cache: use BioC and CRAN; too many interdependencies. always pick packages in CRAN...

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/cran2deb@103 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

diff --git a/pkg/trunk/data/populate_depend_aliases b/pkg/trunk/data/populate_depend_aliases
index 0d5e3f6f807051bc9b974010715cb03bbe549d13..0d218cf8b2ae0985ba67add9039c48dbe59788a3 100644 (file)
--- a/pkg/trunk/data/populate_depend_aliases
+++ b/pkg/trunk/data/populate_depend_aliases
@@ -8,6 +8,7 @@ alias gmp libgmp3-dev
 alias gsl libgsl0-dev
 alias_build ignore build-essential
 alias_build java openjdk-6-jdk
+alias_build java libgcj9-dev
 alias_run java openjdk-6-jre
 alias libatk libatk1.0-dev
 alias libcairo libcairo2-dev

diff --git a/pkg/trunk/exec/update_cache b/pkg/trunk/exec/update_cache
index b7e7429da19579f43bbbb43753528ab6908b39a5..7c13b969fdf4ec347885c561a7a445b8c6279b83 100755 (executable)
--- a/pkg/trunk/exec/update_cache
+++ b/pkg/trunk/exec/update_cache
@@ -10,7 +10,16 @@ mirror <- 'http://cran.r-project.org/'
 
 message('updating list of available R packages...')
 available <- available.packages(contrib.url(mirror))
-#available <- rbind(available,available.packages(contrib.url('http://www.bioconductor.org/')))
+
+available_more <- available.packages(contrib.url('http://www.bioconductor.org/'))
+matches <- match(rownames(available_more),rownames(available))
+matches <- matches[!is.na(matches)]
+if (length(matches) > 0) {
+    message(paste(length(matches),'packages shared between repositories -- siding with CRAN'))
+    available <- rbind(available, available_more[-matches,])
+} else {
+    available <- rbind(available, available_more)
+}
 
 message('updating list of available R task views...')
 ctv.available <- available.views(repo=mirror)