Cufflinks/cuffdiff fails for demo data set about cufflinks HOT 6 OPEN

g++  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3  -DNDEBUG  -pthread -I/usr/local/opt/boost155/include -I/usr/local/include -I/usr/local/include/Eigen/include -L/usr/local/opt/samtools/lib -L/usr/local/opt/boost155/lib -L/usr/local/lib  -L/usr/local/opt/samtools/lib -o gtf_to_sam gtf_to_sam.o libcufflinks.a libgc.a -lboost_thread-mt -lboost_system-mt -lboost_serialization-mt -lbam -lz
...
...
skipping 1000s of lines of warning messages
...
...
Undefined symbols for architecture x86_64:
Undefined symbols for architecture x86_64:
  "_bam_aux2A", referenced from:
  "_bam_aux2A", referenced from:
      BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
      BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
  "_bam_aux2i", referenced from:
  "_bam_aux2i", referenced from:
      BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
      BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
  "_bam_aux_get", referenced from:
  "_bam_aux_get", referenced from:
      BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
      BAMHitFactory::get_hit_from_buf(char const*, ReadHit&, bool, char*, char*) in libcufflinks.a(hits.o)
  "_bam_destroy1", referenced from:
  "_bam_destroy1", referenced from:
      _sampileup in libbam.a(sam.o)
      _sampileup in libbam.a(sam.o)
  "_bam_hdr_destroy", referenced from:
  "_bam_hdr_destroy", referenced from:
      _samclose in libbam.a(sam.o)
      _samclose in libbam.a(sam.o)
  "_bam_init1", referenced from:
  "_bam_init1", referenced from:
      _sampileup in libbam.a(sam.o)
      _sampileup in libbam.a(sam.o)
  "_bam_plp_destroy", referenced from:
  "_bam_plp_destroy", referenced from:
      _bam_plbuf_destroy in libbam.a(bam_plbuf.o)
      _bam_plbuf_destroy in libbam.a(bam_plbuf.o)
  "_bam_plp_init", referenced from:
  "_bam_plp_init", referenced from:
      _bam_plbuf_init in libbam.a(bam_plbuf.o)
      _bam_plbuf_init in libbam.a(bam_plbuf.o)
  "_bam_plp_next", referenced from:
  "_bam_plp_next", referenced from:
      _bam_plbuf_push in libbam.a(bam_plbuf.o)
      _bam_plbuf_push in libbam.a(bam_plbuf.o)
  "_bam_plp_push", referenced from:
  "_bam_plp_push", referenced from:
      _bam_plbuf_push in libbam.a(bam_plbuf.o)
      _bam_plbuf_push in libbam.a(bam_plbuf.o)
  "_bam_plp_reset", referenced from:
  "_bam_plp_reset", referenced from:
      _bam_plbuf_reset in libbam.a(bam_plbuf.o)
      _bam_plbuf_reset in libbam.a(bam_plbuf.o)
  "_bgzf_mt", referenced from:
  "_bgzf_mt", referenced from:
      _samthreads in libbam.a(sam.o)
      _samthreads in libbam.a(sam.o)
  "_bgzf_seek", referenced from:
  "_bgzf_seek", referenced from:
      BAMHitFactory::reset() in libcufflinks.a(hits.o)
      BAMHitFactory::undo_hit() in libcufflinks.a(hits.o)
      BAMHitFactory::reset() in libcufflinks.a(hits.o)
      BAMHitFactory::undo_hit() in libcufflinks.a(hits.o)
  "_fai_build", referenced from:
  "_fai_build", referenced from:
      _samfaipath in libbam.a(sam.o)
      _samfaipath in libbam.a(sam.o)
  "_hts_close", referenced from:
  "_hts_close", referenced from:
      _samclose in libbam.a(sam.o)
      _samclose in libbam.a(sam.o)
  "_hts_get_format", referenced from:
  "_hts_get_format", referenced from:
      _samthreads in libbam.a(sam.o)
      _samopen in libbam.a(sam.o)
      _samthreads in libbam.a(sam.o)
      _samopen in libbam.a(sam.o)
  "_hts_open", referenced from:
  "_hts_open", referenced from:
      _samopen in libbam.a(sam.o)
      _samopen in libbam.a(sam.o)
  "_hts_set_fai_filename", referenced from:
  "_hts_set_fai_filename", referenced from:
      _samopen in libbam.a(sam.o)
      _samopen in libbam.a(sam.o)
  "_hts_verbose", referenced from:
  "_hts_verbose", referenced from:
      _samopen in libbam.a(sam.o)
      _samfaipath in libbam.a(sam.o)
      _samopen in libbam.a(sam.o)
      _samfaipath in libbam.a(sam.o)
  "_sam_hdr_read", referenced from:
  "_sam_hdr_read", referenced from:
      _samopen in libbam.a(sam.o)
      _samopen in libbam.a(sam.o)
  "_sam_hdr_write", referenced from:
  "_sam_hdr_write", referenced from:
      _samopen in libbam.a(sam.o)
      _samopen in libbam.a(sam.o)
  "_sam_read1", referenced from:
  "_sam_read1", referenced from:
      BAMHitFactory::next_record(char const*&, unsigned long&) in libcufflinks.a(hits.o)
      BAMHitFactory::next_record(char const*&, unsigned long&) in libcufflinks.a(hits.o)
      _sampileup in libbam.a(sam.o)
      _sampileup in libbam.a(sam.o)
ld: symbol(s) not found for architecture x86_64
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

$ ls /usr/local/include/bam
bam.h         bam_endian.h  bam_plbuf.h   errmod.h      sam.h         sample.h      stats_isize.h
bam2bcf.h     bam_lpileup.h bam_tview.h   kprobaln.h    sam_header.h  samtools.h    version.h
$
$ ls /usr/local/lib/libbam.a 
/usr/local/lib/libbam.a