Ricardo Wurmus
38b5777ec8
gnu: r-rhdf5filters: Simplify.
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* 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.
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* 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.
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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.
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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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioconductor.scm (r-ballgown): Update to 2.34.0.
Change-Id: Ice69c2be8df89cb103e73de328ac6eb5919f0502
2023-11-03 22:49:27 +01:00
Ricardo Wurmus
7e36e3ed55
gnu: r-guitar: Update to 2.18.0.
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* gnu/packages/bioconductor.scm (r-guitar): Update to 2.18.0.
Change-Id: I2cd39de6e1fedbc3ed9a137373d6836e930296f2
2023-11-03 22:49:27 +01:00
Ricardo Wurmus
0c881be497
gnu: r-chromstar: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-chromstar): Update to 1.28.0.
Change-Id: I48a305a00b1fe7c89ca4f9700ebe6f65a6265080
2023-11-03 22:49:27 +01:00
Ricardo Wurmus
d775b141cf
gnu: r-snpstats: Update to 1.52.0.
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* gnu/packages/bioconductor.scm (r-snpstats): Update to 1.52.0.
Change-Id: Ia770e5b05a7998d552b8ccb5386ddc1ad6722217
2023-11-03 22:49:27 +01:00
Ricardo Wurmus
3b0e948493
gnu: r-snprelate: Update to 1.36.0.
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* gnu/packages/bioconductor.scm (r-snprelate): Update to 1.36.0.
Change-Id: I79ab3d448ab4b10a97d9c9d36b3b849a7c491508
2023-11-03 22:49:27 +01:00
Ricardo Wurmus
bbe5704c17
gnu: r-snapcgh: Update to 1.72.0.
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* gnu/packages/bioconductor.scm (r-snapcgh): Update to 1.72.0.
Change-Id: I7b2adbcb45461b5dc4f8248f92bfbda5f145d906
2023-11-03 22:49:27 +01:00
Ricardo Wurmus
6b8c604e48
gnu: r-pathview: Update to 1.42.0.
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* gnu/packages/bioconductor.scm (r-pathview): Update to 1.42.0.
Change-Id: I56a1425210667cc9b1ee41d20b9a71a749f6ff91
2023-11-03 22:49:27 +01:00
Ricardo Wurmus
740e7ff51b
gnu: r-parody: Update to 1.60.0.
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* gnu/packages/bioconductor.scm (r-parody): Update to 1.60.0.
Change-Id: I409588b32e582c0c6cd631d56a92ca430e2429d4
2023-11-03 22:49:27 +01:00
Ricardo Wurmus
e9618ab210
gnu: r-ldblock: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-ldblock): Update to 1.32.0.
Change-Id: I4183a3b48e050120ffb1e5cbba3894a5637ad1cc
2023-11-03 22:49:27 +01:00
Ricardo Wurmus
9f139605ef
gnu: r-kegggraph: Update to 1.62.0.
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* gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.62.0.
Change-Id: Iadaa3580a5755ca5e611d980241191c4ae8b9452
2023-11-03 22:49:27 +01:00
Ricardo Wurmus
b6288f949f
gnu: r-gwastools: Update to 1.48.0.
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* gnu/packages/bioconductor.scm (r-gwastools): Update to 1.48.0.
[native-inputs]: Add r-knitr.
Change-Id: I0544357b6f954e4812d1cdb983e12ed34f83b0d1
2023-11-03 22:49:27 +01:00
