diff --git a/var/spack/repos/builtin/packages/tophat/package.py b/var/spack/repos/builtin/packages/tophat/package.py
index ec2e478a3f4116..e4c0880c3a0249 100644
--- a/var/spack/repos/builtin/packages/tophat/package.py
+++ b/var/spack/repos/builtin/packages/tophat/package.py
@@ -50,6 +50,11 @@ class Tophat(AutotoolsPackage):
     depends_on('boost@1.47:')
     depends_on('bowtie2', type='run')
 
+    # uses make_pair which changed signature with C++14
+    # a patch exists: https://github.com/DaehwanKimLab/tophat/pull/38
+    # but there might be unexpected side effects
+    conflicts('%gcc@6:')
+
     parallel = False
 
     def configure_args(self):