Hello everybody,
Although there are quite some threads on the forum about compiling samtools under cygwin, I didn't find any that adressed my problem with bcftools under cygwin.
So I've succesfully compiled samtools 1.1 by adjusting the necessary flags in the Makefile (http://seqanswers.com/forums/showthread.php?t=17173), but I am not able to compile bcftools 1.1, even after appending the text -Dexpl=exp -Dlogl=log to the DFLAGS line in the bcftools Makefile as suggested in the previous quoted post.
Here is an excerpt from the output of the $ make bcftools command in cygwin (which should have been installed with all libraries) under win7 x64.
Does anyone have any idea of what went wrong and how I can fix it? Any help would be greatly appreciated.
Thanks,
Dieter
Although there are quite some threads on the forum about compiling samtools under cygwin, I didn't find any that adressed my problem with bcftools under cygwin.
So I've succesfully compiled samtools 1.1 by adjusting the necessary flags in the Makefile (http://seqanswers.com/forums/showthread.php?t=17173), but I am not able to compile bcftools 1.1, even after appending the text -Dexpl=exp -Dlogl=log to the DFLAGS line in the bcftools Makefile as suggested in the previous quoted post.
Here is an excerpt from the output of the $ make bcftools command in cygwin (which should have been installed with all libraries) under win7 x64.
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 vcfcnv.c -o vcfcnv.o
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 HMM.c -o HMM.o
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 vcfplugin.c -o vcfplugin.o
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 ccall.c -o ccall.o
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 em.c -o em.o
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 prob1.c -o prob1.o
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 kmin.c -o kmin.o
gcc -g -Wall -Wc++-compat -O2 -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o ccall.o em.o prob1.o kmin.o htslib-1.1/libhts.a -lpthread -lz -lm -ldl
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 test/test-rbuf.c -o test/test-rbuf.o
gcc -g -Wall -Wc++-compat -O2 -o test/test-rbuf -lm -ldl test/test-rbuf.o
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.1 -fPIC -shared -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -Lhtslib-1.1 -lhts
version.c:1:0: let op: -fPIC ignored for target (all code is position independent) [enabled by default]
/* version.c -- report version numbers for plugins.
^
plugins/fill-AN-AC.c:1:0: let op: -fPIC ignored for target (all code is position independent) [enabled by default]
/* plugins/fill-AN-AC.c -- fills AN and AC INFO fields.
^
htslib-1.1/libhts.a(hts.o): In function `decompress_peek':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:104: undefined reference to `inflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:104: (.text+0x6a): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `inflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:107: undefined reference to `inflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:107: (.text+0x89): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `inflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:110: undefined reference to `inflateEnd'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:110: (.text+0xa3): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `inflateEnd'
htslib-1.1/libhts.a(vcf.o): In function `vcf_hdr_read':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:1203: undefined reference to `gzopen'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:1203: (.text+0x9c7c): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `gzopen'
htslib-1.1/libhts.a(vcf.o): In function `ks_getc':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:45: undefined reference to `gzread'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:45: (.text+0x9f16): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `gzread'
htslib-1.1/libhts.a(vcf.o): In function `vcf_hdr_read':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:1216: undefined reference to `gzclose'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:1216: (.text+0xa15d): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `gzclose'
htslib-1.1/libhts.a(bgzf.o): In function `inflate_gzip_block':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:327: undefined reference to `inflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:327: (.text+0x223): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `inflate'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_compress':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:229: undefined reference to `deflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:229: (.text+0x37d): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `deflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:230: undefined reference to `deflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:230: (.text+0x392): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `deflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:231: undefined reference to `deflateEnd'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:231: (.text+0x3a3): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `deflateEnd'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:237: undefined reference to `crc32'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:237: (.text+0x3f2): additional relocation overflows omitted from the output
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:237: undefined reference to `crc32'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_gzip_compress':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:259: undefined reference to `deflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:252: undefined reference to `deflateInit2_'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_open':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:159: undefined reference to `compressBound'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_dopen':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:181: undefined reference to `compressBound'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_hopen':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:203: undefined reference to `compressBound'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_read_block':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:498: undefined reference to `inflateInit2_'
htslib-1.1/libhts.a(bgzf.o): In function `inflate_block':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:294: undefined reference to `inflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:298: undefined reference to `inflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:303: undefined reference to `inflateEnd'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:299: undefined reference to `inflateEnd'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_close':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:809: undefined reference to `inflateEnd'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:810: undefined reference to `deflateEnd'
htslib-1.1/libhts.a(cram_io.o): In function `zlib_mem_deflate':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:615: undefined reference to `deflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:629: undefined reference to `deflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:636: undefined reference to `deflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:641: undefined reference to `deflateEnd'
htslib-1.1/libhts.a(cram_io.o): In function `zlib_mem_inflate':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:553: undefined reference to `inflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:566: undefined reference to `inflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:584: undefined reference to `inflateEnd'
htslib-1.1/libhts.a(zfio.o): In function `zfputs':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:82: undefined reference to `gzputs'
htslib-1.1/libhts.a(zfio.o): In function `zfpeek':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:99: undefined reference to `gzungetc'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:97: undefined reference to `gzgetc'
htslib-1.1/libhts.a(zfio.o): In function `zfopen':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:167: undefined reference to `gzopen'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:171: undefined reference to `gzopen'
htslib-1.1/libhts.a(zfio.o): In function `zfclose':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:182: undefined reference to `gzclose'
htslib-1.1/libhts.a(zfio.o): In function `zfgets':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:71: undefined reference to `gzgets'
htslib-1.1/libhts.a(zfio.o): In function `zfeof':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:107: undefined reference to `gzeof'
collect2: error: ld returned exit-status 1
Makefile:91: recipe for target 'plugins/fill-AN-AC.so' failed
make: *** [plugins/fill-AN-AC.so] Fout 1
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 HMM.c -o HMM.o
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 vcfplugin.c -o vcfplugin.o
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 ccall.c -o ccall.o
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 em.c -o em.o
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 prob1.c -o prob1.o
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 kmin.c -o kmin.o
gcc -g -Wall -Wc++-compat -O2 -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o ccall.o em.o prob1.o kmin.o htslib-1.1/libhts.a -lpthread -lz -lm -ldl
gcc -c -g -Wall -Wc++-compat -O2 -Dexpl=exp -Dlogl=log -I. -Ihtslib-1.1 test/test-rbuf.c -o test/test-rbuf.o
gcc -g -Wall -Wc++-compat -O2 -o test/test-rbuf -lm -ldl test/test-rbuf.o
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.1 -fPIC -shared -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -Lhtslib-1.1 -lhts
version.c:1:0: let op: -fPIC ignored for target (all code is position independent) [enabled by default]
/* version.c -- report version numbers for plugins.
^
plugins/fill-AN-AC.c:1:0: let op: -fPIC ignored for target (all code is position independent) [enabled by default]
/* plugins/fill-AN-AC.c -- fills AN and AC INFO fields.
^
htslib-1.1/libhts.a(hts.o): In function `decompress_peek':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:104: undefined reference to `inflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:104: (.text+0x6a): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `inflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:107: undefined reference to `inflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:107: (.text+0x89): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `inflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:110: undefined reference to `inflateEnd'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/hts.c:110: (.text+0xa3): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `inflateEnd'
htslib-1.1/libhts.a(vcf.o): In function `vcf_hdr_read':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:1203: undefined reference to `gzopen'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:1203: (.text+0x9c7c): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `gzopen'
htslib-1.1/libhts.a(vcf.o): In function `ks_getc':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:45: undefined reference to `gzread'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:45: (.text+0x9f16): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `gzread'
htslib-1.1/libhts.a(vcf.o): In function `vcf_hdr_read':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:1216: undefined reference to `gzclose'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/vcf.c:1216: (.text+0xa15d): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `gzclose'
htslib-1.1/libhts.a(bgzf.o): In function `inflate_gzip_block':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:327: undefined reference to `inflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:327: (.text+0x223): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `inflate'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_compress':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:229: undefined reference to `deflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:229: (.text+0x37d): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `deflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:230: undefined reference to `deflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:230: (.text+0x392): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `deflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:231: undefined reference to `deflateEnd'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:231: (.text+0x3a3): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `deflateEnd'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:237: undefined reference to `crc32'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:237: (.text+0x3f2): additional relocation overflows omitted from the output
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:237: undefined reference to `crc32'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_gzip_compress':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:259: undefined reference to `deflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:252: undefined reference to `deflateInit2_'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_open':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:159: undefined reference to `compressBound'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_dopen':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:181: undefined reference to `compressBound'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_hopen':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:203: undefined reference to `compressBound'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_read_block':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:498: undefined reference to `inflateInit2_'
htslib-1.1/libhts.a(bgzf.o): In function `inflate_block':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:294: undefined reference to `inflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:298: undefined reference to `inflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:303: undefined reference to `inflateEnd'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:299: undefined reference to `inflateEnd'
htslib-1.1/libhts.a(bgzf.o): In function `bgzf_close':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:809: undefined reference to `inflateEnd'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/bgzf.c:810: undefined reference to `deflateEnd'
htslib-1.1/libhts.a(cram_io.o): In function `zlib_mem_deflate':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:615: undefined reference to `deflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:629: undefined reference to `deflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:636: undefined reference to `deflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:641: undefined reference to `deflateEnd'
htslib-1.1/libhts.a(cram_io.o): In function `zlib_mem_inflate':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:553: undefined reference to `inflateInit2_'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:566: undefined reference to `inflate'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/cram_io.c:584: undefined reference to `inflateEnd'
htslib-1.1/libhts.a(zfio.o): In function `zfputs':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:82: undefined reference to `gzputs'
htslib-1.1/libhts.a(zfio.o): In function `zfpeek':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:99: undefined reference to `gzungetc'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:97: undefined reference to `gzgetc'
htslib-1.1/libhts.a(zfio.o): In function `zfopen':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:167: undefined reference to `gzopen'
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:171: undefined reference to `gzopen'
htslib-1.1/libhts.a(zfio.o): In function `zfclose':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:182: undefined reference to `gzclose'
htslib-1.1/libhts.a(zfio.o): In function `zfgets':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:71: undefined reference to `gzgets'
htslib-1.1/libhts.a(zfio.o): In function `zfeof':
/cygdrive/d/methylome/samtools-1.1/bcftools-1.1/htslib-1.1/cram/zfio.c:107: undefined reference to `gzeof'
collect2: error: ld returned exit-status 1
Makefile:91: recipe for target 'plugins/fill-AN-AC.so' failed
make: *** [plugins/fill-AN-AC.so] Fout 1
Does anyone have any idea of what went wrong and how I can fix it? Any help would be greatly appreciated.
Thanks,
Dieter
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