Merge pull request #6566 from aavogt/master

let generate-cran-packages.R complete without needing to download the whole CRAN

pkgs/development/r-modules/default.nix

@@ -663,7 +663,6 @@ let
     "ArrayBin" # requires SAGx
     "babel" # requires edgeR
     "BACA" # requires RDAVIDWebService
-    "bamboo" # depends on broken jvmr
     "BcDiag" # requires fabia
     "bdvis" # requres taxize
     "beadarrayFilter" # requires beadarray
@@ -761,7 +760,6 @@ let
     "isva" # requires qvalue
     "jomo" # linking errors
     "js" # requires broken V8
-    "jvmr" # tries to download files during its build
     "KANT" # requires affy, and Biobase
     "ktspair" # requires Biobase
     "latticeDensity" # requires spatstat
@@ -909,7 +907,6 @@ let
     "spocc" # requires leafletR
     "SQDA" # requires limma
     "Statomica" # requires Biobase, multtest
-    "StochKit2R" # tarball is invalid on server
     "stpp" # requires spatstat
     "structSSI" # requires multtest
     "strum" # requires Rgraphviz

pkgs/development/r-modules/generate-cran-packages.R

@@ -3,7 +3,12 @@ library(parallel)
 cl <- makeCluster(10)
 options(repos=structure(c(CRAN="http://cran.rstudio.com/")))
 
+
+readFormatted <- as.data.table(read.table(skip=6, sep='"', text=head(readLines('cran-packages.nix'), -1)))
+
 nixPrefetch <- function(name, version) {
+  prevV <- readFormatted$V2 == name & readFormatted$V4 == version
+  if (sum(prevV) == 1) as.character(readFormatted$V6[ prevV ]) else
     system(paste0("nix-prefetch-url --type sha256 http://cran.rstudio.com/src/contrib/", name, "_", version, ".tar.gz"), intern=TRUE)
     # system(paste0("nix-hash --flat --base32 --type sha256 /nix/store/*", name, "_", version, ".tar.gz", "| head -n 1"), intern=TRUE)
 }
@@ -21,7 +26,7 @@ formatPackage <- function(name, version, sha256, depends, imports, linkingTo, kn
     paste0(attr, " = derive { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
 }
 
-clusterExport(cl, c("nixPrefetch"))
+clusterExport(cl, c("nixPrefetch","readFormatted"))
 
 pkgs <- as.data.table(available.packages(filters=c("R_version", "OS_type", "CRAN", "duplicates")))
 pkgs <- subset(pkgs, Repository=="http://cran.rstudio.com/src/contrib")