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* gnu: icedove: Update to 115.10.1.Jonathan Brielmaier2024-08-18
| | | | | | | | | | | | | | | | | | | * gnu/packages/gnuzilla.scm (all-mozilla-102-locales, %icecat-102-base-version, %icecat-102-version, icecat-102-source): Remove variables. (%icedove-build-id, %icedove-version, thunderbird-comm-source): Update for 115.10.1. (thunderbird-comm-l10n): Switch to provided tarball. (icedove-source)[origin]: Add `zstd` package. Use `icecat-source`. Provide l10n folder from tarball. (icedove-minimal)[arguments]: Use MACH_BUILD_PYTHON_NATIVE_PACKAGE_SOURCE instead of deprecated MACH_USE_SYSTEM_PYTHON. Use GUIX_PYTHONPATH and bundled NSS library. [inputs]: Use `icu4c-73`. Add `nspr`. Remove `nss` for now. [native-inputs]: Update clang and llvm to version 15. Use newer `node-lts`. (make-l10n-package)[arguments]: Set GUIX_PYTHONPATH. Change-Id: Ie6d9eb00f609c9872ac985adec72da92ee4be336
* gnu: icu4c: Add patch for VTIMEZONE bug.Jonathan Brielmaier2024-08-18
| | | | | | | | | | | | Icedove@115 does not properly work without this patch. See: https://bugzilla.mozilla.org/show_bug.cgi?id=1843007 * gnu/packages/icu4c.scm (icu4c-73)[source]: Use patch. * gnu/packages/patches/icu4c-icu-22132-fix-vtimezone.patch: New file. * gnu/local.mk (dist_patch_DATA): Register patch. Change-Id: Ie64d1e33afedbaedbaafaeb607a201eb671ac7bd Change-Id: I6d753eacc7daac5663128b20a550044d0fd0ddb7
* system: Add privileged-programs to <operating-system>.Tobias Geerinckx-Rice2024-08-11
| | | | | | | | | | | | | * gnu/system.scm (<operating-system>): Add new privileged-programs field, that defaults to… (%default-privileged-programs): …this new variable, renamed from… (%setuid-programs): …this, which is now defined as the empty list. * doc/guix.texi (Setuid Programs): Rename this… (Privileged Programs): …to this. Adjust all refs. Update all mentions of ‘setuid’ (whether in prose, variable names, or code samples) to use the new ‘privilege[d]’ terminology instead. (operating-system Reference, X Window, Invoking guix system) (Service Reference): Adjust likewise.
* gnu: Replace (almost) all uses of /run/setuid-programs.Tobias Geerinckx-Rice2024-08-11
| | | | | | | | | | | | | | | | | | | | | | | | | …those good for master, anyway. * gnu/packages/admin.scm (ktsuss, opendoas, hosts) [arguments]: Replace /run/setuid-programs with /run/privileged/bin. * gnu/packages/containers.scm (slirp4netns)[arguments]: Likewise. * gnu/packages/debian.scm (pbuilder)[arguments]: Likewise. * gnu/packages/disk.scm (udevil)[arguments]: Likewise. * gnu/packages/enlightenment.scm (efl, enlightenment) [arguments]: Likewise. * gnu/packages/gnome.scm (gdm, gnome-control-center) [arguments]: Likewise. * gnu/packages/linux.scm (singularity)[arguments]: Likewise. * gnu/packages/lxde.scm (spacefm)[arguments]: Likewise. * gnu/packages/monitoring.scm (zabbix-agentd)[arguments]: Likewise. * gnu/packages/virtualization.scm (ganeti)[arguments]: Likewise. * gnu/packages/xdisorg.scm (xsecurelock)[arguments]: Likewise. * gnu/services/dbus.scm (dbus-configuration-directory): Likewise. * gnu/services/ganeti.scm (%default-ganeti-environment-variables): Likewise. * gnu/services/monitoring.scm (zabbix-agent-shepherd-service): Likewise. * gnu/tests/ldap.scm (marionette): Likewise. * gnu/tests/monitoring.scm (os): Likewise.
* gnu: kmonad: Update to 0.4.2-1.07cd1cb.Andrew Tropin2024-08-18
| | | | | | * gnu/packages/haskell-apps.scm (kmonad): Update to 0.4.2-1.07cd1cb. Change-Id: I8a8d36577804d2221b39b430d26e9fd17204c0de
* gnu: r-dmrseq: Update to 1.24.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.24.1. Change-Id: I22fb49eee056e0dd5306fec4575fcb38cbe916aa
* gnu: r-bgeecall: Update to 1.20.1.Ricardo Wurmus2024-08-17
| | | | | | | * gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.20.1. [propagated-inputs]: Add r-txdbmaker. Change-Id: Ia51c1ccdb0e49d8dc74a61f605f00c86718bc1f8
* gnu: r-mscoreutils: Update to 1.16.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.16.1. Change-Id: I233a01625f223c571dae863c977825d4a2909ee7
* gnu: r-scater: Update to 1.32.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-scater): Update to 1.32.1. Change-Id: I0232d463f243505a9b3706d64e6666eb245ceb1c
* gnu: r-hdf5array: Update to 1.32.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.32.1. Change-Id: Iebab45185f6f1fe3e6919a1e70e45127d9f1124f
* gnu: r-s4vectors: Update to 0.42.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.42.1. Change-Id: I58dc50344c5eb477da9d4ddd4447bcb41f456037
* gnu: r-multiassayexperiment: Update to 1.30.3.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.30.3. Change-Id: Iabbd0c74d7515f8f166827b8b99b2ac49b271c13
* gnu: r-universalmotif: Update to 1.22.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.22.1. Change-Id: I60a617d120e5da046decb491b7641f1e10aac0cb
* gnu: r-clusterprofiler: Update to 4.12.2.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.12.2. Change-Id: I17d837fb314c26fcb26c13240a01c91bc2da9797
* gnu: r-enrichplot: Update to 1.24.2.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.24.2. Change-Id: I188e7e908a09337d4bacf4802b1557ddd31048f3
* gnu: r-dose: Update to 3.30.2.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-dose): Update to 3.30.2. Change-Id: Ic07fab82efcbda004d6c7ff21d4ed7b49cc426fb
* gnu: r-chippeakanno: Update to 3.38.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.38.1. Change-Id: Ia4c89074674f3473e11f3b9e1f9ed828701591f6
* gnu: r-qfeatures: Update to 1.14.2.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-qfeatures): Update to 1.14.2. Change-Id: I93c4fc00d19b18a1e0981f21dd0950d1e1a81f37
* gnu: r-seqarray: Update to 1.44.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-seqarray): Update to 1.44.1. Change-Id: I06bb0b45d1a4299e835f7a18c7ed70d847bdb565
* gnu: r-msa: Update to 1.36.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-msa): Update to 1.36.1. Change-Id: I91665d8ff4cd7570b5bcad27ff132611a09b8ecc
* gnu: r-limma: Update to 3.60.4.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-limma): Update to 3.60.4. Change-Id: Iaaf9317ab3921070f5b8e06a7948b42575bbe00b
* gnu: r-raggedexperiment: Update to 1.28.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-raggedexperiment): Update to 1.28.1. Change-Id: If7e8b60435413acda999f055bf9f104929e7f50f
* gnu: r-edger: Update to 4.2.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-edger): Update to 4.2.1. Change-Id: Ia8cb57ada3f036f7fe45972ad1d3a8ff2e53c27b
* gnu: r-iranges: Update to 2.38.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-iranges): Update to 2.38.1. Change-Id: I95d34fb3f339590c1980b7a77093835baa0e0136
* gnu: r-dmrcate: Update to 3.0.5.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-dmrcate): Update to 3.0.5. Change-Id: I88768682f65b821e188f29c4dfee94927040cbbd
* gnu: r-degreport: Update to 1.40.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-degreport): Update to 1.40.1. Change-Id: I35e7284270c81cd10178e7d848dfa5872645405d
* gnu: r-anvil: Update to 1.16.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/bioconductor.scm (r-anvil): Update to 1.16.1. Change-Id: Ief1b321d44a3bd534c6107c4434957c0de2dd977
* gnu: r-desctools: Update to 0.99.55.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-desctools): Update to 0.99.55. Change-Id: Ic6b6222e1702db59786ad2ab73645425645575a1
* gnu: r-exact: Update to 3.3.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-exact): Update to 3.3. Change-Id: If388135e98d31308d6d6170f30038ea9b44c994f
* gnu: r-lme4: Update to 1.1-35.5.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-lme4): Update to 1.1-35.5. Change-Id: I886898d0158ba4a6d29e61e8a19a280ce387ee2e
* gnu: r-rcppeigen: Update to 0.3.4.0.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.4.0.1. Change-Id: I4b7b3569c414d57a1af788fedcdaaf1e59e42fe7
* gnu: r-pcapp: Update to 2.0-4-1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-pcapp): Update to 2.0-4-1. Change-Id: I7a08f67e636843e36bc80af0d94778f6d2b202d6
* gnu: r-sparsem: Update to 1.84-2.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-sparsem): Update to 1.84-2. Change-Id: Id2123705c08bab173a4c8da3029e9bbda4db3ceb
* gnu: r-segmented: Update to 2.1-1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-segmented): Update to 2.1-1. Change-Id: I754caaac1fca6903103b3c36f3d4894350c9a63d
* gnu: r-rcurl: Update to 1.98-1.16.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-rcurl): Update to 1.98-1.16. Change-Id: I7c1570708479711e32a98e586cf51ddf7958e4b6
* gnu: r-bitops: Update to 1.0-8.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-bitops): Update to 1.0-8. Change-Id: I0f5e97d07097a0ec13cce1b1d61e4633cdb9cd70
* gnu: r-rcpparmadillo: Update to 14.0.0-1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 14.0.0-1. Change-Id: I9594cab48497f4767b2f5435828057704efdb01f
* gnu: r-withr: Update to 3.0.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-withr): Update to 3.0.1. Change-Id: Ic9302091cacb203a3d6e45183c871ba12276e3ba
* gnu: r-openssl: Update to 2.2.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-openssl): Update to 2.2.1. Change-Id: Id279140de607eb0f8324ab2e38ce248398110979
* gnu: r-checkmate: Update to 2.3.2.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-checkmate): Update to 2.3.2. Change-Id: I8dbd8ed86a5cc652da180c1bac951abc7ba82fb5
* gnu: r-knitr: Update to 1.48.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-knitr): Update to 1.48. Change-Id: I87ec28f830230f8fd51f7a2701a6bc83c14bd3b6
* gnu: r-yaml: Update to 2.3.10.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-yaml): Update to 2.3.10. Change-Id: I64802f3c68be2498ea48755608ddf55dc3adae3e
* gnu: r-nlme: Update to 3.1-166.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/statistics.scm (r-nlme): Update to 3.1-166. Change-Id: I7df0e68f3e685acb145d3c07f9de14ee1ab141a6
* gnu: r-webmockr: Update to 1.0.0.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/cran.scm (r-webmockr): Update to 1.0.0. Change-Id: I732b25faa1d2cc6cf17fb8c9dfb9dbc7f194c0d9
* gnu: r-crul: Update to 1.5.0.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/cran.scm (r-crul): Update to 1.5.0. Change-Id: Ic25ca2096424aa624eca983b68f622240e212b0a
* gnu: r-paws-common: Update to 0.7.4.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/cran.scm (r-paws-common): Update to 0.7.4. Change-Id: I0bc4341a6cd3ada7bbf7e323a14b4d69083f2ad5
* gnu: r-stars: Update to 0.6-6.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/cran.scm (r-stars): Update to 0.6-6. Change-Id: Ie2b039d28202b9d3f96a740a6883763174e547b6
* gnu: r-pkgdown: Update to 2.1.0.Ricardo Wurmus2024-08-17
| | | | | | | | * gnu/packages/cran.scm (r-pkgdown): Update to 2.1.0. [propagated-inputs]: Remove r-httr, r-magrittr, and r-memoise; add r-fontawesome, r-httr2, and r-openssl. Change-Id: I7cb4e0293ab5ddbc07918c2ee2db84030d2de1e3
* gnu: r-bbotk: Update to 1.0.1.Ricardo Wurmus2024-08-17
| | | | | | * gnu/packages/cran.scm (r-bbotk): Update to 1.0.1. Change-Id: Id2a435d9e9711fff8fae2ff1d2dc5a7ab2a30c85
* gnu: r-mlr3: Update to 0.20.2.Ricardo Wurmus2024-08-17
| | | | | | | * gnu/packages/cran.scm (r-mlr3): Update to 0.20.2. [propagated-inputs]: Remove r-rhpcblasctl. Change-Id: I2d92d399220f3f54d34c6bdc863fd6fb4fc90fb4
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