joelarmstrong
commented
9 years ago Sorry, I think we missed including PCRE as a submodule. It's installed by default on most systems so that may be why.
We might want to include PCRE as a submodule. In the meantime, you can get this to compile by installing pcre:
sudo yum install pcre-devel
or, possibly, by disabling the phast library by using setting the environment variable ENABLE_PHYLOP to 0.
jpearl01
Here's the tail end of the error I received while attempting to build on a CentOS 6 cluster head node.
h5c++ -prefix=/home/josh/external_bio_programs/progressiveCactus/submodules/hdf5 -O3 -g -Wall -funroll-loops -DNDEBUG -I..//../sonLib/lib -I ../lib/ -I../../phast/include -I../../clapack/INCLUDE -c ancestorsMLBed.cpp -o ancestorsMLBed.o ..//../sonLib/lib/sonLib.a ..//../sonLib/lib/cuTest.a ../lib//halLib.a ../../phast/lib/libphast.a ../../phast/lib/liblapack.a ../../phast/lib/libblaswr.a ../../clapack/F2CLIBS/libf2c.a In file included from ../../phast/include/trees.h:25, from ../../phast/include/tree_model.h:26, from ancestorsMLBed.cpp:7: ../../phast/include/stringsplus.h:27:18: error: pcre.h: No such file or directory In file included from ../../phast/include/trees.h:24, from ../../phast/include/tree_model.h:26, from ancestorsMLBed.cpp:7: ../../phast/include/lists.h: In function ‘void lst_arrset(List, int, void_)’: ../../phast/include/lists.h:75: warning: comparison between signed and unsigned integer expressions In file included from ../../phast/include/trees.h:25, from ../../phast/include/treemodel.h:26, from ancestorsMLBed.cpp:7: ../../phast/include/stringsplus.h: At global scope: ../../phast/include/stringsplus.h:60: error: ‘pcre’ does not name a type ../../phast/include/stringsplus.h:388: error: expected constructor, destructor, or type conversion before ‘’ token ../../phast/include/stringsplus.h:394: error: variable or field ‘str_re_free’ declared void ../../phast/include/stringsplus.h:394: error: ‘Regex’ was not declared in this scope ../../phast/include/stringsplus.h:394: error: ‘re’ was not declared in this scope In file included from ../../phast/include/trees.h:25, from ../../phast/include/treemodel.h:26, from ancestorsMLBed.cpp:7: ../../phast/include/stringsplus.h:410: error: ‘Regex’ has not been declared ../../phast/include/stringsplus.h:425: error: ‘Regex’ has not been declared make[3]: ** [../bin//ancestorsML] Error 1 make[3]: Leaving directory
/home/josh/external_bio_programs/progressiveCactus/submodules/hal/modify' make[2]: *** [all.modify] Error 2 make[2]: Leaving directory/home/josh/external_bio_programs/progressiveCactus/submodules/hal' make[1]: * [ucsc.hal] Error 2 make[1]: Leaving directory `/home/josh/external_bio_programs/progressiveCactus/submodules' make: * [all] Error 2Any ideas?
~josh