Update sources

Even when built in /app for flatpaks, modules in the /usr prefix must also
be found, and a /usr/bin/Rscript symlink is needed to resolve shebang
dependencies when building other packages.

.gitignore

@@ -0,0 +1,63 @@
+/xz-5.2.2.tar.bz2
+/zlib-1.2.8.tar.gz
+/bzip2-1.0.6.tar.gz
+/curl-7.48.0.tar.bz2
+/pcre-8.38.tar.bz2
+/R-3.3.1.tar.gz
+/R-3.3.2.tar.gz
+/R-3.3.3.tar.gz
+/zlib-1.2.11.tar.gz
+/bzip2-1.0.6.tar.gz
+/xz-5.2.3.tar.bz2
+/pcre-8.40.tar.bz2
+/curl-7.53.1.tar.bz2
+/R-3.4.0.tar.gz
+/R-3.4.1.tar.gz
+/R-3.4.2.tar.gz
+/pcre-8.41.tar.bz2
+/curl-7.56.1.tar.bz2
+/R-3.4.3.tar.gz
+/R-3.4.4.tar.gz
+/pcre-8.42.tar.bz2
+/curl-7.59.0.tar.bz2
+/xz-5.2.4.tar.bz2
+/R-3.5.0.tar.gz
+/R-3.5.1.tar.gz
+/curl-7.61.1.tar.bz2
+/curl-7.63.0.tar.bz2
+/R-3.5.2.tar.gz
+/R-3.5.3.tar.gz
+/R-3.6.0.tar.gz
+/R-3.6.1.tar.gz
+/R-3.6.2.tar.gz
+/bzip2-1.0.8.tar.gz
+/pcre-8.43.tar.bz2
+/curl-7.67.0.tar.bz2
+/R-3.6.3.tar.gz
+/R-4.0.0.tar.gz
+/R-4.0.1.tar.gz
+/R-4.0.2.tar.gz
+/xz-5.2.5.tar.bz2
+/R-4.0.3.tar.gz
+/pcre-8.44.tar.bz2
+/curl-7.72.0.tar.bz2
+/R-4.0.4.tar.gz
+/R-4.0.5.tar.gz
+/R-4.1.0.tar.gz
+/R-4.1.1.tar.gz
+/R-4.1.2.tar.gz
+/R-4.1.3.tar.gz
+/R-4.2.1.tar.gz
+/R-4.2.2.tar.gz
+/R-4.2.3.tar.gz
+/R-4.3.0.tar.gz
+/R-4.3.1.tar.gz
+/R-4.3.2.tar.gz
+/R-4.3.3.tar.gz
+/R-4.4.0.tar.gz
+/R-4.4.1.tar.gz
+/R-4.4.2.tar.gz
+/R-4.4.3.tar.gz
+/R-4.5.0.tar.gz
+/R-4.5.1.tar.gz
+/R-4.5.2.tar.gz

Makefile

@@ -1,21 +0,0 @@
-# Makefile for source rpm: R
-# $Id$
-NAME := R
-SPECFILE = $(firstword $(wildcard *.spec))
-
-define find-makefile-common
-for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done
-endef
-
-MAKEFILE_COMMON := $(shell $(find-makefile-common))
-
-ifeq ($(MAKEFILE_COMMON),)
-# attept a checkout
-define checkout-makefile-common
-test -f CVS/Root && { cvs -Q -d $$(cat CVS/Root) checkout common && echo "common/Makefile.common" ; } || { echo "ERROR: I can't figure out how to checkout the 'common' module." ; exit -1 ; } >&2
-endef
-
-MAKEFILE_COMMON := $(shell $(checkout-makefile-common))
-endif
-
-include $(MAKEFILE_COMMON)

R-3.3.0-fix-java_path-in-javareconf.patch

@@ -0,0 +1,12 @@
+diff -up R-3.3.0/src/scripts/javareconf.in.fixpath R-3.3.0/src/scripts/javareconf.in
+--- R-3.3.0/src/scripts/javareconf.in.fixpath	2016-05-10 11:13:49.539844250 -0400
++++ R-3.3.0/src/scripts/javareconf.in	2016-05-10 11:15:10.475180907 -0400
+@@ -78,7 +78,7 @@ else
+ 	JAVA_PATH=${PATH}
+     else
+ 	## try jre/bin first just in case we don't have full JDK
+-	JAVA_PATH=${JAVA_HOME}:${JAVA_HOME}/jre/bin:${JAVA_HOME}/bin:${JAVA_HOME}/../bin:${PATH}
++	JAVA_PATH=${JAVA_HOME}:${JAVA_HOME}/jre/bin:${PATH}:${JAVA_HOME}/bin:${JAVA_HOME}/../bin
+     fi
+ fi
+ ## if 'java' is not on the PATH or JAVA_HOME, add some guesses as of

sources

@@ -0,0 +1 @@
+SHA512 (R-4.5.2.tar.gz) = abc4ff1a1b18a1f480e7bceb3267074e30453b5a571034b4c2a1c53e1650a1bafaf86bc6ca37f117a2e4f6617039dedeedef4ba8743f38720fc70e4bed2ff0a4

update-submodules.sh

@@ -0,0 +1,22 @@
+#! /usr/bin/bash
+
+if [ $# -eq 0 ]; then
+    >&2 echo "Usage: ./update-submodules.sh R-<version>.tar.gz"
+    exit 1
+fi
+
+TAR=$1
+DIR=$(tar tf $TAR | cut -d"/" -f1 | uniq)
+SPEC=$PWD/R.spec
+
+tar -xf $TAR
+pushd $DIR/src/library/Recommended
+for PKG in *.tar.gz; do
+    PKG="${PKG%.tar.gz}"
+    PKG_NAME="${PKG%_*}"
+    PKG_VERS="${PKG#*_}"
+    sed -i "s/submodule  $PKG_NAME.*/submodule  $PKG_NAME $PKG_VERS/" $SPEC
+    sed -i "s/R-$PKG_NAME-devel = .*/R-$PKG_NAME-devel = ${PKG_VERS//-/.}/" $SPEC
+done
+popd
+rm -rf $DIR