=> Building biology/paml build started at Sat Oct 8 15:37:37 PDT 2016 port directory: /usr/ports/biology/paml 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: jrm@FreeBSD.org ident warning: no id keywords in /build/boomdata/data/.m/Release46-default/ref/../01//usr/ports/biology/paml/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400600 ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/Release46-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=paml-4.9c_1 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/Release46-default/ref/.p/pool MASTERNAME=Release46-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 paml-4.9c_1: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/biology/paml XDG_CONFIG_HOME=/wrkdirs/biology/paml HOME=/wrkdirs/biology/paml TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/paml XDG_CONFIG_HOME=/wrkdirs/biology/paml HOME=/wrkdirs/biology/paml 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=4.6 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/paml" EXAMPLESDIR="share/examples/paml" DATADIR="share/paml" WWWDIR="www/paml" ETCDIR="etc/paml" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/paml DOCSDIR=/usr/local/share/doc/paml EXAMPLESDIR=/usr/local/share/examples/paml WWWDIR=/usr/local/www/paml ETCDIR=/usr/local/etc/paml --End SUB_LIST-- ---Begin make.conf--- NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> paml-4.9c_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 ===> paml-4.9c_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of paml-4.9c_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.9c_1 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.9c_1 for building => SHA256 Checksum OK for paml4.9c.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.9c_1 for building ===> Extracting for paml-4.9c_1 => SHA256 Checksum OK for paml4.9c.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for paml-4.9c_1 =========================================================================== =================================================== ===> paml-4.9c_1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... `-- Installing indexinfo-0.2.5... `-- Extracting indexinfo-0.2.5: .... done `-- Installing gettext-runtime-0.19.8.1... `-- Extracting gettext-runtime-0.19.8.1: .......... done Extracting gmake-4.2.1_1: .......... done ===> paml-4.9c_1 depends on executable: gmake - found ===> Returning to build of paml-4.9c_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for paml-4.9c_1 =========================================================================== =================================================== ===> Building for paml-4.9c_1 gmake[1]: Entering directory '/wrkdirs/biology/paml/paml4.9c/src' cc -O3 -o baseml baseml.c tools.c -lm cc -O3 -o codeml codeml.c tools.c -lm cc -O3 -o basemlg basemlg.c tools.c -lm In file included from basemlg.c:80:0: treesub.c: In function 'ReadSeq': treesub.c:761:27: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types] printsma(fout,com.spname,com.z,com.ns,com.ls,com.ls,gap,com.seqtype,0,0,NULL); ^ In file included from basemlg.c:11:0: paml.h:143:5: note: expected 'char **' but argument is of type 'unsigned char **' int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, ^ In file included from basemlg.c:80:0: treesub.c:769:23: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types] printsma(fout,com.spname,com.z,com.ns,com.ls,com.ls,gap,com.seqtype,0,0,NULL); ^ In file included from basemlg.c:11:0: paml.h:143:5: note: expected 'char **' but argument is of type 'unsigned char **' int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, ^ In file included from basemlg.c:80:0: treesub.c: In function 'printPatterns': treesub.c:983:23: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types] printsma(fout,com.spname,com.z,com.ns, com.npatt,com.npatt, gap, com.seqtype, 1, 0, NULL); ^ In file included from basemlg.c:11:0: paml.h:143:5: note: expected 'char **' but argument is of type 'unsigned char **' int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, ^ In file included from basemlg.c:80:0: treesub.c: In function 'AllPatterns': treesub.c:1213:23: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types] printsma(fout,com.spname,com.z,com.ns, com.ls, com.ls, gap, com.seqtype, 1, 0, NULL); ^ In file included from basemlg.c:11:0: paml.h:143:5: note: expected 'char **' but argument is of type 'unsigned char **' int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, ^ cc -O3 -o mcmctree mcmctree.c tools.c -lm In file included from mcmctree.c:188:0: mcmctree.c: In function 'ReadSeq': treesub.c:504:42: warning: iteration 1u invokes undefined behavior [-Waggressive-loop-optimizations] for(i=0;i<3;i++) com.lgene[i]=com.ls/3; ^ treesub.c:504:13: note: containing loop for(i=0;i<3;i++) com.lgene[i]=com.ls/3; ^ cc -O3 -o infinitesites -D INFINITESITES mcmctree.c tools.c -lm In file included from mcmctree.c:188:0: mcmctree.c: In function 'ReadSeq': treesub.c:504:42: warning: iteration 1u invokes undefined behavior [-Waggressive-loop-optimizations] for(i=0;i<3;i++) com.lgene[i]=com.ls/3; ^ treesub.c:504:13: note: containing loop for(i=0;i<3;i++) com.lgene[i]=com.ls/3; ^ cc -O3 -o pamp pamp.c tools.c -lm cc -O3 -o evolver evolver.c tools.c -lm cc -O3 -o yn00 yn00.c tools.c -lm cc -O3 -o chi2 chi2.c -lm gmake[1]: Leaving directory '/wrkdirs/biology/paml/paml4.9c/src' =========================================================================== =================================================== =========================================================================== =================================================== ===> Staging for paml-4.9c_1 ===> Generating temporary packing list install -s -m 555 /wrkdirs/biology/paml/paml4.9c/src/baseml /wrkdirs/biology/paml/stage/usr/local/bin install -s -m 555 /wrkdirs/biology/paml/paml4.9c/src/basemlg /wrkdirs/biology/paml/stage/usr/local/bin install -s -m 555 /wrkdirs/biology/paml/paml4.9c/src/chi2 /wrkdirs/biology/paml/stage/usr/local/bin install -s -m 555 /wrkdirs/biology/paml/paml4.9c/src/codeml /wrkdirs/biology/paml/stage/usr/local/bin install -s -m 555 /wrkdirs/biology/paml/paml4.9c/src/evolver /wrkdirs/biology/paml/stage/usr/local/bin install -s -m 555 /wrkdirs/biology/paml/paml4.9c/src/evolverNSbranches /wrkdirs/biology/paml/stage/usr/local/bin install -s -m 555 /wrkdirs/biology/paml/paml4.9c/src/evolverNSbranchsites /wrkdirs/biology/paml/stage/usr/local/bin install -s -m 555 /wrkdirs/biology/paml/paml4.9c/src/evolverNSsites /wrkdirs/biology/paml/stage/usr/local/bin install -s -m 555 /wrkdirs/biology/paml/paml4.9c/src/pamp /wrkdirs/biology/paml/stage/usr/local/bin install -s -m 555 /wrkdirs/biology/paml/paml4.9c/src/yn00 /wrkdirs/biology/paml/stage/usr/local/bin install -m 0644 /wrkdirs/biology/paml/paml4.9c/3s.trees /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/4s.trees /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/5s.trees /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/6s.trees /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/GeneticCode.txt /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/MCaa.dat /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/MCbase.dat /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/MCbaseRandomTree.dat /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/MCcodon.dat /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/aaml.ctl /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/baseml.ctl /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/brown.nuc /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/brown.rooted.trees /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/brown.trees /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/codeml.ctl /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/codonml.ctl /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/mcmctree.ctl /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/pamp.ctl /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/paupblock /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/paupend /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/paupstart /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/stewart.aa /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/stewart.trees /wrkdirs/biology/paml/stage//usr/local/share/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/yn00.ctl /wrkdirs/biology/paml/stage//usr/local/share/paml (cd /wrkdirs/biology/paml/paml4.9c && /bin/sh -c '(/usr/bin/find -d $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null 2>&1) && /usr/bin/find -d $0 $2 -type d -exec chmod 755 $1/{} \; && /usr/bin/find -d $0 $2 -type f -exec chmod 444 $1/{} \;' -- "dat examples Technical" /wrkdirs/biology/paml/stage//usr/local/share/paml) install -m 0644 /wrkdirs/biology/paml/paml4.9c/doc/* /wrkdirs/biology/paml/stage/usr/local/share/doc/paml install -m 0644 /wrkdirs/biology/paml/paml4.9c/README.txt /wrkdirs/biology/paml/stage/usr/local/share/doc/paml ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for paml-4.9c_1 file sizes/checksums [169]: .. done packing files [169]: .. done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for paml-4.9c_1 build of biology/paml ended at Sat Oct 8 15:44:39 PDT 2016 build time: 00:07:02