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Author SHA1 Message Date
Ludovic Courtès 00dfff84c6
packages: 'modify-inputs' preserves outputs in 'replace' clauses. 
Fixes <https://issues.guix.gnu.org/53915>.
Reported by Gordon Quad <gordon@niflheim.info>.

* guix/packages.scm (replace-input): Preserve the outputs of INPUT by
default.
* tests/packages.scm ("modify-inputs, replace, extra output"): New test.
 2022-03-16 15:48:51 +01:00
Ludovic Courtès e3801126a9
tests: Exercise 'modify-inputs' with a 'replace' clause. 
* tests/packages.scm ("modify-inputs, replace")
("modify-inputs, replace, change output"): New tests.
 2022-03-16 15:48:51 +01:00
Fatima Toothpaste 66a4a5ecb2
gnu : nicotine+: Update to 3.2.1. 
* gnu/packages/nicotine.scm (nicotine+): Update to 3.2.1.
  [source]: Delete network requried tests in snippet.
  [arguments]: Remove trailing #t.
  Replae 'check phase to run proper test.
  [inputs]: Add bash-minimal, gspell, libappindicator.
  [native-inputs]: Remove python-pytest. Add xvfb-run.
  [home-page]: Update URL.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-03-16 15:48:51 +01:00
Efraim Flashner 53d986215f
Revert "gnu: %boot3-inputs: Add missing input." 
This reverts commit ed2ca2dcb5.

This is no longer needed after the gcc STARTFILE_PREFIX_SPEC commit.
 2022-03-16 12:17:09 +02:00
Efraim Flashner 030900747b
Revert "gnu: Add %final-inputs-riscv64." 
This reverts commit 0444be8689.

This is no longer necessary after the gcc STARTFILE_PREFIX_SPEC commit.
 2022-03-16 12:16:15 +02:00
Efraim Flashner 32f52f82b3
gnu: gcc: For riscv64-linux remove STARTFILE_PREFIX_SPEC. 
* gnu/packages/gcc.scm (gcc-4.7)[arguments]: When building for
riscv64-linux and the 'gcc/configure/riscv' directory exists adjust the
STARTFILE_PREFIX_SPEC so it doesn't do anything.
 2022-03-16 12:09:42 +02:00
kiasoc5 53370c7b03
gnu: httpie: Update to 3.1.0 [security fixes]. 
Fixes CVE-2022-24737 and CVE-2022-0430.

* gnu/packages/python-web.scm (httpie): Update to 3.1.0.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2022-03-15 20:01:33 -04:00
zimoun 8a0713aef2
gnu: Add r-diffcyt. 
* gnu/packages/bioconductor.scm (r-diffcyt): New variable.
 2022-03-15 22:55:37 +01:00
zimoun 69af58e9a1
gnu: Add r-ga. 
* gnu/packages/cran.scm (r-ga): New variable.
 2022-03-15 22:55:01 +01:00
zimoun 76f96c891c
gnu: Add r-carrier. 
* gnu/packages/cran.scm (r-carrier): New variable.
 2022-03-15 22:54:14 +01:00
zimoun 71ec67ef3f
gnu: Add r-babelwhale. 
* gnu/packages/cran.scm (r-babelwhale): New variable.
 2022-03-15 22:53:09 +01:00
zimoun 59978546fe
gnu: Add r-polychrome. 
* gnu/packages/cran.scm (r-polychrome): New variable.
 2022-03-15 22:52:37 +01:00
zimoun fdbc472bd1
gnu: Add r-scannotatr. 
* gnu/packages/bioconductor.scm (r-scannotatr): New variable.
 2022-03-15 22:50:42 +01:00
Ricardo Wurmus bec806e2fc
gnu: r-sn: Update to 2.0.2. 
* gnu/packages/statistics.scm (r-sn): Update to 2.0.2.
 2022-03-15 22:14:47 +01:00
Ricardo Wurmus b3dbb32bb3
gnu: r-dt: Update to 0.21. 
* gnu/packages/statistics.scm (r-dt): Update to 0.21.
 2022-03-15 22:14:47 +01:00
Ricardo Wurmus b6a1cc89d4
gnu: r-simr: Update to 1.0.6. 
* gnu/packages/statistics.scm (r-simr): Update to 1.0.6.
[propagated-inputs]: Add r-lmertest.
[synopsis]: Change case and spelling.
[description]: Use complete sentences.
 2022-03-15 22:14:47 +01:00
Ricardo Wurmus 6c30609f23
gnu: r-rmarkdown: Update to 2.13. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.13.
[propagated-inputs]: Add r-bslib.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus be72c056f6
gnu: r-withr: Update to 2.5.0. 
* gnu/packages/statistics.scm (r-withr): Update to 2.5.0.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus f077fa0fd0
gnu: r-openssl: Update to 2.0.0. 
* gnu/packages/statistics.scm (r-openssl): Update to 2.0.0.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus 2af90fa53e
gnu: r-commonmark: Update to 1.8.0. 
* gnu/packages/statistics.scm (r-commonmark): Update to 1.8.0.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus 46a1b44782
gnu: r-desc: Update to 1.4.1. 
* gnu/packages/statistics.scm (r-desc): Update to 1.4.1.
[propagated-inputs]: Remove r-crayon; add r-cli.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus f2386cafcf
gnu: r-bbmisc: Update to 1.12. 
* gnu/packages/statistics.scm (r-bbmisc): Update to 1.12.
[propagated-inputs]: Add r-data-table.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus 4bc8d24e16
gnu: r-locfit: Update to 1.5-9.5. 
* gnu/packages/statistics.scm (r-locfit): Update to 1.5-9.5.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus b0e3061665
gnu: r-rlang: Update to 1.0.2. 
* gnu/packages/statistics.scm (r-rlang): Update to 1.0.2.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus 4f9f37cfa9
gnu: r-survival: Update to 3.3-1. 
* gnu/packages/statistics.scm (r-survival): Update to 3.3-1.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus 7751e96df2
gnu: r-bien: Update to 1.2.5. 
* gnu/packages/cran.scm (r-bien): Update to 1.2.5.
[native-inputs]: Remove r-testthat.
 2022-03-15 22:14:46 +01:00
Ricardo Wurmus d66b958b6d
gnu: r-filehash: Update to 2.4-3. 
* gnu/packages/cran.scm (r-filehash): Update to 2.4-3.
 2022-03-15 22:14:45 +01:00
Ricardo Wurmus 88716a4694
gnu: r-pdftools: Update to 3.1.1. 
* gnu/packages/cran.scm (r-pdftools): Update to 3.1.1.
 2022-03-15 22:14:45 +01:00
Ricardo Wurmus aaec4f36a8
gnu: r-mlr3tuning: Update to 0.12.1. 
* gnu/packages/cran.scm (r-mlr3tuning): Update to 0.12.1.
 2022-03-15 22:14:45 +01:00
Ricardo Wurmus 4ad704ee05
gnu: r-bbotk: Update to 0.5.1. 
* gnu/packages/cran.scm (r-bbotk): Update to 0.5.1.
 2022-03-15 22:14:45 +01:00
Ricardo Wurmus c01ae306ad
gnu: r-mlr3: Update to 0.13.3. 
* gnu/packages/cran.scm (r-mlr3): Update to 0.13.3.
 2022-03-15 22:14:45 +01:00
Ricardo Wurmus e14b368dfe
gnu: r-parsnip: Update to 0.2.0. 
* gnu/packages/cran.scm (r-parsnip): Update to 0.2.0.
[propagated-inputs]: Add r-cli, r-ggplot2, and r-withr.
 2022-03-15 22:14:45 +01:00
Ricardo Wurmus f4e5ed1120
gnu: r-posterior: Update to 1.2.1. 
* gnu/packages/cran.scm (r-posterior): Update to 1.2.1.
 2022-03-15 22:14:45 +01:00
Ricardo Wurmus bb98e8bbf6
gnu: r-latex2exp: Update to 0.9.4. 
* gnu/packages/cran.scm (r-latex2exp): Update to 0.9.4.
 2022-03-15 22:14:45 +01:00
Ricardo Wurmus 5fc38f7ab6
gnu: r-shinystan: Update to 2.6.0. 
* gnu/packages/cran.scm (r-shinystan): Update to 2.6.0.
[propagated-inputs]: Remove r-rsconnect.
 2022-03-15 22:14:45 +01:00
Ricardo Wurmus 682d4a4b64
gnu: r-semplot: Update to 1.1.5. 
* gnu/packages/cran.scm (r-semplot): Update to 1.1.5.
 2022-03-15 22:14:44 +01:00
Ricardo Wurmus 3a7e5bb521
gnu: r-qgraph: Update to 1.9.2. 
* gnu/packages/cran.scm (r-qgraph): Update to 1.9.2.
 2022-03-15 22:14:44 +01:00
Ricardo Wurmus 5b992f4b42
gnu: r-openmx: Update to 2.20.6. 
* gnu/packages/cran.scm (r-openmx): Update to 2.20.6.
 2022-03-15 22:14:44 +01:00
Ricardo Wurmus 1e2b297a56
gnu: r-sem: Update to 3.1-14. 
* gnu/packages/cran.scm (r-sem): Update to 3.1-14.
 2022-03-15 22:14:44 +01:00
Ricardo Wurmus 183581903e
gnu: r-quanteda: Update to 3.2.1. 
* gnu/packages/cran.scm (r-quanteda): Update to 3.2.1.
 2022-03-15 22:14:44 +01:00
Ricardo Wurmus 37d4f83a2c
gnu: r-torch: Update to 0.7.2. 
* gnu/packages/cran.scm (r-torch): Update to 0.7.2.
 2022-03-15 22:14:44 +01:00
Ricardo Wurmus e8104d1d63
gnu: r-caret: Update to 6.0-91. 
* gnu/packages/cran.scm (r-caret): Update to 6.0-91.
 2022-03-15 22:14:44 +01:00
Ricardo Wurmus e910b87515
gnu: r-imager: Update to 0.42.13. 
* gnu/packages/cran.scm (r-imager): Update to 0.42.13.
 2022-03-15 22:14:44 +01:00
Ricardo Wurmus 2cc2e440dc
gnu: r-seewave: Update to 2.2.0. 
* gnu/packages/cran.scm (r-seewave): Update to 2.2.0.
 2022-03-15 22:14:44 +01:00
Ricardo Wurmus 0d76859355
gnu: r-sysfonts: Update to 0.8.8. 
* gnu/packages/cran.scm (r-sysfonts): Update to 0.8.8.
 2022-03-15 22:14:43 +01:00
Ricardo Wurmus 13bb00192c
gnu: r-bio3d: Update to 2.4-3. 
* gnu/packages/cran.scm (r-bio3d): Update to 2.4-3.
 2022-03-15 22:14:43 +01:00
Ricardo Wurmus f4f1a353ae
gnu: r-pracma: Update to 2.3.8. 
* gnu/packages/cran.scm (r-pracma): Update to 2.3.8.
 2022-03-15 22:14:43 +01:00
Ricardo Wurmus 84e5b9fac2
gnu: r-parameters: Update to 0.17.0. 
* gnu/packages/cran.scm (r-parameters): Update to 0.17.0.
 2022-03-15 22:14:43 +01:00
Ricardo Wurmus 766f8ea02c
gnu: r-styler: Update to 1.7.0. 
* gnu/packages/cran.scm (r-styler): Update to 1.7.0.
[propagated-inputs]: Remove r-backports, r-glue, and r-xfun.
 2022-03-15 22:14:43 +01:00
Ricardo Wurmus c0d132d4d1
gnu: r-mcmcpack: Update to 1.6-1. 
* gnu/packages/cran.scm (r-mcmcpack): Update to 1.6-1.
 2022-03-15 22:14:43 +01:00