Reduced buffer size and tried to find reason for segfault.

Also added cache invalidation calls when seeking.

com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/conn/DelegateRConnection.java

@@ -57,7 +57,7 @@ import sun.nio.cs.StreamDecoder;
  * </p>
  */
 abstract class DelegateRConnection implements RConnection, ByteChannel {
-    private static final int DEFAULT_CACHE_SIZE = 64 * 1024;
+    private static final int DEFAULT_CACHE_SIZE = 16 * 1024;
     protected final BaseRConnection base;
     private final ByteBuffer cache;
 
@@ -449,14 +449,16 @@ abstract class DelegateRConnection implements RConnection, ByteChannel {
         final int bytesRequested = dst.remaining();
         int totalBytesRead = 0;
         int bytesToRead = 0;
+        boolean eof;
         do {
-            ensureDataAvailable(dst.remaining());
+            eof = ensureDataAvailable(dst.remaining());
             bytesToRead = Math.min(cache.remaining(), dst.remaining());
             cache.get(dst.array(), dst.position(), bytesToRead);
             dst.position(dst.position() + bytesToRead);
             totalBytesRead += bytesToRead;
         } while (totalBytesRead < bytesRequested && bytesToRead > 0);
-        return totalBytesRead;
+        return totalBytesRead == 0 && eof ? -1 : totalBytesRead;
+// return getChannel().read(dst);
     }
 
     @Override
@@ -473,24 +475,34 @@ abstract class DelegateRConnection implements RConnection, ByteChannel {
      * </p>
      */
     protected int readInternal() throws IOException {
-        ensureDataAvailable(1L);
+        ensureDataAvailable(1);
         if (!cache.hasRemaining()) {
             return -1;
         }
         // consider byte to be unsigned
         return cache.get() & 0xFF;
+
+// ByteBuffer buf = ByteBuffer.allocate(1);
+// int n = getChannel().read(buf);
+// if (n <= 0) {
+// return -1;
+// }
+// buf.flip();
+// return buf.get() & 0xFF;
     }
 
-    private void ensureDataAvailable(long i) throws IOException {
+    private boolean ensureDataAvailable(int i) throws IOException {
         if (cache.remaining() < i) {
             byte[] rem = new byte[cache.remaining()];
             cache.get(rem);
             assert !cache.hasRemaining();
             cache.clear();
             cache.put(rem);
-            getChannel().read(cache);
+            int read = getChannel().read(cache);
             cache.flip();
+            return read == -1;
         }
+        return false;
     }
 
     protected void invalidateCache() {

com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/conn/FileConnections.java

@@ -267,6 +267,12 @@ public class FileConnections {
             return true;
         }
 
+        @Override
+        public long seek(long offset, SeekMode seekMode, SeekRWMode seekRWMode) throws IOException {
+            invalidateCache();
+            return DelegateRConnection.seek(channel, offset, seekMode, seekRWMode);
+        }
+
         @Override
         public ByteChannel getChannel() {
             return channel;
@@ -425,6 +431,7 @@ public class FileConnections {
                 default:
                     throw RError.nyi(RError.SHOW_CALLER, "seek mode");
             }
+            invalidateCache();
             return result;
         }
 
@@ -581,6 +588,7 @@ public class FileConnections {
                     writeOffset = offset;
                     break;
             }
+            invalidateCache();
             return result;
         }
 

com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/conn/RawConnections.java

@@ -217,6 +217,7 @@ public class RawConnections {
 
         @Override
         public long seek(long offset, SeekMode seekMode, SeekRWMode seekRWMode) throws IOException {
+            invalidateCache();
             return RawRConnection.seek(channel, offset, seekMode, seekRWMode);
         }