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authorRicardo Wurmus <rekado@elephly.net>2021-02-11 21:31:24 +0100
committerRicardo Wurmus <rekado@elephly.net>2021-02-11 21:33:37 +0100
commitde4fc492700efaf9d8fd4614dfba7fb712446c0c (patch)
tree78014e906ce584e20c8a07ab37fb84704e0fe3b8 /gnu/packages
parentcf3e7038209309316ac676a685000ba20106f611 (diff)
downloadguix-de4fc492700efaf9d8fd4614dfba7fb712446c0c.tar.gz
guix-de4fc492700efaf9d8fd4614dfba7fb712446c0c.zip
gnu: r-scran: Update to 1.18.5.
* gnu/packages/bioconductor.scm (r-scran): Update to 1.18.5.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioconductor.scm4
1 files changed, 2 insertions, 2 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9dbeb915fa..36a104f1f4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8979,14 +8979,14 @@ quality control.")
(define-public r-scran
(package
(name "r-scran")
- (version "1.18.1")
+ (version "1.18.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
- "1zap12rm61z2hg6ykknbif478nr7g468v8mp50bj5hqgi69ywcww"))))
+ "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
e-account-details, username->id, add-account remove-account) (username->contacts, remove-contact, add-contact, set-account-details) (set-all-moderators, username->all-moderators?, username->moderators) (set-moderator): Adjust accordingly. (with-retries, send-dbus, dbus-available-services) (dbus-service-available?): Move to ... * gnu/build/dbus-service.scm: ... this new module. (send-dbus): Rewrite to use the Guile AC/D-Bus library. (%dbus-query-timeout, sleep*): New variables. (%current-dbus-connection): New parameter. (initialize-dbus-connection!, argument->signature-type) (call-dbus-method): New procedures. (dbus-available-services): Adjust accordingly. * gnu/local.mk (GNU_SYSTEM_MODULES): Register new module. * gnu/packages/glib.scm (dbus-for-jami): New variable. * gnu/services/telephony.scm: (jami-configuration)[dbus]: Default to dbus-for-jami. (jami-dbus-session-activation): Write a D-Bus daemon configuration file at '/var/run/jami/session-local.conf'. (jami-shepherd-services): Add the closure of guile-ac-d-bus and guile-fibers as extensions. Adjust imported modules. Remove no longer used parameters. <jami-dbus-session>: Use a PID file, avoiding the need for the manual synchronization. <jami>: Set DBUS_SESSION_BUS_ADDRESS environment variable. Poll using 'jami-service-available?' instead of 'dbus-service-available?'. * gnu/tests/telephony.scm (run-jami-test): Add needed Guile extensions. Set DBUS_SESSION_BUS_ADDRESS environment variable. Adjust all tests to use 'jami-service-available?' to determine if the service is started rather than the now problematic Shepherd's 'start-service'. Maxim Cournoyer 2022-01-13services: Adjust the jami service for the upgraded jami....* gnu/services/telephony.scm (jami-configuration)[jamid]: Rename libring to libjami. * gnu/services/telephony.scm (jami-configuration->command-line-arguments): Adjust daemon file name. * gnu/services/telephony.scm (jami-service-type): Adjust doc. * gnu/tests/telephony.scm (run-jami-test): Check for 'jamid' process, not 'dring'. * doc/guix.texi (Telephony Services): Adjust doc for the jami-qt to jami and libring to libjami packages renaming. Maxim Cournoyer 2021-09-26tests: Reduce boilerplate for users of 'system-test-runner'....* gnu/tests/audio.scm, gnu/tests/base.scm, gnu/tests/ci.scm, gnu/tests/cups.scm, gnu/tests/databases.scm, gnu/tests/desktop.scm, gnu/tests/dict.scm, gnu/tests/docker.scm, gnu/tests/file-sharing.scm, gnu/tests/ganeti.scm, gnu/tests/guix.scm, gnu/tests/ldap.scm, gnu/tests/linux-modules.scm, gnu/tests/mail.scm, gnu/tests/messaging.scm, gnu/tests/monitoring.scm, gnu/tests/networking.scm, gnu/tests/nfs.scm, gnu/tests/package-management.scm, gnu/tests/reconfigure.scm, gnu/tests/rsync.scm, gnu/tests/security-token.scm, gnu/tests/singularity.scm, gnu/tests/ssh.scm, gnu/tests/telephony.scm, gnu/tests/version-control.scm, gnu/tests/virtualization.scm, gnu/tests/web.scm: Remove (mkdir #$output) (chdir #$output) and pass #$output as argument to 'system-test-runner'. Ludovic Courtès 2021-09-25tests: Adjust to SRFI-64 as found in Guile 3.0.7....In Guile 3.0.7, 'test-runner-current' is set to #f upon 'test-end'. Consequently, the previous strategy, where we'd call 'test-runner-current' after 'test-end', no longer works. Instead, set the test runner in each test right before 'test-begin'. * gnu/build/marionette.scm (system-test-runner): New procedure. * gnu/tests/audio.scm (run-mpd-test): Replace (exit (= ...)) idiom by (test-runner-current (system-test-runner)). * gnu/tests/base.scm (run-basic-test) (run-cleanup-test, run-mcron-test, run-nss-mdns-test): Likewise. * gnu/tests/ci.scm (run-laminar-test): Likewise. * gnu/tests/cups.scm (run-cups-test): Likewise. * gnu/tests/databases.scm (run-memcached-test) (run-postgresql-test, run-mysql-test): Likewise. * gnu/tests/desktop.scm (run-elogind-test): Likewise. * gnu/tests/dict.scm (run-dicod-test): Likewise. * gnu/tests/docker.scm (run-docker-test): Likewise. (run-docker-system-test): Likewise. * gnu/tests/file-sharing.scm (run-transmission-daemon-test): Likewise. * gnu/tests/ganeti.scm (run-ganeti-test): Likewise. * gnu/tests/guix.scm (run-guix-build-coordinator-test): Likewise. (run-guix-data-service-test): Likewise. * gnu/tests/ldap.scm (run-ldap-test): Likewise. * gnu/tests/linux-modules.scm (run-loadable-kernel-modules-test-base): Likewise. * gnu/tests/mail.scm (run-opensmtpd-test) (run-exim-test, run-dovecot-test, run-getmail-test): Likewise. * gnu/tests/messaging.scm (run-xmpp-test) (run-bitlbee-test, run-quassel-test): Likewise. * gnu/tests/monitoring.scm (run-prometheus-node-exporter-server-test) (run-zabbix-server-test): Likewise. * gnu/tests/networking.scm (run-inetd-test, run-openvswitch-test) (run-dhcpd-test, run-tor-test, run-iptables-test, run-ipfs-test): Likewise. * gnu/tests/nfs.scm (run-nfs-test) (run-nfs-server-test, run-nfs-root-fs-test): Likewise. * gnu/tests/package-management.scm (run-nix-test): Likewise. * gnu/tests/reconfigure.scm (run-switch-to-system-test) (run-upgrade-services-test, run-install-bootloader-test): Likewise. * gnu/tests/rsync.scm (run-rsync-test): Likewise. * gnu/tests/security-token.scm (run-pcscd-test): Likewise. * gnu/tests/singularity.scm (run-singularity-test): Likewise. * gnu/tests/ssh.scm (run-ssh-test): Likewise. * gnu/tests/telephony.scm (run-jami-test): Likewise. * gnu/tests/version-control.scm (run-cgit-test): Likewise. (run-git-http-test, run-gitolite-test, run-gitile-test): Likewise. * gnu/tests/virtualization.scm (run-libvirt-test, run-childhurd-test): Likewise. * gnu/tests/web.scm (run-webserver-test, run-php-fpm-test) (run-hpcguix-web-server-test, run-tailon-test, run-patchwork-test): Likewise. Ludovic Courtès 2021-08-29Migrate to the new 'targets' field of bootloader-configuration....The old 'target' field is deprecated; adjust the sources to use the new 'targets' one instead. * doc/guix-cookbook.texi<target>: Replace by 'targets'. * gnu/bootloader/grub.scm: Likewise. * gnu/installer/parted.scm: Likewise. * gnu/machine/digital-ocean.scm: Likewise. * gnu/system/examples/asus-c201.tmpl: Likewise * gnu/system/examples/bare-bones.tmpl: Likewise * gnu/system/examples/bare-hurd.tmpl: Likewise * gnu/system/examples/beaglebone-black.tmpl: Likewise * gnu/system/examples/desktop.tmpl: Likewise * gnu/system/examples/docker-image.tmpl: Likewise * gnu/system/examples/lightweight-desktop.tmpl: Likewise * gnu/system/examples/vm-image.tmpl: Likewise * gnu/system/examples/yggdrasil.tmpl: Likewise * gnu/system/hurd.scm: Likewise * gnu/system/images/hurd.scm: Likewise * gnu/system/images/novena.scm: Likewise * gnu/system/images/pine64.scm: Likewise * gnu/system/images/pinebook-pro.scm: Likewise * gnu/system/images/rock64.scm: Likewise * gnu/system/install.scm: Likewise * gnu/system/vm.scm: Likewise * gnu/tests.scm: Likewise * gnu/tests/ganeti.scm: Likewise * gnu/tests/install.scm: Likewise * gnu/tests/nfs.scm: Likewise * gnu/tests/telephony.scm: Likewise * tests/boot-parameters.scm: Likewise * tests/system.scm: Likewise Maxim Cournoyer 2021-08-02Reinstate "services: Add a service for Jami."...This reverts commit 4673f817938d9d2b1b40a072ab2e0c44a32ccc97, which reverted commit 69dcc24c9f0cdfea674eb690e7755d26a25ced2b with the fix detailed below. Thanks to Christopher Baines for reporting the failure and proposing a fix. * guix/self.scm (compiled-guix) [*system-test-modules*]: Add the test data files via the 'extra-files' argument. * gnu/local.mk (dist_patch_DATA): Move the tests/data/jami-dummy-account.dat file to... * gnu/local.mk (MODULES_NOT_COMPILED): ... here. Maxim Cournoyer 2021-08-02Revert "services: Add a service for Jami."...This reverts commit 69dcc24c9f0cdfea674eb690e7755d26a25ced2b. It broke 'guix pull'. Maxim Cournoyer 2021-08-02services: Add a service for Jami....* gnu/services/telephony.scm (string-or-computed-file?) (string-list?, account-fingerprint-list?): New procedures. (maybe-string-list, maybe-account-fingerprint-list) (maybe-boolean, maybe-string, jami-account-list): New configuration field types. (serialize-string-list, serialize-boolean, serialize-string) (jami-account, jami-account->alist, jami-configuration) (jami-account-list?, jami-account-list-maybe): New procedures. (%jami-accounts): New variable. (jami-configuration->command-line-arguments): New procedure. (jami-dbus-session-activation, jami-shepherd-services): New procedures. (jami-service-type): New variable. * gnu/build/jami-service.scm: New file. * gnu/tests/data/jami-dummy-account.dat: Likewise. * gnu/tests/telephony.scm: Likewise. * gnu/local.mk (GNU_SYSTEM_MODULES): Register them. * Makefile.am (SCM_TESTS): Register the test file. (dist_patch_DATA): Register the new data file. * doc/guix.texi (Telephony Services): Document it. Maxim Cournoyer