=> Building biology/paml Started : Thursday, 7 JUN 2018 at 05:51:19 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.242.g757c0-DEVELOPMENT #30: Tue May 8 14:06:27 PDT 2018 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.2-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.2-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-4.9h: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> 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 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=5.2 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-5.2 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 _PERL5_FROM_BIN=5.26.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500200 OSVERSION=9999999 OSREL=5.2 _OSRELEASE=5.2-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> paml-4.9h 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 ===> paml-4.9h depends on file: /usr/local/sbin/pkg - found ===> Returning to build of paml-4.9h -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user => paml4.9h.tgz doesn't seem to exist in /distfiles/. => Attempting to fetch http://abacus.gene.ucl.ac.uk/software/paml4.9h.tgz paml4.9h.tgz 6094 kB 0 Bps ===> Fetching all distfiles required by paml-4.9h for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.9h for building => SHA256 Checksum OK for paml4.9h.tgz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.9h for building ===> Extracting for paml-4.9h => SHA256 Checksum OK for paml4.9h.tgz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for paml-4.9h ===> Converting DOS text files to UNIX text files -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> paml-4.9h 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-4.9h depends on executable: gmake - found ===> Returning to build of paml-4.9h -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for paml-4.9h -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for paml-4.9h gmake[1]: Entering directory '/construction/biology/paml/paml4.9h/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:849:28: 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:144:5: 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:857:25: 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:144:5: 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:1075:22: 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:144:5: 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:1343:22: 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:144:5: 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:191:0: mcmctree.c: In function 'ReadSeq': treesub.c:586:50: warning: iteration 1u invokes undefined behavior [-Waggressive-loop-optimizations] for (i = 0; i < 3; i++) com.lgene[i] = com.ls / 3; ^ treesub.c:586:13: 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:191:0: mcmctree.c: In function 'ReadSeq': treesub.c:586:50: warning: iteration 1u invokes undefined behavior [-Waggressive-loop-optimizations] for (i = 0; i < 3; i++) com.lgene[i] = com.ls / 3; ^ treesub.c:586:13: 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/paml4.9h/src' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for paml-4.9h ===> Generating temporary packing list install -s -m 555 /construction/biology/paml/paml4.9h/src/baseml /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9h/src/basemlg /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9h/src/chi2 /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9h/src/codeml /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9h/src/evolver /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9h/src/evolverNSbranches /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9h/src/evolverNSbranchsites /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9h/src/evolverNSsites /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9h/src/pamp /construction/biology/paml/stage/usr/local/bin install -s -m 555 /construction/biology/paml/paml4.9h/src/yn00 /construction/biology/paml/stage/usr/local/bin install -m 0644 /construction/biology/paml/paml4.9h/doc/* /construction/biology/paml/stage/usr/local/share/doc/paml install -m 0644 /construction/biology/paml/paml4.9h/README.txt /construction/biology/paml/stage/usr/local/share/doc/paml (cd /construction/biology/paml/paml4.9h && /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 Technical" /construction/biology/paml/stage/usr/local/share/examples/paml) (cd /construction/biology/paml/paml4.9h/examples && /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 . /construction/biology/paml/stage/usr/local/share/examples/paml) install -m 0644 /construction/biology/paml/paml4.9h/*.aa /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9h/*.ctl /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9h/*.dat /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9h/*.nuc /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9h/*.trees /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9h/*.txt /construction/biology/paml/stage/usr/local/share/examples/paml install -m 0644 /construction/biology/paml/paml4.9h/paup* /construction/biology/paml/stage/usr/local/share/examples/paml ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for paml-4.9h file sizes/checksums [175]: .. done packing files [175]: .. done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 7 JUN 2018 at 05:55:08 UTC Duration: 00:03:48