From eb5a0c49e2fd95918e3e43ddf923ecdc54e64026 Mon Sep 17 00:00:00 2001
From: Chris O'Neill <chris@redgrovecomputing.com>
Date: Sun, 10 Dec 2017 17:31:35 +0000
Subject: [PATCH] Close textConnections after data has been read within
 read.markup.RCC() to avoid exhausting the 125 user allocatable connections.

---
 R/read.markup.RCC.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/read.markup.RCC.R b/R/read.markup.RCC.R
index a86b550..f3a6bb0 100755
--- a/R/read.markup.RCC.R
+++ b/R/read.markup.RCC.R
@@ -51,17 +51,21 @@ read.markup.RCC <- function(rcc.path = ".", rcc.pattern = "*.RCC|*.rcc", exclude
 		# convert data into table for all data structures
 		header.con <- textConnection(as.character(header.info$text));
 		header.data <- read.csv(header.con, header = FALSE, stringsAsFactors = FALSE);
+		close(header.con)
 
 		sample.con <- textConnection(as.character(sample.info$text));
 		sample.data <- read.csv(sample.con, header = FALSE, stringsAsFactors = FALSE);
 		sample.data[which(sample.data[, 1] == "ID"), 1] <- "sample.id";
+		close(sample.con)
 
 		lane.con <- textConnection(as.character(lane.info$text));
 		lane.data <- read.csv(lane.con, header = FALSE, stringsAsFactors = FALSE);
 		lane.data[which(lane.data[, 1] == "ID"), 1] <- "lane.id";
+		close(lane.con)
 
 		code.con <- textConnection(as.character(code.info$text));
 		code.data <- read.csv(code.con, header = TRUE, stringsAsFactors = FALSE);
+		close(code.con)
 
 		# combine metadata
 		rcc.header <- do.call(rbind, list(header.data, sample.data, lane.data));