Undefined reference to symbol 'exp@@GLIBC_2.2.5'

Question

I am trying to compile Bavieca (for a few weeks now tbh), at the same time becoming accustomed with compiling in Linux, learning about static and dynamic libraries etc, so I'm a little new to this area. Bavieca depends on the BLAS/LAPACK libraries. I am using the atlas respective libraries after unsuccessfully trying the dependent ones.

I can compile successfully the first two parts of the distribution (api & common), but compilation fails in the third (tools).

Makefile:

include ../Makefile.defines

INC = -I./algebra -I./alignment -I./audio -I./base -I./decoding -I./dynamicdecoder -I./estimation -I./config -I./hmm \
-I./io -I./other -I./param -I./text -I./transform -I./wfsadecoder ${INCS_DIR_CBLAS} ${INCS_DIR_LAPACK} 

SRC_DIR = ../common
OBJ_DIR = ../../obj/$(ARCH)-$(OS)/common
LIB_DIR = ../../lib/$(ARCH)-$(OS)
OBJFILES_BASE = $(patsubst $(SRC_DIR)/%,$(OBJ_DIR)/%,$(patsubst %.cpp,%.o,$(wildcard $(SRC_DIR)/*/*.cpp)))

static: CPPFLAGS_ = $(CPPFLAGS)
pic: CPPFLAGS_ = $(CPPFLAGS_SHARED)

# targets (pic stands for position independent code)

static: createDirectories libcommon.a

pic: createDirectories libcommon_pic.a

clean: 
    rm -rf $(OBJ_DIR)
    rm -rf $(LIB_DIR)/libcommon.a
    rm -rf $(LIB_DIR)/libcommon_pic.a

createDirectories: 
    (mkdir -p $(LIB_DIR))
    (mkdir -p $(OBJ_DIR)/algebra)
    (mkdir -p $(OBJ_DIR)/alignment)
    (mkdir -p $(OBJ_DIR)/audio)
    (mkdir -p $(OBJ_DIR)/base)
    (mkdir -p $(OBJ_DIR)/config)
    (mkdir -p $(OBJ_DIR)/decoding)
    (mkdir -p $(OBJ_DIR)/dynamicdecoder)
    (mkdir -p $(OBJ_DIR)/estimation)
    (mkdir -p $(OBJ_DIR)/hmm)
    (mkdir -p $(OBJ_DIR)/io)
    (mkdir -p $(OBJ_DIR)/other)
    (mkdir -p $(OBJ_DIR)/param)
    (mkdir -p $(OBJ_DIR)/sadmodule)
    (mkdir -p $(OBJ_DIR)/text)
    (mkdir -p $(OBJ_DIR)/transform)
    (mkdir -p $(OBJ_DIR)/vtlestimator)
    (mkdir -p $(OBJ_DIR)/wfsabuilder)
    (mkdir -p $(OBJ_DIR)/wfsadecoder)

# ----------------------------------------------
# create the static library
#-----------------------------------------------

libcommon.a: $(OBJFILES_BASE)
    $(AR) $@ $?
    (mv libcommon.a $(LIB_DIR))
    rm -rf $(OBJ_DIR)

libcommon_pic.a: $(OBJFILES_BASE)
    $(AR) $@ $?
    (mv libcommon_pic.a $(LIB_DIR))
    rm -rf $(OBJ_DIR)

# ----------------------------------------------
# create the object files from the source files
# ----------------------------------------------

$(OBJ_DIR)/algebra/%.o: $(SRC_DIR)/algebra/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/alignment/%.o: $(SRC_DIR)/alignment/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/audio/%.o: $(SRC_DIR)/audio/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/base/%.o: $(SRC_DIR)/base/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/config/%.o: $(SRC_DIR)/config/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/decoding/%.o: $(SRC_DIR)/decoding/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/dynamicdecoder/%.o: $(SRC_DIR)/dynamicdecoder/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/estimation/%.o: $(SRC_DIR)/estimation/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/hmm/%.o: $(SRC_DIR)/hmm/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/io/%.o: $(SRC_DIR)/io/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/other/%.o: $(SRC_DIR)/other/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/param/%.o: $(SRC_DIR)/param/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/sadmodule/%.o: $(SRC_DIR)/sadmodule/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/text/%.o: $(SRC_DIR)/text/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/transform/%.o: $(SRC_DIR)/transform/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/vtlestimator/%.o: $(SRC_DIR)/vtlestimator/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/wfsabuilder/%.o: $(SRC_DIR)/wfsabuilder/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

$(OBJ_DIR)/wfsadecoder/%.o: $(SRC_DIR)/wfsadecoder/%.cpp
    $(XCC) $(CPPFLAGS_) $(INC) -c $< -o $@

Makefile.defines:

# ---------------------------------------
# Arch and Operating System settings
# ---------------------------------------

MAKE = make --quiet -w
ARCH := $(shell uname -m | sed s/' '//g)
OS   := $(shell uname -s)

# ---------------------------------------
# Linux compile options
# ---------------------------------------

XCC          = gcc

# SIMD flags (vector based arithmetic operations)
#SIMD_FLAGS =
# SSE is enabled by default on gcc-4.0 and higher. If SSE is enabled, the C preprocessor symbol __SSE__ is defined
SIMD_FLAGS = -msse3
# AVX is available on Sandy Bridge and later Intel and AMD architectures. If AVX is enabled the C preprocessor symbol __AVX__ is defined
#SIMD_FLAGS = -march=corei7-avx


#CPPFLAGS     = -g -Wno-deprecated -Wall -O2 -finline-functions $(SIMD_FLAGS)
CPPFLAGS     = -g -Wno-deprecated -O2 -finline-functions $(SIMD_FLAGS)
# -fPIC generates Position Independent Code, which is needed to build shared libraries 
# so they can be dynamically relocated, however it may slowdown the code, for this reason
# it should be avoided for object files that build executables or static libraries
CPPFLAGS_SHARED = $(CPPFLAGS) -fPIC
AR       = ar rs

# ---------------------------------------
# CBLAS and LAPACK includes/libraries
# ---------------------------------------

BASE = /usr

INCS_DIR_CBLAS = -I$(BASE)/include/atlas
INCS_DIR_LAPACK = -I$(BASE)/include/atlas
LIBS_DIR_CBLAS = -L$(BASE)/lib/atlas-base
LIBS_DIR_LAPACK = -L$(BASE)/lib/atlas-base/atlas
LIB_CBLAS = -lcblas -lblas -lgfortran -lf2c
LIB_LAPACK = -llapack

# ----------------------------------------------------
# Java JNI (Java Native Interface) includes/libraries
# ----------------------------------------------------

JAVA_BASE = /usr/lib/jvm/java-1.7.0-openjdk-amd64
INCS_DIR_JNI = -I$(JAVA_BASE)/include -I$(JAVA_BASE)/include/linux

The output is the following:

(mkdir -p ../../obj/x86_64-Linux/tools)
(mkdir -p ../../bin/x86_64-Linux)
gcc -g -Wno-deprecated -O2 -finline-functions -msse3 -L../../lib/x86_64-Linux/ -L/usr/lib/atlas-base -L/usr/lib/atlas-base/atlas -o ../../bin/x86_64-Linux/aligner ../../obj/x86_64-Linux/tools/mainAligner.o -lcommon -llapack -lcblas -lblas -lgfortran -lf2c  
/usr/bin/ld: ../../lib/x86_64-Linux//libcommon.a(HMMStateDecoding.o): undefined reference to symbol 'exp@@GLIBC_2.2.5'
//lib/x86_64-linux-gnu/libm.so.6: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make: *** [aligner] Error 1

Now, I've googled and searched and found out that I need to append -lm to the linker phase. Which I did, resulting in multiple undefined references. This is a small sample of the output in this case:

../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `ParameterValue':
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/./config/ParameterManager.h:92: undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&)'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/./config/ParameterManager.h:92: undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&)'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `std::string::_Rep::_M_dispose(std::allocator<char> const&)':
/usr/include/c++/4.8/bits/basic_string.h:240: undefined reference to `std::string::_Rep::_S_empty_rep_storage'
/usr/include/c++/4.8/bits/basic_string.h:240: undefined reference to `std::string::_Rep::_S_empty_rep_storage'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `std::_Rb_tree_iterator<std::pair<std::string const, std::string> >::operator++()':
/usr/include/c++/4.8/bits/stl_tree.h:189: undefined reference to `std::_Rb_tree_increment(std::_Rb_tree_node_base*)'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `_Alloc_hider':
/usr/include/c++/4.8/bits/basic_string.h:275: undefined reference to `std::string::_Rep::_S_empty_rep_storage'
/usr/include/c++/4.8/bits/basic_string.h:275: undefined reference to `std::string::_Rep::_S_empty_rep_storage'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `std::string::operator=(std::string const&)':
/usr/include/c++/4.8/bits/basic_string.h:547: undefined reference to `std::string::assign(std::string const&)'
/usr/include/c++/4.8/bits/basic_string.h:547: undefined reference to `std::string::assign(std::string const&)'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `std::string::_Rep::_M_dispose(std::allocator<char> const&)':
/usr/include/c++/4.8/bits/basic_string.h:240: undefined reference to `std::string::_Rep::_S_empty_rep_storage'
/usr/include/c++/4.8/bits/basic_string.h:240: undefined reference to `std::string::_Rep::_S_empty_rep_storage'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `__gnu_cxx::new_allocator<Bavieca::ParameterValue>::deallocate(Bavieca::ParameterValue*, unsigned long)':
/usr/include/c++/4.8/ext/new_allocator.h:110: undefined reference to `operator delete(void*)'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `std::string::_Rep::_M_dispose(std::allocator<char> const&)':
/usr/include/c++/4.8/bits/basic_string.h:249: undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
/usr/include/c++/4.8/bits/basic_string.h:249: undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
/usr/include/c++/4.8/bits/basic_string.h:249: undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
/usr/include/c++/4.8/bits/basic_string.h:249: undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `Bavieca::ConfigurationFeatures::load()':
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/param/ConfigurationFeatures.cpp:110: undefined reference to `__cxa_get_exception_ptr'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `runtime_error':
/usr/include/c++/4.8/stdexcept:112: undefined reference to `vtable for std::runtime_error'
/usr/include/c++/4.8/stdexcept:112: undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&)'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `Bavieca::ConfigurationFeatures::load()':
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/param/ConfigurationFeatures.cpp:110: undefined reference to `__cxa_begin_catch'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/param/ConfigurationFeatures.cpp:111: undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::operator<< <std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*)'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/param/ConfigurationFeatures.cpp:110: undefined reference to `std::runtime_error::~runtime_error()'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/param/ConfigurationFeatures.cpp:110: undefined reference to `__cxa_end_catch'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/param/ConfigurationFeatures.cpp:110: undefined reference to `std::runtime_error::~runtime_error()'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/param/ConfigurationFeatures.cpp:110: undefined reference to `__cxa_end_catch'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `runtime_error':
/usr/include/c++/4.8/stdexcept:112: undefined reference to `std::exception::~exception()'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `Bavieca::ConfigurationFeatures::load()':
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/param/ConfigurationFeatures.cpp:110: undefined reference to `std::terminate()'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `~basic_string':
/usr/include/c++/4.8/bits/basic_string.h:539: undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o):(.gcc_except_table+0xe4): undefined reference to `typeinfo for std::runtime_error'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o): In function `__static_initialization_and_destruction_0':
/usr/include/c++/4.8/iostream:74: undefined reference to `std::ios_base::Init::Init()'
/usr/include/c++/4.8/iostream:74: undefined reference to `std::ios_base::Init::~Init()'
../../lib/x86_64-Linux//libcommon.a(ConfigurationFeatures.o):(.eh_frame+0x13): undefined reference to `__gxx_personality_v0'
../../lib/x86_64-Linux//libcommon.a(AudioFile.o): In function `Bavieca::AudioFile::load(char const*, int*)':
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/audio/AudioFile.cpp:48: undefined reference to `operator new[](unsigned long)'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/audio/AudioFile.cpp:53: undefined reference to `__cxa_get_exception_ptr'
../../lib/x86_64-Linux//libcommon.a(AudioFile.o): In function `runtime_error':
/usr/include/c++/4.8/stdexcept:112: undefined reference to `vtable for std::runtime_error'
/usr/include/c++/4.8/stdexcept:112: undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&)'
../../lib/x86_64-Linux//libcommon.a(AudioFile.o): In function `Bavieca::AudioFile::load(char const*, int*)':
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/audio/AudioFile.cpp:53: undefined reference to `__cxa_begin_catch'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/audio/AudioFile.cpp:54: undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::operator<< <std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*)'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/audio/AudioFile.cpp:54: undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::operator<< <std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*)'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/audio/AudioFile.cpp:53: undefined reference to `std::runtime_error::~runtime_error()'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/audio/AudioFile.cpp:53: undefined reference to `__cxa_end_catch'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/audio/AudioFile.cpp:53: undefined reference to `std::runtime_error::~runtime_error()'
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/audio/AudioFile.cpp:53: undefined reference to `__cxa_end_catch'
../../lib/x86_64-Linux//libcommon.a(AudioFile.o): In function `runtime_error':
/usr/include/c++/4.8/stdexcept:112: undefined reference to `std::exception::~exception()'
../../lib/x86_64-Linux//libcommon.a(AudioFile.o): In function `Bavieca::AudioFile::load(char const*, int*)':
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/audio/AudioFile.cpp:53: undefined reference to `std::terminate()'
../../lib/x86_64-Linux//libcommon.a(AudioFile.o):(.gcc_except_table+0x48): undefined reference to `typeinfo for std::runtime_error'
../../lib/x86_64-Linux//libcommon.a(AudioFile.o): In function `__static_initialization_and_destruction_0':
/usr/include/c++/4.8/iostream:74: undefined reference to `std::ios_base::Init::Init()'
/usr/include/c++/4.8/iostream:74: undefined reference to `std::ios_base::Init::~Init()'
../../lib/x86_64-Linux//libcommon.a(AudioFile.o):(.eh_frame+0x53): undefined reference to `__gxx_personality_v0'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `basic_ios':
/usr/include/c++/4.8/bits/basic_ios.h:456: undefined reference to `std::ios_base::ios_base()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `basic_ostream':
/usr/include/c++/4.8/ostream:385: undefined reference to `VTT for std::basic_ofstream<char, std::char_traits<char> >'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `basic_ios':
/usr/include/c++/4.8/bits/basic_ios.h:456: undefined reference to `vtable for std::basic_ios<char, std::char_traits<char> >'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `basic_ostream':
/usr/include/c++/4.8/ostream:385: undefined reference to `VTT for std::basic_ofstream<char, std::char_traits<char> >'
/usr/include/c++/4.8/ostream:385: undefined reference to `std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `basic_ofstream':
/usr/include/c++/4.8/fstream:625: undefined reference to `vtable for std::basic_ofstream<char, std::char_traits<char> >'
/usr/include/c++/4.8/fstream:625: undefined reference to `vtable for std::basic_ofstream<char, std::char_traits<char> >'
/usr/include/c++/4.8/fstream:625: undefined reference to `std::basic_filebuf<char, std::char_traits<char> >::basic_filebuf()'
/usr/include/c++/4.8/fstream:626: undefined reference to `std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `_Alloc_hider':
/usr/include/c++/4.8/bits/basic_string.h:275: undefined reference to `std::string::_Rep::_S_empty_rep_storage'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `std::string::assign(char const*)':
/usr/include/c++/4.8/bits/basic_string.h:1131: undefined reference to `std::string::assign(char const*, unsigned long)'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_ios':
/usr/include/c++/4.8/bits/basic_ios.h:276: undefined reference to `vtable for std::basic_ios<char, std::char_traits<char> >'
/usr/include/c++/4.8/bits/basic_ios.h:276: undefined reference to `std::ios_base::~ios_base()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_string':
/usr/include/c++/4.8/bits/basic_string.h:539: undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `Bavieca::FileOutput::FileOutput(char const*, bool)':
/home/spgeo/Desktop/bavieca/bavieca-code/src/common/../common/io/FileOutput.cpp:26: undefined reference to `std::basic_ofstream<char, std::char_traits<char> >::~basic_ofstream()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `basic_ofstream':
/usr/include/c++/4.8/fstream:625: undefined reference to `std::basic_filebuf<char, std::char_traits<char> >::~basic_filebuf()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_ostream':
/usr/include/c++/4.8/ostream:93: undefined reference to `VTT for std::basic_ofstream<char, std::char_traits<char> >'
/usr/include/c++/4.8/ostream:93: undefined reference to `VTT for std::basic_ofstream<char, std::char_traits<char> >'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `std::string::_Rep::_M_dispose(std::allocator<char> const&)':
/usr/include/c++/4.8/bits/basic_string.h:240: undefined reference to `std::string::_Rep::_S_empty_rep_storage'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_ofstream':
/usr/include/c++/4.8/fstream:674: undefined reference to `vtable for std::basic_ofstream<char, std::char_traits<char> >'
/usr/include/c++/4.8/fstream:674: undefined reference to `vtable for std::basic_ofstream<char, std::char_traits<char> >'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_filebuf':
/usr/include/c++/4.8/fstream:220: undefined reference to `vtable for std::basic_filebuf<char, std::char_traits<char> >'
/usr/include/c++/4.8/fstream:220: undefined reference to `std::basic_filebuf<char, std::char_traits<char> >::close()'
/usr/include/c++/4.8/fstream:220: undefined reference to `std::__basic_file<char>::~__basic_file()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_streambuf':
/usr/include/c++/4.8/streambuf:198: undefined reference to `vtable for std::basic_streambuf<char, std::char_traits<char> >'
/usr/include/c++/4.8/streambuf:198: undefined reference to `std::locale::~locale()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_ostream':
/usr/include/c++/4.8/ostream:93: undefined reference to `VTT for std::basic_ofstream<char, std::char_traits<char> >'
/usr/include/c++/4.8/ostream:93: undefined reference to `VTT for std::basic_ofstream<char, std::char_traits<char> >'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_ios':
/usr/include/c++/4.8/bits/basic_ios.h:276: undefined reference to `vtable for std::basic_ios<char, std::char_traits<char> >'
/usr/include/c++/4.8/bits/basic_ios.h:276: undefined reference to `std::ios_base::~ios_base()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `std::string::_Rep::_M_dispose(std::allocator<char> const&)':
/usr/include/c++/4.8/bits/basic_string.h:249: undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_streambuf':
/usr/include/c++/4.8/streambuf:198: undefined reference to `vtable for std::basic_streambuf<char, std::char_traits<char> >'
/usr/include/c++/4.8/streambuf:198: undefined reference to `std::locale::~locale()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_ostream':
/usr/include/c++/4.8/ostream:93: undefined reference to `VTT for std::basic_ofstream<char, std::char_traits<char> >'
/usr/include/c++/4.8/ostream:93: undefined reference to `VTT for std::basic_ofstream<char, std::char_traits<char> >'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_ios':
/usr/include/c++/4.8/bits/basic_ios.h:276: undefined reference to `vtable for std::basic_ios<char, std::char_traits<char> >'
/usr/include/c++/4.8/bits/basic_ios.h:276: undefined reference to `std::ios_base::~ios_base()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `~basic_filebuf':
/usr/include/c++/4.8/fstream:220: undefined reference to `std::__basic_file<char>::~__basic_file()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `std::basic_ofstream<char, std::char_traits<char> >::open(char const*, std::_Ios_Openmode)':
/usr/include/c++/4.8/fstream:716: undefined reference to `std::basic_filebuf<char, std::char_traits<char> >::open(char const*, std::_Ios_Openmode)'
/usr/include/c++/4.8/fstream:721: undefined reference to `std::basic_ios<char, std::char_traits<char> >::clear(std::_Ios_Iostate)'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `std::basic_filebuf<char, std::char_traits<char> >::is_open() const':
/usr/include/c++/4.8/fstream:228: undefined reference to `std::__basic_file<char>::is_open() const'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `operator<< <std::char_traits<char> >':
/usr/include/c++/4.8/ostream:535: undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)'
/usr/include/c++/4.8/ostream:535: undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `std::basic_ios<char, std::char_traits<char> >::setstate(std::_Ios_Iostate)':
/usr/include/c++/4.8/bits/basic_ios.h:152: undefined reference to `std::basic_ios<char, std::char_traits<char> >::clear(std::_Ios_Iostate)'
/usr/include/c++/4.8/bits/basic_ios.h:152: undefined reference to `std::basic_ios<char, std::char_traits<char> >::clear(std::_Ios_Iostate)'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `std::basic_ofstream<char, std::char_traits<char> >::close()':
/usr/include/c++/4.8/fstream:755: undefined reference to `std::basic_filebuf<char, std::char_traits<char> >::close()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `std::basic_ios<char, std::char_traits<char> >::setstate(std::_Ios_Iostate)':
/usr/include/c++/4.8/bits/basic_ios.h:152: undefined reference to `std::basic_ios<char, std::char_traits<char> >::clear(std::_Ios_Iostate)'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o): In function `__static_initialization_and_destruction_0':
/usr/include/c++/4.8/iostream:74: undefined reference to `std::ios_base::Init::Init()'
/usr/include/c++/4.8/iostream:74: undefined reference to `std::ios_base::Init::~Init()'
../../lib/x86_64-Linux//libcommon.a(FileOutput.o):(.eh_frame+0x13): undefined reference to `__gxx_personality_v0'
collect2: error: ld returned 1 exit status
make: *** [param] Error 1

Now I am in a dead-end. I have no experience or knowledge either as to what to do next. Could it be that libm is not functioning properly? The other answers in similar questions in this site didn't apply to my case.

EDIT: Changing in Makefile.defined the "gcc" to "g++" results in the following output error: undefined reference to cblas_sgemm(CBLAS_ORDER, CBLAS_TRANSPOSE, CBLAS_TRANSPOSE, int, int, int, float, float const*, int, float const*, int, float, float*, int) collect2: error: ld returned 1 exit status make: *** [param] Error 1

It seems unable to find the cblas library, even though I've linked both the include and lib directory.

score 1 · Answer 1 · answered Feb 09 '15 at 20:41

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This looks like a pretty broken makefile... You are compiling a C++ library (as it needs std::string) with a C compiler (gcc). It can't work. Try replacing gcc by g++ in Makefile.defines, and in any case report your bad experience to the developers of the library.

answered Feb 09 '15 at 20:41

Vincent Fourmond

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1
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You were right, I suspect this is my fault though.. changing in g++ results in the following output error: `undefined reference to cblas_sgemm(CBLAS_ORDER, CBLAS_TRANSPOSE, CBLAS_TRANSPOSE, int, int, int, float, float const*, int, float const*, int, float, float*, int) collect2: error: ld returned 1 exit status make: *** [param] Error 1` – Ata3ias Feb 09 '15 at 22:10
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@Ata3ias Are you linking to the blas libraries. If yes, then it means that the original sources are missing a proper extern "C" { ... } wrapping. This will be painful to fix. – Vincent Fourmond Feb 11 '15 at 10:54

Undefined reference to symbol 'exp@@GLIBC_2.2.5'

1 Answers1