JAL-3840 don’t update the modal residue count for gaps

[jalview.git] / build.gradle

diff --git a/build.gradle b/build.gradle
index 2c1a56d..41a972b 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -1369,13 +1369,12 @@ task linkCheck(type: JavaExec) {
   args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
 
   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
-  def errFOS = outFOS
   standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    standardOutput)
+    System.out)
   errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    errorOutput)
+    System.err)
 
   inputs.dir(helpBuildDir)
   outputs.file(helpLinksCheckerOutFile)
@@ -2548,12 +2547,12 @@ DEBUG: ${eclipseDebug}
         new org.apache.tools.ant.util.TeeOutputStream(
           logOutFOS,
           stdout),
-        standardOutput)
+        System.out)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         new org.apache.tools.ant.util.TeeOutputStream(
           logErrFOS,
           stderr),
-        errorOutput)
+        System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,