configure error: We could not detect the bam libraries

[matteodelucchi]

early steps I tried first to install the precompiled version:

wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
tar zxvpf cufflinks-2.2.1.Linux_x86_64.tar.gz
rm cufflinks-2.2.1.Linux_x86_64.tar.gz
cd cufflinks-2.2.1.Linux_x86_64/
echo -e "\nexport PATH=$PATH:/dataT/dlc/programs/cufflinks-2.2.1.Linux_x86_64
" >> ~/.bashrc

which resulted in the following error:

wget https://github.com/cole-trapnell-lab/cufflinks/blob/master/external_tests/tiny_tests/2x75/accepted_hits.sam
$ ./cufflinks accepted_hits.sam 
-bash: ./cufflinks: cannot execute binary file

compiling the binaries Therefore I tried to compile it from scratch which resulted in the common error:

$ autoreconf --install
$ ./configure \
--prefix=/dataT/dlc/programs/cufflinks  \
--boost=$MODULEPATH \
--eigen=/dataT/dlc/programs/eigen-eigen-323c052e1731/build_dir \
--with-bam=/dataT/dlc/programs/samtools-1.9
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/dataT/dlc/programs/cufflinks-2.2.1/build-aux/missing: Unknown `--is-lightweight' option
Try `/dataT/dlc/programs/cufflinks-2.2.1/build-aux/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
... 
<diverse success stating messages came here >
...
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.

I tried:

1. checked if samtools and htslib are in my PATH
2. set BAM_ROOT variable to my samtools folder: /dataT/dlc/programs/samtools-1.9 which contains the file bam.h
3. copied the file /dataT/dlc/programs/samtools-1.9/version.h to version.hpp
4. created the directory /dataT/dlc/programs/samtools-1.9/include/bam and copied the file bam.h into it and put it into my PATH variable

I repeated the above "autoconf - ./configure"-procedure after each step with and without specifying the --with-bam argument but resulted always the same error. The URL stated in the error message is not available anymore (belongs to a chess club...).

system info Red Hat Enterprise Linux Server release 7.6 (Maipo) Architecture: ppc64le Byte Order: Little Endian

[barracuda156]

Fails on MacOS also:

--->  Configuring cufflinks
Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-2.2.1" && ./configure --prefix=/opt/local --with-bam=/opt/local --with-boost=/opt/local/libexec/boost/1.71 --with-eigen=/opt/local --with-zlib=/opt/local 
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether ccache /usr/bin/g++-4.2 accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of ccache /usr/bin/g++-4.2... gcc3
checking for gcc... ccache /usr/bin/gcc-4.2
checking whether we are using the GNU C compiler... yes
checking whether ccache /usr/bin/gcc-4.2 accepts -g... yes
checking for ccache /usr/bin/gcc-4.2 option to accept ISO C89... none needed
checking dependency style of ccache /usr/bin/gcc-4.2... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.5
checking for python platform... darwin
checking for python script directory... ${prefix}/lib/python2.5/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.5/site-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.
Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-2.2.1" && ./configure --prefix=/opt/local --with-bam=/opt/local --with-boost=/opt/local/libexec/boost/1.71 --with-eigen=/opt/local --with-zlib=/opt/local 
Exit code: 1
Error: Failed to configure cufflinks: consult /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-2.2.1/config.log
Error: Failed to configure cufflinks: configure failure: command execution failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_cufflinks/cufflinks/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets if you believe there
is a bug.
Error: Processing of port cufflinks failed