e16d152463
gnu: Add r-dnamcrosshyb.
...
* gnu/packages/bioinformatics.scm (r-dnamcrosshyb): New variable.
Change-Id: I19e332e6adf0ce9cc721d89bb74a1aa709778873
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-04 16:30:11 +01:00
cb0e60cccf
gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked.
...
* gnu/packages/bioconductor.scm
(r-bsgenome-hsapiens-ucsc-hg38-masked): New variable.
Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b
2023-11-04 16:30:11 +01:00
9dcd8802f5
gnu: python-pikepdf: Fix embedded version string.
...
* gnu/packages/python-xyz.scm (python-pikepdf)[native-inputs]: Add
python-setuptools-scm to correct embedded version form 0.0.0 to 1.17.0.
Change-Id: I659ed3e725fff6afe17abe6f55449567ba84cdfc
2023-11-04 19:05:28 +08:00
33644303a1
gnu: emacs-org-ql-dynamic-agenda: Rename to emacs-org-dynamic-agenda-ql.
...
* /gnu/packages/emacs-xyz.scm (emacs-org-ql-dynamic-agenda): Rename to…
(emacs-org-dynamic-agenda-ql): …this.
[arguments]<#:include>: Adjust according to source change.
Change-Id: I4b09933a17d301e3017f1628414eade1ee174538
2023-11-04 19:03:39 +08:00
7eeab6417f
gnu: Add r-methylaid.
...
* gnu/packages/bioconductor.scm (r-methylaid): New variable.
Change-Id: I7839035e5316bdbe5f1386b7b41ed2fc440fb432
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-04 11:37:15 +01:00
f54f36b363
gnu: passff-host: Add explicit references to inputs and remove some.
...
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
2023-11-04 00:52:39 +01:00
625cfb4c4c
gnu: password-store: Add missing ‘tail’ input.
...
* gnu/packages/password-utils.scm (password-store)[arguments]: Add “tail” to
the list of requisites.
[inputs]: Add COREUTILS.
Change-Id: I7f59e6c0abfb5396b9548edaec08d3b0a7c0eb23
2023-11-04 00:52:38 +01:00
10d728139d
gnu: Add r-ggbreak.
...
* gnu/packages/cran.scm (r-ggbreak): New variable.
Change-Id: I27d62d0110fb56e77dc8cf82581adb6259317c2d
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-03 23:39:57 +01:00
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
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
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
96e8502faa
gnu: Add python-emcee.
...
* gnu/packages/statistics.scm (python-emcee): New variable.
2023-11-03 19:25:35 -03:00
a7d56852e3
gnu: Add python-salib.
...
* gnu/packages/python-science.scm (python-salib): New variable.
2023-11-03 19:25:35 -03:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Mădălin Ionel Patrașcu
Jack Hill
Nicolas Graves
Clément Lassieur
Afkhami, Navid
Vinicius Monego
Ricardo Wurmus