Cygwin linking problems: no -rdynamic, plugins can't be built #377
Comments
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Windows and Cygwin do not support dynamic linking in the same way as the other platforms that bcftools is often compiled on (Linux and other Unixes, OS X). So the parts of htslib and bcftools that need dynamic linking (HTSlib's hfile* plugins and bcftools's plugins) do not yet work on Cygwin. You have seen this with the lack of the Unfortunately at the moment, the plugins are unsupported on Cygwin. Someone who is familiar with this level of Cygwin programming will need to supply the equivalent Cygwin linker options needed to build plugin-style dynamic objects so that we can add support to the makefile. In the meantime, the good news is that you can probably get a lot of work done even without the plugins! |
jmarshall
changed the title
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(All the |
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I still get left with make failed the foloowing lines are the error/s area Bob gcc -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 consensus.o ploidy.o version.o ccall.o em.o prob1.o kmin.o htslib-1.3/libhts.a -lpthread -lz -lm gcc -g -Wc++-compat -O2 -std=gnu99 -I. -Dexpl=exp -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec/bcftools" -c -o test/test-rbuf.o test/test-rbuf.c gcc -o test/test-rbuf test/test-rbuf.o -lm gcc -fPIC -shared -g -Wc++-compat -O2 -std=gnu99 -I. -Dexpl=exp -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec/bcftools" -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c |
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Yes, Bob. Those are the same errors as originally reported. They mean you can't build these plugins on Cygwin. |
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OK thanks John |
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fyi... I am also having this same error upon installation: % make plugins gcc -fPIC -shared -g -Wall -Wc++-compat -O2 -I. -I../htslib -DPLUGINPATH="/usr/local/libexec/bcftools" -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c |
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htslib just added support for Cygwin. With the recent checkin from https://github.com/jmarshall the Cygwin dll can now be created. Here is the commit which adds Cygwin support for htslib |
Good day.
Now, I am trying to compile bcftools 1.3 through Cygwin. I have removed "-rdynamic" from the makefile as I encountered an error, the same error I got when I tried to compile samtools in Cygwin. However, after doing this, another error occurred (see below):
echo '#define BCFTOOLS_VERSION "1.3"' > version.h
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o main.o main.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfindex.o vcfindex.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o tabix.o tabix.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfstats.o vcfstats.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfisec.o vcfisec.c
vcfisec.c: In function ‘main_vcfisec’:
vcfisec.c:556:21: warning: array subscript has type ‘char’ [-Wchar-subscripts]
else if ( isdigit(p) ) args->isec_op = OP_EQUAL;
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfmerge.o vcfmerge.c
vcfmerge.c: In function ‘merge_alleles’:
vcfmerge.c:542:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
for (j=0; j<len; j++) a[i][j] = toupper(a[i][j]);
^
vcfmerge.c:547:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
for (j=0; j<len; j++) b[i][j] = toupper(b[i][j]);
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfquery.o vcfquery.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcffilter.o vcffilter.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o filter.o filter.c
filter.c: In function ‘filters_next_token’:
filter.c:109:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *tmp && isspace(tmp) ) tmp++;
^
filter.c:114:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( isdigit(str[0]) || *str[0]=='.' ) // strtod would eat +/-
^
filter.c:117:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( *str!=tmp && (!tmp[0] || !isalnum(tmp[0])) )
^
filter.c:141:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *tmp && !isspace(tmp) && tmp!='=' && *tmp!='!' ) tmp++;
^
filter.c:150:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( isspace(tmp[0]) ) break;
^
filter.c: In function ‘filters_init1’:
filter.c:1173:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *se && !isspace(se) ) se++;
^
filter.c: In function ‘filter_init’:
filter.c:1479:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( tmp && !isspace(tmp) ) error("Could not parse the expression : [%s]\n", str);
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfsom.o vcfsom.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfnorm.o vcfnorm.c
vcfnorm.c: In function ‘replace_iupac_codes’:
vcfnorm.c:88:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
char c = toupper(seq[i]);
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfgtcheck.o vcfgtcheck.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfview.o vcfview.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfannotate.o vcfannotate.c
vcfannotate.c: In function ‘set_samples’:
vcfannotate.c:1033:9: warning: array subscript has type ‘char’ [-Wchar-subscript s]
while ( se && !isspace(se) ) se++;
^
vcfannotate.c:1049:9: warning: array subscript has type ‘char’ [-Wchar-subscript s]
while ( isspace(ss) ) ss++;
^
vcfannotate.c:1051:9: warning: array subscript has type ‘char’ [-Wchar-subscript s]
while ( *se && !isspace(se) ) se++;
^
vcfannotate.c: In function ‘rename_chrs’:
vcfannotate.c:1357:9: warning: array subscript has type ‘char’ [-Wchar-subscript s]
while ( ss && !isspace(ss) ) ss++;
^
vcfannotate.c:1367:9: warning: array subscript has type ‘char’ [-Wchar-subscript s]
while ( ss && isspace(ss) ) ss++;
^
vcfannotate.c:1369:9: warning: array subscript has type ‘char’ [-Wchar-subscript s]
while ( se && !isspace(se) ) se++;
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfroh.o vcfroh.c
vcfroh.c: In function ‘load_genmap’:
vcfroh.c:229:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( tmp && !isspace(tmp) ) tmp++;
^
vcfroh.c: In function ‘read_AF’:
vcfroh.c:439:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( tmp && !isspace(tmp) )
^
vcfroh.c:441:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( str[0]=='.' && (!str[1] || isspace(str[1])) ) return -1; // missin g value
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfconcat.o vcfconcat.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfcall.o vcfcall.c
vcfcall.c: In function ‘parse_ped_samples’:
vcfcall.c:201:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( isspace(tmp) )
^
vcfcall.c:205:17: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( isspace(tmp) ) tmp++; // allow multiple spaces
^
vcfcall.c: In function ‘set_samples’:
vcfcall.c:283:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( ss && isspace(ss) ) ss++;
^
vcfcall.c:287:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( se && !isspace(se) ) se++;
^
vcfcall.c:294:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( ss && isspace(ss) ) ss++;
^
vcfcall.c:297:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( se && !isspace(se) ) se++;
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o mcall.o mcall.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcmp.o vcmp.c
vcmp.c: In function ‘vcmp_set_ref’:
vcmp.c:57:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( a && *b && toupper(a)==toupper(b) ) { a++; b++; }
^
vcmp.c:57:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
vcmp.c:68:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
for (i=0; indref; i++) vcmp->dref[i] = toupper(ref1[vcmp->nmatch +i]);
^
vcmp.c:78:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
for (i=0; indref; i++) vcmp->dref[i] = toupper(ref2[vcmp->nmatch+i]) ;
^
vcmp.c: In function ‘vcmp_find_allele’:
vcmp.c:90:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( a && *b && toupper(a)==toupper(b) ) { a++; b++; }
^
vcmp.c:90:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
vcmp.c:103:17: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( !a[j] || toupper(a[j])!=vcmp->dref[j] ) break;
^
vcmp.c:110:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( !b[j] || toupper(b[j])!=vcmp->dref[j] ) break;
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o gvcf.o gvcf.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o reheader.o reheader.c
reheader.c: In function ‘read_header_file’:
reheader.c:65:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--; // remove traili ng newlines
^
reheader.c: In function ‘set_sample_pairs’:
reheader.c:79:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *value && !isspace(value) ) value++;
^
reheader.c:82:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( isspace(value) ) value++;
^
reheader.c:91:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--; // remove traili ng newlines
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o convert.o convert.c
convert.c: In function ‘parse_subscript’:
convert.c:781:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *q && *q!='}' && isdigit(q) ) q++;
^
convert.c: In function ‘parse_tag’:
convert.c:791:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( q && (isalnum(q) || q=='' || *q=='.') ) q++;
^
convert.c:806:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *q && (isalnum(q) || q=='' || *q=='.') ) q++;
^
convert.c:848:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *q && (isalnum(q) || q=='' || *q=='.') ) q++;
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfconvert.o vcfconvert.c
In file included from vcfconvert.c:42:0:
tsv2vcf.h: In function ‘tsv_next’:
tsv2vcf.h:68:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *tsv->se && !isspace(tsv->se) ) tsv->se++;
^
tsv2vcf.h:71:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( tsv->se && isspace(tsv->se) ) tsv->se++;
^
tsv2vcf.h:73:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( tsv->se && !isspace(tsv->se) ) tsv->se++;
^
vcfconvert.c: In function ‘tsv_setter_chrom_pos_ref_alt’:
vcfconvert.c:161:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( se < tsv->se && se!='' && isspace(tsv->se) ) se++;
^
vcfconvert.c:162:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( se < tsv->se && se!='' && isspace(tsv->se) ) error("Could not parse ALT in CHROM:POS_REF_ALT id: %s\n", tsv->ss);
^
vcfconvert.c: In function ‘tsv_setter_verify_ref_alt’:
vcfconvert.c:195:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( tsv->se && isspace(tsv->se) ) tsv->se++;
^
vcfconvert.c:197:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( tsv->se && !isspace(tsv->se) ) tsv->se++;
^
vcfconvert.c: In function ‘gensample_to_vcf’:
vcfconvert.c:354:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( se && !isspace(se) ) se++;
^
vcfconvert.c:378:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
se = samples[i]; while ( se && !isspace(se) ) se++;
^
vcfconvert.c: In function ‘haplegendsample_to_vcf’:
vcfconvert.c:502:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
se = samples[i]; while ( se && !isspace(se) ) se++;
^
vcfconvert.c: In function ‘hapsample_to_vcf’:
vcfconvert.c:615:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
se = samples[i]; while ( se && !isspace(se) ) se++;
^
vcfconvert.c: In function ‘tsv_setter_aa1’:
vcfconvert.c:1069:5: warning: array subscript has type ‘char’ [-Wchar-subscripts ]
int a0 = acgt_to_5(toupper(ss[0]));
^
vcfconvert.c:1070:5: warning: array subscript has type ‘char’ [-Wchar-subscripts ]
int a1 = ss[1] ? acgt_to_5(toupper(ss[1])) : a0;
^
vcfconvert.c: In function ‘tsv_setter_aa’:
vcfconvert.c:1094:5: warning: array subscript has type ‘char’ [-Wchar-subscripts ]
ref[0] = toupper(ref[0]);
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o tsv2vcf.o tsv2vcf.c
In file included from tsv2vcf.c:27:0:
tsv2vcf.h: In function ‘tsv_next’:
tsv2vcf.h:68:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( tsv->se && !isspace(tsv->se) ) tsv->se++;
^
tsv2vcf.h:71:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( tsv->se && isspace(tsv->se) ) tsv->se++;
^
tsv2vcf.h:73:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( tsv->se && !isspace(tsv->se) ) tsv->se++;
^
tsv2vcf.c: In function ‘tsv_parse’:
tsv2vcf.c:81:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( tsv->se && !isspace(tsv->se) ) tsv->se++;
^
tsv2vcf.c:88:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( tsv->se && isspace(tsv->se) ) tsv->se++;
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfcnv.o vcfcnv.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o HMM.o HMM.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o vcfplugin.o vcfplugin.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o consensus.o consensus.c
consensus.c: In function ‘init_region’:
consensus.c:239:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( se && !isspace(se) && se!=':' ) se++;
^
consensus.c:253:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( ss==se || (se && !isspace(se)) ) { from = 0; to = 0; }
^
consensus.c: In function ‘apply_variant’:
consensus.c:452:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
for (i=0; id.allele[ialt][i] = toupper(rec->d.allele[i alt][i]);
^
consensus.c:454:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
for (i=0; id.allele[ialt][i] = tolower(rec->d.allele[i alt][i]);
^
consensus.c: In function ‘consensus’:
consensus.c:542:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( args->fa_case==-1 ) args->fa_case = toupper(str.s[0])==str.s[0] ? 1 : 0;
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o ploidy.o ploidy.c
ploidy.c: In function ‘ploidy_parse’:
ploidy.c:65:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *ss && isspace(ss) ) ss++;
^
ploidy.c:66:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
if ( ss[0]=='' && (!ss[1] || isspace(ss[1])) )
^
ploidy.c:77:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *ss && isspace(ss) ) ss++;
^
ploidy.c:80:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( ss && !isspace(ss) ) ss++;
^
ploidy.c:82:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( ss && isspace(ss) ) ss++;
^
ploidy.c:88:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( se && !isspace(se) ) se++;
^
ploidy.c:105:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( se && isspace(se) ) se++;
^
ploidy.c: In function ‘ploidy_init_string’:
ploidy.c:151:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( ss && isspace(ss) ) ss++;
^
ploidy.c:157:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( se && isspace(se) ) se++;
^
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o version.o version.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o ccall.o ccall.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o em.o em.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o prob1.o prob1.c
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o kmin.o kmin.c
gcc -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfqu ery.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 vcf convert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o cc all.o em.o prob1.o kmin.o htslib-1.3/libhts.a -lpthread -lz -lm -ldl
gcc -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr/local/libexec /bcftools" -c -o test/test-rbuf.o test/test-rbuf.c
gcc -o test/test-rbuf test/test-rbuf.o -lm
gcc -fPIC -shared -g -Wall -Wc++-compat -O2 -I. -Ihtslib-1.3 -DPLUGINPATH="/usr /local/libexec/bcftools" -o plugins/fill-AN-AC.so version.c plugins/fill-AN-A C.c
version.c:1:0: warning: -fPIC ignored for target (all code is position independe nt)
/_ version.c -- report version numbers for plugins.
^
plugins/fill-AN-AC.c:1:0: warning: -fPIC ignored for target (all code is positio n independent)
/* plugins/fill-AN-AC.c -- fills AN and AC INFO fields.
^
/tmp/cca9Flmb.o: In function version': /cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/version.c:35: undefin ed reference tohts_version'
/cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/version.c:35:(.text+0 x13): relocation truncated to fit: R_X86_64_PC32 against undefined symbol hts_v ersion' /tmp/ccLHH1WC.o: In functioninit':
/cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/plugins/fill-AN-AC.c: 43: undefined reference to bcf_hdr_append' /cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/plugins/fill-AN-AC.c: 43:(.text+0x2d): relocation truncated to fit: R_X86_64_PC32 against undefined sy mbolbcf_hdr_append'
/cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/plugins/fill-AN-AC.c: 44: undefined reference to bcf_hdr_append' /cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/plugins/fill-AN-AC.c: 44:(.text+0x40): relocation truncated to fit: R_X86_64_PC32 against undefined sy mbolbcf_hdr_append'
/tmp/ccLHH1WC.o: In function process': /cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/plugins/fill-AN-AC.c: 51: undefined reference tobcf_calc_ac'
/cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/plugins/fill-AN-AC.c: 51:(.text+0x82): relocation truncated to fit: R_X86_64_PC32 against undefined sy mbol bcf_calc_ac' /cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/plugins/fill-AN-AC.c: 56: undefined reference tobcf_update_info'
/cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/plugins/fill-AN-AC.c: 56:(.text+0xe9): relocation truncated to fit: R_X86_64_PC32 against undefined sy mbol bcf_update_info' /cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/plugins/fill-AN-AC.c: 57: undefined reference tobcf_update_info'
/cygdrive/c/Users/NicoleJohnMagculia/Home/bin/bcftools-1.3/plugins/fill-AN-AC.c: 57:(.text+0x11d): relocation truncated to fit: R_X86_64_PC32 against undefined s ymbol `bcf_update_info'
collect2: error: ld returned 1 exit status
Makefile:125: recipe for target 'plugins/fill-AN-AC.so' failed
make: *** [plugins/fill-AN-AC.so] Error 1
What seems to be the problem? I badly need your expertise on this matter. Thanks.
Sincerely,
Nicole John
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