=> Building biology/bwa build started at Tue Oct 4 23:50:48 PDT 2016 port directory: /usr/ports/biology/bwa building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: bacon4000@gmail.com ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../10//usr/ports/biology/bwa/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=bwa-0.7.9a OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/biology/bwa XDG_CONFIG_HOME=/wrkdirs/biology/bwa HOME=/wrkdirs/biology/bwa TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/bwa XDG_CONFIG_HOME=/wrkdirs/biology/bwa HOME=/wrkdirs/biology/bwa TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -msse2 -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -msse2 -O2 -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-- OSREL=4.7 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 PROFILE="@comment " DOCSDIR="share/doc/bwa" EXAMPLESDIR="share/examples/bwa" DATADIR="share/bwa" WWWDIR="www/bwa" ETCDIR="etc/bwa" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bwa DOCSDIR=/usr/local/share/doc/bwa EXAMPLESDIR=/usr/local/share/examples/bwa WWWDIR=/usr/local/www/bwa ETCDIR=/usr/local/etc/bwa --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> bwa-0.7.9a depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> bwa-0.7.9a depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bwa-0.7.9a =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.9a for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.9a for building => SHA256 Checksum OK for bwa-0.7.9a.tar.bz2. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.9a for building ===> Extracting for bwa-0.7.9a => SHA256 Checksum OK for bwa-0.7.9a.tar.bz2. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bwa-0.7.9a ===> Applying ports patches for bwa-0.7.9a =========================================================================== =================================================== =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for bwa-0.7.9a =========================================================================== =================================================== ===> Building for bwa-0.7.9a --- utils.o --- --- kthread.o --- --- kstring.o --- --- ksw.o --- --- bwt.o --- --- utils.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o --- kthread.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o --- kstring.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o --- ksw.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o --- bwt.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o --- bntseq.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o --- bwa.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o --- bwamem.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o --- bwamem_pair.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o --- bwamem_extra.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o --- malloc_wrap.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o --- QSufSort.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o --- bwt_gen.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o --- bwase.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o --- bwaseqio.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o --- bwtgap.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o --- bwtaln.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o --- bamlite.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o --- is.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o --- bwtindex.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o --- bwape.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o --- kopen.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o --- pemerge.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o --- bwtsw2_core.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o --- bwtsw2_main.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o --- bwtsw2_aux.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o --- bwt_lite.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o --- bwtsw2_chain.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o --- fastmap.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o --- bwtsw2_pair.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o --- main.o --- cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o --- libbwa.a --- ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o --- bwa --- cc -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread =========================================================================== =================================================== ===> bwa-0.7.9a depends on package: perl5>=5.20<5.21 - not found ===> Installing existing package /packages/All/perl5-5.20.3_15.txz Installing perl5-5.20.3_15... Extracting perl5-5.20.3_15: .......... done Message from perl5-5.20.3_15: 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. ===> bwa-0.7.9a depends on package: perl5>=5.20<5.21 - found ===> Returning to build of bwa-0.7.9a =========================================================================== =================================================== ===> Staging for bwa-0.7.9a ===> Generating temporary packing list install -s -m 555 /wrkdirs/biology/bwa/bwa-0.7.9a/bwa /wrkdirs/biology/bwa/stage/usr/local/bin install -m 555 /wrkdirs/biology/bwa/bwa-0.7.9a/*.pl /wrkdirs/biology/bwa/stage/usr/local/bin install -m 444 /wrkdirs/biology/bwa/bwa-0.7.9a/*.1 /wrkdirs/biology/bwa/stage/usr/local/man/man1 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for bwa-0.7.9a file sizes/checksums [7]: . done packing files [7]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for bwa-0.7.9a build of biology/bwa ended at Tue Oct 4 23:51:07 PDT 2016 build time: 00:00:19