=> Building biology/mrbayes build started at Sat Oct 8 16:25:59 PDT 2016 port directory: /usr/ports/biology/mrbayes 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: mzaki@m.u-tokyo.ac.jp ident warning: no id keywords in /build/boomdata/data/.m/Release46-default/ref/../02//usr/ports/biology/mrbayes/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=mrbayes-3.1.2_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 mrbayes-3.1.2_1: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/biology/mrbayes XDG_CONFIG_HOME=/wrkdirs/biology/mrbayes HOME=/wrkdirs/biology/mrbayes TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/mrbayes XDG_CONFIG_HOME=/wrkdirs/biology/mrbayes HOME=/wrkdirs/biology/mrbayes 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="-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 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/mrbayes" EXAMPLESDIR="share/examples/mrbayes" DATADIR="share/mrbayes" WWWDIR="www/mrbayes" ETCDIR="etc/mrbayes" --End PLIST_SUB-- --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 --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--- =================================================== =========================================================================== =================================================== ===> mrbayes-3.1.2_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 ===> mrbayes-3.1.2_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mrbayes-3.1.2_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by mrbayes-3.1.2_1 for building =========================================================================== =================================================== ===> Fetching all distfiles required by mrbayes-3.1.2_1 for building => SHA256 Checksum OK for mrbayes-3.1.2.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by mrbayes-3.1.2_1 for building ===> Extracting for mrbayes-3.1.2_1 => SHA256 Checksum OK for mrbayes-3.1.2.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for mrbayes-3.1.2_1 ===> Applying ports patches for mrbayes-3.1.2_1 =========================================================================== =================================================== ===> mrbayes-3.1.2_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 ===> mrbayes-3.1.2_1 depends on executable: gmake - found ===> Returning to build of mrbayes-3.1.2_1 =========================================================================== =================================================== ===> mrbayes-3.1.2_1 depends on shared library: libreadline.so.6 - not found ===> Installing existing package /packages/All/readline-6.3.8.txz Installing readline-6.3.8... `-- Installing ncurses-6.0_5... `-- Extracting ncurses-6.0_5: .......... done Extracting readline-6.3.8: .......... done Message from ncurses-6.0_5: ===> NOTICE: The ncurses 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 ===> mrbayes-3.1.2_1 depends on shared library: libreadline.so.6 - found (/usr/local/lib/libreadline.so.6) ===> Returning to build of mrbayes-3.1.2_1 =========================================================================== =================================================== ===> Configuring for mrbayes-3.1.2_1 =========================================================================== =================================================== ===> Building for mrbayes-3.1.2_1 gmake[1]: Entering directory '/wrkdirs/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 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; ^ 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; ^ cc -pipe -O2 -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o plot.o plot.c 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 '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; ^ 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; ^ 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 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 '/wrkdirs/biology/mrbayes/mrbayes-3.1.2' =========================================================================== =================================================== =========================================================================== =================================================== ===> Staging for mrbayes-3.1.2_1 ===> Generating temporary packing list install -s -m 555 /wrkdirs/biology/mrbayes/mrbayes-3.1.2/mb /wrkdirs/biology/mrbayes/stage/usr/local/bin/ install -m 0644 /wrkdirs/biology/mrbayes/mrbayes-3.1.2/adh.nex /wrkdirs/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /wrkdirs/biology/mrbayes/mrbayes-3.1.2/anolis.nex /wrkdirs/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /wrkdirs/biology/mrbayes/mrbayes-3.1.2/avian_ovomucoids.nex /wrkdirs/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /wrkdirs/biology/mrbayes/mrbayes-3.1.2/bglobin.nex /wrkdirs/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /wrkdirs/biology/mrbayes/mrbayes-3.1.2/cynmix.nex /wrkdirs/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /wrkdirs/biology/mrbayes/mrbayes-3.1.2/kim.nex /wrkdirs/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /wrkdirs/biology/mrbayes/mrbayes-3.1.2/primates.nex /wrkdirs/biology/mrbayes/stage/usr/local/share/examples/mrbayes install -m 0644 /wrkdirs/biology/mrbayes/mrbayes-3.1.2/replicase.nex /wrkdirs/biology/mrbayes/stage/usr/local/share/examples/mrbayes ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for mrbayes-3.1.2_1 file sizes/checksums [9]: . done packing files [9]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for mrbayes-3.1.2_1 build of biology/mrbayes ended at Sat Oct 8 16:27:28 PDT 2016 build time: 00:01:29