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127179 Commits (220759226e93d76d8d80058f69f9d8b29714bbde)

Author SHA1 Message Date
Efraim Flashner 4826856977
gnu: icedtea-7: Fix building on powerpc-linux. 
* gnu/packages/java.scm (icedtea-7)[arguments]: Adjust custom
'install-libjvm phase to add support for powerpc-linux.

Change-Id: Ie77a2b53fdef1e0ddc0351e6c2d0241d08b80508
 2023-11-05 08:42:48 +02:00
Mădălin Ionel Patrașcu adf716c171
gnu: Add r-screpertoire. 
* gnu/packages/bioconductor.scm (r-screpertoire): New variable.

Change-Id: Iaa876f787d5e39ca2888bf2082da3d7839224e15
 2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu 01b7d917a2
gnu: Add r-powertcr. 
* gnu/packages/bioconductor.scm (r-powertcr): New variable.

Change-Id: I75fc30a7021d6199b768318da3afcfeaaafcf027
 2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu 1678be98f2
gnu: Add r-evmix. 
* gnu/packages/cran.scm (r-evmix): New variable.

Change-Id: I93152dee218e9cef85dd66e17231f1728f0ffb52
 2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu ab64815f6a
gnu: Add r-truncdist. 
* gnu/packages/cran.scm (r-truncdist): New variable.

Change-Id: Icb9f06a36e5ee5a58828dc2f496b71a850a911b9
 2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu 3f991b817d
gnu: Add r-evd. 
* gnu/packages/cran.scm (r-evd): New variable.

Change-Id: I1f3b2ee5829807f6f76cf87b4df43ae8005688bc
 2023-11-04 23:13:51 +01:00
Wilko Meyer e3f318f048
gnu: linux-libre 5.10: Fix the hash of the deblob-scripts. 
This is a followup to commit e672066097.

* gnu/packages/linux.scm (deblob-scripts 5.10): Update hash.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: I0fe56dd2694185b6c77468ecc844aaf25ec7564a
 2023-07-23 22:26:01 -04:00
Wilko Meyer 3bb6938ffc
gnu: linux-libre 5.15: Fix the hash of the deblob-scripts. 
This is a followup to commit b26526ea05.

* gnu/packages/linux.scm (deblob-scripts 5.15): Update hash.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: Ia59003f2ccfe98e2390593d1ca0b7077f0b7bd5d
 2023-07-23 22:26:00 -04:00
Wilko Meyer 1d4813f275
gnu: linux-libre 6.1: Fix the hash of the deblob-scripts. 
This is a followup to commit 26709726a8.

* gnu/packages/linux.scm (deblob-scripts 6.1): Update hash.

Signed-off-by: Leo Famulari <leo@famulari.name>
Change-Id: I0035078f4c229763e56cf70ccae730804b123640
 2023-07-23 22:26:00 -04:00
Mădălin Ionel Patrașcu 58786c82df
gnu: Add r-rnbeads. 
* gnu/packages/bioconductor.scm (r-rnbeads): New variable.

Change-Id: I78b248a449473fc37ac414295faa6e61269b8625
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-04 17:09:53 +01:00
Mădălin Ionel Patrașcu 4c17016019
gnu: Add r-ewastools. 
* gnu/packages/bioinformatics.scm (r-ewastools): New variable.

Change-Id: I4117dbee188c7d9547fe63b2b89ec9258bbda60b
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-04 17:03:24 +01:00
Mădălin Ionel Patrașcu a04800b811
gnu: Add r-mblm. 
* gnu/packages/cran.scm (r-mblm): New variable.

Change-Id: Iddfa9bc03a4e5782623253cb70d1ae888545e2ec
 2023-11-04 17:03:24 +01:00
Mădălin Ionel Patrașcu 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
Mădălin Ionel Patrașcu 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
Jack Hill 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
Nicolas Graves 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
Mădălin Ionel Patrașcu 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
Clément Lassieur 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
Clément Lassieur 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
Afkhami, Navid 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
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