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Message-ID: <BAY175-W14DF8CC504AF6F9213BF6CADC70@phx.gbl>
From: Robert May <tpibob AT gmail DOT com>
To: "cygwin AT cygwin DOT com" <cygwin AT cygwin DOT com>
Subject: bcftools error running Make after installing update 2.4.1.1 to Cygwin64
Date: Tue, 26 Jan 2016 07:00:36 +1000
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error running Make after installing update 2.4.1.1 to Cygwin64

Robert AT 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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