr" ,emacs-xr)))
(home-page "https://github.com/mattiase/relint")
@@ -2473,7 +2474,7 @@ column by drawing a thin line down the length of the editing window.")
(define-public emacs-inf-ruby
(package
(name "emacs-inf-ruby")
- (version "2.5.1")
+ (version "2.5.2")
(source
(origin
(method git-fetch)
@@ -2482,7 +2483,7 @@ column by drawing a thin line down the length of the editing window.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "1r452h6cyypqlc59q8dx5smkwhck4qjcg1pf9qdw539cpva5q77z"))))
+ (base32 "0a1hhvfbl6mq8rjsi77fg9fh5a91hi5scjrg9rjqc5ffbql67y0v"))))
(build-system emacs-build-system)
(home-page "https://github.com/nonsequitur/inf-ruby")
(synopsis "Provides a REPL buffer connected to a Ruby subprocess in Emacs")
@@ -3389,6 +3390,76 @@ for the current function or variable in the minibuffer.")
completion candidate when using the Company text completion framework.")
(license license:gpl3+)))
+(define-public emacs-math-symbol-lists
+ (let ((commit "dc7531cff0c845d5470a50c24d5d7309b2ced7eb")
+ (revision "1"))
+ (package
+ (name "emacs-math-symbol-lists")
+ (version (git-version "1.2.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vspinu/math-symbol-lists.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "094m21i9rns6m59cmhxcivxxafbg52w8f8na4y3v47aq67zmhhqm"))))
+ (build-system emacs-build-system)
+ (home-page "https://github.com/vspinu/math-symbol-lists")
+ (synopsis "Lists of Unicode math symbols and @code{LaTeX} commands")
+ (description "This is a storage package used by completion engines like
+@code{company-math}.")
+ (license license:gpl3+))))
+
+(define-public emacs-company-math
+ (let ((commit "600e49449644f6835f9dc3501bc58461999e8ab9")
+ (revision "1"))
+ (package
+ (name "emacs-company-math")
+ (version (git-version "1.3" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vspinu/company-math.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1ps2lpkzn8mjbpcbvvy1qz3xbgrh6951x8y9bsd1fm32drdph9lh"))))
+ (build-system emacs-build-system)
+ (propagated-inputs
+ `(("emacs-math-symbol-lists" ,emacs-math-symbol-lists)
+ ("emacs-company" ,emacs-company)))
+ (home-page "https://github.com/vspinu/company-math")
+ (synopsis "Completion backends for Unicode math symbols and @code{LaTeX} tags")
+ (description "This package provides a backend for use with
+@code{company-mode} allowing for completion of common math symbols.")
+ (license license:gpl3+))))
+
+(define-public emacs-nswbuff
+ (let ((commit "362da7f3687e2eb5bb11667347de85f4a9d002bc")
+ (revision "1"))
+ (package
+ (name "emacs-nswbuff")
+ (version (git-version "1.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/joostkremers/nswbuff.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0l2xfz8z5qd4hz3kv6zn7h6qq3narkilri8a071y1n8j31jps4ma"))))
+ (build-system emacs-build-system)
+ (home-page "https://github.com/joostkremers/nswbuff")
+ (synopsis "Quickly switch between buffers")
+ (description "This package allows for navigating between buffers within
+a customizable list.")
+ (license license:gpl3+))))
+
(define-public emacs-multiple-cursors
(package
(name "emacs-multiple-cursors")
@@ -3410,6 +3481,32 @@ completion candidate when using the Company text completion framework.")
simultaneous cursors.")
(license license:gpl3+)))
+(define-public emacs-mc-extras
+ (let ((commit "053abc52181b8718559d7361a587bbb795faf164")
+ (revision "1"))
+ (package
+ (name "emacs-mc-extras")
+ (version (git-version "1.2.4" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/knu/mc-extras.el.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "16y48qrd20m20vypvys5jp4v4gc1qrqlkm75s1pk1r68i9zrw481"))))
+ (build-system emacs-build-system)
+ (propagated-inputs
+ `(("emacs-multiple-cursors" ,emacs-multiple-cursors)))
+ (home-page "https://github.com/knu/mc-extras.el")
+ (synopsis "Extra functions for manipulating multiple cursors")
+ (description
+ "This package provides additional functions for
+@code{multiple-cursors}, including functions for marking s-expressions,
+comparing characters, removing cursors, and more.")
+ (license license:bsd-2))))
+
(define-public emacs-typo
(package
(name "emacs-typo")
@@ -4011,6 +4108,38 @@ minutes is started automatically. Every 4 breaks a long break is
started with 20 minutes. All values are customizable.")
(license license:gpl3+)))
+(define-public emacs-org-sidebar
+ (let ((commit "74ca98b9920f3de3f13d49866581435e1ec63ec5")
+ (revision "1"))
+ (package
+ (name "emacs-org-sidebar")
+ (version (git-version "0.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/alphapapa/org-sidebar.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "03p1ndyw2qp2skib5hszc4xyh84w7p2mhkd4a9dy6qv8q47xpsqn"))))
+ (build-system emacs-build-system)
+ (propagated-inputs
+ `(("emacs-dash" ,emacs-dash)
+ ("emacs-org-super-agenda" ,emacs-org-super-agenda)
+ ("emacs-org" ,emacs-org)
+ ("emacs-org-ql" ,emacs-org-ql)
+ ("emacs-s" ,emacs-s)))
+ (home-page "https://github.com/alphapapa/org-sidebar")
+ (synopsis "Helpful sidebar for Org buffers")
+ (description "This package provides a sidebar for Org buffers. At the
+top is a chronological list of scheduled and deadlined tasks in the current
+buffer (similar to the Org agenda ,but without all its features), and below
+that is a list of all other non-done to-do items. If the buffer is narrowed,
+the sidebar only shows items in the narrowed portion; this allows seeing an
+overview of tasks in a subtree.")
+ (license license:gpl3+))))
+
(define-public emacs-org-trello
(package
(name "emacs-org-trello")
@@ -4604,45 +4733,50 @@ automatically.")
(license license:gpl3+)))
(define-public emacs-ivy
- (package
- (name "emacs-ivy")
- (version "0.12.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/abo-abo/swiper.git")
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0xgngn3jhmyn6mlkk9kmgfgh0w5i50b27syr4cgfgarg6p77j05w"))))
- (build-system emacs-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'install 'install-doc
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (info (string-append out "/share/info")))
- (with-directory-excursion "doc"
- (invoke "makeinfo" "ivy.texi")
- (install-file "ivy.info" info)
- #t)))))))
- (propagated-inputs
- `(("emacs-hydra" ,emacs-hydra)))
- (native-inputs
- `(("texinfo" ,texinfo)))
- (home-page "http://oremacs.com/swiper/")
- (synopsis "Incremental vertical completion for Emacs")
- (description
- "This package provides @code{ivy-read} as an alternative to
+ ;; The latest release version introduced a new feature, swiper-isearch, that
+ ;; generally works well but had some noticeable bugs; this later commit
+ ;; includes fixes for several of them.
+ (let ((commit "d3e4514fd72f217c704ae18afdf711bb9036a04d")
+ (revision "1"))
+ (package
+ (name "emacs-ivy")
+ (version (git-version "0.12.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/abo-abo/swiper.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "142axxc6vsl14cfyvzj9csiykxdn7vhw88fy955hzx7av4qfqg4x"))))
+ (build-system emacs-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'install 'install-doc
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (info (string-append out "/share/info")))
+ (with-directory-excursion "doc"
+ (invoke "makeinfo" "ivy.texi")
+ (install-file "ivy.info" info)
+ #t)))))))
+ (propagated-inputs
+ `(("emacs-hydra" ,emacs-hydra)))
+ (native-inputs
+ `(("texinfo" ,texinfo)))
+ (home-page "http://oremacs.com/swiper/")
+ (synopsis "Incremental vertical completion for Emacs")
+ (description
+ "This package provides @code{ivy-read} as an alternative to
@code{completing-read} and similar functions. No attempt is made to determine
the best candidate. Instead, the user can navigate candidates with
@code{ivy-next-line} and @code{ivy-previous-line}. The matching is done by
splitting the input text by spaces and re-building it into a regular
expression.")
- (license license:gpl3+)))
+ (license license:gpl3+))))
(define-public emacs-ivy-pass
(let ((commit "5b523de1151f2109fdd6a8114d0af12eef83d3c5")
@@ -5228,7 +5362,7 @@ strings, and code folding.")
(define-public emacs-nodejs-repl
(package
(name "emacs-nodejs-repl")
- (version "0.2.1")
+ (version "0.2.2")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -5237,7 +5371,7 @@ strings, and code folding.")
(file-name (git-file-name name version))
(sha256
(base32
- "05ccv87rnw7fss3lib8m9sywjrj6n92fnd7mmhmjh27g2klqc83z"))))
+ "1kkj888k9x5n0i7xkia177gzsa84my3g8n0n7v65281cc4f1yhk5"))))
(build-system emacs-build-system)
(home-page "https://github.com/abicky/nodejs-repl.el")
(synopsis "Node.js REPL inside Emacs")
@@ -5580,28 +5714,35 @@ environments (virtualenv) inside Emacs.")
(license license:gpl3+)))
(define-public emacs-highlight-indentation
- (package
- (name "emacs-highlight-indentation")
- (version "0.7.0")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/antonj/Highlight-Indentation-for-Emacs.git")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "00l54k75qk24a0znzl4ij3s3nrnr2wy9ha3za8apphzlm98m907k"))))
- (build-system emacs-build-system)
- (home-page "https://github.com/antonj/Highlight-Indentation-for-Emacs/")
- (synopsis "Highlighting indentation for Emacs")
- (description "Provides two minor modes to highlight indentation guides in Emacs:
+ ;; Last release version is from 2015.
+ (let ((commit "d03803f2c06749c430443a3d24e039cbafc9c58f")
+ (revision "1"))
+ (package
+ (name "emacs-highlight-indentation")
+ (version (git-version "0.7.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/antonj/Highlight-Indentation-for-Emacs.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1jq0gf4kcx9hvrw40rnw5c2qynjpjw1vsjbi2i4lqjbsnfnxn4wz"))))
+ (build-system emacs-build-system)
+ (home-page "https://github.com/antonj/Highlight-Indentation-for-Emacs/")
+ (synopsis "Highlighting indentation for Emacs")
+ (description "This package provides two minor modes to highlight
+indentation guides in Emacs:
+
@enumerate
@item @code{highlight-indentation-mode}, which displays guidelines
-indentation (space indentation only).
-@item @code{highlight-indentation-current-column-mode}, which displays guidelines for the current-point indentation (space indentation only).
+ indentation (space indentation only).
+@item @code{highlight-indentation-current-column-mode}, which displays
+ guidelines for the current-point indentation (space indentation only).
@end enumerate")
- (license license:gpl2+)))
+ (license license:gpl2+))))
(define-public emacs-elpy
(package
@@ -5931,7 +6072,7 @@ ack, ag, helm and pt.")
(define-public emacs-helm
(package
(name "emacs-helm")
- (version "3.2")
+ (version "3.3")
(source
(origin
(method git-fetch)
@@ -5940,7 +6081,7 @@ ack, ag, helm and pt.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "12yyprpgh2by2pd41i4z9gz55fxg0f90x03bfrsf791xwbhf6931"))))
+ (base32 "0fqhw7r9fcsja5d3pgbipw7pkw9nj534faav6hi45413hc3gyv92"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-async" ,emacs-async)
@@ -6119,21 +6260,21 @@ xref, etc...) are still available, but with better integration.")
(license license:gpl3+))))
(define-public emacs-lua-mode
- (let ((commit "652e299cb967fccca827dda381d61a9c144d97de")
- (revision "1"))
+ (let ((commit "95c64bb5634035630e8c59d10d4a1d1003265743")
+ (revision "2"))
(package
(name "emacs-lua-mode")
- (version (string-append "20151025." revision "-" (string-take commit 9)))
+ (version (git-version "20151025" revision commit))
(home-page "https://github.com/immerrr/lua-mode/")
(source (origin
(method git-fetch)
(uri (git-reference
(url home-page)
(commit commit)))
- (file-name (string-append name "-" version ".checkout"))
+ (file-name (git-file-name name version))
(sha256
(base32
- "053025k930wh0lak6rc1973ynfrmm8zsyzfqhhd39x7abkl41hc9"))))
+ "1mra4db25ds64526dsj8m5yv0kfq3lgggjh1x6xmqypdaryddbcp"))))
(build-system emacs-build-system)
(synopsis "Major mode for lua")
(description
@@ -6399,12 +6540,11 @@ aligning text objects based on separators.")
(license license:gpl3+))))
(define-public emacs-evil-expat
- (let ((commit "4c344ea19b789002d759a202ffbf594730d2c59a")
- (version "0.0.1")
+ (let ((commit "f4fcd0aa3edc359adb5c986b5dd9188d220d84e2")
(revision "1"))
(package
(name "emacs-evil-expat")
- (version (git-version version revision commit))
+ (version (git-version "0.0.1" revision commit))
(source
(origin
(method git-fetch)
@@ -6414,7 +6554,7 @@ aligning text objects based on separators.")
(file-name (git-file-name name version))
(sha256
(base32
- "16v7fnldxag6l1lsnrnhdjkga9qi78lbdfbb82k6pmv04991mbkr"))))
+ "0872ix682hkdz0k8pn6sb54rqkx00rz5fxpd5j2snx406yagpaxz"))))
(build-system emacs-build-system)
(propagated-inputs `(("emacs-evil" ,emacs-evil)))
(home-page "https://github.com/edkolev/evil-expat")
@@ -6587,14 +6727,14 @@ passive voice.")
(name "emacs-org")
;; emacs-org-contrib inherits from this package. Please update its sha256
;; checksum as well.
- (version "9.2.3")
+ (version "9.2.5")
(source (origin
(method url-fetch)
- (uri (string-append "http://elpa.gnu.org/packages/org-"
+ (uri (string-append "https://elpa.gnu.org/packages/org-"
version ".tar"))
(sha256
(base32
- "0hqy4lns9q5p0l1ylgmlckqprn9sbasszhznanmv0rsh0gzhsbyw"))))
+ "1pid1sykgz83i4ry5n8f270finag6sm7ckqxn5lkikyya43wlzx1"))))
(build-system emacs-build-system)
(home-page "https://orgmode.org/")
(synopsis "Outline-based notes management and organizer")
@@ -6608,14 +6748,14 @@ programming and reproducible research.")
(package
(inherit emacs-org)
(name "emacs-org-contrib")
- (version "20190715")
+ (version "20190805")
(source (origin
(method url-fetch)
(uri (string-append "https://orgmode.org/elpa/org-plus-contrib-"
version ".tar"))
(sha256
(base32
- "0yxxkcaxhp5bmjsfdd9pz79rj9s7nb4gj5ci51sh4pf8mimk9542"))))
+ "1mw91hwbqyjq5pyz9hzdhvjlc2bphqpi23yqd3sdk1crpc87s40c"))))
(arguments
`(#:modules ((guix build emacs-build-system)
(guix build utils)
@@ -7159,6 +7299,56 @@ find files owned by packages... And much more, including performing all the
above over the network.")
(license license:gpl3+))))
+(define-public emacs-helm-org-rifle
+ (package
+ (name "emacs-helm-org-rifle")
+ (version "1.6.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/alphapapa/helm-org-rifle")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1r38xhwvgbv6kn5x159phz3xgss7f1rc7icq27rnr4d8aj91wm6k"))))
+ (build-system emacs-build-system)
+ (propagated-inputs
+ `(("emacs-dash" ,emacs-dash)
+ ("emacs-f" ,emacs-f)
+ ("emacs-helm" ,emacs-helm)
+ ("emacs-s" ,emacs-s)))
+ (home-page "https://github.com/alphapapa/helm-org-rifle")
+ (synopsis "Rifle through Org files")
+ (description "This package searches both headings and contents of entries
+in Org buffers and displays matching entries.")
+ (license license:gpl3+)))
+
+(define-public emacs-dired-toggle-sudo
+ (package
+ (name "emacs-dired-toggle-sudo")
+ (version "1.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/renard/dired-toggle-sudo")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0ajj8d6k5in2hclcrqckinfh80ylddplva0ryfbkzsjkfq167cv2"))
+ (patches
+ (search-patches
+ "emacs-dired-toggle-sudo-emacs-26.patch"))))
+ (build-system emacs-build-system)
+ (home-page "https://github.com/renard/dired-toggle-sudo")
+ (synopsis "Browse directory with @code{sudo} privileges")
+ (description "This package allows for the use of @code{dired} with
+@code{sudo} privileges.")
+ (license license:wtfpl2)))
+
(define-public emacs-memoize
(package
(name "emacs-memoize")
@@ -8528,12 +8718,11 @@ the actual transformations.")
(license license:gpl2+))))
(define-public emacs-dired-hacks
- (let ((commit "2c1234592aee91dcd9401bcd67213e6a4a464fd9")
- (revision "1"))
+ (let ((commit "886befe113fae397407c804f72c45613d1d43535")
+ (revision "2"))
(package
(name "emacs-dired-hacks")
- (version (string-append "0.0.1-" revision "."
- (string-take commit 7)))
+ (version (git-version "0.0.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -8542,7 +8731,7 @@ the actual transformations.")
(file-name (git-file-name name version))
(sha256
(base32
- "1g7mky41cahpryzj6frdgzdymknpqq7pidzfjj9304887kijmhj3"))))
+ "1cvibg90ggyrivpjmcfprpi2fx7dpa68f8kzg08s88gw5ib75djl"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-dash" ,emacs-dash)
@@ -8553,7 +8742,9 @@ the actual transformations.")
(synopsis
"Collection of useful dired additions")
(description
- "Collection of Emacs dired mode additions:
+ "This package provides the following collection of Emacs dired mode
+additions:
+
@itemize
@item dired-avfs
@item dired-columns
@@ -8623,6 +8814,32 @@ available key bindings that follow C-x (or as many as space allows given your
settings).")
(license license:gpl3+)))
+(define-public emacs-hercules
+ (let ((commit "3345904a0dab4c7a4d4478f0766f1d9f5d1bb501")
+ (revision "1"))
+ (package
+ (name "emacs-hercules")
+ (version (git-version "0.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/jjzmajic/hercules.el.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0cpq8h6l47nqhzch6snax5yrhxl8p4wn35q13ci35lj3iq8kmlk8"))))
+ (build-system emacs-build-system)
+ (propagated-inputs
+ `(("emacs-which-key" ,emacs-which-key)))
+ (home-page "https://gitlab.com/jjzmajic/hercules.el")
+ (synopsis "Call a chain of related commands without repeated prefix keys")
+ (description
+ "This package provides sticky-key-like functionality to obviate the
+need for repeated prefix-key sequences, and can reuse existing keymaps. The
+list of commands is displayed in a handy popup.")
+ (license license:gpl3+))))
+
(define-public emacs-ws-butler
(package
(name "emacs-ws-butler")
@@ -10433,29 +10650,32 @@ as well as functions for navigating between these headings.")
(license license:gpl3+)))
(define-public emacs-org-super-agenda
- (package
- (name "emacs-org-super-agenda")
- (version "1.1")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/alphapapa/org-super-agenda")
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0vzf91lsxnhwf52kvm8ycpf0wb9c8l91689vyhwgv4wz8q6cvjwp"))))
- (build-system emacs-build-system)
- (propagated-inputs
- `(("emacs-org" ,emacs-org)
- ("emacs-dash" ,emacs-dash)
- ("emacs-ht" ,emacs-ht)
- ("emacs-s" ,emacs-s)))
- (home-page "https://github.com/alphapapa/org-super-agenda")
- (synopsis "Supercharged Org agenda")
- (description "This package allows items in the Org agenda to be grouped
+ ;; emacs-org-sidebar depends on a newer commit than the latest release version.
+ (let ((commit "375bde4ca72494ac88a2a9738754f047fe45cc4e")
+ (revision "1"))
+ (package
+ (name "emacs-org-super-agenda")
+ (version (git-version "1.1.1" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/alphapapa/org-super-agenda")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0hrwf02fqjm0d9gj146ax67ib76093qpqh7066dcxj2gy20625yj"))))
+ (build-system emacs-build-system)
+ (propagated-inputs
+ `(("emacs-org" ,emacs-org)
+ ("emacs-dash" ,emacs-dash)
+ ("emacs-ht" ,emacs-ht)
+ ("emacs-s" ,emacs-s)))
+ (home-page "https://github.com/alphapapa/org-super-agenda")
+ (synopsis "Supercharged Org agenda")
+ (description "This package allows items in the Org agenda to be grouped
into sections while preserving the structure imposed by any timestamps.")
- (license license:gpl3+)))
+ (license license:gpl3+))))
(define-public emacs-org-make-toc
(package
@@ -11752,7 +11972,7 @@ downloading manager for Emacs.")
(define-public emacs-helpful
(package
(name "emacs-helpful")
- (version "0.16")
+ (version "0.17")
(source
(origin
(method git-fetch)
@@ -11761,7 +11981,7 @@ downloading manager for Emacs.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "1pzlx3galyryd3hd84hnd7r5s6yl9sdrfhy1s6dgz40glw41wmpr"))))
+ (base32 "0v2y0x9pwi08y2mgjjiw5brfb5haa7pbmy4540glw904ffxxcblj"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-elisp-refs" ,emacs-elisp-refs)
@@ -12676,6 +12896,29 @@ When @code{gac-automatically-push-p} is non-nil, it also tries to push to
the current upstream.")
(license license:gpl3+)))
+(define-public emacs-scroll-on-drag
+ (let ((commit "888abd04c34753b1fc4b2fe541bc004ebec5c996")
+ (revision "1"))
+ (package
+ (name "emacs-scroll-on-drag")
+ (version (git-version "0.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/ideasman42/emacs-scroll-on-drag.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1si4hdqa3jw1inbyh3wb3i5i9grbms1nwky3vyk9zg7iznwm8a9p"))))
+ (build-system emacs-build-system)
+ (home-page "https://gitlab.com/ideasman42/emacs-scroll-on-drag")
+ (synopsis "Interactive scrolling")
+ (description "This package permits scrolling at increasing speeds based
+on drag distance.")
+ (license license:gpl3+))))
+
(define-public emacs-company-restclient
(package
(name "emacs-company-restclient")
@@ -13692,12 +13935,11 @@ server with @code{M-x pinentry-start}.")
(license license:gpl3+))))
(define-public emacs-so-long
- (let ((commit "3ebe97decdb5cbbfba82ca686e0ad2c7d2722b4a")
- (version "1.0")
- (revision "1"))
+ (let ((commit "cfae473b1bf65f78ddb015159e667ec0103d881c")
+ (revision "2"))
(package
(name "emacs-so-long")
- (version (git-version version revision commit))
+ (version (git-version "1.0" revision commit))
(source
(origin
(method git-fetch)
@@ -13707,7 +13949,7 @@ server with @code{M-x pinentry-start}.")
(file-name (git-file-name name version))
(sha256
(base32
- "0fi71g5rsdsi978jz8406k8hvzgnssm9wxar8yqfhs97178r9s5m"))))
+ "0g943n5cl9lz5s7hszg6yvp10xd1xvd8mfgxyg0yckmp8fqkswin"))))
(build-system emacs-build-system)
(home-page "https://www.emacswiki.org/emacs/SoLong")
(synopsis "Improve performance in files with long lines")
@@ -13744,12 +13986,13 @@ accept and reject GitHub pull requests.")
(license license:gpl3+))))
(define-public emacs-deadgrep
- (let ((commit "caeb37b8d6ab83f0eba353d6bbb29678190d4419")
- (version "0.7")
+ ;; We prefer a newer commit (four commits newer than release) because of a
+ ;; bugfix for globbing.
+ (let ((commit "329119c65126f7917d3910bc584f4191ba8f21ac")
(revision "1"))
(package
(name "emacs-deadgrep")
- (version (git-version version revision commit))
+ (version (git-version "0.8" revision commit))
(source
(origin
(method git-fetch)
@@ -13759,7 +14002,7 @@ accept and reject GitHub pull requests.")
(file-name (git-file-name name version))
(sha256
(base32
- "158fqha8nilwfzmw15lcsq8b099j8wclzq303md0j4mfr2q2gfvs"))))
+ "0fxf7gq9sjfkgpdfqx10w3l3nd4rwa8kv9plyxk1fqacb3s5m6ai"))))
(build-system emacs-build-system)
(inputs
`(("emacs-dash" ,emacs-dash)
@@ -14142,7 +14385,7 @@ buffers – other modes on the TODO list).
(define-public emacs-magit-todos
(package
(name "emacs-magit-todos")
- (version "1.2")
+ (version "1.3")
(source
(origin
(method git-fetch)
@@ -14152,7 +14395,7 @@ buffers – other modes on the TODO list).
(file-name (git-file-name name version))
(sha256
(base32
- "17a18gszbypz82bj36xbfyykc4s9rz83vwmpxvlf65svhd51c0nh"))))
+ "0gfm6wn2a4v5i9lfsvvin0kwpr9n96ddm3z4yf50jd3kg2igzry1"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-async" ,emacs-async)
@@ -16189,7 +16432,7 @@ previewed by scrolling up and down within a @code{dired} buffer.")
(define-public emacs-counsel-etags
(package
(name "emacs-counsel-etags")
- (version "1.8.4")
+ (version "1.8.7")
(source
(origin
(method git-fetch)
@@ -16199,7 +16442,7 @@ previewed by scrolling up and down within a @code{dired} buffer.")
(file-name (git-file-name name version))
(sha256
(base32
- "14my9jvxl26a5yn381h5pi5481y9d9gyk7wnxxd0s4sjc964c5h5"))))
+ "0vjcjspfrz1csnmfi6r7p7f070a496adxkqnsxwx1gx8cpylwp1g"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-ivy" ,emacs-ivy)))
@@ -16632,6 +16875,30 @@ provided. Those alternative commands are and bound by default to their
corresponding Evil keys.")
(license license:expat))))
+(define-public emacs-evil-traces
+ (let ((commit "b41b7432b8110378c199a3d25af464083777f453")
+ (revision "1"))
+ (package
+ (name "emacs-evil-traces")
+ (version (git-version "0.0.1" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mamapanda/evil-traces.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0a15f2saynz9fws1h5s7py3cshsk4xs1kwgwj1m5rsin36g0j6hc"))))
+ (build-system emacs-build-system)
+ (propagated-inputs
+ `(("emacs-evil" ,emacs-evil)))
+ (home-page "https://github.com/mamapanda/evil-traces")
+ (synopsis "Visual hints for @code{evil-ex}")
+ (description "This package adds visual hints to certain @code{ex}
+commands in @code{evil-mode}.")
+ (license license:gpl3+))))
+
(define-public emacs-xterm-color
(let ((commit "a452ab38a7cfae97078062ff8885b5d74fd1e5a6")
(version "1.8")
@@ -16846,6 +17113,29 @@ convert the resulting @code{.epub} to a @code{.mobi} file. Needs a working
zip utility (default is @code{zip}).")
(license license:gpl3+)))
+(define-public emacs-ox-hugo
+ (package
+ (name "emacs-ox-hugo")
+ (version "0.8")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/kaushalmodi/ox-hugo.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "11h464cyc28ld0b0zridgm4drydc1qjxbm1y24zrwlkyqqjk6yr7"))))
+ (build-system emacs-build-system)
+ (home-page "https://ox-hugo.scripter.co")
+ (synopsis "Hugo markdown back-end for Org export engine")
+ (description
+ "Ox-hugo is an Org exporter backend that exports Org to Hugo-compatible
+Markdown, Blackfriday, and also generates the front-matter in TOML or YAML
+format.")
+ (license license:gpl3+)))
+
(define-public emacs-ox-pandoc
(package
(name "emacs-ox-pandoc")
@@ -16926,3 +17216,28 @@ time.")
(description "@code{mastodon.el} is an Emacs client for Mastodon, the
federated microblogging social network.")
(license license:gpl3+)))
+
+;; The last release tarball is for version 0.6. We pick a commit close to
+;; version 0.6.10, which doesn't have a release tarball.
+(define-public emacs-ebdb
+ (let ((commit "2a87f5ed2a53e3a4e91e8c88ba5afc49f5e945df")
+ (revision "0"))
+ (package
+ (name "emacs-ebdb")
+ (version (git-version "0.6.10" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/girzel/ebdb.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0fidy7z0c86dpqiss97sg5s92fd3fj4bdl8pqqdgg2m00jx4mrjz"))))
+ (build-system emacs-build-system)
+ (home-page "https://github.com/girzel/ebdb")
+ (synopsis "EIEIO port of BBDB, Emacs's contact-management package")
+ (description "EBDB is a contact management/addressbook package for
+Emacs. It's a re-write of the Insidious Big Brother Database (BBDB) using
+Emacs Lisp's (relatively new) EIEIO object oriented libraries.")
+ (license license:gpl3+))))
diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index bf638525df..fa2bf786c2 100644
--- a/gnu/packages/emulators.scm
+++ b/gnu/packages/emulators.scm
@@ -119,8 +119,8 @@
;; Building from recent Git because the official 5.0 release no longer builds.
(define-public dolphin-emu
- (let ((commit "2c57e709d0f9e4010a4415de4192de887e37f187")
- (revision "5"))
+ (let ((commit "24718c1a389e4f51db974575cd15c372485b92e2")
+ (revision "6"))
(package
(name "dolphin-emu")
(version (git-version "5.0" revision commit))
@@ -146,7 +146,7 @@
#t))
(sha256
(base32
- "0aszfdfvs7yg4bmrd3qxwsiz7hx3mrj29f4aw86bz7h9j7hkh57f"))))
+ "1d92rhnw307j3m6swk6bycb8fyc7vw2hfgakd5hpsc4qw65vxfq8"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f
@@ -244,12 +244,6 @@ turbo speed, networked multiplayer, and graphical enhancements.")
(base32
"02i648i50dwicv1vaql15rccv4g8h5blf5g6inv67lrfxpbkvlf0"))))
(build-system gnu-build-system)
- (arguments
- `(#:phases (modify-phases %standard-phases
- (add-after
- 'unpack 'autogen.sh
- (lambda _
- (invoke "sh" "autogen.sh"))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)))
@@ -1185,7 +1179,7 @@ play them on systems for which they were never designed!")
(define-public mame
(package
(name "mame")
- (version "0.211")
+ (version "0.212")
(source
(origin
(method git-fetch)
@@ -1195,7 +1189,11 @@ play them on systems for which they were never designed!")
(file-name (git-file-name name version))
(sha256
(base32
- "0gbxgncbzmmplijg0c1ibwsb87fbmfvs1kjflh002yyx8yvfw83z"))
+ "0p3zcb9l624dsy2gyv23ppp1k1iwd1vrg8cbn5v4fx1s44mx7f5c"))
+ (patches
+ ;; FIXME: Remove once 0.213 is out. Applied upstream as
+ ;; 0b5b13cf1e28550b49c387dec93f9801f029e313.
+ (search-patches "mame-rapidjson-fix.patch"))
(modules '((guix build utils)))
(snippet
;; Remove bundled libraries.
diff --git a/gnu/packages/enchant.scm b/gnu/packages/enchant.scm
index ce148b47a5..cfec161784 100644
--- a/gnu/packages/enchant.scm
+++ b/gnu/packages/enchant.scm
@@ -33,7 +33,7 @@
(define-public enchant
(package
(name "enchant")
- (version "2.2.4")
+ (version "2.2.5")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/AbiWord/enchant/releases"
@@ -41,7 +41,7 @@
version ".tar.gz"))
(sha256
(base32
- "1p6a3qmrh8bjzds6x7rg9da0ir44gg804jzkf634h39wsa4vdmpm"))))
+ "0iqwzs11i9fvqdxv5kn0svcn2mzymn657qf3j66lg8dx1nh4xkpz"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags '("--disable-static"
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 7d48414889..a1f222bed4 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -11,6 +11,7 @@
;;; Copyright © 2018, 2019 Jonathan Brielmaier <jonathan.brielmaier@web.de>
;;; Copyright © 2018, 2019 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2019 Tim Stahel <swedneck@swedneck.xyz>
+;;; Copyright © 2019 Jovany Leandro G.C <bit4bit@riseup.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -2062,3 +2063,49 @@ purpose circuit simulator and can perform DC and transient analyses, fourier
analysis and AC analysis. The engine is designed to do true mixed-mode
simulation.")
(license license:gpl3+)))
+
+(define-public cutter
+ (package
+ (name "cutter")
+ (version "1.8.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/radareorg/cutter")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "03f3cdckh51anx9gd1b0ndb2fg7061hqngvygf32ky29mm2m2lyv"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (radare2 (assoc-ref inputs "radare2")))
+ ;; fix pkg-config detection ./src/lib_radare2.pri:PREFIX=/usr/lib
+ ;; override `qmake PREFIX=`
+ (substitute* "./src/lib_radare2.pri"
+ (("PREFIX") "R2PREFIX")
+ (("R2PREFIX=/usr") (string-append "R2PREFIX=" radare2)))
+ (invoke "qmake"
+ (string-append "PREFIX=" out)
+ "./src/Cutter.pro")))))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("qtbase" ,qtbase)
+ ("qtsvg" ,qtsvg)
+ ("openssl" ,openssl)
+ ("radare2" ,radare2)))
+ (home-page "https://github.com/radareorg/cutter")
+ (synopsis "GUI for radare2 reverse engineering framework")
+ (description "Cutter is a GUI for radare2 reverse engineering framework.
+Its goal is making an advanced andcustomizable reverse-engineering platform
+while keeping the user experience at mind. Cutter is created by reverse
+engineers for reverse engineers.")
+ (license (list license:cc-by-sa3.0 ;the "Iconic" icon set
+ license:gpl3+)))) ;everything else
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 8556677e74..87775c68fe 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -13,6 +13,7 @@
;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2019 Tanguy Le Carrour <tanguy@bioneland.org>
+;;; Copyright © 2019 Martin Becze <mjbecze@riseup.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -38,6 +39,7 @@
#:use-module (guix build-system cmake)
#:use-module (guix build-system python)
#:use-module (guix build-system glib-or-gtk)
+ #:use-module (guix build-system go)
#:use-module (guix utils)
#:use-module (gnu packages)
#:use-module (gnu packages base)
@@ -357,7 +359,7 @@ do so.")
(define-public electrum
(package
(name "electrum")
- (version "3.3.6")
+ (version "3.3.8")
(source
(origin
(method url-fetch)
@@ -365,7 +367,7 @@ do so.")
version "/Electrum-"
version ".tar.gz"))
(sha256
- (base32 "0am5ki3z0yvhrz16vp2jjy5fkxxqph0mj9qqpbw3kpql65shykwz"))
+ (base32 "1g00cj1pmckd4xis8r032wmraiv3vd3zc803hnyxa2bnhj8z3bg2"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -715,9 +717,6 @@ the Monero GUI client.")
Ledger Nano as a hardware SSH/GPG agent.")
(license license:lgpl3)))
-(define-public python2-trezor-agent
- (package-with-python2 python-trezor-agent))
-
(define-public python-mnemonic
(package
(name "python-mnemonic")
@@ -813,9 +812,6 @@ Ledger Blue/Nano S.")
TREZOR Hardware Wallet.")
(license license:lgpl3)))
-(define-public python2-trezor
- (package-with-python2 python-trezor))
-
(define-public python-keepkey
(package
(name "python-keepkey")
@@ -965,7 +961,7 @@ Luhn and family of ISO/IEC 7064 check digit algorithms. ")
(define-public python-duniterpy
(package
(name "python-duniterpy")
- (version "0.54.3")
+ (version "0.55.1")
(source
(origin
(method git-fetch)
@@ -976,7 +972,7 @@ Luhn and family of ISO/IEC 7064 check digit algorithms. ")
(file-name (git-file-name name version))
(sha256
(base32
- "1k3rpfc9zxj9z50cr4zjfyzdla9ap5mj1v1rlcriqmflgb5cmiba"))))
+ "07zsbbkzmnvyv5v0vw2d42vw3ar4iqhlidy9376ysk4ldlj1igf7"))))
(build-system python-build-system)
(arguments
;; Tests fail with "AttributeError: module 'attr' has no attribute 's'".
@@ -1023,7 +1019,7 @@ main features are:
(define-public silkaj
(package
(name "silkaj")
- (version "0.7.2")
+ (version "0.7.3")
(source
(origin
(method git-fetch)
@@ -1033,7 +1029,7 @@ main features are:
(file-name (git-file-name name version))
(sha256
(base32
- "059k2kil2l8jcm4wp86w1z7y8p26rww7d3l5fzds0qq2dzvkvzgs"))))
+ "0yk2574yb0d0k0rg7qf0pkmjidblsad04x8hhqpy9k80rvgjcr5w"))))
(build-system python-build-system)
(arguments
`(#:tests? #f)) ;no test
@@ -1095,3 +1091,26 @@ financial years, budget estimates, bankcard management and other
information.")
(home-page "http://grisbi.org")
(license license:gpl2+)))
+
+(define-public trezord
+ (package
+ (name "trezord")
+ (version "2.0.17")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/trezor/trezord-go.git")
+ (commit (string-append "v" version))))
+ (sha256
+ (base32
+ "0nqzpq0i3crh0i4r1cppja5sn3rwi1fv9afxzwzv63096x5l30a7"))
+ (file-name (git-file-name name version))))
+ (build-system go-build-system)
+ (arguments
+ '(#:import-path "github.com/trezor/trezord-go"))
+ (home-page "https://trezor.io")
+ (synopsis "Trezor Communication Daemon aka Trezor Bridge (written in Go)")
+ (description "This allows a Trezor hardware wallet to communicate to the
+Trezor wallet.")
+ (license license:lgpl3+)))
diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index 713c49259c..c4f82cde19 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -644,7 +644,7 @@ for use at smaller text sizes")))
(define-public font-gnu-unifont
(package
(name "font-gnu-unifont")
- (version "12.1.02")
+ (version "12.1.03")
(source
(origin
(method url-fetch)
@@ -654,7 +654,7 @@ for use at smaller text sizes")))
(string-append "mirror://gnu/unifont/unifont-"
version "/unifont-" version ".tar.gz")))
(sha256
- (base32 "12wdxnlyz5gl5d7h6pazcz8d7h81fwkng1xrayxsgrzh6bqdq4p8"))))
+ (base32 "10mr3ax19v5pa6a791fk2j3k45fpa8n5r36kq9gs8lk95wfnxmf1"))))
(build-system gnu-build-system)
(outputs '("out" ; TrueType version
"pcf" ; PCF (bitmap) version
diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm
index fe9e77d8c7..041c1b3b6b 100644
--- a/gnu/packages/fontutils.scm
+++ b/gnu/packages/fontutils.scm
@@ -637,7 +637,7 @@ definitions.")
opentype fonts. You can save fonts in many different outline formats, and
generate bitmaps.")
(license license:gpl3+)
- (home-page "https://fontforge.github.io/en-US/")))
+ (home-page "https://fontforge.github.io")))
(define-public python2-ufolib
(package
diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index 7cd959d2f1..b1368cb72e 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -723,7 +723,7 @@ multiplexer to the KMS/DRM Linux kernel devices.")
(define-public exempi
(package
(name "exempi")
- (version "2.5.0")
+ (version "2.5.1")
(source (origin
(method url-fetch)
(uri (string-append
@@ -731,7 +731,7 @@ multiplexer to the KMS/DRM Linux kernel devices.")
name "-" version ".tar.bz2"))
(sha256
(base32
- "06vi7dc2gappwqm3xpfyy5ihxq14bmvj3bd47yk482jlq0jgr0nw"))))
+ "1j4vx054l1c2cggw4aka4iw48jkcf68qk5y064pbqw1k3ddks2qh"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags (list (string-append "--with-boost="
@@ -741,7 +741,7 @@ multiplexer to the KMS/DRM Linux kernel devices.")
(inputs
`(("expat" ,expat)
("zlib" ,zlib)))
- (home-page "https://wiki.freedesktop.org/libopenraw/Exempi")
+ (home-page "https://libopenraw.freedesktop.org/exempi/")
(synopsis "XMP metadata handling library")
(description "Exempi is an implementation of the Extensible Metadata
Platform (@dfn{XMP}), which enables embedding metadata in PDF and image
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 66b642ebd2..1aa2f92c02 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -4974,6 +4974,10 @@ Crowther & Woods, its original authors, in 1995. It has been known as
("luajit" ,luajit)))
(arguments
`(#:make-flags '("CC=gcc" "config=release")
+ ;; XXX: Building in parallel occasionally causes this build failure:
+ ;; ../src/luajit2/src/host/buildvm.c:73:10: fatal error: buildvm_arch.h:
+ ;; No such file or directory
+ #:parallel-build? #f
#:phases (modify-phases %standard-phases
(delete 'bootstrap)
(replace 'configure
diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm
index e7d50a5b8a..9aaeab6e2c 100644
--- a/gnu/packages/gl.scm
+++ b/gnu/packages/gl.scm
@@ -64,14 +64,14 @@
(define-public glu
(package
(name "glu")
- (version "9.0.0")
+ (version "9.0.1")
(source (origin
(method url-fetch)
(uri (string-append "ftp://ftp.freedesktop.org/pub/mesa/glu/glu-"
version ".tar.gz"))
(sha256
(base32
- "0r72yyhj09x3krn3kn629jqbwyq50ji8w5ri2pn6zwrk35m4g1s3"))))
+ "1xqhk9bn10nbvffw3r4p4rjslwz1l7gaycc0x2pqkr2irp7q9x7n"))))
(build-system gnu-build-system)
(propagated-inputs
`(("mesa" ,mesa))) ; according to glu.pc
@@ -227,7 +227,7 @@ also known as DXTn or DXTC) for Mesa.")
(define-public mesa
(package
(name "mesa")
- (version "19.1.1")
+ (version "19.1.4")
(source
(origin
(method url-fetch)
@@ -239,7 +239,7 @@ also known as DXTn or DXTC) for Mesa.")
version "/mesa-" version ".tar.xz")))
(sha256
(base32
- "10amy5sdmpjbskr3xazgk0jyli8xpgi0y1nsmjr76hx8nhb4n4bj"))
+ "1yvb7ja09i36zjifpyrf8jmbm9z0wqs2w3x8dlmxkkzdv6knilm6"))
(patches
(search-patches "mesa-skip-disk-cache-test.patch"))))
(build-system meson-build-system)
@@ -291,7 +291,7 @@ also known as DXTn or DXTC) for Mesa.")
;; TODO: Fix svga driver for aarch64 and armhf.
'("-Dgallium-drivers=etnaviv,freedreno,nouveau,r300,r600,swrast,tegra,v3d,vc4,virgl"))
(_
- '("-Dgallium-drivers=nouveau,r300,r600,radeonsi,svga,swrast,virgl")))
+ '("-Dgallium-drivers=iris,nouveau,r300,r600,radeonsi,svga,swrast,virgl")))
;; Enable various optional features. TODO: opencl requires libclc,
;; omx requires libomxil-bellagio
"-Dplatforms=x11,drm,surfaceless,wayland"
@@ -308,11 +308,8 @@ also known as DXTn or DXTC) for Mesa.")
;; Enable Vulkan on i686-linux and x86-64-linux.
,@(match (%current-system)
- ("x86_64-linux"
+ ((or "i686-linux" "x86_64-linux")
'("-Dvulkan-drivers=intel,amd"))
- ;; TODO: Fix intel driver on i686-linux.
- ("i686-linux"
- '("-Dvulkan-drivers=amd"))
(_
'("-Dvulkan-drivers=auto")))
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index e2ecc1bb6a..e295725c51 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -38,6 +38,7 @@
;;; Copyright © 2019 Florian Pelz <pelzflorian@pelzflorian.de>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2019 Jelle Licht <jlicht@fsfe.org>
+;;; Copyright © 2019 Jonathan Frederickson <jonathan@terracrypt.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -5538,6 +5539,57 @@ Compatible with Cisco VPN concentrators configured to use IPsec.")
(license license:gpl2+)
(properties `((upstream-name . "NetworkManager-vpnc")))))
+(define-public network-manager-openconnect
+ (package
+ (name "network-manager-openconnect")
+ (version "1.2.6")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "mirror://gnome/sources/NetworkManager-openconnect/"
+ (version-major+minor version)
+ "/NetworkManager-openconnect-" version ".tar.xz"))
+ (sha256
+ (base32
+ "0nlp290nkawc4wqm978n4vhzg3xdqi8kpjjx19l855vab41rh44m"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:configure-flags '("--enable-absolute-paths" "--localstatedir=/var")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'configure 'patch-path
+ (lambda* (#:key inputs outputs #:allow-other-keys #:rest args)
+ (let* ((openconnect (string-append (assoc-ref inputs "openconnect")
+ "/sbin/openconnect"))
+ (modprobe (string-append (assoc-ref inputs "kmod")
+ "/bin/modprobe"))
+ (pretty-ovpn (string-append "\"" openconnect "\"")))
+ (substitute* "src/nm-openconnect-service.c"
+ (("\"/usr/local/sbin/openconnect\"") pretty-ovpn)
+ (("\"/usr/sbin/openconnect\"") pretty-ovpn)
+ (("/sbin/modprobe") modprobe)))
+ #t)))))
+ (native-inputs
+ `(("intltool" ,intltool)
+ ("network-manager-applet" ,network-manager-applet) ;for libnma
+ ("pkg-config" ,pkg-config)))
+ (inputs
+ `(("gcr" ,gcr)
+ ("gtk+" ,gtk+)
+ ("kmod" ,kmod)
+ ("libsecret" ,libsecret)
+ ("libxml2" ,libxml2)
+ ("network-manager" ,network-manager)
+ ("openconnect" ,openconnect)))
+ (home-page "https://wiki.gnome.org/Projects/NetworkManager/VPN")
+ (synopsis "OpenConnect plug-in for NetworkManager")
+ (description
+ "This extension of NetworkManager allows it to take care of connections
+to @acronym{VPNs, virtual private networks} via OpenConnect, an open client for
+Cisco's AnyConnect SSL VPN.")
+ (license license:gpl2+)
+ (properties `((upstream-name . "NetworkManager-openconnect")))))
+
(define-public mobile-broadband-provider-info
(package
(name "mobile-broadband-provider-info")
@@ -8175,15 +8227,18 @@ advanced image management tool")
(inputs
`(("cairo" ,cairo)
("gobject-introspection" ,gobject-introspection)
+ ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
("python2-pycairo" ,python2-pycairo)
("python2-pygobject" ,python2-pygobject)
("python2-psutil" ,python2-psutil)
("vte" ,vte)))
- (propagated-inputs
- ;; Terminator refuses to start when these are not present.
- `(("gsettings-desktop-schemas" ,gsettings-desktop-schemas)))
(arguments
- `(#:python ,python-2 ;Python 3 not supported
+ `(#:python ,python-2 ; Python 3 isn't supported
+ #:imported-modules ((guix build glib-or-gtk-build-system)
+ ,@%python-build-system-modules)
+ #:modules ((guix build python-build-system)
+ ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
+ (guix build utils))
#:phases
(modify-phases %standard-phases
(add-after
@@ -8194,10 +8249,60 @@ advanced image management tool")
(wrap-program prog
`("PYTHONPATH" = (,(getenv "PYTHONPATH")))
`("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH"))))
- #t))))))
+ #t)))
+ (add-after 'wrap-program 'glib-or-gtk-wrap
+ (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
(home-page "https://gnometerminator.blogspot.com/")
(synopsis "Store and run multiple GNOME terminals in one window")
(description
"Terminator allows you to run multiple GNOME terminals in a grid and
+tabs, and it supports drag and drop re-ordering of terminals.")
(license license:gpl2)))
+
+(define-public libhandy
+ (package
+ (name "libhandy")
+ (version "0.0.10")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://source.puri.sm/Librem5/libhandy")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1702hbdqhfpgw0c4vj2ag08vgl83byiryrbngbq11b9azmj3jhzs"))))
+ (build-system meson-build-system)
+ (arguments
+ `(#:configure-flags
+ '("-Dglade_catalog=disabled"
+ "-Dgtk_doc=true")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'disable-broken-test
+ (lambda _
+ ;; This test fails for unknown reasons
+ (substitute* "tests/meson.build"
+ (("'test-dialog',") ""))
+ #t))
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; Tests require a running X server.
+ (system "Xvfb :1 &")
+ (setenv "DISPLAY" ":1")
+ #t)))))
+ (inputs
+ `(("gtk+" ,gtk+)))
+ (native-inputs
+ `(("glib:bin" ,glib "bin")
+ ("gobject-introspection" ,gobject-introspection) ; for g-ir-scanner
+ ("vala" ,vala)
+ ("gtk-doc" ,gtk-doc)
+ ("pkg-config" ,pkg-config)
+ ("gettext" ,gettext-minimal)
+ ("xorg-server" ,xorg-server)))
+ (home-page "https://source.puri.sm/Librem5/libhandy")
+ (synopsis "Library full of GTK+ widgets for mobile phones")
+ (description "The aim of the handy library is to help with developing user
+intefaces for mobile devices using GTK+.")
+ (license license:lgpl2.1+)))
diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 3dc2f2fe8f..a0a1baa9a2 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -1218,8 +1218,8 @@ for a variety of protocols to proxy network data.")
(license license:bsd-3))))
(define-public go-golang-org-x-sys-unix
- (let ((commit "5ed2794edfdc1c54dfb61d619c5944285f35d444")
- (revision "3"))
+ (let ((commit "04f50cda93cbb67f2afa353c52f342100e80e625")
+ (revision "4"))
(package
(name "go-golang-org-x-sys-unix")
(version (git-version "0.0.0" revision commit))
@@ -1231,7 +1231,7 @@ for a variety of protocols to proxy network data.")
(file-name (git-file-name name version))
(sha256
(base32
- "1qy8hmv5nwpcywk7sh1pg0s32jwpd4ykh492xzl4mmxy8galwsr5"))))
+ "0hmfsz9y1ingwsn482hlzzmzs7kr3cklm0ana0mbdk70isw2bxnw"))))
(build-system go-build-system)
(arguments
`(#:import-path "golang.org/x/sys/unix"
@@ -3617,7 +3617,7 @@ error handling primitives in Go.")
(define-public go-github-com-maruel-panicparse
(package
(name "go-github-com-maruel-panicparse")
- (version "1.2.1")
+ (version "1.3.0")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -3626,7 +3626,7 @@ error handling primitives in Go.")
(file-name (git-file-name name version))
(sha256
(base32
- "05hf68ifb7ww4rpmxyywbj9r0kyap45p1273ncq4qy2ydv042l8j"))))
+ "13qkn7f64yln8jdmma37h6ra4c7anxkp3vfgvfyb6lb07dpr1ibq"))))
(build-system go-build-system)
(arguments
'(#:import-path "github.com/maruel/panicparse"))
diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm
index f4f9228a07..1eedcfec7b 100644
--- a/gnu/packages/graphics.scm
+++ b/gnu/packages/graphics.scm
@@ -160,9 +160,7 @@
"Blender is a 3D graphics creation suite. It supports the entirety of
the 3D pipeline—modeling, rigging, animation, simulation, rendering,
compositing and motion tracking, even video editing and game creation. The
-application can be customized via its API for Python scripting.
-
-WARNING: This is a release candidate build of Blender.")
+application can be customized via its API for Python scripting.")
(license license:gpl2+)))
(define-public blender-2.79
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 9086e4945b..b80a0f799a 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -729,9 +729,7 @@ application suites.")
(define-public gtk+
(package (inherit gtk+-2)
(name "gtk+")
- ;; NOTE: When updating the version of 'gtk+', the hash of 'mate-themes' in
- ;; mate.scm will also need to be updated.
- (version "3.24.9")
+ (version "3.24.10")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
@@ -739,7 +737,7 @@ application suites.")
name "-" version ".tar.xz"))
(sha256
(base32
- "0dg6jf2763sp740ls6b5y86b5b9zhz3zj0sbmar2xpws1lkv0zjp"))
+ "00qvq1r96ikdalv7xzgng1kad9i0rcahqk01gwhxl3xrw83z3a1m"))
(patches (search-patches "gtk3-respect-GUIX_GTK3_PATH.patch"
"gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch"))))
(outputs '("out" "bin" "doc"))
diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm
index 6dcdcedccf..8c36658361 100644
--- a/gnu/packages/guile-xyz.scm
+++ b/gnu/packages/guile-xyz.scm
@@ -907,27 +907,30 @@ tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
(define-public guile-email
(package
(name "guile-email")
- (version "0.1.0")
+ (version "0.2.0")
(source
(origin
(method url-fetch)
(uri (string-append
- "https://git.systemreboot.net/guile-email/snapshot/guile-email-"
- version ".tar.xz"))
+ "https://guile-email.systemreboot.net/releases/guile-email-"
+ version ".tar.lz"))
(sha256
(base32
- "0p2v8q2kkz8m6vf2rsjvz3dj1mvnx7dxakjf72dwkndbgk3rp79f"))))
+ "05pm0rwdxhjdlpmvhn0kyfslph6j5m1gv76givs0hshb30nirl2x"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
- ("autoconf" ,autoconf)
- ("automake" ,automake)))
+ ("lzip" ,lzip)))
(inputs
`(("guile" ,guile-2.2)))
- (home-page "https://git.systemreboot.net/guile-email")
+ (arguments
+ '(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ; to prevent guild warnings
+ (home-page "https://guile-email.systemreboot.net")
(synopsis "Guile email parser")
- (description "This package provides an email parser written in pure
-Guile.")
+ (description "guile-email is a collection of email utilities implemented
+in pure guile. It supports parsing MIME (Multipurpose Internet Mail
+Extensions) compliant email messages and reading emails from the mbox
+format.")
(license license:agpl3+)))
(define-public guile-debbugs-next
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index df71965e81..b07a570654 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -261,29 +261,27 @@ without requiring the source code to be rewritten.")
(define-public guile-next
;; This is the upcoming Guile 3.0, with JIT support.
- (let ((commit "6f3357b0df64c4be17e72079864c09a542f1c779")
- (revision "1"))
- (package
- (inherit guile-2.2)
- (name "guile-next")
- (version "2.9.2")
- (source (origin
- (inherit (package-source guile-2.2))
- (uri (string-append "ftp://alpha.gnu.org/gnu/guile/guile-"
- version ".tar.xz"))
- (sha256
- (base32
- "1w358df2wmcyzk2ziqrj2zhwqisaqraqfa3008ay23nf1a7bw0z4"))))
- (native-search-paths
- (list (search-path-specification
- (variable "GUILE_LOAD_PATH")
- (files '("share/guile/site/3.0")))
- (search-path-specification
- (variable "GUILE_LOAD_COMPILED_PATH")
- (files '("lib/guile/3.0/site-ccache"
- "share/guile/site/3.0")))))
- (properties '((ftp-server . "alpha.gnu.org")
- (upstream-name . "guile"))))))
+ (package
+ (inherit guile-2.2)
+ (name "guile-next")
+ (version "2.9.3")
+ (source (origin
+ (inherit (package-source guile-2.2))
+ (uri (string-append "ftp://alpha.gnu.org/gnu/guile/guile-"
+ version ".tar.xz"))
+ (sha256
+ (base32
+ "14990wcpysgw58kij03wbgiggmi5z94jmy7wdcqnn6ny7cimkkgr"))))
+ (native-search-paths
+ (list (search-path-specification
+ (variable "GUILE_LOAD_PATH")
+ (files '("share/guile/site/3.0")))
+ (search-path-specification
+ (variable "GUILE_LOAD_COMPILED_PATH")
+ (files '("lib/guile/3.0/site-ccache"
+ "share/guile/site/3.0")))))
+ (properties '((ftp-server . "alpha.gnu.org")
+ (upstream-name . "guile")))))
(define (make-guile-readline guile)
(package
diff --git a/gnu/packages/haskell-apps.scm b/gnu/packages/haskell-apps.scm
index e01f796178..e77f6d113b 100644
--- a/gnu/packages/haskell-apps.scm
+++ b/gnu/packages/haskell-apps.scm
@@ -6,6 +6,7 @@
;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
+;;; Copyright © 2019 Kyle Meyer <kyle@kyleam.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -142,7 +143,7 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
(define-public git-annex
(package
(name "git-annex")
- (version "6.20180926")
+ (version "7.20190708")
(source
(origin
(method url-fetch)
@@ -150,15 +151,20 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
"git-annex/git-annex-" version ".tar.gz"))
(sha256
(base32
- "1251rj8h63y30sfqk0zh670yhz14p256y59n3590pg015pf3575d"))))
+ "18s563swrp8mx479995pdhhmn40y3xwlbm1z3w63qsnjqmj7zlij"))))
(build-system haskell-build-system)
(arguments
`(#:configure-flags
'("--flags=-Android -Assistant -Pairing -S3 -Webapp -WebDAV")
#:phases
(modify-phases %standard-phases
- (add-before 'configure 'patch-shell
+ (add-before 'configure 'patch-shell-for-tests
(lambda _
+ ;; Shell.hs defines "/bin/sh" that is used in Git hooks. We
+ ;; shouldn't patch hooks with Guix's current bash because the
+ ;; hooks can exist after that bash is garbage collected, but
+ ;; let's temporarily patch it so that we can run the tests.
+ (copy-file "Utility/Shell.hs" "/tmp/Shell.hs")
(substitute* "Utility/Shell.hs"
(("/bin/sh") (which "sh")))
#t))
@@ -192,6 +198,11 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
(symlink "git-annex" "git-annex-shell"))
(invoke "git-annex" "test")
#t))
+ (add-after 'check 'unpatch-shell-and-rebuild
+ (lambda args
+ ;; Undo `patch-shell-for-tests'.
+ (copy-file "/tmp/Shell.hs" "Utility/Shell.hs")
+ (apply (assoc-ref %standard-phases 'build) args)))
(add-after 'install 'install-symlinks
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@@ -208,6 +219,7 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
("ghc-bloomfilter" ,ghc-bloomfilter)
("ghc-byteable" ,ghc-byteable)
("ghc-case-insensitive" ,ghc-case-insensitive)
+ ("ghc-concurrent-output" ,ghc-concurrent-output)
("ghc-crypto-api" ,ghc-crypto-api)
("ghc-cryptonite" ,ghc-cryptonite)
("ghc-data-default" ,ghc-data-default)
diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index 2f0b842cae..589eee74d9 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -811,7 +811,7 @@ implementations of cryptographic ciphers.")
"0xz10ycdm5vk9nrcym1fi83k19frfwqz18bz8bnpzwvaj0j41yfj"))))
(build-system haskell-build-system)
(inputs
- `(("ghc-ansi-terminal" ,ghc-ansi-terminal-0.8)
+ `(("ghc-ansi-terminal" ,ghc-ansi-terminal)
("ghc-async" ,ghc-async)
("ghc-concurrent-output" ,ghc-concurrent-output)
("ghc-exceptions" ,ghc-exceptions)
diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index 28a1647fd1..882773ab68 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -25,6 +25,8 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages haskell)
#:use-module (gnu packages haskell-check)
+ #:use-module (gnu packages haskell-xyz)
+ #:use-module (gnu packages tls)
#:use-module (guix build-system haskell)
#:use-module (guix download)
#:use-module ((guix licenses) #:prefix license:)
@@ -775,3 +777,64 @@ Ephemeral (Elliptic curve and regular) Diffie Hellman key exchanges, and many
extensions.")
(license license:bsd-3)))
+(define-public ghc-hsopenssl
+ (package
+ (name "ghc-hsopenssl")
+ (version "0.11.4.15")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "HsOpenSSL/HsOpenSSL-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0idmak6d8mpbxphyq9hkxkmby2wnzhc1phywlgm0zw6q47pwxgff"))))
+ (build-system haskell-build-system)
+ (inputs
+ `(("ghc-network" ,ghc-network)
+ ("openssl" ,openssl)))
+ (arguments
+ `(#:cabal-revision
+ ("1" "0bkcw2pjfgv1bhgkrpncvwq9czfr7cr4ak14n0v8c2y33i33wk5z")))
+ (home-page "https://github.com/vshabanov/HsOpenSSL")
+ (synopsis "Partial OpenSSL binding for Haskell")
+ (description "HsOpenSSL is an OpenSSL binding for Haskell. It can
+generate RSA and DSA keys, read and write PEM files, generate message
+digests, sign and verify messages, encrypt and decrypt messages. It has
+also some capabilities of creating SSL clients and servers. This
+package is in production use by a number of Haskell based systems and
+stable. You may also be interested in the tls package,
+@uref{http://hackage.haskell.org/package/tls}, which is a pure Haskell
+implementation of SSL.")
+ (license license:public-domain)))
+
+(define-public ghc-openssl-streams
+ (package
+ (name "ghc-openssl-streams")
+ (version "1.2.1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "openssl-streams/openssl-streams-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0pwghr7ygv59k572xsj1j97rilkbjz66qaiyj0ra2wfg6pl70wfw"))))
+ (build-system haskell-build-system)
+ (inputs
+ `(("ghc-hsopenssl" ,ghc-hsopenssl)
+ ("ghc-io-streams" ,ghc-io-streams)
+ ("ghc-network" ,ghc-network)))
+ (native-inputs
+ `(("ghc-hunit" ,ghc-hunit)
+ ("ghc-test-framework" ,ghc-test-framework)
+ ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))
+ (arguments
+ `(#:cabal-revision
+ ("2" "1004kgdryflpkp19dv4ikilhcn0xbfc5dsp6v3ib34580pcfj7wy")))
+ (home-page "http://hackage.haskell.org/package/openssl-streams")
+ (synopsis "OpenSSL network support for io-streams")
+ (description "This library contains io-streams routines for secure
+networking using OpenSSL (by way of HsOpenSSL).")
+ (license license:bsd-3)))
diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 4bb790d93c..7cbf8932e6 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -28,6 +28,7 @@
#:use-module (gnu packages haskell)
#:use-module (gnu packages haskell-check)
#:use-module (gnu packages haskell-crypto)
+ #:use-module (gnu packages haskell-xyz)
#:use-module (guix build-system haskell)
#:use-module (guix download)
#:use-module ((guix licenses) #:prefix license:)
@@ -1294,3 +1295,171 @@ derivations of regular expressions.")
"The Haskell XML Toolbox bases on the ideas of HaXml and HXML, but
introduces a more general approach for processing XML with Haskell.")
(license license:expat)))
+
+(define-public ghc-http-common
+ (package
+ (name "ghc-http-common")
+ (version "0.8.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "http-common/http-common-" version ".tar.gz"))
+ (sha256
+ (base32
+ "14s5a178sb2vm5k00rs21760mds5dz2gs10k9iyn22h01mxyf599"))))
+ (build-system haskell-build-system)
+ (inputs
+ `(("ghc-base64-bytestring" ,ghc-base64-bytestring)
+ ("ghc-blaze-builder" ,ghc-blaze-builder)
+ ("ghc-case-insensitive" ,ghc-case-insensitive)
+ ("ghc-network" ,ghc-network)
+ ("ghc-unordered-containers" ,ghc-unordered-containers)))
+ (home-page "https://github.com/afcowie/http-streams/")
+ (synopsis "Common types for HTTP clients and servers")
+ (description "Base types used by a variety of HTTP clients and
+servers. See http-streams @code{Network.Http.Client} or pipes-http
+@code{Pipes.Http.Client} for full documentation. You can import
+@code{Network.Http.Types} if you like, but both http-streams and
+pipes-http re-export this package's types and functions.")
+ (license license:bsd-3)))
+
+(define-public ghc-http-streams
+ (package
+ (name "ghc-http-streams")
+ (version "0.8.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "http-streams/http-streams-" version ".tar.gz"))
+ (sha256
+ (base32
+ "18vxd35n7s3z4gjvad94bknc8z1w9d7ccgphnhsxlz5cackizmxq"))))
+ (build-system haskell-build-system)
+ (inputs
+ `(("ghc-attoparsec" ,ghc-attoparsec)
+ ("ghc-base64-bytestring" ,ghc-base64-bytestring)
+ ("ghc-blaze-builder" ,ghc-blaze-builder)
+ ("ghc-case-insensitive" ,ghc-case-insensitive)
+ ("ghc-io-streams" ,ghc-io-streams)
+ ("ghc-hsopenssl" ,ghc-hsopenssl)
+ ("ghc-openssl-streams" ,ghc-openssl-streams)
+ ("ghc-unordered-containers" ,ghc-unordered-containers)
+ ("ghc-aeson" ,ghc-aeson)
+ ("ghc-http-common" ,ghc-http-common)
+ ("ghc-network-uri" ,ghc-network-uri)
+ ("ghc-network" ,ghc-network)))
+ (arguments
+ `(#:tests? #f)) ; tests rely on an outdated version of snap-server
+ (home-page "https://github.com/afcowie/http-streams/")
+ (synopsis "HTTP client using io-streams")
+ (description "An HTTP client using the Snap Framework's io-streams
+library to handle the streaming IO. The API is optimized for ease of
+use for the rather common case of code needing to query web services and
+deal with the result.")
+ (license license:bsd-3)))
+
+(define-public ghc-snap-core
+ (package
+ (name "ghc-snap-core")
+ (version "1.0.3.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "snap-core/snap-core-" version ".tar.gz"))
+ (sha256
+ (base32
+ "136q7l4hd5yn5hb507q1ziqx124ma1lkzh5dx0n150p8dx3rhhsc"))))
+ (build-system haskell-build-system)
+ (inputs
+ `(("ghc-old-locale" ,ghc-old-locale)
+ ("ghc-hunit" ,ghc-hunit)
+ ("ghc-attoparsec" ,ghc-attoparsec)
+ ("ghc-bytestring-builder" ,ghc-bytestring-builder)
+ ("ghc-case-insensitive" ,ghc-case-insensitive)
+ ("ghc-lifted-base" ,ghc-lifted-base)
+ ("ghc-io-streams" ,ghc-io-streams)
+ ("ghc-hashable" ,ghc-hashable)
+ ("ghc-monad-control" ,ghc-monad-control)
+ ("ghc-random" ,ghc-random)
+ ("ghc-readable" ,ghc-readable)
+ ("ghc-regex-posix" ,ghc-regex-posix)
+ ("ghc-transformers-base" ,ghc-transformers-base)
+ ("ghc-unix-compat" ,ghc-unix-compat)
+ ("ghc-unordered-containers" ,ghc-unordered-containers)
+ ("ghc-vector" ,ghc-vector)
+ ("ghc-network-uri" ,ghc-network-uri)
+ ("ghc-network" ,ghc-network)))
+ (native-inputs
+ `(("ghc-quickcheck" ,ghc-quickcheck)
+ ("ghc-parallel" ,ghc-parallel)
+ ("ghc-test-framework" ,ghc-test-framework)
+ ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+ ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
+ ("ghc-zlib" ,ghc-zlib)))
+ (arguments
+ `(#:cabal-revision
+ ("3" "0wlhn33r7c9g7j23y006ddq9d87lkmianvvfrbl8jd8mvjvj2gfa")))
+ (home-page "http://snapframework.com/")
+ (synopsis "Haskell Web Framework (core interfaces and types)")
+ (description "Snap is a simple and fast web development framework
+and server written in Haskell. For more information, you can visit the
+Snap project website at @uref{http://snapframework.com/}. This library
+contains the core definitions and types for the Snap framework.")
+ (license license:bsd-3)))
+
+(define-public ghc-snap-server
+ (package
+ (name "ghc-snap-server")
+ (version "1.1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "snap-server/snap-server-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0vvw9n8xs272qdlrf3dxhnva41zh3awi7pf022rrjj75lj8a77i4"))))
+ (build-system haskell-build-system)
+ (inputs
+ `(("ghc-attoparsec" ,ghc-attoparsec)
+ ("ghc-blaze-builder" ,ghc-blaze-builder)
+ ("ghc-bytestring-builder" ,ghc-bytestring-builder)
+ ("ghc-case-insensitive" ,ghc-case-insensitive)
+ ("ghc-clock" ,ghc-clock)
+ ("ghc-io-streams" ,ghc-io-streams)
+ ("ghc-io-streams-haproxy" ,ghc-io-streams-haproxy)
+ ("ghc-lifted-base" ,ghc-lifted-base)
+ ("ghc-network" ,ghc-network)
+ ("ghc-old-locale" ,ghc-old-locale)
+ ("ghc-snap-core" ,ghc-snap-core)
+ ("ghc-unix-compat" ,ghc-unix-compat)
+ ("ghc-vector" ,ghc-vector)))
+ (native-inputs
+ `(("ghc-base16-bytestring" ,ghc-base16-bytestring)
+ ("ghc-monad-control" ,ghc-monad-control)
+ ("ghc-random" ,ghc-random)
+ ("ghc-threads" ,ghc-threads)
+ ("ghc-hunit" ,ghc-hunit)
+ ("ghc-quickcheck" ,ghc-quickcheck)
+ ("ghc-http-streams" ,ghc-http-streams)
+ ("ghc-http-common" ,ghc-http-common)
+ ("ghc-parallel" ,ghc-parallel)
+ ("ghc-test-framework" ,ghc-test-framework)
+ ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+ ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
+ (arguments
+ `(#:cabal-revision
+ ("3" "0a9d3nqb5rvgm25nak68lp6yj9m6cwhbgdbg5l7ib5i2czcg7yjh")))
+ (home-page "http://snapframework.com/")
+ (synopsis "Web server for the Snap Framework")
+ (description "Snap is a simple and fast web development framework
+and server written in Haskell. For more information, you can visit the
+Snap project website at @uref{http://snapframework.com/}. The Snap HTTP
+server is a high performance web server library written in Haskell.
+Together with the snap-core library upon which it depends, it provides a
+clean and efficient Haskell programming interface to the HTTP
+protocol.")
+ (license license:bsd-3)))
diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm
new file mode 100644
index 0000000000..53c4dcc5ff
--- /dev/null
+++ b/gnu/packages/haskell-xyz.scm
@@ -0,0 +1,276 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Robert Vollmert <rob@vllmrt.net>
+;;;
+;;; 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 haskell-xyz)
+ #:use-module (gnu packages)
+ #:use-module (gnu packages haskell)
+ #:use-module (gnu packages haskell-check)
+ #:use-module (guix build-system haskell)
+ #:use-module (guix download)
+ #:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix packages))
+
+(define-public ghc-concurrent-extra
+ (package
+ (name "ghc-concurrent-extra")
+ (version "0.7.0.12")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "concurrent-extra/concurrent-extra-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1y8xk460fvnw0idzdiylmm874sjny4q9jxb1js9fjz8lw2wns3h4"))))
+ (build-system haskell-build-system)
+ (arguments
+ ;; XXX: The ReadWriteLock 'stressTest' fails.
+ `(#:tests? #f))
+ (inputs
+ `(("ghc-unbounded-delays" ,ghc-unbounded-delays)))
+ (native-inputs
+ `(("ghc-async" ,ghc-async)
+ ("ghc-hunit" ,ghc-hunit)
+ ("ghc-random" ,ghc-random)
+ ("ghc-test-framework" ,ghc-test-framework)
+ ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))
+ (home-page "https://github.com/basvandijk/concurrent-extra")
+ (synopsis "Extra concurrency primitives")
+ (description "This Haskell library offers (among other things) the
+following selection of synchronisation primitives:
+
+@itemize
+@item @code{Broadcast}: Wake multiple threads by broadcasting a value.
+@item @code{Event}: Wake multiple threads by signalling an event.
+@item @code{Lock}: Enforce exclusive access to a resource. Also known
+as a binary semaphore or mutex. The package additionally provides an
+alternative that works in the STM monad.
+@item @code{RLock}: A lock which can be acquired multiple times by the
+same thread. Also known as a reentrant mutex.
+@item @code{ReadWriteLock}: Multiple-reader, single-writer locks. Used
+to protect shared resources which may be concurrently read, but only
+sequentially written.
+@item @code{ReadWriteVar}: Concurrent read, sequential write variables.
+@end itemize
+
+Please consult the API documentation of the individual modules for more
+detailed information.
+
+This package was inspired by the concurrency libraries of Java and
+Python.")
+ (license license:bsd-3)))
+
+(define-public ghc-io-streams
+ (package
+ (name "ghc-io-streams")
+ (version "1.5.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "io-streams/io-streams-" version ".tar.gz"))
+ (sha256
+ (base32
+ "12rcdg2d70644bvn838fxcjkssqj8pssnx5y657si5rijcbkgjsx"))))
+ (build-system haskell-build-system)
+ (inputs
+ `(("ghc-attoparsec" ,ghc-attoparsec)
+ ("ghc-bytestring-builder" ,ghc-bytestring-builder)
+ ("ghc-network" ,ghc-network)
+ ("ghc-primitive" ,ghc-primitive)
+ ("ghc-vector" ,ghc-vector)
+ ("ghc-zlib-bindings" ,ghc-zlib-bindings)))
+ (native-inputs
+ `(("ghc-hunit" ,ghc-hunit)
+ ("ghc-quickcheck" ,ghc-quickcheck)
+ ("ghc-test-framework" ,ghc-test-framework)
+ ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+ ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
+ ("ghc-zlib" ,ghc-zlib)))
+ (arguments
+ `(#:cabal-revision
+ ("2" "1mcab95d6hm098myh9gp7sh10srigjphgvm8s9pfs7jg5hzghy14")))
+ (home-page "http://hackage.haskell.org/package/io-streams")
+ (synopsis "Simple and composable stream I/O")
+ (description "This library contains simple and easy-to-use
+primitives for I/O using streams.")
+ (license license:bsd-3)))
+
+(define-public ghc-io-streams-haproxy
+ (package
+ (name "ghc-io-streams-haproxy")
+ (version "1.0.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "io-streams-haproxy/io-streams-haproxy-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "11nh9q158mgnvvb23s5ffg87lkhl5smk039yl43jghxmb214z0bp"))))
+ (build-system haskell-build-system)
+ (inputs
+ `(("ghc-attoparsec" ,ghc-attoparsec)
+ ("ghc-io-streams" ,ghc-io-streams)
+ ("ghc-network" ,ghc-network)))
+ (native-inputs
+ `(("ghc-hunit" ,ghc-hunit)
+ ("ghc-test-framework" ,ghc-test-framework)
+ ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))
+ (arguments
+ `(#:cabal-revision
+ ("4" "06c51a057n5bc9xfbp2m4jz5ds4z1xvmsx5mppch6qfwbz7x5i9l")))
+ (home-page "http://snapframework.com/")
+ (synopsis "HAProxy protocol 1.5 support for io-streams")
+ (description "HAProxy protocol version 1.5 support
+(see @uref{http://haproxy.1wt.eu/download/1.5/doc/proxy-protocol.txt})
+for applications using io-streams. The proxy protocol allows information
+about a networked peer (like remote address and port) to be propagated
+through a forwarding proxy that is configured to speak this protocol.")
+ (license license:bsd-3)))
+
+(define-public ghc-language-glsl
+ (package
+ (name "ghc-language-glsl")
+ (version "0.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "language-glsl/language-glsl-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0hdg67ainlqpjjghg3qin6fg4p783m0zmjqh4rd5gyizwiplxkp1"))))
+ (build-system haskell-build-system)
+ (inputs `(("ghc-prettyclass" ,ghc-prettyclass)))
+ (arguments
+ `(#:tests? #f
+ #:cabal-revision
+ ("1" "10ac9pk4jy75k03j1ns4b5136l4kw8krr2d2nw2fdmpm5jzyghc5")))
+ (home-page "http://hackage.haskell.org/package/language-glsl")
+ (synopsis "GLSL abstract syntax tree, parser, and pretty-printer")
+ (description "This package is a Haskell library for the
+representation, parsing, and pretty-printing of GLSL 1.50 code.")
+ (license license:bsd-3)))
+
+(define-public ghc-prettyclass
+ (package
+ (name "ghc-prettyclass")
+ (version "1.0.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "prettyclass/prettyclass-" version ".tar.gz"))
+ (sha256
+ (base32
+ "11l9ajci7nh1r547hx8hgxrhq8mh5gdq30pdf845wvilg9p48dz5"))))
+ (build-system haskell-build-system)
+ (home-page "http://hackage.haskell.org/package/prettyclass")
+ (synopsis "Pretty printing class similar to Show")
+ (description "This package provides a pretty printing class similar
+to @code{Show}, based on the HughesPJ pretty printing library. It
+provides the pretty printing class and instances for the Prelude
+types.")
+ (license license:bsd-3)))
+
+(define-public ghc-readable
+ (package
+ (name "ghc-readable")
+ (version "0.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "readable/readable-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1ja39cg26wy2fs00gi12x7iq5k8i366pbqi3p916skfa5jnkfc3h"))))
+ (build-system haskell-build-system)
+ (home-page "https://github.com/mightybyte/readable")
+ (synopsis "Type class for reading from Text and ByteString")
+ (description "This package provides a @code{Readable} type class for
+reading data types from @code{ByteString} and @code{Text}. It also
+includes efficient implementations for common data types.")
+ (license license:bsd-3)))
+
+(define-public ghc-threads
+ (package
+ (name "ghc-threads")
+ (version "0.5.1.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "threads/threads-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0bjnjhnq3km6xqk0fn1fgyz5xdw4h6lylbwwbcmkkfzwcz0c76hk"))))
+ (build-system haskell-build-system)
+ (native-inputs
+ `(("ghc-concurrent-extra" ,ghc-concurrent-extra)
+ ("ghc-hunit" ,ghc-hunit)
+ ("ghc-test-framework" ,ghc-test-framework)
+ ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))
+ (home-page "https://github.com/basvandijk/threads")
+ (synopsis "Fork threads and wait for their result")
+ (description "This package provides functions to fork threads and
+wait for their result, whether it's an exception or a normal value.
+Besides waiting for the termination of a single thread this package also
+provides functions to wait for a group of threads to terminate. This
+package is similar to the @code{threadmanager}, @code{async} and
+@code{spawn} packages. The advantages of this package are:
+
+@itemize
+@item Simpler API.
+@item More efficient in both space and time.
+@item No space-leak when forking a large number of threads.
+@item Correct handling of asynchronous exceptions.
+@item GHC specific functionality like @code{forkOn} and
+@code{forkIOWithUnmask}.
+@end itemize")
+ (license license:bsd-3)))
+
+(define-public ghc-zlib-bindings
+ (package
+ (name "ghc-zlib-bindings")
+ (version "0.1.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "zlib-bindings/zlib-bindings-" version ".tar.gz"))
+ (sha256
+ (base32
+ "02ciywlz4wdlymgc3jsnicz9kzvymjw1www2163gxidnz4wb8fy8"))))
+ (build-system haskell-build-system)
+ (inputs
+ `(("ghc-zlib" ,ghc-zlib)))
+ (native-inputs
+ `(("ghc-hspec" ,ghc-hspec)
+ ("ghc-quickcheck" ,ghc-quickcheck)))
+ (arguments
+ `(#:cabal-revision
+ ("2" "0fq49694gqkab8m0vq4i879blswczwd66n7xh4r4gwiahf0ryvqc")))
+ (home-page "https://github.com/snapframework/zlib-bindings")
+ (synopsis "Low-level bindings to the @code{zlib} package")
+ (description "This package provides low-level bindings to the
+@code{zlib} package.")
+ (license license:bsd-3)))
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b59553f501..8787f10789 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -73,6 +73,7 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix utils)
+ #:use-module (ice-9 match)
#:use-module (ice-9 regex)
#:use-module ((srfi srfi-1) #:select (alist-delete)))
@@ -440,7 +441,7 @@ interactive environment for the functional language Haskell.")
interactive environment for the functional language Haskell.")
(license license:bsd-3)))
-(define-public ghc-8
+(define-public ghc-8.4
(package (inherit ghc-8.0)
(name "ghc")
(version "8.4.3")
@@ -572,6 +573,53 @@ interactive environment for the functional language Haskell.")
(file-pattern ".*\\.conf\\.d$")
(file-type 'directory))))))
+(define-public ghc-8.6
+ (package (inherit ghc-8.4)
+ (name "ghc")
+ (version "8.6.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://www.haskell.org/ghc/dist/"
+ version "/" name "-" version "-src.tar.xz"))
+ (sha256
+ (base32 "0qg3zsmbk4rkwkc3jpas3zs74qaxmw4sp4v1mhsbj0a0dzls2jjd"))))
+ (native-inputs
+ `(;; GHC 8.6.5 must be built with GHC >= 8.2.
+ ("ghc-bootstrap" ,ghc-8.4)
+ ("ghc-testsuite"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://www.haskell.org/ghc/dist/"
+ version "/" name "-" version "-testsuite.tar.xz"))
+ (sha256
+ (base32
+ "0pw9r91g2np3i806g2f4f8z4jfdd7mx226cmdizk4swa7av1qf91"))))
+ ,@(filter (match-lambda
+ (("ghc-bootstrap" . _) #f)
+ (("ghc-testsuite" . _) #f)
+ (_ #t))
+ (package-native-inputs ghc-8.4))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments ghc-8.4)
+ ((#:make-flags make-flags ''())
+ `(cons "EXTRA_RUNTEST_OPTS=--skip-perf-tests"
+ ,make-flags))
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ ;; These two tests refer to the root user, which doesn't exist
+ ;; (see <https://bugs.gnu.org/36692>).
+ (add-after 'unpack-testsuite 'skip-tests
+ (lambda _
+ (substitute* "libraries/unix/tests/all.T"
+ (("^test\\('T8108'") "# guix skipped: test('T8108'"))
+ (substitute* "libraries/unix/tests/libposix/all.T"
+ (("^test\\('posix010'") "# guix skipped: test('posix010'"))
+ #t))))))))
+
+(define-public ghc-8 ghc-8.4)
+
(define-public ghc ghc-8)
(define-public ghc-hostname
@@ -1054,28 +1102,6 @@ the ‘haddock’ package.")
documentation-generation tool for Haskell libraries.")
(license license:bsd-3)))
-(define-public ghc-haddock-test
- (package
- (name "ghc-haddock-test")
- (version "0.0.1")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "https://hackage.haskell.org/package/"
- "haddock-test/haddock-test-"
- version ".tar.gz"))
- (sha256
- (base32
- "1ax8fnfrwx66csj952f3virxzapipan9da7z5l1zc12nqkifbs7w"))))
- (build-system haskell-build-system)
- (inputs
- `(("ghc-xml" ,ghc-xml)
- ("ghc-syb" ,ghc-syb)))
- (home-page "http://www.haskell.org/haddock/")
- (synopsis "Test utilities for Haddock")
- (description "This package provides test utilities for Haddock.")
- (license license:bsd-3)))
-
(define-public ghc-haddock
(package
(name "ghc-haddock")
@@ -2903,30 +2929,6 @@ Haskell library @code{regex-base}.")
@code{regex-posix} to replace @code{Text.Regex}.")
(license license:bsd-3)))
-(define-public ghc-regex-tdfa-rc
- (package
- (name "ghc-regex-tdfa-rc")
- (version "1.1.8.3")
- (source
- (origin
- (method url-fetch)
- (uri (string-append
- "https://hackage.haskell.org/package/regex-tdfa-rc/regex-tdfa-rc-"
- version
- ".tar.gz"))
- (sha256
- (base32
- "1vi11i23gkkjg6193ak90g55akj69bhahy542frkwb68haky4pp3"))))
- (build-system haskell-build-system)
- (inputs
- `(("ghc-regex-base" ,ghc-regex-base)))
- (home-page
- "https://hackage.haskell.org/package/regex-tdfa")
- (synopsis "Tagged DFA regex engine for Haskell")
- (description "A new all-Haskell \"tagged\" DFA regex engine, inspired by
-@code{libtre} (fork by Roman Cheplyaka).")
- (license license:bsd-3)))
-
(define-public ghc-regex-tdfa-text
(package
(name "ghc-regex-tdfa-text")
@@ -3041,6 +3043,7 @@ the parsers provided by @code{parsec}, @code{attoparsec} and @code{base}'s
(base32
"0hznd8i65s81xy13i2qc7cvipw3lfb2yhkv53apbdsh6sbljz5sk"))))
(build-system haskell-build-system)
+ (arguments `(#:tests? #f)) ; doctest suite fails to build on i686
(inputs
`(("ghc-reducers" ,ghc-reducers)
("ghc-semigroups" ,ghc-semigroups)
@@ -3990,7 +3993,7 @@ instances of the @code{Pretty} class.")
"0gnb4mkqryv08vncxnj0bzwcnd749613yw3cxfzw6y3nsldp4c56"))))
(build-system haskell-build-system)
(inputs
- `(("ghc-ansi-terminal" ,ghc-ansi-terminal-0.8)))
+ `(("ghc-ansi-terminal" ,ghc-ansi-terminal)))
(home-page "https://github.com/ekmett/ansi-wl-pprint")
(synopsis "Wadler/Leijen Pretty Printer for colored ANSI terminal output")
(description "This is a pretty printing library based on Wadler's paper
@@ -4235,7 +4238,7 @@ interface.")
(define-public ghc-ansi-terminal
(package
(name "ghc-ansi-terminal")
- (version "0.9.1")
+ (version "0.8.0.4")
(source
(origin
(method url-fetch)
@@ -4245,7 +4248,7 @@ interface.")
".tar.gz"))
(sha256
(base32
- "1yr0ld0kqns3w3j9gl62bdwshvyazidx4dv1qkvq19ivnf08w23l"))))
+ "0428gq8m3fdnb7ldcsyk97qcch76hcxbgh2666p6f76fs2qbhg7b"))))
(build-system haskell-build-system)
(inputs
`(("ghc-colour" ,ghc-colour)))
@@ -4256,21 +4259,6 @@ allows cursor movement, screen clearing, color output showing or hiding the
cursor, and changing the title.")
(license license:bsd-3)))
-(define-public ghc-ansi-terminal-0.8
- (package (inherit ghc-ansi-terminal)
- (name "ghc-ansi-terminal")
- (version "0.8.0.4")
- (source
- (origin
- (method url-fetch)
- (uri (string-append
- "https://hackage.haskell.org/package/ansi-terminal/ansi-terminal-"
- version
- ".tar.gz"))
- (sha256
- (base32
- "0428gq8m3fdnb7ldcsyk97qcch76hcxbgh2666p6f76fs2qbhg7b"))))))
-
(define-public ghc-vault
(package
(name "ghc-vault")
@@ -5909,35 +5897,6 @@ within an enclosed computation, while remaining responsive to (external)
asynchronous exceptions.")
(license license:expat)))
-(define-public ghc-packedstring
- (package
- (name "ghc-packedstring")
- (version "0.1.0.1")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://hackage.haskell.org/package/"
- "packedstring/packedstring-"
- version ".tar.gz"))
- (sha256
- (base32
- "1x78pzzdlnpcmh9p37rlf8m5cxf3yqm2alf3whl4zpr9w25r0qj8"))))
- (build-system haskell-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'enable-extension
- (lambda _
- ;; This package won't compile without the StandaloneDeriving
- ;; extension.
- (substitute* "packedstring.cabal"
- (("CPP") "CPP, StandaloneDeriving"))
- #t)))))
- (home-page "https://hackage.haskell.org/package/packedstring")
- (synopsis "Library for packed strings")
- (description
- "This deprecated library provides an implementation of packed strings.")
- (license license:bsd-3)))
-
(define-public ghc-th-abstraction
(package
(name "ghc-th-abstraction")
@@ -6252,6 +6211,9 @@ back-ends.")
(base32
"0cbsyh4ilvjzq1q7pxls43k6pdqxg1l85xzibcwpbvmlvrizh86w"))))
(build-system haskell-build-system)
+ ;; The tests are broken on i686. They are fixed in 0.10.3.0.
+ ;; See https://github.com/snoyberg/yaml/issues/158
+ (arguments `(#:tests? #f))
(inputs
`(("ghc-conduit" ,ghc-conduit)
("ghc-resourcet" ,ghc-resourcet)
@@ -11278,6 +11240,9 @@ imported with the correct Haskell types.")
(base32
"1931m23iqb4wddpdidm4ph746zpaw41kkjzmb074j7yyfpk7x1jv"))))
(build-system haskell-build-system)
+ ;; Tests fail on i686.
+ ;; See https://github.com/vimus/libmpd-haskell/issues/112
+ (arguments `(#:tests? #f))
(inputs
`(("ghc-attoparsec" ,ghc-attoparsec)
("ghc-old-locale" ,ghc-old-locale)
@@ -11821,7 +11786,7 @@ default)
(define-public ghc-validation
(package
(name "ghc-validation")
- (version "1.1")
+ (version "1")
(source
(origin
(method url-fetch)
@@ -11831,18 +11796,11 @@ default)
".tar.gz"))
(sha256
(base32
- "1acj7mh3581ks405xswxw6667z7y1y0slisg6jvp6chc191ji9l5"))))
+ "08drmdvyzg2frbb26icy1mlz52xv0l6gi3v8gb7xp0vrcci5libh"))))
(build-system haskell-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'add-setup-script
- (lambda _
- ;; The usual "Setup.hs" script is missing from the source.
- (with-output-to-file "Setup.hs"
- (lambda ()
- (format #t "import Distribution.Simple~%")
- (format #t "main = defaultMain~%"))))))))
+ `(#:cabal-revision
+ ("1" "1x1g4nannz81j1h64l1m3ancc96zc57d1bjhj1wk7bwn1xxbi5h3")))
(inputs
`(("ghc-semigroups" ,ghc-semigroups)
("ghc-semigroupoids" ,ghc-semigroupoids)
@@ -11875,7 +11833,7 @@ example of, \"An applicative functor that is not a monad.\"")
(define-public ghc-concurrent-output
(package
(name "ghc-concurrent-output")
- (version "1.10.10")
+ (version "1.10.9")
(source
(origin
(method url-fetch)
@@ -11885,7 +11843,7 @@ example of, \"An applicative functor that is not a monad.\"")
".tar.gz"))
(sha256
(base32
- "1wnjxnwbc3l853kiiijagzjyb6fmhz3lmkwls24plbximl1qrr22"))))
+ "0mwf155w89nbbkjln7hhbn8k3f8p0ylcvgrg31cm7ijpx4499i4c"))))
(build-system haskell-build-system)
(inputs
`(("ghc-async" ,ghc-async)
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 38780e93fe..93eccf842d 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -577,9 +577,6 @@ collection of tools for doing simple manipulations of TIFF images.")
(arguments
'(#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'autogen
- (lambda _
- (invoke "sh" "autobuild")))
(add-after 'unpack 'patch-reg-wrapper
(lambda _
(substitute* "prog/reg_wrapper.sh"
@@ -1004,7 +1001,7 @@ language bindings to VIGRA.")
(define-public libwebp
(package
(name "libwebp")
- (version "1.0.2")
+ (version "1.0.3")
(source
(origin
;; No tarballs are provided for >0.6.1.
@@ -1015,7 +1012,7 @@ language bindings to VIGRA.")
(file-name (git-file-name name version))
(sha256
(base32
- "1ay0sai7f74dyk2gi975qfllmq534vnsx456npf16583mqb6ib2q"))))
+ "1l8h9d3z3kla567ilmymrgg8vc2n763g8qss1hah8dg832hbqkxf"))))
(build-system gnu-build-system)
(inputs
`(("freeglut" ,freeglut)
@@ -1074,14 +1071,14 @@ channels.")
(define-public exiv2
(package
(name "exiv2")
- (version "0.27.1")
+ (version "0.27.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.exiv2.org/builds/exiv2-" version
"-Source.tar.gz"))
(sha256
- (base32 "109hbfk63dh14fz20ivq20gcclb9jj9jmh48w4lcn6zxh1ljh9gi"))))
+ (base32 "0gqminvj14xm3rgbnydbywf22608js80rp7nmxxk4497j5mzali6"))))
(build-system cmake-build-system)
(arguments '(#:tests? #f)) ; no test suite
(propagated-inputs
@@ -1206,12 +1203,6 @@ ISO/IEC 15444-1).")
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)))
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'autogen
- (lambda _
- (invoke "sh" "autogen.sh"))))))
(synopsis "Scaling, colorspace conversion, and dithering library")
(description "Zimg implements the commonly required image processing basics
of scaling, colorspace conversion, and depth conversion. A simple API enables
diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm
index 39fcf61a12..807fd43b9b 100644
--- a/gnu/packages/imagemagick.scm
+++ b/gnu/packages/imagemagick.scm
@@ -48,14 +48,14 @@
;; The 7 release series has an incompatible API, while the 6 series is still
;; maintained. Don't update to 7 until we've made sure that the ImageMagick
;; users are ready for the 7-series API.
- (version "6.9.10-51")
+ (version "6.9.10-58")
(source (origin
(method url-fetch)
(uri (string-append "mirror://imagemagick/ImageMagick-"
version ".tar.xz"))
(sha256
(base32
- "03c5r14ycp7mmlk6pryfcnpvjjnghk3z7dbjd1b7m1bgzmw21jhj"))))
+ "1hrd408lqgwg70aaif8g60lipwsplsg61722kpmx7a08pygs46hf"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")
diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm
index b5b1d4eb20..d8c0649131 100644
--- a/gnu/packages/kde.scm
+++ b/gnu/packages/kde.scm
@@ -320,7 +320,7 @@ plugins, as well as code to create plugins, or complete applications.")
(define-public krita
(package
(name "krita")
- (version "4.2.2")
+ (version "4.2.5")
(source (origin
(method url-fetch)
(uri (string-append
@@ -329,7 +329,7 @@ plugins, as well as code to create plugins, or complete applications.")
"/krita-" version ".tar.gz"))
(sha256
(base32
- "1pzk5bqp3kh22djhvsvmsc7ybirs4hsnkpg1y9677m2gxwbqnnps"))))
+ "1f14r2mrqasl6nr3sss0xy2h8xlxd5wdcjcd64m9nz2gwlm39r7w"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f
diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm
index 58c451a4e9..ae87671611 100644
--- a/gnu/packages/libevent.scm
+++ b/gnu/packages/libevent.scm
@@ -41,7 +41,7 @@
(define-public libevent
(package
(name "libevent")
- (version "2.1.10")
+ (version "2.1.11")
(source (origin
(method url-fetch)
(uri (string-append
@@ -49,7 +49,7 @@
version "-stable/libevent-" version "-stable.tar.gz"))
(sha256
(base32
- "1c25928gdv495clxk2v1d4gkr5py7ack4gx2n7d13frnld0syr78"))))
+ "0g988zqm45sj1hlhhz4il5z4dpi5dl74hzjwzl4md37a09iaqnx6"))))
(build-system gnu-build-system)
(arguments
;; This skips some of the tests which fail on armhf and aarch64.
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 998f197304..f2e36ee7b4 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -349,42 +349,42 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
"linux-" version ".tar.xz"))
(sha256 hash)))
-(define-public linux-libre-5.2-version "5.2.4")
+(define-public linux-libre-5.2-version "5.2.8")
(define-public linux-libre-5.2-pristine-source
(let ((version linux-libre-5.2-version)
- (hash (base32 "0hzfayq79bksng09ngw3k3h3zkd6ndfn059rvwpznypy1fg8pkdi")))
+ (hash (base32 "0dv91zfjkil29lp2l35lswkrhrqbc4kjh965ciaqwih1rh3cs9x1")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.2)))
-(define-public linux-libre-4.19-version "4.19.62")
+(define-public linux-libre-4.19-version "4.19.66")
(define-public linux-libre-4.19-pristine-source
(let ((version linux-libre-4.19-version)
- (hash (base32 "1p6s1ksrsq3za7644j0qf9brf6brwq39jxpfln5ypmyfi5qn9gh7")))
+ (hash (base32 "0r6vzarmi77fhivd1n6f667sgcw8zd54ykmhmp6rd52bbkhsp0f9")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.19)))
-(define-public linux-libre-4.14-version "4.14.134")
+(define-public linux-libre-4.14-version "4.14.138")
(define-public linux-libre-4.14-pristine-source
(let ((version linux-libre-4.14-version)
- (hash (base32 "0b9xj1rwr5fpw2giirfghzxxc0wp1hwf4nqvalx314pxxysyf88b")))
+ (hash (base32 "0yw39cqpk6g42q0xcv2aq8yyzsi0kzx9nvlfbw0iyg58wcfvsl7j")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.14)))
-(define-public linux-libre-4.9-version "4.9.186")
+(define-public linux-libre-4.9-version "4.9.189")
(define-public linux-libre-4.9-pristine-source
(let ((version linux-libre-4.9-version)
- (hash (base32 "0sjbp7m6d625rw06wv34a0805d1lgldii4pxiqfpja871m1q8914")))
+ (hash (base32 "1cyhwnxkjd0qa5d48657yppjnzbi830q0p25jjv2dxs629k4bnck")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.9)))
-(define-public linux-libre-4.4-version "4.4.186")
+(define-public linux-libre-4.4-version "4.4.189")
(define-public linux-libre-4.4-pristine-source
(let ((version linux-libre-4.4-version)
- (hash (base32 "113rjf8842glzi23y1g1yrwncihv2saah6wz0r726r06bk9p64hb")))
+ (hash (base32 "0nc8v62gw89m3ykqg6nqf749fzm8y1n481ns8vny4gbinyikjhlp")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.4)))
@@ -1397,15 +1397,18 @@ Zerofree requires the file system to be unmounted or mounted read-only.")
(define-public strace
(package
(name "strace")
- (version "5.1")
+ (version "5.2")
(home-page "https://strace.io")
(source (origin
(method url-fetch)
(uri (string-append home-page "/files/" version
"/strace-" version ".tar.xz"))
+ ;; XXX Remove the 'regenerate-tests' phase below when
+ ;; "strace-ipc-tests.patch" is no longer applied.
+ (patches (search-patches "strace-ipc-tests.patch"))
(sha256
(base32
- "12wsga1v3rab24gr0mpfip7j7gwr90m8f9h6fviqxa3xgnwl38zm"))))
+ "1li49i75wrdw91hchyyd8spnzfcmxcfyfb5g9zbaza89aq4bq4ym"))))
(build-system gnu-build-system)
(arguments
'(#:phases
@@ -1414,7 +1417,14 @@ Zerofree requires the file system to be unmounted or mounted read-only.")
(lambda _
(substitute* "strace.c"
(("/bin/sh") (which "sh")))
- #t)))
+ #t))
+ (add-before 'configure 'regenerate-tests
+ ;; XXX Remove this phase when "strace-ipc-tests.patch" is no longer
+ ;; applied in the 'source' field above. This phase is needed to
+ ;; regenerate many other files from tests/gen_tests.in, which is
+ ;; modified by the aforementioned patch.
+ (lambda _
+ (invoke "tests/gen_tests.sh"))))
;; Don't fail if the architecture doesn't support different personalities.
#:configure-flags '("--enable-mpers=check")
;; See <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=32459>.
@@ -4613,7 +4623,7 @@ are exceeded.")
(define-public mtd-utils
(package
(name "mtd-utils")
- (version "2.0.2")
+ (version "2.1.1")
(source (origin
(method url-fetch)
(uri (string-append
@@ -4621,17 +4631,19 @@ are exceeded.")
"mtd-utils-" version ".tar.bz2"))
(sha256
(base32
- "1f30jszknc5v6ykmil8ajxgksmcg54q3rsp84jsancp9x0dycggv"))))
+ "1lijl89l7hljx8xx70vrz9srd3h41v5gh4b0lvqnlv831yvyh5cd"))))
(arguments
'(#:configure-flags '("--enable-unit-tests")))
(native-inputs
`(("cmocka" ,cmocka)
("pkg-config" ,pkg-config)))
(inputs
- `(("acl" ,acl) ; for XATTR
+ `(("acl" ,acl) ; extended attributes (xattr)
("libuuid" ,util-linux)
("lzo" ,lzo)
- ("zlib" ,zlib)))
+ ("openssl" ,openssl) ; optional crypto support
+ ("zlib" ,zlib)
+ ("zstd" ,zstd "lib")))
(build-system gnu-build-system)
(synopsis "MTD Flash Storage Utilities")
(description "This package provides utilities for testing, partitioning, etc
diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index e7d0d5a44f..d2bed231bd 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm