Attachment 157382 Details for Bug 200603 – Poudriere Log for 9.3

Poudriere Log for 9.3

releng_9_3.txt (text/plain), 33.50 KB, created by cartwright on 2015-06-02 20:05:50 UTC

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Creator: cartwright

Created: 2015-06-02 20:05:50 UTC

Size: 33.50 KB

patch

obsolete

>[00:00:00] ====>> Creating the reference jail... done
>[00:00:01] ====>> Mounting system devices for releng_9_3-default
>[00:00:01] ====>> Mounting ports/packages/distfiles
>[00:00:01] ====>> Stashing existing package repository
>[00:00:01] ====>> Mounting packages from: /usr/local/poudriere/data/packages/releng_9_3-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
>/etc/resolv.conf -> /usr/local/poudriere/data/.m/releng_9_3-default/ref/etc/resolv.conf
>[00:00:01] ====>> Starting jail releng_9_3-default
>[00:00:01] ====>> Logs: /usr/local/poudriere/data/logs/bulk/releng_9_3-default/2015-06-02_12h52m18s
>[00:00:01] ====>> Loading MOVED
>[00:00:02] ====>> Calculating ports order and dependencies
>[00:00:03] ====>> Sanity checking the repository
>[00:00:03] ====>> Checking packages for incremental rebuild needed
>[00:00:03] ====>> Deleting gmake-4.1_1.txz: new version: 4.1_2
>[00:00:03] ====>> Deleting pkg-1.5.1.txz: new version: 1.5.3
>[00:00:03] ====>> Deleting stale symlinks
>[00:00:03] ====>> Deleting empty directories
>[00:00:03] ====>> Cleaning the build queue
>[00:00:04] ====>> Recording filesystem state for prepkg... done
>[00:00:04] ====>> Building 2 packages using 2 builders
>[00:00:04] ====>> Starting/Cloning builders
>[00:00:06] ====>> Hit CTRL+t at any time to see build progress and stats
>[00:00:06] ====>> [01][00:00:00] Starting build of ports-mgmt/pkg
>[00:01:07] ====>> [01][00:01:01] Finished build of ports-mgmt/pkg: Success
>[00:01:08] ====>> [01][00:00:00] Starting build of devel/gmake
>[00:01:27] ====>> [01][00:00:19] Finished build of devel/gmake: Success
>[00:01:28] ====>> Stopping 2 builders
>[00:01:37] ====>> Creating pkgng repository
>Creating repository in /tmp/packages... done
>Packing files for repository... done
>[00:01:38] ====>> Committing packages to repository
>[00:01:38] ====>> Removing old packages
>[00:01:38] ====>> Portlint check
>WARN: Makefile: [45]: use ${VARIABLE}, instead of $(VARIABLE).
>0 fatal errors and 1 warning found.
>[00:01:38] ====>> Building with flags: 
>[00:01:38] ====>> Removing existing /usr/local
>build started at Tue Jun  2 12:53:56 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 382111 2015-03-24 16:01:21Z marino $
>Poudriere version: 3.1.6
>Host OSVERSION: 1001000
>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=/usr/local/poudriere/data/.m/releng_9_3-default/ref/.p/pool
>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=3.1.6
>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-7.221:
>     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--
>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 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-7.221 depends on file: /usr/local/sbin/pkg - not found
>===>    Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg
>===>   Installing existing package /packages/All/pkg-1.5.3.txz
>[releng_9_3-default] Installing pkg-1.5.3...
>[releng_9_3-default] Extracting pkg-1.5.3... done
>Message for pkg-1.5.3:
>If you are upgrading from the old package format, first run:
>
>  # pkg2ng
>===>   Returning to build of mafft-7.221
>===========================================================================
>=======================<phase: fetch-depends  >============================
>===========================================================================
>=======================<phase: fetch          >============================
>===>  License BSD2CLAUSE accepted by the user
>===>  Found saved configuration for mafft-7.149_1
>===>   mafft-7.221 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by mafft-7.221 for building
>===========================================================================
>=======================<phase: checksum       >============================
>===>  License BSD2CLAUSE accepted by the user
>===>  Found saved configuration for mafft-7.149_1
>===>   mafft-7.221 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by mafft-7.221 for building
>=> SHA256 Checksum OK for mafft-7.221-without-extensions-src.tgz.
>===========================================================================
>=======================<phase: extract-depends>============================
>===========================================================================
>=======================<phase: extract        >============================
>===>  License BSD2CLAUSE accepted by the user
>===>  Found saved configuration for mafft-7.149_1
>===>   mafft-7.221 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by mafft-7.221 for building
>===>  Extracting for mafft-7.221
>=> SHA256 Checksum OK for mafft-7.221-without-extensions-src.tgz.
>===========================================================================
>=======================<phase: patch-depends  >============================
>===========================================================================
>=======================<phase: patch          >============================
>===>  Patching for mafft-7.221
>===========================================================================
>=======================<phase: build-depends  >============================
>===>   mafft-7.221 depends on executable: gmake - not found
>===>    Verifying install for gmake in /usr/ports/devel/gmake
>===>   Installing existing package /packages/All/gmake-4.1_2.txz
>[releng_9_3-default] Installing gmake-4.1_2...
>[releng_9_3-default] `-- Installing gettext-runtime-0.19.4...
>[releng_9_3-default] |   `-- Installing indexinfo-0.2.3...
>[releng_9_3-default] |   `-- Extracting indexinfo-0.2.3... done
>[releng_9_3-default] |   `-- Installing libiconv-1.14_8...
>[releng_9_3-default] |   `-- Extracting libiconv-1.14_8... done
>[releng_9_3-default] `-- Extracting gettext-runtime-0.19.4... done
>[releng_9_3-default] Extracting gmake-4.1_2... done
>===>   Returning to build of mafft-7.221
>===========================================================================
>=======================<phase: lib-depends    >============================
>===========================================================================
>====>> Recording filesystem state for prebuild... done
>=======================<phase: configure      >============================
>===>   mafft-7.221 depends on executable: gmake - found
>===>  Configuring for mafft-7.221
>===========================================================================
>=======================<phase: build          >============================
>===>  Building for mafft-7.221
>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 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 f2cl mtxutl.o io.o f2cl.o constants.o defs.o  -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -lpthread
>cc -o countlen mtxutl.o io.o countlen.o defs.o  -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -lpthread
>cc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o  -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -lpthread
>cc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.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  -lpthread
>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  -lpthread
>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  -lpthread
>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  -lpthread
>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  -lpthread
>cc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.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  -lpthread
>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  -lpthread
>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  -lpthread
>cc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.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  -lpthread
>cc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.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  -lpthread
>cc -o splittbfast 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 Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o  -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -lpthread
>cc -o disttbfast 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 disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o  -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -lpthread
>cc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.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  -lpthread
>cc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.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  -lpthread
>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  -lpthread
>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  -lpthread
>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  -lpthread
>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  -lpthread
>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 getlag.o defs.o fft.o fftFunctions.o  -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -lpthread
>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  -lpthread
>cc -o setcore 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 setcore.o defs.o fft.o fftFunctions.o  -Denablemultithread -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector  -fstack-protector -lm  -lpthread
>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  -lpthread
>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  -lpthread
>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  -lpthread
>cc -o makedirectionlist 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 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  -lpthread
>cp mafft mafft-homologs.rb ../scripts
>chmod 755 ../scripts/*
>cp mafftash_premafft.pl seekquencer_premafft.pl 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 ../binaries
>chmod 755 ../binaries/*
>cp mafft.1 mafft-homologs.1 ../binaries
>done.
>===========================================================================
>====>> Checking for filesystem violations... done
>=======================<phase: run-depends    >============================
>===========================================================================
>====>> Recording filesystem state for prestage... done
>=======================<phase: stage          >============================
>===>  Staging for mafft-7.221
>===>   Generating temporary packing list
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/dvtditr /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/dndfast7 /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/dndblast /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/sextet5 /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/mafft-distance /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/pairlocalalign /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/pair2hat3s /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/multi2hat3s /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/pairash /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/addsingle /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/splittbfast /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/disttbfast /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/tbfast /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/mafft-profile /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/f2cl /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/mccaskillwrap /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/contrafoldwrap /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/countlen /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/seq2regtable /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/regtable2seq /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/score /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/getlag /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/dndpre /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/setcore /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/replaceu /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/restoreu /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/setdirection /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/makedirectionlist /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -s -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/version /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/mafftash_premafft.pl /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/seekquencer_premafft.pl /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/libexec/mafft
>install  -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/scripts/mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin
>install  -m 555 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/scripts/mafft-homologs.rb /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/einsi
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/fftns
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/fftnsi
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/ginsi
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/linsi
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-einsi
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-fftns
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-fftnsi
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-ginsi
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-linsi
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-nwns
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-nwnsi
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-qinsi
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-xinsi
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/nwns
>/bin/ln -sf mafft /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/nwnsi
>/bin/ln -sf ../libexec/mafft/mafft-distance /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-distance
>/bin/ln -sf ../libexec/mafft/mafft-profile /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/bin/mafft-profile
>install  -m 444 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/mafft.1 /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/man/man1
>install  -m 444 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/binaries/mafft-homologs.1 /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/man/man1
>install  -m 0644 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-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-7.221-without-extensions/readme /wrkdirs/usr/ports/biology/mafft/work/stage/usr/local/share/doc/mafft
>install  -m 0644 /wrkdirs/usr/ports/biology/mafft/work/mafft-7.221-without-extensions/license /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-7.221
>===========================================================================
>=======================<phase: install-mtree  >============================
>===========================================================================
>====>> Recording filesystem state for preinst... done
>=======================<phase: install        >============================
>===>  Installing for mafft-7.221
>===>  Checking if mafft already installed
>===>   Registering installation for mafft-7.221
>[releng_9_3-default] Installing mafft-7.221...
>===========================================================================
>====>> 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-7.221
>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-7.221
>
>The operation will free 7 MiB.
>[releng_9_3-default] [1/1] Deinstalling mafft-7.221...
>[releng_9_3-default] [1/1] Deleting files for mafft-7.221... done
>===========================================================================
>====>> Checking for extra files and directories
>[00:01:58] ====>> Installing from package
>[releng_9_3-default] Installing mafft-7.221...
>[releng_9_3-default] Extracting mafft-7.221... done
>[00:01:58] ====>> Cleaning up
>===>  Cleaning for mafft-7.221
>[00:01:58] ====>> 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-7.221
>
>The operation will free 7 MiB.
>[releng_9_3-default] [1/1] Deinstalling mafft-7.221...
>[releng_9_3-default] [1/1] Deleting files for mafft-7.221... done
>build of biology/mafft ended at Tue Jun  2 12:54:16 MST 2015
>build time: 00:00:20
>[00:01:58] ====>> Cleaning up
>[00:01:58] ====>> Umounting file systems

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Attachments on bug 200603: 157380 | 157381 | 157382