ld: library not found for -lcrt0.o

vckngs7 (89)
I am trying to compile a program package for my computer called DSSP. It requires the boost library. I have boost on my computer and it should be working fine. When I type make I get the following errors.

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[0] 02:20: dssp-2.0.4$make
linking mkdssp
clang: warning: argument unused during compilation: '-pthread'
ld: library not found for -lcrt0.o
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mkdssp] Error 1


I have done a search around the internet and have not turned up anything. I do not know what lcrt0.o is, nor could I find useful information about it. Anyone have any ideas?
vckngs7 (89)
Update:

I've removed an option -pthread from the make file as well as the option which caused the library error for -lcrt0.o.

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[0] 02:44: dssp-2.0.4$make
linking mkdssp
ld: library not found for -lboost_thread-mt
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mkdssp] Error 1


The makefile is as follows (this is not in violation of the license agreement).

Note: I am using bash
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# Makefile for mkdssp
#
#  Copyright Maarten L. Hekkelman, Radboud University 2008-2011.
# Distributed under the Boost Software License, Version 1.0.
#    (See accompanying file LICENSE_1_0.txt or copy at
#          http://www.boost.org/LICENSE_1_0.txt)
#
# This makefile includes a file called make.config. It will create a
# new one if it doesn't exist. In this make.config you can set site
# specific variables like the Boost library location.

firstTarget: mkdssp

include make.config

VERSION                         = 2.0.4

DEST_DIR                        ?= /usr/local/
LIB_DIR                         = $(BOOST_LIB_DIR)
INC_DIR                         = $(BOOST_INC_DIR)

MAN_DIR                         = $(DEST_DIR)man/man1/

BOOST_LIBS                      = thread regex filesystem program_options date_time iostreams math_c99 system
LIBS                            = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2

DEFINES                         = USE_COMPRESSION LINUX VERSION='"$(VERSION)"'
CC                              = c++

CFLAGS                          = $(INC_DIR:%=-I%) -iquote src -g -Wall -Wno-multichar -pthread
LDOPTS                          = $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -g 

OBJ_DIR                         = obj

ifeq ($(DEBUG),1)
OBJ_DIR                         := $(OBJ_DIR).dbg
CFLAGS                          += -g3
else
DEFINES                         += NDEBUG
CFLAGS                          += -O3
endif

CFLAGS                          += $(DEFINES:%=-D%)

DIST_NAME                       = dssp-$(VERSION)

VPATH += src

OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ_DIR)/structure.o $(OBJ_DIR)/utils.o

mkdssp: $(OBJECTS)
        @ echo linking $@
        @ $(CC) -o $@ $^ $(LDOPTS)
        @ echo OK


There is more to the makefile but it doesn't even pass this step so in order to save space I thought I'd post this and then deal with the rest of other problems arise.
kbw (9488)
I'm assuning you're using GNU Make.

Is BOOST_LIB_DIR set? What's it's value? You can check it by running:
 
 
make -pn | grep ^BOOST_LIB_DIR


You should be using the C++ linker, not the C linker. So the target should be:
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mkdssp: $(OBJECTS)
        $(LINK.cc) -o $@ $^ $(LDOPTS)
Indented by a tab, not spaces.

CFLAGS sets C program options, CPPFLAGS sets C and C++, CXXFLAGS sets C++ only.

You're using CFLAGS, but you should be using CPPFLAGS instead. So you need to replace all instances.

It would be interesting to see the content of make.config.
Last edited on
vckngs7 (89)
I wanted to be a bit more descriptive so I've posted below the two changes I have made so far to the makefile and which error they eliminated.

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[0] 14:00: dssp-2.0.4 2$make
linking mkdssp
clang: warning: argument unused during compilation: '-pthread'
ld: warning: directory not found for option '-L/usr/local/boost/libs'
ld: library not found for -lcrt0.o
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mkdssp] Error 1


ORIGINAL
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mkdssp: $(OBJECTS)
	@ echo linking $@
	@ $(CC) -static -o $@ $^ $(LDOPTS)
	@ echo OK


ALTERED
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mkdssp: $(OBJECTS)
	@ echo linking $@
	@ $(CC) -o $@ $^ $(LDOPTS)
	@ echo OK


With the above change I now get the following error

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[0] 14:03: dssp-2.0.4 2$make
linking mkdssp
clang: warning: argument unused during compilation: '-pthread'
ld: warning: directory not found for option '-L/usr/local/boost/libs'
OK


The above error was fixed by configuring in my .bashrc file the following settings

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#Configureation for Boost                                                                                                       
export BOOST_LIB_DIR="/usr/local/boost_1_52_0/boost/libs"
export BOOST_INC_DIR="/usr/local/include/boost"
export boost="/usr/local/include/boost"


So as far as I can tell I've solved the problem. Though, I will admit I think the solution was just happened upon. In short, DSSP has quite a few little bugs to work out in order to install properly on OS X.
kbw (9488)
I wanted to be a bit more descriptive so I've posted below the two changes I have made so far to the makefile
So you've ignored my recommended changes? I've explained that the makefile is wrong and why and given you the fix.

Good luck.
vckngs7 (89)
I didn't ignore them, I tried to recreate my problems as I went through them so I could describe what was happened and instead of getting the same results I found one other fix and I solved the problem without needing to implement your changes.

Had I not been successful I would have used your changed and reported back.

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