liuhui@pine:~/bin/cufflinks-master$ ./configure --with-bam=/usr/local/include/bam

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... /bin/mkdir -p

checking for gawk... no

checking for mawk... mawk

checking whether make sets $(MAKE)... yes

checking for gawk... (cached) mawk

checking for g++... g++

checking whether the C++ compiler works... yes

checking for C++ compiler default output file name... a.out

checking for suffix of executables...

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

checking for style of include used by make... GNU

checking dependency style of g++... gcc3

checking for gcc... gcc

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking dependency style of gcc... gcc3

checking whether make sets $(MAKE)... (cached) yes

checking for ranlib... ranlib

checking for ar... ar

checking the archiver (ar) interface... ar

checking for a Python interpreter with version >= 2.4... python

checking for python... /usr/bin/python

checking for python version... 2.7

checking for python platform... linux2

checking for python script directory... ${prefix}/lib/python2.7/dist-packages

checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages

checking for boostlib >= 1.47.0... yes

checking for bamlib... configure: error: We could not detect the bam libraries (version  or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option.  If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.

Fixed it by modifying the read permissions

chmod 755 /usr/local/lib/libbam.a

chmod 755 /usr/local/include/bam/*.h