Attachment 164573 Details for Bug 205558 – poudriere testport output for releng_9_3

poudriere testport output for releng_9_3

mafft_9.txt (text/plain), 27.29 KB, created by cartwright on 2015-12-23 23:50:50 UTC

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Creator: cartwright

Created: 2015-12-23 23:50:50 UTC

Size: 27.29 KB

patch

obsolete

>[00:00:00] ====>> Creating the reference jail... done
>[00:00:00] ====>> Mounting system devices for releng_9_3-default
>[00:00:00] ====>> Mounting ports/packages/distfiles
>[00:00:00] ====>> Stashing existing package repository
>[00:00:00] ====>> Mounting packages from: /usr/local/poudriere/data/packages/releng_9_3-default
>[00:00:00] ====>> Copying /var/db/ports from: /usr/local/etc/poudriere.d/options
>[00:00:00] ====>> Appending to make.conf: /usr/local/etc/poudriere.d/make.conf
>/etc/resolv.conf -> /usr/local/poudriere/data/.m/releng_9_3-default/ref/etc/resolv.conf
>[00:00:00] ====>> Starting jail releng_9_3-default
>[00:00:01] ====>> Logs: /usr/local/poudriere/data/logs/bulk/releng_9_3-default/2015-12-23_16h45m41s
>[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
>looks fine.
>[00:00:05] ====>> Building with flags: 
>[00:00:05] ====>> Removing existing /usr/local
>build started at Wed Dec 23 16:45:46 MST 2015
>port directory: /usr/ports/biology/mafft
>building for: FreeBSD releng_9_3-default 9.3-RELEASE FreeBSD 9.3-RELEASE amd64
>maintained by: cartwright@asu.edu
>Makefile ident:      $FreeBSD: head/biology/mafft/Makefile 390711 2015-06-27 14:30:19Z bapt $
>Poudriere version: 3.1.8
>Host OSVERSION: 1002000
>Jail OSVERSION: 903000
>
>---Begin Environment---
>PKGREPOSITORY=/tmp/pkgs
>PACKAGES=/tmp/pkgs
>OSVERSION=903000
>UNAME_v=FreeBSD 9.3-RELEASE
>UNAME_r=9.3-RELEASE
>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_9_3-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_9_3-default/ref/usr/ports/biology/mafft
>MASTERNAME=releng_9_3-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 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/usr/ports/biology/mafft/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mafft/work  HOME=/wrkdirs/usr/ports/biology/mafft/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh
>--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="/bin/ln" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mafft/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mafft/work  HOME=/wrkdirs/usr/ports/biology/mafft/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 -fstack-protector"  CPP="cpp" CPPFLAGS=""  LDFLAGS=" -fstack-protector" LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -O2 -fno-strict-aliasing -pipe -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--
>OSREL=9.3
>PREFIX=%D
>LOCALBASE=/usr/local
>RESETPREFIX=/usr/local
>PORTDOCS=""
>PORTEXAMPLES=""
>LIB32DIR=lib
>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
>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
>
>---End make.conf---
>=======================<phase: check-sanity   >============================
>===>  License BSD2CLAUSE accepted by the user
>===>  Found saved configuration for mafft-7.149_1
>===========================================================================
>=======================<phase: pkg-depends    >============================
>===>   mafft-7.266 depends on file: /usr/local/sbin/pkg - not found
>===>   Installing existing package /packages/All/pkg-1.6.2.txz
>[releng_9_3-default] Installing pkg-1.6.2...
>[releng_9_3-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
>===>   mafft-7.266 depends on file: /usr/local/sbin/pkg - found
>===>   Returning to build of mafft-7.266
>===========================================================================
>=======================<phase: fetch-depends  >============================
>===========================================================================
>=======================<phase: fetch          >============================
>===>  License BSD2CLAUSE accepted by the user
>===>  Found saved configuration for mafft-7.149_1
>===>   mafft-7.266 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by mafft-7.266 for building
>===========================================================================
>=======================<phase: checksum       >============================
>===>  License BSD2CLAUSE accepted by the user
>===>  Found saved configuration for mafft-7.149_1
>===>   mafft-7.266 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by mafft-7.266 for building
>=> SHA256 Checksum OK for mafft-7.266-without-extensions-src.tgz.
>===========================================================================
>=======================<phase: extract-depends>============================
>===========================================================================
>=======================<phase: extract        >============================
>===>  License BSD2CLAUSE accepted by the user
>===>  Found saved configuration for mafft-7.149_1
>===>   mafft-7.266 depends on file: /usr/local/sbin/pkg - found
>===> 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.
>===========================================================================
>=======================<phase: patch-depends  >============================
>===========================================================================
>=======================<phase: patch          >============================
>===>  Patching for mafft-7.266
>===>  Applying FreeBSD patches for mafft-7.266
>===========================================================================
>=======================<phase: build-depends  >============================
>===>   mafft-7.266 depends on executable: gmake - not found
>===>   Installing existing package /packages/All/gmake-4.1_2.txz
>[releng_9_3-default] Installing gmake-4.1_2...
>[releng_9_3-default] `-- Installing indexinfo-0.2.4...
>[releng_9_3-default] `-- Extracting indexinfo-0.2.4: .... done
>[releng_9_3-default] `-- Installing libiconv-1.14_9...
>[releng_9_3-default] `-- Extracting libiconv-1.14_9: .......... done
>[releng_9_3-default] `-- Installing gettext-runtime-0.19.6...
>[releng_9_3-default] `-- Extracting gettext-runtime-0.19.6: .......... done
>[releng_9_3-default] Extracting gmake-4.1_2: .......... done
>===>   mafft-7.266 depends on executable: gmake - found
>===>   Returning to build of mafft-7.266
>===========================================================================
>=======================<phase: lib-depends    >============================
>===========================================================================
>====>> Recording filesystem state for prebuild... done
>=======================<phase: configure      >============================
>===>   mafft-7.266 depends on executable: gmake - found
>===>  Configuring for mafft-7.266
>===========================================================================
>=======================<phase: build          >============================
>===>  Building for mafft-7.266
>cp mafftash_premafft.tmpl mafftash_premafft.pl
>cp seekquencer_premafft.tmpl seekquencer_premafft.pl
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c mtxutl.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c io.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c mltaln9.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c tddis.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c constants.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c nj.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c partSalignmm.c  
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c Lalignmm.c 
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c rna.c 
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c Salignmm.c 
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c Dalignmm.c 
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c Falign.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c Falign_localhom.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c Galign11.c 
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c MSalignmm.c 
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c fftFunctions.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c fft.c 
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c tditeration.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c dvtditr.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c defs.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c SAalignmm.c -o SAalignmm.o
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c treeOperation.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c addfunctions.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c dndfast7.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c dndblast.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c sextet5.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c mafft-distance.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c MSalign11.c 
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c suboptalign11.c 
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c genalign11.c 
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c Lalign11.c 
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c pairlocalalign.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c pair2hat3s.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c multi2hat3s.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c pairash.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c addsingle.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c splittbfast.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c disttbfast.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c tbfast.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c mafft-profile.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c f2cl.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c mccaskillwrap.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c contrafoldwrap.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c countlen.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c seq2regtable.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c regtable2seq.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c score.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c getlag.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c dndpre.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c setcore.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c replaceu.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c restoreu.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c setdirection.c
>cc -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -c makedirectionlist.c
>cc -o version version.c -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector
>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 -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -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 -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o pair2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o pair2hat3s.o defs.o fft.o fftFunctions.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -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 -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -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 -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -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 -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -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 -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -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 -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>cc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -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 -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -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 -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -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 -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -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 -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -pthread
>===========================================================================
>====>> Checking for filesystem violations... done
>=======================<phase: run-depends    >============================
>===========================================================================
>====>> Recording filesystem state for prestage... done
>=======================<phase: stage          >============================
>===>  Staging for mafft-7.266
>===>   Generating temporary packing list
>/bin/mkdir -p /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/man/man1
>install  -m 555 mafft mafft-homologs.rb  /wrkdirs/usr/ports/biology/mafft/work/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/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -m 555 mafftash_premafft.pl seekquencer_premafft.pl /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -m 0644 mafft.1 mafft-homologs.1 /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/man/man1
>/bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/linsi; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/ginsi; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/fftns; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/fftnsi; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/nwns; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/nwnsi; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/einsi; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-linsi; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-ginsi; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-fftns; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-fftnsi; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-nwns; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-nwnsi; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-einsi; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-xinsi; /bin/ln -s mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-qinsi;
>/bin/ln -s ../libexec/mafft/mafft-profile /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-profile
>/bin/ln -s ../libexec/mafft/mafft-distance /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-distance
>install  -m 0644 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.266-without-extensions/test/* /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/share/examples/mafft
>install  -m 0644 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.266-without-extensions/readme /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/share/doc/mafft
>====> 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 mafft-7.266
>===========================================================================
>=======================<phase: install-mtree  >============================
>===========================================================================
>====>> Recording filesystem state for preinst... done
>=======================<phase: install        >============================
>===>  Installing for mafft-7.266
>===>  Checking if mafft already installed
>===>   Registering installation for mafft-7.266
>[releng_9_3-default] Installing mafft-7.266...
>===========================================================================
>====>> Checking shared library dependencies
> 0x0000000000000001 (NEEDED)             Shared library: [libc.so.7]
> 0x0000000000000001 (NEEDED)             Shared library: [libm.so.5]
> 0x0000000000000001 (NEEDED)             Shared library: [libthr.so.3]
>=======================<phase: deinstall      >============================
>===>  Deinstalling for mafft
>===>   Deinstalling mafft-7.266
>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:
>	mafft-7.266
>
>The operation will free 8 MiB.
>[releng_9_3-default] [1/1] Deinstalling mafft-7.266...
>[releng_9_3-default] [1/1] Deleting files for mafft-7.266: .......... done
>===========================================================================
>====>> Checking for extra files and directories
>[00:00:20] ====>> Installing from package
>[releng_9_3-default] Installing mafft-7.266...
>[releng_9_3-default] Extracting mafft-7.266: .......... done
>[00:00:20] ====>> Cleaning up
>===>  Cleaning for mafft-7.266
>[00:00:21] ====>> 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:
>	mafft-7.266
>
>The operation will free 8 MiB.
>[releng_9_3-default] [1/1] Deinstalling mafft-7.266...
>[releng_9_3-default] [1/1] Deleting files for mafft-7.266: .......... done
>build of biology/mafft ended at Wed Dec 23 16:46:02 MST 2015
>build time: 00:00:16
>[00:00:21] ====>> Cleaning up
>[00:00:21] ====>> Umounting file systems

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Attachments on bug 205558: 164571 | 164572 | 164573