From 37076660acdbcfc0da9d645a7fc3d59a32711b03 Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Mon, 25 Feb 2013 18:30:33 -0800 Subject: [PATCH] use package filters and use omegahat in addition to bioc --- trunk/exec/update_cache | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/trunk/exec/update_cache b/trunk/exec/update_cache index ebf1d3e..8107b74 100755 --- a/trunk/exec/update_cache +++ b/trunk/exec/update_cache @@ -14,18 +14,20 @@ ctv.available <- NULL mirrors <- NULL mirrors <- c(mirrors,CRAN='http://cran.r-project.org') -#mirrors <- c(mirrors,BioC='http://www.bioconductor.org/packages/2.2') -mirrors <- c(mirrors,BioC='http://www.bioconductor.org/packages/2.7') +mirrors <- c(mirrors,BioC='http://www.bioconductor.org/packages/2.11') +mirrors <- c(mirrors,Omegahat="http://www.omegahat.org/R/src/contrib") verbose<-TRUE debug<-FALSE +package.filters <- c("OS_type","duplicates") for (mirror.name in names(mirrors)) { mirror.url<-mirrors[mirror.name] message(paste("Updating list of available R packages from ",mirror.name," [",mirror.url,"].\n",sep="")) packages.retrieved <- NULL if ("CRAN" == mirror.name) { - packages.retrieved <- available.packages(contrib.url(mirror.url)) + packages.retrieved <- available.packages(contrib.url(mirror.url),filters=package.filters) + print(packages.retrieved[grep("SNP",rownames(packages.retrieved)),]) } else if ("BioC" == mirror.name) { repos <- c( "bioc" @@ -36,11 +38,11 @@ for (mirror.name in names(mirrors)) { for (s in repos) { packages.retrieved <- rbind( packages.retrieved, - available.packages(contrib.url(paste(mirror.url,s,sep="/"))) + available.packages(contrib.url(paste(mirror.url,s,sep="/")),filters=package.filters) ) } } else { - packages.retrieved <- available.packages(mirror.url) + packages.retrieved <- available.packages(mirror.url,filters=package.filters) } if (verbose) message(paste("Retrieved ",nrow(packages.retrieved)," package descriptions.\n",sep="")) available <- rbind(available, packages.retrieved) @@ -52,7 +54,11 @@ for (mirror.name in names(mirrors)) { dupes <- duplicated(rownames(available), fromLast=T) if (sum(dupes)>0) { - if (verbose) cat("Found ",sum(dupes)," packages with the same name in different distributions. Those are now removed.\n",sep="") + if (verbose) { + cat("Found ",sum(dupes)," packages with the same name in different distributions. Those are now removed.\n",sep="") + print(available[dupes,]) + } + available <- available[!dupes,,drop=F] } else { if (length(mirrors)>1) cat("All packages have different names.") -- 2.39.2