=> Building biology/mafft build started at Tue Oct 4 23:38:51 PDT 2016 port directory: /usr/ports/biology/mafft 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: cartwright@asu.edu ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../03//usr/ports/biology/mafft/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=mafft-7.266 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--- ===> The following configuration options are available for mafft-7.266: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/biology/mafft XDG_CONFIG_HOME=/wrkdirs/biology/mafft HOME=/wrkdirs/biology/mafft TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- INSTALL_LIB="install -s -m 444" INSTALL_DATA="install -m 0644" INSTALL_PROGRAM="install -s -m 555" INSTALL_SCRIPT="install -m 555" MKDIR="/bin/mkdir -p" LN="ln" XDG_DATA_HOME=/wrkdirs/biology/mafft XDG_CONFIG_HOME=/wrkdirs/biology/mafft HOME=/wrkdirs/biology/mafft 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 -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -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 PROFILE="@comment " DOCSDIR="share/doc/mafft" EXAMPLESDIR="share/examples/mafft" DATADIR="share/mafft" WWWDIR="www/mafft" ETCDIR="etc/mafft" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mafft DOCSDIR=/usr/local/share/doc/mafft EXAMPLESDIR=/usr/local/share/examples/mafft WWWDIR=/usr/local/www/mafft ETCDIR=/usr/local/etc/mafft --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 BSD2CLAUSE accepted by the user =========================================================================== =================================================== ===> mafft-7.266 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 ===> mafft-7.266 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mafft-7.266 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by mafft-7.266 for building =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by mafft-7.266 for building => SHA256 Checksum OK for mafft-7.266-without-extensions-src.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by mafft-7.266 for building ===> Extracting for mafft-7.266 => SHA256 Checksum OK for mafft-7.266-without-extensions-src.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for mafft-7.266 ===> Applying ports patches for mafft-7.266 =========================================================================== =================================================== ===> mafft-7.266 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... `-- Installing indexinfo-0.2.5... `-- Extracting indexinfo-0.2.5: .... done `-- Installing gettext-runtime-0.19.8.1... `-- Extracting gettext-runtime-0.19.8.1: .......... done Extracting gmake-4.2.1_1: .......... done ===> mafft-7.266 depends on executable: gmake - found ===> Returning to build of mafft-7.266 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for mafft-7.266 =========================================================================== =================================================== ===> Building for mafft-7.266 gmake[1]: Entering directory '/wrkdirs/biology/mafft/mafft-7.266-without-extensions/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c mtxutl.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c io.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c mltaln9.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c tddis.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c constants.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c nj.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c partSalignmm.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Lalignmm.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c rna.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Salignmm.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Dalignmm.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Falign.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Falign_localhom.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Galign11.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c MSalignmm.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c fftFunctions.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c fft.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c tditeration.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c dvtditr.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c defs.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c SAalignmm.c -o SAalignmm.o cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c treeOperation.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c addfunctions.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c dndfast7.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c dndblast.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c sextet5.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c mafft-distance.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c MSalign11.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c suboptalign11.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c genalign11.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Lalign11.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c pairlocalalign.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c pair2hat3s.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c multi2hat3s.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c pairash.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c addsingle.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c splittbfast.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c disttbfast.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c tbfast.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c mafft-profile.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c f2cl.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c mccaskillwrap.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c contrafoldwrap.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c countlen.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c seq2regtable.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c regtable2seq.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c score.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c getlag.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c dndpre.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c setcore.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c replaceu.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c restoreu.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c setdirection.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c makedirectionlist.c cc -o version version.c -Denablemultithread -pipe -O2 -fno-strict-aliasing sed "s:_LIBDIR:/usr/local/libexec/mafft:" mafft.tmpl > mafft sed "s:_BINDIR:/usr/local/bin:" mafft-homologs.tmpl > mafft-homologs.rb cc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genalign11.o Lalign11.o SAalignmm.o pairlocalalign.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o pair2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o pair2hat3s.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genalign11.o Lalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o Lalign11.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o addsingle.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread gmake[1]: Leaving directory '/wrkdirs/biology/mafft/mafft-7.266-without-extensions/core' =========================================================================== =================================================== =========================================================================== =================================================== ===> Staging for mafft-7.266 ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/biology/mafft/mafft-7.266-without-extensions/core' /bin/mkdir -p /wrkdirs/biology/mafft/stage/usr/local/libexec/mafft /wrkdirs/biology/mafft/stage/usr/local/bin /wrkdirs/biology/mafft/stage/usr/local/man/man1 install -m 555 mafft mafft-homologs.rb /wrkdirs/biology/mafft/stage/usr/local/bin install -s -m 555 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s pairash addsingle splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version /wrkdirs/biology/mafft/stage/usr/local/libexec/mafft install -m 555 mafftash_premafft.pl seekquencer_premafft.pl /wrkdirs/biology/mafft/stage/usr/local/libexec/mafft install -m 0644 mafft.1 mafft-homologs.1 /wrkdirs/biology/mafft/stage/usr/local/man/man1 ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/linsi; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/ginsi; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/fftns; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/fftnsi; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/nwns; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/nwnsi; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/einsi; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/mafft-linsi; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/mafft-ginsi; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/mafft-fftns; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/mafft-fftnsi; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/mafft-nwns; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/mafft-nwnsi; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/mafft-einsi; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/mafft-xinsi; ln -s mafft /wrkdirs/biology/mafft/stage/usr/local/bin/mafft-qinsi; ln -s ../libexec/mafft/mafft-profile /wrkdirs/biology/mafft/stage/usr/local/bin/mafft-profile ln -s ../libexec/mafft/mafft-distance /wrkdirs/biology/mafft/stage/usr/local/bin/mafft-distance gmake[1]: Leaving directory '/wrkdirs/biology/mafft/mafft-7.266-without-extensions/core' install -m 0644 /wrkdirs/biology/mafft/mafft-7.266-without-extensions/test/* /wrkdirs/biology/mafft/stage/usr/local/share/examples/mafft install -m 0644 /wrkdirs/biology/mafft/mafft-7.266-without-extensions/readme /wrkdirs/biology/mafft/stage/usr/local/share/doc/mafft ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for mafft-7.266 file sizes/checksums [70]: . done packing files [70]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for mafft-7.266 build of biology/mafft ended at Tue Oct 4 23:39:32 PDT 2016 build time: 00:00:41