phasegenomics / FALCON-Phase

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds
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bam_filt.o:(.bss+0x50): multiple definition of `rp' #84

Open bingochenbin opened 2 years ago

bingochenbin commented 2 years ago

Hi, I encountered the following error when I install FALCON-Phase

make[1]: Entering directory `/users/chenb/Software/biosoft/FALCON-Phase/htslib'
gcc -Wall -g -O2 -I.  -c -o kfunc.o kfunc.c
gcc -Wall -g -O2 -I.  -c -o knetfile.o knetfile.c
gcc -Wall -g -O2 -I.  -c -o kstring.o kstring.c
gcc -Wall -g -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -Wall -g -O2 -I.  -c -o bgzf.o bgzf.c
gcc -Wall -g -O2 -I.  -c -o errmod.o errmod.c
gcc -Wall -g -O2 -I.  -c -o faidx.o faidx.c
gcc -Wall -g -O2 -I.  -c -o hfile.o hfile.c
gcc -Wall -g -O2 -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
gcc -Wall -g -O2 -I.  -c -o hts.o hts.c
hts.c: In function ‘hts_idx_init’:
hts.c:1366:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow]
 1366 |     idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
      |                                                           ^~~
gcc -Wall -g -O2 -I.  -c -o hts_os.o hts_os.c
gcc -Wall -g -O2 -I.  -c -o md5.o md5.c
gcc -Wall -g -O2 -I.  -c -o multipart.o multipart.c
gcc -Wall -g -O2 -I.  -c -o probaln.o probaln.c
gcc -Wall -g -O2 -I.  -c -o realn.o realn.c
gcc -Wall -g -O2 -I.  -c -o regidx.o regidx.c
gcc -Wall -g -O2 -I.  -c -o sam.o sam.c
In file included from /usr/include/string.h:633,
                 from sam.c:31:
sam.c: In function ‘bam_hdr_write’:
sam.c:233:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  233 |     strncpy(buf, "BAM\1", 4);
      |     ^~~~~~~
gcc -Wall -g -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -Wall -g -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
...
gcc -Wall -g -O2 -I.  -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/users/chenb/Software/anaconda3/envs/denovo_asm/lib -Wl,-rpath-link,/users/chenb/Software/anaconda3/envs/denovo_asm/lib -L/users/chenb/Software/anaconda3/envs/denovo_asm/lib  -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
make[1]: Leaving directory `/users/chenb/Software/biosoft/FALCON-Phase/htslib'
gcc -Wall -O3 -I../htslib -Isrc  -c matrix.c -o matrix.o
gcc -Wall -O3 -I../htslib -Isrc  -c bam_filt.c -o bam_filt.o
bam_filt.c: In function ‘filter_bam’:
bam_filt.c:416:6: warning: variable ‘okay’ set but not used [-Wunused-but-set-variable]
  416 |  int okay;
      |      ^~~~
gcc -Wall -O3 -I../htslib -Isrc  -c count_motif.c -o count_motif.o
gcc -Wall -O3 -I../htslib -Isrc  -c dna.c -o dna.o
gcc -Wall -O3 -I../htslib -Isrc  -c run_phasing.c -o run_phasing.o
gcc -Wall -O3 -I../htslib -Isrc  -c string_parser.c -o string_parser.o
gcc -Wall -O3 main.c matrix.o bam_filt.o count_motif.o dna.o run_phasing.o string_parser.o  -I../htslib -Isrc  ../htslib/libhts.a  -lbz2 -llzma -lz -lm -lpthread -o ../bin/falcon-phase
bam_filt.o:(.bss+0x50): multiple definition of `rp'
/tmp/ccMrEQYU.o:(.bss+0x70): first defined here
run_phasing.o:(.bss+0x0): multiple definition of `global_opts_phasing'
/tmp/ccMrEQYU.o:(.bss+0x20): first defined here
...
../htslib/libhts.a(hfile_libcurl.o): In function `libcurl_exit':
/users/chenb/Software/biosoft/FALCON-Phase/htslib/hfile_libcurl.c:289: undefined reference to `curl_global_cleanup'
../htslib/libhts.a(hfile_s3.o): In function `s3_sign':
/users/chenb/Software/biosoft/FALCON-Phase/htslib/hfile_s3.c:77: undefined reference to `EVP_sha1'
/users/chenb/Software/biosoft/FALCON-Phase/htslib/hfile_s3.c:77: undefined reference to `HMAC'
collect2: error: ld returned 1 exit status
make: *** [../bin/falcon-phase] Error 1

Can someone please advise. Thank you in advance!