Attachment 166524 Details for Bug 206900 – Poudriere log

Poudriere log

samtools01-0.1.19.log-10-1-i386 (text/plain), 32.44 KB, created by Jason W. Bacon on 2016-02-03 19:24:37 UTC

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Creator: Jason W. Bacon

Created: 2016-02-03 19:24:37 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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Attachments on bug 206900: 166521 | 166522 | 166523 | 166524 | 166559