libmaus fails without boost

[kgutwin]

Boost is not installed 'natively' on this system. During a run of bcbio_nextgen_install.py, I get this output:

==> Installing libmaus
==> Downloading https://github.com/gt1/libmaus/archive/0.0.117-release-20140501103431.tar.gz
==> ./configure --prefix=/pkg/bcbio/2014.05/Linux/x86_64/Cellar/libmaus/0.0.117 --with-io-lib=/pkg/bcbio/2014.05/Linux/x86_64/opt/staden_io_lib
checking whether std::shared_ptr exists... no
checking boost/interprocess/smart_ptr/unique_ptr.hpp usability... no
checking boost/interprocess/smart_ptr/unique_ptr.hpp presence... no
checking for boost/interprocess/smart_ptr/unique_ptr.hpp... no
configure: error: Required unique_ptr class not found (not in standard and not in boost)

READ THIS: https://github.com/Homebrew/homebrew/wiki/troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
  https://github.com/chapmanb/homebrew-homebrew-cbl/issues

Fatal error: local() encountered an error (return code 1) while executing 'export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/pkg/bcbio/2014.05/Linux/x86_64/lib/perl5:${PERL5LIB} && /pkg/bcbio/2014.05/Linux/x86_64/bin/brew install  --env=inherit libmaus'

Aborting.

I don't know much about Homebrew but it appears that a dependency needs to be added to libmaus.rb to pull in the correct boost library.

[chapmanb]

Thanks for the report and sorry about the issue. What system are you running on, and what version of gcc are you compiling with? My understanding is that you either need gcc > 4.2 or boost installed. I didn't include boost by default since I hoped most folks would have a more recent gcc and it is a pretty heavy dependency. If you have an older gcc the fix is either to upgrade or install boost via brew:

export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && /pkg/bcbio/2014.05/Linux/x86_64/bin/brew install  --env=inherit -v boost

If your system setup is different happy to debug more to figure out what is happening. Hope this helps.

[kgutwin]

I was using RHEL 5.7 with gcc 4.1.2 - the bcbio installation instructions (https://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html) didn’t specify a particular version of gcc. We also have gcc 4.6.2 installed as an optional module, and building using that seems to bypass the issue.

Thanks for the suggestion!

On May 5, 2014, at 3:02 PM, Brad Chapman notifications@github.com wrote:

Thanks for the report and sorry about the issue. What system are you running on, and what version of gcc are you compiling with? My understanding is that you either need gcc > 4.2 or boost installed. I didn't include boost by default since I hoped most folks would have a more recent gcc and it is a pretty heavy dependency. If you have an older gcc the fix is either to upgrade or install boost via brew:

export CC=${CC:-which gcc} && export CXX=${CXX:-which g++} && /pkg/bcbio/2014.05/Linux/x86_64/bin/brew install --env=inherit -v boost If your system setup is different happy to debug more to figure out what is happening. Hope this helps.

— Reply to this email directly or view it on GitHub.

[chapmanb]

Glad things are working now, and thank you for the suggestion. We haven't extensively tested lots of gcc versions but added language to the documentation to suggest upgrading to recent versions. Thanks again for the report and feedback.