I am programming a module for my Alderbaran Nao V5 robot. Alderbaran recommends using qibuild to compile a module, and I was able to successfully do so, but now I am trying to migrate towards writing my own makefile and using g++.
I am encountering the following error:
/usr/lib/gcc/i686-pc-linux-gnu/4.5.3/../../../../lib/crt1.o: In function
`_start':
(.text+0x18): undefined reference to `main'
/home/nao/naoqi-sdk-2.1.3.3-linux32/lib/libqimessaging.so: undefined reference to `std::__detail::_List_node_base::swap(std::__detail::_List_node_base&, std::__detail::_List_node_base&)#GLIBCXX_3.4.15'
/home/nao/naoqi-sdk-2.1.3.3-linux32/lib/libqi.so: undefined reference to `std::invalid_argument::~invalid_argument()#GLIBCXX_3.4.15'
/home/nao/naoqi-sdk-2.1.3.3-linux32/lib/libqitype.so: undefined reference to `std::out_of_range::~out_of_range()#GLIBCXX_3.4.15'
/home/nao/naoqi-sdk-2.1.3.3-linux32/lib/libqitype.so: undefined reference to `std::__detail::_List_node_base::_M_transfer(std::__detail::_List_node_base*, std::__detail::_List_node_base*)#GLIBCXX_3.4.15'
/home/nao/naoqi-sdk-2.1.3.3-linux32/lib/libqimessaging.so: undefined reference to `std::__detail::_List_node_base::_M_unhook()#GLIBCXX_3.4.15'
/home/nao/naoqi-sdk-2.1.3.3-linux32/lib/libqimessaging.so: undefined reference to `std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)#GLIBCXX_3.4.15'
/home/nao/naoqi-sdk-2.1.3.3-linux32/lib/libqi.so: undefined reference to `posix_spawnp#GLIBC_2.15'
collect2: ld returned 1 exit status
make: *** [shm.so] Error 1
Here is the makefile I am using:
#Variables
CXXFLAGS=-Wall -g
CXX = g++
NaoQi_INC = /home/nao/naoqi-sdk-2.1.3.3-linux32/include
NaoQi_LIB = -L/home/nao/naoqi-sdk-2.1.3.3-linux32/lib -lalcommon -lalerror -lalproxies -lalvalue -lqimessaging -lqitype -lqi
#Object Targets
main.o: main.cpp shm.h
$(CXX) $(CXXFLAGS) -c -I$(NaoQi_INC) main.cpp
shm.o: shm.cpp shm.h $(NaoQi_INC)/alcommon/alproxy.h $(NaoQi_INC)/alcommon/albroker.h $(NaoQi_INC)/alcommon/almodule.h
$(CXX) $(CXXFLAGS) -c -I$(NaoQi_INC) shm.cpp
#Library Targets
shm.so: main.o shm.o
$(CXX) $(CXXFLAGS) -o shm.so main.o shm.o -L/usr/local/lib -lm $(NaoQi_LIB)
clean:
rm -f *o main
rm -f *o shm
all: shm.o main.o shm.so
I noticed that the gentoo operating system I am compiling on has up to GLIBCXX_3.4.14 but does not have GLIBCXX_3.4.15. How can I fix this issue? Why would this issue not present itself when I build the module using qibuild?
Interestingly, the problem was that my .so linking command was missing a -shared flag. Not sure why that gave all of the errors I ran into, however.
Related
Actually, I am working with the well-known SVM-struct project (http://www.cs.cornell.edu/people/tj/svm_light/svm_struct.html)on Ubuntu 16.04. I followed the instructions in http://www.cs.cornell.edu/people/tj/svm_light/svm_multiclass.html to use SVM-multiclass, downloaded the source code and make. But I met some errors when building the project:
$ make
cd svm_light; make svm_learn_hideo_noexe
make[1]: Entering directory '/home/parallels/CLionProjects/svm_multiclass/svm_light'
make[1]: Nothing to be done for 'svm_learn_hideo_noexe'.
make[1]: Leaving directory '/home/parallels/CLionProjects/svm_multiclass/svm_light'
cd svm_struct; make svm_struct_noexe
make[1]: Entering directory '/home/parallels/CLionProjects/svm_multiclass/svm_struct'
make[1]: Nothing to be done for 'svm_struct_noexe'.
make[1]: Leaving directory '/home/parallels/CLionProjects/svm_multiclass/svm_struct'
gcc -O3 -lm -Wall svm_struct/svm_struct_learn.o svm_struct_learn_custom.o svm_struct_api.o svm_light/svm_hideo.o svm_light/svm_learn.o svm_light/svm_common.o svm_struct/svm_struct_common.o svm_struct/svm_struct_main.o -o svm_multiclass_learn
svm_light/svm_learn.o: In function `estimate_sphere':
svm_learn.c:(.text+0x6e88): undefined reference to `sqrt'
svm_light/svm_learn.o: In function `estimate_r_delta':
svm_learn.c:(.text+0x7053): undefined reference to `sqrt'
svm_light/svm_learn.o: In function `estimate_r_delta_average':
svm_learn.c:(.text+0x7b04): undefined reference to `sqrt'
svm_light/svm_learn.o: In function `length_of_longest_document_vector':
svm_learn.c:(.text+0x7b86): undefined reference to `sqrt'
svm_light/svm_learn.o: In function `incorporate_unlabeled_examples':
svm_learn.c:(.text+0x89eb): undefined reference to `sqrt'
svm_light/svm_learn.o:svm_learn.c:(.text+0xc952): more undefined references to `sqrt' follow
svm_light/svm_common.o: In function `classify_example':
svm_common.c:(.text+0x38f): undefined reference to `tanh'
svm_common.c:(.text+0x42d): undefined reference to `exp'
svm_common.c:(.text+0x4a7): undefined reference to `pow'
svm_light/svm_common.o: In function `kernel':
svm_common.c:(.text+0x870): undefined reference to `tanh'
svm_common.c:(.text+0x90d): undefined reference to `exp'
svm_common.c:(.text+0x988): undefined reference to `pow'
svm_light/svm_common.o: In function `model_length_s':
svm_common.c:(.text+0x2c8d): undefined reference to `sqrt'
svm_light/svm_common.o: In function `model_length_n':
svm_common.c:(.text+0x2f5c): undefined reference to `sqrt'
svm_light/svm_common.o: In function `cholesky_matrix':
svm_common.c:(.text+0x3c6f): undefined reference to `sqrt'
svm_light/svm_common.o: In function `find_indep_subset_of_matrix':
svm_common.c:(.text+0x3f41): undefined reference to `sqrt'
svm_light/svm_common.o: In function `single_kernel':
svm_common.c:(.text+0xc0c): undefined reference to `tanh'
svm_common.c:(.text+0xc84): undefined reference to `pow'
svm_common.c:(.text+0xcfb): undefined reference to `exp'
collect2: error: ld returned 1 exit status
Makefile:48: recipe for target 'svm_multiclass_learn' failed
make: *** [svm_multiclass_learn] Error 1
I think the Makefile has already included -lm.
# Makefile for SVM-multiclass, 03.07.04
#Use the following to compile under unix or cygwin
CC = gcc
LD = gcc
#Call 'make' using the following line to make CYGWIN produce stand-alone Windows executables
# make 'SFLAGS=-mno-cygwin'
CFLAGS = $(SFLAGS) -O3 -fomit-frame-pointer -ffast-math -Wall
LDFLAGS = $(SFLAGS) -O3 -lm -Wall
#CFLAGS = $(SFLAGS) -pg -Wall
#LDFLAGS = $(SFLAGS) -pg -lm -Wall
all: svm_multiclass_learn svm_multiclass_classify
.PHONY: clean
clean: svm_light_clean svm_struct_clean
rm -f *.o *.tcov *.d core gmon.out *.stackdump
#-----------------------#
#---- SVM-light ----#
#-----------------------#
svm_light_hideo_noexe:
cd svm_light; make svm_learn_hideo_noexe
svm_light_clean:
cd svm_light; make clean
#----------------------#
#---- STRUCT SVM ----#
#----------------------#
svm_struct_noexe:
cd svm_struct; make svm_struct_noexe
svm_struct_clean:
cd svm_struct; make clean
#-------------------------#
#---- SVM MULTICLASS ----#
#-------------------------#
svm_multiclass_classify: svm_light_hideo_noexe svm_struct_noexe svm_struct_api.o svm_struct/svm_struct_classify.o svm_struct/svm_struct_common.o svm_struct/svm_struct_main.o
$(LD) $(LDFLAGS) svm_struct_api.o svm_struct/svm_struct_classify.o svm_light/svm_common.o svm_struct/svm_struct_common.o -o svm_multiclass_classify $(LIBS)
svm_multiclass_learn: svm_light_hideo_noexe svm_struct_noexe svm_struct_api.o svm_struct_learn_custom.o svm_struct/svm_struct_learn.o svm_struct/svm_struct_common.o svm_struct/svm_struct_main.o
$(LD) $(LDFLAGS) svm_struct/svm_struct_learn.o svm_struct_learn_custom.o svm_struct_api.o svm_light/svm_hideo.o svm_light/svm_learn.o svm_light/svm_common.o svm_struct/svm_struct_common.o svm_struct/svm_struct_main.o -o svm_multiclass_learn $(LIBS)
svm_struct_api.o: svm_struct_api.c svm_struct_api.h svm_struct_api_types.h svm_struct/svm_struct_common.h
$(CC) -c $(CFLAGS) svm_struct_api.c -o svm_struct_api.o
svm_struct_learn_custom.o: svm_struct_learn_custom.c svm_struct_api.h svm_light/svm_common.h svm_struct_api_types.h svm_struct/svm_struct_common.h
$(CC) -c $(CFLAGS) svm_struct_learn_custom.c -o svm_struct_learn_custom.o
The linker collects dependencies first (svm_light/svm_learn.o) and fills them in when it sees a definition (-lm).
You seem to already have a $(LIBS) at the end of your ld invocation, so just:
LIBS += -lm
should fix it.
Other tips:
you can replace the pattern cd X; make TARGET with make -C X TARGET
you can refer to the target as $# and the first prerequisite in the dependency list as $<, so your last rule can be written as:
svm_struct_learn_custom.o: svm_struct_learn_custom.c svm_struct_api.h svm_light/svm_common.h svm_struct_api_types.h svm_struct/svm_struct_common.h
$(CC) -c $(CFLAGS) $< -o $#
where the recipe redefinition of the built-in recipe for compiling .c files, so it suffices to simply list the headers as (extra) prerequisites:
svm_struct_learn_custom.o: svm_struct_api.h svm_light/svm_common.h svm_struct_api_types.h svm_struct/svm_struct_common.h
There are a couple similar problems to this but they all seem to have answers that don't work.
I've installed opencv4 onto an image of Ubuntu and I know the opencv files are install correctly
$ pkg-config --cflags opencv
-I/usr/include/opencv
and have a proper .cp file
/usr/local/lib/pkgconfig$ ls
gpr.pc grpc++.pc grpc++_unsecure.pc protobuf-lite.pc
grpc.pc grpc_unsecure.pc opencv4.pc protobuf.pc
But even though it's all installed correctly it's giving me this error.
~/neuralink/neuralink-image-service-prompt/proto$ make g++ -std=c++11 `pkg-config --cflags opencv protobuf grpc` -L/usr/local/lib `pkg-config --libs opencv protobuf grpc++` -Wl,--no-as-needed -lgrpc++_reflection -Wl,--as-needed -ldl foo.cpp -o foo
/tmp/ccnfoOEl.o: In function `main':
foo.cpp:(.text+0x48): undefined reference to `cv::imread(cv::String const&, int)'
/tmp/ccnfoOEl.o: In function `cv::String::String(char const*)':
foo.cpp:(.text._ZN2cv6StringC2EPKc[_ZN2cv6StringC5EPKc]+0x4d): undefined reference to `cv::String::allocate(unsigned long)'
/tmp/ccnfoOEl.o: In function `cv::String::~String()':
foo.cpp:(.text._ZN2cv6StringD2Ev[_ZN2cv6StringD5Ev]+0x14): undefined reference to `cv::String::deallocate()'
/tmp/ccnfoOEl.o: In function `cv::String::operator=(cv::String const&)':
foo.cpp:(.text._ZN2cv6StringaSERKS0_[_ZN2cv6StringaSERKS0_]+0x28): undefined reference to `cv::String::deallocate()'
/tmp/ccnfoOEl.o: In function `cv::Mat::~Mat()':
foo.cpp:(.text._ZN2cv3MatD2Ev[_ZN2cv3MatD5Ev]+0x39): undefined reference to `cv::fastFree(void*)'
/tmp/ccnfoOEl.o: In function `cv::Mat::release()':
foo.cpp:(.text._ZN2cv3Mat7releaseEv[_ZN2cv3Mat7releaseEv]+0x4b): undefined reference to `cv::Mat::deallocate()'
collect2: error: ld returned 1 exit status
<builtin>: recipe for target 'foo' failed
make: *** [foo] Error 1
Some people have already tried answering similar questions (such as Undefined reference to cv::imread(cv::String const&, int) and linking opencv libraries with g++) however these don't help, as the user didn't add opencv to their makefile and I have.
Here is my make makefile
LDFLAGS = -L/usr/local/lib `pkg-config --libs opencv protobuf grpc++`\
-Wl,--no-as-needed -lgrpc++_reflection -Wl,--as-needed\
-ldl
CXX = g++
CPPFLAGS += `pkg-config --cflags opencv protobuf grpc`
CXXFLAGS += -std=c++11
GRPC_CPP_PLUGIN = grpc_cpp_plugin
GRPC_CPP_PLUGIN_PATH ?= `which $(GRPC_CPP_PLUGIN)`
all: foo
client: image.pb.o image.grpc.pb.o client.o
$(CXX) $^ $(LDFLAGS) -o $#
server: image.pb.o image.grpc.pb.o server.o
$(CXX) $^ $(LDFLAGS) -o $#
%.grpc.pb.cc: %.proto
protoc --grpc_out=. --plugin=protoc-gen-grpc=$(GRPC_CPP_PLUGIN_PATH) $<
%.pb.cc: %.proto
protoc --cpp_out=. $<
clean:
rm -f *.o *.pb.cc *.pb.h client server
And I wrote a simple program that still throws the error
#include <opencv2/opencv.hpp>
#include <stdio.h>
int main() {
cv::Mat frame = cv::imread("sylvania.png", cv::IMREAD_UNCHANGED);
printf("Image size is %i x %i\n", frame.rows, frame.cols);
}
Everything seems to compile fine but I keep getting this linker issue. I don't seem to get the issue when I compile it on another computer (my mac) for what it's worth. Also I have the gRPC and Protoc files because I need them for the project, I just didn't use those file as an example since they're quite long.
I agree with Micka, here is a Makefile of one of my projects:
CPPFLAGS=-g -Wall -I. -DDEBUG
LDFLAGS=-g
LDLIBS=-lopencv_core -lopencv_calib3d -lopencv_highgui -lopencv_imgproc -lopencv_stitching -lopencv_video
main: main.o AffineKalmanLP.o
g++ $(LDFLAGS) -o main main.o AffineKalmanLP.o $(LDLIBS)
main.o: main.cpp main.h
g++ $(CPPFLAGS) -c main.cpp
AffineKalmanLP.o: AffineKalmanLP.cpp AffineKalmanLP.h
g++ $(CPPFLAGS) -c AffineKalmanLP.cpp
clean:
rm main main.o AffineKalmanLP.o
You need to add it to LDLIBS.
If I remove that line, I get undefined reference for various things as well.
I ran into an issue with make. I have 3 files.
main.cpp | src/Math/Vector2.cpp | src/Math/Vector2.hpp
Here is my MakeFile:
main: vector2.o main.o
g++ -o main.o vector2.o
main.o: main.cpp
g++ -o main.o main.cpp -c
vector2.o: src/Math/Vector2.cpp src/Math/Vector2.hpp
g++ -o vector2.o src/Math/Vector2.cpp -lm -c
When i copy these commands manually , it compiles perfectly fine.
However $make main returns
g++ main.cpp -o main
/tmp/ccnRZ4UD.o: In function `main':
main.cpp:(.text+0x42): undefined reference to `
phy2d::Maths::Vector2f::Vector2f(double, double)'
main.cpp:(.text+0x66): undefined reference to `
phy2d::Maths::Vector2f::Vector2f(double, double)'
main.cpp:(.text+0x79): undefined reference to `
phy2d::Maths::Vector2f::distance(phy2d::Maths::Vector2f const&)
const'
collect2: error: ld returned 1 exit status
<builtin>: recipe for target 'main' failed
make: *** [main] Error 1
Any ideas??
There's no way that the makefile you provide will give the output you show.
In your comment you said Here is my MakeFile. Note that make will not read a file named MakeFile. It will read files named Makefile and makefile, but if you're using a case-sensitive filesystem then one explanation for the behavior you're seeing is that you've used MakeFile for your makefile name and make can't find it.
Or, you could have simply been imprecise in your question, but then this can't be the makefile that make is using for some other reason.
Also, there are numerous errors with your makefile:
You have two different targets main and main.o where the command generates the same file, -o main.o
You are adding libraries -lm to your compile line for vector2.o; libraries should go on the link line.
In general you should be using automatic variables to make sure your makefile is agreeing with what you want it to do.
Here's a reasonable makefile for your situation:
CXX = g++
main: vector2.o main.o
$(CXX) -o $# $^ -lm
main.o: main.cpp
$(CXX) -c -o $# $<
vector2.o: src/Math/Vector2.cpp src/Math/Vector2.hpp
$(CXX) -c -o $# $<
I have been scratching my head since yesterday trying to make gtest work but I just can't fix it after reading the links below.
undefined reference to `pthread_key_create' (linker error)
error during making GTest
The compilation error displayed is this:
g++ main.o tests.o var.o -L ../gmock/lib/.libs -L ../gmock/gtest/lib/.libs
-lgtest -lgmock -lpthread -o test
../gmock/gtest/lib/.libs/libgtest.so: undefined reference to `pthread_key_create'
../gmock/gtest/lib/.libs/libgtest.so: undefined reference to `pthread_getspecific'
../gmock/gtest/lib/.libs/libgtest.so: undefined reference to `pthread_key_delete'
../gmock/gtest/lib/.libs/libgtest.so: undefined reference to `pthread_setspecific'
collect2: error: ld returned 1 exit status
make: *** [test] Error 1
My Makefile is:
CXXFLAGS=-I ../gmock/include -I ../gmock/gtest/include
test:main.o tests.o var.o
g++ $^ -L ../gmock/lib/.libs -L ../gmock/gtest/lib/.libs -lgtest -lgmock -lpthread -o $#
I am still in the process of learning Linux, compiling and linking source files.
The Error is about linking error on pthread.
You have to make the pthread flag to -pthread and the follow CXX should do the trick.
LDLIBS = -L../gmock/lib/.libs -L../gmock/gtest/lib/.libs -lgtest -lgmock
test:main.o tests.o var.o
g++ -isystem $(LDLIBS) -pthread $^ -o $#
This link have a good Makefile which addresses all your problems and it follows general standards on creating a Makefile
I'm current working on a C++ that I edit locally on my Mac but run on an Ubuntu server. I always make sure that the code compiles on my mac before uploading it to the server to compile it there, where I have to use a makefile to link with libraries that are installed in my local directory. Basically, I had edited a significant portion of my code, found that it compiled on my mac, and uploaded it to the server to compile, but it doesn't compile! Luckily, I had a backup version of the code, so I tried that on the server, and that won't compile anymore either! In between the last time I knew that my code compiled on the server and now, I know that they ran some updates, but that's all I can think of that's different. For reference, here's my make file:
LOCAL_INCLUDE = /home/schraiber/.local/include
LOCAL_LIB = /home/schraiber/.local/lib
CXXFLAGS = -I$(LOCAL_INCLUDE)
CXX_LDFLAGS = -L$(LOCAL_LIB) -lgsl -lm -lgslcblas -lpthread
CoalHMMgf: main.o IOUtilities.o parameters.o Algorithms.o Optimization.o probabilities.o RNGUtilities.o Data.o ThreadData.h
g++ $(CXXFLAGS) $(CXX_LDFLAGS) main.o IOUtilities.o parameters.o Algorithms.o Optimization.o probabilities.o RNGUtilities.o Data.o -o CoalHMMgf
main.o: main.cpp IOUtilities.h parameters.h Algorithms.h Optimization.h probabilities.h ThreadData.h Data.h
g++ $(CXXFLAGS) $(CXX_LDFLAGS) -c main.cpp
IOutilities.o: IOUtilities.h IOUtilities.cpp parameters.h data.h
g++ $(CXXFLAGS) $(CXX_LDFLAGS) -c IOUtilities.cpp
parameters.o: parameters.h parameters.cpp
g++ $(CXXFLAGS) $(CXX_LDFLAGS) -c parameters.cpp
Algorithms.o: Algorithms.h Algorithms.cpp
g++ $(CXXFLAGS) $(CXX_LDFLAGS) -c Algorithms.cpp
Optimization.o: Optimization.h Optimization.cpp Algorithms.h parameters.h probabilities.h RNGUtilities.h ThreadData.h IOUtilities.h
g++ $(CXXFLAGS) $(CXX_LDFLAGS) -c Optimization.cpp
probabilities.o: probabilities.h probabilities.cpp parameters.h
g++ $(CXXFLAGS) $(CXX_LDFLAGS) -c probabilities.cpp
RNGUtilities.o: RNGUtilities.h RNGUtilities.cpp
g++ $(CXXFLAGS) $(CXX_LDFLAGS) -c RNGUtilities.cpp
Data.o: Data.h Data.cpp
g++ $(CXXFLAGS) $(CXX_LDFLAGS) -c Data.cpp
and the error:
g++ -I/home/schraiber/.local/include -L/home/schraiber/.local/lib -lgsl -lm -lgslcblas -lpthread main.o IOUtilities.o parameters.o Algorithms.o Optimization.o probabilities.o RNGUtilities.o Data.o -o CoalHMMgf
main.o: In function `main':
main.cpp:(.text+0xbf1): undefined reference to `pthread_create'
main.cpp:(.text+0xd0e): undefined reference to `pthread_join'
Optimization.o: In function `my_df(gsl_vector const*, void*, gsl_vector*)':
Optimization.cpp:(.text+0x3149): undefined reference to `gsl_vector_alloc'
Optimization.cpp:(.text+0x316b): undefined reference to `gsl_vector_get'
Optimization.cpp:(.text+0x3180): undefined reference to `gsl_vector_set'
Optimization.cpp:(.text+0x31bc): undefined reference to `gsl_vector_get'
Optimization.cpp:(.text+0x31ec): undefined reference to `gsl_vector_set'
Optimization.cpp:(.text+0x323b): undefined reference to `gsl_vector_set'
Optimization.cpp:(.text+0x327e): undefined reference to `gsl_vector_set'
Optimization.cpp:(.text+0x32c9): undefined reference to `gsl_vector_set'
Optimization.o: In function `MHthreaded(void*)':
Optimization.cpp:(.text+0x3489): undefined reference to `gsl_rng_env_setup'
Optimization.cpp:(.text+0x3490): undefined reference to `gsl_rng_default'
Optimization.cpp:(.text+0x360b): undefined reference to `gsl_rng_uniform'
Optimization.cpp:(.text+0x3653): undefined reference to `gsl_ran_gaussian'
Optimization.cpp:(.text+0x3686): undefined reference to `gsl_ran_gaussian'
Optimization.cpp:(.text+0x377f): undefined reference to `gsl_rng_uniform'
RNGUtilities.o: In function `AllocRNG(gsl_rng*&, gsl_rng_type const*, int)':
RNGUtilities.cpp:(.text+0x9a): undefined reference to `gsl_rng_alloc'
RNGUtilities.cpp:(.text+0xba): undefined reference to `gsl_rng_set'
RNGUtilities.o: In function `FreeRNG(gsl_rng*&)':
RNGUtilities.cpp:(.text+0xe3): undefined reference to `gsl_rng_free'
collect2: ld returned 1 exit status
make: *** [CoalHMMgf] Error 1
and just to verify that gsl is installed in the local directory:
schraiber#trump:~/test_rsync$ ls ~/.local/lib
libbpp-core.a libbpp-core.so.2.0.0 libbpp-seq.so.9 libgslcblas.a libgslcblas.so.0 libgsl.so pkgconfig
libbpp-core.so libbpp-seq.a libbpp-seq.so.9.1.0 libgslcblas.la libgslcblas.so.0.0.0 libgsl.so.0 python2.7
libbpp-core.so.2 libbpp-seq.so libgsl.a libgslcblas.so libgsl.la libgsl.so.0.16.0
schraiber#trump:~/test_rsync$ ls ~/.local/include/
Bpp gsl
An interesting thing to note is that my program is also supposed to link with Bpp, and it does that just fine as far as I can tell.
Your "-lfoo" parameters should come last on your "g++" command line. So, for example, make this change in your makefile:
CoalHMMgf: main.o IOUtilities.o parameters.o Algorithms.o Optimization.o probabilities.o RNGUtilities.o Data.o ThreadData.h
g++ $(CXXFLAGS) main.o IOUtilities.o parameters.o Algorithms.o Optimization.o probabilities.o RNGUtilities.o Data.o -o CoalHMMgf $(CXX_LDFLAGS)
Libraries have to be defined on the link line such that the library containing no other references is the very last one. Libraries that depend on code from a second library need to be listed first. They must be listed after the .o files, or else the .o files are assumed to be self-contained and don't need the libraries.