=> Building biology/mrbayes Started : Wednesday, 18 APR 2018 at 02:10:32 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 mrbayes-3.1.2_2: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/mrbayes XDG_CONFIG_HOME=/construction/biology/mrbayes HOME=/construction/biology/mrbayes TMPDIR="/tmp" PATH=/construction/biology/mrbayes/.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/mrbayes XDG_CONFIG_HOME=/construction/biology/mrbayes HOME=/construction/biology/mrbayes TMPDIR="/tmp" PATH=/construction/biology/mrbayes/.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="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib" 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/mrbayes/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/mrbayes" EXAMPLESDIR="share/examples/mrbayes" DATADIR="share/mrbayes" WWWDIR="www/mrbayes" ETCDIR="etc/mrbayes" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mrbayes DOCSDIR=/usr/local/share/doc/mrbayes EXAMPLESDIR=/usr/local/share/examples/mrbayes WWWDIR=/usr/local/www/mrbayes ETCDIR=/usr/local/etc/mrbayes -------------------------------------------------- -- /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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> mrbayes-3.1.2_2 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 ===> mrbayes-3.1.2_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mrbayes-3.1.2_2 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by mrbayes-3.1.2_2 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by mrbayes-3.1.2_2 for building => SHA256 Checksum OK for mrbayes-3.1.2.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by mrbayes-3.1.2_2 for building ===> Extracting for mrbayes-3.1.2_2 => SHA256 Checksum OK for mrbayes-3.1.2.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for mrbayes-3.1.2_2 ===> Applying ports patches for mrbayes-3.1.2_2 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> mrbayes-3.1.2_2 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 ===> mrbayes-3.1.2_2 depends on executable: gmake - found ===> Returning to build of mrbayes-3.1.2_2 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> mrbayes-3.1.2_2 depends on shared library: libreadline.so.7 - not found ===> Installing existing package /packages/All/readline-7.0.3_1.txz Installing readline-7.0.3_1... `-- Installing ncurses-6.0.0s20171223_1... `-- Extracting ncurses-6.0.0s20171223_1: .......... done Extracting readline-7.0.3_1: .......... done ===> mrbayes-3.1.2_2 depends on shared library: libreadline.so.7 - found (/usr/local/lib/libreadline.so.7) ===> Returning to build of mrbayes-3.1.2_2 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for mrbayes-3.1.2_2 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for mrbayes-3.1.2_2 gmake[1]: Entering directory '/construction/biology/mrbayes/mrbayes-3.1.2' cc -pipe -O2 -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o mb.o mb.c cc -pipe -O2 -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o mcmc.o mcmc.c cc -pipe -O2 -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o command.o command.c cc -pipe -O2 -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o mbmath.o mbmath.c cc -pipe -O2 -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o model.o model.c cc -pipe -O2 -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o plot.o plot.c mbmath.c: In function 'MultiplyMatrixNTimes': mbmath.c:4399:24: warning: variable 'numRemaining' set but not used [-Wunused-but-set-variable] int k, numSquares, numRemaining; ^ mbmath.c: In function 'QuantileGamma': mbmath.c:4727:10: warning: variable 'lnga1' set but not used [-Wunused-but-set-variable] MrBFlt lnga1, quantile; ^ plot.c: In function 'DoPlot': plot.c:70:20: warning: variable 'numLinesToRead' set but not used [-Wunused-but-set-variable] numParamLines, numLinesToRead, numLinesRead, firstNumCols=0, nLines, ^ command.c: In function 'DoPartition': command.c:5463:22: warning: variable 'numDivs' set but not used [-Wunused-but-set-variable] int i, j, howMany, numDivs, partTypes[MAX_NUM_DIVS], checkEachPart[MAX_NUM_DIVS]; ^ command.c: In function 'GetToken': command.c:7813:3: warning: value computed is not used [-Wunused-value] *tokenP++; ^ mcmc.c: In function 'CheckSetConstraints': mcmc.c:3496:47: warning: variable 'nextActiveConstraint' set but not used [-Wunused-but-set-variable] int a, b, i, j, k, nLongsNeeded, foundIt, nextActiveConstraint; ^ mcmc.c: In function 'GetParsimonyDownStates': mcmc.c:10639:11: warning: variable 'nSitesOfPat' set but not used [-Wunused-but-set-variable] CLFlt *nSitesOfPat; ^ mcmc.c: In function 'GetSprParsimonyLengths': mcmc.c:11147:11: warning: variable 'nSitesOfPat' set but not used [-Wunused-but-set-variable] CLFlt *nSitesOfPat; ^ mcmc.c: In function 'InitSprParsSets': mcmc.c:12522:28: warning: variable 'nIntNodes' set but not used [-Wunused-but-set-variable] int c, i, j, d, chain, nIntNodes, nNodes; ^ mcmc.c: In function 'Likelihood_ParsCodon': mcmc.c:14216:13: warning: variable 'q' set but not used [-Wunused-but-set-variable] TreeNode *q; ^ mcmc.c:14215:12: warning: variable 'y' set but not used [-Wunused-but-set-variable] int x, y; ^ mcmc.c:14215:9: warning: variable 'x' set but not used [-Wunused-but-set-variable] int x, y; ^ mcmc.c: In function 'Likelihood_ParsStd': mcmc.c:14269:30: warning: variable 'oldpP' set but not used [-Wunused-but-set-variable] long *pL, *pR, *pP, *pA, *oldpP, x; ^ mcmc.c: In function 'Move_Aamodel': mcmc.c:15116:15: warning: variable 'x' set but not used [-Wunused-but-set-variable] MrBFlt *bs, x, *subValue; ^ mcmc.c: In function 'Move_BiasedSpr': mcmc.c:15422:54: warning: variable 'origRoot' set but not used [-Wunused-but-set-variable] **subTree1DP, **subTree2DP, *newAttachmentNode, *origRoot; ^ mcmc.c:15418:24: warning: variable 'isBranchAnc' set but not used [-Wunused-but-set-variable] int i, isVPriorExp, isBranchAnc, nNodes1, nNodes2; ^ mcmc.c: In function 'Move_LocalClock': mcmc.c:21707:17: warning: variable 'tuning' set but not used [-Wunused-but-set-variable] MrBFlt x, y, tuning, minV, maxV, h1, h2, h3, h[3], tempD, ran, distUv, distCv, ^ mcmc.c:21706:38: warning: variable 'aSister' set but not used [-Wunused-but-set-variable] int topologyHasChanged, vIsRoot, aSister, bSister, cSister; ^ mcmc.c: In function 'Move_NNI': mcmc.c:22193:8: warning: variable 'i' set but not used [-Wunused-but-set-variable] int i; ^ mcmc.c: In function 'Move_OmegaNeu': mcmc.c:23297:15: warning: variable 'mp' set but not used [-Wunused-but-set-variable] ModelParams *mp; ^ mcmc.c: In function 'Move_OmegaPur': mcmc.c:23486:15: warning: variable 'mp' set but not used [-Wunused-but-set-variable] ModelParams *mp; ^ mcmc.c: In function 'Move_SPRClock': mcmc.c:26841:22: warning: variable 'newPathLengthB' set but not used [-Wunused-but-set-variable] newPathLengthA, newPathLengthB; ^ mcmc.c: In function 'PrintChainCondLikes': mcmc.c:29624:16: warning: variable 'mp' set but not used [-Wunused-but-set-variable] ModelParams *mp; ^ cc -pipe -O2 -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o sump.o sump.c sump.c: In function 'DoSump': sump.c:78:20: warning: variable 'numLinesToRead' set but not used [-Wunused-but-set-variable] numParamLines, numLinesToRead, numLinesRead, firstNumCols=0, nLines, ^ sump.c: In function 'PrintAATable': sump.c:1564:16: warning: variable 'len' set but not used [-Wunused-but-set-variable] int i, j, k, len, startReading; ^ sump.c: In function 'PrintOverlayPlot': sump.c:1672:23: warning: variable 'len' set but not used [-Wunused-but-set-variable] int i, j, k, k2, n, len, screenHeight, screenWidth, numY[60], whichIsX, whichIsY; ^ sump.c: In function 'PrintPlot': sump.c:1976:16: warning: variable 'len' set but not used [-Wunused-but-set-variable] int i, j, k, len, numY[60], screenWidth, screenHeight, whichIsX, whichIsY; ^ mcmc.c: In function 'SetProteinQMatrix': mcmc.c:37783:16: warning: variable 'mp' set but not used [-Wunused-but-set-variable] ModelParams *mp; ^ mcmc.c: In function 'SetUpTermState': mcmc.c:39383:31: warning: variable 'nReps' set but not used [-Wunused-but-set-variable] int i, j, k, n, c, d, x=0, nReps; ^ command.c: In function 'DoCalibrateParm': command.c:1227:11: warning: 'tempD' may be used uninitialized in this function [-Wmaybe-uninitialized] MrBFlt tempD; ^ cc -pipe -O2 -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o sumt.o sumt.c sumt.c: In function 'CheckSumtSpecies': sumt.c:936:32: warning: variable 'numNotFound' set but not used [-Wunused-but-set-variable] int i, nNodes, whichTaxon, numNotFound; ^ sumt.c: In function 'FindTree': sumt.c:5086:32: warning: variable 'whichTree' set but not used [-Wunused-but-set-variable] int i, n, foundTree, nDiff, whichTree, *x; ^ sumt.c: In function 'ShowConPhylogram': sumt.c:6728:36: warning: variable 'treeWidth' set but not used [-Wunused-but-set-variable] int i, j, k, nLines, from, to, treeWidth, barLength; ^ cc -pipe -O2 -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o bayes.o bayes.c cc -L/usr/local/lib -pipe -O2 -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall mb.o bayes.o command.o mbmath.o mcmc.o model.o plot.o sump.o sumt.o -lncurses -lreadline -lm -o mb gmake[1]: Leaving directory '/construction/biology/mrbayes/mrbayes-3.1.2' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for mrbayes-3.1.2_2 ===> Generating temporary packing list install -s -m 555 /construction/biology/mrbayes/mrbayes-3.1.2/mb /construction/biology/mrbayes/stage/usr/local/bin/ install -m 0644 /construction/biology/mrbayes/mrbayes-3.1.2/adh.nex /construction/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /construction/biology/mrbayes/mrbayes-3.1.2/anolis.nex /construction/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /construction/biology/mrbayes/mrbayes-3.1.2/avian_ovomucoids.nex /construction/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /construction/biology/mrbayes/mrbayes-3.1.2/bglobin.nex /construction/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /construction/biology/mrbayes/mrbayes-3.1.2/cynmix.nex /construction/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /construction/biology/mrbayes/mrbayes-3.1.2/kim.nex /construction/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /construction/biology/mrbayes/mrbayes-3.1.2/primates.nex /construction/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /construction/biology/mrbayes/mrbayes-3.1.2/replicase.nex /construction/biology/mrbayes/stage/usr/local/share/examples/mrbayes ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for mrbayes-3.1.2_2 file sizes/checksums [9]: . done packing files [9]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 18 APR 2018 at 02:11:39 UTC Duration: 00:01:07