Wednesday, November 19, 2014

Problem troubleshooted while installing Phylobayes on Mavericks by LM Davalos:

Problem: Parallel phylobayes (pb_mpi1.5a) does not compile from source on multi-processor mac running OS 10.9. After clearing out any errors having to do with open-mpi, these errors persist:

file BP2util.h
shell: fatal error: 'tr1/unordered_map' file not found
#include <tr1/unordered_map>

original #include <tr1/unordered_map> #tr1 is deprecated in 10.9 and will not compile
modified: #include <unordered_map>

shell: error: use of undeclared identifier 'tr1'
original: class BipartitionHashTable : public tr1::unordered_map<string,T> {};
modified: class BipartitionHashTable : public unordered_map<string,T> {};

file BP2Stat.h
shell: fatal error: 'tr1/unordered_map' file not found
#include <tr1/unordered_map>

original: #include <tr1/unordered_map>
modified: #include <unordered_map>
#define hash_map std::unordered_map

file PolyNode.cpp
shell: error: variable length array of non-POD element type 'string'
original:  string retval[degree]; #line 431
modified:  string *retval = new string[degree]; #line 431


  1. Before getting here, make clean, the sources include .o and need to be removed.