diff --git a/build.xml b/build.xml
index ef662a160..f3f88fdf7 100644
--- a/build.xml
+++ b/build.xml
@@ -547,12 +547,10 @@
 
     <target name="vcf.jar" depends="gatk.compile,init.jar">
         <jar jarfile="${dist.dir}/vcf.jar">
-            <fileset dir="${java.classes}">
-              <include name="**/utils/codecs/**/*.class"/>
-              <include name="**/utils/variantcontext/**/*.class"/>
-              <include name="org/broadinstitute/sting/utils/exceptions/**"/>
-	      <include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
-            </fileset>
+	    <classfileset dir="${java.classes}">
+	      <rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/codecs/vcf/**/*.class" />
+	      <rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/variantcontext/**/*.class" />
+	    </classfileset>
         </jar>
     </target>
 
diff --git a/public/R/src/gsalib/R/gsa.read.gatkreport.R b/public/R/src/gsalib/R/gsa.read.gatkreport.R
index 011b5240d..46bbf7eda 100644
--- a/public/R/src/gsalib/R/gsa.read.gatkreport.R
+++ b/public/R/src/gsalib/R/gsa.read.gatkreport.R
@@ -99,5 +99,5 @@ gsa.read.gatkreport <- function(filename) {
         .gsa.assignGATKTableToEnvironment(tableName, tableHeader, tableRows, tableEnv);
     }
 
-    gatkreport = as.list(tableEnv);
+    gatkreport = as.list(tableEnv, all.names=TRUE);
 }