From 6432ac63081a6e6d1a38cdcaac7195df479d3294 Mon Sep 17 00:00:00 2001 From: blundellc Date: Sat, 13 Sep 2008 13:23:56 +0000 Subject: [PATCH] cache: use BioC and CRAN; too many interdependencies. always pick packages in CRAN over those in BioC. add build depends for java on libgcj9-dev (jni) git-svn-id: svn://svn.r-forge.r-project.org/svnroot/cran2deb@103 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- pkg/trunk/data/populate_depend_aliases | 1 + pkg/trunk/exec/update_cache | 11 ++++++++++- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/pkg/trunk/data/populate_depend_aliases b/pkg/trunk/data/populate_depend_aliases index 0d5e3f6..0d218cf 100644 --- 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 b7e7429..7c13b96 100755 --- 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) -- 2.39.5