rJava: depend upon autotools-dev, run R CMD javareconf before build.

build hook for R CMD javareconf is hacky and needs to be replaced, but
works for now. rJava needs to depend upon autotools-dev to ensure it has
up to date configure scripts.

also drop BioC for now.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/cran2deb@116 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

diff --git a/pkg/trunk/R/zzz.R b/pkg/trunk/R/zzz.R
index 39a935eca7122944c94bf2bd9c958a227b09f632..fe75b9a6b6a67e8a7c7e7c5bad9536315327c673 100644 (file)
--- a/pkg/trunk/R/zzz.R
+++ b/pkg/trunk/R/zzz.R
@@ -10,7 +10,7 @@
     global("dinstall_archive", file.path(root,'var/archive'))
     global("r_depend_fields", c('Depends','Imports')) # Suggests, Enhances
     # git_revision {
-    global("git_revision","0a42c69323bbf485eb18fc4345253bee2efd7aff")
+    global("git_revision","3278eadbf43c0c5a8a46f2298a38860c34f07ba4")
     # git_revision }
     global("changesfile", function(srcname,version='*') {
         return(file.path(pbuilder_results

diff --git a/pkg/trunk/data/populate_depend_aliases b/pkg/trunk/data/populate_depend_aliases
index b36f53625a41352eb5c09745c2338d659a4604cd..175d74a0c2871b92b0430bc165583fd256a2292f 100644 (file)
--- a/pkg/trunk/data/populate_depend_aliases
+++ b/pkg/trunk/data/populate_depend_aliases
@@ -37,3 +37,4 @@ alias_run sqlite libsqlite3-0
 alias_build sqlite libsqlite3-dev
 alias zlib zlib1g-dev
 alias cshell tsch|csh|c-shell
+alias_build autotools autotools-dev

diff --git a/pkg/trunk/data/populate_forcedep b/pkg/trunk/data/populate_forcedep
index 5da35da47495d057973875f6de830748085f6c85..cdd8495f04124d65e53778514d6898e5b92a149a 100644 (file)
--- a/pkg/trunk/data/populate_forcedep
+++ b/pkg/trunk/data/populate_forcedep
@@ -1,4 +1,5 @@
 force java rJava
+force autotools rJava
 force sqlite RSQLite
 force sqlite SQLiteDF
 force boost RBGL

diff --git a/pkg/trunk/exec/update_cache b/pkg/trunk/exec/update_cache
index 9fc98a285890e1d02081c128f320a683ea1b4d61..5370210c02c1bab56e218554f5eb650618a3b6c8 100755 (executable)
--- a/pkg/trunk/exec/update_cache
+++ b/pkg/trunk/exec/update_cache
@@ -11,10 +11,9 @@ 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/')))
-# prefer CRAN
-dupes <- duplicated(rownames(available), fromLast=T)
-available <- available[!dupes,]
+#available <- rbind(available,available.packages(contrib.url('http://www.bioconductor.org/')))
+#dupes <- duplicated(rownames(available), fromLast=T)
+#available <- available[!dupes,]
 
 message('updating list of available R task views...')
 ctv.available <- available.views(repo=mirror)

diff --git a/pkg/trunk/inst/etc/hook/A80rjava b/pkg/trunk/inst/etc/hook/A80rjava
new file mode 100755 (executable)
index 0000000..1d37c8b
--- /dev/null
+++ b/pkg/trunk/inst/etc/hook/A80rjava
@@ -0,0 +1,4 @@
+if [ -n "$(which java)" ]
+then
+    R CMD javareconf
+fi