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127159 Commits (7995a474eab286a0eb05b065716ecd026a681d56)

Author SHA1 Message Date
Vinicius Monego 479fdc8451
gnu: python-pymc: Update to 5.9.1. 
* gnu/packages/statistics.scm (python-pymc): Update to 5.9.1.

Change-Id: I3d7927e7173f36ba4edeab06bd930c285432c29f
 2023-11-03 19:25:36 -03:00
Vinicius Monego 43d9fa0802
gnu: python-pytensor: Update to 2.17.3. 
* gnu/packages/python-science.scm (python-pytensor): Update to 2.17.3.

Change-Id: I2843aca1df4d43883bf643e6e363bd3700202c45
 2023-11-03 19:25:36 -03:00
Vinicius Monego 1879bfd88f
gnu: python-deepxde: Update to 1.10.0. 
* gnu/packages/machine-learning.scm (python-deepxde): Update to 1.10.0.

Change-Id: Ibc37f9e7df45c49f590beb1dda87236e853b88c1
 2023-11-03 19:25:36 -03:00
Vinicius Monego 96e8502faa
gnu: Add python-emcee. 
* gnu/packages/statistics.scm (python-emcee): New variable.
 2023-11-03 19:25:35 -03:00
Vinicius Monego a7d56852e3
gnu: Add python-salib. 
* gnu/packages/python-science.scm (python-salib): New variable.
 2023-11-03 19:25:35 -03:00
Vinicius Monego 9642b1c7af
gnu: python-openturns: Update to 1.21.1. 
* gnu/packages/statistics.scm (python-openturns): Update to 1.21.1.
 2023-11-03 19:25:35 -03:00
Vinicius Monego a55c3110be
gnu: python-opentsne: Update to 1.0.0. 
* gnu/packages/machine-learning.scm (python-opentsne): Update to 1.0.0.
 2023-11-03 19:25:35 -03:00
Vinicius Monego ef473d3422
gnu: symengine: Update to 0.11.1. 
* gnu/packages/algebra.scm (symengine): Update to 0.11.1.
 2023-11-03 19:25:31 -03:00
Ricardo Wurmus eb93ab2d14
gnu: r-gdata: Remove Excel from description. 
gdata 3.0.0 has removed support for reading Excel files.

* gnu/packages/statistics.scm (r-gdata)[description]: Update it.

Change-Id: Ic4090bc765d330d38136bf1b1dbbb6bb136edd39
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 8be2f44765
gnu: Remove r-sigpathway. 
This package has been removed with the release of Bioconductor 3.18.

* gnu/packages/bioconductor.scm (r-sigpathway): Remove variable.

Change-Id: I5cb9d938f370aa28b196f9cea95fb6024c2e6e37
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 38b5777ec8
gnu: r-rhdf5filters: Simplify. 
* gnu/packages/bioconductor.scm (r-rhdf5filters)[arguments]: Remove
'use-system-libraries phase and pass configure flags to disable bundled
libraries.

Change-Id: I2fb115e7b3df00cccb3f8d6659d465075d21f19b
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 78641cf9da
gnu: r-spams: Build with C++11. 
* gnu/packages/statistics.scm (r-spams)[arguments]: Add phase 'use-c++11.

Change-Id: Ie477af6afe8993919090f6c81e071cee542e69bc
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 142313cf0c
gnu: Remove r-genomegraphs. 
This package had been removed from Bioconductor with release 3.11.

* gnu/packages/bioconductor.scm (r-genomegraphs): Remove variable.

Change-Id: I73cc8cc8546089d91212176939b8c0c0a7afc309
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 0150529188
gnu: Remove r-wavetiling. 
This package had been removed from Bioconductor since release 3.12.

* gnu/packages/bioconductor.scm (r-wavetiling): Remove variable.

Change-Id: I5eb624d975f0eb170b263266b144eacf11944580
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus abaca151b2
gnu: r-mpo-db: Include HPO sqlite database. 
* 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
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus b30127052e
gnu: r-readwriter: Update to 0.3.2-1.12d32cb. 
* gnu/packages/bioinformatics.scm (r-readwriter): Update to 0.3.2-1.12d32cb.

Change-Id: I412190ce94bee4e7b5fce27db7ef8a72188e74f4
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus c66c66ee3f
gnu: r-hpo-db: Include HPO sqlite database. 
* 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
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus a938342899
gnu: r-rhdf5lib: Adjust modifications to Makevars. 
* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Adjust patch.

Change-Id: Iaef3d2d80c22de1c2a0b64e7c13f5fa3b8e5719d
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus c82c9c8090
gnu: r-phyloseq: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.46.0.

Change-Id: Id11b5e913529ac8efce0d046168f4a9dbe0dbabd
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 1c3e8ab395
gnu: r-tximeta: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.20.0.

Change-Id: I8d9c5d01efc8f6c64290cdfdd193d95cd1da9152
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 270d7e1079
gnu: r-tricycle: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.10.0.

Change-Id: I72a9e1140c17ce8605bfe6e83cc290eb1ae2fad2
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 9ee38f4ee6
gnu: r-tcgabiolinks: Update to 2.30.0. 
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.30.0.

Change-Id: If7e571bfa6454bfa94dd395606575391dc506ecd
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 28480926a5
gnu: r-biscuiteer: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.16.0.

Change-Id: Ib6cffbbeedfe87932acfcbfb2b789b4c92a9bf81
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 53ebbff56c
gnu: r-omnipathr: Update to 3.10.1. 
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.10.1.
[propagated-inputs]: Add r-lubridate and r-stringi.

Change-Id: Ia18b66848cd6996dfdc551bf4b182bb5ac3e17a8
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 41a4f01473
gnu: r-omicade4: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-omicade4): Update to 1.42.0.

Change-Id: I4369e5721116bf73f096ee39a516ada94c348872
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 73efb254d8
gnu: r-dmrseq: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.22.0.

Change-Id: I738c2fb7e0fa3e816d3767f854b8f9ed77425591
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus f6e56299e7
gnu: r-dada2: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-dada2): Update to 1.30.0.

Change-Id: I0955c3a61b4d81cd6809e2eb287d8acfcccfb789
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 407e9b2710
gnu: r-bsseq: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.38.0.

Change-Id: Ie31f0b5c726da98a0caa4c658a5c62c1a5f40eaa
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 69d7d7a6db
gnu: r-biotmle: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.26.0.

Change-Id: Ied1d1e649fba277aa724040af31334f664d2debd
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 9f2c8b711b
gnu: r-biotip: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-biotip): Update to 1.16.0.

Change-Id: I73503554b0271e5fe950c6da367b4893972f27e9
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus a7d1b8832a
gnu: r-bioqc: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-bioqc): Update to 1.30.0.

Change-Id: I0b5fd7cac1283a7f12a1221ad453eb56767e8b90
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus ee259a9ad9
gnu: r-bionetstat: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.22.0.

Change-Id: I92f2ebef0b65b947a719bdd1008f07ce279263a4
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus b0190a7d5c
gnu: r-bionet: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-bionet): Update to 1.62.0.

Change-Id: I0712a4ba67c27b32d6666e91d9515f0299e61848
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus 63f3a845ea
gnu: r-bionero: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-bionero): Update to 1.10.0.

Change-Id: I396a37dd28571a471b45d4d8aca6ce40a1cbd384
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus 4ccceb31b9
gnu: r-biomvcclass: Update to 1.70.0. 
* gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.70.0.

Change-Id: I0c6214669ec284d314eb7dc90270558934070e4b
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus b4e803a8a9
gnu: r-mvcclass: Update to 1.76.0. 
* gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.76.0.

Change-Id: I6e7fa851c804009ae41a955b117d95b33fd1b2f0
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus c91a1a8bc8
gnu: r-biomformat: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.30.0.

Change-Id: I661d11f81a0dedbc8381b5ba1806643b5ff52aa6
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus 2b4dcd4a7b
gnu: r-biodb: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-biodb): Update to 1.10.0.

Change-Id: If1d14855b2bf134741c54c0a51daefdf2b80a49f
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus 9480ea5046
gnu: r-biocthis: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.12.0.

Change-Id: I8400ebfd178f916488e022152e75db59f05994e6
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus 327c9bd7c8
gnu: r-basilisk: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.14.0.

Change-Id: I86f5306de138eb1fedffbae65c14f9acd504c86c
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus b5527cc3c6
gnu: r-basilisk-utils: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.14.0.

Change-Id: I6113042a10770ee50e4ef997ee41fe109f917885
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus b2389dcfc1
gnu: r-dir-expiry: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.10.0.

Change-Id: I1081ec981a52a51a351d98e5079f8fd4bcc399d0
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus d5026a9e16
gnu: r-genetclassifier: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-genetclassifier): Update to 1.42.0.

Change-Id: I323ca2d408c640b05c9d845570ee7af28616cce2
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus 31fef7c331
gnu: r-minet: Update to 3.60.0. 
* gnu/packages/bioconductor.scm (r-minet): Update to 3.60.0.

Change-Id: I4944d2e34aacc6d3ba8c5a2d2176ecf7b33ca6b8
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus ae127ddf0d
gnu: r-biobtreer: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-biobtreer): Update to 1.14.0.

Change-Id: Icf0458c6931237a405178361778a68c1a068337c
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus d40b4c5063
gnu: r-bgeedb: Update to 2.28.0. 
* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.28.0.

Change-Id: I558f36065a9a751710843f21c6089231309705ca
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus 38f88c84bf
gnu: r-bgeecall: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.18.1.

Change-Id: I5db747786c63f248dec01879e41a9837c94d6d6c
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus 58661d1d54
gnu: r-beclear: Update to 2.18.0. 
* gnu/packages/bioconductor.scm (r-beclear): Update to 2.18.0.

Change-Id: Ia52d2072c95c4ff68cabe22cd6f9da8f3f7833b3
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus 6ddf9ed610
gnu: r-megadepth: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-megadepth): Update to 1.12.0.

Change-Id: Ia8424334f3183442a8e7ffb21ba664b93f6342a3
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus 9d0492c750
gnu: r-ballgown: Update to 2.34.0. 
* gnu/packages/bioconductor.scm (r-ballgown): Update to 2.34.0.

Change-Id: Ice69c2be8df89cb103e73de328ac6eb5919f0502
 2023-11-03 22:49:27 +01:00