search

bcgsc / biobloom

Create Bloom filters for a given reference and then use it to categorize sequences
http://www.bcgsc.ca/platform/bioinfo/software/biobloomtools
GNU General Public License v3.0
75 stars 15 forks source link

Build issues with Boost #29

Closed conchoecia closed 6 years ago

conchoecia commented 6 years ago

Hello again,

Now I am having trouble running /.configure. I see some complaints that configure found the boost files but was not able to compile them. My hunch is that this is actually something failing upstream and causing downstream problems. I will attach the log as well.

Thanks!

checking boost/property_tree/ptree.hpp usability... no
checking boost/property_tree/ptree.hpp presence... yes
configure: WARNING: boost/property_tree/ptree.hpp: present but cannot be compiled
configure: WARNING: boost/property_tree/ptree.hpp:     check for missing prerequisite headers?
configure: WARNING: boost/property_tree/ptree.hpp: see the Autoconf documentation
configure: WARNING: boost/property_tree/ptree.hpp:     section "Present But Cannot Be Compiled"
configure: WARNING: boost/property_tree/ptree.hpp: proceeding with the compiler's result
configure: WARNING:     ## ------------------------------- ##
configure: WARNING:     ## Report this to cjustin@bcgsc.ca ##
configure: WARNING:     ## ------------------------------- ##
checking for boost/property_tree/ptree.hpp... no
checking boost/property_tree/ini_parser.hpp usability... no
checking boost/property_tree/ini_parser.hpp presence... yes
configure: WARNING: boost/property_tree/ini_parser.hpp: present but cannot be compiled
configure: WARNING: boost/property_tree/ini_parser.hpp:     check for missing prerequisite headers?
configure: WARNING: boost/property_tree/ini_parser.hpp: see the Autoconf documentation
configure: WARNING: boost/property_tree/ini_parser.hpp:     section "Present But Cannot Be Compiled"
configure: WARNING: boost/property_tree/ini_parser.hpp: proceeding with the compiler's result
configure: WARNING:     ## ------------------------------- ##
configure: WARNING:     ## Report this to cjustin@bcgsc.ca ##
configure: WARNING:     ## ------------------------------- ##
checking for boost/property_tree/ini_parser.hpp... no
checking google/dense_hash_map usability... no
checking google/dense_hash_map presence... yes
configure: WARNING: google/dense_hash_map: present but cannot be compiled
configure: WARNING: google/dense_hash_map:     check for missing prerequisite headers?
configure: WARNING: google/dense_hash_map: see the Autoconf documentation
configure: WARNING: google/dense_hash_map:     section "Present But Cannot Be Compiled"
configure: WARNING: google/dense_hash_map: proceeding with the compiler's result
configure: WARNING:     ## ------------------------------- ##
configure: WARNING:     ## Report this to cjustin@bcgsc.ca ##
configure: WARNING:     ## ------------------------------- ##
checking for google/dense_hash_map... no
checking btl_bloomfilter/BloomFilter.hpp usability... no
checking btl_bloomfilter/BloomFilter.hpp presence... yes
configure: WARNING: btl_bloomfilter/BloomFilter.hpp: present but cannot be compiled
configure: WARNING: btl_bloomfilter/BloomFilter.hpp:     check for missing prerequisite headers?
configure: WARNING: btl_bloomfilter/BloomFilter.hpp: see the Autoconf documentation
configure: WARNING: btl_bloomfilter/BloomFilter.hpp:     section "Present But Cannot Be Compiled"
configure: WARNING: btl_bloomfilter/BloomFilter.hpp: proceeding with the compiler's result
configure: WARNING:     ## ------------------------------- ##
configure: WARNING:     ## Report this to cjustin@bcgsc.ca ##
configure: WARNING:     ## ------------------------------- ##
checking for btl_bloomfilter/BloomFilter.hpp... no
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
configure: error: Requires the Boost C++ libraries, which may
    be downloaded from here: http://www.boost.org/users/download/
    The following commands will download and install Boost:
    cd /usr/local/bin/biobloom
    wget http://downloads.sourceforge.net/project/boost/boost/1.58.0/1_58_0.tar.bz2
    tar jxf 1_58_0.tar.bz2
    cd -

config.log

JustinChu commented 6 years ago

I'm noticing in the log that headers from /usr/local/include/ and /usr/include/ are both being used. The strange thing is that /usr/local/include seems to have system(?) headers (/usr/local/include/except.h) but I'd expect them to be in /usr/include.

Maybe different installs of gcc are interfering with each other?

What are you putting into the --with-boost parameter? Try running installing boost in your home directory somewhere using that instead?

conchoecia commented 6 years ago

Hmm, weird. Thanks for taking a look! I tried sudo ./configure --with-boost=/usr/include and everything worked, including make install. I do have multiple GCC installs, so maybe that it is. I wonder if anyone else has had this problem before?