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2024-01-23gnu: Add flash.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flash): New variable. Change-Id: Id657ba7850031ad24b4333b6bc79401511e00a85
2024-01-23gnu: Add isolator.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (isolator): New variable. Change-Id: I950baca5b6898576f358b3364b1fe541b3333298
2024-01-23ci: Don't cross compile to or1k-elf.Mathieu Othacehe
* gnu/ci.scm (cross-jobs)[pointless?]: Don't build any packages for or1k-elf. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Change-Id: I294429d5318b94fb8e7780a37f3608b5321cf6ca
2024-01-23gnu: Add metal.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (metal): New variable. Change-Id: I70fd30c18303f61a9f6720e70d4b4e57140a7140
2024-01-23gnu: Add randfold.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (randfold): New variable. Change-Id: If2cea9c8d5323296015dc21ea7a3d1b677ae2798
2024-01-23gnu: Add python-pyfasta.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfasta): New variable. Change-Id: Ib2ab0a6eb250309633d5be33c18409227bce84ba
2024-01-23gnu: Add python-fcsparser.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-fcsparser): New variable. Change-Id: I87ed7f10bbfdf7d689cb6289a5f5ad31872f9de0
2024-01-23gnu: Add lsgkm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (lsgkm): New variable. Change-Id: I0ea35354c7856e7425567cd4ac27ab7fc2ab0d9e
2024-01-23gnu: icecat: Update to 115.7.0-guix0-preview1 [security fixes].Mark H Weaver
Includes fixes for CVE-2024-0741, CVE-2024-0742, CVE-2024-0746, CVE-2024-0747, CVE-2024-0749, CVE-2024-0750, CVE-2024-0751, CVE-2024-0753, and CVE-2024-0755. * gnu/packages/gnuzilla.scm (%icecat-base-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes.
2024-01-23Revert "gnu: source-highlight: Wrap scripts."Efraim Flashner
This package causes the rebuild of more than 9000 packages. This reverts commit 367bc2d198f57bc34522441820f761b61fed0ce0.
2024-01-23gnu: kubo: Update to 0.18.0.Artyom V. Poptsov
* gnu/packages/ipfs.scm (kubo): Update to 0.18.0. [inputs]: Add go-github-com-gorilla-mux. Change-Id: I4eccdfcf9eadbdf25728fcca766c5238efb0d57f Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2024-01-23gnu: source-highlight: Wrap scripts.Efraim Flashner
* gnu/packages/pretty-print.scm (source-highlight)[arguments]: Add a phase to wrap shell scripts so they can find the source-hightlight binary. [inputs]: Add guile-3.0. Change-Id: Ia8d006d969385210d5c82b4a0dd1f78178306ac2
2024-01-23gnu: trurl: Update to 0.9.Sharlatan Hellseher
* gnu/packages/curl.scm (trurl): Update to 0.9. Change-Id: Ieb0f19e6d48897dceb32e317613a301f521c9b94
2024-01-23gnu: Add eddylab-squid.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (eddylab-squid): New variable. Change-Id: Icb02f42fc95d2001a639e22608a01ef9074158bc
2024-01-23gnu: Add python-magic-impute.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-magic-impute): New variable. Change-Id: Iba5240e9920a1045078c736553cb1d56069963b5
2024-01-23gnu: Add python-graphtools.Ricardo Wurmus
* gnu/packages/graph.scm (python-graphtools): New variable. Change-Id: If08b1460447702f7ec2e64f013a52a7065076b01
2024-01-23gnu: Add python-tasklogger.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-tasklogger): New variable. Change-Id: I53319b70b7788090e8873a912d7c56044c0bb5b2
2024-01-23gnu: python-nose2: Update to 0.14.0.Ricardo Wurmus
* gnu/packages/check.scm (python-nose2): Update to 0.14.0. [native-inputs]: Remove python-coverage. [propagated-inputs]: Remove python-six. Change-Id: I15a30723fe49cca9929524e543d12c9e2f4b02ca
2024-01-23gnu: python-scikit-learn: Disable one test.Ricardo Wurmus
This test fails with the upgrade of scipy. * gnu/packages/machine-learning.scm (python-scikit-learn)[arguments]: Disable test_singular_matrix test. Change-Id: I47627403826bb5c52f4d578399c7cabaa3f8838d
2024-01-23gnu: Add python-pygsp.Ricardo Wurmus
* gnu/packages/graph.scm (python-pygsp): New variable. Change-Id: I8dd195216617e5cdb4a7453ecbe23cd9ff9e06a3
2024-01-23gnu: Add r-scenic.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scenic): New variable. Change-Id: Iff1f501a406ba1a12e49093a575e03facc98f303
2024-01-23gnu: python-scipy: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/python-science.scm (python-scipy): Update to 1.12.0. [propagated-inputs]: Add python-jupytext, python-mpmath, python-mypy, python-numpydoc, python-pydata-sphinx-theme, python-pydevtool, python-rich-click, python-sphinx, python-threadpoolctl, and python-typing-extensions; remove python-pyparsing. [native-inputs]: Add python-hypothesis, python-pycodestyle, python-pytest-cov, and python-pytest-xdist; remove python-threadpoolctl. Change-Id: I81a4831e3d94c58416f7d35ec47de90370b88210
2024-01-23gnu: r-desctools: Update to 0.99.53.Ricardo Wurmus
* gnu/packages/statistics.scm (r-desctools): Update to 0.99.53. Change-Id: I425b37907b51a93fafa193d217bdf68636f608a7
2024-01-23gnu: r-plotly: Update to 4.10.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-plotly): Update to 4.10.4. Change-Id: Idd10685b1ab521056e0468f0c0c188543c11c96a
2024-01-23gnu: r-xml: Update to 3.99-0.16.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml): Update to 3.99-0.16.1. Change-Id: I2936eac03ec20b091e45b920f946d92028099973
2024-01-23gnu: r-rsqlite: Update to 2.3.5.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.3.5. Change-Id: I43e95bc4ff0b0dc36cf9f3de1705d63bc5681286
2024-01-23gnu: r-roxygen2: Update to 7.3.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-roxygen2): Update to 7.3.1. Change-Id: I5d23ee576beb4dc4dc1e49d13cc38ffef0d33512
2024-01-23gnu: r-maldiquant: Update to 1.22.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-maldiquant): Update to 1.22.2. Change-Id: Ia483cff36bb3a2cbf4b691bb4832ce98757aabe0
2024-01-23gnu: r-modeldata: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-modeldata): Update to 1.3.0. Change-Id: Ibaef5366948e9ca45325d279a99f14417ca43e8e
2024-01-23gnu: r-yardstick: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-yardstick): Update to 1.3.0. [propagated-inputs]: Add r-withr. Change-Id: I00a5d74cca4396e685df32f85d998004a3e94edc
2024-01-23gnu: r-lightgbm: Update to 4.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-lightgbm): Update to 4.3.0. Change-Id: I9da6fbcf9558f1ed47b41abd7183f3c53ba1ec67
2024-01-23gnu: r-rstanarm: Update to 2.32.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-rstanarm): Update to 2.32.1. Change-Id: Ib83276a66add397aeacd830803f94f713f0c22e3
2024-01-23gnu: r-matrixextra: Update to 0.1.15.Ricardo Wurmus
* gnu/packages/cran.scm (r-matrixextra): Update to 0.1.15. Change-Id: I72c274e3075cc40d0f6aafb8199a4594c1a518c6
2024-01-23gnu: r-graphlayouts: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-graphlayouts): Update to 1.1.0. Change-Id: I5056c2158af15aeed9d5b53a52149e67d6d50b56
2024-01-23gnu: r-mcmcpack: Update to 1.7-0.Ricardo Wurmus
* gnu/packages/cran.scm (r-mcmcpack): Update to 1.7-0. Change-Id: I2e480dee05c23158b9ab58de5f9a90e623a7f6b2
2024-01-23gnu: r-ggfun: Update to 0.1.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggfun): Update to 0.1.4. Change-Id: I08cf695cd03bf28aaa2f2b7b4a35c6632a7027c4
2024-01-23gnu: r-rmpfr: Update to 0.9-5.Ricardo Wurmus
* gnu/packages/cran.scm (r-rmpfr): Update to 0.9-5. Change-Id: I32ba06d98406989aca7129f9f647e836e06663f8
2024-01-23gnu: r-bigrquery: Update to 1.5.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-bigrquery): Update to 1.5.0. [propagated-inputs]: Remove r-assertthat, r-glue, r-progress, r-rcpp, and r-withr; add r-clock and r-cpp11. Change-Id: I3f1eb2e32ce901231303a2eb905e8fd7aa0f995a
2024-01-23gnu: r-fmsb: Update to 0.7.6.Ricardo Wurmus
* gnu/packages/cran.scm (r-fmsb): Update to 0.7.6. Change-Id: I9acec8e49ba036f263223a37c53cf9d4a82ba59f
2024-01-23gnu: r-quickjsr: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-quickjsr): Update to 1.1.0. Change-Id: Ic2fb19a11c781c25b63cc2ed1bf185201aca0fe8
2024-01-23gnu: r-cmplot: Update to 4.5.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-cmplot): Update to 4.5.1. Change-Id: I34faf9e7c4b786aaae660ba18c65b429304db601
2024-01-23gnu: r-nodbi: Update to 0.10.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-nodbi): Update to 0.10.0. [propagated-inputs]: Add r-r-utils and r-v8. Change-Id: I1cc2c0c99f15cde415c90fa8959f3e0ffc546458
2024-01-23gnu: r-overlap: Update to 0.3.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-overlap): Update to 0.3.9. [propagated-inputs]: Add r-suntools. Change-Id: I3dc9817e0c7a5b4c4422e285aa5ccf4320047bd6
2024-01-23gnu: r-import: Update to 1.3.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-import): Update to 1.3.2. Change-Id: Ic78d705b104683e14f3b1848ba0218bfcc6e8ab1
2024-01-23gnu: r-xts: Update to 0.13.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-xts): Update to 0.13.2. Change-Id: I0f551d91a7012fabb117160c54e9c17883a48ca9
2024-01-23gnu: r-psych: Update to 2.4.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-psych): Update to 2.4.1. Change-Id: Iebac111c7dd7a8bab9df6789c9861e499b4439d3
2024-01-23gnu: r-timechange: Update to 0.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-timechange): Update to 0.3.0. Change-Id: I5c8dce37f2f268145b7288845ef0c7d1115eb445
2024-01-23gnu: r-ctrdata: Update to 1.17.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-ctrdata): Update to 1.17.0. [propagated-inputs]: Add r-digest. Change-Id: I505ea3605193eb461001c8e58cd9ef8d725d8f63
2024-01-23gnu: r-ps: Update to 1.7.6.Ricardo Wurmus
* gnu/packages/cran.scm (r-ps): Update to 1.7.6. Change-Id: Id7ef2ce2c709c8bffb7d3257324390400d55b29e
2024-01-23gnu: r-paletteer: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paletteer): Update to 1.6.0. Change-Id: Iff3c0636541bf3deb7a50706a62a44331a77e820
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