=> Building biology/migrate Started : Thursday, 30 AUG 2018 at 13:03:50 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-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 -------------------------------------------------- ===> The following configuration options are available for migrate-3.6.11: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples THREAD=off: Build with THREAD support ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- ac_cv_prog_GMAKE="/usr/bin/make" XDG_DATA_HOME=/construction/biology/migrate XDG_CONFIG_HOME=/construction/biology/migrate HOME=/construction/biology/migrate TMPDIR="/tmp" PATH=/construction/biology/migrate/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/migrate XDG_CONFIG_HOME=/construction/biology/migrate HOME=/construction/biology/migrate TMPDIR="/tmp" PATH=/construction/biology/migrate/.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=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local 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 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- PRETTYCFLAGS="-pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++" DESTDIR=/construction/biology/migrate/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/migrate" EXAMPLESDIR="share/examples/migrate" DATADIR="share/migrate" WWWDIR="www/migrate" ETCDIR="etc/migrate" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/migrate DOCSDIR=/usr/local/share/doc/migrate EXAMPLESDIR=/usr/local/share/examples/migrate WWWDIR=/usr/local/www/migrate ETCDIR=/usr/local/etc/migrate -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem 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=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> NOTICE: The migrate port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> migrate-3.6.11 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> migrate-3.6.11 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of migrate-3.6.11 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: The migrate port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by migrate-3.6.11 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: The migrate port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by migrate-3.6.11 for building => SHA256 Checksum OK for migrate-3.6.11.src.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: The migrate port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by migrate-3.6.11 for building ===> Extracting for migrate-3.6.11 => SHA256 Checksum OK for migrate-3.6.11.src.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for migrate-3.6.11 ===> Applying ports patches for migrate-3.6.11 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for migrate-3.6.11 configure: loading site script /xports/Templates/config.site checking build system type... x86_64-portbld-dragonfly5.3 checking host system type... x86_64-portbld-dragonfly5.3 checking target system type... x86_64-portbld-dragonfly5.3 ./configure: USERFLAGS+=-pipe: not found checking for gmake... (cached) /usr/bin/make ======================================================================= Migrate subversion: Hardware: portbld System OS: dragonfly5.3 DragonFly System CPU: x86_64 ----------------------------------------------------------------------- checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes ./configure: CFLAGS+=: not found C-compiler: cc C++-compiler:c++ CFLAGS: -pipe -O2 -fno-strict-aliasing ======================================================================= checking for a BSD-compatible install... /usr/bin/install -c checking for pthread_create in -lpthread... yes checking for MPI_Init in -lmpi... no checking for exp in -lm... yes checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for limits.h... (cached) yes checking for strings.h... (cached) yes checking for pthread.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking for int... (cached) yes checking whether struct tm is in sys/time.h or time.h... time.h checking for inline... inline checking return type of signal handlers... void checking for strftime... (cached) yes checking for strcspn... (cached) yes checking for strsep... (cached) yes checking for lgamma... yes checking which zlib implementation to use... autodetect checking for main in -lz... yes checking for gzbuffer... no configure: creating ./config.status config.status: creating Makefile config.status: creating conf.h config.status: conf.h is unchanged MIGRATE-N is now setup to compile the program you need to type one of the commands below (ordered by preference): SINGLE CPU machines make # with PDF output support # this might fail on first attempt, # if the make fails, please let me know # often linking fails because the C++ pdf library # and the core migrate parts (C) mismatch # check the Makefile line for STDLIB= -lstdc++ SMP machines more than 1 CPU in machine make thread # uses the thread library if present make # on macs running macos 10.6+ using GrandCentral PARALLEL Computers, Clusters with MPI software make mpis # each cpu-core can be treated as a node make mpis-thread # experimental, may increase load per node! ------------------------------------------------------------------------ SPEED and other TESTING the migrate website contains a testsuite.tar.gz that has many tests for single, parallel and thread compilations the tests are driven by a python script rt (see the README in the testsuite) and a submit script that allows to streamline submissions to a batch queue system, currently supported systems are SUN/ORACLE GRIDENGINE, TORQUE/MOAB, and NONE ------------------------------------------------------------------------ In case there are problems with the compile send a message to the migrate-support@google.com usergroup, include a log of ./configure make ======================================================================= -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for migrate-3.6.11 --- haru --- --- zlibsystem --- Using system zlib architecture --- haru --- (cd ./haru ; /usr/bin/make -f makefile.gcc "CC=c++" "CPP=cc" "ARCH=x86_64" "MACOSVERSION=" "MYCPPFLAGS=-pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ ") --- PdfExceptions.o --- --- PdfList.o --- --- PdfUtils.o --- --- PdfStreams.o --- --- PdfAutoPtrObjects.o --- --- PdfObjects.o --- --- PdfContents.o --- --- PdfPages.o --- --- PdfFonts.o --- --- PdfXref.o --- --- PdfDestinations.o --- --- PdfOutlines.o --- --- PdfExceptions.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfExceptions.cc --- PdfList.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfList.cc --- PdfUtils.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfUtils.cc --- PdfStreams.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfStreams.cc --- PdfAutoPtrObjects.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfAutoPtrObjects.cc --- PdfObjects.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfObjects.cc --- PdfContents.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfContents.cc --- PdfPages.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfPages.cc --- PdfFonts.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfFonts.cc --- PdfXref.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfXref.cc --- PdfDestinations.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfDestinations.cc --- PdfOutlines.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfOutlines.cc --- PdfBorderStyle.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfBorderStyle.cc --- PdfAnnotations.o --- --- PdfDoc.o --- --- PdfCatalog.o --- --- PdfAnnotations.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfAnnotations.cc --- PdfDoc.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfDoc.cc --- PdfCatalog.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfCatalog.cc --- PdfInfo.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfInfo.cc --- PdfEncoding.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfEncoding.cc --- PdfFontDef.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfFontDef.cc --- PdfXObjects.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfXObjects.cc --- PdfFontDef_Courier.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfFontDef_Courier.cc --- PdfFontDef_Helvetica.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfFontDef_Helvetica.cc --- PdfFontDef_Times.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfFontDef_Times.cc --- PdfFontDef_Symbol.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfFontDef_Symbol.cc --- PdfFontDef_ZapfDingbats.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfFontDef_ZapfDingbats.cc --- PdfEncoding_ISO8859.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfEncoding_ISO8859.cc --- PdfEncoding_KOI8.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfEncoding_KOI8.cc --- PdfEncoding_MSCP.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfEncoding_MSCP.cc --- PdfMbFonts.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfMbFonts.cc --- PdfCMap.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfCMap.cc --- PdfUnicodeText.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfUnicodeText.cc --- PdfMbFontDef_Gothic.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfMbFontDef_Gothic.cc --- PdfMbFontDef_Mincyo.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfMbFontDef_Mincyo.cc --- PdfMbFontDef_SimHei.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfMbFontDef_SimHei.cc --- PdfMbFontDef_SimSun.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfMbFontDef_SimSun.cc --- PdfMbFontDef_Ming.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfMbFontDef_Ming.cc --- PdfMbFontDef_Batang.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfMbFontDef_Batang.cc --- PdfMbFontDef_Dotum.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfMbFontDef_Dotum.cc --- PdfCMap_RKSJ.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfCMap_RKSJ.cc --- PdfCMap_EUC.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfCMap_EUC.cc --- PdfCMap_GB_EUC.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfCMap_GB_EUC.cc --- PdfCMap_ETen_B5.o --- --- PdfCMap_KSCms_UHC.o --- --- PdfCMap_ETen_B5.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfCMap_ETen_B5.cc --- PdfCMap_KSCms_UHC.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfCMap_KSCms_UHC.cc --- PdfCMap_KSC_EUC.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfCMap_KSC_EUC.cc --- PdfPngImage.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfPngImage.cc --- PdfJpegImage.o --- --- PdfEncrypt.o --- --- PdfJpegImage.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfJpegImage.cc --- PdfEncrypt.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c PdfEncrypt.cc --- libharuc.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c libharuc.cc --- libharuc_jpfonts.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c libharuc_jpfonts.cc --- libharuc_krfonts.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c libharuc_krfonts.cc --- libharuc_cnsfonts.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c libharuc_cnsfonts.cc --- libharuc_cntfonts.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c libharuc_cntfonts.cc --- libharu_png.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c libharu_png.cc --- libharu_jpeg.o --- cc -I. -DNDEBUG -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c libharu_jpeg.cc --- libharu.a --- ar rc libharu.a PdfExceptions.o PdfList.o PdfUtils.o PdfStreams.o PdfAutoPtrObjects.o PdfObjects.o PdfContents.o PdfPages.o PdfFonts.o PdfXref.o PdfDestinations.o PdfOutlines.o PdfBorderStyle.o PdfAnnotations.o PdfDoc.o PdfCatalog.o PdfInfo.o PdfEncoding.o PdfFontDef.o PdfXObjects.o PdfFontDef_Courier.o PdfFontDef_Helvetica.o PdfFontDef_Times.o PdfFontDef_Symbol.o PdfFontDef_ZapfDingbats.o PdfEncoding_ISO8859.o PdfEncoding_KOI8.o PdfEncoding_MSCP.o PdfMbFonts.o PdfCMap.o PdfUnicodeText.o PdfMbFontDef_Gothic.o PdfMbFontDef_Mincyo.o PdfMbFontDef_SimHei.o PdfMbFontDef_SimSun.o PdfMbFontDef_Ming.o PdfMbFontDef_Batang.o PdfMbFontDef_Dotum.o PdfCMap_RKSJ.o PdfCMap_EUC.o PdfCMap_GB_EUC.o PdfCMap_ETen_B5.o PdfCMap_KSCms_UHC.o PdfCMap_KSC_EUC.o PdfPngImage.o PdfJpegImage.o PdfEncrypt.o libharuc.o libharuc_jpfonts.o libharuc_krfonts.o libharuc_cnsfonts.o libharuc_cntfonts.o libharu_png.o libharu_jpeg.o ranlib libharu.a --- all --- /usr/bin/make migrate-n "CFLAGS = -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION=\"\\\"June-18-15\\\"\" -DMIGRATEVERSION=\"\\\"3.6.11\\\"\" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++" "LIBS = -Lharu -lharu -lz -lm" "LDFLAGS = " --- aic.o --- --- altivec.o --- --- autotune.o --- --- bayes.o --- --- broyden.o --- --- calculator.o --- --- combroyden2.o --- --- data.o --- --- correlation.o --- --- gammalike.o --- --- fst.o --- --- heating.o --- --- aic.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c aic.c --- altivec.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c altivec.c --- autotune.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c autotune.c --- bayes.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c bayes.c --- broyden.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c broyden.c --- calculator.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c calculator.c --- combroyden2.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c combroyden2.c --- data.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c data.c --- correlation.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c correlation.c --- gammalike.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c gammalike.c --- fst.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c fst.c --- heating.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c heating.c --- histogram.o --- --- inthp.o --- --- histogram.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c histogram.c --- inthp.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c inthp.c --- joint-chains.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c joint-chains.c --- laguerre.o --- --- lrt.o --- --- laguerre.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c laguerre.c --- lrt.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c lrt.c --- main.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c main.c --- migrate_mpi.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c migrate_mpi.c --- mutationmodel.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c mutationmodel.c --- mcmc1.o --- --- mcmc2.o --- --- mcmc1.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c mcmc1.c --- mcmc2.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c mcmc2.c --- menu.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c menu.c --- migevents.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c migevents.c --- options.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c options.c --- priors.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c priors.c --- profile.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c profile.c --- random.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c random.c --- reporter.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c reporter.c --- spline.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c spline.c --- tools.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c tools.c --- tree.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c tree.c --- sequence.o --- --- sighandler.o --- --- sequence.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c sequence.c --- sighandler.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c sighandler.c --- slice.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c slice.c --- sort.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c sort.c --- uep.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c uep.c --- world.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c world.c --- pretty.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c pretty.c --- skyline.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c skyline.c --- watterson.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c watterson.c --- znzlib.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c znzlib.c --- pretty-win32.o --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -c pretty-win32.cpp --- migrate-n --- cc -pipe -O2 -fno-strict-aliasing -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937 -DMIGRATESUBVERSION="\"June-18-15\"" -DMIGRATEVERSION="\"3.6.11\"" -pipe -O2 -fno-strict-aliasing -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++ -o migrate-n aic.o altivec.o autotune.o bayes.o broyden.o calculator.o combroyden2.o data.o correlation.o gammalike.o fst.o heating.o histogram.o inthp.o joint-chains.o laguerre.o lrt.o main.o migrate_mpi.o mutationmodel.o mcmc1.o mcmc2.o menu.o migevents.o options.o priors.o profile.o random.o reporter.o spline.o tools.o tree.o sequence.o sighandler.o slice.o sort.o uep.o world.o pretty.o skyline.o watterson.o znzlib.o pretty-win32.o -Lharu -lharu -lz -lm ; -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for migrate-3.6.11 ===> Generating temporary packing list install -s -m 555 /construction/biology/migrate/migrate-3.6.11/src/migrate-n /construction/biology/migrate/stage/usr/local/bin ln -sf migrate-n /construction/biology/migrate/stage/usr/local/bin/migrate install -m 444 /construction/biology/migrate/migrate-3.6.11/src/migrate.1 /construction/biology/migrate/stage/usr/local/man/man1 ln -sf migrate.1 /construction/biology/migrate/stage/usr/local/man/man1/migrate-n.1 install -m 0644 /construction/biology/migrate/migrate-3.6.11/src/../HISTORY /construction/biology/migrate/migrate-3.6.11/src/../README /construction/biology/migrate/migrate-3.6.11/src/../README_PARALLEL_GENERAL /construction/biology/migrate/migrate-3.6.11/src/../migrate.html /construction/biology/migrate/stage/usr/local/share/doc/migrate install -m 0644 /construction/biology/migrate/migrate-3.6.11/src/../graphics/* /construction/biology/migrate/stage/usr/local/share/doc/migrate/graphics install -m 0644 /construction/biology/migrate/migrate-3.6.11/src/../example/[A-Za-z]* /construction/biology/migrate/stage/usr/local/share/examples/migrate ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for migrate-3.6.11 file sizes/checksums [39]: . done packing files [39]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:05:48 UTC Duration: 00:01:58