FreeBSD Bugzilla – Attachment 166570 Details for
Bug 206926
[NEW PORT] biology/vcftools: Tools for working with VCF genomics files
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Poudriere log
samtools01-0.1.19.log-10-1-i386 (text/plain), 32.44 KB, created by
Jason W. Bacon
on 2016-02-04 16:22:23 UTC
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Description:
Poudriere log
Filename:
MIME Type:
Creator:
Jason W. Bacon
Created:
2016-02-04 16:22:23 UTC
Size:
32.44 KB
patch
obsolete
>build started at Wed Feb 3 13:16:26 CST 2016 >port directory: /usr/ports/biology/samtools0119 >building for: FreeBSD 10-1-i386-default 10.1-RELEASE-p29 FreeBSD 10.1-RELEASE-p29 i386 >maintained by: bacon4000@gmail.com >ident warning: no id keywords in /usr/local/poudriere/data/.m/10-1-i386-default/ref//usr/ports/biology/samtools0119/Makefile >Makefile ident: >Poudriere version: 3.1.10 >Host OSVERSION: 1001000 >Jail OSVERSION: 1001000 > >---Begin Environment--- >PKGREPOSITORY=/tmp/pkgs >PACKAGES=/tmp/pkgs >UNAME_p=i386 >UNAME_m=i386 >OSVERSION=1001000 >UNAME_v=FreeBSD 10.1-RELEASE-p29 >UNAME_r=10.1-RELEASE-p29 >BLOCKSIZE=K >MAIL=/var/mail/root >STATUS=1 >WARNING_WAIT=0 >SAVED_TERM=xterm >NO_WARNING_PKG_INSTALL_EOL=yes >MASTERMNT=/usr/local/poudriere/data/.m/10-1-i386-default/ref >FORCE_PACKAGE=yes >PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin >POUDRIERE_BUILD_TYPE=bulk >OLDPWD=/usr/home/bacon >PWD=/ >MASTERNAME=10-1-i386-default >SCRIPTPREFIX=/usr/local/share/poudriere >USER=root >HOME=/root >POUDRIERE_VERSION=3.1.10 >SCRIPTPATH=/usr/local/share/poudriere/testport.sh >TRYBROKEN=yes >LIBEXECPREFIX=/usr/local/libexec/poudriere >LOCALBASE=/usr/local >PACKAGE_BUILDING=yes >DEV_WARNING_WAIT=0 >---End Environment--- > >---Begin OPTIONS List--- >---End OPTIONS List--- > >--CONFIGURE_ARGS-- > >--End CONFIGURE_ARGS-- > >--CONFIGURE_ENV-- >MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/samtools0119/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/samtools0119/work HOME=/wrkdirs/usr/ports/biology/samtools0119/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh >--End CONFIGURE_ENV-- > >--MAKE_ENV-- >XDG_DATA_HOME=/wrkdirs/usr/ports/biology/samtools0119/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/samtools0119/work HOME=/wrkdirs/usr/ports/biology/samtools0119/work TMPDIR="/tmp" NO_PIE=yes NO_DEBUG_FILES=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" >--End MAKE_ENV-- > >--PLIST_SUB-- >PYTHON_INCLUDEDIR=include/python2.7 >PYTHON_LIBDIR=lib/python2.7 >PYTHON_PLATFORM=freebsd10 >PYTHON_SITELIBDIR=lib/python2.7/site-packages >PYTHON_VER=2.7 >PYTHON_VERSION=python2.7 >OSREL=10.1 >PREFIX=%D >LOCALBASE=/usr/local >RESETPREFIX=/usr/local >PORTDOCS="" >PORTEXAMPLES="" >LIB32DIR=lib >PERL_VERSION=5.20.3 >PERL_VER=5.20 >PERL5_MAN1=lib/perl5/site_perl/man/man1 >PERL5_MAN3=lib/perl5/site_perl/man/man3 >SITE_PERL=lib/perl5/site_perl >SITE_ARCH=lib/perl5/site_perl/mach/5.20 >DOCSDIR="share/doc/samtools" >EXAMPLESDIR="share/examples/samtools" >DATADIR="share/samtools" >WWWDIR="www/samtools" >ETCDIR="etc/samtools" >--End PLIST_SUB-- > >--SUB_LIST-- >PREFIX=/usr/local >LOCALBASE=/usr/local >DATADIR=/usr/local/share/samtools >DOCSDIR=/usr/local/share/doc/samtools >EXAMPLESDIR=/usr/local/share/examples/samtools >WWWDIR=/usr/local/www/samtools >ETCDIR=/usr/local/etc/samtools >--End SUB_LIST-- > >---Begin make.conf--- >MACHINE=i386 >MACHINE_ARCH=i386 >ARCH=${MACHINE_ARCH} >USE_PACKAGE_DEPENDS=yes >BATCH=yes >WRKDIRPREFIX=/wrkdirs >PORTSDIR=/usr/ports >PACKAGES=/packages >DISTDIR=/distfiles >---End make.conf--- >=======================<phase: check-sanity >============================ >===> License MIT accepted by the user >=========================================================================== >=======================<phase: pkg-depends >============================ >===> samtools01-0.1.19 depends on file: /usr/local/sbin/pkg - not found >===> Installing existing package /packages/All/pkg-1.6.3.txz >[10-1-i386-default] Installing pkg-1.6.3... >[10-1-i386-default] Extracting pkg-1.6.3: .......... done >Message from pkg-1.6.3: >If you are upgrading from the old package format, first run: > > # pkg2ng >===> samtools01-0.1.19 depends on file: /usr/local/sbin/pkg - found >===> Returning to build of samtools01-0.1.19 >=========================================================================== >=======================<phase: fetch-depends >============================ >=========================================================================== >=======================<phase: fetch >============================ >===> License MIT accepted by the user >===> samtools01-0.1.19 depends on file: /usr/local/sbin/pkg - found >===> Fetching all distfiles required by samtools01-0.1.19 for building >=========================================================================== >=======================<phase: checksum >============================ >===> License MIT accepted by the user >===> samtools01-0.1.19 depends on file: /usr/local/sbin/pkg - found >===> Fetching all distfiles required by samtools01-0.1.19 for building >=> SHA256 Checksum OK for samtools-0.1.19.tar.bz2. >=========================================================================== >=======================<phase: extract-depends>============================ >=========================================================================== >=======================<phase: extract >============================ >===> License MIT accepted by the user >===> samtools01-0.1.19 depends on file: /usr/local/sbin/pkg - found >===> Fetching all distfiles required by samtools01-0.1.19 for building >===> Extracting for samtools01-0.1.19 >=> SHA256 Checksum OK for samtools-0.1.19.tar.bz2. >=========================================================================== >=======================<phase: patch-depends >============================ >=========================================================================== >=======================<phase: patch >============================ >===> Patching for samtools01-0.1.19 >===> Applying FreeBSD patches for samtools01-0.1.19 >/usr/bin/sed -i.bak -e "s|/software/bin/python|/usr/local/bin/python|g" /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/*.py >=========================================================================== >=======================<phase: build-depends >============================ >===> samtools01-0.1.19 depends on executable: gmake - not found >===> Installing existing package /packages/All/gmake-4.1_2.txz >[10-1-i386-default] Installing gmake-4.1_2... >[10-1-i386-default] `-- Installing indexinfo-0.2.4... >[10-1-i386-default] `-- Extracting indexinfo-0.2.4: .... done >[10-1-i386-default] `-- Installing gettext-runtime-0.19.6... >[10-1-i386-default] `-- Extracting gettext-runtime-0.19.6: .......... done >[10-1-i386-default] Extracting gmake-4.1_2: .......... done >===> samtools01-0.1.19 depends on executable: gmake - found >===> Returning to build of samtools01-0.1.19 >===> samtools01-0.1.19 depends on package: perl5>=5.20<5.21 - not found >===> Installing existing package /packages/All/perl5-5.20.3_8.txz >[10-1-i386-default] Installing perl5-5.20.3_8... >[10-1-i386-default] Extracting perl5-5.20.3_8: .......... done >Message from perl5-5.20.3_8: >The /usr/bin/perl symlink has been removed starting with Perl 5.20. >For shebangs, you should either use: > >#!/usr/local/bin/perl > >or > >#!/usr/bin/env perl > >The first one will only work if you have a /usr/local/bin/perl, >the second will work as long as perl is in PATH. >===> samtools01-0.1.19 depends on package: perl5>=5.20<5.21 - found >===> Returning to build of samtools01-0.1.19 >=========================================================================== >=======================<phase: lib-depends >============================ >=========================================================================== >====>> Recording filesystem state for prebuild... done >=======================<phase: configure >============================ >===> samtools01-0.1.19 depends on executable: gmake - found >===> samtools01-0.1.19 depends on package: perl5>=5.20<5.21 - found >===> Configuring for samtools01-0.1.19 >=========================================================================== >=======================<phase: build >============================ >===> Building for samtools01-0.1.19 >gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19' >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o >gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19' >gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19' >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -o razip razip.o razf.o knetfile.o -lz >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o >bam_import.c:179:67: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] > fprintf(stderr,"realloc failed to alloc %ld bytes\n", y); > ~~~ ^ > %zu >bam_import.c:186:71: warning: format specifies type 'long' but the argument has type 'unsigned int' [-Wformat] > fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y); > ~~~ ^~~~~~~~~~~~~~~~~~~~~~~ > %u >bam_import.c:186:116: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] > fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y); > ~~~ ^ > %zu >bam_import.c:186:118: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] > fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y); > ~~~ ^ > %zu >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o >4 warnings generated. >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o >bam2bcf_indel.c:32:52: warning: for loop has empty body [-Wempty-body] > for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; > ^ >bam2bcf_indel.c:32:52: note: put the semicolon on a separate line to silence this warning >bam2bcf_indel.c:33:52: warning: for loop has empty body [-Wempty-body] > for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; > ^ >bam2bcf_indel.c:33:52: note: put the semicolon on a separate line to silence this warning >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o >errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare] > if (m > m) return -1; > ^ >2 warnings generated. >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o >1 warning generated. >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o >ar cr libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o >/usr/bin/ranlib libbam.a >gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19' >padding.c:173:153: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] >gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/bcftools' > fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l); > ~~~ ^~~ > %zu >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o >1 warning generated. >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o >ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o >gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/bcftools' >gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc' >gmake[3]: Nothing to be done for 'lib'. >gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc' >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -fstack-protector libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread >gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19' >gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/bcftools' >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread >gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/bcftools' >gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc' >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -DMD5SUM_MAIN -o md5sum-lite.o md5.c >cc -c -O2 -pipe -fstack-protector -fno-strict-aliasing -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -c -I.. -o md5fa.o md5fa.c >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -o maq2sam-short maq2sam.c -lz >md5.cmd5.c:155:27: warning: 'memset' call operates on objects of type 'struct MD5Context' while the size is based on a different type 'struct MD5Context *' [-Wsizeof-pointer-memaccess] > memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ > ~~~ ^~~ >:155:27:md5.c:155:27: warning: 'memset' call operates on objects of type 'struct MD5Context' while the size is based on a different type 'struct MD5Context *' [-Wsizeof-pointer-memaccess] > memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ > ~~~ ^~~ >md5.c:155:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)? > memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ > ^~~ > note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)? > memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ > ^~~ >1 warning generated. >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz >1 warning generated. >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -c -I.. -o ace2sam.o ace2sam.c >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -c -I.. -o wgsim.o wgsim.c >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -c -I.. -o bamcheck.o bamcheck.c >ace2sam.c:112:54: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] > fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line > ~~~ ^~~~~~~~~~~~~~~~~~ > %zu >bamcheck.c:1420:14: warning: implicit declaration of function 'isatty' is invalid in C99 [-Wimplicit-function-declaration] > if ( isatty(fileno((FILE *)stdin)) ) > ^ >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -o md5sum-lite md5sum-lite.o >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -o md5fa md5.o md5fa.o -lz >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -o wgsim wgsim.o -lm -lz >1 warning generated. >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -o ace2sam ace2sam.o -lz >1 warning generated. >cc -O2 -pipe -fstack-protector -fno-strict-aliasing -O -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz >gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc' >gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19' >=========================================================================== >====>> Checking for filesystem violations... done >=======================<phase: run-depends >============================ >===> samtools01-0.1.19 depends on file: /usr/local/bin/python2.7 - not found >===> Installing existing package /packages/All/python27-2.7.11_1.txz >[10-1-i386-default] Installing python27-2.7.11_1... >[10-1-i386-default] `-- Installing libffi-3.2.1... >[10-1-i386-default] `-- Extracting libffi-3.2.1: .......... done >[10-1-i386-default] Extracting python27-2.7.11_1: .......... done >Message from python27-2.7.11_1: >=========================================================================== > >Note that some standard Python modules are provided as separate ports >as they require additional dependencies. They are available as: > >bsddb databases/py-bsddb >gdbm databases/py-gdbm >sqlite3 databases/py-sqlite3 >tkinter x11-toolkits/py-tkinter > >=========================================================================== >===> samtools01-0.1.19 depends on file: /usr/local/bin/python2.7 - found >===> Returning to build of samtools01-0.1.19 >===> samtools01-0.1.19 depends on package: perl5>=5.20<5.21 - found >=========================================================================== >====>> Recording filesystem state for prestage... done >=======================<phase: stage >============================ >===> Staging for samtools01-0.1.19 >===> samtools01-0.1.19 depends on file: /usr/local/bin/python2.7 - found >===> samtools01-0.1.19 depends on package: perl5>=5.20<5.21 - found >===> Generating temporary packing list >install -s -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/samtools /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -s -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/razip /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -s -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/bcftools/bcftools /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -s -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/ace2sam /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -s -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/bamcheck /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -s -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/maq2sam-long /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -s -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/maq2sam-short /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -s -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/md5fa /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -s -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/md5sum-lite /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -s -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/wgsim /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/*.pl /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/plot-bamcheck /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/*.py /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -m 555 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/misc/*.lua /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/bin >install -m 0644 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/libbam.a /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/lib >install -m 444 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/samtools.1 /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/man/man1 >/bin/mkdir -p /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/include/bam >install -m 0644 /wrkdirs/usr/ports/biology/samtools0119/work/samtools-0.1.19/*.h /wrkdirs/usr/ports/biology/samtools0119/work/stage/usr/local/include/bam >====> Compressing man pages (compress-man) >=========================================================================== >====> Running Q/A tests (stage-qa) >====> Checking for pkg-plist issues (check-plist) >===> Parsing plist >===> Checking for items in STAGEDIR missing from pkg-plist >===> Checking for items in pkg-plist which are not in STAGEDIR >===> No pkg-plist issues found (check-plist) >====>> Checking for staging violations... done >=======================<phase: package >============================ >===> Building package for samtools01-0.1.19 >=========================================================================== >=======================<phase: install-mtree >============================ >=========================================================================== >====>> Recording filesystem state for preinst... done >=======================<phase: install >============================ >===> Installing for samtools01-0.1.19 >===> samtools01-0.1.19 depends on file: /usr/local/bin/python2.7 - found >===> samtools01-0.1.19 depends on package: perl5>=5.20<5.21 - found >===> Checking if samtools01 already installed >===> Registering installation for samtools01-0.1.19 >[10-1-i386-default] Installing samtools01-0.1.19... >=========================================================================== >====>> Checking shared library dependencies > 0x00000001 (NEEDED) Shared library: [libc.so.7] > 0x00000001 (NEEDED) Shared library: [libm.so.5] > 0x00000001 (NEEDED) Shared library: [libncurses.so.8] > 0x00000001 (NEEDED) Shared library: [libthr.so.3] > 0x00000001 (NEEDED) Shared library: [libz.so.6] >=======================<phase: deinstall >============================ >===> Deinstalling for samtools01 >===> Deinstalling samtools01-0.1.19 >Updating database digests format: ........ done >Checking integrity... done (0 conflicting) >Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): > >Installed packages to be REMOVED: > samtools01-0.1.19 > >The operation will free 1 MiB. >[10-1-i386-default] [1/1] Deinstalling samtools01-0.1.19... >[10-1-i386-default] [1/1] Deleting files for samtools01-0.1.19: .......... done >=========================================================================== >====>> Checking for extra files and directories >[00:00:17] ====>> Installing from package >[10-1-i386-default] Installing samtools01-0.1.19... >[10-1-i386-default] Extracting samtools01-0.1.19: .......... done >[00:00:17] ====>> Cleaning up >===> Cleaning for samtools01-0.1.19 >[00:00:17] ====>> Deinstalling package >Updating database digests format: . done >Checking integrity... done (0 conflicting) >Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): > >Installed packages to be REMOVED: > samtools01-0.1.19 > >The operation will free 1 MiB. >[10-1-i386-default] [1/1] Deinstalling samtools01-0.1.19... >[10-1-i386-default] [1/1] Deleting files for samtools01-0.1.19: .......... done >build of biology/samtools0119 ended at Wed Feb 3 13:16:40 CST 2016 >build time: 00:00:14
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