tophat-2.0.6 build error with clang-4.1 on OSX, non-POD variable length arrays

error.log

$ make -j1
/usr/bin/make  all-recursive
Making all in src
c++ -DHAVE_CONFIG_H -I. -I. -I..     -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3  -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -I./SeqAn-1.3 -c -o segment_juncs.o segment_juncs.cpp
brew: superenv removed: -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -I/usr/local/include -I/usr/local/include
segment_juncs.cpp:4857:47: error: variable length array of non-POD element type 'std::set<Junction, skip_count_lt>'
  std::set<Junction, skip_count_lt> vseg_juncs[num_threads];
                                              ^
segment_juncs.cpp:4863:32: error: variable length array of non-POD element type 'std::set<Deletion>'
  std::set<Deletion> vdeletions[num_threads];
                               ^
segment_juncs.cpp:4864:34: error: variable length array of non-POD element type 'std::set<Insertion>'
  std::set<Insertion> vinsertions[num_threads];
                                 ^
segment_juncs.cpp:4865:27: error: variable length array of non-POD element type 'FusionSimpleSet' (aka 'map<Fusion, FusionSimpleStat>')
  FusionSimpleSet vfusions[num_threads];
                          ^
4 errors generated.
make[2]: *** [segment_juncs.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2