link error occurred in running ./setup.sh <install_path>

[zhangzhen]

GCC 10.4.0 was used in compilation.

Several link errors happened in compilation of HTSLIB as follows:

gcc -Wall -I/dshare/home/zhangz/NanoSeq/include -D HAVE_LIBDEFLATE -fvisibility=hidden -I.  -c -o hts.o hts.c
gcc -shared -Wl,-soname,libhts.so.3 -L/dshare/home/zhangz/NanoSeq/lib -fvisibility=hidden  -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -llzma -lbz2 -lz -lm -l:libdeflate.a  -lcurl -lcrypto -lpthread
gcc -L/dshare/home/zhangz/NanoSeq/lib -fvisibility=hidden  -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm -l:libdeflate.a  -lcurl -lcrypto
gcc -L/dshare/home/zhangz/NanoSeq/lib -fvisibility=hidden  -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm -l:libdeflate.a  -lcurl -lcrypto
/usr/bin/ld: /dshare/home/zhangz/NanoSeq/lib/libdeflate.a(deflate_decompress.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /dshare/home/zhangz/NanoSeq/lib/libdeflate.a(deflate_compress.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /dshare/home/zhangz/NanoSeq/lib/libdeflate.a(crc32.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC

Any help is appreciated to solve this problem!

[fa8sanger]

I am not sure. The error message suggests using option -fPIC.
In addition, I would try to download htslib myself and install it myself, just to make sure it works.