aboutsummaryrefslogtreecommitdiff
# GNU Guix --- Functional package management for GNU
# Copyright © 2018, 2019 Ludovic Courtès <ludo@gnu.org>
#
# 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/>.

#
# Test the 'guix pack --localstatedir' command-line utility.
#

guix pack --version

# 'guix pack --localstatedir' produces derivations that depend on
# guile-sqlite3 and guile-gcrypt.  To make that relatively inexpensive, run
# the test in the user's global store if possible, on the grounds that
# binaries may already be there or can be built or downloaded inexpensively.

storedir="`guile -c '(use-modules (guix config))(display %storedir)'`"
localstatedir="`guile -c '(use-modules (guix config))(display %localstatedir)'`"
NIX_STORE_DIR="$storedir"
GUIX_DAEMON_SOCKET="$localstatedir/guix/daemon-socket/socket"
export NIX_STORE_DIR GUIX_DAEMON_SOCKET

if ! guile -c '(use-modules (guix)) (exit (false-if-exception (open-connection)))'
then
    exit 77
fi

# Build a tarball with '--localstatedir'
the_pack="`guix pack -C none --localstatedir --profile-name=current-guix \
            guile-bootstrap`"
test_directory="`mktemp -d`"
trap 'chmod -Rf +w "$test_directory"; rm -rf "$test_directory"' EXIT

cd "$test_directory"
tar -xf "$the_pack"

profile="`find -name current-guix`"
test "`readlink $profile`" = "current-guix-1-link"
test -s "`dirname $profile`/../../../db/db.sqlite"
test -x ".`guix build guile-bootstrap`/bin/guile"
cd -

# Make sure the store database is not completely bogus.
guile -c "(use-modules (sqlite3) (guix config) (ice-9 match))

  (define db
    (sqlite-open (string-append \"$test_directory\"
                                %localstatedir
                               \"/guix/db/db.sqlite\")
                 SQLITE_OPEN_READONLY))

  (define stmt
    (sqlite-prepare db \"SELECT * FROM ValidPaths;\"))

  (match (sqlite-fold cons '() stmt)
    ((#(ids paths hashes times derivers sizes) ...)
     (exit (member \"`guix build guile-bootstrap`\" paths))))"
-ad384816fe260be98bc53701d9d761197ef162fc.zip
Merge branch 'staging' into core-updates
Diffstat (limited to 'gnu')
-rw-r--r--gnu/bootloader.scm1
-rw-r--r--gnu/ci.scm61
-rw-r--r--gnu/home.scm2
-rw-r--r--gnu/home/services.scm5
-rw-r--r--gnu/home/services/ssh.scm12
-rw-r--r--gnu/installer/parted.scm1
-rw-r--r--gnu/local.mk13
-rw-r--r--gnu/packages/admin.scm55
-rw-r--r--gnu/packages/algebra.scm12
-rw-r--r--gnu/packages/animation.scm49
-rw-r--r--gnu/packages/assembly.scm7
-rw-r--r--gnu/packages/audio.scm32
-rw-r--r--gnu/packages/benchmark.scm4
-rw-r--r--gnu/packages/bioconductor.scm207
-rw-r--r--gnu/packages/bioinformatics.scm473
-rw-r--r--gnu/packages/bittorrent.scm3
-rw-r--r--gnu/packages/bootloaders.scm6
-rw-r--r--gnu/packages/browser-extensions.scm4
-rw-r--r--gnu/packages/build-tools.scm4
-rw-r--r--gnu/packages/c.scm4
-rw-r--r--gnu/packages/cdrom.scm83
-rw-r--r--gnu/packages/check.scm37
-rw-r--r--gnu/packages/chromium.scm6
-rw-r--r--gnu/packages/ci.scm22
-rw-r--r--gnu/packages/code.scm4
-rw-r--r--gnu/packages/coq.scm13
-rw-r--r--gnu/packages/cpp.scm34
-rw-r--r--gnu/packages/cran.scm238
-rw-r--r--gnu/packages/crates-io.scm328
-rw-r--r--gnu/packages/cups.scm35
-rw-r--r--gnu/packages/databases.scm109
-rw-r--r--gnu/packages/debian.scm6
-rw-r--r--gnu/packages/dezyne.scm4
-rw-r--r--gnu/packages/diffoscope.scm4
-rw-r--r--gnu/packages/dns.scm12
-rw-r--r--gnu/packages/documentation.scm12
-rw-r--r--gnu/packages/dunst.scm4
-rw-r--r--gnu/packages/ebook.scm4
-rw-r--r--gnu/packages/emacs-xyz.scm468
-rw-r--r--gnu/packages/engineering.scm80
-rw-r--r--gnu/packages/file-systems.scm44
-rw-r--r--gnu/packages/finance.scm175
-rw-r--r--gnu/packages/firmware.scm8
-rw-r--r--gnu/packages/fonts.scm25
-rw-r--r--gnu/packages/fontutils.scm10
-rw-r--r--gnu/packages/fpga.scm6
-rw-r--r--gnu/packages/game-development.scm87
-rw-r--r--gnu/packages/games.scm396
-rw-r--r--gnu/packages/gcc.scm4
-rw-r--r--gnu/packages/geo.scm41
-rw-r--r--gnu/packages/gnome-xyz.scm3
-rw-r--r--gnu/packages/gnome.scm86
-rw-r--r--gnu/packages/gnuzilla.scm247
-rw-r--r--gnu/packages/golang.scm106
-rw-r--r--gnu/packages/graph.scm4
-rw-r--r--gnu/packages/graphics.scm15
-rw-r--r--gnu/packages/graphviz.scm2
-rw-r--r--gnu/packages/gstreamer.scm2
-rw-r--r--gnu/packages/gtk.scm19
-rw-r--r--gnu/packages/guile-xyz.scm97
-rw-r--r--gnu/packages/hardware.scm90
-rw-r--r--gnu/packages/haskell.scm486
-rw-r--r--gnu/packages/image-viewers.scm50
-rw-r--r--gnu/packages/image.scm26
-rw-r--r--gnu/packages/instrumentation.scm35
-rw-r--r--gnu/packages/irc.scm4
-rw-r--r--gnu/packages/java.scm3
-rw-r--r--gnu/packages/julia.scm39
-rw-r--r--gnu/packages/libreoffice.scm5
-rw-r--r--gnu/packages/linux.scm123
-rw-r--r--gnu/packages/lisp-xyz.scm34
-rw-r--r--gnu/packages/lisp.scm8
-rw-r--r--gnu/packages/lxde.scm150
-rw-r--r--gnu/packages/lxqt.scm445
-rw-r--r--gnu/packages/machine-learning.scm8
-rw-r--r--gnu/packages/mail.scm49
-rw-r--r--gnu/packages/maths.scm64
-rw-r--r--gnu/packages/maven.scm4
-rw-r--r--gnu/packages/messaging.scm31
-rw-r--r--gnu/packages/moe.scm5
-rw-r--r--gnu/packages/music.scm21
-rw-r--r--gnu/packages/networking.scm19
-rw-r--r--gnu/packages/ocaml.scm394
-rw-r--r--gnu/packages/ocr.scm186
-rw-r--r--gnu/packages/package-management.scm17
-rw-r--r--gnu/packages/patches/crawl-upgrade-saves.patch4
-rw-r--r--gnu/packages/patches/guile-fibers-epoll-instance-is-dead.patch99
-rw-r--r--gnu/packages/patches/lcalc-default-parameters-1.patch26
-rw-r--r--gnu/packages/patches/lcalc-default-parameters-2.patch58
-rw-r--r--gnu/packages/patches/lcalc-lcommon-h.patch13
-rw-r--r--gnu/packages/patches/lcalc-using-namespace-std.patch43
-rw-r--r--gnu/packages/patches/lrcalc-includes.patch92
-rw-r--r--gnu/packages/patches/perl-class-methodmaker-reproducible.patch21
-rw-r--r--gnu/packages/patches/polkit-CVE-2021-4034.patch82
-rw-r--r--gnu/packages/patches/polkit-configure-elogind.patch15
-rw-r--r--gnu/packages/patches/polkit-use-duktape.patch5030
-rw-r--r--gnu/packages/patches/python-dateutil-pytest-compat.patch43
-rw-r--r--gnu/packages/patches/python-mypy-12332.patch68
-rw-r--r--gnu/packages/patches/python-mypy-use-sys-path.patch130
-rw-r--r--gnu/packages/perl-check.scm6
-rw-r--r--gnu/packages/perl.scm10
-rw-r--r--gnu/packages/plotutils.scm4
-rw-r--r--gnu/packages/polkit.scm108
-rw-r--r--gnu/packages/pulseaudio.scm55
-rw-r--r--gnu/packages/python-check.scm12
-rw-r--r--gnu/packages/python-compression.scm47
-rw-r--r--gnu/packages/python-crypto.scm29
-rw-r--r--gnu/packages/python-science.scm2
-rw-r--r--gnu/packages/python-web.scm25
-rw-r--r--gnu/packages/python-xyz.scm404
-rw-r--r--gnu/packages/qt.scm101
-rw-r--r--gnu/packages/radio.scm10
-rw-r--r--gnu/packages/rsync.scm4
-rw-r--r--gnu/packages/sagemath.scm72
-rw-r--r--gnu/packages/search.scm10
-rw-r--r--gnu/packages/security-token.scm8
-rw-r--r--gnu/packages/selinux.scm384
-rw-r--r--gnu/packages/shells.scm13
-rw-r--r--gnu/packages/sphinx.scm26
-rw-r--r--gnu/packages/syncthing.scm18
-rw-r--r--gnu/packages/telegram.scm2
-rw-r--r--gnu/packages/telephony.scm2
-rw-r--r--gnu/packages/terminals.scm56
-rw-r--r--gnu/packages/tex.scm2
-rw-r--r--gnu/packages/text-editors.scm4
-rw-r--r--gnu/packages/time.scm1
-rw-r--r--gnu/packages/tor.scm47
-rw-r--r--gnu/packages/upnp.scm4
-rw-r--r--gnu/packages/version-control.scm10
-rw-r--r--gnu/packages/video.scm94
-rw-r--r--gnu/packages/vim.scm8
-rw-r--r--gnu/packages/vpn.scm6
-rw-r--r--gnu/packages/web.scm117
-rw-r--r--gnu/packages/wm.scm10
-rw-r--r--gnu/packages/xfce.scm38
-rw-r--r--gnu/packages/xiph.scm12
-rw-r--r--gnu/packages/xorg.scm20
-rw-r--r--gnu/services/base.scm24
-rw-r--r--gnu/services/configuration.scm40
-rw-r--r--gnu/services/desktop.scm23
-rw-r--r--gnu/services/file-sharing.scm11
-rw-r--r--gnu/services/getmail.scm6
-rw-r--r--gnu/services/kerberos.scm1
-rw-r--r--gnu/services/messaging.scm17
-rw-r--r--gnu/services/networking.scm2
-rw-r--r--gnu/services/telephony.scm6
-rw-r--r--gnu/tests/desktop.scm17
147 files changed, 5342 insertions, 8441 deletions
diff --git a/gnu/bootloader.scm b/gnu/bootloader.scm
index 9cf5457873..70e1836179 100644
--- a/gnu/bootloader.scm
+++ b/gnu/bootloader.scm
@@ -69,7 +69,6 @@
bootloader-configuration-terminal-inputs
bootloader-configuration-serial-unit
bootloader-configuration-serial-speed
- bootloader-configuration-additional-configuration
%bootloaders
lookup-bootloader-by-name
diff --git a/gnu/ci.scm b/gnu/ci.scm
index 9cc3a1a81f..2c51ea7387 100644
--- a/gnu/ci.scm
+++ b/gnu/ci.scm
@@ -254,37 +254,40 @@ otherwise use the IMAGE name."
(parameterize ((%graft? #f))
(derivation->job name drv))))
-(define (image-jobs store system)
+(define* (image-jobs store system
+ #:key source commit)
"Return a list of jobs that build images for SYSTEM."
(define MiB
(expt 2 20))
- (if (member system %guix-system-supported-systems)
- `(,(image->job store
- (image
- (inherit efi-disk-image)
- (operating-system installation-os))
- #:name "usb-image"
- #:system system)
- ,(image->job
- store
- (image
- (inherit (image-with-label
- iso9660-image
- (string-append "GUIX_" system "_"
- (if (> (string-length %guix-version) 7)
- (substring %guix-version 0 7)
- %guix-version))))
- (operating-system installation-os))
- #:name "iso9660-image"
- #:system system)
- ;; Only cross-compile Guix System images from x86_64-linux for now.
- ,@(if (string=? system "x86_64-linux")
- (map (cut image->job store <>
- #:system system)
- %guix-system-images)
- '()))
- '()))
+ (parameterize ((current-guix-package
+ (channel-source->package source #:commit commit)))
+ (if (member system %guix-system-supported-systems)
+ `(,(image->job store
+ (image
+ (inherit efi-disk-image)
+ (operating-system installation-os))
+ #:name "usb-image"
+ #:system system)
+ ,(image->job
+ store
+ (image
+ (inherit (image-with-label
+ iso9660-image
+ (string-append "GUIX_" system "_"
+ (if (> (string-length %guix-version) 7)
+ (substring %guix-version 0 7)
+ %guix-version))))
+ (operating-system installation-os))
+ #:name "iso9660-image"
+ #:system system)
+ ;; Only cross-compile Guix System images from x86_64-linux for now.
+ ,@(if (string=? system "x86_64-linux")
+ (map (cut image->job store <>
+ #:system system)
+ %guix-system-images)
+ '()))
+ '())))
(define* (system-test-jobs store system
#:key source commit)
@@ -527,7 +530,9 @@ names."
hello system))))
('images
;; Build Guix System images only.
- (image-jobs store system))
+ (image-jobs store system
+ #:source source
+ #:commit commit))
('system-tests
;; Build Guix System tests only.
(system-test-jobs store system
diff --git a/gnu/home.scm b/gnu/home.scm
index 4ddbafe412..c95d1e0818 100644
--- a/gnu/home.scm
+++ b/gnu/home.scm
@@ -96,7 +96,7 @@
(home-environment-essential-services he))))
(define* (home-environment-derivation he)
- "Return a derivation that builds OS."
+ "Return a derivation that builds home environment."
(let* ((services (home-environment-services he))
(home (fold-services services
#:target-type home-service-type)))
diff --git a/gnu/home/services.scm b/gnu/home/services.scm
index 75ea54743d..99035686f1 100644
--- a/gnu/home/services.scm
+++ b/gnu/home/services.scm
@@ -420,8 +420,9 @@ extended with one gexp.")))
(he-path (string-append (getenv "HOME") "/.guix-home"))
(new-home-env (getenv "GUIX_NEW_HOME"))
(new-home (or new-home-env
- ;; Path of the activation file if called interactively
- (dirname (car (command-line)))))
+ ;; Absolute path of the directory of the activation
+ ;; file if called interactively.
+ (canonicalize-path (dirname (car (command-line))))))
(old-home-env (getenv "GUIX_OLD_HOME"))
(old-home (or old-home-env
(if (file-exists? (he-init-file he-path))
diff --git a/gnu/home/services/ssh.scm b/gnu/home/services/ssh.scm
index f0987aee23..d15f5ee912 100644
--- a/gnu/home/services/ssh.scm
+++ b/gnu/home/services/ssh.scm
@@ -69,17 +69,19 @@
" " value "\n"))
(define (address-family? obj)
- (memv obj (list 'unset AF_INET AF_INET6)))
+ (memv obj (list AF_INET AF_INET6)))
+
+(define-maybe address-family)
(define (serialize-address-family field family)
- (if (eq? 'unset family)
- ""
+ (if (maybe-value-set? family)
(string-append " " (serialize-field-name field) " "
(cond ((= family AF_INET) "inet")
((= family AF_INET6) "inet6")
;; The 'else' branch is unreachable.
(else (raise (condition (&error)))))
- "\n")))
+ "\n")
+ ""))
(define (natural-number? obj)
(and (integer? obj) (exact? obj) (> obj 0)))
@@ -115,7 +117,7 @@
maybe-string
"Host name---e.g., @code{\"foo.example.org\"} or @code{\"192.168.1.2\"}.")
(address-family
- address-family
+ maybe-address-family
"Address family to use when connecting to this host: one of
@code{AF_INET} (for IPv4 only), @code{AF_INET6} (for IPv6 only).
Additionally, the field can be left unset to allow any address family.")
diff --git a/gnu/installer/parted.scm b/gnu/installer/parted.scm
index d942a2f49b..641a1f45e8 100644
--- a/gnu/installer/parted.scm
+++ b/gnu/installer/parted.scm
@@ -80,7 +80,6 @@
efi-installation?
default-esp-mount-point
- with-delay-device-in-use?
force-device-sync
eligible-devices
partition-user-type
diff --git a/gnu/local.mk b/gnu/local.mk
index a4238e5141..f061f1d4dd 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1246,6 +1246,7 @@ dist_patch_DATA = \
%D%/packages/patches/guile-ac-d-bus-fix-tests.patch \
%D%/packages/patches/guile-cross-compilation.patch \
%D%/packages/patches/guile-fibers-destroy-peer-schedulers.patch \
+ %D%/packages/patches/guile-fibers-epoll-instance-is-dead.patch \
%D%/packages/patches/guile-fibers-wait-for-io-readiness.patch \
%D%/packages/patches/guile-gdbm-ffi-support-gdbm-1.14.patch \
%D%/packages/patches/guile-git-adjust-for-libgit2-1.2.0.patch \
@@ -1370,10 +1371,6 @@ dist_patch_DATA = \
%D%/packages/patches/kodi-set-libcurl-ssl-parameters.patch \
%D%/packages/patches/kodi-skip-test-449.patch \
%D%/packages/patches/laby-make-install.patch \
- %D%/packages/patches/lcalc-default-parameters-1.patch \
- %D%/packages/patches/lcalc-default-parameters-2.patch \
- %D%/packages/patches/lcalc-lcommon-h.patch \
- %D%/packages/patches/lcalc-using-namespace-std.patch \
%D%/packages/patches/ldns-drill-examples.patch \
%D%/packages/patches/leela-zero-gtest.patch \
%D%/packages/patches/less-hurd-path-max.patch \
@@ -1461,7 +1458,6 @@ dist_patch_DATA = \
%D%/packages/patches/llvm-roc-4.0.0-remove-isystem-usr-include.patch \
%D%/packages/patches/llvm-roc-5.0.0-linkdl.patch \
%D%/packages/patches/lm-sensors-hwmon-attrs.patch \
- %D%/packages/patches/lrcalc-includes.patch \
%D%/packages/patches/lsh-fix-x11-forwarding.patch \
%D%/packages/patches/lsof-fatal-test-failures.patch \
%D%/packages/patches/lua-CVE-2014-5461.patch \
@@ -1614,6 +1610,7 @@ dist_patch_DATA = \
%D%/packages/patches/perl-5.14-module-pluggable-search.patch \
%D%/packages/patches/perl-5.14-no-sys-dirs.patch \
%D%/packages/patches/perl-autosplit-default-time.patch \
+ %D%/packages/patches/perl-class-methodmaker-reproducible.patch \
%D%/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch \
%D%/packages/patches/perl-image-exiftool-CVE-2021-22204.patch \
%D%/packages/patches/perl-net-amazon-s3-moose-warning.patch \
@@ -1640,9 +1637,6 @@ dist_patch_DATA = \
%D%/packages/patches/plib-CVE-2011-4620.patch \
%D%/packages/patches/plib-CVE-2012-4552.patch \
%D%/packages/patches/plotutils-spline-test.patch \
- %D%/packages/patches/polkit-CVE-2021-4034.patch \
- %D%/packages/patches/polkit-configure-elogind.patch \
- %D%/packages/patches/polkit-use-duktape.patch \
%D%/packages/patches/portaudio-audacity-compat.patch \
%D%/packages/patches/portmidi-modular-build.patch \
%D%/packages/patches/postgresql-disable-resolve_symlinks.patch \
@@ -1680,6 +1674,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-argcomplete-1.11.1-fish31.patch \
%D%/packages/patches/python-cross-compile.patch \
%D%/packages/patches/python-configobj-setuptools.patch \
+ %D%/packages/patches/python-dateutil-pytest-compat.patch \
%D%/packages/patches/python-debugpy-unbundle-pydevd.patch \
%D%/packages/patches/python-docopt-pytest6-compat.patch \
%D%/packages/patches/python-execnet-read-only-fix.patch \
@@ -1721,8 +1716,6 @@ dist_patch_DATA = \
%D%/packages/patches/python-versioneer-guix-support.patch \
%D%/packages/patches/python-waitress-fix-tests.patch \
%D%/packages/patches/python-werkzeug-tests.patch \
- %D%/packages/patches/python-mypy-12332.patch \
- %D%/packages/patches/python-mypy-use-sys-path.patch \
%D%/packages/patches/python-zeep-Fix-pytest_httpx-test-cases.patch \
%D%/packages/patches/qemu-build-info-manual.patch \
%D%/packages/patches/qemu-glibc-2.27.patch \
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 06bc566cc7..db3e881228 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -784,7 +784,7 @@ memory, disks, network and processes. It's a Python port and continuation of
(define-public pies
(package
(name "pies")
- (version "1.7")
+ (version "1.8")
(source
(origin
(method url-fetch)
@@ -792,7 +792,16 @@ memory, disks, network and processes. It's a Python port and continuation of
version ".tar.bz2"))
(sha256
(base32
- "0ajcah2y6n55qc0ckspcx0hfpm1yb2xa1apcyij7mclic4q2y330"))))
+ "0v0xcq0mfil440xq2pa5mjkyva5c9ahqda54z5w2ksl2d78v8a35"))
+ (snippet
+ #~(begin
+ (use-modules (guix build utils))
+ (for-each delete-file
+ (append
+ ;; Generated by flex.
+ (find-files "gres/src" "lex\\.c$")
+ ;; Generated by bison.
+ (find-files "gres/src" "-gram\\.[ch]$")))))))
(build-system gnu-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
@@ -804,6 +813,7 @@ memory, disks, network and processes. It's a Python port and continuation of
(substitute* '("src/progman.c" "src/comp.c")
(("\"/bin/sh\"")
(string-append "\"" bash "/bin/sh\"")))))))))
+ (native-inputs (list bison flex))
(home-page "https://www.gnu.org.ua/software/pies/")
(synopsis "Program invocation and execution supervisor")
(description
@@ -4193,7 +4203,7 @@ Python loading in HPC environments.")
(let ((real-name "inxi"))
(package
(name "inxi-minimal")
- (version "3.3.19-1")
+ (version "3.3.20-1")
(source
(origin
(method git-fetch)
@@ -4202,7 +4212,7 @@ Python loading in HPC environments.")
(commit version)))
(file-name (git-file-name real-name version))
(sha256
- (base32 "0g5m43cj4534gb181zy1hwjz5il88xibf8psxw8a4s6jnaq1zdlk"))))
+ (base32 "182lczpa217gpzn58nfdzjbbinp3bw9lbm1x9lck1mkdmqklgl2a"))))
(build-system trivial-build-system)
(inputs
`(("bash" ,bash-minimal)
@@ -5444,3 +5454,40 @@ attempts, it cannot eliminate the risk presented by weak authentication. Set
up services to use only two factor, or public/private authentication
mechanisms if you really want to protect services.")
(license license:gpl2+)))
+
+(define-public rex
+ (package
+ (name "rex")
+ (version "4.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://download.gnu.org.ua/pub/releases/rex/rex-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1arb8z602invwavskq36nhwy42a3v14iyhi06iqlngfai2k93fai"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:tests? #f ; no tests
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; No configure script and Makefile.
+ (delete 'configure)
+ (delete 'build)
+ (add-before 'install 'patch-exec-expect
+ (lambda _
+ (substitute* "rex"
+ (("exec expect") (string-append "exec " (which "expect"))))))
+ (replace 'install
+ (lambda _
+ (invoke "./install"
+ (string-append "--prefix=" #$output)))))))
+ (inputs (list expect))
+ (home-page "https://www.gnu.org.ua/software/rex/")
+ (synopsis "Remote execution utility")
+ (description "@command{rex} runs a supplied command or shell script on
+several hosts in succession or in parallel. It can also be used to copy a
+file or files to several hosts.")
+ (license license:gpl3+)))
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index b3f0823daf..8ccb44c434 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -1628,7 +1628,7 @@ John Cremona to compute his elliptic curve database.")
(define-public lrcalc
(package
(name "lrcalc")
- (version "1.2")
+ (version "2.1")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1637,18 +1637,10 @@ John Cremona to compute his elliptic curve database.")
(file-name (git-file-name name version))
(sha256
(base32
- "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
- (patches (search-patches "lrcalc-includes.patch"))))
+ "0s3amf3z75hnrjyszdndrvk4wp5p630dcgyj341i6l57h43d1p4k"))))
(build-system gnu-build-system)
(native-inputs
(list autoconf automake libtool))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-before 'build 'fix-permission
- (lambda _
- (chmod "lrcalc.maple.src" #o644)
- #t)))))
(synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
(description "The Littlewood-Richardson Calculator (lrcalc) is a
program designed to compute Littlewood-Richardson coefficients. It computes
diff --git a/gnu/packages/animation.scm b/gnu/packages/animation.scm
index ba8ce00fbd..b8524681fa 100644
--- a/gnu/packages/animation.scm
+++ b/gnu/packages/animation.scm
@@ -2,7 +2,7 @@
;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Pkill -9 <pkill9@runbox.com>
-;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -323,7 +323,7 @@ audio or video backends, ensuring good performance.")
(define-public lightspark
(package
(name "lightspark")
- (version "0.8.5")
+ (version "0.8.6")
(source
(origin
(method git-fetch)
@@ -332,7 +332,7 @@ audio or video backends, ensuring good performance.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "00535ndzjbz5xyr95cih01wlkc2mgvg60bv6amz4lnnglk0c5v0p"))))
+ (base32 "0v7d7vwb0xqkk3v8dyks0wyk52ga57v5lg93y74v1d2wh7spmmzw"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;requires Adobe Flex SDK, see README.tests
@@ -352,29 +352,28 @@ audio or video backends, ensuring good performance.")
(when tests?
(invoke "./tests")))))))
(native-inputs
- `(("gettext" ,gettext-minimal)
- ("glib:bin" ,glib "bin")
- ("nasm" ,nasm)
- ("perl" ,perl)
- ("pkg-config" ,pkg-config)
- ("python" ,python-wrapper)))
+ (list gettext-minimal
+ `(,glib "bin")
+ nasm
+ perl
+ pkg-config
+ python-wrapper))
(inputs
- `(("cairo" ,cairo)
- ("curl" ,curl)
- ("ffmpeg" ,ffmpeg)
- ("freeglut" ,freeglut)
- ("glew" ,glew)
- ("glibmm" ,glibmm)
- ("gnash" ,gnash)
- ("gnutls" ,gnutls)
- ("libjpeg" ,libjpeg-turbo)
- ("openssl" ,openssl)
- ("pango" ,pango)
- ("pcre2" ,pcre2)
- ("rtmpdump" ,rtmpdump)
- ("sdl2" ,sdl2)
- ("sdl2-mixer" ,sdl2-mixer)
- ("zlib" ,zlib)))
+ (list cairo
+ curl
+ ffmpeg
+ freeglut
+ glew
+ glibmm
+ gnutls
+ libjpeg-turbo
+ openssl
+ pango
+ pcre2
+ rtmpdump
+ sdl2
+ sdl2-mixer
+ zlib))
(home-page "https://lightspark.github.io/")
(synopsis "Flash player implementation")
(description
diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm
index ca50b00a06..df6587385f 100644
--- a/gnu/packages/assembly.scm
+++ b/gnu/packages/assembly.scm
@@ -291,7 +291,7 @@ runtime")
(define-public rgbds
(package
(name "rgbds")
- (version "0.4.2")
+ (version "0.5.2")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -300,7 +300,7 @@ runtime")
(file-name (git-file-name name version))
(sha256
(base32
- "0lygj7jzjlq4w0mkiir7ycysrd1p1akyvzrppjcchja05mi8wy9p"))))
+ "13zy05xzh2yxyvzf78a5h59pabwrfr6qs5m453pfbdyd3msg2s7w"))))
(build-system gnu-build-system)
(arguments
`(#:phases
@@ -312,8 +312,7 @@ runtime")
(("pkg-config")
(or (which "pkg-config")
(string-append ,(%current-target-system)
- "-pkg-config"))))
- #t))
+ "-pkg-config"))))))
(replace 'check
(lambda _
(with-directory-excursion "test/asm"
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index aad86bac06..8795caef71 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -38,6 +38,7 @@
;;; Copyright © 2021 Aleksandr Vityazev <avityazev@posteo.org>
;;; Copyright © 2022 Arjan Adriaanse <arjan@adriaan.se>
;;; Copyright © 2022 Juliana Sims <jtsims@protonmail.com>
+;;; Copyright © 2022 Simon Streit <simon@netpanic.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -875,6 +876,10 @@ engineers, musicians, soundtrack editors and composers.")
(lambda* (#:key inputs #:allow-other-keys)
(substitute* '("libraries/lib-files/FileNames.cpp")
(("\"/usr/include/linux/magic.h\"") "<linux/magic.h>"))))
+ (add-after 'install 'delete-gratuitous-script
+ (lambda* (#:key outputs #:allow-other-keys)
+ (delete-file (string-append (assoc-ref outputs "out")
+ "/audacity"))))
(add-after 'wrap-program 'glib-or-gtk-wrap
(assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))
;; The test suite is not "well exercised" according to the developers,
@@ -5863,3 +5868,30 @@ framework. It provides a visual interface to audio and video connections
managed by PipeWire.")
(home-page "https://gitlab.freedesktop.org/rncbc/qpwgraph")
(license license:gpl2)))
+
+(define-public streamripper
+ (package
+ (name "streamripper")
+ (version "1.64.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://sourceforge.net/projects/streamripper"
+ "/files/streamripper%20(current)/"
+ version "/streamripper-" version ".tar.gz"))
+ (sha256
+ (base32 "0hnyv3206r0rfprn3k7k6a0j959kagsfyrmyjm3gsf3vkhp5zmy1"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Delete bundled copy of libmad.
+ '(delete-file-recursively "libmad-0.15.1b"))))
+ (build-system gnu-build-system)
+ (native-inputs (list pkg-config))
+ (inputs (list faad2 glib libmad libvorbis))
+ (home-page "http://streamripper.sourceforge.net")
+ (synopsis "Record audio streams to your hard drive")
+ (description "Streamripper records shoutcast-compatible
+streams. For shoutcast style streams it finds the “meta data” or track
+separation data, and uses that as a marker for where the track should
+be separated.")
+ (license license:gpl2+)))
diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index 7be932f528..1b036e9bd4 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -72,14 +72,14 @@
(define-public fio
(package
(name "fio")
- (version "3.30")
+ (version "3.31")
(source (origin
(method url-fetch)
(uri (string-append "https://brick.kernel.dk/snaps/"
"fio-" version ".tar.bz2"))
(sha256
(base32
- "1qjivkisn7dxk8irrb0rglmmdpbnai6n7vindf18ln0j24cc1x56"))))
+ "03x0n18f2wsyjh6qv57kvgqcwga54rzngwzr6fzlrjsalqw7mxlp"))))
(build-system gnu-build-system)
(arguments
(list #:modules
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 94c92abefa..facfb75abf 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -35,6 +35,7 @@
#:use-module (guix git-download)
#:use-module (guix build-system r)
#:use-module (gnu packages)
+ #:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
@@ -1220,6 +1221,27 @@ demonstration purposes in the @code{AneuFinder} package.")
from Illumina 450k methylation arrays.")
(license license:artistic2.0)))
+(define-public r-bladderbatch
+ (package
+ (name "r-bladderbatch")
+ (version "1.34.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bladderbatch" version
+ 'experiment))
+ (sha256
+ (base32
+ "1dpbaqsqizyi99r0imf5m4lndhhrkyiaqii9bi8rp18fjbjdd72k"))))
+ (properties `((upstream-name . "bladderbatch")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biobase))
+ (home-page "https://bioconductor.org/packages/bladderbatch")
+ (synopsis "Bladder gene expression data illustrating batch effects")
+ (description
+ "This package contains microarray gene expression data on 57 bladder samples from
+5 batches. The data are used as an illustrative example for the sva package.")
+ (license license:artistic2.0)))
+
(define-public r-biscuiteerdata
(package
(name "r-biscuiteerdata")
@@ -1540,6 +1562,30 @@ harmonized subsetting of rows (features) and columns (patients / samples)
across the entire multi-'omics experiment.")
(license license:artistic2.0)))
+(define-public r-parathyroidse
+ (package
+ (name "r-parathyroidse")
+ (version "1.34.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "parathyroidSE" version
+ 'experiment))
+ (sha256
+ (base32
+ "1h33x55c4gbzmh085skqif04wdcvjp2l9fm55qzwws27kwd30c16"))))
+ (properties `((upstream-name . "parathyroidSE")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-summarizedexperiment))
+ (home-page "https://bioconductor.org/packages/parathyroidSE")
+ (synopsis "RangedSummarizedExperiment for RNA-Seq of parathyroid tumors")
+ (description
+ "This package provides @code{RangedSummarizedExperiment} objects of read
+counts in genes and exonic parts for paired-end RNA-Seq data from experiments on
+primary cultures of parathyroid tumors. The sequencing was performed on tumor
+cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).")
+ ;; The author(s) mentions only LGPL without any specific version.
+ (license license:lgpl2.1+)))
+
(define-public r-tcgabiolinksgui-data
(package
(name "r-tcgabiolinksgui-data")
@@ -2090,8 +2136,8 @@ canonical cancer pathways.")
(description
"The project is intended to support the use of @dfn{sequins}(synthetic
sequencing spike-in controls) owned and made available by the Garvan Institute
-of Medical Research. The goal is to provide a standard open source library for
-quantitative analysis, modelling and visualization of spike-in controls.")
+of Medical Research. The goal is to provide a standard library for quantitative
+analysis, modelling, and visualization of spike-in controls.")
(license license:bsd-3)))
(define-public r-aneufinder
@@ -5016,6 +5062,45 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has
previously been used in XCMS.")
(license license:artistic2.0)))
+(define-public r-organism-dplyr
+ (package
+ (name "r-organism-dplyr")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Organism.dplyr" version))
+ (sha256
+ (base32
+ "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as"))))
+ (properties `((upstream-name . "Organism.dplyr")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-annotationdbi
+ r-annotationfilter
+ r-biocfilecache
+ r-dbi
+ r-dbplyr
+ r-dplyr
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-rlang
+ r-rsqlite
+ r-s4vectors
+ r-tibble))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/Organism.dplyr")
+ (synopsis "Dplyr-based access to Bioconductor annotation resources")
+ (description
+ "This package provides an alternative interface to Bioconductor @code{
+annotation} resources, in particular the gene identifier mapping functionality
+of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate
+functionality of the @code{TxDb} packages (e.g.,
+@code{TxDb.Hsapiens.UCSC.hg38.knownGene}).")
+ (license license:artistic2.0)))
+
(define-public r-organismdbi
(package
(name "r-organismdbi")
@@ -5048,6 +5133,61 @@ annotation packages each of which has its own schema by taking advantage of
the fact that each of these packages implements a select methods.")
(license license:artistic2.0)))
+(define-public r-pcaexplorer
+ (package
+ (name "r-pcaexplorer")
+ (version "2.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "pcaExplorer" version))
+ (sha256
+ (base32
+ "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl"))))
+ (properties `((upstream-name . "pcaExplorer")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-annotationdbi
+ r-base64enc
+ r-biomart
+ r-deseq2
+ r-dt
+ r-genefilter
+ r-genomicranges
+ r-ggplot2
+ r-ggrepel
+ r-go-db
+ r-gostats
+ r-heatmaply
+ r-iranges
+ r-knitr
+ r-limma
+ r-nmf
+ r-pheatmap
+ r-plotly
+ r-plyr
+ r-rmarkdown
+ r-s4vectors
+ r-scales
+ r-shiny
+ r-shinyace
+ r-shinybs
+ r-shinydashboard
+ r-summarizedexperiment
+ r-threejs
+ r-tidyr
+ r-topgo))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/federicomarini/pcaExplorer")
+ (synopsis
+ "Interactive Visualization of RNA-seq Data Using a Principal Components Approach")
+ (description
+ "This package provides functionality for interactive visualization of RNA-seq
+datasets based on Principal Components Analysis. The methods provided allow for
+quick information extraction and effective data exploration. A Shiny
+application encapsulates the whole analysis.")
+ (license license:expat)))
+
(define-public r-pcamethods
(package
(name "r-pcamethods")
@@ -5611,6 +5751,38 @@ a scRNA-seq experiment onto the cell-types or individual cells identified in a
different experiment.")
(license license:gpl3)))
+(define-public r-scry
+ (package
+ (name "r-scry")
+ (version "1.8.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scry" version))
+ (sha256
+ (base32
+ "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193"))))
+ (properties `((upstream-name . "scry")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocsingular
+ r-delayedarray
+ r-glmpca
+ r-hdf5array
+ r-matrix
+ r-singlecellexperiment
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/scry.html")
+ (synopsis "Small-count analysis methods for high-dimensional data")
+ (description
+ "Many modern biological datasets consist of small counts that are not
+well fit by standard linear-Gaussian methods such as principal component
+analysis. This package provides implementations of count-based feature
+selection and dimension reduction algorithms. These methods can be used to
+facilitate unsupervised analysis of any high-dimensional data such as
+single-cell RNA-seq.")
+ (license license:artistic2.0)))
+
(define-public r-seqlogo
(package
(name "r-seqlogo")
@@ -6541,9 +6713,10 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/yixuan/RcppNumerical")
(synopsis "Rcpp integration for numerical computing libraries")
- (description "This package provides a collection of open source libraries
-for numerical computing (numerical integration, optimization, etc.) and their
-integration with @code{Rcpp}.")
+ (description
+ "This package provides a collection of libraries for numerical computing
+(numerical integration, optimization, etc.) and their integration with
+@code{Rcpp}.")
(license license:gpl2+)))
(define-public r-apeglm
@@ -7917,6 +8090,16 @@ coordinates.")
(base32
"0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
(build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'make-build-order-reproducible
+ (lambda _
+ (substitute* '("src/SYMPHONY/Cgl/configure.ac"
+ "src/SYMPHONY/Cgl/configure")
+ (("for file in `ls \\*/Makefile.in`")
+ "for file in `ls */Makefile.in | sort`")))))))
(inputs
(list zlib))
(native-inputs
@@ -12985,8 +13168,22 @@ gene expression.")
"0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
(properties `((upstream-name . "bgx")))
(build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'do-not-tune-cflags-for-reproducibility
+ (lambda _
+ (substitute* "configure.ac"
+ (("AX_GCC_ARCHFLAG.*") ""))
+ (delete-file "configure")
+ (invoke "autoreconf" "-vif"))))))
+ (inputs
+ (list boost))
(propagated-inputs
(list r-affy r-biobase r-gcrma r-rcpp))
+ (native-inputs
+ (list autoconf automake))
(home-page "https://bioconductor.org/packages/bgx/")
(synopsis "Bayesian gene expression")
(description
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 054776da5b..ba8c47451f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3985,26 +3985,44 @@ HMMs).")
(define-public htseq
(package
(name "htseq")
- (version "0.12.3")
+ (version "2.0.2")
+ ;; Sources on pypi do not include everything needed to run the tests.
(source (origin
- (method url-fetch)
- (uri (pypi-uri "HTSeq" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/htseq/htseq")
+ (commit (string-append "release_" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0pk41vkzxsbb5nv644325mh8akmz4zdply9r2s80dgg5b21pgp0b"))))
+ "1kbr4ydjjhizz6r5m3xd4f0wj7qnn8zs0vnzghhgaa0yhbya5r19"))))
(build-system python-build-system)
- (native-inputs
- (list python-cython))
- ;; Numpy needs to be propagated when htseq is used as a Python library.
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ ;; Avoid rebuilding the extension. Everything is built during the
+ ;; 'install phase anyway.
+ (delete 'build)
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest" "-v")))))))
(propagated-inputs
- (list python-numpy))
- (inputs
- (list python-pysam python-matplotlib))
- (home-page "https://htseq.readthedocs.io/")
- (synopsis "Analysing high-throughput sequencing data with Python")
+ (list python-matplotlib
+ python-numpy
+ python-pysam))
+ (native-inputs
+ (list python-cython
+ python-pandas
+ python-pytest
+ python-scipy
+ swig))
+ (home-page "https://github.com/htseq")
+ (synopsis "Framework for analyzing high-throughput sequencing data")
(description
- "HTSeq is a Python package that provides infrastructure to process data
-from high-throughput sequencing assays.")
+ "This package provides a framework to process and analyze data from
+high-throughput sequencing (HTS) assays")
(license license:gpl3+)))
(define-public java-htsjdk
@@ -6276,36 +6294,37 @@ subsequent visualization, annotation and storage of results.")
(base32 "0m8wkyvbgvcr5kzc284w8fbhpxwglh2c1xq0yc3yv00a53gs7rv0"))))
(build-system gnu-build-system)
(arguments
- `(#:make-flags
- ,#~(list "BLASFLAGS=-llapack -lopenblas"
- (string-append "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1"
- " -I" (search-input-directory
- %build-inputs "include/simde"))
- "ZLIB=-lz"
- "BIN=plink prettify"
- (string-append "CC=" #$(cc-for-target))
- (string-append "PREFIX=" #$output)
- "DESTDIR=")
- #:phases
- (modify-phases %standard-phases
+ (list
+ #:tests? #false ;TEST_EXTRACT_CHR doesn't produce expected files
+ #:make-flags
+ #~(list "BLASFLAGS=-llapack -lopenblas"
+ "NO_SSE42=1"
+ "NO_AVX2=1"
+ "STATIC_ZSTD="
+ (string-append "CC=" #$(cc-for-target))
+ (string-append "PREFIX=" #$output)
+ "DESTDIR=")
+ #:phases
+ '(modify-phases %standard-phases
(add-after 'unpack 'chdir
- (lambda _ (chdir "1.9")))
- (delete 'configure) ; no "configure" script
+ (lambda _ (chdir "2.0/build_dynamic")))
+ (delete 'configure) ; no "configure" script
(replace 'check
(lambda* (#:key tests? inputs #:allow-other-keys)
(when tests?
- (symlink "plink" "plink19")
- (symlink (search-input-file inputs "/bin/plink") "plink107")
(setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
- (with-directory-excursion "tests"
- ;; The model test fails because of a 0.0001 difference.
- (substitute* "tests.py"
- (("diff -q test1.model test2.model")
- "echo yes"))
- (invoke "bash" "test_setup.sh")
- (invoke "python3" "tests.py"))))))))
+ (with-directory-excursion "../Tests"
+ (substitute* "run_tests.sh"
+ (("^./run_tests" m)
+ (string-append (which "bash") " " m)))
+ (invoke "bash" "run_tests.sh")))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (install-file "plink2"
+ (string-append
+ (assoc-ref outputs "out") "/bin")))))))
(inputs
- (list lapack openblas zlib))
+ (list lapack openblas zlib `(,zstd "lib")))
(native-inputs
(list diffutils plink python simde)) ; for tests
(home-page "https://www.cog-genomics.org/plink/")
@@ -6430,6 +6449,86 @@ Values such as sequence name, sequence description, sequence quality and the
sequence itself can be retrieved from these databases.")
(license license:bsd-3)))
+(define-public python-taggd
+ (package
+ (name "python-taggd")
+ (version "0.3.6")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/SpatialTranscriptomicsResearch/taggd")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0j19ah81z7aqrdljah9hyarp91gvgbk63pz6fz3pdpksy1yqyi6k"))
+ (modules '((guix build utils)))
+ (snippet
+ '(for-each delete-file
+ (find-files "taggd" "\\.c$")))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'disable-broken-tests
+ (lambda _
+ (substitute* "tests/taggd_demultiplex_test.py"
+ (("def test_normal_bam_run")
+ "def _disabled_test_normal_bam_run")))))))
+ (propagated-inputs
+ (list python-numpy python-pysam python-setuptools))
+ (native-inputs
+ (list python-cython))
+ (home-page "https://github.com/SpatialTranscriptomicsResearch/taggd")
+ (synopsis "Genetic barcode demultiplexing")
+ (description "This package provides TagGD barcode demultiplexing utilities
+for Spatial Transcriptomics data.")
+ (license license:bsd-3)))
+
+(define-public stpipeline
+ (package
+ (name "stpipeline")
+ (version "1.8.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "stpipeline" version))
+ (sha256
+ (base32
+ "0har2g42fvaqpiz66lincy86aj1hvwzds26kxhxfamvyvv4721wk"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "requirements.txt"
+ (("argparse.*") "")))))))
+ (propagated-inputs
+ (list htseq
+ python-cython
+ python-invoke
+ python-numpy
+ python-pandas
+ python-pympler
+ python-pysam
+ python-regex
+ python-scikit-learn
+ python-scipy
+ python-seaborn
+ python-setuptools
+ python-sqlitedict
+ python-taggd
+ samtools
+ star))
+ (home-page "https://github.com/SpatialTranscriptomicsResearch/st_pipeline")
+ (synopsis "Pipeline for spatial mapping of unique transcripts")
+ (description
+ "This package provides an automated pipeline for spatial mapping of
+unique transcripts.")
+ (license license:expat)))
+
(define-public sra-tools
(package
(name "sra-tools")
@@ -11292,13 +11391,13 @@ cases include:
(define-public python-mappy
(package
(name "python-mappy")
- (version "2.18")
+ (version "2.24")
(source (origin
(method url-fetch)
(uri (pypi-uri "mappy" version))
(sha256
(base32
- "1a05p7rkmxa6qhm108na8flzj2v45jab06drk59kzk1ip2sgvzqq"))))
+ "1ycszza87p9qvx8mis9v1hry0ac465x1xcxbsn1k45qlxxrzp8im"))))
(build-system python-build-system)
(native-inputs
(list python-cython))
@@ -16097,6 +16196,32 @@ control samples and applying quantile normalization on all markers of
interest.")
(license license:gpl2+))))
+(define-public r-kbet
+ (let ((commit "f35171dfb04c7951b8a09ac778faf7424c4b6bc0")
+ (revision "1"))
+ (package
+ (name "r-kbet")
+ (version (git-version "0.99.6" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/theislab/kBET")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1r91prl2kki3zk694vhlmxdlqh0ixlhs8jfcqw6wc7cdsa0nv67k"))))
+ (properties `((upstream-name . "kBET")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-cluster r-fnn r-ggplot2 r-mass r-rcolorbrewer))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/theislab/kBET")
+ (synopsis "k-nearest neighbour batch effect test")
+ (description
+ "This tool detects batch effects in high-dimensional data based on chi^2-test.")
+ ;; Any version of the GPL
+ (license license:gpl3+))))
+
(define-public ccwl
(package
(name "ccwl")
@@ -16330,3 +16455,271 @@ alignment algorithm. It completes MashMap with a high-performance alignment
module capable of computing base-level alignments for very large sequences.")
(home-page "https://github.com/ekg/wfmash")
(license license:expat)))
+
+(define-public flair
+ (package
+ (name "flair")
+ (version "1.6.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BrooksLabUCSC/flair")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "106swb2q7l20ki58fca1hg95q5f79bgp9gjb0clr2243ycrzyxf8"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:tests? #false ;there are none
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; TODO: implement as a feature of python-build-system (PEP-621,
+ ;; PEP-631, PEP-660)
+ (replace 'build
+ (lambda _
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
+ ;; ZIP does not support timestamps before 1980.
+ (setenv "SOURCE_DATE_EPOCH" "315532800")
+ (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
+ (replace 'install
+ (lambda _
+ (apply invoke "pip" "--no-cache-dir" "--no-input"
+ "install" "--no-deps" "--prefix" #$output
+ (find-files "dist" "\\.whl$")))))))
+ (propagated-inputs
+ (list python-mappy
+ python-ncls
+ python-pybedtools
+ python-pysam
+ python-tqdm))
+ (native-inputs
+ (list python-pypa-build python-setuptools))
+ (home-page "https://flair.readthedocs.io/en/latest/")
+ (synopsis "Full-length alternative isoform analysis of RNA")
+ (description "This package implements FLAIR (Full-Length Alternative
+Isoform analysis of RNA) for the correction, isoform definition, and
+alternative splicing analysis of noisy reads. FLAIR has primarily been used
+for nanopore cDNA, native RNA, and PacBio sequencing reads.")
+ (license license:bsd-3)))
+
+(define-public go-github-com-biogo-graph
+ (package
+ (name "go-github-com-biogo-graph")
+ (version "0.0.0-20150317020928-057c1989faed")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biogo/graph")
+ (commit (go-version->git-ref version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1kpzs5dfd5dsk4mg1g2qjz1prqd84ixhrcxxnf90hq25vxcnk7lh"))))
+ (build-system go-build-system)
+ (arguments
+ '(#:import-path "github.com/biogo/graph"
+ #:tests? #false)) ;TODO: one of 13 tests fails for unknown reasons
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (home-page "https://github.com/biogo/graph")
+ (synopsis "Undirected graph analysis for biogo")
+ (description "The package @code{graph} implements graph manipulation
+functions.")
+ (license license:bsd-3)))
+
+(define-public go-github-com-biogo-store-interval
+ (package
+ (name "go-github-com-biogo-store-interval")
+ (version "0.0.0-20201120204734-aad293a2328f")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biogo/store")
+ (commit (go-version->git-ref version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0skizrp1j6vgbl0g1kmh73picagqlvwckaqs0gkl6rai5lckxj8a"))))
+ (build-system go-build-system)
+ (arguments
+ '(#:import-path "github.com/biogo/store/interval"
+ #:unpack-path "github.com/biogo/store"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github-com-kr-pretty))
+ (home-page "https://github.com/biogo/store")
+ (synopsis "Interval store type for biogo")
+ (description
+ "The @code{store} package provides a number of data store types that are
+useful for bioinformatic analysis.")
+ (license license:bsd-3)))
+
+(define-public go-github-com-biogo-store-kdtree
+ (package
+ (inherit go-github-com-biogo-store-interval)
+ (name "go-github-com-biogo-store-kdtree")
+ (arguments
+ '(#:import-path "github.com/biogo/store/kdtree"
+ #:unpack-path "github.com/biogo/store"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github-com-kr-pretty))
+ (synopsis "kdtree store type for biogo")))
+
+(define-public go-github-com-biogo-store-llrb
+ (package
+ (inherit go-github-com-biogo-store-interval)
+ (name "go-github-com-biogo-store-llrb")
+ (arguments
+ '(#:import-path "github.com/biogo/store/llrb"
+ #:unpack-path "github.com/biogo/store"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github-com-kr-pretty))
+ (synopsis "LLRB store for biogo")))
+
+(define-public go-github-com-biogo-store-step
+ (package
+ (inherit go-github-com-biogo-store-interval)
+ (name "go-github-com-biogo-store-step")
+ (arguments
+ '(#:import-path "github.com/biogo/store/step"
+ #:unpack-path "github.com/biogo/store"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github-com-kr-pretty))
+ (synopsis "Step store for biogo")))
+
+(define-public go-github-com-biogo-hts-bam
+ (package
+ (name "go-github-com-biogo-hts-bam")
+ (version "1.4.3")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biogo/hts")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "013ga6ilc4m3hyfr3yyiva9g4vs81afhj73v2sy7r75b5zxw7lx1"))))
+ (build-system go-build-system)
+ (arguments
+ '(#:import-path "github.com/biogo/hts/bam"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (home-page "https://github.com/biogo/hts")
+ (synopsis "HTS BAM module for biogo")
+ (description "This package provides tools for handling BAM files.")
+ (license license:bsd-3)))
+
+(define-public go-github-com-biogo-hts-sam
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-sam")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/sam"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (synopsis "HTS SAM module for biogo")
+ (description "This package provides tools for handling SAM files.")))
+
+(define-public go-github-com-biogo-hts-tabix
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-tabix")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/tabix"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (synopsis "HTS Tabix module for biogo")
+ (description "This package provides tools for handling Tabix files.")))
+
+(define-public go-github-com-biogo-hts-bgzf
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-bgzf")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/bgzf"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (synopsis "HTS bgzf module for biogo")
+ (description "This package provides tools for handling bgzf files.")))
+
+(define-public go-github-com-biogo-hts-cram
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-cram")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/cram"
+ #:unpack-path "github.com/biogo/hts"
+ #:tests? #false)) ;require network access
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github.com-ulikunitz-xz
+ go-github-com-kortschak-utter))
+ (synopsis "HTS CRAM module for biogo")
+ (description "This package provides tools for handling CRAM files.")))
+
+(define-public go-github-com-biogo-hts-csi
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-csi")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/csi"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (synopsis "Coordinate sorted indexing for biogo")
+ (description "This package implements CSIv1 and CSIv2 coordinate sorted
+indexing.")))
+
+(define-public go-github-com-biogo-hts-fai
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-fai")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/fai"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (synopsis "Fasta sequence file index handling for biogo")
+ (description "This package implements FAI fasta sequence file index
+handling.")))
+
+(define-public go-github-com-biogo-biogo
+ (package
+ (name "go-github-com-biogo-biogo")
+ (version "1.0.4")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biogo/biogo")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0ali1mqf3dc26myv6l7wmqfr8i25461rbq3qdad8s0wi29622199"))))
+ (build-system go-build-system)
+ (arguments
+ '(#:import-path "github.com/biogo/biogo"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github-com-biogo-store-interval
+ go-github-com-biogo-store-kdtree
+ go-github-com-biogo-store-llrb
+ go-github-com-biogo-store-step
+ go-github-com-biogo-hts-bam
+ go-github-com-biogo-graph))
+ (home-page "https://github.com/biogo/biogo")
+ (synopsis "Bioinformatics library for Go")
+ (description
+ "Bíogo is a bioinformatics library for the Go language.")
+ (license license:bsd-3)))
diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm
index fcb59368e9..4fc250e7b6 100644
--- a/gnu/packages/bittorrent.scm
+++ b/gnu/packages/bittorrent.scm
@@ -16,6 +16,7 @@
;;; Copyright © 2021 Josselin Poiret <josselin.poiret@protonmail.ch>
;;; Copyright © 2022 Brice Waegeneire <brice@waegenei.re>
;;; Copyright © 2022 Jacob Hart <hartja1@yahoo.com>
+;;; Copyright © 2022 Simon Streit <simon@netpanic.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -132,7 +133,7 @@
(string-append gui "/share/man/man1/transmission-gtk.1"))
#t))))))
(inputs
- (list libevent curl openssl zlib gtk+))
+ (list libevent curl openssl zlib gtk+ libappindicator))
(native-inputs
(list intltool pkg-config))
(home-page "https://transmissionbt.com/")
diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index d19cf55bc4..b521b57ecd 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -7,7 +7,7 @@
;;; Copyright © 2016, 2017 Danny Milosavljevic <dannym@scratchpost.org>
;;; Copyright © 2016, 2017 David Craven <david@craven.ch>
;;; Copyright © 2017, 2018, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018–2022 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 nee <nee@cock.li>
;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
@@ -1157,14 +1157,14 @@ tools, and more.")
(define-public os-prober
(package
(name "os-prober")
- (version "1.80")
+ (version "1.81")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://debian/pool/main/o/os-prober/os-prober_"
version ".tar.xz"))
(sha256
- (base32 "13z3rshgz5xj0328a80wavdimjw925yha9s1ks398sq0kn5w6qw0"))))
+ (base32 "10w8jz6mqhp0skdcam9mpgv79vx1sv7lkpra3rqjg0jkhvn2in9g"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build gnu-build-system)
diff --git a/gnu/packages/browser-extensions.scm b/gnu/packages/browser-extensions.scm
index 1012e4b643..63bd11b226 100644
--- a/gnu/packages/browser-extensions.scm
+++ b/gnu/packages/browser-extensions.scm
@@ -51,7 +51,7 @@ supported content to the Kodi media center.")
(define ublock-origin
(package
(name "ublock-origin")
- (version "1.43.0")
+ (version "1.44.0")
(home-page "https://github.com/gorhill/uBlock")
(source (origin
(method git-fetch)
@@ -62,7 +62,7 @@ supported content to the Kodi media center.")
(file-name (git-file-name name version))
(sha256
(base32
- "0w0by41v1s1cbd3bfjlb7kxr2bl6r5z3jvizlx02x14hqlppma9k"))))
+ "0sws7xd8nvxnzcyw92i9sc5xv3hpqw1kzdj9vm8bhfxlh042l7ly"))))
(build-system gnu-build-system)
(outputs '("xpi" "firefox" "chromium"))
(arguments
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 1134b8eb3c..38a7ee2783 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -102,7 +102,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
(define-public bear
(package
(name "bear")
- (version "3.0.19")
+ (version "3.0.20")
(source
(origin
(method git-fetch)
@@ -111,7 +111,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "05jbcx5m923dg27j3i442hc73hdci5n7vp7a671x1w7bdivgqg96"))))
+ (base32 "0k89ccp9vz3x71w3r2wfpng9b8s0rxp4qr0ch9q32wq6y1ik847j"))))
(build-system cmake-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm
index 39f048e993..d7d649488b 100644
--- a/gnu/packages/c.scm
+++ b/gnu/packages/c.scm
@@ -463,7 +463,7 @@ as dictionaries, skip lists, and memory pools.")
(define-public packcc
(package
(name "packcc")
- (version "1.7.2")
+ (version "1.8.0")
(home-page "https://github.com/arithy/packcc")
(source (origin
(method git-fetch)
@@ -473,7 +473,7 @@ as dictionaries, skip lists, and memory pools.")
(file-name (git-file-name name version))
(sha256
(base32
- "1mb6ys5ylvjz0xpq6769ir98s80p98s9ahd0c9k8p2ra1w20vz33"))))
+ "0b25p7ri1l2l20awyknljfnj7r4rg7cf2x3bljijx5q6j8rxdcsg"))))
(build-system gnu-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm
index 56a4ab8a10..6391bd6fec 100644
--- a/gnu/packages/cdrom.scm
+++ b/gnu/packages/cdrom.scm
@@ -408,58 +408,59 @@ or @command{xorrisofs} to create ISO 9660 images.")
(define-public dvdisaster
(package
(name "dvdisaster")
- (version "0.79.9")
+ (version "0.79.10")
(source
(origin
(method url-fetch)
(uri (string-append "https://dvdisaster.jcea.es/downloads/dvdisaster-"
version ".tar.bz2"))
(sha256
- (base32 "1hz3fvqfdrwb7dn6ggqkpcgyjag37ivm1layw27ncjz9glklxjbr"))))
+ (base32 "1s3z4098ixdjr3gjs36fg7rykqs0zz1rnvz2v9rvyj0s5zv9y2nx"))))
(build-system gnu-build-system)
(inputs
(list gtk+-2))
(native-inputs
- `(("gettext" ,gettext-minimal)
- ("pkg-config" ,pkg-config)
- ("which" ,which)))
+ (list gettext-minimal pkg-config which))
(arguments
- `(;; Parallel builds appear to be unsafe, see
- ;; <http://hydra.gnu.org/build/49331/nixlog/1/raw>.
- #:parallel-build? #f
- #:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (with-directory-excursion "regtest"
- (substitute* "common.bash"
- (("ISODIR=/var/tmp/regtest") "ISODIR=/tmp"))
- (for-each invoke (find-files "." "rs.*\\.bash")))))
- (add-after 'install 'install-desktop
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((datadir (string-append (assoc-ref outputs "out") "/share")))
- (substitute* "contrib/dvdisaster.desktop"
- (("dvdisaster48.png") "dvdisaster.png"))
- (install-file "contrib/dvdisaster.desktop"
- (string-append datadir "/applications"))
- (for-each
- (lambda (png)
- (let* ((size (substring png
- (string-index png char-set:digit)
- (string-rindex png #\.)))
- (icondir (string-append datadir "/icons/"
- size "x" size "/apps")))
- (mkdir-p icondir)
- (copy-file png (string-append icondir "/dvdisaster.png"))))
- (find-files "contrib" "dvdisaster[0-9]*\\.png"))
- (mkdir-p (string-append datadir "/pixmaps"))
- (copy-file "contrib/dvdisaster48.xpm"
- (string-append datadir "/pixmaps/dvdisaster.xpm")))))
- (add-after 'install 'remove-uninstall-script
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out")))
- (delete-file
- (string-append out "/bin/dvdisaster-uninstall.sh"))))))))
+ (list #:parallel-build? #f ; http://hydra.gnu.org/build/49331/nixlog/1/raw
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (with-directory-excursion "regtest"
+ (substitute* "common.bash"
+ (("ISODIR=/var/tmp/regtest") "ISODIR=/tmp"))
+ (for-each invoke (find-files "." "rs.*\\.bash")))))
+ (add-after 'install 'install-desktop
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((datadir (string-append (assoc-ref outputs "out")
+ "/share")))
+ (substitute* "contrib/dvdisaster.desktop"
+ (("dvdisaster48.png") "dvdisaster.png"))
+ (install-file "contrib/dvdisaster.desktop"
+ (string-append datadir "/applications"))
+ (for-each
+ (lambda (png)
+ (let* ((size (substring
+ png
+ (string-index png char-set:digit)
+ (string-rindex png #\.)))
+ (icondir (string-append datadir "/icons/"
+ size "x" size "/apps")))
+ (mkdir-p icondir)
+ (copy-file png
+ (string-append icondir
+ "/dvdisaster.png"))))
+ (find-files "contrib" "dvdisaster[0-9]*\\.png"))
+ (mkdir-p (string-append datadir "/pixmaps"))
+ (copy-file "contrib/dvdisaster48.xpm"
+ (string-append datadir
+ "/pixmaps/dvdisaster.xpm")))))
+ (add-after 'install 'remove-uninstall-script
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out")))
+ (delete-file
+ (string-append out "/bin/dvdisaster-uninstall.sh"))))))))
(home-page "https://dvdisaster.jcea.es/")
(synopsis "Error correcting codes for optical media images")
(description "Optical media (CD,DVD,BD) keep their data only for a
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index aa7dd41af4..d7920ee27b 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm