=> Building biology/phyml build started at Wed Oct 5 12:44:05 PDT 2016 port directory: /usr/ports/biology/phyml building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: ports@FreeBSD.org ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../08//usr/ports/biology/phyml/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=phyml-3.2.0,1 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for phyml-3.2.0,1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ====> MPI (Message Passing Interface) support: you can only select none or one of them MPICH2=off: Parallel processing support via MPICH2 OPENMPI=off: Parallel processing support via Open MPI ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --disable-beagle --disable-mpi --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/biology/phyml XDG_CONFIG_HOME=/wrkdirs/biology/phyml HOME=/wrkdirs/biology/phyml TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/phyml XDG_CONFIG_HOME=/wrkdirs/biology/phyml HOME=/wrkdirs/biology/phyml TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/phyml" EXAMPLESDIR="share/examples/phyml" DATADIR="share/phyml" WWWDIR="www/phyml" ETCDIR="etc/phyml" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/phyml DOCSDIR=/usr/local/share/doc/phyml EXAMPLESDIR=/usr/local/share/examples/phyml WWWDIR=/usr/local/www/phyml ETCDIR=/usr/local/etc/phyml --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> NOTICE: The phyml 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 ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===> phyml-3.2.0,1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> phyml-3.2.0,1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of phyml-3.2.0,1 =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The phyml 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 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by phyml-3.2.0,1 for building =========================================================================== =================================================== ===> NOTICE: The phyml 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 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by phyml-3.2.0,1 for building => SHA256 Checksum OK for stephaneguindon-phyml-v3.2.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The phyml 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 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by phyml-3.2.0,1 for building ===> Extracting for phyml-3.2.0,1 => SHA256 Checksum OK for stephaneguindon-phyml-v3.2.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for phyml-3.2.0,1 =========================================================================== =================================================== ===> phyml-3.2.0,1 depends on executable: autoconf-2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_1.txz Installing autoconf-2.69_1... `-- Installing indexinfo-0.2.5... `-- Extracting indexinfo-0.2.5: .... done `-- Installing autoconf-wrapper-20131203... `-- Extracting autoconf-wrapper-20131203: ........ done `-- Installing perl5-5.20.3_15... `-- Extracting perl5-5.20.3_15: .......... done `-- Installing m4-1.4.17_1,1... `-- Extracting m4-1.4.17_1,1: .......... done Extracting autoconf-2.69_1: .......... done Message from perl5-5.20.3_15: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> phyml-3.2.0,1 depends on executable: autoconf-2.69 - found ===> Returning to build of phyml-3.2.0,1 ===> phyml-3.2.0,1 depends on executable: autoheader-2.69 - found ===> phyml-3.2.0,1 depends on executable: autoreconf-2.69 - found ===> phyml-3.2.0,1 depends on executable: aclocal-1.15 - not found ===> Installing existing package /packages/All/automake-1.15_1.txz Installing automake-1.15_1... `-- Installing automake-wrapper-20131203... `-- Extracting automake-wrapper-20131203: ... done Extracting automake-1.15_1: .......... done ===> phyml-3.2.0,1 depends on executable: aclocal-1.15 - found ===> Returning to build of phyml-3.2.0,1 ===> phyml-3.2.0,1 depends on executable: automake-1.15 - found ===> phyml-3.2.0,1 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.4.6.txz Installing libtool-2.4.6... Extracting libtool-2.4.6: .......... done ===> phyml-3.2.0,1 depends on executable: libtoolize - found ===> Returning to build of phyml-3.2.0,1 ===> phyml-3.2.0,1 depends on package: pkgconf>=0.9.10 - not found ===> Installing existing package /packages/All/pkgconf-1.0.1.txz Installing pkgconf-1.0.1... Extracting pkgconf-1.0.1: .......... done ===> phyml-3.2.0,1 depends on package: pkgconf>=0.9.10 - found ===> Returning to build of phyml-3.2.0,1 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for phyml-3.2.0,1 libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:17: installing './compile' configure.ac:5: installing './missing' src/Makefile.am: installing './depcomp' configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking build system type... x86_64-portbld-dragonfly4.7 checking host system type... x86_64-portbld-dragonfly4.7 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 cc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... (cached) gcc3 checking for log 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 float.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... (cached) yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... (cached) yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes configure: "On arch x86_64-portbld-dragonfly4.7 use MSSE = -msse" checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 262144 checking how to convert x86_64-portbld-dragonfly4.7 file names to x86_64-portbld-dragonfly4.7 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly4.7 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... dragonfly4.7 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking pkg-config is at least version 0.9.0... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands =========================================================================== =================================================== ===> Building for phyml-3.2.0,1 --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in src --- intro --- --- main.o --- --- utilities.o --- --- optimiz.o --- --- lk.o --- --- intro --- .: Building [phyml]. Version 20161005 :. --- utilities.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT utilities.o -MD -MP -MF .deps/utilities.Tpo -c -o utilities.o utilities.c --- main.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c --- optimiz.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT optimiz.o -MD -MP -MF .deps/optimiz.Tpo -c -o optimiz.o optimiz.c --- bionj.o --- --- lk.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT lk.o -MD -MP -MF .deps/lk.Tpo -c -o lk.o lk.c --- bionj.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT bionj.o -MD -MP -MF .deps/bionj.Tpo -c -o bionj.o bionj.c mv -f .deps/bionj.Tpo .deps/bionj.Po --- models.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT models.o -MD -MP -MF .deps/models.Tpo -c -o models.o models.c models.c: In function 'General_Dist': models.c:1171:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0) ^ models.c: In function 'GTR_Dist': models.c:1273:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0) {Free(pi); return -1.;} ^ --- main.o --- mv -f .deps/main.Tpo .deps/main.Po --- free.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT free.o -MD -MP -MF .deps/free.Tpo -c -o free.o free.c --- models.o --- mv -f .deps/models.Tpo .deps/models.Po --- help.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT help.o -MD -MP -MF .deps/help.Tpo -c -o help.o help.c --- free.o --- mv -f .deps/free.Tpo .deps/free.Po --- simu.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT simu.o -MD -MP -MF .deps/simu.Tpo -c -o simu.o simu.c --- help.o --- mv -f .deps/help.Tpo .deps/help.Po --- eigen.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT eigen.o -MD -MP -MF .deps/eigen.Tpo -c -o eigen.o eigen.c --- optimiz.o --- mv -f .deps/optimiz.Tpo .deps/optimiz.Po --- pars.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT pars.o -MD -MP -MF .deps/pars.Tpo -c -o pars.o pars.c --- simu.o --- mv -f .deps/simu.Tpo .deps/simu.Po --- alrt.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT alrt.o -MD -MP -MF .deps/alrt.Tpo -c -o alrt.o alrt.c --- lk.o --- mv -f .deps/lk.Tpo .deps/lk.Po --- interface.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c --- alrt.o --- mv -f .deps/alrt.Tpo .deps/alrt.Po --- cl.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT cl.o -MD -MP -MF .deps/cl.Tpo -c -o cl.o cl.c --- eigen.o --- mv -f .deps/eigen.Tpo .deps/eigen.Po --- spr.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT spr.o -MD -MP -MF .deps/spr.Tpo -c -o spr.o spr.c --- pars.o --- mv -f .deps/pars.Tpo .deps/pars.Po --- draw.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT draw.o -MD -MP -MF .deps/draw.Tpo -c -o draw.o draw.c --- interface.o --- mv -f .deps/interface.Tpo .deps/interface.Po --- stats.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT stats.o -MD -MP -MF .deps/stats.Tpo -c -o stats.o stats.c --- draw.o --- mv -f .deps/draw.Tpo .deps/draw.Po --- rates.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT rates.o -MD -MP -MF .deps/rates.Tpo -c -o rates.o rates.c --- cl.o --- mv -f .deps/cl.Tpo .deps/cl.Po --- mcmc.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT mcmc.o -MD -MP -MF .deps/mcmc.Tpo -c -o mcmc.o mcmc.c --- rates.o --- mv -f .deps/rates.Tpo .deps/rates.Po --- times.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT times.o -MD -MP -MF .deps/times.Tpo -c -o times.o times.c --- spr.o --- mv -f .deps/spr.Tpo .deps/spr.Po --- tiporder.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT tiporder.o -MD -MP -MF .deps/tiporder.Tpo -c -o tiporder.o tiporder.c mv -f .deps/tiporder.Tpo .deps/tiporder.Po --- mg.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT mg.o -MD -MP -MF .deps/mg.Tpo -c -o mg.o mg.c --- times.o --- mv -f .deps/times.Tpo .deps/times.Po --- m4.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT m4.o -MD -MP -MF .deps/m4.Tpo -c -o m4.o m4.c --- utilities.o --- mv -f .deps/utilities.Tpo .deps/utilities.Po --- io.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT io.o -MD -MP -MF .deps/io.Tpo -c -o io.o io.c --- mcmc.o --- mv -f .deps/mcmc.Tpo .deps/mcmc.Po --- make.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT make.o -MD -MP -MF .deps/make.Tpo -c -o make.o make.c mv -f .deps/make.Tpo .deps/make.Po --- nexus.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT nexus.o -MD -MP -MF .deps/nexus.Tpo -c -o nexus.o nexus.c mv -f .deps/nexus.Tpo .deps/nexus.Po --- init.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT init.o -MD -MP -MF .deps/init.Tpo -c -o init.o init.c --- m4.o --- mv -f .deps/m4.Tpo .deps/m4.Po --- xml.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT xml.o -MD -MP -MF .deps/xml.Tpo -c -o xml.o xml.c --- mg.o --- mv -f .deps/mg.Tpo .deps/mg.Po --- mixt.o --- cc -I. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT mixt.o -MD -MP -MF .deps/mixt.Tpo -c -o mixt.o mixt.c --- xml.o --- mv -f .deps/xml.Tpo .deps/xml.Po --- stats.o --- mv -f .deps/stats.Tpo .deps/stats.Po --- mixt.o --- mv -f .deps/mixt.Tpo .deps/mixt.Po --- io.o --- mv -f .deps/io.Tpo .deps/io.Po --- init.o --- mv -f .deps/init.Tpo .deps/init.Po --- phyml --- /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o -lm -lm libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o -lm --- all-am --- Done. =========================================================================== =================================================== =========================================================================== =================================================== ===> Staging for phyml-3.2.0,1 ===> Generating temporary packing list Making install in src .: Building [phyml]. Version 20161005 :. Done. /bin/mkdir -p '/wrkdirs/biology/phyml/stage/usr/local/bin' /bin/sh ../libtool --mode=install install -s -m 555 phyml '/wrkdirs/biology/phyml/stage/usr/local/bin' libtool: install: install -m 555 -s phyml /wrkdirs/biology/phyml/stage/usr/local/bin/phyml (cd /wrkdirs/biology/phyml/phyml-3.2.0/doc && install -m 0644 *.pdf /wrkdirs/biology/phyml/stage/usr/local/share/doc/phyml) ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for phyml-3.2.0,1 file sizes/checksums [16]: . done packing files [16]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for phyml-3.2.0,1 build of biology/phyml ended at Wed Oct 5 12:44:43 PDT 2016 build time: 00:00:38