Date: Sun, 22 Oct 2017 01:42:01 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110armv6-quarterly][biology/mrbayes] Failed for mrbayes-3.1.2_2 in build Message-ID: <201710220142.v9M1g18K007571@beefy15.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: mzaki@m.u-tokyo.ac.jp Last committer: sunpoet@FreeBSD.org Ident: $FreeBSD: branches/2017Q4/biology/mrbayes/Makefile 444463 2017-06-27 13:46:53Z sunpoet $ Log URL: http://beefy15.nyi.freebsd.org/data/110armv6-quarterly/452586/logs/mrbayes-3.1.2_2.log Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=110armv6-quarterly&build=452586 Log: ====>> Building biology/mrbayes build started at Sun Oct 22 01:41:30 UTC 2017 port directory: /usr/ports/biology/mrbayes building for: FreeBSD 110armv6-quarterly-job-15 11.0-RELEASE-p13 FreeBSD 11.0-RELEASE-p13 1100122 arm maintained by: mzaki@m.u-tokyo.ac.jp Makefile ident: $FreeBSD: branches/2017Q4/biology/mrbayes/Makefile 444463 2017-06-27 13:46:53Z sunpoet $ Poudriere version: 3.1.21 Host OSVERSION: 1200040 Jail OSVERSION: 1100122 Job Id: 15 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p13 1100122 UNAME_r=11.0-RELEASE-p13 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110armv6-quarterly/ref QEMU_EMULATING=1 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=mrbayes-3.1.2_2 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110armv6-quarterly/ref/.p/pool MASTERNAME=110armv6-quarterly SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.21 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> 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 ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mrbayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mrbayes/work HOME=/wrkdirs/usr/ports/biology/mrbayes/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mrbayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mrbayes/work HOME=/wrkdirs/usr/ports/biology/mrbayes/work TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -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" --End MAKE_ENV-- --PLIST_SUB-- OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib 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--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes MACHINE=arm MACHINE_ARCH=armv6 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### ARCH=armv6 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=11.0 OSVERSION=1100122 PYTHONBASE=/usr/local UID=0 _JAVA_OS_LIST_REGEXP=native|linux _JAVA_VENDOR_LIST_REGEXP=openjdk|oracle|sun _JAVA_VERSION_LIST_REGEXP=1.6|1.7|1.8|1.6\+|1.7\+|1.8\+ _OSRELEASE=11.0-RELEASE-p13 #### Misc Poudriere #### GID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<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-1.10.1.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-15] Installing pkg-1.10.1... [110armv6-quarterly-job-15] Extracting pkg-1.10.1: .......... 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 FreeBSD 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_1.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-15] Installing gmake-4.2.1_1... [110armv6-quarterly-job-15] `-- Installing gettext-runtime-0.19.8.1_1... [110armv6-quarterly-job-15] | `-- Installing indexinfo-0.2.6... [110armv6-quarterly-job-15] | `-- Extracting indexinfo-0.2.6: .... done [110armv6-quarterly-job-15] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [110armv6-quarterly-job-15] Extracting gmake-4.2.1_1: .......... 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.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-15] Installing readline-7.0.3... [110armv6-quarterly-job-15] Extracting readline-7.0.3: .......... 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 '/wrkdirs/usr/ports/biology/mrbayes/work/mrbayes-3.1.2' /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o mb.o mb.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o mcmc.o mcmc.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o bayes.o bayes.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o command.o command.c command.c:1371:12: warning: variable 'tempD' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (calibrationPtr->prior == offsetExponential) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ command.c:1403:25: note: uninitialized use occurs here sprintf (s, "%1.2lf", tempD); ^~~~~ command.c:1371:8: note: remove the 'if' if its condition is always true else if (calibrationPtr->prior == offsetExponential) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ command.c:1227:16: note: initialize the variable 'tempD' to silence this warning MrBFlt tempD; ^ = 0.0 command.c:7813:3: warning: expression result unused [-Wunused-value] *tokenP++; ^~~~~~~~~ 2 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o mbmath.o mbmath.c mbmath.c:4788:5: warning: use of unary operator that may be intended as compound assignment (-=) r =- log(RandomNumber(seed)); ^~ 1 warning generated. /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o model.o model.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o plot.o plot.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o sump.o sump.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o sumt.o sumt.c /nxb-bin/usr/bin/cc -L/usr/local/lib -O2 -pipe -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 mbmath.o: In function `ComplexExponentiation': mbmath.c:(.text+0x2ffc): undefined reference to `sincos' cc: error: linker command failed with exit code 1 (use -v to see invocation) gmake[1]: *** [<builtin>: mb] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/mrbayes/work/mrbayes-3.1.2' *** Error code 1 Stop. make: stopped in /usr/ports/biology/mrbayes
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