Ubuntu won't make htslib-1.3.1
Nobody has claimed this yet.
Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 20/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c, ubuntu
- Domain
- build-system
Research direction
Start with zfio.c and the bgzip build target shown in the report, then reproduce the failure with the provided configure and make commands on Ubuntu 12.04. Trace the undefined gzgetc_ reference and confirm that a successful build of bgzip completes without the linker error.
Written by the indexing model from the issue text.
Description
Hello
I am trying to install htslib-1.3.1 on Ubuntu 12.04 using ./configure and make but getting the following error message. Also I have verified that zlib1g-dev is installed and up to date on the server.
Any help would be much appreciated.
Matt
gcc -g -O2 -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -O2 -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -O2 -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -I. -fpic -c -o cram/thread_pool.pico cram/thread_pool.c
gcc -g -O2 -I. -fpic -c -o cram/vlen.pico cram/vlen.c
gcc -g -O2 -I. -fpic -c -o cram/zfio.pico cram/zfio.c
gcc -shared -Wl,-soname,libhts.so.2 -pthread -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.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_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico -lz -lm
ln -sf libhts.so libhts.so.2
gcc -g -O2 -I. -c -o bgzip.o bgzip.c
gcc -pthread -o bgzip bgzip.o libhts.a -lz
libhts.a(zfio.o): In function zfpeek': zfio.c:(.text+0x121): undefined reference togzgetc_'
collect2: error: ld returned 1 exit status
make: *** [bgzip] Error 1
- Dominant language
- C
- Stars
- 950
- Forks
- 475
- Avg merge
- 3d 13h
- Merged PRs (30d)
- 11
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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