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Updated Cygwin64 with 2.4.1.1
- From: Robert May <tpibob at gmail dot com>
- To: "cygwin at cygwin dot com" <cygwin at cygwin dot com>
- Date: Mon, 25 Jan 2016 09:39:27 +1000
- Subject: Updated Cygwin64 with 2.4.1.1
- Authentication-results: sourceware.org; auth=none
- References: <BAY175-W1506B08F4E02E2A7091D3FADC60 at phx dot gbl>
Instalation error
-/unknown package
x3270.sh exit code 1
htslib configure - make - make install ok
samtools configure ok
Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3
$ ./configure
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking location of HTSlib source tree... htslib-1.3
checking for NcursesW wide-character library... yes
checking for working ncursesw/curses.h... yes
checking for working ncursesw.h... no
checking for working ncurses.h... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
config.status: config.h is unchanged
=== configuring in htslib-1.3 (/usr/local/bin/samtools-1.3/htslib-1.3)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' --cache-file=/dev/null --srcdir=.
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
config.status: config.h is unchanged
samtools make big PROBLEM
Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3
$ make
make: *** No rule to make target 'kfunc.c', needed by 'kfunc.o'. Stop.
Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3
$ make clean
rm -f test/*.tmp test/*.tmp.*
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f libhts.so libhts.so.*
rm -f libhts.a bgzip htsfile tabix test/fieldarith test/hfile test/sam test/test-regidx test/test_view test/test-vcf-api test/test-vcf-sweep
bcftools Make
Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3
$ cd c:/cygwin64/usr/local/bin/bcftools-1.3
Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3
$ ./configure
-bash: ./configure: No such file or directory
Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3
$ make
Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3
$ make
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]
}
^
Makefile:103: recipe for target 'vcfcnv.o' failed
make: *** [vcfcnv.o] Error 1
Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3
$ make clean
rm -f test/*.o test/*~ test/test-rbuf
rm -f plugins/*.so plugins/*.P
rm -rf plugins/*.dSYM
rm -f gmon.out *.o *~ bcftools version.h plugins/*.so plugins/*.P
rm -rf *.dSYM plugins/*.dSYM test/*.dSYM
bwa that didn'y go far
Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3
$Robert@DESKTOP-14EL82S /usr/local/bin/bwa-0.7.12
$ ./configure
-bash: ./configure: No such file or directory
Robert@DESKTOP-14EL82S /usr/local/bin/bwa-0.7.12
$ make
make: Nothing to be done for 'all'.
Robert@DESKTOP-14EL82S /usr/local/bin/bwa-0.7.12
$ make install
make: *** No rule to make target 'install'. Stop.
Robert@DESKTOP-14EL82S /usr/local/bin/bwa-0.7.12
$ make clean
rm -f gmon.out *.o a.out bwa *~ *.a
Robert@DESKTOP-14EL82S /usr/local/bin/bwa-0.7.12
$ cd c:/cygwin64/usr/local/bin/Platypus_0.8.1
Platypus
Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1
$ ./buildPlatypus.sh
Building Platypus
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_ext
building 'htslibWrapper' extension
gcc -fno-strict-aliasing -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python/python-2.7.10-1.x86_64/build=/usr/src/debug/python-2.7.10-1 -fdebug-prefix-map=/usr/src/ports/python/python-2.7.10-1.x86_64/src/Python-2.7.10=/usr/src/debug/python-2.7.10-1 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c htslibWrapper.c -o build/temp.cygwin-2.4.0-x86_64-2.7/htslibWrapper.o -msse2 -msse3 -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC
htslibWrapper.c:1:0: warning: -fPIC ignored for target (all code is position independent)
/* Generated by Cython 0.21.1 */
^
gcc -shared -Wl,--enable-auto-image-base -L. build/temp.cygwin-2.4.0-x86_64-2.7/htslibWrapper.o -L/usr/lib/python2.7/config -L/usr/lib -lhts -lpython2.7 -o build/lib.cygwin-2.4.0-x86_64-2.7/htslibWrapper.dll
/usr/lib/gcc/x86_64-pc-cygwin/4.9.3/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lhts
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
Setup failed. Check previous lines for errors
Stampy
Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1
$ cd c:cygwin64/usr/local/bin/stampy-1.0.28
Robert@DESKTOP-14EL82S /cygdrive/c/cygwin64/usr/local/bin/stampy-1.0.28
$ ./configure
-bash: ./configure: No such file or directory
Robert@DESKTOP-14EL82S /cygdrive/c/cygwin64/usr/local/bin/stampy-1.0.28
$ ./buildStampy-1.0.28
-bash: ./buildStampy-1.0.28: No such file or directory
Robert@DESKTOP-14EL82S /cygdrive/c/cygwin64/usr/local/bin/stampy-1.0.28
$ make
makefile:1: *** missing separator. Stop.
Robert@DESKTOP-14EL82S /cygdrive/c/cygwin64/usr/local/bin/stampy-1.0.28
$ cd c:/cygwin64/usr/local/bin/tree-puzzle-5.3.rc16-windows
Robert@DESKTOP-14EL82S /usr/local/bin/tree-puzzle-5.3.rc16-windows
$ ./configure
checking build system type... ./config.guess: unable to guess system type
This script, last modified 2004-08-11, has failed to recognize
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from
ftp://ftp.gnu.org/pub/gnu/config/
If the version you run (./config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to <config-patches@gnu.org> in order to provide the needed
information to handle your system.
config.guess timestamp = 2004-08-11
uname -m = x86_64
uname -r = 2.4.0(0.293/5/3)
uname -s = CYGWIN_NT-10.0
uname -v = 2016-01-15 16:16
/usr/bin/uname -p = unknown
/bin/uname -X =
hostinfo =
/bin/universe =
/usr/bin/arch -k =
/bin/arch = x86_64
/usr/bin/oslevel =
/usr/convex/getsysinfo =
UNAME_MACHINE = x86_64
UNAME_RELEASE = 2.4.0(0.293/5/3)
UNAME_SYSTEM = CYGWIN_NT-10.0
UNAME_VERSION = 2016-01-15 16:16
configure: error: cannot guess build type; you must specify one
Robert@DESKTOP-14EL82S /usr/local/bin/tree-puzzle-5.3.rc16-windows
$ make
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure CFLAGS=-static -DSPRNG -DHHH -Wall -pedantic -std=c99 -O -g --no-create --no-recursion
checking build system type... ./config.guess: unable to guess system type
This script, last modified 2004-08-11, has failed to recognize
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from
ftp://ftp.gnu.org/pub/gnu/config/
If the version you run (./config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to <config-patches@gnu.org> in order to provide the needed
information to handle your system.
config.guess timestamp = 2004-08-11
uname -m = x86_64
uname -r = 2.4.0(0.293/5/3)
uname -s = CYGWIN_NT-10.0
uname -v = 2016-01-15 16:16
/usr/bin/uname -p = unknown
/bin/uname -X =
hostinfo =
/bin/universe =
/usr/bin/arch -k =
/bin/arch = x86_64
/usr/bin/oslevel =
/usr/convex/getsysinfo =
UNAME_MACHINE = x86_64
UNAME_RELEASE = 2.4.0(0.293/5/3)
UNAME_SYSTEM = CYGWIN_NT-10.0
UNAME_VERSION = 2016-01-15 16:16
configure: error: cannot guess build type; you must specify one
Makefile:355: recipe for target 'config.status' failed
make: *** [config.status] Error 1
Robert@DESKTOP-14EL82S /usr/local/bin/tree-puzzle-5.3.rc16-windows
$
Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree
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