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bcftools error running Make after installing update 2.4.1.1 to Cygwin64
- From: Robert May <tpibob at gmail dot com>
- To: "cygwin at cygwin dot com" <cygwin at cygwin dot com>
- Date: Tue, 26 Jan 2016 07:00:36 +1000
- Subject: bcftools error running Make after installing update 2.4.1.1 to Cygwin64
- Authentication-results: sourceware.org; auth=none
error running Make after installing update 2.4.1.1 to Cygwin64
Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3
$ make
many warnings are given in the following text - see end for error message
echo '#define BCFTOOLS_VERSION "1.3"'> version.h
gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o main.o main.c
gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o vcfindex.o vcfindex.c
vcfindex.c: In function ‘main_vcfindex’:
vcfindex.c:209:9: warning: implicit declaration of function ‘alloca’ [-Wimplicit-function-declaration]
char *idx_fname = (char*)alloca(strlen(fname) + 5);
^
vcfindex.c:209:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
char *idx_fname = (char*)alloca(strlen(fname) + 5);
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o tabix.o tabix.c
tabix.c: In function ‘main_tabix’:
tabix.c:97:13: warning: implicit declaration of function ‘alloca’ [-Wimplicit-function-declaration]
fn = (char*)alloca(strlen(argv[optind]) + 5);
^
tabix.c:97:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
fn = (char*)alloca(strlen(argv[optind]) + 5);
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o vcfstats.o vcfstats.c
vcfstats.c: In function ‘main_vcfstats’:
vcfstats.c:1558:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -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 -std=c99 -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 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o vcfquery.o vcfquery.c
vcfquery.c: In function ‘main_vcfquery’:
vcfquery.c:285:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o vcffilter.o vcffilter.c
vcffilter.c: In function ‘main_vcffilter’:
vcffilter.c:501:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -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 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o vcfsom.o vcfsom.c
gcc -g -Wall -Wc++-compat -O2 -std=c99 -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]);
^
vcfnorm.c: In function ‘main_vcfnorm’:
vcfnorm.c:1785:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o vcfgtcheck.o vcfgtcheck.c
vcfgtcheck.c: In function ‘main_vcfgtcheck’:
vcfgtcheck.c:780:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o vcfview.o vcfview.c
vcfview.c: In function ‘main_vcfview’:
vcfview.c:696:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -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-subscripts]
while ( *se && !isspace(*se) ) se++;
^
vcfannotate.c:1049:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( isspace(*ss) ) ss++;
^
vcfannotate.c:1051:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *se && !isspace(*se) ) se++;
^
vcfannotate.c: In function ‘rename_chrs’:
vcfannotate.c:1357:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *ss && !isspace(*ss) ) ss++;
^
vcfannotate.c:1367:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *ss && isspace(*ss) ) ss++;
^
vcfannotate.c:1369:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
while ( *se && !isspace(*se) ) se++;
^
vcfannotate.c: In function ‘main_vcfannotate’:
vcfannotate.c:1716:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -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; // missing value
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o vcfconcat.o vcfconcat.c
gcc -g -Wall -Wc++-compat -O2 -std=c99 -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++;
^
vcfcall.c: In function ‘main_vcfcall’:
vcfcall.c:739:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
if ( !isatty(fileno((FILE *)stdin)) ) args.bcf_fname = "-"; // reading from stdin
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o mcall.o mcall.c
gcc -g -Wall -Wc++-compat -O2 -std=c99 -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; i<vcmp->ndref; i++) vcmp->dref[i] = toupper(ref1[vcmp->nmatch+i]);
^
vcmp.c:78:5: warning: array subscript has type ‘char’ [-Wchar-subscripts]
for (i=0; i<vcmp->ndref; 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 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o gvcf.o gvcf.c
gcc -g -Wall -Wc++-compat -O2 -std=c99 -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 trailing 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 trailing newlines
^
reheader.c: In function ‘reheader_vcf_gz’:
reheader.c:227:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
bgzf_out = bgzf_dopen(fileno(stdout), "w");
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -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 -std=c99 -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]);
^
vcfconvert.c: In function ‘main_vcfconvert’:
vcfconvert.c:1436:13: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
if ( !isatty(fileno((FILE *)stdin)) ) args->infname = "-";
^
gcc -g -Wall -Wc++-compat -O2 -std=c99 -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 -std=c99 -I. -Ihtslib-1.3 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -c -o vcfcnv.o vcfcnv.c
vcfcnv.c: In function ‘norm_prob’:
vcfcnv.c:602:93: error: ‘M_PI’ undeclared (first use in this function)
return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev2) / param->norm / sqrt(2*M_PI*param->dev2);
^
vcfcnv.c:602:93: note: each undeclared identifier is reported only once for each function it appears in
vcfcnv.c: In function ‘main_vcfcnv’:
vcfcnv.c:1349:9: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration]
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";
^
vcfcnv.c: In function ‘norm_prob’:
vcfcnv.c:603:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
With this final error message
Makefile:103: recipe for target 'vcfcnv.o' failed
make: *** [vcfcnv.o] Error 1
Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree
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