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Merged
jbedo merged 15 commits into from
Jun 23, 2025
Merged

R updates #416842

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181c75a
R: 4.5.0 -> 4.5.1
jbedo Jun 15, 2025
2e555c4
rPackages: CRAN and BioC update
jbedo Jun 15, 2025
4376b2a
rPackages.BAT: fix build
jbedo Jun 15, 2025
6c412ad
rPackages.pak: fix build
jbedo Jun 15, 2025
dc86a95
rPackages.baseline: fix build
jbedo Jun 15, 2025
8e54329
rPackages.orbweaver: fixed build
b-rodrigues Jun 17, 2025
c119e10
rPackages.tergo: fixed build
b-rodrigues Jun 17, 2025
90bd848
rPackages.tabs: fixed build
b-rodrigues Jun 17, 2025
08e2c2d
rPackages.gglinedensity: fixed build
b-rodrigues Jun 17, 2025
f3d037c
rPackages.red: fixed build
b-rodrigues Jun 17, 2025
d252979
rPackages.orbweaver: fixed build (#417448)
jbedo Jun 18, 2025
a8c1f55
rPackages.tergo: fixed build (#417449)
jbedo Jun 18, 2025
8f98e32
rPackages.tabs: fixed build (#417526)
jbedo Jun 18, 2025
530ff65
rPackages.gglinedensity: fixed build (#417529)
jbedo Jun 18, 2025
de89502
rPackages.red: fixed build (#417531)
jbedo Jun 18, 2025
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4 changes: 2 additions & 2 deletions pkgs/applications/science/math/R/default.nix
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Original file line number Diff line number Diff line change
Expand Up @@ -47,15 +47,15 @@ assert (!blas.isILP64) && (!lapack.isILP64);

stdenv.mkDerivation (finalAttrs: {
pname = "R";
version = "4.5.0";
version = "4.5.1";

src =
let
inherit (finalAttrs) pname version;
in
fetchurl {
url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
sha256 = "sha256-OzPqET4NHdyXk4dNWUnOwsc4b2bkq/sc75rsIoRsPOE=";
hash = "sha256-tCp5IUADhmRbEBBbkcaHKHh9tcTIPJ9sMKzc5jLhu3A=";
};

outputs = [
Expand Down
4 changes: 2 additions & 2 deletions pkgs/development/r-modules/bioc-annotation-packages.json
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Original file line number Diff line number Diff line change
Expand Up @@ -1043,8 +1043,8 @@
},
"IlluminaHumanMethylationMSAmanifest": {
"name": "IlluminaHumanMethylationMSAmanifest",
"version": "0.1.0",
"sha256": "01q7i5a2zc9pby9ivsqq8pdp80732akq4g8d594h9dn6qgm0znz3",
"version": "0.1.1",
"sha256": "1ksw8nr4ghvih4imc9bj7xm1wvnw5wg4mhzw8mcvdvw3bjz4ly64",
"depends": ["minfi"]
},
"JASPAR2018": {
Expand Down
21 changes: 10 additions & 11 deletions pkgs/development/r-modules/bioc-experiment-packages.json
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Original file line number Diff line number Diff line change
Expand Up @@ -555,6 +555,12 @@
"sha256": "0rmp259r5n0dqf8zn9wwfqlcbdan1qs3ni0f4izv4nj3mym435y9",
"depends": ["ExperimentHub", "S4Vectors", "SummarizedExperiment"]
},
"Hiiragi2013": {
"name": "Hiiragi2013",
"version": "1.44.2",
"sha256": "0kl423kr19ai4kz7a5dv3d0swgzp3911pgxyp8qf8kgy952a1rr1",
"depends": ["Biobase", "KEGGREST", "MASS", "RColorBrewer", "affy", "boot", "clue", "cluster", "genefilter", "geneplotter", "gplots", "gtools", "lattice", "latticeExtra", "mouse4302_db", "xtable"]
},
"HumanAffyData": {
"name": "HumanAffyData",
"version": "1.34.0",
Expand Down Expand Up @@ -905,8 +911,8 @@
},
"ProteinGymR": {
"name": "ProteinGymR",
"version": "1.2.0",
"sha256": "0li7kra2p2hg77x2jsy96dz0q052lf05kr9y4v3r35p62rzhnc35",
"version": "1.2.1",
"sha256": "1xwva9gnfldgx2bw62zwz3wlc84k4jlnybq81nr0xqa6xdr9fycl",
"depends": ["AnnotationHub", "ComplexHeatmap", "ExperimentHub", "bio3d", "circlize", "dplyr", "forcats", "ggExtra", "ggdist", "gghalves", "ggplot2", "htmltools", "lifecycle", "pals", "purrr", "queryup", "r3dmol", "rlang", "spdl", "stringr", "tidyr", "tidyselect"]
},
"PtH2O2lipids": {
Expand Down Expand Up @@ -2471,8 +2477,8 @@
},
"systemPipeRdata": {
"name": "systemPipeRdata",
"version": "2.12.0",
"sha256": "04xxwdcznxdhxhmn73b9njj0mrd5bn3bwznnx5wf3p5qkfdckl9g",
"version": "2.12.2",
"sha256": "12vxhm096gwy026gnh1ql1749gpxdsch70x3bc2a2pcnc74kk2hf",
"depends": ["BiocGenerics", "Biostrings", "jsonlite", "remotes"]
},
"tartare": {
Expand Down Expand Up @@ -2632,13 +2638,6 @@
"depends": ["AnnotationDbi", "Biobase", "GGBase", "illuminaHumanv1_db", "snpStats"],
"broken": true
},
"Hiiragi2013": {
"name": "Hiiragi2013",
"version": "1.41.0",
"sha256": "0z8ns2qsnng3kvzcris3hxggy1jmzrl8jwy0ndf6sbn1cqj1pnkl",
"depends": ["Biobase", "KEGGREST", "MASS", "RColorBrewer", "affy", "boot", "clue", "cluster", "genefilter", "geneplotter", "gplots", "gtools", "lattice", "latticeExtra", "mouse4302_db", "xtable"],
"broken": true
},
"MAQCsubsetAFX": {
"name": "MAQCsubsetAFX",
"version": "1.8.0",
Expand Down
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