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Merge pull request #127790 from PhDyellow/r_bioc_updater_revised

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r-modules: R bioc updater revised
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Justin Bedő 2021-09-16 09:36:18 +00:00 committed by GitHub
commit 29595eba18
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3 changed files with 28 additions and 8 deletions
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20
pkgs/development/r-modules/default.nix
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@ -43,21 +43,29 @@ let
#
deriveBioc = mkDerive {
mkHomepage = {name, biocVersion, ...}: "https://bioconductor.org/packages/${biocVersion}/bioc/html/${name}.html";
mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/bioc/src/contrib/${name}_${version}.tar.gz"
"mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}/${name}_${version}.tar.gz"
"mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}_${version}.tar.gz" ];
mkUrls = {name, version, biocVersion}: [
"mirror://bioc/${biocVersion}/bioc/src/contrib/${name}_${version}.tar.gz"
"mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}/${name}_${version}.tar.gz"
"mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}_${version}.tar.gz"
];
};
deriveBiocAnn = mkDerive {
mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html";
mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ];
mkUrls = {name, version, biocVersion}: [
"mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz"
];
};
deriveBiocExp = mkDerive {
mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html";
mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz" ];
mkUrls = {name, version, biocVersion}: [
"mirror://bioc/${biocVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz"
];
};
deriveCran = mkDerive {
mkHomepage = {name, snapshot, ...}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/";
mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ];
mkUrls = {name, version, snapshot}: [
"http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz"
];
};
# Overrides package definitions with nativeBuildInputs.

9
pkgs/development/r-modules/generate-r-packages.R
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@ -1,9 +1,16 @@
#!/usr/bin/env Rscript
library(data.table)
library(parallel)
library(BiocManager)
cl <- makeCluster(10)
biocVersion <- 3.12
biocVersion <- BiocManager:::.version_map()
biocVersion <- biocVersion[biocVersion$R == getRversion()[, 1:2],c("Bioc", "BiocStatus")]
if ("release" %in% biocVersion$BiocStatus) {
biocVersion <- as.numeric(as.character(biocVersion[biocVersion$BiocStatus == "release", "Bioc"]))
} else {
biocVersion <- max(as.numeric(as.character(biocVersion$Bioc)))
}
snapshotDate <- Sys.Date()-1
mirrorUrls <- list( bioc=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/bioc/src/contrib/")

7
pkgs/development/r-modules/generate-shell.nix
View File

@ -5,13 +5,18 @@ stdenv.mkDerivation {
buildCommand = "exit 1";
buildInputs = [ wget ];
buildInputs = [
wget
cacert
nix
];
nativeBuildInputs = [
(rWrapper.override {
packages = with rPackages; [
data_table
parallel
BiocManager
];
})
];