=> Building biology/paml Started : Wednesday, 18 APR 2018 at 02:13:44 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.81.g32506c-DEVELOPMENT #29: Tue Apr 10 08:49:52 PDT 2018 marino@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.0-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.0-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 paml-4.9c_1: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/paml XDG_CONFIG_HOME=/construction/biology/paml HOME=/construction/biology/paml TMPDIR="/tmp" PATH=/construction/biology/paml/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/paml XDG_CONFIG_HOME=/construction/biology/paml HOME=/construction/biology/paml TMPDIR="/tmp" PATH=/construction/biology/paml/.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 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 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/paml/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/paml" EXAMPLESDIR="share/examples/paml" DATADIR="share/paml" WWWDIR="www/paml" ETCDIR="etc/paml" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.0 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=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500000 OSVERSION=9999999 OSREL=5.0 _OSRELEASE=5.0-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> paml-4.9c_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5.txz Installing pkg-1.10.5... Extracting pkg-1.10.5: .......... done ===> paml-4.9c_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of paml-4.9c_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.9c_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.9c_1 for building => SHA256 Checksum OK for paml4.9c.tgz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> 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. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for paml-4.9c_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> paml-4.9c_1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz Installing gmake-4.2.1_2... `-- Installing gettext-runtime-0.19.8.1_1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_2: .......... done ===> paml-4.9c_1 depends on executable: gmake - found ===> Returning to build of paml-4.9c_1 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for paml-4.9c_1 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for paml-4.9c_1 gmake[1]: Entering directory '/construction/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 '/construction/biology/paml/paml4.9c/src' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for paml-4.9c_1 ===> Generating temporary packing list install -s -m 555 /construction/biology/paml/paml4.9c/src/baseml /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9c/src/basemlg /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9c/src/chi2 /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9c/src/codeml /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9c/src/evolver /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9c/src/evolverNSbranches /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9c/src/evolverNSbranchsites /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9c/src/evolverNSsites /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9c/src/pamp /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9c/src/yn00 /construction/biology/paml/stage/usr/local/bin install -m 0644 /construction/biology/paml/paml4.9c/3s.trees /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/4s.trees /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/5s.trees /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/6s.trees /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/GeneticCode.txt /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/MCaa.dat /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/MCbase.dat /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/MCbaseRandomTree.dat /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/MCcodon.dat /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/aaml.ctl /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/baseml.ctl /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/brown.nuc /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/brown.rooted.trees /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/brown.trees /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/codeml.ctl /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/codonml.ctl /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/mcmctree.ctl /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/pamp.ctl /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/paupblock /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/paupend /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/paupstart /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/stewart.aa /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/stewart.trees /construction/biology/paml/stage//usr/local/share/paml install -m 0644 /construction/biology/paml/paml4.9c/yn00.ctl /construction/biology/paml/stage//usr/local/share/paml (cd /construction/biology/paml/paml4.9c && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE "dat examples Technical" /construction/biology/paml/stage//usr/local/share/paml) install -m 0644 /construction/biology/paml/paml4.9c/doc/* /construction/biology/paml/stage/usr/local/share/doc/paml install -m 0644 /construction/biology/paml/paml4.9c/README.txt /construction/biology/paml/stage/usr/local/share/doc/paml ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for paml-4.9c_1 file sizes/checksums [169]: .. done packing files [169]: .. done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 18 APR 2018 at 02:18:01 UTC Duration: 00:04:16