not compile make file

[199413]

gcc -Wall -O3 src/matlock.c src/matrix.o src/bam_filt.o src/count_motif.o src/dna.o src/read_count.o -Ihtslib -Isrc htslib/libhts.a -lbz2 -llzma -lz -lm -lpthread -lgsl -lgslcblas -o bin/matlock
/usr/bin/ld: src/bam_filt.o:(.bss+0x50): multiple definition of `rp'; /tmp/ccu2Wv02.o:(.bss+0x20): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:16: bin/matlock] Error 1

[aijigekoukou-shen]

gcc -Wall -O3 src/matlock.c src/matrix.o src/bam_filt.o src/count_motif.o src/dna.o src/read_count.o -Ihtslib -Isrc htslib/libhts.a -lbz2 -llzma -lz -lm -lpthread -lgsl -lgslcblas -o bin/matlock /usr/bin/ld: src/bam_filt.o:(.bss+0x50): multiple definition of `rp'; /tmp/ccu2Wv02.o:(.bss+0x20): first defined here collect2: error: ld returned 1 exit status make: *** [Makefile:16: bin/matlock] Error 1

Hi. Are you solve this problem？

[amvarani]

Hi there
It would help if you used the flag: -Wl,--allow-multiple-definition
This is not the correct and good solution but should work

gcc -Wall -O3 src/matlock.c src/matrix.o src/bam_filt.o src/count_motif.o src/dna.o src/read_count.o -Ihtslib -Isrc htslib/libhts.a -lbz2 -llzma -lz -lm -lpthread -lgsl -lgslcblas -Wl,--allow-multiple-definition -o bin/matlock

The best solution is to use conda

conda install bioconda::matlock