=>> Building biology/plinkseq build started at Fri Apr 12 01:13:16 UTC 2019 port directory: /usr/ports/biology/plinkseq package name: plinkseq-0.10_1 building for: FreeBSD ppcports 13.0-CURRENT FreeBSD 13.0-CURRENT 1300013 powerpc maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/plinkseq/Makefile 460452 2018-01-31 01:07:07Z jwb $ Poudriere version: 3.2.8 Host OSVERSION: 1300012 Jail OSVERSION: 1300013 Job Id: 31 !!! Jail is newer than host. (Jail: 1300013, Host: 1300012) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300013 UNAME_v=FreeBSD 13.0-CURRENT 1300013 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root TRYBROKEN=yes LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/zfs/poudriere/data/.m/head-head-powerpc64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen GID=0 UID=0 PWD=/zfs/poudriere/data/.m/head-head-powerpc64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-head-powerpc64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/zfs/poudriere/data/.m/head-head-powerpc64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/plinkseq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/plinkseq/work HOME=/wrkdirs/usr/ports/biology/plinkseq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/plinkseq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/plinkseq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/plinkseq/work HOME=/wrkdirs/usr/ports/biology/plinkseq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/plinkseq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="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=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/plinkseq" EXAMPLESDIR="share/examples/plinkseq" DATADIR="share/plinkseq" WWWDIR="www/plinkseq" ETCDIR="etc/plinkseq" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/plinkseq DOCSDIR=/usr/local/share/doc/plinkseq EXAMPLESDIR=/usr/local/share/examples/plinkseq WWWDIR=/usr/local/www/plinkseq ETCDIR=/usr/local/etc/plinkseq --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300013 PYTHONBASE=/usr/local _SMP_CPUS=80 CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### DISABLE_MAKE_JOBS=poudriere ---End make.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-- =================================================== ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===> plinkseq-0.10_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [ppcports] Installing pkg-1.10.5_5... [ppcports] Extracting pkg-1.10.5_5: .......... done ===> plinkseq-0.10_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of plinkseq-0.10_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.10_1 for building =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.10_1 for building => SHA256 Checksum OK for plinkseq-src-0.10.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.10_1 for building ===> Extracting for plinkseq-0.10_1 => SHA256 Checksum OK for plinkseq-src-0.10.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for plinkseq-0.10_1 ===> Applying FreeBSD patches for plinkseq-0.10_1 /usr/bin/sed -i.bak -e 's|PF_INET|AF_INET|g' /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/mongoose/sources/lib/mongoose.c /usr/bin/sed -i.bak -e 's|g++|c++|g' -e 's|gcc|cc|g' -e 's|CXXFLAGS = -O3|CXXFLAGS = -O2 -pipe -fno-strict-aliasing |g' -e 's|ALL_CFLAGS =-O3|ALL_CFLAGS = -O2 -pipe -fno-strict-aliasing |g' /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/config_defs.Makefile /usr/bin/sed -i.bak -e 's| -ldl||g' -e 's| $(STATIC_FLAG)||g' /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/Makefile =========================================================================== =================================================== ===> plinkseq-0.10_1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz [ppcports] Installing gmake-4.2.1_3... [ppcports] `-- Installing gettext-runtime-0.19.8.1_2... [ppcports] | `-- Installing indexinfo-0.3.1... [ppcports] | `-- Extracting indexinfo-0.3.1: .... done [ppcports] `-- Extracting gettext-runtime-0.19.8.1_2: .......... done [ppcports] Extracting gmake-4.2.1_3: .......... done ===> plinkseq-0.10_1 depends on executable: gmake - found ===> Returning to build of plinkseq-0.10_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for plinkseq-0.10_1 =========================================================================== =================================================== ===> Building for plinkseq-0.10_1 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10' mkdir -p build/lib mkdir -p build/execs making depend sources/execs/pseq.cpp making depend sources/execs/gcol.cpp making depend sources/execs/browser.cpp making depend sources/execs/behead.cpp making depend sources/execs/mm.cpp making depend sources/execs/smp.cpp making depend sources/execs/tab2vcf.cpp making depend sources/execs/mongoose.cpp making depend sources/execs/pdas.cpp gmake ./sources/plinkseq ./sources/pseq ./sources/util ./sources/mongoose ./sources/browser ./sources/pdas ./sources/ext gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10' gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/plinkseq gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/plinkseq' mkdir -p build/lib making depend sources/lib/sqlite3.c making depend sources/lib/network.cpp making depend sources/lib/seqdb.cpp making depend sources/lib/genotype.cpp making depend sources/lib/reffuncs.cpp making depend sources/lib/r8lib.cpp making depend sources/lib/statistics.cpp making depend sources/lib/netfunc.cpp making depend sources/lib/filemap.cpp making depend sources/lib/matrix.cpp making depend sources/lib/allele.cpp making depend sources/lib/locdb.cpp making depend sources/lib/vcf.cpp making depend sources/lib/varmeta.cpp making depend sources/lib/globals.cpp making depend sources/lib/dcdflib.cpp making depend sources/lib/inddb.cpp making depend sources/lib/eval.cpp making depend sources/lib/matrix.pb.cpp making depend sources/lib/matdb.cpp making depend sources/lib/segments.cpp making depend sources/lib/c8lib.cpp making depend sources/lib/dose.cpp making depend sources/lib/variant.cpp making depend sources/lib/varfunc.cpp making depend sources/lib/indmap.cpp making depend sources/lib/individual.cpp making depend sources/lib/annot.cpp making depend sources/lib/iterate.cpp making depend sources/lib/crandom.cpp making depend sources/lib/em.cpp making depend sources/lib/bed.cpp making depend sources/lib/vcfiterate.cpp making depend sources/lib/zfstream.cpp making depend sources/lib/netdb.cpp making depend sources/lib/permute.cpp making depend sources/lib/helper.cpp making depend sources/lib/glm.cpp making depend sources/lib/prob.cpp making depend sources/lib/phmap.cpp making depend sources/lib/variant.pb.cpp making depend sources/lib/svar.cpp making depend sources/lib/output.cpp making depend sources/lib/vardb.cpp making depend sources/lib/vgroup.cpp making depend sources/lib/vcfz.cpp making depend sources/lib/protdb.cpp making depend sources/lib/matrix_exponential.cpp making depend sources/lib/gstore.cpp making depend sources/lib/mask.cpp making depend sources/lib/regions.cpp making depend sources/lib/token.cpp making depend sources/lib/fisher.cpp making depend sources/lib/refdb.cpp making depend sources/lib/meta.cpp making depend sources/lib/defs.cpp making depend sources/lib/sqlwrap.cpp making depend sources/lib/bcf.cpp making depend sources/lib/bgzf.cpp c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/bgzf.cpp -o build/lib/bgzf.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/bcf.cpp -o build/lib/bcf.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/sqlwrap.cpp -o build/lib/sqlwrap.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/defs.cpp -o build/lib/defs.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/meta.cpp -o build/lib/meta.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/refdb.cpp -o build/lib/refdb.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/fisher.cpp -o build/lib/fisher.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/token.cpp -o build/lib/token.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/regions.cpp -o build/lib/regions.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/mask.cpp -o build/lib/mask.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/gstore.cpp -o build/lib/gstore.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/matrix_exponential.cpp -o build/lib/matrix_exponential.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/protdb.cpp -o build/lib/protdb.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vcfz.cpp -o build/lib/vcfz.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vgroup.cpp -o build/lib/vgroup.o make: Working in: /usr/ports/biology/plinkseq c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vardb.cpp -o build/lib/vardb.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/output.cpp -o build/lib/output.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/svar.cpp -o build/lib/svar.o c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/variant.pb.cpp -o build/lib/variant.pb.o In file included from ../ext/sources/include/google/protobuf/stubs/once.h:81, from sources/lib/variant.pb.cpp:10: ../ext/sources/include/google/protobuf/stubs/atomicops.h:188: error: stray '#' in program ../ext/sources/include/google/protobuf/stubs/atomicops.h:188: error: expected constructor, destructor, or type conversion before string constant gmake[3]: *** [../../config_rules.Makefile:16: build/lib/variant.pb.o] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/plinkseq' gmake[2]: *** [Makefile:170: sources/plinkseq] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10' gmake[1]: *** [Makefile:165: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10' *** Error code 1 Stop. make: stopped in /usr/ports/biology/plinkseq =>> Cleaning up wrkdir ===> Cleaning for plinkseq-0.10_1 build of biology/plinkseq | plinkseq-0.10_1 ended at Fri Apr 12 01:24:18 UTC 2019 build time: 00:11:02 !!! build failure encountered !!!