From afa892195222cb90f0264f527c0864cf78c05176 Mon Sep 17 00:00:00 2001
From: "Andre L. Martins" <alm253@cornell.edu>
Date: Tue, 14 Oct 2014 16:41:20 +0100
Subject: [PATCH] Improve twoBit R interface compilation

- Add missing symlinks for twobit.h twobit.c (and drop them from .gitignore)
- Add Roxygen script to support roxygen2 systems (> 4.0)
---
 .gitignore       |  2 --
 Makefile         |  2 +-
 Roxygen          | 30 ++++++++++++++++++++++++++++++
 pkg/src/twobit.c |  1 +
 pkg/src/twobit.h |  1 +
 5 files changed, 33 insertions(+), 3 deletions(-)
 create mode 100755 Roxygen
 create mode 120000 pkg/src/twobit.c
 create mode 120000 pkg/src/twobit.h

diff --git a/.gitignore b/.gitignore
index 6424f0c..a099ccb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,3 @@
-pkg/src/twobit.c
-pkg/src/twobit.h
 *.roxygen
 2bit_ls
 test
diff --git a/Makefile b/Makefile
index e5da1d5..200f6d0 100644
--- a/Makefile
+++ b/Makefile
@@ -11,5 +11,5 @@ twobit.so: twobit.c
 
 twoBit.pkg:
 	rm -Rf pkg.roxygen
-	R CMD roxygen pkg
+	(R CMD roxygen pkg)||(./Roxygen pkg)
 	R CMD INSTALL pkg.roxygen
diff --git a/Roxygen b/Roxygen
new file mode 100755
index 0000000..6c953f7
--- /dev/null
+++ b/Roxygen
@@ -0,0 +1,30 @@
+#!/usr/bin/Rscript
+library(methods)
+library(utils)
+library(roxygen2)
+
+args <- commandArgs(TRUE)
+
+sourcePath = args[1]
+
+tmp = charToRaw(sourcePath)
+if (tmp[length(tmp)] == charToRaw("/"))
+  tmp = tmp[1:(length(tmp) - 1)]
+sourcePath = rawToChar(tmp)
+
+output = paste(sourcePath, ".roxygen", sep='')
+
+#
+# stupid roxygen no longer supports separte output path
+#
+res = system(paste("mkdir", output), intern = FALSE, wait = TRUE)
+if (res != 0)
+ stop("failed to create output folder")
+
+res = system(paste("cp -Rf ", sourcePath, "/* ", output, sep=''), intern = FALSE, wait = TRUE)
+if (res != 0)
+ stop("failed to copy input to output folder")
+
+#roxygenize(sourcePath, output)
+#roxygenize(output, output)
+roxygenize(output)
diff --git a/pkg/src/twobit.c b/pkg/src/twobit.c
new file mode 120000
index 0000000..0df528e
--- /dev/null
+++ b/pkg/src/twobit.c
@@ -0,0 +1 @@
+../../twobit.c
\ No newline at end of file
diff --git a/pkg/src/twobit.h b/pkg/src/twobit.h
new file mode 120000
index 0000000..afd4a0e
--- /dev/null
+++ b/pkg/src/twobit.h
@@ -0,0 +1 @@
+../../twobit.h
\ No newline at end of file