=> Building biology/bwa Started : Sunday, 7 JUL 2019 at 16:36:13 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/bwa XDG_CONFIG_HOME=/construction/biology/bwa HOME=/construction/biology/bwa TMPDIR="/tmp" PATH=/construction/biology/bwa/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/bwa XDG_CONFIG_HOME=/construction/biology/bwa HOME=/construction/biology/bwa TMPDIR="/tmp" PATH=/construction/biology/bwa/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local 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 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/bwa/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 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/5.28 PROFILE="@comment " DOCSDIR="share/doc/bwa" EXAMPLESDIR="share/examples/bwa" DATADIR="share/bwa" WWWDIR="www/bwa" ETCDIR="etc/bwa" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bwa-0.7.17 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.17 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.17 for building => SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.17 for building ===> Extracting for bwa-0.7.17 => SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for bwa-0.7.17 ===> Applying ports patches for bwa-0.7.17 ===> Applying dragonfly patches for bwa-0.7.17 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> bwa-0.7.17 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.20.1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> bwa-0.7.17 depends on executable: gmake - found ===> Returning to build of bwa-0.7.17 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for bwa-0.7.17 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for bwa-0.7.17 gmake[1]: Entering directory '/construction/biology/bwa/bwa-0.7.17' cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o 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 QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') cc -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.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 gmake[1]: Leaving directory '/construction/biology/bwa/bwa-0.7.17' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> bwa-0.7.17 depends on package: perl5>=5.28.r1<5.29 - not found ===> Installing existing package /packages/All/perl5-5.28.2.txz Installing perl5-5.28.2... Extracting perl5-5.28.2: .......... done Message from perl5-5.28.2: 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-0.7.17 depends on package: perl5>=5.28.r1<5.29 - found ===> Returning to build of bwa-0.7.17 -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for bwa-0.7.17 ===> Generating temporary packing list install -s -m 555 /construction/biology/bwa/bwa-0.7.17/bwa /construction/biology/bwa/stage/usr/local/bin install -m 555 /construction/biology/bwa/bwa-0.7.17/*.pl /construction/biology/bwa/stage/usr/local/bin install -m 444 /construction/biology/bwa/bwa-0.7.17/*.1 /construction/biology/bwa/stage/usr/local/man/man1 ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for bwa-0.7.17 file sizes/checksums [7]: . done packing files [7]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 16:36:36 UTC Duration: 00:00:22