Working with BioConductor.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/cran2deb@343 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

diff --git a/trunk/exec/update_cache b/trunk/exec/update_cache
index b47921be8c3d0561de67a57c2e23a06852de4319..e9bb8900f5e54a3ce41e39283d81d132657ce4a8 100755 (executable)
--- a/trunk/exec/update_cache
+++ b/trunk/exec/update_cache
@@ -14,9 +14,11 @@ ctv.available <- NULL
 
 mirrors <- NULL
 mirrors <- c(mirrors,CRAN='http://cran.r-project.org')
-#mirrors <- c(mirrors,BioC='http://www.bioconductor.org/packages/2.7')
+#mirrors <- c(mirrors,BioC='http://www.bioconductor.org/packages/2.2')
+mirrors <- c(mirrors,BioC='http://www.bioconductor.org/packages/2.7')
 
 verbose<-TRUE
+debug<-FALSE
 
 for (mirror.name in names(mirrors)) {
        mirror.url<-mirrors[mirror.name]
@@ -25,8 +27,17 @@ for (mirror.name in names(mirrors)) {
        if ("CRAN" == mirror.name) {
                packages.retrieved <- available.packages(contrib.url(mirror.url))
        } else if ("BioC" == mirror.name) {
-               for (s in c('bioc')) {
-                       packages.retrieved <- rbind(packages.retrieved,contrib.url(available.packages(paste(mirror.url,s,sep="/"))))
+               repos <- c(
+                       "bioc"
+                       ,"data/annotation"
+                       ,"data/experiment"
+                       ,"extra"
+               )
+               for (s in repos) {
+                       packages.retrieved <- rbind(
+                               packages.retrieved,
+                               available.packages(contrib.url(paste(mirror.url,s,sep="/")))
+                       )
                }
        } else {
                packages.retrieved <- available.packages(mirror.url)
@@ -62,7 +73,7 @@ if (any(grep("^E:",base_pkgs,value=FALSE))) {
 }
 
 
-if (verbose) {
+if (debug) {
        cat("The following base packages were determined:\n")
        print(base_pkgs)
 }