Bosst configure error

Question

[Andrey Yurchenko]

​Dear Abyss team, I have ​complied boost and used this cl to configure Abyss:

./configure --exec-prefix=/export/home/aay2c/app/abyss --with-boost=/export/home/aay2c/app/boostok/include --prefix=/export/home/aay2c/app/abyss CPPFLAGS=-I/export/home/aay2c/app/sparsehash/include --with-sqlite=/export/home/aay2c/app/sqlite

But got the error, What It can be??

checking tr1/functional usability... yes

checking tr1/functional presence... yes

checking for tr1/functional... yes

checking boost/functional/hash.hpp usability... no

checking boost/functional/hash.hpp presence... yes

configure: WARNING: boost/functional/hash.hpp: present but cannot be compiled

configure: WARNING: boost/functional/hash.hpp:     check for missing prerequisite headers?

configure: WARNING: boost/functional/hash.hpp: see the Autoconf documentation

configure: WARNING: boost/functional/hash.hpp:     section "Present But Cannot Be Compiled"

configure: WARNING: boost/functional/hash.hpp: proceeding with the compiler's result

configure: WARNING:     ## ----------------------------------- ##

configure: WARNING:     ## Report this to [e-mail] ##

configure: WARNING:     ## ----------------------------------- ##

checking for boost/functional/hash.hpp... no

checking boost/property_map/property_map.hpp usability... yes

checking boost/property_map/property_map.hpp presence... yes

checking for boost/property_map/property_map.hpp... yes

checking google/sparse_hash_map usability... yes

checking google/sparse_hash_map presence... yes

checking for google/sparse_hash_map... yes

checking unordered_map usability... no

checking unordered_map presence... no

checking for unordered_map... no

checking tr1/unordered_map usability... yes

checking tr1/unordered_map presence... yes

checking for tr1/unordered_map... yes

checking unordered_set usability... no

checking unordered_set presence... no

checking for unordered_set... no

checking tr1/unordered_set usability... yes

checking tr1/unordered_set presence... yes

checking for tr1/unordered_set... yes

checking boost/unordered_set.hpp usability... no

checking boost/unordered_set.hpp presence... yes

configure: WARNING: boost/unordered_set.hpp: present but cannot be compiled

configure: WARNING: boost/unordered_set.hpp:     check for missing prerequisite headers?

configure: WARNING: boost/unordered_set.hpp: see the Autoconf documentation

configure: WARNING: boost/unordered_set.hpp:     section "Present But Cannot Be Compiled"

configure: WARNING: boost/unordered_set.hpp: proceeding with the compiler's result

configure: WARNING:     ## ----------------------------------- ##

configure: WARNING:     ## Report this to [e-mail] ##

configure: WARNING:     ## ----------------------------------- ##

checking for boost/unordered_set.hpp... no

Thank you!!!

[GenoMax]

What OS is this? You should also consider emailing the abyss-users list as indicated in the message above.

[benv]

It is really hard to tell what is wrong from the configure output alone. If you look for the Boost checks in the config.log file it will give you more info about why the checks failed. If you like, you can post your config.log (post here, send e-mail to benv at bcgsc dot ca, or post to GitHub gist) and I can have a look for you.

Answer 1

[benv]

Hi Andrey,

Not sure, but you may be able to determine the nature of the error by looking in the config.log generated by the configure command.

Assuming you are not able to install boost with a package manager (e.g. apt or yum), you can set up the required boost headers by:

1. downloading a recent boost source tarball (e.g. https://sourceforge.net/projects/boost/files/boost/1.61.0/boost_1_61_0.tar.gz)
2. unpacking the tarball
3. copying the boost directory from the unpacked tarball directory into /home/andrey/include (for example)
4. adding --with-boost=/home/andrey to your configure command

The value of --with-boost should be a directory that contains include/boost/unordered_set.hpp underneath it (for example).

Answer 2

[mike]

I had the same problem and could not get around it until I installed the sqlite dev libraries.