C "undefined reference to" error while compiling COSEG from RepeatMasker developers - c

Question

I'm trying to compile COSEG, a program from the RepeatMasker developers (link: http://www.repeatmasker.org/COSEGDownload.html) on Xubuntu.
After unpacking the distribution I enter the directory and try to run make in my terminal but I get many "undefined reference to" errors:
massimiliano#compaq2:~/Programs/coseg$ make
cc -O4 -lm version.o coseg.o -o coseg
coseg.o: In function `compute_siegel_tri_pvalue.part.0':
coseg.c:(.text+0xa1): undefined reference to `log'
coseg.c:(.text+0xae): undefined reference to `exp'
coseg.c:(.text+0x47b): undefined reference to `log'
coseg.c:(.text+0x4c2): undefined reference to `exp'
coseg.c:(.text+0x4d7): undefined reference to `log'
coseg.c:(.text+0x683): undefined reference to `log'
coseg.c:(.text+0x6d7): undefined reference to `exp'
coseg.c:(.text+0x6e4): undefined reference to `log'
coseg.c:(.text+0x70f): undefined reference to `sqrt'
coseg.c:(.text+0x72d): undefined reference to `sqrt'
coseg.c:(.text+0x757): undefined reference to `sqrt'
coseg.o: In function `compute_siegel_pvalue.part.1':
coseg.c:(.text+0x7da): undefined reference to `log'
coseg.c:(.text+0x7e7): undefined reference to `exp'
coseg.c:(.text+0x97f): undefined reference to `exp'
coseg.c:(.text+0x98c): undefined reference to `log'
coseg.c:(.text+0x9ff): undefined reference to `log'
coseg.c:(.text+0xad7): undefined reference to `exp'
coseg.c:(.text+0xae4): undefined reference to `log'
coseg.c:(.text+0xb4d): undefined reference to `log'
coseg.c:(.text+0xbe7): undefined reference to `sqrt'
coseg.c:(.text+0xc05): undefined reference to `sqrt'
coseg.o: In function `compute_pvalue.part.2':
coseg.c:(.text+0xd3b): undefined reference to `log'
coseg.c:(.text+0xd4c): undefined reference to `log'
coseg.c:(.text+0xe24): undefined reference to `exp'
coseg.c:(.text+0xe86): undefined reference to `log'
coseg.c:(.text+0xe97): undefined reference to `log'
coseg.o: In function `compute_tri_pvalue.part.3':
coseg.c:(.text+0x10e4): undefined reference to `exp'
coseg.o: In function `inverseNormalCDF':
coseg.c:(.text+0x141e): undefined reference to `log'
coseg.c:(.text+0x150f): undefined reference to `sqrt'
coseg.o: In function `allocate_memory':
coseg.c:(.text+0x15de): undefined reference to `log'
coseg.c:(.text+0x166c): undefined reference to `log'
coseg.c:(.text+0x16cc): undefined reference to `log'
coseg.o: In function `compute_tri_pvalue':
coseg.c:(.text+0x303a): undefined reference to `log'
coseg.c:(.text+0x3047): undefined reference to `exp'
coseg.o: In function `compute_pvalue':
coseg.c:(.text+0x31e6): undefined reference to `log'
coseg.c:(.text+0x31f3): undefined reference to `exp'
coseg.o: In function `compute_score':
coseg.c:(.text+0x32cd): undefined reference to `log'
coseg.c:(.text+0x32da): undefined reference to `exp'
coseg.o: In function `compute_tri_score':
coseg.c:(.text+0x3386): undefined reference to `log'
coseg.c:(.text+0x3393): undefined reference to `exp'
coseg.o: In function `compute_tri_bestmut':
coseg.c:(.text+0x628c): undefined reference to `log'
coseg.c:(.text+0x629b): undefined reference to `exp'
coseg.o: In function `split_pvaluelocal':
coseg.c:(.text+0x6e55): undefined reference to `log'
coseg.c:(.text+0x734d): undefined reference to `log'
coseg.c:(.text+0x735a): undefined reference to `exp'
coseg.o: In function `compute_bestmut':
coseg.c:(.text+0x7ff3): undefined reference to `log'
coseg.c:(.text+0x8000): undefined reference to `exp'
coseg.o: In function `union_tri_pvalue':
coseg.c:(.text+0x91fd): undefined reference to `log'
coseg.c:(.text+0x920a): undefined reference to `exp'
coseg.c:(.text+0x934e): undefined reference to `log'
coseg.c:(.text+0x935b): undefined reference to `exp'
coseg.o: In function `union_pvalue':
coseg.c:(.text+0x9e1c): undefined reference to `log'
coseg.c:(.text+0x9e29): undefined reference to `exp'
coseg.o: In function `build_MST':
coseg.c:(.text+0xb232): undefined reference to `exp'
coseg.o: In function `compute_sigma':
coseg.c:(.text+0xb7d4): undefined reference to `log'
coseg.c:(.text+0xb7e1): undefined reference to `exp'
coseg.o: In function `compute_bestmut1':
coseg.c:(.text+0xbb27): undefined reference to `log'
coseg.c:(.text+0xbb34): undefined reference to `exp'
coseg.o: In function `build_new_subfamily2':
coseg.c:(.text+0xd265): undefined reference to `exp'
coseg.c:(.text+0xd2a6): undefined reference to `log'
coseg.c:(.text+0xd4ad): undefined reference to `exp'
coseg.c:(.text+0xd4ee): undefined reference to `log'
coseg.o: In function `sigmage_to_logpvalue':
coseg.c:(.text+0xd8a8): undefined reference to `exp'
coseg.c:(.text+0xd8ec): undefined reference to `log'
coseg.o: In function `build_new_singlemut_subfamily':
coseg.c:(.text+0xdb4d): undefined reference to `exp'
coseg.c:(.text+0xdb8e): undefined reference to `log'
coseg.c:(.text+0xdd7d): undefined reference to `exp'
coseg.c:(.text+0xddbe): undefined reference to `log'
coseg.o: In function `build_singlemut_MST':
coseg.c:(.text+0xe608): undefined reference to `log'
coseg.c:(.text+0xe615): undefined reference to `exp'
coseg.c:(.text+0xe8ce): undefined reference to `log'
coseg.c:(.text+0xe8db): undefined reference to `exp'
coseg.o: In function `build_MST2':
coseg.c:(.text+0xf38f): undefined reference to `exp'
coseg.c:(.text+0xf5d0): undefined reference to `exp'
coseg.c:(.text+0xf7c9): undefined reference to `exp'
coseg.c:(.text+0xf814): undefined reference to `log'
coseg.c:(.text+0xf85f): undefined reference to `exp'
coseg.c:(.text+0xfb3c): undefined reference to `exp'
coseg.c:(.text+0xfb97): undefined reference to `log'
coseg.c:(.text+0xfbf6): undefined reference to `exp'
coseg.c:(.text+0xfcd8): undefined reference to `sqrt'
coseg.c:(.text+0xfd51): undefined reference to `sqrt'
coseg.o: In function `print_subfamilies':
coseg.c:(.text+0xffe0): undefined reference to `exp'
coseg.c:(.text+0x10024): undefined reference to `log'
collect2: ld returned 1 exit status
make: *** [coseg] Error 1
Searching the internet I have found that probably it is a 'linking' problem and I have to add/modify some lines of code in the makefile but this kind of stuffs are very new to me and I am not a programmer, so I feel a bit confused.
Do you have some tips or suggestions to help me to solve this problem, please?
Thank you very much for your time!
Massimiliano.
Update:
Trying to compile the previous version of the program, gives me an additional warning:
echo "char const* Version = \"0.2.1\";" > version.c
cc -O4 -lm -c -o version.o version.c
cc -O4 -lm -c -o coseg.o coseg.c
coseg.c: In function ‘inverseNormalCDF’:
coseg.c:973:5: warning: format ‘%lf’ expects a matching ‘double’ argument [-Wformat]
Update - Makefile:
This is the Makefile unpacked with the distribution:
##
## Makefile for coseg project
##
VERSION=0.2.2
INSTALLDIR=/usr/local/coseg-${VERSION}
## Basic
CC = cc -O4 -lm
## A nice memory leak checker:
#CC = bgcc -O4 -fbounds-checking -lm
all: coseg
version.c: Makefile
echo "char const* Version = \"$(VERSION)\";" > version.c
coseg: version.o coseg.o
${CC} version.o coseg.o -o coseg
beautify:
indent -bap -cdb -bl -bli0 -npcs -nut -lp coseg.c
install: coseg
-mkdir ${INSTALLDIR}
cp coseg ${INSTALLDIR}
cp README ${INSTALLDIR}
cp preprocessAlignments.pl ${INSTALLDIR}
cp postprocess.pl ${INSTALLDIR}
cp runcoseg.pl ${INSTALLDIR}
cp extractSubSeqs.pl ${INSTALLDIR}
cp refineConsSeqs.pl ${INSTALLDIR}
cp ALU.cons ${INSTALLDIR}
cp ALU.ins ${INSTALLDIR}
cp ALU.seqs ${INSTALLDIR}
cp LINE1 ${INSTALLDIR}
dist:
-mkdir dist
-mkdir dist/coseg
cp ALU.cons dist/coseg
cp ALU.ins dist/coseg
cp ALU.seqs dist/coseg
cp LINE1 dist/coseg
cp Makefile dist/coseg
cp README dist/coseg
cp coseg.c dist/coseg
cp coseg.h dist/coseg
cp postprocess.pl dist/coseg
cp preprocessAlignments.pl dist/coseg
cp runcoseg.pl dist/coseg
cp extractSubSeqs.pl dist/coseg
cp refineConsSeqs.pl dist/coseg
(cd dist; tar zcvf coseg-$(VERSION).tar.gz coseg)
clean:
-rm *.o
-rm coseg
-rm version.c
-rm ALU.seqs.subfamilies.seq
-rm ALU.seqs.assign
-rm ALU.seqs.log
-rm ALU.seqs.subfamilies
-rm ALU.seqs.tree.viz
ALU.seqs.subfamilies.seq: coseg
./runcoseg.pl -d -filePrefix ALU
t/kothi.seqs.subfamilies.seq: coseg
./runcoseg.pl -u1 -t -m 5 -filePrefix t/kothi
test: ALU.seqs.subfamilies.seq t/kothi.seqs.subfamilies.seq
diff ALU.seqs.subfamilies.seq t
diff t/kothi.seqs.subfamilies.seq t/kothi-baseline

Answer 1

Some linkers (including yours) need to have the libraries specified after the object files (or other libraries), which use symbols from it. This can even lead to the necessity to specify libraries multiply if cyclic dependencies are involved.
In your case coseg.o uses symbols from libm, so you would have to specify -lm after coseg.o in your command: cc -O4 version.o coseg.o -lm -o coseg
I suggest you change your Makefile to:
##
## Makefile for coseg project
##
VERSION=0.2.2
INSTALLDIR=/usr/local/coseg-${VERSION}
## Basic
CC = cc
CFLAGS = -O4
LDFLAGS = -lm
## A nice memory leak checker:
#CC = bgcc -O4 -fbounds-checking -lm
all: coseg
version.c: Makefile
echo "char const* Version = \"$(VERSION)\";" > version.c
coseg: version.o coseg.o
${CC} version.o coseg.o ${LDFLAGS} -o coseg
... rest of makefile ...
That should fix your problem.