------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for mrbayes-3.2.7_2: AVX=off: Use AVX optimized routines DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples FMA=off: Use FMA optimized routines SSE=on: Use SSE optimized routines ====> MPI (Message Passing Interface) support: you can only select none or one of them MPICH=off: Parallel processing support via MPICH 3 OPENMPI=off: Parallel processing support via Open MPI ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_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 SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- --disable-avx --disable-fma --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/mrbayes/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=6.1 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/ncurses-6.2.20210313_1.txz ===== Message from ncurses-6.2.20210313_1: -- { type: install message: < mrbayes-3.2.7_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> mrbayes-3.2.7_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mrbayes-3.2.7_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> mrbayes-3.2.7_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mrbayes-3.2.7_2 for building => SHA256 Checksum OK for NBISweden-MrBayes-v3.2.7_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> mrbayes-3.2.7_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mrbayes-3.2.7_2 for building ===> Extracting for mrbayes-3.2.7_2 => SHA256 Checksum OK for NBISweden-MrBayes-v3.2.7_GH0.tar.gz. Extracted Memory Use: 15.96M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for mrbayes-3.2.7_2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> mrbayes-3.2.7_2 depends on shared library: libreadline.so.8 - found (/usr/local/lib/libreadline.so.8) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> mrbayes-3.2.7_2 depends on shared library: libreadline.so.8 - found (/usr/local/lib/libreadline.so.8) ===> Configuring for mrbayes-3.2.7_2 configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... x86_64-portbld-dragonfly6.1 checking host system type... x86_64-portbld-dragonfly6.1 checking for pkg-config... no checking for pdflatex... no checking for bibtex... no configure: WARNING: pdflatex or bibtex is missing, documentation will not be rebuilt checking for style of include used by make... GNU checking whether to compile using MPI... no checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for sqrt in -lm... yes checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes configure: Trying to locate Beagle (hmsbeagle-1) in '/usr/local' checking libhmsbeagle/beagle.h usability... no checking libhmsbeagle/beagle.h presence... no checking for libhmsbeagle/beagle.h... no checking for beagleCreateInstance in -lhmsbeagle... no configure: Trying to locate Beagle (hmsbeagle-1) in '/usr' checking libhmsbeagle/beagle.h usability... no checking libhmsbeagle/beagle.h presence... no checking for libhmsbeagle/beagle.h... no checking for beagleCreateInstance in -lhmsbeagle... (cached) no configure: WARNING: Failed to locate Beagle, falling back on pkg-config checking for BEAGLE... no checking for a readline compatible library... -lreadline checking readline.h usability... no checking readline.h presence... no checking for readline.h... no checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking whether readline supports history... yes checking history.h usability... no checking history.h presence... no checking for history.h... no checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for memory.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for size_t... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for C compiler vendor... gnu checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for C compiler version... 8.3.0 checking CFLAGS for maximum warnings... -Wall checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... 14:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:0:0:0 checking for x86 cpuid 0x00000001 output... 406f1:5100800:7ffefbff:bfebfbff checking for x86 cpuid 0x00000007 output... 0:21cbfbb:0:0 checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800 checking for x86-AVX xgetbv 0x00000000 output... 7:0 checking whether RDRND is supported by the processor... yes checking whether RDRND is supported by the processor and OS... yes checking whether C compiler accepts -mrdrnd... yes checking whether BMI1 is supported by the processor... yes checking whether BMI1 is supported by the processor and OS... yes checking whether C compiler accepts -mbmi... yes checking whether BMI2 is supported by the processor... yes checking whether BMI2 is supported by the processor and OS... yes checking whether C compiler accepts -mbmi2... yes checking whether ADX is supported by the processor... yes checking whether ADX is supported by the processor and OS... yes checking whether C compiler accepts -madx... yes checking whether MPX is supported by the processor... no checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C compiler accepts -mabm... yes checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... no checking whether SHA is supported by the processor... no checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... yes checking whether FMA3 is supported by the processor and OS... yes checking whether C compiler accepts -mfma... yes checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... yes checking whether AVX2 is supported by the processor and OS... yes checking whether C compiler accepts -mavx2... yes checking whether AVX512-F is supported by the processor... no checking whether AVX512-CD is supported by the processor... no checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... no checking whether AVX512-BW is supported by the processor... no checking whether AVX512-DQ is supported by the processor... no checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking for floor... yes checking for memset... (cached) yes checking for pow... yes checking for sqrt... yes checking for strchr... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/manual/Makefile config.status: creating doc/tutorial/Makefile config.status: creating examples/Makefile config.status: creating src/Makefile config.status: creating src/config.h config.status: executing depfiles commands SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for mrbayes-3.2.7_2 --- all-recursive --- Making all in src --- all --- /usr/bin/make all-am --- mb-bayes.o --- --- mb-best.o --- --- mb-command.o --- --- mb-likelihood.o --- --- mb-mbbeagle.o --- --- mb-mcmc.o --- --- mb-model.o --- --- mb-proposal.o --- --- mb-sumpt.o --- --- mb-utils.o --- --- mb-best.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -DNDEBUG -std=c99 -pedantic -pipe -O2 -fno-strict-aliasing -Wall -MT mb-best.o -MD -MP -MF .deps/mb-best.Tpo -c -o mb-best.o `test -f 'best.c' || echo './'`best.c --- mb-command.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -DNDEBUG -std=c99 -pedantic -pipe -O2 -fno-strict-aliasing -Wall -MT mb-command.o -MD -MP -MF .deps/mb-command.Tpo -c -o mb-command.o `test -f 'command.c' || echo './'`command.c --- mb-mbbeagle.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -DNDEBUG -std=c99 -pedantic -pipe -O2 -fno-strict-aliasing -Wall -MT mb-mbbeagle.o -MD -MP -MF .deps/mb-mbbeagle.Tpo -c -o mb-mbbeagle.o `test -f 'mbbeagle.c' || echo './'`mbbeagle.c --- mb-mcmc.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -DNDEBUG -std=c99 -pedantic -pipe -O2 -fno-strict-aliasing -Wall -MT mb-mcmc.o -MD -MP -MF .deps/mb-mcmc.Tpo -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c --- mb-bayes.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -DNDEBUG -std=c99 -pedantic -pipe -O2 -fno-strict-aliasing -Wall -MT mb-bayes.o -MD -MP -MF .deps/mb-bayes.Tpo -c -o mb-bayes.o `test -f 'bayes.c' || echo './'`bayes.c --- mb-model.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -DNDEBUG -std=c99 -pedantic -pipe -O2 -fno-strict-aliasing -Wall -MT mb-model.o -MD -MP -MF .deps/mb-model.Tpo -c -o mb-model.o `test -f 'model.c' || echo './'`model.c --- mb-proposal.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -DNDEBUG -std=c99 -pedantic -pipe -O2 -fno-strict-aliasing -Wall -MT mb-proposal.o -MD -MP -MF .deps/mb-proposal.Tpo -c -o mb-proposal.o `test -f 'proposal.c' || echo './'`proposal.c --- mb-sumpt.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -DNDEBUG -std=c99 -pedantic -pipe -O2 -fno-strict-aliasing -Wall -MT mb-sumpt.o -MD -MP -MF .deps/mb-sumpt.Tpo -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c --- mb-utils.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -DNDEBUG -std=c99 -pedantic -pipe -O2 -fno-strict-aliasing -Wall -MT mb-utils.o -MD -MP -MF .deps/mb-utils.Tpo -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c --- mb-likelihood.o --- cc -DHAVE_CONFIG_H -I. -I/usr/local/include -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -DNDEBUG -std=c99 -pedantic -pipe -O2 -fno-strict-aliasing -Wall -MT mb-likelihood.o -MD -MP -MF .deps/mb-likelihood.Tpo -c -o mb-likelihood.o `test -f 'likelihood.c' || echo './'`likelihood.c --- mb-mbbeagle.o --- mv -f .deps/mb-mbbeagle.Tpo .deps/mb-mbbeagle.Po --- mb-bayes.o --- mv -f .deps/mb-bayes.Tpo .deps/mb-bayes.Po --- mb-best.o --- mv -f .deps/mb-best.Tpo .deps/mb-best.Po --- mb-sumpt.o --- sumpt.c: In function 'ExamineSumpFile': sumpt.c:1778:5: warning: 'strcpy' accessing 1 byte at offsets [0, 9223372036854775807] and 0 may overlap 1 byte at offset 0 [-Wrestrict] strcpy(headerLine, s); ^~~~~~~~~~~~~~~~~~~~~ sumpt.c:1778:5: warning: 'strcpy' accessing 1 byte at offsets [0, 9223372036854775807] and 0 may overlap 1 byte at offset 0 [-Wrestrict] --- mb-utils.o --- utils.c: In function 'CopyResults': utils.c:311:9: warning: 'strncpy' accessing between 0 and 2147483647 bytes at offsets [0, 9223372036854775807] and 0 may overlap up to 2147483647 bytes at offset 2147483646 [-Wrestrict] strncpy (strCpy,strBuf,longestLine); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c: In function 'CopyProcessSsFile': utils.c:350:9: warning: 'strncpy' accessing between 0 and 2147483647 bytes at offsets [0, 9223372036854775807] and 0 may overlap up to 2147483647 bytes at offset 2147483646 [-Wrestrict] strncpy (strCpy,strBuf,longestLine); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c: In function 'CopyTreeResults': utils.c:422:9: warning: 'strncpy' accessing between 0 and 2147483647 bytes at offsets [0, 9223372036854775807] and 0 may overlap up to 2147483647 bytes at offset 2147483646 [-Wrestrict] strncpy (strCpy,strBuf,longestLine); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- mb-sumpt.o --- sumpt.c: In function 'DoSump': sumpt.c:335:5: warning: 'strncpy' output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation] strncpy (temp, sumpParams.sumpOutfile, 90); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoCompRefTree': sumpt.c:4612:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 7 and 126 [-Wformat-overflow=] sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1); ^~ sumpt.c:4612:33: note: directive argument in the range [1, 2147483647] sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1); ^~~~~~~~~~~~ sumpt.c:4612:13: note: 'sprintf' output between 8 and 136 bytes into a destination of size 130 sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function 'ShowConTree': sumpt.c:8173:21: warning: '__builtin_strcpy' accessing 1 byte at offsets [0, 9223372036854775807] and 0 may overlap 1 byte at offset 0 [-Wrestrict] sprintf (printLine+treeWidth+1,"%s", label); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- mb-likelihood.o --- mv -f .deps/mb-likelihood.Tpo .deps/mb-likelihood.Po --- mb-sumpt.o --- sumpt.c: In function 'DoSumt': sumpt.c:4958:39: warning: '.run' directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); ^~~~ sumpt.c:4958:36: note: directive argument in the range [-2147483647, 2147483647] sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); ^~~~~~~~~~~~ sumpt.c:4958:17: note: 'sprintf' output between 8 and 137 bytes into a destination of size 120 sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:4956:39: warning: '.t' directive writing 2 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tempName, "%s.t", fileName); ^~ sumpt.c:4956:17: note: 'sprintf' output between 3 and 122 bytes into a destination of size 120 sprintf (tempName, "%s.t", fileName); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- mb-proposal.o --- mv -f .deps/mb-proposal.Tpo .deps/mb-proposal.Po --- mb-mcmc.o --- mcmc.c: In function 'ReusePreviousResults.part.10': mcmc.c:15950:52: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 3 and 210 [-Wformat-overflow=] sprintf (fileName, "%s%s.tree%d.run%d.t", workingDir, localFileName, i+1, n+1); ^~ mcmc.c:15950:36: note: directive argument in the range [1, 2147483647] sprintf (fileName, "%s%s.tree%d.run%d.t", workingDir, localFileName, i+1, n+1); ^~~~~~~~~~~~~~~~~~~~~ mcmc.c:15950:17: note: 'sprintf' output between 14 and 230 bytes into a destination of size 220 sprintf (fileName, "%s%s.tree%d.run%d.t", workingDir, localFileName, i+1, n+1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- mb-sumpt.o --- mv -f .deps/mb-sumpt.Tpo .deps/mb-sumpt.Po --- mb-mcmc.o --- mcmc.c: In function 'ReopenMBPrintFiles': mcmc.c:15467:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 2 and 110 [-Wformat-overflow=] sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); ^~ mcmc.c:15467:36: note: directive argument in the range [1, 2147483647] sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); ^~~~~~~~~~~~~~~~~~~ mcmc.c:15467:17: note: 'sprintf' output between 14 and 131 bytes into a destination of size 120 sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- mb-utils.o --- mv -f .deps/mb-utils.Tpo .deps/mb-utils.Po --- mb-mcmc.o --- mcmc.c: In function 'RunChain': mcmc.c:17362:46: warning: '.ss' directive writing 3 bytes into a region of size between 1 and 220 [-Wformat-overflow=] sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS); ^~~ mcmc.c:17362:21: note: 'sprintf' output between 5 and 234 bytes into a destination of size 220 sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/mb-mcmc.Tpo .deps/mb-mcmc.Po --- mb-command.o --- command.c: In function 'DoExecute': command.c:3560:5: warning: 'strncpy' output may be truncated copying 98 bytes from a string of length 99 [-Wstringop-truncation] strncpy (exeFileName, inputFileName, 98); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/mb-command.Tpo .deps/mb-command.Po --- mb-model.o --- model.c: In function 'SetModelParams': model.c:19111:48: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf (tempMult, "g_m{%d}", i+1); ^ model.c:19111:21: note: 'sprintf' output between 7 and 16 bytes into a destination of size 15 sprintf (tempMult, "g_m{%d}", i+1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/mb-model.Tpo .deps/mb-model.Po --- mb --- cc -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -madx -mabm -O3 -DNDEBUG -std=c99 -pedantic -pipe -O2 -fno-strict-aliasing -Wall -L/usr/local/lib -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -lm -lreadline Making all in doc --- all-recursive --- Making all in manual Making all in tutorial Making all in examples SUCCEEDED 00:01:26 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for mrbayes-3.2.7_2 ===> Generating temporary packing list Making install in src /bin/mkdir -p '/construction/biology/mrbayes/stage/usr/local/bin' install -s -m 555 mb '/construction/biology/mrbayes/stage/usr/local/bin' Making install in doc Making install in manual /bin/mkdir -p '/construction/biology/mrbayes/stage/usr/local/share/doc/mrbayes' install -m 0644 Manual_MrBayes_v3.2.pdf '/construction/biology/mrbayes/stage/usr/local/share/doc/mrbayes' Making install in tutorial /bin/mkdir -p '/construction/biology/mrbayes/stage/usr/local/share/doc/mrbayes' install -m 0644 hym.nex '/construction/biology/mrbayes/stage/usr/local/share/doc/mrbayes' /bin/mkdir -p '/construction/biology/mrbayes/stage/usr/local/share/doc/mrbayes' install -m 0644 MBDating.pdf '/construction/biology/mrbayes/stage/usr/local/share/doc/mrbayes' Making install in examples /bin/mkdir -p '/construction/biology/mrbayes/stage/usr/local/share/examples/mrbayes' install -m 0644 avian_ovomucoids.nex codon.nex cynmix.nex finch.nex hymfossil.nex primates.nex replicase.nex sceloporus.nex '/construction/biology/mrbayes/stage/usr/local/share/examples/mrbayes' /bin/mkdir -p '/construction/biology/mrbayes/stage/usr/local/share/doc/mrbayes' install -m 0644 COPYING README NEWS '/construction/biology/mrbayes/stage/usr/local/share/doc/mrbayes' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for mrbayes-3.2.7_2 file sizes/checksums [15]: 0% file sizes/checksums [15]: 100% packing files [15]: 0% packing files [15]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:06 TOTAL TIME 00:01:48