Attachment 164512 Details for Bug 205524 – poudriere testport output for releng_10_2

poudriere testport output for releng_10_2

htslib-1.3_releng_10.txt (text/plain), 31.58 KB, created by cartwright on 2015-12-22 23:21:16 UTC

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Creator: cartwright

Created: 2015-12-22 23:21:16 UTC

Size: 31.58 KB

patch

obsolete

>[00:00:00] ====>> Creating the reference jail... done
>[00:00:00] ====>> Mounting system devices for releng_10_1-default
>[00:00:00] ====>> Mounting ports/packages/distfiles
>[00:00:00] ====>> Stashing existing package repository
>[00:00:01] ====>> Mounting packages from: /usr/local/poudriere/data/packages/releng_10_1-default
>[00:00:01] ====>> Copying /var/db/ports from: /usr/local/etc/poudriere.d/options
>[00:00:01] ====>> Appending to make.conf: /usr/local/etc/poudriere.d/make.conf
>[00:00:01] ====>> Appending to make.conf: /usr/local/etc/poudriere.d/releng_10_1-make.conf
>/etc/resolv.conf -> /usr/local/poudriere/data/.m/releng_10_1-default/ref/etc/resolv.conf
>[00:00:01] ====>> Starting jail releng_10_1-default
>[00:00:01] ====>> Logs: /usr/local/poudriere/data/logs/bulk/releng_10_1-default/2015-12-22_16h04m18s
>[00:00:01] ====>> Loading MOVED
>[00:00:01] ====>> Calculating ports order and dependencies
>[00:00:02] ====>> Sanity checking the repository
>[00:00:02] ====>> Checking packages for incremental rebuild needed
>[00:00:03] ====>> Deleting stale symlinks
>[00:00:03] ====>> Deleting empty directories
>[00:00:03] ====>> Cleaning the build queue
>[00:00:03] ====>> Recording filesystem state for prepkg... done
>[00:00:04] ====>> Committing packages to repository
>[00:00:04] ====>> Removing old packages
>[00:00:04] ====>> Portlint check
>WARN: Makefile: [26]: possible direct use of command "file" found. use ${FILE} instead.
>0 fatal errors and 1 warning found.
>[00:00:05] ====>> Building with flags: 
>[00:00:05] ====>> Removing existing /usr/local
>build started at Tue Dec 22 16:04:23 MST 2015
>port directory: /usr/ports/biology/htslib
>building for: FreeBSD releng_10_1-default 10.2-RELEASE-p8 FreeBSD 10.2-RELEASE-p8 amd64
>maintained by: cartwright@asu.edu
>Makefile ident:      $FreeBSD: head/biology/htslib/Makefile 385521 2015-05-06 15:16:53Z mat $
>Poudriere version: 3.1.8
>Host OSVERSION: 1002000
>Jail OSVERSION: 1002000
>
>---Begin Environment---
>PKGREPOSITORY=/tmp/pkgs
>PACKAGES=/tmp/pkgs
>OSVERSION=1002000
>UNAME_v=FreeBSD 10.2-RELEASE-p8
>UNAME_r=10.2-RELEASE-p8
>BLOCKSIZE=K
>MAIL=/var/mail/root
>STATUS=1
>WARNING_WAIT=0
>SAVED_TERM=xterm-256color
>NO_WARNING_PKG_INSTALL_EOL=yes
>MASTERMNT=/usr/local/poudriere/data/.m/releng_10_1-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=/
>PWD=/usr/local/poudriere/data/.m/releng_10_1-default/ref/usr/ports/biology/htslib
>MASTERNAME=releng_10_1-default
>SCRIPTPREFIX=/usr/local/share/poudriere
>USER=root
>HOME=/root
>POUDRIERE_VERSION=3.1.8
>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---
>===> The following configuration options are available for htslib-1.3:
>     libcurl=on: Use libcurl for network file access (HTTPS and S3 support).
>===> Use 'make config' to modify these settings
>---End OPTIONS List---
>
>--CONFIGURE_ARGS--
>--enable-libcurl --prefix=/usr/local ${_LATE_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 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/htslib/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/htslib/work  HOME=/wrkdirs/usr/ports/biology/htslib/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144
>--End CONFIGURE_ENV--
>
>--MAKE_ENV--
>INSTALL_LIB="install  -s -m 444"  INSTALL_DATA="install  -m 0644"  INSTALL_PROGRAM="install  -s -m 555"  INSTALL_DIR="/bin/mkdir -p" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/htslib/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/htslib/work  HOME=/wrkdirs/usr/ports/biology/htslib/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 -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector"  CPP="cpp" CPPFLAGS="-I/usr/local/include"  LDFLAGS=" -L/usr/local/lib -fstack-protector" LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector "  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--
>PORTVERSION="1.3"
>OSREL=10.2
>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/htslib"
>EXAMPLESDIR="share/examples/htslib"
>DATADIR="share/htslib"
>WWWDIR="www/htslib"
>ETCDIR="etc/htslib"
>--End PLIST_SUB--
>
>--SUB_LIST--
>PREFIX=/usr/local
>LOCALBASE=/usr/local
>DATADIR=/usr/local/share/htslib
>DOCSDIR=/usr/local/share/doc/htslib
>EXAMPLESDIR=/usr/local/share/examples/htslib
>WWWDIR=/usr/local/www/htslib
>ETCDIR=/usr/local/etc/htslib
>--End SUB_LIST--
>
>---Begin make.conf---
>USE_PACKAGE_DEPENDS=yes
>BATCH=yes
>WRKDIRPREFIX=/wrkdirs
>USE_PACKAGE_DEPENDS=yes
>BATCH=yes
>WRKDIRPREFIX=/wrkdirs
>PORTSDIR=/usr/ports
>PACKAGES=/packages
>DISTDIR=/distfiles
>#### /usr/local/etc/poudriere.d/make.conf ####
>CFLAGS += -O2 -fno-strict-aliasing -pipe
>
>#DEFAULT_VERSIONS=python=2.7 python2=2.7 python3=3.4
>#WITH_BDB_VER=6
>#WITH_BDB6_PERMITTED=yes
>TEX_DEFAULT=texlive
>
>MAKE_JOBS_NUMBER_LIMIT=8
>
>#### /usr/local/etc/poudriere.d/releng_10_1-make.conf ####
>CPUTYPE?=bdver1
>
>---End make.conf---
>=======================<phase: check-sanity   >============================
>===>  License BSD3CLAUSE MIT accepted by the user
>===========================================================================
>=======================<phase: pkg-depends    >============================
>===>   htslib-1.3 depends on file: /usr/local/sbin/pkg - not found
>===>   Installing existing package /packages/All/pkg-1.6.2.txz
>[releng_10_1-default] Installing pkg-1.6.2...
>[releng_10_1-default] Extracting pkg-1.6.2: .......... done
>Message from pkg-1.6.2:
>If you are upgrading from the old package format, first run:
>
>  # pkg2ng
>===>   htslib-1.3 depends on file: /usr/local/sbin/pkg - found
>===>   Returning to build of htslib-1.3
>===========================================================================
>=======================<phase: fetch-depends  >============================
>===========================================================================
>=======================<phase: fetch          >============================
>===>  License BSD3CLAUSE MIT accepted by the user
>===>   htslib-1.3 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by htslib-1.3 for building
>===========================================================================
>=======================<phase: checksum       >============================
>===>  License BSD3CLAUSE MIT accepted by the user
>===>   htslib-1.3 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by htslib-1.3 for building
>=> SHA256 Checksum OK for samtools-htslib-1.3_GH0.tar.gz.
>===========================================================================
>=======================<phase: extract-depends>============================
>===========================================================================
>=======================<phase: extract        >============================
>===>  License BSD3CLAUSE MIT accepted by the user
>===>   htslib-1.3 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by htslib-1.3 for building
>===>  Extracting for htslib-1.3
>=> SHA256 Checksum OK for samtools-htslib-1.3_GH0.tar.gz.
>===========================================================================
>=======================<phase: patch-depends  >============================
>===========================================================================
>=======================<phase: patch          >============================
>===>  Patching for htslib-1.3
>===>  Applying FreeBSD patches for htslib-1.3
>===========================================================================
>=======================<phase: build-depends  >============================
>===>   htslib-1.3 depends on executable: autoconf-2.69 - not found
>===>   Installing existing package /packages/All/autoconf-2.69.txz
>[releng_10_1-default] Installing autoconf-2.69...
>[releng_10_1-default] `-- Installing indexinfo-0.2.4...
>[releng_10_1-default] `-- Extracting indexinfo-0.2.4: .... done
>[releng_10_1-default] `-- Installing autoconf-wrapper-20131203...
>[releng_10_1-default] `-- Extracting autoconf-wrapper-20131203: ........ done
>[releng_10_1-default] `-- Installing perl5-5.20.3_8...
>[releng_10_1-default] `-- Extracting perl5-5.20.3_8: .......... done
>[releng_10_1-default] `-- Installing m4-1.4.17_1,1...
>[releng_10_1-default] `-- Extracting m4-1.4.17_1,1: .......... done
>[releng_10_1-default] Extracting autoconf-2.69: .......... 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.
>===>   htslib-1.3 depends on executable: autoconf-2.69 - found
>===>   Returning to build of htslib-1.3
>===>   htslib-1.3 depends on executable: autoheader-2.69 - found
>===>   htslib-1.3 depends on executable: autoreconf-2.69 - found
>===>   htslib-1.3 depends on executable: aclocal-1.15 - not found
>===>   Installing existing package /packages/All/automake-1.15_1.txz
>[releng_10_1-default] Installing automake-1.15_1...
>[releng_10_1-default] `-- Installing automake-wrapper-20131203...
>[releng_10_1-default] `-- Extracting automake-wrapper-20131203: ... done
>[releng_10_1-default] Extracting automake-1.15_1: .......... done
>===>   htslib-1.3 depends on executable: aclocal-1.15 - found
>===>   Returning to build of htslib-1.3
>===>   htslib-1.3 depends on executable: automake-1.15 - found
>===>   htslib-1.3 depends on executable: gmake - not found
>===>   Installing existing package /packages/All/gmake-4.1_2.txz
>[releng_10_1-default] Installing gmake-4.1_2...
>[releng_10_1-default] `-- Installing gettext-runtime-0.19.6...
>[releng_10_1-default] `-- Extracting gettext-runtime-0.19.6: .......... done
>[releng_10_1-default] Extracting gmake-4.1_2: .......... done
>===>   htslib-1.3 depends on executable: gmake - found
>===>   Returning to build of htslib-1.3
>===========================================================================
>=======================<phase: lib-depends    >============================
>===>   htslib-1.3 depends on shared library: libcurl.so - not found
>===>   Installing existing package /packages/All/curl-7.46.0_1.txz
>[releng_10_1-default] Installing curl-7.46.0_1...
>[releng_10_1-default] `-- Installing ca_root_nss-3.20.1...
>[releng_10_1-default] `-- Extracting ca_root_nss-3.20.1: ....... done
>[releng_10_1-default] Extracting curl-7.46.0_1: .......... done
>Message from ca_root_nss-3.20.1:
>********************************* WARNING *********************************
>
>FreeBSD does not, and can not warrant that the certification authorities
>whose certificates are included in this package have in any way been
>audited for trustworthiness or RFC 3647 compliance.
>
>Assessment and verification of trust is the complete responsibility of the
>system administrator.
>
>*********************************** NOTE **********************************
>
>This package installs symlinks to support root certificates discovery by
>default for software that uses OpenSSL.
>
>This enables SSL Certificate Verification by client software without manual
>intervention.
>
>If you prefer to do this manually, replace the following symlinks with
>either an empty file or your site-local certificate bundle.
>
>  * /etc/ssl/cert.pem
>  * /usr/local/etc/ssl/cert.pem
>  * /usr/local/openssl/cert.pem
>
>***************************************************************************
>===>   htslib-1.3 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so)
>===>   Returning to build of htslib-1.3
>===========================================================================
>====>> Recording filesystem state for prebuild... done
>=======================<phase: configure      >============================
>===>   htslib-1.3 depends on executable: autoconf-2.69 - found
>===>   htslib-1.3 depends on executable: autoheader-2.69 - found
>===>   htslib-1.3 depends on executable: autoreconf-2.69 - found
>===>   htslib-1.3 depends on executable: aclocal-1.15 - found
>===>   htslib-1.3 depends on executable: automake-1.15 - found
>===>   htslib-1.3 depends on executable: gmake - found
>===>   htslib-1.3 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so)
>===>  Configuring for htslib-1.3
>configure: loading site script /usr/ports/Templates/config.site
>checking for gcc... cc
>checking whether the C compiler works... yes
>checking for C compiler default output file name... a.out
>checking for suffix of executables... 
>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 cc accepts -g... yes
>checking for cc option to accept ISO C89... none needed
>checking for ranlib... ranlib
>checking how to run the C preprocessor... cpp
>checking for grep that handles long lines and -e... (cached) /usr/bin/grep
>checking for egrep... (cached) /usr/bin/egrep
>checking for ANSI C header files... (cached) yes
>checking for sys/types.h... (cached) yes
>checking for sys/stat.h... (cached) yes
>checking for stdlib.h... (cached) yes
>checking for string.h... (cached) yes
>checking for memory.h... (cached) yes
>checking for strings.h... (cached) yes
>checking for inttypes.h... (cached) yes
>checking for stdint.h... (cached) yes
>checking for unistd.h... (cached) yes
>checking for stdlib.h... (cached) yes
>checking for unistd.h... (cached) yes
>checking for sys/param.h... (cached) yes
>checking for getpagesize... (cached) yes
>checking for working mmap... (cached) yes
>checking for gmtime_r... yes
>checking for zlib.h... (cached) yes
>checking for inflate in -lz... yes
>checking for curl_easy_pause in -lcurl... yes
>checking for CCHmac... no
>checking for library containing HMAC... -lcrypto
>configure: creating ./config.status
>config.status: creating config.mk
>config.status: creating config.h
>===========================================================================
>=======================<phase: build          >============================
>===>  Building for htslib-1.3
>gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/htslib/work/htslib-1.3'
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o kfunc.o kfunc.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o knetfile.o knetfile.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o kstring.o kstring.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o bgzf.o bgzf.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o faidx.o faidx.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o hfile.o hfile.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o hfile_net.o hfile_net.c
>echo '#define HTS_VERSION "1.3"' > version.h
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o md5.o md5.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o regidx.o regidx.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o sam.o sam.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o synced_bcf_reader.o synced_bcf_reader.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o vcf_sweep.o vcf_sweep.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o tbx.o tbx.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o vcf.o vcf.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o vcfutils.o vcfutils.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/cram_codecs.o cram/cram_codecs.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/cram_decode.o cram/cram_decode.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/cram_encode.o cram/cram_encode.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/cram_external.o cram/cram_external.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/cram_index.o cram/cram_index.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/cram_io.o cram/cram_io.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/cram_samtools.o cram/cram_samtools.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/cram_stats.o cram/cram_stats.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/files.o cram/files.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/mFILE.o cram/mFILE.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/open_trace_file.o cram/open_trace_file.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/pooled_alloc.o cram/pooled_alloc.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/rANS_static.o cram/rANS_static.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/sam_header.o cram/sam_header.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/string_alloc.o cram/string_alloc.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/thread_pool.o cram/thread_pool.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/vlen.o cram/vlen.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o cram/zfio.o cram/zfio.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o hfile_libcurl.o hfile_libcurl.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o kfunc.pico kfunc.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o knetfile.pico knetfile.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o kstring.pico kstring.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o bgzf.pico bgzf.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o faidx.pico faidx.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o hfile.pico hfile.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o hfile_net.pico hfile_net.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o hts.pico hts.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o md5.pico md5.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o regidx.pico regidx.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o sam.pico sam.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o vcf_sweep.pico vcf_sweep.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o tbx.pico tbx.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o vcf.pico vcf.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o vcfutils.pico vcfutils.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_external.pico cram/cram_external.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_index.pico cram/cram_index.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_io.pico cram/cram_io.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/files.pico cram/files.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/mFILE.pico cram/mFILE.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/sam_header.pico cram/sam_header.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/thread_pool.pico cram/thread_pool.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/vlen.pico cram/vlen.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/zfio.pico cram/zfio.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o bgzip.o bgzip.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o htsfile.o htsfile.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o tabix.o tabix.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -I. -I/usr/local/include -c -o hts.o hts.c
>cc -shared -Wl,-soname,libhts.so.1 -pthread -L/usr/local/lib -fstack-protector  -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico hfile_libcurl.pico -lz -lm   -lcurl -lcrypto
>ln -sf libhts.so libhts.so.1
>ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o  hfile_libcurl.o
>ranlib libhts.a
>cc -pthread -L/usr/local/lib -fstack-protector  -o bgzip bgzip.o libhts.a -lz   -lcurl -lcrypto
>cc -pthread -L/usr/local/lib -fstack-protector  -o htsfile htsfile.o libhts.a -lz   -lcurl -lcrypto
>cc -pthread -L/usr/local/lib -fstack-protector  -o tabix tabix.o libhts.a -lz   -lcurl -lcrypto
>gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/htslib/work/htslib-1.3'
>===========================================================================
>====>> Checking for filesystem violations... done
>=======================<phase: run-depends    >============================
>===========================================================================
>====>> Recording filesystem state for prestage... done
>=======================<phase: stage          >============================
>===>  Staging for htslib-1.3
>===>   htslib-1.3 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so)
>===>   Generating temporary packing list
>gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/htslib/work/htslib-1.3'
>/bin/mkdir -p /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/include /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/include/htslib /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/man/man1 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/man/man5 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/libdata/pkgconfig
>if test -n ""; then /bin/mkdir -p /wrkdirs/usr/ports/biology/htslib/work/stage; fi
>install  -s -m 444 libhts.so /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.so.1.3
>ln -sf libhts.so.1.3 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.so
>ln -sf libhts.so.1.3 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.so.1
>sed -e 's#@includedir@#/usr/local/include#g;s#@libdir@#/usr/local/lib#g;s#@PACKAGE_VERSION@#1.3#g' htslib.pc.in > /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/libdata/pkgconfig/htslib.pc
>chmod 644 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/libdata/pkgconfig/htslib.pc
>install  -s -m 555 bgzip htsfile tabix /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/bin
>if test -n ""; then install  -s -m 555  /wrkdirs/usr/ports/biology/htslib/work/stage; fi
>install  -m 0644 htslib/*.h /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/include/htslib
>install  -m 0644 libhts.a /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.a
>install  -m 0644 htsfile.1 tabix.1 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/man/man1
>install  -m 0644 faidx.5 sam.5 vcf.5 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/man/man5
>gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/htslib/work/htslib-1.3'
>====> 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 htslib-1.3
>===========================================================================
>=======================<phase: install-mtree  >============================
>===========================================================================
>====>> Recording filesystem state for preinst... done
>=======================<phase: install        >============================
>===>  Installing for htslib-1.3
>===>   htslib-1.3 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so)
>===>  Checking if htslib already installed
>===>   Registering installation for htslib-1.3
>[releng_10_1-default] Installing htslib-1.3...
>===========================================================================
>====>> Checking shared library dependencies
> 0x0000000000000001 (NEEDED)             Shared library: [libc.so.7]
> 0x0000000000000001 (NEEDED)             Shared library: [libcrypto.so.7]
> 0x0000000000000001 (NEEDED)             Shared library: [libcurl.so.4]
> 0x0000000000000001 (NEEDED)             Shared library: [libm.so.5]
> 0x0000000000000001 (NEEDED)             Shared library: [libthr.so.3]
> 0x0000000000000001 (NEEDED)             Shared library: [libz.so.6]
>=======================<phase: deinstall      >============================
>===>  Deinstalling for htslib
>===>   Deinstalling htslib-1.3
>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:
>	htslib-1.3
>
>The operation will free 3 MiB.
>[releng_10_1-default] [1/1] Deinstalling htslib-1.3...
>[releng_10_1-default] [1/1] Deleting files for htslib-1.3: .......... done
>===========================================================================
>====>> Checking for extra files and directories
>[00:00:25] ====>> Installing from package
>[releng_10_1-default] Installing htslib-1.3...
>[releng_10_1-default] Extracting htslib-1.3: .......... done
>[00:00:25] ====>> Cleaning up
>===>  Cleaning for htslib-1.3
>[00:00:25] ====>> 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:
>	htslib-1.3
>
>The operation will free 3 MiB.
>[releng_10_1-default] [1/1] Deinstalling htslib-1.3...
>[releng_10_1-default] [1/1] Deleting files for htslib-1.3: .......... done
>build of biology/htslib ended at Tue Dec 22 16:04:43 MST 2015
>build time: 00:00:20
>[00:00:25] ====>> Cleaning up
>[00:00:26] ====>> Umounting file systems

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Attachments on bug 205524: 164511 | 164512 | 164513