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2023-11-03gnu: r-trajectoryutils: Update to 1.10.0....* gnu/packages/bioconductor.scm (r-trajectoryutils): Update to 1.10.0. Change-Id: I55d3dd66077721eba7b5de5c6f4d8e8dce18243c Ricardo Wurmus
2023-11-03gnu: r-transcriptr: Update to 1.30.0....* gnu/packages/bioconductor.scm (r-transcriptr): Update to 1.30.0. Change-Id: I63bdde62a0afe545c5538b8dc8c84c5b220d659b Ricardo Wurmus
2023-11-03gnu: r-trackviewer: Update to 1.38.0....* gnu/packages/bioconductor.scm (r-trackviewer): Update to 1.38.0. Change-Id: I7e13ad40fef06848d4002875c6640406f0e2c8cd Ricardo Wurmus
2023-11-03gnu: r-tkwidgets: Update to 1.80.0....* gnu/packages/bioconductor.scm (r-tkwidgets): Update to 1.80.0. Change-Id: I3164946bdf1665872b5d96acdaa0b53103bb9440 Ricardo Wurmus
2023-11-03gnu: r-tcgautils: Update to 1.22.0....* gnu/packages/bioconductor.scm (r-tcgautils): Update to 1.22.0. Change-Id: I032c2f7fe6dcd40ade4ed736052e1caad79610e6 Ricardo Wurmus
2023-11-03gnu: r-singscore: Update to 1.22.0....* gnu/packages/bioconductor.scm (r-singscore): Update to 1.22.0. Change-Id: Iad1bd17ce29ecb3118a4998ab53c3deebbe3354d Ricardo Wurmus
2023-11-03gnu: r-simplifyenrichment: Update to 1.12.0....* gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 1.12.0. Change-Id: I3ad0ec6e0e990048d1847e5915d9a63b7efc1db4 Ricardo Wurmus
2023-11-03gnu: r-shortread: Update to 1.60.0....* gnu/packages/bioconductor.scm (r-shortread): Update to 1.60.0. Change-Id: I130c2f6de4a31c639da2cbddc5d3dd9ef35e3dfb Ricardo Wurmus
2023-11-03gnu: r-shinymethyl: Update to 1.38.0....* gnu/packages/bioconductor.scm (r-shinymethyl): Update to 1.38.0. Change-Id: I84bf96c91ec31578af9522ccd69693c91d8ac72f Ricardo Wurmus
2023-11-03gnu: r-sesame: Update to 1.20.0....* gnu/packages/bioconductor.scm (r-sesame): Update to 1.20.0. Change-Id: I9ab2fb2cf0a8e65308820b0e93ed6a9c74fd11e5 Ricardo Wurmus
2023-11-03gnu: r-seqpattern: Update to 1.34.0....* gnu/packages/bioconductor.scm (r-seqpattern): Update to 1.34.0. Change-Id: Iaca71f59f8399e2fe27ab545b128dbc16097ac72 Ricardo Wurmus
2023-11-03gnu: r-seqlogo: Update to 1.68.0....* gnu/packages/bioconductor.scm (r-seqlogo): Update to 1.68.0. Change-Id: Ie71132c07d393633dfc20b2dd43f29621627a615 Ricardo Wurmus
2023-11-03gnu: r-seqarray: Update to 1.42.0....* gnu/packages/bioconductor.scm (r-seqarray): Update to 1.42.0. Change-Id: I0efc86ef3f9c0a798ee7cb4434092bea8aa143c5 Ricardo Wurmus
2023-11-03gnu: r-scry: Update to 1.14.0....* gnu/packages/bioconductor.scm (r-scry): Update to 1.14.0. Change-Id: I3138f53e6133f96ecd1efb0ccbc002a53d04b6ab Ricardo Wurmus
2023-11-03gnu: r-scmap: Update to 1.24.0....* gnu/packages/bioconductor.scm (r-scmap): Update to 1.24.0. Change-Id: I894d2be7b665d64a3278027b93d36910dcc59114 Ricardo Wurmus
2023-11-03gnu: r-scdblfinder: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-scdblfinder): Update to 1.16.0. Change-Id: I9978ed4ba4de89ac1a97a4606498eb0bffe4b47c Ricardo Wurmus
2023-11-03gnu: r-scannotatr: Update to 1.8.0....* gnu/packages/bioconductor.scm (r-scannotatr): Update to 1.8.0. Change-Id: Ic38511c26633c146aeab43e51420f8cb66d81557 Ricardo Wurmus
2023-11-03gnu: r-saturn: Update to 1.10.0....* gnu/packages/bioconductor.scm (r-saturn): Update to 1.10.0. Change-Id: I2d79ca29c9fe303fef07d046fab802932f62ef6c Ricardo Wurmus
2023-11-03gnu: r-rtracklayer: Update to 1.62.0....* gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.62.0. Change-Id: Icc6a2074292ad9426cb9eb2a50c31b307a724202 Ricardo Wurmus
2023-11-03gnu: r-rtcgatoolbox: Update to 2.32.1....* gnu/packages/bioconductor.scm (r-rtcgatoolbox): Update to 2.32.1. [propagated-inputs]: Remove r-rcircos. Change-Id: I1676a7c25e97fa990e855c2d26ecd268b08c8d94 Ricardo Wurmus
2023-11-03gnu: r-rtcga: Update to 1.32.0....* gnu/packages/bioconductor.scm (r-rtcga): Update to 1.32.0. Change-Id: I34d49096aee9329730b009209d60471f0b97ce1a Ricardo Wurmus
2023-11-03gnu: r-rsamtools: Update to 2.18.0....* gnu/packages/bioconductor.scm (r-rsamtools): Update to 2.18.0. [propagated-inputs]: Add r-zlibbioc. Change-Id: I5276250da7f390358cb62e3934aedf61b4a36d67 Ricardo Wurmus
2023-11-03gnu: r-rhdf5filters: Update to 1.14.0....* gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.14.0. [native-inputs]: Remove r-biocstyle and r-rmarkdown. Change-Id: I14e7f0e2c5986c35b9c6ca36dcb3f4127cf348aa Ricardo Wurmus
2023-11-03gnu: r-rhdf5: Update to 2.46.0....* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.46.0. [propagated-inputs]: Add r-s4vectors. Change-Id: I6423f6b8a92b2053039c2af7f52cbfe047d9f75f Ricardo Wurmus
2023-11-03gnu: r-regioner: Update to 1.34.0....* gnu/packages/bioconductor.scm (r-regioner): Update to 1.34.0. Change-Id: I1b8b0d031065a2462d9a812a2ceccf58bf31ff37 Ricardo Wurmus
2023-11-03gnu: r-rcas: Update to 1.28.2....* gnu/packages/bioconductor.scm (r-rcas): Update to 1.28.2. Change-Id: I2406be8ad960d235124eabd3d1dab9605994d707 Ricardo Wurmus
2023-11-03gnu: r-rbgl: Update to 1.78.0....* gnu/packages/bioconductor.scm (r-rbgl): Update to 1.78.0. Change-Id: I2f99033a91cfd9085df7388bb51418887a70735d Ricardo Wurmus
2023-11-03gnu: r-protgenerics: Update to 1.34.0....* gnu/packages/bioconductor.scm (r-protgenerics): Update to 1.34.0. Change-Id: Iede0129b8b5a5164f7efe982d4863e61e526444b Ricardo Wurmus
2023-11-03gnu: r-piano: Update to 2.18.0....* gnu/packages/bioconductor.scm (r-piano): Update to 2.18.0. Change-Id: I3511dae77061b5fca24b8b077b1fba34d613be7c Ricardo Wurmus
2023-11-03gnu: r-pfamanalyzer: Update to 1.2.0....* gnu/packages/bioconductor.scm (r-pfamanalyzer): Update to 1.2.0. Change-Id: I31ab67f4ac5b5846038e4896fc44a65da8717b27 Ricardo Wurmus
2023-11-03gnu: r-pcamethods: Update to 1.94.0....* gnu/packages/bioconductor.scm (r-pcamethods): Update to 1.94.0. Change-Id: I67ae7bd85bf7353b038f85842b930337878ea313 Ricardo Wurmus
2023-11-03gnu: r-pcaexplorer: Update to 2.28.0....* gnu/packages/bioconductor.scm (r-pcaexplorer): Update to 2.28.0. Change-Id: If0d0369c364c5c665a9cdfe71fb6ce7c4b466b40 Ricardo Wurmus
2023-11-03gnu: r-oscope: Update to 1.32.0....* gnu/packages/bioconductor.scm (r-oscope): Update to 1.32.0. Change-Id: Ie2f593d31f51d6fd4954d6eaa633a60e02f8cbee Ricardo Wurmus
2023-11-03gnu: r-organismdbi: Update to 1.44.0....* gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.44.0. Change-Id: I8c018e323daab03e758e8690b31a75c06ae7d748 Ricardo Wurmus
2023-11-03gnu: r-organism-dplyr: Update to 1.30.1....* gnu/packages/bioconductor.scm (r-organism-dplyr): Update to 1.30.1. Change-Id: Ib8c833cd10fa5cc845c954b97a587279cb29127f Ricardo Wurmus
2023-11-03gnu: r-mzr: Update to 2.36.0....* gnu/packages/bioconductor.scm (r-mzr): Update to 2.36.0. Change-Id: I72f45ac3dbfea48e1327ab6bf87d5ee3eebd5b3d Ricardo Wurmus
2023-11-03gnu: r-mzid: Update to 1.40.0....* gnu/packages/bioconductor.scm (r-mzid): Update to 1.40.0. Change-Id: Ie85887d844236cc8217f7ccabec284fc4040d3f7 Ricardo Wurmus
2023-11-03gnu: r-msnid: Update to 1.36.0....* gnu/packages/bioconductor.scm (r-msnid): Update to 1.36.0. Change-Id: I2461051259efcfa92694569689a374a60224e07c Ricardo Wurmus
2023-11-03gnu: r-msnbase: Update to 2.28.0....* gnu/packages/bioconductor.scm (r-msnbase): Update to 2.28.0. Change-Id: If193d2756124c63fb308c62c4803378641b5a5d1 Ricardo Wurmus
2023-11-03gnu: r-msa: Update to 1.34.0....* gnu/packages/bioconductor.scm (r-msa): Update to 1.34.0. Change-Id: Ief67a7396f222a640a3c481cc1ac66c725204e00 Ricardo Wurmus
2023-11-03gnu: r-mutationalpatterns: Update to 3.12.0....* gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.12.0. Change-Id: Ia0dd49b80c91865677cdba3f03f6acabfb5b155f Ricardo Wurmus
2023-11-03gnu: r-muscat: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-muscat): Update to 1.16.0. Change-Id: Idf30d38c285a0fddd2aab924ca3017dfd25b587a Ricardo Wurmus
2023-11-03gnu: r-mmuphin: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-mmuphin): Update to 1.16.0. Change-Id: Ib8d6583456e76abea75d08dc21aaedffe5a46053 Ricardo Wurmus
2023-11-03gnu: r-mfuzz: Update to 2.62.0....* gnu/packages/bioconductor.scm (r-mfuzz): Update to 2.62.0. Change-Id: If08902a17ecf2be089677634ee9d348e46295245 Ricardo Wurmus
2023-11-03gnu: r-methylkit: Update to 1.28.0....* gnu/packages/bioconductor.scm (r-methylkit): Update to 1.28.0. Change-Id: I3040045d082d80a8e1f1e68691ad3c7bc561d3d3 Ricardo Wurmus
2023-11-03gnu: r-metaneighbor: Update to 1.22.0....* gnu/packages/bioconductor.scm (r-metaneighbor): Update to 1.22.0. Change-Id: I24a17f7af9ccfb6a942bd0f24b187948d16bc07a Ricardo Wurmus
2023-11-03gnu: r-metagenomeseq: Update to 1.43.0....* gnu/packages/bioconductor.scm (r-metagenomeseq): Update to 1.43.0. Change-Id: Ia7e010752cb480bec3270f79dca748e2ccf4c53b Ricardo Wurmus
2023-11-03gnu: r-mdqc: Update to 1.64.0....* gnu/packages/bioconductor.scm (r-mdqc): Update to 1.64.0. Change-Id: If60e2e8f16e27362542298799dd30c70f91840fe Ricardo Wurmus
2023-11-03gnu: r-maser: Update to 1.20.0....* gnu/packages/bioconductor.scm (r-maser): Update to 1.20.0. Change-Id: I02074e2ef18c4e2b3414d1d1ac3b325b3a28ee8b Ricardo Wurmus
2023-11-03gnu: r-manor: Update to 1.74.0....* gnu/packages/bioconductor.scm (r-manor): Update to 1.74.0. Change-Id: I646db2726748aefdd8f6a437571cd5e9ad613862 Ricardo Wurmus
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2023-12-22tests: jami: Double timeouts....* gnu/tests/telephony.scm (run-jami-test): Pass #:timeout to ‘wait-for-service’. Double number passed to ‘with-retries’. Change-Id: Ib3c81a770c2d52b2eb40e4f28abc8e33f5c71fc8 Ludovic Courtès 2023-12-22tests: jami: Check status of Jami D-Bus session....* gnu/tests/telephony.scm (run-jami-test)["dbus session is up"]: New test. Reviewed-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Change-Id: Ifa9b57c732f3c64e1ec6bf3028b69a57cee56320 Ludovic Courtès 2023-12-14services: Add rspamd-service-type....* gnu/services/mail.scm (rspamd-service-type): New variable. * gnu/tests/mail.scm (%test-rspamd): New variable. * doc/guix.texi: Document it. Co-authored-by: Saku Laesvuori <saku@laesvuori.fi> Change-Id: I7196643f087ffe9fc91aab231b69d5ed8dc9d198 Signed-off-by: Ludovic Courtès <ludo@gnu.org> Thomas Ieong 2023-12-14tests: childhurd: Prefer “-cpu max” over “-cpu host”....“-cpu host” can sometimes, for unclear reasons, lead to this error from QEMU 8.1.1: qemu-system-x86_64: CPU model 'host' requires KVM or HVF This commit fixes it. Inspired by <https://github.com/matthewbauer/nixpkgs/commit/47b56e7c19c2e3af685ee408f02f232efb3d12b1>. * gnu/tests/virtualization.scm (run-childhurd-test)[test]: Prefer “-cpu max” over “-cpu host”. Change-Id: I11a8a68bb0532fe1f3fd2c34b4a7a5fdb7bccb57 Ludovic Courtès 2023-11-05tests: inetd: Avoid race condition when looking for PID file....* gnu/tests/networking.scm (run-inetd-test): Use ‘wait-for-file’ instead of ‘file-exists?’. Change-Id: I3e596814485428fb81595d81c4e03519340c6576 Ludovic Courtès 2023-10-11services: static-networking: Add support for bonding....* gnu/services/base.scm (<network-link>): Add mac-address field. Set type field to #f by default, so it won't be mandatory. network-link without a type will be used for existing interfaces. (assert-network-link-mac-address, mac-address?): Add sanitizer. Allow valid mac-address or #f. (assert-network-link-type): Add sanitizer. Allow symbol or #f. * gnu/services/base.scm (network-set-up/linux, network-tear-down/linux): Adapt to new structure. * doc/guix.texi (Networking Setup): Document it. * gnu/tests/networking.scm (run-static-networking-advanced-test): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Alexey Abramov 2023-10-05tests: childhurd: Test SSH connection with a non-root user....* gnu/tests/virtualization.scm (%childhurd-os): Remove ‘services’ and add ‘users’ to the GNU/Hurd ‘operating-system’ declaration. (run-childhurd-test)[run-command-over-ssh]: Log in as “test” instead of “root”. Ludovic Courtès 2023-10-01services: hurd-vm: Implement zero-configuration offloading....This allows for zero-configuration offloading to a childhurd. * gnu/services/virtualization.scm (operating-system-with-offloading-account): New procedure. (<hurd-vm-configuration>)[offloading?]: New field. (hurd-vm-disk-image): Define ‘transform’ and use it. (hurd-vm-activation): Generate SSH key for user ‘offloading’ and add authorize it via /etc/childhurd/etc/ssh/authorized_keys.d. (hurd-vm-configuration-offloading-ssh-key) (hurd-vm-guix-extension): New procedures. (hurd-vm-service-type): Add GUIX-SERVICE-TYPE extension. * gnu/tests/virtualization.scm (run-childhurd-test)[import-module?]: New procedure. [os]: Add (gnu build install) and its closure to #:import-modules. [test]: Add “copy-on-write store” and “offloading” tests. * doc/guix.texi (Virtualization Services): Document it. Ludovic Courtès 2023-10-01services: hurd-vm: Disable password-based authentication for root....With offloading to a childhurd is enabled, allowing password-less root login in the childhurd to anyone amounts to providing write access to the host’s store to anyone. Thus, disable password-based root logins in the childhurd. * gnu/services/virtualization.scm (%hurd-vm-operating-system): Change ‘permit-root-login’ to 'prohibit-password. * gnu/tests/virtualization.scm (%childhurd-os): Provide a custom ‘os’ field for ‘hurd-vm-configuration’. * doc/guix.texi (Virtualization Services): Remove mention of password-less root login. Ludovic Courtès 2023-10-01tests: hurd-vm: Remove custom disk image configuration....This was added in 18e76f89055f25f015fadb7c999b410f38a88cc6. Presumably, the problem was that using compressed QCOW2 images makes the childhurd slower, so it’s eventually marked as failing to start. By enabling KVM inside the Guix System VM, we allow the childhurd to run on KVM, which compensates the slowdown due to the use of a compressed image. * gnu/tests/virtualization.scm (hurd-vm-disk-image-raw): Remove. (%childhurd-os): Use default config for ‘hurd-vm-service-type’. (run-childhurd-test)[test]: Pass “-cpu host” to the run-vm script. Ludovic Courtès 2023-10-01services: hurd-vm: ‘image’ field has to be an <image> record....* gnu/services/virtualization.scm (<hurd-vm-configuration>)[image]: Document as being an <image> record. (hurd-vm-disk-image): Remove call to ‘system-image’. (hurd-vm-shepherd-service): Add call to ‘system-image’. * gnu/tests/virtualization.scm (hurd-vm-disk-image-raw): Remove call to ‘system-image’. * doc/guix.texi (Virtualization Services): Adjust accordingly. Ludovic Courtès 2023-09-17tests: childhurd: Add missing module imports....Fixes a regression introduced in a09c7da8f8d8e732f969cf0a09aaa78f87032ab1. * gnu/tests/virtualization.scm (run-childhurd-test)[test]: Import (ice-9 textual-ports) and (ice-9 match) in the marionette when needed. Ludovic Courtès 2023-09-15services: guix: Add bffe-service-type....This is intended to replace the functionality of the Guix Build Coordinator queue builds script, and also provide a web interface for build farms. * gnu/services/guix.scm (<bffe-configuration>): New record type. (bffe-configuration, bffe-configuration?, bffe-configuration-package, bffe-configuration-user, bffe-configuration-group, bffe-configuration-arguments bffe-configuration-extra-environment-variables): New procedures. (bffe-service-type): New variable. * gnu/tests/guix.scm (%test-bffe): New variable. * doc/guix.texi (Guix Services): Document the new service. Christopher Baines 2023-09-08services: ganeti: Fix tests....* gnu/tests/ganeti.scm (run-ganeti-test)["force-start wconfd"]: Don't use INVOKE. ["gnt-os list"]: Import (ice-9 textual-ports). Marius Bakke