error compiling - multiple difinitions of variables

[jdmontenegro]

Dear Sir,

I tried to compile this tool locally in my server and downloaded the source code from version 1.5.6. The first error was that I had no permissions to download the additional source code with "git clone --recursive" command. After downloading the remaining of the source I cd'd inot src and ran the following:

...software/deSALT-1.5.6/src> make
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   main.c -o main.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   desalt_index.c -o desalt_index.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   read_seeding.c -o read_seeding.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   bit_operation.c -o bit_operation.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   format.c -o format.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   ktime.c -o ktime.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   binarys_qsort.c -o binarys_qsort.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   hash_index.c -o hash_index.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   aln_2pass.c -o aln_2pass.o
aln_2pass.c: In function ‘load_fasta_2pass’:
aln_2pass.c:3835:27: warning: ‘qual0[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 3835 |     qual0[0][i] = qual0[1][seqlen - 1 - i] = s_io->qual[i] - 33;
      |                           ^
aln_2pass.c:3806:22: note: ‘qual0[1]’ was declared here
 3806 |  uint8_t *qseq0[2], *qual0[2];
      |                      ^~~~~
aln_2pass.c:3947:22: warning: ‘qual0[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 3947 |  if (opt->with_qual) kfree(km, qual0[0]);
      |                      ^~~~~~~~~~~~~~~~~~~
aln_2pass.c:3806:22: note: ‘qual0[0]’ was declared here
 3806 |  uint8_t *qseq0[2], *qual0[2];
      |                      ^~~~~
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   splic_junction.c -o splic_junction.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   bseq.c -o bseq.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   load_unipath_size.c -o load_unipath_size.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   graph.c -o graph.o
cc -c -DHAVE_KALLOC -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function   kalloc.c -o kalloc.o
cc -c -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function  -msse2 -DHAVE_KALLOC  ksw2_ll_sse.c -o ksw2_ll_sse.o
cc -c -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function  -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH  ksw2_extz2_sse.c -o ksw2_extz2_sse41.o
cc -c -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function  -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH  ksw2_extd2_sse.c -o ksw2_extd2_sse41.o
cc -c -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function  -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH  ksw2_exts2_sse.c -o ksw2_exts2_sse41.o
cc -c -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function  -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY  ksw2_extz2_sse.c -o ksw2_extz2_sse2.o
cc -c -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function  -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY  ksw2_extd2_sse.c -o ksw2_extd2_sse2.o
cc -c -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function  -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY  ksw2_exts2_sse.c -o ksw2_exts2_sse2.o
cc -c -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function  -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH  ksw2_dispatch.c -o ksw2_dispatch.o
cc -g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function  main.o desalt_index.o read_seeding.o bit_operation.o format.o ktime.o binarys_qsort.o hash_index.o aln_2pass.o splic_junction.o bseq.o load_unipath_size.o graph.o kalloc.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o -lm -lz -lpthread -lgomp -o deSALT
read_seeding.o:(.bss+0x16e42e8): multiple definition of `secondary_ratio'
main.o:(.bss+0x16e3e28): first defined here
read_seeding.o:(.bss+0x16e42fa): multiple definition of `top_n'
main.o:(.bss+0x16e3e3a): first defined here
read_seeding.o:(.bss+0x16e42f4): multiple definition of `uni_pos_n_max'
main.o:(.bss+0x16e3e34): first defined here
read_seeding.o:(.bss+0x16e42f9): multiple definition of `seed_step'
main.o:(.bss+0x16e3e39): first defined here
read_seeding.o:(.bss+0x16e42fd): multiple definition of `re_b'
main.o:(.bss+0x16e3e3d): first defined here
read_seeding.o:(.bss+0x16e42fb): multiple definition of `re_2bt'
main.o:(.bss+0x16e3e3b): first defined here
read_seeding.o:(.bss+0x16e42fe): multiple definition of `k_r'
main.o:(.bss+0x16e3e3e): first defined here
read_seeding.o:(.bss+0x16e42f8): multiple definition of `seed_offset'
main.o:(.bss+0x16e3e38): first defined here
read_seeding.o:(.bss+0x16e42f6): multiple definition of `pos_n_max'
main.o:(.bss+0x16e3e36): first defined here
read_seeding.o:(.bss+0x16e4310): multiple definition of `vertexm'
main.o:(.bss+0x16e3e50): first defined here
read_seeding.o:(.bss+0x16e4308): multiple definition of `vertexu'
main.o:(.bss+0x16e3e48): first defined here
read_seeding.o:(.bss+0x16e42e4): multiple definition of `min_chain_score'
main.o:(.bss+0x16e3e24): first defined here
read_seeding.o:(.bss+0x16e42e0): multiple definition of `max_read_join_gap'
main.o:(.bss+0x16e3e20): first defined here
read_seeding.o:(.bss+0x16e4300): multiple definition of `query_info'
main.o:(.bss+0x16e3e40): first defined here
read_seeding.o: In function `get_skeleton_anchor':
/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:915: multiple definition of `read_bit1'
main.o:(.bss+0x0): first defined here
read_seeding.o:(.bss+0x16e4320): multiple definition of `rwlock'
main.o:(.bss+0x16e3e60): first defined here
read_seeding.o:(.bss+0x16e42f0): multiple definition of `batch_size'
main.o:(.bss+0x16e3e30): first defined here
read_seeding.o:(.bss+0x16e42fc): multiple definition of `re_bt'
main.o:(.bss+0x16e3e3c): first defined here
read_seeding.o:(.bss+0x16e3ee0): multiple definition of `temp_anchor_dir'
main.o:(.bss+0x16e3a20): first defined here
read_seeding.o:(.bss+0x16e3ac8): multiple definition of `fp_tff'
main.o:(.bss+0x16e3608): first defined here
read_seeding.o:(.bss+0x16e3ae0): multiple definition of `temp_binary_pos'
main.o:(.bss+0x16e3620): first defined here
read_seeding.o:(.bss+0x16e3ac0): multiple definition of `fp_temp'
main.o:(.bss+0x16e3600): first defined here
read_seeding.o:(.bss+0x16e42ec): multiple definition of `seed_num'
main.o:(.bss+0x16e3e2c): first defined here
format.o:(.bss+0x0): multiple definition of `read_bit1'
main.o:(.bss+0x0): first defined here
format.o:(.bss+0x16e3600): multiple definition of `fp_temp'
main.o:(.bss+0x16e3600): first defined here
format.o:(.bss+0x16e3608): multiple definition of `fp_tff'
main.o:(.bss+0x16e3608): first defined here
format.o:(.bss+0x16e3620): multiple definition of `temp_binary_pos'
main.o:(.bss+0x16e3620): first defined here
format.o:(.bss+0x16e3a20): multiple definition of `temp_anchor_dir'
main.o:(.bss+0x16e3a20): first defined here
format.o:(.bss+0x16e3e20): multiple definition of `max_read_join_gap'
main.o:(.bss+0x16e3e20): first defined here
format.o:(.bss+0x16e3e24): multiple definition of `min_chain_score'
main.o:(.bss+0x16e3e24): first defined here
format.o:(.bss+0x16e3e28): multiple definition of `secondary_ratio'
main.o:(.bss+0x16e3e28): first defined here
format.o:(.bss+0x16e3e2c): multiple definition of `seed_num'
main.o:(.bss+0x16e3e2c): first defined here
format.o:(.bss+0x16e3e30): multiple definition of `batch_size'
main.o:(.bss+0x16e3e30): first defined here
format.o:(.bss+0x16e3e34): multiple definition of `uni_pos_n_max'
main.o:(.bss+0x16e3e34): first defined here
format.o:(.bss+0x16e3e36): multiple definition of `pos_n_max'
main.o:(.bss+0x16e3e36): first defined here
format.o:(.bss+0x16e3e38): multiple definition of `seed_offset'
main.o:(.bss+0x16e3e38): first defined here
format.o:(.bss+0x16e3e39): multiple definition of `seed_step'
main.o:(.bss+0x16e3e39): first defined here
format.o:(.bss+0x16e3e3a): multiple definition of `top_n'
main.o:(.bss+0x16e3e3a): first defined here
format.o:(.bss+0x16e3e3b): multiple definition of `re_2bt'
main.o:(.bss+0x16e3e3b): first defined here
format.o:(.bss+0x16e3e3c): multiple definition of `re_bt'
main.o:(.bss+0x16e3e3c): first defined here
format.o:(.bss+0x16e3e3d): multiple definition of `re_b'
main.o:(.bss+0x16e3e3d): first defined here
format.o:(.bss+0x16e3e3e): multiple definition of `k_r'
main.o:(.bss+0x16e3e3e): first defined here
format.o:(.bss+0x16e3e40): multiple definition of `query_info'
main.o:(.bss+0x16e3e40): first defined here
format.o:(.bss+0x16e3e48): multiple definition of `vertexu'
main.o:(.bss+0x16e3e48): first defined here
format.o:(.bss+0x16e3e50): multiple definition of `vertexm'
main.o:(.bss+0x16e3e50): first defined here
format.o:(.bss+0x16e3e60): multiple definition of `rwlock'
main.o:(.bss+0x16e3e60): first defined here
binarys_qsort.o:(.bss+0x0): multiple definition of `e_shift'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:682: first defined here
binarys_qsort.o: In function `binsearch_range':
/proj/jmontenegro/software/deSALT-1.5.6/src/binarys_qsort.c:10: multiple definition of `hash_kmer'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
binarys_qsort.o: In function `binsearch_range':
/proj/jmontenegro/software/deSALT-1.5.6/src/binarys_qsort.c:10: multiple definition of `splice_offset'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
binarys_qsort.o: In function `binsearch_range':
/proj/jmontenegro/software/deSALT-1.5.6/src/binarys_qsort.c:7: multiple definition of `merge_anchor_cnt'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
binarys_qsort.o: In function `binsearch_range':
/proj/jmontenegro/software/deSALT-1.5.6/src/binarys_qsort.c:7: multiple definition of `seqio'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:680: first defined here
binarys_qsort.o: In function `binsearch_range':
/proj/jmontenegro/software/deSALT-1.5.6/src/binarys_qsort.c:10: multiple definition of `EXON_T'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
binarys_qsort.o: In function `binsearch_range':
/proj/jmontenegro/software/deSALT-1.5.6/src/binarys_qsort.c:39: multiple definition of `strand_arr'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
binarys_qsort.o: In function `binsearch_range':
/proj/jmontenegro/software/deSALT-1.5.6/src/binarys_qsort.c:36: multiple definition of `QUERY_pos'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:674: first defined here
binarys_qsort.o: In function `binsearch_range':
/proj/jmontenegro/software/deSALT-1.5.6/src/binarys_qsort.c:38: multiple definition of `REF_pos'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:915: first defined here
binarys_qsort.o: In function `binsearch_range':
/proj/jmontenegro/software/deSALT-1.5.6/src/binarys_qsort.c:36: multiple definition of `read_bit1'
main.o:(.bss+0x0): first defined here
binarys_qsort.o:(.bss+0x16e3640): multiple definition of `fp_temp'
main.o:(.bss+0x16e3600): first defined here
binarys_qsort.o:(.bss+0x16e3648): multiple definition of `fp_tff'
main.o:(.bss+0x16e3608): first defined here
binarys_qsort.o:(.bss+0x16e3660): multiple definition of `temp_binary_pos'
main.o:(.bss+0x16e3620): first defined here
binarys_qsort.o:(.bss+0x16e3a60): multiple definition of `temp_anchor_dir'
main.o:(.bss+0x16e3a20): first defined here
binarys_qsort.o:(.bss+0x16e3e60): multiple definition of `max_read_join_gap'
main.o:(.bss+0x16e3e20): first defined here
binarys_qsort.o:(.bss+0x16e3e64): multiple definition of `min_chain_score'
main.o:(.bss+0x16e3e24): first defined here
binarys_qsort.o:(.bss+0x16e3e68): multiple definition of `secondary_ratio'
main.o:(.bss+0x16e3e28): first defined here
binarys_qsort.o:(.bss+0x16e3e6c): multiple definition of `seed_num'
main.o:(.bss+0x16e3e2c): first defined here
binarys_qsort.o:(.bss+0x16e3e70): multiple definition of `batch_size'
main.o:(.bss+0x16e3e30): first defined here
binarys_qsort.o:(.bss+0x16e3e74): multiple definition of `uni_pos_n_max'
main.o:(.bss+0x16e3e34): first defined here
binarys_qsort.o:(.bss+0x16e3e76): multiple definition of `pos_n_max'
main.o:(.bss+0x16e3e36): first defined here
binarys_qsort.o:(.bss+0x16e3e78): multiple definition of `seed_offset'
main.o:(.bss+0x16e3e38): first defined here
binarys_qsort.o:(.bss+0x16e3e79): multiple definition of `seed_step'
main.o:(.bss+0x16e3e39): first defined here
binarys_qsort.o:(.bss+0x16e3e7a): multiple definition of `top_n'
main.o:(.bss+0x16e3e3a): first defined here
binarys_qsort.o:(.bss+0x16e3e7b): multiple definition of `re_2bt'
main.o:(.bss+0x16e3e3b): first defined here
binarys_qsort.o:(.bss+0x16e3e7c): multiple definition of `re_bt'
main.o:(.bss+0x16e3e3c): first defined here
binarys_qsort.o:(.bss+0x16e3e7d): multiple definition of `re_b'
main.o:(.bss+0x16e3e3d): first defined here
binarys_qsort.o:(.bss+0x16e3e7e): multiple definition of `k_r'
main.o:(.bss+0x16e3e3e): first defined here
binarys_qsort.o:(.bss+0x16e3e80): multiple definition of `query_info'
main.o:(.bss+0x16e3e40): first defined here
binarys_qsort.o:(.bss+0x16e3e88): multiple definition of `vertexu'
main.o:(.bss+0x16e3e48): first defined here
binarys_qsort.o:(.bss+0x16e3e90): multiple definition of `vertexm'
main.o:(.bss+0x16e3e50): first defined here
binarys_qsort.o:(.bss+0x16e3ea0): multiple definition of `rwlock'
main.o:(.bss+0x16e3e60): first defined here
hash_index.o:(.data+0x0): multiple definition of `hash_kmer'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
hash_index.o: In function `initHashTable':
/proj/jmontenegro/software/deSALT-1.5.6/src/hash_index.c:27: multiple definition of `read_bit1'
main.o:(.bss+0x0): first defined here
hash_index.o:(.bss+0x16e3620): multiple definition of `fp_temp'
main.o:(.bss+0x16e3600): first defined here
hash_index.o:(.bss+0x16e3628): multiple definition of `fp_tff'
main.o:(.bss+0x16e3608): first defined here
hash_index.o:(.bss+0x16e3640): multiple definition of `temp_binary_pos'
main.o:(.bss+0x16e3620): first defined here
hash_index.o:(.bss+0x16e3a40): multiple definition of `temp_anchor_dir'
main.o:(.bss+0x16e3a20): first defined here
hash_index.o:(.bss+0x16e3e40): multiple definition of `max_read_join_gap'
main.o:(.bss+0x16e3e20): first defined here
hash_index.o:(.bss+0x16e3e44): multiple definition of `min_chain_score'
main.o:(.bss+0x16e3e24): first defined here
hash_index.o:(.bss+0x16e3e48): multiple definition of `secondary_ratio'
main.o:(.bss+0x16e3e28): first defined here
hash_index.o:(.bss+0x16e3e4c): multiple definition of `seed_num'
main.o:(.bss+0x16e3e2c): first defined here
hash_index.o:(.bss+0x16e3e50): multiple definition of `batch_size'
main.o:(.bss+0x16e3e30): first defined here
hash_index.o:(.bss+0x16e3e54): multiple definition of `uni_pos_n_max'
main.o:(.bss+0x16e3e34): first defined here
hash_index.o:(.bss+0x16e3e56): multiple definition of `pos_n_max'
main.o:(.bss+0x16e3e36): first defined here
hash_index.o:(.bss+0x16e3e58): multiple definition of `seed_offset'
main.o:(.bss+0x16e3e38): first defined here
hash_index.o:(.bss+0x16e3e59): multiple definition of `seed_step'
main.o:(.bss+0x16e3e39): first defined here
hash_index.o:(.bss+0x16e3e5a): multiple definition of `top_n'
main.o:(.bss+0x16e3e3a): first defined here
hash_index.o:(.bss+0x16e3e5b): multiple definition of `re_2bt'
main.o:(.bss+0x16e3e3b): first defined here
hash_index.o:(.bss+0x16e3e5c): multiple definition of `re_bt'
main.o:(.bss+0x16e3e3c): first defined here
hash_index.o:(.bss+0x16e3e5d): multiple definition of `re_b'
main.o:(.bss+0x16e3e3d): first defined here
hash_index.o:(.bss+0x16e3e5e): multiple definition of `k_r'
main.o:(.bss+0x16e3e3e): first defined here
hash_index.o:(.bss+0x16e3e60): multiple definition of `query_info'
main.o:(.bss+0x16e3e40): first defined here
hash_index.o:(.bss+0x16e3e68): multiple definition of `vertexu'
main.o:(.bss+0x16e3e48): first defined here
hash_index.o:(.bss+0x16e3e70): multiple definition of `vertexm'
main.o:(.bss+0x16e3e50): first defined here
hash_index.o:(.bss+0x16e3e80): multiple definition of `rwlock'
main.o:(.bss+0x16e3e60): first defined here
aln_2pass.o:(.bss+0x16e36c0): multiple definition of `temp_binary_pos'
main.o:(.bss+0x16e3620): first defined here
aln_2pass.o: In function `get_refseq':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:48: multiple definition of `hash_kmer'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
aln_2pass.o: In function `get_refseq':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:48: multiple definition of `e_shift'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:682: first defined here
aln_2pass.o: In function `refine_site':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:1109: multiple definition of `REF_pos'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:915: first defined here
aln_2pass.o: In function `refine_site':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:1109: multiple definition of `QUERY_pos'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:674: first defined here
aln_2pass.o: In function `get_refseq':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:48: multiple definition of `merge_anchor_cnt'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
aln_2pass.o: In function `get_refseq':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:50: multiple definition of `seqio'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:680: first defined here
aln_2pass.o: In function `get_refseq':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:50: multiple definition of `EXON_T'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
aln_2pass.o: In function `get_refseq':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:48: multiple definition of `strand_arr'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
aln_2pass.o: In function `get_refseq':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:50: multiple definition of `THREAD_READ_I'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:933: first defined here
aln_2pass.o:(.bss+0x16e3ac0): multiple definition of `temp_anchor_dir'
main.o:(.bss+0x16e3a20): first defined here
aln_2pass.o: In function `get_refseq':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:48: multiple definition of `splice_offset'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
aln_2pass.o: In function `get_refseq':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:50: multiple definition of `hit_num'
hash_index.o:/proj/jmontenegro/software/deSALT-1.5.6/src/hash_index.c:27: first defined here
aln_2pass.o: In function `get_refseq':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:50: multiple definition of `value_num'
hash_index.o:/proj/jmontenegro/software/deSALT-1.5.6/src/hash_index.c:31: first defined here
aln_2pass.o: In function `get_refseq':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:50: multiple definition of `bucket_num'
hash_index.o:/proj/jmontenegro/software/deSALT-1.5.6/src/hash_index.c:31: first defined here
aln_2pass.o: In function `refine_site':
/proj/jmontenegro/software/deSALT-1.5.6/src/aln_2pass.c:1109: multiple definition of `read_bit1'
main.o:(.bss+0x0): first defined here
aln_2pass.o:(.bss+0x16e36a0): multiple definition of `fp_temp'
main.o:(.bss+0x16e3600): first defined here
aln_2pass.o:(.bss+0x16e36a8): multiple definition of `fp_tff'
main.o:(.bss+0x16e3608): first defined here
aln_2pass.o:(.bss+0x16e3ec0): multiple definition of `max_read_join_gap'
main.o:(.bss+0x16e3e20): first defined here
aln_2pass.o:(.bss+0x16e3ec4): multiple definition of `min_chain_score'
main.o:(.bss+0x16e3e24): first defined here
aln_2pass.o:(.bss+0x16e3ec8): multiple definition of `secondary_ratio'
main.o:(.bss+0x16e3e28): first defined here
aln_2pass.o:(.bss+0x16e3ecc): multiple definition of `seed_num'
main.o:(.bss+0x16e3e2c): first defined here
aln_2pass.o:(.bss+0x16e3ed0): multiple definition of `batch_size'
main.o:(.bss+0x16e3e30): first defined here
aln_2pass.o:(.bss+0x16e3ed4): multiple definition of `uni_pos_n_max'
main.o:(.bss+0x16e3e34): first defined here
aln_2pass.o:(.bss+0x16e3ed6): multiple definition of `pos_n_max'
main.o:(.bss+0x16e3e36): first defined here
aln_2pass.o:(.bss+0x16e3ed8): multiple definition of `seed_offset'
main.o:(.bss+0x16e3e38): first defined here
aln_2pass.o:(.bss+0x16e3ed9): multiple definition of `seed_step'
main.o:(.bss+0x16e3e39): first defined here
aln_2pass.o:(.bss+0x16e3eda): multiple definition of `top_n'
main.o:(.bss+0x16e3e3a): first defined here
aln_2pass.o:(.bss+0x16e3edb): multiple definition of `re_2bt'
main.o:(.bss+0x16e3e3b): first defined here
aln_2pass.o:(.bss+0x16e3edc): multiple definition of `re_bt'
main.o:(.bss+0x16e3e3c): first defined here
aln_2pass.o:(.bss+0x16e3edd): multiple definition of `re_b'
main.o:(.bss+0x16e3e3d): first defined here
aln_2pass.o:(.bss+0x16e3ede): multiple definition of `k_r'
main.o:(.bss+0x16e3e3e): first defined here
aln_2pass.o:(.bss+0x16e3ee0): multiple definition of `query_info'
main.o:(.bss+0x16e3e40): first defined here
aln_2pass.o:(.bss+0x16e3ee8): multiple definition of `vertexu'
main.o:(.bss+0x16e3e48): first defined here
aln_2pass.o:(.bss+0x16e3ef0): multiple definition of `vertexm'
main.o:(.bss+0x16e3e50): first defined here
aln_2pass.o:(.bss+0x16e3f00): multiple definition of `rwlock'
main.o:(.bss+0x16e3e60): first defined here
bseq.o:(.bss+0x0): multiple definition of `read_bit1'
main.o:(.bss+0x0): first defined here
bseq.o:(.bss+0x16e3600): multiple definition of `fp_temp'
main.o:(.bss+0x16e3600): first defined here
bseq.o:(.bss+0x16e3608): multiple definition of `fp_tff'
main.o:(.bss+0x16e3608): first defined here
bseq.o:(.bss+0x16e3620): multiple definition of `temp_binary_pos'
main.o:(.bss+0x16e3620): first defined here
bseq.o:(.bss+0x16e3a20): multiple definition of `temp_anchor_dir'
main.o:(.bss+0x16e3a20): first defined here
bseq.o:(.bss+0x16e3e20): multiple definition of `max_read_join_gap'
main.o:(.bss+0x16e3e20): first defined here
bseq.o:(.bss+0x16e3e24): multiple definition of `min_chain_score'
main.o:(.bss+0x16e3e24): first defined here
bseq.o:(.bss+0x16e3e28): multiple definition of `secondary_ratio'
main.o:(.bss+0x16e3e28): first defined here
bseq.o:(.bss+0x16e3e2c): multiple definition of `seed_num'
main.o:(.bss+0x16e3e2c): first defined here
bseq.o:(.bss+0x16e3e30): multiple definition of `batch_size'
main.o:(.bss+0x16e3e30): first defined here
bseq.o:(.bss+0x16e3e34): multiple definition of `uni_pos_n_max'
main.o:(.bss+0x16e3e34): first defined here
bseq.o:(.bss+0x16e3e36): multiple definition of `pos_n_max'
main.o:(.bss+0x16e3e36): first defined here
bseq.o:(.bss+0x16e3e38): multiple definition of `seed_offset'
main.o:(.bss+0x16e3e38): first defined here
bseq.o:(.bss+0x16e3e39): multiple definition of `seed_step'
main.o:(.bss+0x16e3e39): first defined here
bseq.o:(.bss+0x16e3e3a): multiple definition of `top_n'
main.o:(.bss+0x16e3e3a): first defined here
bseq.o:(.bss+0x16e3e3b): multiple definition of `re_2bt'
main.o:(.bss+0x16e3e3b): first defined here
bseq.o:(.bss+0x16e3e3c): multiple definition of `re_bt'
main.o:(.bss+0x16e3e3c): first defined here
bseq.o:(.bss+0x16e3e3d): multiple definition of `re_b'
main.o:(.bss+0x16e3e3d): first defined here
bseq.o:(.bss+0x16e3e3e): multiple definition of `k_r'
main.o:(.bss+0x16e3e3e): first defined here
bseq.o:(.bss+0x16e3e40): multiple definition of `query_info'
main.o:(.bss+0x16e3e40): first defined here
bseq.o:(.bss+0x16e3e48): multiple definition of `vertexu'
main.o:(.bss+0x16e3e48): first defined here
bseq.o:(.bss+0x16e3e50): multiple definition of `vertexm'
main.o:(.bss+0x16e3e50): first defined here
bseq.o:(.bss+0x16e3e60): multiple definition of `rwlock'
main.o:(.bss+0x16e3e60): first defined here
graph.o:(.bss+0x16e3e96): multiple definition of `pos_n_max'
main.o:(.bss+0x16e3e36): first defined here
graph.o: In function `initGraph':
/proj/jmontenegro/software/deSALT-1.5.6/src/graph.c:36: multiple definition of `e_shift'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:682: first defined here
graph.o: In function `initGraph':
/proj/jmontenegro/software/deSALT-1.5.6/src/graph.c:37: multiple definition of `hash_kmer'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
graph.o: In function `initGraph':
/proj/jmontenegro/software/deSALT-1.5.6/src/graph.c:37: multiple definition of `splice_offset'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
graph.o: In function `initGraph':
/proj/jmontenegro/software/deSALT-1.5.6/src/graph.c:37: multiple definition of `merge_anchor_cnt'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
graph.o: In function `initGraph':
/proj/jmontenegro/software/deSALT-1.5.6/src/graph.c:39: multiple definition of `seqio'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:680: first defined here
graph.o: In function `initGraph':
/proj/jmontenegro/software/deSALT-1.5.6/src/graph.c:41: multiple definition of `EXON_T'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
graph.o: In function `initGraph':
/proj/jmontenegro/software/deSALT-1.5.6/src/graph.c:41: multiple definition of `strand_arr'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:676: first defined here
graph.o: In function `initGraph':
/proj/jmontenegro/software/deSALT-1.5.6/src/graph.c:41: multiple definition of `QUERY_pos'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:674: first defined here
graph.o: In function `initGraph':
/proj/jmontenegro/software/deSALT-1.5.6/src/graph.c:41: multiple definition of `REF_pos'
read_seeding.o:/proj/jmontenegro/software/deSALT-1.5.6/src/read_seeding.c:915: first defined here
graph.o: In function `initGraph':
/proj/jmontenegro/software/deSALT-1.5.6/src/graph.c:39: multiple definition of `read_bit1'
main.o:(.bss+0x0): first defined here
graph.o:(.bss+0x16e3660): multiple definition of `fp_temp'
main.o:(.bss+0x16e3600): first defined here
graph.o:(.bss+0x16e3668): multiple definition of `fp_tff'
main.o:(.bss+0x16e3608): first defined here
graph.o:(.bss+0x16e3680): multiple definition of `temp_binary_pos'
main.o:(.bss+0x16e3620): first defined here
graph.o:(.bss+0x16e3a80): multiple definition of `temp_anchor_dir'
main.o:(.bss+0x16e3a20): first defined here
graph.o:(.bss+0x16e3e80): multiple definition of `max_read_join_gap'
main.o:(.bss+0x16e3e20): first defined here
graph.o:(.bss+0x16e3e84): multiple definition of `min_chain_score'
main.o:(.bss+0x16e3e24): first defined here
graph.o:(.bss+0x16e3e88): multiple definition of `secondary_ratio'
main.o:(.bss+0x16e3e28): first defined here
graph.o:(.bss+0x16e3e8c): multiple definition of `seed_num'
main.o:(.bss+0x16e3e2c): first defined here
graph.o:(.bss+0x16e3e90): multiple definition of `batch_size'
main.o:(.bss+0x16e3e30): first defined here
graph.o:(.bss+0x16e3e94): multiple definition of `uni_pos_n_max'
main.o:(.bss+0x16e3e34): first defined here
graph.o:(.bss+0x16e3e98): multiple definition of `seed_offset'
main.o:(.bss+0x16e3e38): first defined here
graph.o:(.bss+0x16e3e99): multiple definition of `seed_step'
main.o:(.bss+0x16e3e39): first defined here
graph.o:(.bss+0x16e3e9a): multiple definition of `top_n'
main.o:(.bss+0x16e3e3a): first defined here
graph.o:(.bss+0x16e3e9b): multiple definition of `re_2bt'
main.o:(.bss+0x16e3e3b): first defined here
graph.o:(.bss+0x16e3e9c): multiple definition of `re_bt'
main.o:(.bss+0x16e3e3c): first defined here
graph.o:(.bss+0x16e3e9d): multiple definition of `re_b'
main.o:(.bss+0x16e3e3d): first defined here
graph.o:(.bss+0x16e3e9e): multiple definition of `k_r'
main.o:(.bss+0x16e3e3e): first defined here
graph.o:(.bss+0x16e3ea0): multiple definition of `query_info'
main.o:(.bss+0x16e3e40): first defined here
graph.o:(.bss+0x16e3ea8): multiple definition of `vertexu'
main.o:(.bss+0x16e3e48): first defined here
graph.o:(.bss+0x16e3eb0): multiple definition of `vertexm'
main.o:(.bss+0x16e3e50): first defined here
graph.o:(.bss+0x16e3ec0): multiple definition of `rwlock'
main.o:(.bss+0x16e3e60): first defined here
collect2: error: ld returned 1 exit status
make: *** [deSALT] Error 1

As you can see, gcc is complianing about variables with multiple definitions and then it does not finish compilation. Could you help me find a workaround this issue?

Thank you,

Juan D. Montenegro

[Eric-Kobayashi]

you can add -fcommon to workaround this issue
make CFLAGS=-fcommon

[aowenson-imm]

make CFLAGS="-fcommon" does not solve error. But this does: make CC="gcc -fcommon".