Troubleshooting fastx-toolkit. Trying to resolve this error. I have uninstalled the newer versions of both libgtextutils and fastx_toolkit and am reverting to hopefully a more stable version. 

The "Abort trap: 6" was never really resolved for me but after running this version and compiling from source, the error does go away (can't say it is resolved). However, a new suite of errors with the older version pops up. Curiously, this is accounted for in the newer version. The errors are similar to the installation of phylobayes. I have troubleshooted them here and have a successful installation. Now hopefully I can move on with my life. I am going to try something new.

Anyways, here is the installation error workaround:

cd /usr/local/bin/
wget http://cancan.cshl.edu/labmembers/gordon/files/libgtextutils-0.6.tar.bz2 #note this is not latest version
tar -xjf libgtextutils-0.6.tar.bz2
cd libgtextutils-0.6
./configure
make
sudo make install

wget http://cancan.cshl.edu/labmembers/gordon/files/fastx_toolkit-0.0.12.tar.bz2 #note this is not latest version
tar -xjf fastx_toolkit-0.0.12.tar.bz2  
cd fastx_toolkit-0.0.12
./configure
make
g++ -DHAVE_CONFIG_H -I. -I../..   -I../libfastx   -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -MT fastx_collapser.o -MD -MP -MF .deps/fastx_collapser.Tpo -c -o fastx_collapser.o fastx_collapser.cpp
fastx_collapser.cpp:50:10: fatal error: 'tr1/unordered_map' file not found
#include <tr1/unordered_map>
         ^
1 error generated.
make[3]: *** [fastx_collapser.o] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
cd src/
cd fastx_collapser
vi fastx_collapser.cpp
#press i to edit in vi

#original
#include <tr/unordered_map>
#new

#include <unordered_map>
#save and exit, press ESC and then type ":wq!"

cd ../..
make
fastx_collapser.cpp:51:6: error: no member named 'tr1' in namespace 'std'
std::tr1::unordered_map<string,size_t> collapsed_sequences;
~~~~~^
1 error generated.
make[3]: *** [fastx_collapser.o] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
cd src/fastx_collapser
vi fastx_collapser.cpp
#original

std::tr1::unordered_map<string,size_t> collapsed_sequences;
#new

std::unordered_map<string,size_t> collapsed_sequences;
sudo make install

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

Fail.

succeeded(0), failed(58736)   99.9949% completed.    libc++abi.dylib: terminating with uncaught exception of type std::length_error: vector::_M_fill_insert

succeeded(0), failed(58737)   99.9966% completed.    libc++abi.dylib: terminating with uncaught exception of type std::length_error: vector::_M_fill_insert

succeeded(0), failed(58738)   99.9983% completed.    libc++abi.dylib: terminating with uncaught exception of type std::length_error: vector::_M_fill_insert

succeeded(0), failed(58739)   100% completed.

We are sorry, commands in file: [failed_quantify_graph_commands.6513.txt] failed.  :-(

Error, cmd: /usr/local/Cellar/trinity/r20131110/trinity-plugins/parafly/bin/ParaFly -c /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_004_Arjam_MOE/trinity_output//chrysalis/quantifyGraph_commands -CPU 4 -failed_cmds failed_quantify_graph_commands.6513.txt -v -shuffle  died with ret 256 at /usr/local/bin/Trinity.pl line 1793.

This is to be continued. At least they put a frowny face in the error message.