Commit graph

117066 commits

Author SHA1 Message Date
Ricardo Wurmus 44e149cfaa
gnu: r-googledrive: Update to 2.1.1.
* gnu/packages/cran.scm (r-googledrive): Update to 2.1.1.
2023-07-12 14:29:03 +02:00
Ricardo Wurmus 1d6792cf83
gnu: r-datawizard: Update to 0.8.0.
* gnu/packages/cran.scm (r-datawizard): Update to 0.8.0.
2023-07-12 14:29:03 +02:00
Ricardo Wurmus bb570c1534
gnu: r-ggpicrust2: Update to 1.7.1.
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 1.7.1.
[propagated-inputs]: Remove r-phyloseq; add r-ggh4x.
2023-07-12 14:29:03 +02:00
Ricardo Wurmus d669b30658
gnu: r-scistreer: Update to 1.2.0.
* gnu/packages/bioconductor.scm (r-scistreer): Update to 1.2.0.
2023-07-12 14:29:03 +02:00
Ricardo Wurmus 5f8104b3a4
gnu: r-numbat: Update to 1.3.2-1.
* gnu/packages/bioconductor.scm (r-numbat): Update to 1.3.2-1.
2023-07-12 14:29:03 +02:00
Ricardo Wurmus 347e3b1b75
gnu: r-biomartr: Update to 1.0.4.
* gnu/packages/bioconductor.scm (r-biomartr): Update to 1.0.4.
2023-07-12 14:29:03 +02:00
Ricardo Wurmus 49fe6b3d66
gnu: apache-arrow: Update to 12.0.1.
* gnu/packages/databases.scm (apache-arrow): Update to 12.0.1.
2023-07-12 14:29:03 +02:00
Ricardo Wurmus abd0c1b29d
gnu: r-mlr3: Update to 0.16.1.
* gnu/packages/cran.scm (r-mlr3): Update to 0.16.1.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 66e988201d
gnu: r-igraph: Update to 1.5.0.
* gnu/packages/cran.scm (r-igraph): Update to 1.5.0.
[propagated-inputs]: Add r-cli.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 56b8a26951
gnu: r-terra: Update to 1.7-39.
* gnu/packages/cran.scm (r-terra): Update to 1.7-39.
[inputs]: Add curl, openssh, openssl, and pcre2.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 5dea2079b1
gnu: r-leidenalg: Update to 1.1.0.
* gnu/packages/cran.scm (r-leidenalg): Update to 1.1.0.
[properties]: Add hint for updater to keep gmp as input.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 5aca0cd1e3
gnu: Add r-envstats.
* gnu/packages/cran.scm (r-envstats): New variable.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 64b18f3282
gnu: r-gmp: Update to 0.7-2.
* gnu/packages/cran.scm (r-gmp): Update to 0.7-2.
[arguments]: Remove obsolete build phase.
[properties]: Tell updater that "gmp" is an extra input.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 2c04ca3de0
gnu: r-haven: Update to 2.5.3.
* gnu/packages/cran.scm (r-haven): Update to 2.5.3.
[properties]: Declare readstat as an extra input.
[native-inputs]: Add pkg-config.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 95a4fc7e9c
gnu: r-gprofiler2: Update to 0.2.2.
* gnu/packages/cran.scm (r-gprofiler2): Update to 0.2.2.
[native-inputs]: Add r-rmarkdown.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 1223a87a14
gnu: r-v8: Update to 4.3.2.
* gnu/packages/cran.scm (r-v8): Update to 4.3.2.
[properties]: Declare libnode as an extra input, not an ignored input.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 1b09d2e9ae
gnu: r-lme4: Update to 1.1-34.
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-34.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 138d0dd9ad
gnu: r-digest: Update to 0.6.33.
* gnu/packages/statistics.scm (r-digest): Update to 0.6.33.
[native-inputs]: Add r-simplermarkdown.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus febe08ee8a
import/cran: Add one more package name transformation.
* guix/import/cran.scm (transform-sysname): Add entry for "zlib-devel".
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 60c70a9009
gnu: r-plotly: Update to 4.10.2.
* gnu/packages/statistics.scm (r-plotly): Update to 4.10.2.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus 7c2290f663
gnu: r-opencpu: Update to 2.2.10.
* gnu/packages/cran.scm (r-opencpu): Update to 2.2.10.
[properties]: Add hints for updater.
2023-07-12 14:29:02 +02:00
Ricardo Wurmus cca7d7ea4c
gnu: r-rgl: Update to 1.2.1.
* gnu/packages/cran.scm (r-rgl): Update to 1.2.1.
[properties]: Tell updater to not remove glu and libx11.
2023-07-12 14:29:01 +02:00
Ricardo Wurmus 2680ec55ff
gnu: r-bslib: Update to 0.5.0.
* gnu/packages/cran.scm (r-bslib): Update to  0.5.0.
[source]: Delete minified JavaScript for components.
[arguments]: Update 'process-javascript phase to generate components from
source.
[native-inputs]: Add typescript-components.
2023-07-12 14:29:01 +02:00
Ricardo Wurmus b43841c124
refresh: Sort update specs by package location.
Fixes <https://issues.guix.gnu.org/64358>.

* guix/scripts/refresh.scm (guix-refresh): Sort update specs by location from
bottom to top before updating packages.
2023-07-12 14:29:01 +02:00
jgart 4a027d2b0e
gnu: rr: Fix typo in synopsis.
* gnu/packages/debug.scm (rr)
[synopsis]: Fix typo.
2023-07-11 22:43:35 -05:00
jgart cf3bd63b06
gnu: keepassxc: Fix broken home-page url.
* gnu/packages/password-utils.scm (keepassxc): Fix broken url.
[home-page]: Fix broken url.
2023-07-11 22:43:05 -05:00
Zhu Zihao b5baa98053
gnu: nix: Update to 2.16.1.
* gnu/packages/package-management.scm (nix): Update to 2.16.1.
[source]: Use HTTPS for package source.
[inputs]: Add nlohmann-json.
[native-inputs]: Add rapidcheck.
[arguments]<#:phases>: In phase "check", change the value of environment
variable  "NIX_STORE" to "/nix/store" temporarily.

* gnu/packages/patches/nix-dont-build-html-doc.diff: Update.

Co-authored-by: jgart <jgart@dismail.de>
2023-07-11 22:28:52 -05:00
Zhu Zihao 38f050193b
gnu: Add rapidcheck.
* gnu/packages/check.scm (rapidcheck): New variable.
2023-07-11 21:39:35 -05:00
AwesomeAdam54321 b073fb9896
gnu: Add python-redo.
* gnu/packages/python-xyz.scm (python-redo): New variable.
2023-07-11 21:39:27 -05:00
Daniel Meißner 64b720e65e
gnu: Add python-cloup.
* gnu/packages/python-xyz.scm (python-cloup): New variable.

Co-authored-by: jgart <jgart@dismail.de>
2023-07-11 20:33:15 -05:00
John Kehayias 15f9870eb3
gnu: rocm: Update to 5.6.0.
Update all of the ROCm packages at the same time as they share a version
number and should be upgraded together, including llvm-for-rocm.

* gnu/packages/llvm.scm (llvm-for-rocm): Update to 5.6.0.
[source]{patches}: Remove unneeded patches (linkdl and remove-isystem-usr-include).
* gnu/packages/rocm.scm (rocm-cmake, roct-thunk-interface): Update
to 5.6.0.
(rocclr-src): Update to 5.6.0.
[source]{patches}: Add enable-gfx800 patch.
(rocm-device-libs):  Update to 5.6.0.
[inputs]: Update style.
(rocm-comgr): Update to 5.6.0.
[inputs]: Remove lld.  Update style.
(rocr-runtime): Update to 5.6.0.
[arguments]: Use gexps.  Remove configure-flags.  Add add-rocm-device-lib-path
phase.
[inputs]: Add libdrm.  Update style.
[native-inputs]: Add pkg-config.  Update style.
(rocm-opencl-runtime): Update to 5.6.0.
[source]{patches}: Remove noopencl patch.
[arguments]{configure-flags}: Add BUILD_ICD=OFF and
FILE_REORG_BACKWARD_COMPATIBILITY=OFF flags.
[inputs]: Add opencl-headers.
(rocminfo): Update to 5.6.0.
[arguments]: Use gexps.  Use search-input-file instead of assoc-ref and which.
(rocm-bandwidth-test): Update to 5.6.0.
[source]{patches}: Add fix-includes patch.
* gnu/packages/patches/rocm-comgr-3.1.0-dependencies.patch,
gnu/packages/patches/rocm-opencl-runtime-4.3-noclinfo.patch: Update patches.
* gnu/packages/patches/llvm-roc-4.0.0-remove-isystem-usr-include.patch,
gnu/packages/patches/llvm-roc-5.0.0-linkdl.patch,
gnu/packages/patches/rocm-opencl-runtime-4.3-noopencl.patch: Delete files.
* gnu/packages/patches/rocm-bandwidth-test-5.5.0-fix-includes.patch,
gnu/packages/patches/rocclr-5.6.0-enable-gfx800.patch: New files.
* gnu/local.mk (dist_patch_DATA): Update patches.
2023-07-11 12:21:00 -04:00
Ahmad Draidi 0cce3ac36e
gnu: Add emacs-sakura-theme.
* gnu/packages/emacs-xyz.scm (emacs-sakura-theme): New variable.

Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-07-11 20:06:12 +04:00
Ahmad Draidi ebaeeacc84
gnu: Add emacs-abyss-theme.
* gnu/packages/emacs-xyz.scm (emacs-abyss-theme): New variable.

Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-07-11 20:06:11 +04:00
Ahmad Draidi 3b77a06f3b
gnu: Add emacs-starlit-theme.
* gnu/packages/emacs-xyz.scm (emacs-starlit-theme): New variable.

Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-07-11 20:06:10 +04:00
Ahmad Draidi 686a3ca7c5
gnu: emacs-dumbparens: Update to 0-1.59bb5ae.
* gnu/packages/emacs-xyz.scm (emacs-dumbparens): Update to 0-1.59bb5ae.
[source]: Download from new upstream URL.
[home-page]: Use new home-page.

Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-07-11 20:06:09 +04:00
Ahmad Draidi 355391419b
gnu: emacs-scroll-on-drag: Update to 0.1-2.179c2ac.
* gnu/packages/emacs-xyz.scm (emacs-scroll-on-drag): Update to 0.1-2.179c2ac.
[source]: Download from new upstream URL.
[home-page]: Use new home-page.

Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-07-11 20:06:08 +04:00
Ahmad Draidi 7c6237ccbb
gnu: emacs-mode-line-idle: Update to 0.2-0.1dc0115.
* gnu/packages/emacs-xyz.scm (emacs-mode-line-idle): Update to 0.2-0.1dc0115.
[source]: Download from new upstream URL.
[home-page]: Use new home-page.

Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-07-11 20:06:07 +04:00
Ahmad Draidi e7d554c8ad
gnu: emacs-undo-fu-session: Update to 0.6-0.a6c4f73.
* gnu/packages/emacs-xyz.scm (emacs-undo-fu-session): Update to 0.6-0.a6c4f73.
[source]: Download from new upstream URL.
[arguments]: Update #:test-command. Fix tests by adding
'--eval (setq undo-fu-session-ignore-temp-files nil)' to #:test-command.
[home-page]: Use new home-page.

Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-07-11 20:06:06 +04:00
Ahmad Draidi 9a214850f0
gnu: emacs-undo-fu: Update to 0.5-0.0e22308.
* gnu/packages/emacs-xyz.scm (emacs-undo-fu): Update to 0.5-0.0e22308.
[source]: Download from new upstream URL.
[home-page]: Use new home-page.

Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-07-11 20:06:05 +04:00
Ahmad Draidi 507d2648c1
gnu: emacs-spell-fu: Update to 0.3-1.67a26b7.
* gnu/packages/emacs-xyz.scm (emacs-spell-fu): Update to 0.3-1.67a26b7.
[source]: Download from new upstream URL.
[home-page]: Use new home-page.

Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-07-11 20:06:04 +04:00
Paul A. Patience 7858b74b77
gnu: gnuplot: Update to 5.4.8.
* gnu/packages/maths.scm (gnuplot): Update to 5.4.8.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-07-11 16:58:04 +02:00
Paul A. Patience 7761495ccb
gnu: gmsh: Update to 4.11.1.
* gnu/packages/maths.scm (gmsh): Update to 4.11.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-07-11 16:15:01 +02:00
Bruno Victal fc25bd72b2
gnu: desktop-file-utils: Format description.
* gnu/packages/freedesktop.scm (desktop-file-utils)[description]: Format
description.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-07-11 16:12:25 +02:00
Bruno Victal e12a0cb3db
gnu: guile-hashing: Fix description.
* gnu/packages/guile-xyz.scm (guile-hashing)[description]: Fix typo.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-07-11 16:12:23 +02:00
Timotej Lazar 355e3c6e1c
gnu: rxvt-unicode: Use helper procedure to make desktop files.
* gnu/packages/xdisorg.scm (rxvt-unicode)[arguments]: Replace custom code with
make-desktop-entry-file. Specify categories and icon in desktop files.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-07-11 16:06:52 +02:00
Timotej Lazar f969f45fa8
gnu: rxvt-unicode: Use new package style.
* gnu/packages/xdisorg.scm (rxvt-unicode)[arguments]: Use gexps.
[inputs]: Drop input labels.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-07-11 16:06:51 +02:00
Timotej Lazar f0dfb2a8e9
gnu: rxvt-unicode: Update to 9.31 [fixes CVE-2022-4170].
* gnu/packages/xdisorg.scm (rxvt-unicode): Update to 9.31.
[inputs]: Add libxext.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-07-11 16:06:49 +02:00
Timotej Lazar 09d1e04230
gnu: qbittorrent{,-nox}: Use qt-build-system.
CMake is now upstream’s preferred build system.

* gnu/packages/bittorrent.scm (qbittorrent)[build-system]: Use qt-build-system.
[arguments]: Drop custom wrap phase. (Re-)enable tests.
[inputs]: Remove input labels. Drop qtbase-5.
[native-inputs]: Drop pkg-config.
(qbittorrent-nox)[arguments]: Adjust configure-flags. Keep the wrap-qt phase
since the non-GUI version is also a QT program.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-07-11 16:05:50 +02:00
Timotej Lazar f561e8a0ed
gnu: qbittorrent: Update to 4.5.4.
* gnu/packages/bittorrent.scm (qbittorrent): Update to 4.5.4.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-07-11 16:05:48 +02:00
Zac Berkowitz b716d17e1c
gnu: mit-scheme: Fix building
* gnu/packages/scheme.scm (mit-scheme)[arguments] Add 'set-env
  before 'configure, setting -Wno-array-parameter in CFLAGS and
  CPPFLAGS to ignore warning causing build break.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-07-11 16:04:44 +02:00