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2023-11-04gnu: passff-host: Add explicit references to inputs and remove some.Clément Lassieur
This removes ‘coreutils’, ‘grep’, ‘sed’, ‘which’, ‘bash-minimal’ and ‘gnu-make’ inputs, which were only used by the Makefile and install_host_app.sh. Instead of running install_host_app.sh (through ‘make’) which does a few text substitutions, do the text substitutions with Scheme code. This simplifies things and avoids unnecessary native inputs. * gnu/packages/browser-extensions.scm (passff-host)[build-system]: Change to copy-build-system. [arguments]: Copy passff.json and passff.py. Do text substitutions on them rather than running make. Refer to ‘password-store’ and ‘python’ through inputs rather than directly. [inputs]: Add PASSWORD-STORE and PYTHON. Change-Id: I8fdb757516a7c30eae36b15f2a8d91e1445b19a5
2023-11-04gnu: password-store: Add missing ‘tail’ input.Clément Lassieur
* gnu/packages/password-utils.scm (password-store)[arguments]: Add “tail” to the list of requisites. [inputs]: Add COREUTILS. Change-Id: I7f59e6c0abfb5396b9548edaec08d3b0a7c0eb23
2023-11-03gnu: Add r-ggbreak.Afkhami, Navid
* gnu/packages/cran.scm (r-ggbreak): New variable. Change-Id: I27d62d0110fb56e77dc8cf82581adb6259317c2d Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-03gnu: python-pymc: Update to 5.9.1.Vinicius Monego
* gnu/packages/statistics.scm (python-pymc): Update to 5.9.1. Change-Id: I3d7927e7173f36ba4edeab06bd930c285432c29f
2023-11-03gnu: python-pytensor: Update to 2.17.3.Vinicius Monego
* gnu/packages/python-science.scm (python-pytensor): Update to 2.17.3. Change-Id: I2843aca1df4d43883bf643e6e363bd3700202c45
2023-11-03gnu: python-deepxde: Update to 1.10.0.Vinicius Monego
* gnu/packages/machine-learning.scm (python-deepxde): Update to 1.10.0. Change-Id: Ibc37f9e7df45c49f590beb1dda87236e853b88c1
2023-11-03gnu: Add python-emcee.Vinicius Monego
* gnu/packages/statistics.scm (python-emcee): New variable.
2023-11-03gnu: Add python-salib.Vinicius Monego
* gnu/packages/python-science.scm (python-salib): New variable.
2023-11-03gnu: python-openturns: Update to 1.21.1.Vinicius Monego
* gnu/packages/statistics.scm (python-openturns): Update to 1.21.1.
2023-11-03gnu: python-opentsne: Update to 1.0.0.Vinicius Monego
* gnu/packages/machine-learning.scm (python-opentsne): Update to 1.0.0.
2023-11-03gnu: symengine: Update to 0.11.1.Vinicius Monego
* gnu/packages/algebra.scm (symengine): Update to 0.11.1.
2023-11-03gnu: r-gdata: Remove Excel from description.Ricardo Wurmus
gdata 3.0.0 has removed support for reading Excel files. * gnu/packages/statistics.scm (r-gdata)[description]: Update it. Change-Id: Ic4090bc765d330d38136bf1b1dbbb6bb136edd39
2023-11-03gnu: Remove r-sigpathway.Ricardo Wurmus
This package has been removed with the release of Bioconductor 3.18. * gnu/packages/bioconductor.scm (r-sigpathway): Remove variable. Change-Id: I5cb9d938f370aa28b196f9cea95fb6024c2e6e37
2023-11-03gnu: r-rhdf5filters: Simplify.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5filters)[arguments]: Remove 'use-system-libraries phase and pass configure flags to disable bundled libraries. Change-Id: I2fb115e7b3df00cccb3f8d6659d465075d21f19b
2023-11-03gnu: r-spams: Build with C++11.Ricardo Wurmus
* gnu/packages/statistics.scm (r-spams)[arguments]: Add phase 'use-c++11. Change-Id: Ie477af6afe8993919090f6c81e071cee542e69bc
2023-11-03gnu: Remove r-genomegraphs.Ricardo Wurmus
This package had been removed from Bioconductor with release 3.11. * gnu/packages/bioconductor.scm (r-genomegraphs): Remove variable. Change-Id: I73cc8cc8546089d91212176939b8c0c0a7afc309
2023-11-03gnu: Remove r-wavetiling.Ricardo Wurmus
This package had been removed from Bioconductor since release 3.12. * gnu/packages/bioconductor.scm (r-wavetiling): Remove variable. Change-Id: I5eb624d975f0eb170b263266b144eacf11944580
2023-11-03gnu: r-mpo-db: Include HPO sqlite database.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mpo-db)[arguments]: Bypass fetching of the database from the internet when in build environment. [native-inputs]: Add MPO.sqlite. Change-Id: Ic7228322b89ce78a85a9bd5ffbd985ccd906d268
2023-11-03gnu: r-readwriter: Update to 0.3.2-1.12d32cb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-readwriter): Update to 0.3.2-1.12d32cb. Change-Id: I412190ce94bee4e7b5fce27db7ef8a72188e74f4
2023-11-03gnu: r-hpo-db: Include HPO sqlite database.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hpo-db)[arguments]: Bypass fetching of the database from the internet when in build environment. [native-inputs]: Add HPO.sqlite. Change-Id: Ie01605ef2531d992fb85c07bae5cfaabda626ea6
2023-11-03gnu: r-rhdf5lib: Adjust modifications to Makevars.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Adjust patch. Change-Id: Iaef3d2d80c22de1c2a0b64e7c13f5fa3b8e5719d
2023-11-03gnu: r-phyloseq: Update to 1.46.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.46.0. Change-Id: Id11b5e913529ac8efce0d046168f4a9dbe0dbabd
2023-11-03gnu: r-tximeta: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.20.0. Change-Id: I8d9c5d01efc8f6c64290cdfdd193d95cd1da9152
2023-11-03gnu: r-tricycle: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.10.0. Change-Id: I72a9e1140c17ce8605bfe6e83cc290eb1ae2fad2
2023-11-03gnu: r-tcgabiolinks: Update to 2.30.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.30.0. Change-Id: If7e571bfa6454bfa94dd395606575391dc506ecd
2023-11-03gnu: r-biscuiteer: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.16.0. Change-Id: Ib6cffbbeedfe87932acfcbfb2b789b4c92a9bf81
2023-11-03gnu: r-omnipathr: Update to 3.10.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.10.1. [propagated-inputs]: Add r-lubridate and r-stringi. Change-Id: Ia18b66848cd6996dfdc551bf4b182bb5ac3e17a8
2023-11-03gnu: r-omicade4: Update to 1.42.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-omicade4): Update to 1.42.0. Change-Id: I4369e5721116bf73f096ee39a516ada94c348872
2023-11-03gnu: r-dmrseq: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.22.0. Change-Id: I738c2fb7e0fa3e816d3767f854b8f9ed77425591
2023-11-03gnu: r-dada2: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dada2): Update to 1.30.0. Change-Id: I0955c3a61b4d81cd6809e2eb287d8acfcccfb789
2023-11-03gnu: r-bsseq: Update to 1.38.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.38.0. Change-Id: Ie31f0b5c726da98a0caa4c658a5c62c1a5f40eaa
2023-11-03gnu: r-biotmle: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.26.0. Change-Id: Ied1d1e649fba277aa724040af31334f664d2debd
2023-11-03gnu: r-biotip: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biotip): Update to 1.16.0. Change-Id: I73503554b0271e5fe950c6da367b4893972f27e9
2023-11-03gnu: r-bioqc: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bioqc): Update to 1.30.0. Change-Id: I0b5fd7cac1283a7f12a1221ad453eb56767e8b90
2023-11-03gnu: r-bionetstat: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.22.0. Change-Id: I92f2ebef0b65b947a719bdd1008f07ce279263a4
2023-11-03gnu: r-bionet: Update to 1.62.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bionet): Update to 1.62.0. Change-Id: I0712a4ba67c27b32d6666e91d9515f0299e61848
2023-11-03gnu: r-bionero: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bionero): Update to 1.10.0. Change-Id: I396a37dd28571a471b45d4d8aca6ce40a1cbd384
2023-11-03gnu: r-biomvcclass: Update to 1.70.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.70.0. Change-Id: I0c6214669ec284d314eb7dc90270558934070e4b
2023-11-03gnu: r-mvcclass: Update to 1.76.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.76.0. Change-Id: I6e7fa851c804009ae41a955b117d95b33fd1b2f0
2023-11-03gnu: r-biomformat: Update to 1.30.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.30.0. Change-Id: I661d11f81a0dedbc8381b5ba1806643b5ff52aa6
2023-11-03gnu: r-biodb: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biodb): Update to 1.10.0. Change-Id: If1d14855b2bf134741c54c0a51daefdf2b80a49f
2023-11-03gnu: r-biocthis: Update to 1.12.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.12.0. Change-Id: I8400ebfd178f916488e022152e75db59f05994e6
2023-11-03gnu: r-basilisk: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.14.0. Change-Id: I86f5306de138eb1fedffbae65c14f9acd504c86c
2023-11-03gnu: r-basilisk-utils: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.14.0. Change-Id: I6113042a10770ee50e4ef997ee41fe109f917885
2023-11-03gnu: r-dir-expiry: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.10.0. Change-Id: I1081ec981a52a51a351d98e5079f8fd4bcc399d0
2023-11-03gnu: r-genetclassifier: Update to 1.42.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genetclassifier): Update to 1.42.0. Change-Id: I323ca2d408c640b05c9d845570ee7af28616cce2
2023-11-03gnu: r-minet: Update to 3.60.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-minet): Update to 3.60.0. Change-Id: I4944d2e34aacc6d3ba8c5a2d2176ecf7b33ca6b8
2023-11-03gnu: r-biobtreer: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biobtreer): Update to 1.14.0. Change-Id: Icf0458c6931237a405178361778a68c1a068337c
2023-11-03gnu: r-bgeedb: Update to 2.28.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.28.0. Change-Id: I558f36065a9a751710843f21c6089231309705ca
2023-11-03gnu: r-bgeecall: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.18.1. Change-Id: I5db747786c63f248dec01879e41a9837c94d6d6c
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