From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: (qmail 35115 invoked by alias); 24 Jan 2016 23:39:37 -0000 Mailing-List: contact cygwin-help@cygwin.com; run by ezmlm Precedence: bulk List-Id: List-Subscribe: List-Archive: List-Post: List-Help: , Sender: cygwin-owner@cygwin.com Mail-Followup-To: cygwin@cygwin.com Received: (qmail 34960 invoked by uid 89); 24 Jan 2016 23:39:35 -0000 Authentication-Results: sourceware.org; auth=none X-Virus-Found: No X-Spam-SWARE-Status: No, score=3.0 required=5.0 tests=AWL,BAYES_50,FREEMAIL_FROM,RCVD_IN_DNSWL_LOW,SPF_PASS autolearn=ham version=3.3.2 spammy=cram, 195, H*r:sk:col004-, H*r:sk:COL004- X-HELO: mail-pf0-f173.google.com Received: from mail-pf0-f173.google.com (HELO mail-pf0-f173.google.com) (209.85.192.173) by sourceware.org (qpsmtpd/0.93/v0.84-503-g423c35a) with (AES128-GCM-SHA256 encrypted) ESMTPS; Sun, 24 Jan 2016 23:39:32 +0000 Received: by mail-pf0-f173.google.com with SMTP id q63so74010332pfb.1 for ; Sun, 24 Jan 2016 15:39:31 -0800 (PST) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:message-id:from:to:subject:date:importance :in-reply-to:references:content-type:content-transfer-encoding :mime-version; bh=KhR4PjMh5uGMXV3FwUXjf+mi18w3KfYnPlXttyk1Bms=; b=TbUIgYPfbwoxNB0wCjpqFQP3EbrbTrg4J1/Krca/7uNICBeloyK55WQkd2YNtEzaTj 4m4Gy0VgIK+xxVMY0NHEpK/MzFeycMNCGJLD24kpIlJC/hVvKeFnHYjKCUYvGaZeRPBE SI6WnC93fKsN3j2UXqvZnGKbzrwvd4hKmPy8Mzd/sp1CXwDquWVjnukqnJMVNGO7NSrb DJlGLCF1Puacn1lBnGRX9guXTK8eHkH240zN0MRtQRtY2MkPNnud2tI+H6mZHpwjD6Ye LZnCEnH4sO5DW+43Yw5TXPwjUKxJ7Eckm2mq2IODddo5Z+PQ4Xs3sYMn27GT/zNjLtaY 3hRg== X-Gm-Message-State: AG10YOTxm9FcO3UoKoHJSlfjq1VuQN05qB5X2sOxApmmr+4ji5wJjBzlLdu5pY5BWB0vQQ== X-Received: by 10.98.72.132 with SMTP id q4mr21334834pfi.53.1453678770130; Sun, 24 Jan 2016 15:39:30 -0800 (PST) Received: from mail.hotmail.com (col004-wss1s3.hotmail.com. [157.56.23.10]) by smtp.gmail.com with ESMTPSA id i76sm23780302pfj.68.2016.01.24.15.39.29 for (version=TLSv1/SSLv3 cipher=OTHER); Sun, 24 Jan 2016 15:39:29 -0800 (PST) Received: from BAY175-W51 ([157.56.23.7]) by COL004-WSS1S3.hotmail.com over TLS secured channel with Microsoft SMTPSVC(7.5.7601.23008); Sun, 24 Jan 2016 15:39:28 -0800 X-TMN: [KiejoTfcMzGlimk45LfXBo17Cb0E9Br/] Message-ID: From: Robert May To: "cygwin@cygwin.com" Subject: Updated Cygwin64 with 2.4.1.1 Date: Mon, 25 Jan 2016 03:06:00 -0000 In-Reply-To: References: Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-SW-Source: 2016-01/txt/msg00340.txt.bz2 Instalation error -/unknown package x3270.sh exit code 1 htslib configure - make - make install ok samtools configure ok=20 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 =3D=3D=3D configuring in htslib-1.3 (/usr/local/bin/samtools-1.3/htslib-1.3) configure: running /bin/sh ./configure --disable-option-checking '--prefix= =3D/usr/local'=A0 --cache-file=3D/dev/null --srcdir=3D. 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'.=A0 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=A0 test/fieldarith test/hfile test/sam t= est/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=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o main.o main.c gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfindex.o vcfindex.c vcfindex.c: In function =91main_vcfindex=92: vcfindex.c:209:9: warning: implicit declaration of function =91alloca=92 [-= Wimplicit-function-declaration] =A0=A0=A0=A0=A0=A0=A0=A0 char *idx_fname =3D (char*)alloca(strlen(fname) + = 5); =A0=A0=A0=A0=A0=A0=A0=A0 ^ vcfindex.c:209:27: warning: cast to pointer from integer of different size = [-Wint-to-pointer-cast] =A0=A0=A0=A0=A0=A0=A0=A0 char *idx_fname =3D (char*)alloca(strlen(fname) + = 5); =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0 ^ gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o tabix.o tabix.c tabix.c: In function =91main_tabix=92: tabix.c:97:13: warning: implicit declaration of function =91alloca=92 [-Wim= plicit-function-declaration] =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 fn =3D (char*)alloca(strlen(argv[optin= d]) + 5); =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^ tabix.c:97:18: warning: cast to pointer from integer of different size [-Wi= nt-to-pointer-cast] =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 fn =3D (char*)alloca(strlen(argv[optin= d]) + 5); =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^ gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfstats.o vcfstats.c vcfstats.c: In function =91main_vcfstats=92: vcfstats.c:1558:9: warning: implicit declaration of function =91fileno=92 [= -Wimplicit-function-declaration] =A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) fname =3D "-= ";=A0 // reading from stdin =A0=A0=A0=A0=A0=A0=A0=A0 ^ gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfisec.o vcfisec.c vcfisec.c: In function =91main_vcfisec=92: vcfisec.c:556:21: warning: array subscript has type =91char=92 [-Wchar-subs= cripts] =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 else if ( isdi= git(*p) ) args->isec_op =3D OP_EQUAL; =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^ gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfmerge.o vcfmerge.c vcfmerge.c: In function =91merge_alleles=92: vcfmerge.c:542:13: warning: array subscript has type =91char=92 [-Wchar-sub= scripts] =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 for (j=3D0; jndref; i++) vcmp->dref[i] =3D = toupper(ref1[vcmp->nmatch+i]); =A0=A0=A0=A0=A0=A0=A0=A0 ^ vcmp.c:78:5: warning: array subscript has type =91char=92 [-Wchar-subscript= s] =A0=A0=A0=A0 for (i=3D0; indref; i++) vcmp->dref[i] =3D toupper(ref2= [vcmp->nmatch+i]); =A0=A0=A0=A0 ^ vcmp.c: In function =91vcmp_find_allele=92: vcmp.c:90:9: warning: array subscript has type =91char=92 [-Wchar-subscript= s] =A0=A0=A0=A0=A0=A0=A0=A0 while ( *a && *b && toupper(*a)=3D=3Dtoupper(*b) )= { a++; b++; } =A0=A0=A0=A0=A0=A0=A0=A0 ^ vcmp.c:90:9: warning: array subscript has type =91char=92 [-Wchar-subscript= s] vcmp.c:103:17: warning: array subscript has type =91char=92 [-Wchar-subscri= pts] =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 if ( !a[j] || toupper(a[j]= )!=3Dvcmp->dref[j] ) break; =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^ vcmp.c:110:13: warning: array subscript has type =91char=92 [-Wchar-subscri= pts] =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 if ( !b[j] || toupper(b[j])!=3Dvcmp->d= ref[j] ) break; =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^ gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o gvcf.o gvcf.c gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o reheader.o reheader.c reheader.c: In function =91read_header_file=92: reheader.c:65:5: warning: array subscript has type =91char=92 [-Wchar-subsc= ripts] =A0=A0=A0=A0 while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--;=A0 /= / remove trailing newlines =A0=A0=A0=A0 ^ reheader.c: In function =91set_sample_pairs=92: reheader.c:79:9: warning: array subscript has type =91char=92 [-Wchar-subsc= ripts] =A0=A0=A0=A0=A0=A0=A0=A0 while ( *value && !isspace(*value) ) value++; =A0=A0=A0=A0=A0=A0=A0=A0 ^ reheader.c:82:9: warning: array subscript has type =91char=92 [-Wchar-subsc= ripts] =A0=A0=A0=A0=A0=A0=A0=A0 while ( isspace(*value) ) value++; =A0=A0=A0=A0=A0=A0=A0=A0 ^ reheader.c:91:5: warning: array subscript has type =91char=92 [-Wchar-subsc= ripts] =A0=A0=A0=A0 while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--;=A0 /= / remove trailing newlines =A0=A0=A0=A0 ^ reheader.c: In function =91reheader_vcf_gz=92: reheader.c:227:9: warning: implicit declaration of function =91fileno=92 [-= Wimplicit-function-declaration] =A0=A0=A0=A0=A0=A0=A0=A0 bgzf_out =3D bgzf_dopen(fileno(stdout), "w"); =A0=A0=A0=A0=A0=A0=A0=A0 ^ gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o convert.o convert.c convert.c: In function =91parse_subscript=92: convert.c:781:5: warning: array subscript has type =91char=92 [-Wchar-subsc= ripts] =A0=A0=A0=A0 while ( *q && *q!=3D'}' && isdigit(*q) ) q++; =A0=A0=A0=A0 ^ convert.c: In function =91parse_tag=92: convert.c:791:5: warning: array subscript has type =91char=92 [-Wchar-subsc= ripts] =A0=A0=A0=A0 while ( *q && (isalnum(*q) || *q=3D=3D'_' || *q=3D=3D'.') ) q+= +; =A0=A0=A0=A0 ^ convert.c:806:13: warning: array subscript has type =91char=92 [-Wchar-subs= cripts] =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 while ( *q && (isalnum(*q) || *q=3D=3D= '_' || *q=3D=3D'.') ) q++; =A0^ convert.c:848:13: warning: array subscript has type =91char=92 [-Wchar-subs= cripts] =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 while ( *q && (isalnum(*q) || *q=3D=3D= '_' || *q=3D=3D'.') ) q++; =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^ gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfconvert.o vcfconvert.c In file included from vcfconvert.c:42:0: tsv2vcf.h: In function =91tsv_next=92: tsv2vcf.h:68:9: warning: array subscript has type =91char=92 [-Wchar-subscr= ipts] =A0=A0=A0=A0=A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; =A0=A0=A0=A0=A0=A0=A0=A0 ^ tsv2vcf.h:71:5: warning: array subscript has type =91char=92 [-Wchar-subscr= ipts] =A0=A0=A0=A0 while ( *tsv->se && isspace(*tsv->se) ) tsv->se++; =A0=A0=A0=A0 ^ tsv2vcf.h:73:5: warning: array subscript has type =91char=92 [-Wchar-subscr= ipts] =A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; =A0=A0=A0=A0 ^ vcfconvert.c: In function =91tsv_setter_chrom_pos_ref_alt=92: vcfconvert.c:161:5: warning: array subscript has type =91char=92 [-Wchar-su= bscripts] =A0=A0=A0=A0 while ( se < tsv->se && *se!=3D'_' && isspace(*tsv->se) ) se++; =A0=A0=A0=A0 ^ vcfconvert.c:162:5: warning: array subscript has type =91char=92 [-Wchar-su= bscripts] =A0=A0=A0=A0 if ( se < tsv->se && *se!=3D'_' && isspace(*tsv->se) ) error("= Could not parse ALT in CHROM:POS_REF_ALT id: %s\n", tsv->ss); =A0=A0=A0=A0 ^ vcfconvert.c: In function =91tsv_setter_verify_ref_alt=92: vcfconvert.c:195:5: warning: array subscript has type =91char=92 [-Wchar-su= bscripts] =A0=A0=A0=A0 while ( *tsv->se && isspace(*tsv->se) ) tsv->se++; =A0=A0=A0=A0 ^ vcfconvert.c:197:5: warning: array subscript has type =91char=92 [-Wchar-su= bscripts] =A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; =A0=A0=A0=A0 ^ vcfconvert.c: In function =91gensample_to_vcf=92: vcfconvert.c:354:5: warning: array subscript has type =91char=92 [-Wchar-su= bscripts] =A0=A0=A0=A0 while ( *se && !isspace(*se) ) se++; =A0=A0=A0=A0 ^ vcfconvert.c:378:9: warning: array subscript has type =91char=92 [-Wchar-su= bscripts] =A0=A0=A0=A0=A0=A0=A0=A0 se =3D samples[i]; while ( *se && !isspace(*se) ) = se++; =A0=A0=A0=A0=A0=A0=A0=A0 ^ vcfconvert.c: In function =91haplegendsample_to_vcf=92: vcfconvert.c:502:9: warning: array subscript has type =91char=92 [-Wchar-su= bscripts] =A0=A0=A0=A0=A0=A0=A0=A0 se =3D samples[i]; while ( *se && !isspace(*se) ) = se++; =A0=A0=A0=A0=A0=A0=A0=A0 ^ vcfconvert.c: In function =91hapsample_to_vcf=92: vcfconvert.c:615:9: warning: array subscript has type =91char=92 [-Wchar-su= bscripts] =A0=A0=A0=A0=A0=A0=A0=A0 se =3D samples[i]; while ( *se && !isspace(*se) ) = se++; =A0=A0=A0=A0=A0=A0=A0=A0 ^ vcfconvert.c: In function =91tsv_setter_aa1=92: vcfconvert.c:1069:5: warning: array subscript has type =91char=92 [-Wchar-s= ubscripts] =A0=A0=A0=A0 int a0 =3D acgt_to_5(toupper(ss[0])); =A0=A0=A0=A0 ^ vcfconvert.c:1070:5: warning: array subscript has type =91char=92 [-Wchar-s= ubscripts] =A0=A0=A0=A0 int a1 =3D ss[1] ? acgt_to_5(toupper(ss[1])) : a0; =A0=A0=A0=A0 ^ vcfconvert.c: In function =91tsv_setter_aa=92: vcfconvert.c:1094:5: warning: array subscript has type =91char=92 [-Wchar-s= ubscripts] =A0=A0=A0=A0 ref[0] =3D toupper(ref[0]); =A0=A0=A0=A0 ^ vcfconvert.c: In function =91main_vcfconvert=92: vcfconvert.c:1436:13: warning: implicit declaration of function =91fileno= =92 [-Wimplicit-function-declaration] =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) = args->infname =3D "-"; =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^ gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o tsv2vcf.o tsv2vcf.c In file included from tsv2vcf.c:27:0: tsv2vcf.h: In function =91tsv_next=92: tsv2vcf.h:68:9: warning: array subscript has type =91char=92 [-Wchar-subscr= ipts] =A0=A0=A0=A0=A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; =A0=A0=A0=A0=A0=A0=A0=A0 ^ tsv2vcf.h:71:5: warning: array subscript has type =91char=92 [-Wchar-subscr= ipts] =A0=A0=A0=A0 while ( *tsv->se && isspace(*tsv->se) ) tsv->se++; =A0=A0=A0=A0 ^ tsv2vcf.h:73:5: warning: array subscript has type =91char=92 [-Wchar-subscr= ipts] =A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; =A0=A0=A0=A0 ^ tsv2vcf.c: In function =91tsv_parse=92: tsv2vcf.c:81:9: warning: array subscript has type =91char=92 [-Wchar-subscr= ipts] =A0=A0=A0=A0=A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++; =A0=A0=A0=A0=A0=A0=A0=A0 ^ tsv2vcf.c:88:9: warning: array subscript has type =91char=92 [-Wchar-subscr= ipts] =A0=A0=A0=A0=A0=A0=A0=A0 while ( *tsv->se && isspace(*tsv->se) ) tsv->se++; =A0=A0=A0=A0=A0=A0=A0=A0 ^ gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH= =3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfcnv.o vcfcnv.c vcfcnv.c: In function =91norm_prob=92: vcfcnv.c:602:93: error: =91M_PI=92 undeclared (first use in this function) =A0=A0=A0=A0 return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev= 2) / param->norm / sqrt(2*M_PI*param->dev2); =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^ vcfcnv.c:602:93: note: each undeclared identifier is reported only once for= each function it appears in vcfcnv.c: In function =91main_vcfcnv=92: vcfcnv.c:1349:9: warning: implicit declaration of function =91fileno=92 [-W= implicit-function-declaration] =A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) fname =3D "-= "; =A0=A0=A0=A0=A0=A0=A0=A0 ^ vcfcnv.c: In function =91norm_prob=92: vcfcnv.c:603:1: warning: control reaches end of non-void function [-Wreturn= -type] =A0} =A0^ 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'.=A0 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 -f= debug-prefix-map=3D/usr/src/ports/python/python-2.7.10-1.x86_64/build=3D/us= r/src/debug/python-2.7.10-1 -fdebug-prefix-map=3D/usr/src/ports/python/pyth= on-2.7.10-1.x86_64/src/Python-2.7.10=3D/usr/src/debug/python-2.7.10-1 -DNDE= BUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c ht= slibWrapper.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=3D64 -fPIC htslibWrapper.c:1:0: warning: -fPIC ignored for target (all code is positio= n independent) =A0/* Generated by Cython 0.21.1 */ =A0^ 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: ca= nnot 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.=A0 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 =A0=A0=A0 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 in order to provide the needed information to handle your system. config.guess timestamp =3D 2004-08-11 uname -m =3D x86_64 uname -r =3D 2.4.0(0.293/5/3) uname -s =3D CYGWIN_NT-10.0 uname -v =3D 2016-01-15 16:16 /usr/bin/uname -p =3D unknown /bin/uname -X=A0=A0=A0=A0 =3D hostinfo=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =3D /bin/universe=A0=A0=A0=A0=A0=A0=A0=A0=A0 =3D /usr/bin/arch -k=A0=A0=A0=A0=A0=A0 =3D /bin/arch=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =3D x86_64 /usr/bin/oslevel=A0=A0=A0=A0=A0=A0 =3D /usr/convex/getsysinfo =3D UNAME_MACHINE =3D x86_64 UNAME_RELEASE =3D 2.4.0(0.293/5/3) UNAME_SYSTEM=A0 =3D CYGWIN_NT-10.0 UNAME_VERSION =3D 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=3D/bin/sh /bin/sh ./configure CFLAGS=3D-static -DSPRNG= -DHHH -Wall -pedantic -std=3Dc99 -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 =A0=A0=A0 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 in order to provide the needed information to handle your system. config.guess timestamp =3D 2004-08-11 uname -m =3D x86_64 uname -r =3D 2.4.0(0.293/5/3) uname -s =3D CYGWIN_NT-10.0 uname -v =3D 2016-01-15 16:16 /usr/bin/uname -p =3D unknown /bin/uname -X=A0=A0=A0=A0 =3D hostinfo=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =3D /bin/universe=A0=A0=A0=A0=A0=A0=A0=A0=A0 =3D /usr/bin/arch -k=A0=A0=A0=A0=A0=A0 =3D /bin/arch=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =3D x86_64 /usr/bin/oslevel=A0=A0=A0=A0=A0=A0 =3D /usr/convex/getsysinfo =3D UNAME_MACHINE =3D x86_64 UNAME_RELEASE =3D 2.4.0(0.293/5/3) UNAME_SYSTEM=A0 =3D CYGWIN_NT-10.0 UNAME_VERSION =3D 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 $ =A0Bob May DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surn= ame and ISOGG=A0YTree=20=09=09=20=09=20=20=20=09=09=20=20=20=09=09=20=09=20= =20=20=09=09=20=20 -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple