From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 26 Feb 2013 02:30:33 +0000 (-0800)
Subject: use package filters and use omegahat in addition to bioc
X-Git-Url: https://git.donarmstrong.com/?p=cran2deb.git;a=commitdiff_plain;h=refs%2Fheads%2Flocaluser

use package filters and use omegahat in addition to bioc
---

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.")