=> Building biology/plinkseq Started : Wednesday, 11 APR 2018 at 02:40:37 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=5.2-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.2-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 -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/plinkseq XDG_CONFIG_HOME=/construction/biology/plinkseq HOME=/construction/biology/plinkseq TMPDIR="/tmp" PATH=/construction/biology/plinkseq/.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/plinkseq XDG_CONFIG_HOME=/construction/biology/plinkseq HOME=/construction/biology/plinkseq TMPDIR="/tmp" PATH=/construction/biology/plinkseq/.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="" LDFLAGS="" 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/plinkseq/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/plinkseq" EXAMPLESDIR="share/examples/plinkseq" DATADIR="share/plinkseq" WWWDIR="www/plinkseq" ETCDIR="etc/plinkseq" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.2 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=500200 OSVERSION=9999999 OSREL=5.2 _OSRELEASE=5.2-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> plinkseq-0.10_1 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 ===> plinkseq-0.10_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of plinkseq-0.10_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.10_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> 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. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> 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. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for plinkseq-0.10_1 ===> Applying ports patches for plinkseq-0.10_1 /usr/bin/sed -i.bak -e 's|PF_INET|AF_INET|g' /construction/biology/plinkseq/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 = -pipe -O2 -fno-strict-aliasing|g' -e 's|ALL_CFLAGS =-O3|ALL_CFLAGS = -pipe -O2 -fno-strict-aliasing|g' /construction/biology/plinkseq/plinkseq-0.10/config_defs.Makefile /usr/bin/sed -i.bak -e 's| -ldl||g' -e 's| $(STATIC_FLAG)||g' /construction/biology/plinkseq/plinkseq-0.10/Makefile -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> plinkseq-0.10_1 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 ===> plinkseq-0.10_1 depends on executable: gmake - found ===> Returning to build of plinkseq-0.10_1 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for plinkseq-0.10_1 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for plinkseq-0.10_1 gmake[1]: Entering directory '/construction/biology/plinkseq/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/mongoose.cpp making depend sources/execs/pdas.cpp making depend sources/execs/tab2vcf.cpp gmake ./sources/plinkseq ./sources/pseq ./sources/util ./sources/mongoose ./sources/browser ./sources/pdas ./sources/ext gmake[2]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10' gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/plinkseq gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/pseq gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/util gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/mongoose gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/browser gmake[3]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/plinkseq' gmake[3]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/pseq' gmake[3]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/util' gmake[3]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/mongoose' gmake[3]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/browser' mkdir -p build/lib mkdir -p build/lib mkdir -p build/lib making depend sources/lib/util.cpp making depend sources/lib/lines.cpp making depend sources/lib/char_tok.cpp mkdir -p build/lib making depend sources/lib/sqlite3.c mkdir -p build/lib making depend sources/lib/mongoose.c c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include sources/lib/char_tok.cpp -o build/lib/char_tok.o making depend sources/lib/sockets.cpp cc -c -pipe -O2 -fno-strict-aliasing -DSQLITE_OMIT_LOAD_EXTENSION -I./sources/include sources/lib/mongoose.c -o build/lib/mongoose.o making depend sources/lib/ibd.cpp c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../plinkseq/sources/include/ -I../ext/sources/include/ sources/lib/lines.cpp -o build/lib/lines.o making depend sources/lib/extra.cpp making depend sources/lib/network.cpp making depend sources/lib/matdb.cpp ar rv build/lib/libutil.a build/lib/char_tok.o /usr/libexec/binutils227/elf/ar: creating build/lib/libutil.a a - build/lib/char_tok.o ranlib build/lib/libutil.a gmake[3]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/util' making depend sources/lib/ibs.cpp making depend sources/lib/seqdb.cpp gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/pdas gmake[3]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/pdas' mkdir -p build/lib making depend sources/lib/socks.cpp making depend sources/lib/func.cpp c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../plinkseq/sources/include/ -I../ext/sources/include/ sources/lib/socks.cpp -o build/lib/socks.o making depend sources/lib/genotype.cpp making depend sources/lib/webcheck.cpp making depend sources/lib/genic.cpp making depend sources/lib/varmeta.cpp making depend sources/lib/varfunc.cpp making depend sources/lib/r8lib.cpp making depend sources/lib/reffuncs.cpp making depend sources/lib/assoc.cpp making depend sources/lib/netfunc.cpp making depend sources/lib/filemap.cpp making depend sources/lib/prot.cpp making depend sources/lib/matdb.cpp making depend sources/lib/allele.cpp making depend sources/lib/loaders.cpp making depend sources/lib/locdb.cpp making depend sources/lib/compare.cpp making depend sources/lib/netassoc.cpp making depend sources/lib/annot.cpp making depend sources/lib/stepup.cpp making depend sources/lib/protdb.cpp making depend sources/lib/summaries.cpp making depend sources/lib/svar.cpp ar rv build/lib/libpdas.a build/lib/socks.o /usr/libexec/binutils227/elf/ar: creating build/lib/libpdas.a a - build/lib/socks.o ranlib build/lib/libpdas.a gmake[3]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/pdas' making depend sources/lib/eval.cpp gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/ext gmake[3]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext' cd protobuf \ && ./configure --prefix=`pwd`/../sources/include/DUMMY --exec-prefix=`pwd`/../build \ && gmake && gmake install making depend sources/lib/cnv.cpp making depend sources/lib/vcfz.cpp making depend sources/lib/davies.cpp making depend sources/lib/clusters.cpp making depend sources/lib/matrix.pb.cpp making depend sources/lib/em.cpp making depend sources/lib/kbac.cpp making depend sources/lib/c8lib.cpp making depend sources/lib/pops.cpp making depend sources/lib/meta.cpp making depend sources/lib/variant.cpp making depend sources/lib/skat.cpp making depend sources/lib/zfstream.cpp making depend sources/lib/varfunc.cpp making depend sources/lib/gseq.cpp making depend sources/lib/output.cpp checking whether to enable maintainer-specific portions of Makefiles... yes making depend sources/lib/glm-tests.cpp making depend sources/lib/phmap.cpp making depend sources/lib/views.cpp ar rv build/lib/libbrowser.a build/lib/lines.o /usr/libexec/binutils227/elf/ar: creating build/lib/libbrowser.a a - build/lib/lines.o ranlib build/lib/libbrowser.a making depend sources/lib/inddb.cpp gmake[3]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/browser' making depend sources/lib/iterate.cpp checking build system type... making depend sources/lib/nets.cpp making depend sources/lib/chet.cpp making depend sources/lib/bed.cpp making depend sources/lib/vcf.cpp making depend sources/lib/variant.pb.cpp c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/chet.cpp -o build/lib/chet.o making depend sources/lib/vcfiterate.cpp making depend sources/lib/sqlwrap.cpp x86_64-unknown-dragonfly5.2 checking host system type... x86_64-unknown-dragonfly5.2 checking target system type... x86_64-unknown-dragonfly5.2 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... making depend sources/lib/globals.cpp making depend sources/lib/permute.cpp making depend sources/lib/helper.cpp making depend sources/lib/statistics.cpp making depend sources/lib/prob.cpp making depend sources/lib/crandom.cpp making depend sources/lib/token.cpp making depend sources/lib/matrix.cpp making depend sources/lib/dcdflib.cpp making depend sources/lib/vardb.cpp c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/nets.cpp -o build/lib/nets.o making depend sources/lib/vgroup.cpp making depend sources/lib/refdb.cpp making depend sources/lib/individual.cpp making depend sources/lib/matrix_exponential.cpp making depend sources/lib/gstore.cpp making depend sources/lib/glm.cpp ar rv build/lib/libmongoose.a build/lib/mongoose.o /usr/libexec/binutils227/elf/ar: creating build/lib/libmongoose.a a - build/lib/mongoose.o ranlib build/lib/libmongoose.a gmake[3]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/mongoose' c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/views.cpp -o build/lib/views.o making depend sources/lib/mask.cpp making depend sources/lib/regions.cpp yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for gcc... cc making depend sources/lib/netdb.cpp checking whether the C compiler works... making depend sources/lib/segments.cpp yes checking for C compiler default output file name... a.out checking for suffix of executables... making depend sources/lib/fisher.cpp making depend sources/lib/dose.cpp checking whether we are cross compiling... making depend sources/lib/indmap.cpp no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... making depend sources/lib/defs.cpp yes checking for cc option to accept ISO C89... making depend sources/lib/bcf.cpp none needed checking for style of include used by make... GNU checking dependency style of cc... making depend sources/lib/bgzf.cpp gcc3 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/bgzf.cpp -o build/lib/bgzf.o checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking how to run the C++ preprocessor... c++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/bcf.cpp -o build/lib/bcf.o yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking C++ compiler flags...... use user-supplied: -pipe -O2 -fno-strict-aliasing checking whether __SUNPRO_CC is declared... no checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking how to convert x86_64-unknown-dragonfly5.2 file names to x86_64-unknown-dragonfly5.2 format... func_convert_file_noop checking how to convert x86_64-unknown-dragonfly5.2 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from cc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... dragonfly5.2 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... dragonfly5.2 ld.so checking how to hardcode library paths into programs... immediate checking for ANSI C header files... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inttypes.h... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for working memcmp... yes checking for working strtod... yes checking for ftruncate... yes checking for memset... yes checking for mkdir... yes checking for strchr... yes checking for strerror... yes checking for strtol... yes checking zlib version... ok (1.2.0.4 or later) checking for library containing zlibVersion... -lz checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking whether to check for GCC pthread/shared inconsistencies... yes checking whether -pthread is sufficient with -shared... yes checking whether what we have so far is sufficient with -nostdlib... no checking whether -lpthread saves the day... yes checking the location of hash_map... configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating protobuf.pc config.status: creating protobuf-lite.pc config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/defs.cpp -o build/lib/defs.o config.status: executing libtool commands === configuring in gtest (/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/gtest) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY' '--exec-prefix=/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build' 'CC=cc' 'CFLAGS=-pipe -O2 -fno-strict-aliasing' 'LDFLAGS=' 'LIBS=' 'CPPFLAGS=' 'CXX=c++' 'CXXFLAGS=-pipe -O2 -fno-strict-aliasing ' --cache-file=/dev/null --srcdir=. c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/indmap.cpp -o build/lib/indmap.o checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... build-aux/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for gcc... cc checking whether the C compiler works... c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/glm-tests.cpp -o build/lib/glm-tests.o 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 for style of include used by make... GNU checking dependency style of cc... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking build system type... x86_64-unknown-dragonfly5.2 checking host system type... x86_64-unknown-dragonfly5.2 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/dose.cpp -o build/lib/dose.o /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking how to convert x86_64-unknown-dragonfly5.2 file names to x86_64-unknown-dragonfly5.2 format... func_convert_file_noop checking how to convert x86_64-unknown-dragonfly5.2 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from cc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... cpp checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... dragonfly5.2 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/gseq.cpp -o build/lib/gseq.o yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... dragonfly5.2 ld.so checking how to hardcode library paths into programs... immediate checking for python... : checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking whether to check for GCC pthread/shared inconsistencies... yes checking whether -pthread is sufficient with -shared... yes configure: creating ./config.status c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/skat.cpp -o build/lib/skat.o config.status: creating Makefile config.status: creating scripts/gtest-config config.status: creating build-aux/config.h config.status: build-aux/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands gmake[4]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake all-recursive gmake[5]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' Making all in . gmake[6]: Entering directory 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sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ google/protobuf/stubs/strutil.cc: In function 'char* google::protobuf::DoubleToBuffer(double, char*)': google/protobuf/stubs/strutil.cc:1058:39: warning: typedef 'DBL_DIG_is_too_big' locally defined but not used [-Wunused-local-typedefs] GOOGLE_COMPILE_ASSERT(DBL_DIG < 20, DBL_DIG_is_too_big); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ google/protobuf/stubs/strutil.cc: In function 'char* google::protobuf::FloatToBuffer(float, char*)': google/protobuf/stubs/strutil.cc:1113:39: warning: typedef 'FLT_DIG_is_too_big' locally defined but not used [-Wunused-local-typedefs] GOOGLE_COMPILE_ASSERT(FLT_DIG < 10, FLT_DIG_is_too_big); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT strutil.lo -MD -MP -MF .deps/strutil.Tpo -c google/protobuf/stubs/strutil.cc -o strutil.o >/dev/null 2>&1 mv -f .deps/strutil.Tpo .deps/strutil.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT substitute.lo -MD -MP -MF .deps/substitute.Tpo -c -o substitute.lo `test -f 'google/protobuf/stubs/substitute.cc' || echo './'`google/protobuf/stubs/substitute.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT substitute.lo -MD -MP -MF .deps/substitute.Tpo -c google/protobuf/stubs/substitute.cc -fPIC -DPIC -o .libs/substitute.o In file included from ./google/protobuf/stubs/substitute.h:35:0, from google/protobuf/stubs/substitute.cc:33: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT substitute.lo -MD -MP -MF .deps/substitute.Tpo -c google/protobuf/stubs/substitute.cc -o substitute.o >/dev/null 2>&1 mv -f .deps/substitute.Tpo .deps/substitute.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT structurally_valid.lo -MD -MP -MF .deps/structurally_valid.Tpo -c -o structurally_valid.lo `test -f 'google/protobuf/stubs/structurally_valid.cc' || echo './'`google/protobuf/stubs/structurally_valid.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT structurally_valid.lo -MD -MP -MF .deps/structurally_valid.Tpo -c google/protobuf/stubs/structurally_valid.cc -fPIC -DPIC -o .libs/structurally_valid.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT structurally_valid.lo -MD -MP -MF .deps/structurally_valid.Tpo -c google/protobuf/stubs/structurally_valid.cc -o structurally_valid.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT descriptor.lo -MD -MP -MF .deps/descriptor.Tpo -c -o descriptor.lo `test -f 'google/protobuf/descriptor.cc' || echo './'`google/protobuf/descriptor.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT descriptor.lo -MD -MP -MF .deps/descriptor.Tpo -c google/protobuf/descriptor.cc -fPIC -DPIC -o .libs/descriptor.o mv -f .deps/structurally_valid.Tpo .deps/structurally_valid.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vgroup.cpp -o build/lib/vgroup.o In file included from ./google/protobuf/stubs/hash.h:39:0, from google/protobuf/descriptor.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT descriptor.pb.lo -MD -MP -MF .deps/descriptor.pb.Tpo -c -o descriptor.pb.lo `test -f 'google/protobuf/descriptor.pb.cc' || echo './'`google/protobuf/descriptor.pb.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT descriptor.pb.lo -MD -MP -MF .deps/descriptor.pb.Tpo -c google/protobuf/descriptor.pb.cc -fPIC -DPIC -o .libs/descriptor.pb.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/summaries.cpp -o build/lib/summaries.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT descriptor_database.lo -MD -MP -MF .deps/descriptor_database.Tpo -c -o descriptor_database.lo `test -f 'google/protobuf/descriptor_database.cc' || echo './'`google/protobuf/descriptor_database.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT descriptor_database.lo -MD -MP -MF .deps/descriptor_database.Tpo -c google/protobuf/descriptor_database.cc -fPIC -DPIC -o .libs/descriptor_database.o In file included from ./google/protobuf/descriptor_database.h:44:0, from google/protobuf/descriptor_database.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT descriptor_database.lo -MD -MP -MF .deps/descriptor_database.Tpo -c google/protobuf/descriptor_database.cc -o descriptor_database.o >/dev/null 2>&1 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vardb.cpp -o build/lib/vardb.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT descriptor.pb.lo -MD -MP -MF .deps/descriptor.pb.Tpo -c google/protobuf/descriptor.pb.cc -o descriptor.pb.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT descriptor.lo -MD -MP -MF .deps/descriptor.Tpo -c google/protobuf/descriptor.cc -o descriptor.o >/dev/null 2>&1 mv -f .deps/descriptor_database.Tpo .deps/descriptor_database.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/dcdflib.cpp -o build/lib/dcdflib.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT dynamic_message.lo -MD -MP -MF .deps/dynamic_message.Tpo -c -o dynamic_message.lo `test -f 'google/protobuf/dynamic_message.cc' || echo './'`google/protobuf/dynamic_message.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT dynamic_message.lo -MD -MP -MF .deps/dynamic_message.Tpo -c google/protobuf/dynamic_message.cc -fPIC -DPIC -o .libs/dynamic_message.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/stepup.cpp -o build/lib/stepup.o mv -f .deps/descriptor.pb.Tpo .deps/descriptor.pb.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/matrix.cpp -o build/lib/matrix.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT dynamic_message.lo -MD -MP -MF .deps/dynamic_message.Tpo -c google/protobuf/dynamic_message.cc -o dynamic_message.o >/dev/null 2>&1 mv -f .deps/dynamic_message.Tpo .deps/dynamic_message.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/token.cpp -o build/lib/token.o mv -f .deps/descriptor.Tpo .deps/descriptor.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT extension_set_heavy.lo -MD -MP -MF .deps/extension_set_heavy.Tpo -c -o extension_set_heavy.lo `test -f 'google/protobuf/extension_set_heavy.cc' || echo './'`google/protobuf/extension_set_heavy.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT extension_set_heavy.lo -MD -MP -MF .deps/extension_set_heavy.Tpo -c google/protobuf/extension_set_heavy.cc -fPIC -DPIC -o .libs/extension_set_heavy.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT generated_message_reflection.lo -MD -MP -MF .deps/generated_message_reflection.Tpo -c -o generated_message_reflection.lo `test -f 'google/protobuf/generated_message_reflection.cc' || echo './'`google/protobuf/generated_message_reflection.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT generated_message_reflection.lo -MD -MP -MF .deps/generated_message_reflection.Tpo -c google/protobuf/generated_message_reflection.cc -fPIC -DPIC -o .libs/generated_message_reflection.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT message.lo -MD -MP -MF .deps/message.Tpo -c -o message.lo `test -f 'google/protobuf/message.cc' || echo './'`google/protobuf/message.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT message.lo -MD -MP -MF .deps/message.Tpo -c google/protobuf/message.cc -fPIC -DPIC -o .libs/message.o In file included from ./google/protobuf/stubs/hash.h:39:0, from google/protobuf/message.cc:37: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/netassoc.cpp -o build/lib/netassoc.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT extension_set_heavy.lo -MD -MP -MF .deps/extension_set_heavy.Tpo -c google/protobuf/extension_set_heavy.cc -o extension_set_heavy.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT message.lo -MD -MP -MF .deps/message.Tpo -c google/protobuf/message.cc -o message.o >/dev/null 2>&1 mv -f .deps/extension_set_heavy.Tpo .deps/extension_set_heavy.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/crandom.cpp -o build/lib/crandom.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT generated_message_reflection.lo -MD -MP -MF .deps/generated_message_reflection.Tpo -c google/protobuf/generated_message_reflection.cc -o generated_message_reflection.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT reflection_ops.lo -MD -MP -MF .deps/reflection_ops.Tpo -c -o reflection_ops.lo `test -f 'google/protobuf/reflection_ops.cc' || echo './'`google/protobuf/reflection_ops.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT reflection_ops.lo -MD -MP -MF .deps/reflection_ops.Tpo -c google/protobuf/reflection_ops.cc -fPIC -DPIC -o .libs/reflection_ops.o In file included from ./google/protobuf/reflection_ops.h:41:0, from google/protobuf/reflection_ops.cc:38: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT reflection_ops.lo -MD -MP -MF .deps/reflection_ops.Tpo -c google/protobuf/reflection_ops.cc -o reflection_ops.o >/dev/null 2>&1 mv -f .deps/message.Tpo .deps/message.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/prob.cpp -o build/lib/prob.o mv -f .deps/reflection_ops.Tpo .deps/reflection_ops.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/statistics.cpp -o build/lib/statistics.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/compare.cpp -o build/lib/compare.o mv -f .deps/generated_message_reflection.Tpo .deps/generated_message_reflection.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT service.lo -MD -MP -MF .deps/service.Tpo -c -o service.lo `test -f 'google/protobuf/service.cc' || echo './'`google/protobuf/service.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT service.lo -MD -MP -MF .deps/service.Tpo -c google/protobuf/service.cc -fPIC -DPIC -o .libs/service.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT service.lo -MD -MP -MF .deps/service.Tpo -c google/protobuf/service.cc -o service.o >/dev/null 2>&1 mv -f .deps/service.Tpo .deps/service.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT text_format.lo -MD -MP -MF .deps/text_format.Tpo -c -o text_format.lo `test -f 'google/protobuf/text_format.cc' || echo './'`google/protobuf/text_format.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT text_format.lo -MD -MP -MF .deps/text_format.Tpo -c google/protobuf/text_format.cc -fPIC -DPIC -o .libs/text_format.o In file included from ./google/protobuf/text_format.h:44:0, from google/protobuf/text_format.cc:42: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/loaders.cpp -o build/lib/loaders.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT unknown_field_set.lo -MD -MP -MF .deps/unknown_field_set.Tpo -c -o unknown_field_set.lo `test -f 'google/protobuf/unknown_field_set.cc' || echo './'`google/protobuf/unknown_field_set.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT unknown_field_set.lo -MD -MP -MF .deps/unknown_field_set.Tpo -c google/protobuf/unknown_field_set.cc -fPIC -DPIC -o .libs/unknown_field_set.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/helper.cpp -o build/lib/helper.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT unknown_field_set.lo -MD -MP -MF .deps/unknown_field_set.Tpo -c google/protobuf/unknown_field_set.cc -o unknown_field_set.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT wire_format.lo -MD -MP -MF .deps/wire_format.Tpo -c -o wire_format.lo `test -f 'google/protobuf/wire_format.cc' || echo './'`google/protobuf/wire_format.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT wire_format.lo -MD -MP -MF .deps/wire_format.Tpo -c google/protobuf/wire_format.cc -fPIC -DPIC -o .libs/wire_format.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT text_format.lo -MD -MP -MF .deps/text_format.Tpo -c google/protobuf/text_format.cc -o text_format.o >/dev/null 2>&1 mv -f .deps/unknown_field_set.Tpo .deps/unknown_field_set.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/permute.cpp -o build/lib/permute.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT wire_format.lo -MD -MP -MF .deps/wire_format.Tpo -c google/protobuf/wire_format.cc -o wire_format.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT gzip_stream.lo -MD -MP -MF .deps/gzip_stream.Tpo -c -o gzip_stream.lo `test -f 'google/protobuf/io/gzip_stream.cc' || echo './'`google/protobuf/io/gzip_stream.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT gzip_stream.lo -MD -MP -MF .deps/gzip_stream.Tpo -c google/protobuf/io/gzip_stream.cc -fPIC -DPIC -o .libs/gzip_stream.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT gzip_stream.lo -MD -MP -MF .deps/gzip_stream.Tpo -c google/protobuf/io/gzip_stream.cc -o gzip_stream.o >/dev/null 2>&1 mv -f .deps/gzip_stream.Tpo .deps/gzip_stream.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/globals.cpp -o build/lib/globals.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT printer.lo -MD -MP -MF .deps/printer.Tpo -c -o printer.lo `test -f 'google/protobuf/io/printer.cc' || echo './'`google/protobuf/io/printer.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT printer.lo -MD -MP -MF .deps/printer.Tpo -c google/protobuf/io/printer.cc -fPIC -DPIC -o .libs/printer.o mv -f .deps/wire_format.Tpo .deps/wire_format.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/sqlwrap.cpp -o build/lib/sqlwrap.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vcfiterate.cpp -o build/lib/vcfiterate.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/prot.cpp -o build/lib/prot.o mv -f .deps/text_format.Tpo .deps/text_format.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/variant.pb.cpp -o build/lib/variant.pb.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT printer.lo -MD -MP -MF .deps/printer.Tpo -c google/protobuf/io/printer.cc -o printer.o >/dev/null 2>&1 mv -f .deps/printer.Tpo .deps/printer.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT tokenizer.lo -MD -MP -MF .deps/tokenizer.Tpo -c -o tokenizer.lo `test -f 'google/protobuf/io/tokenizer.cc' || echo './'`google/protobuf/io/tokenizer.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT tokenizer.lo -MD -MP -MF .deps/tokenizer.Tpo -c google/protobuf/io/tokenizer.cc -fPIC -DPIC -o .libs/tokenizer.o In file included from ./google/protobuf/io/tokenizer.h:42:0, from google/protobuf/io/tokenizer.cc:91: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT zero_copy_stream_impl.lo -MD -MP -MF .deps/zero_copy_stream_impl.Tpo -c -o zero_copy_stream_impl.lo `test -f 'google/protobuf/io/zero_copy_stream_impl.cc' || echo './'`google/protobuf/io/zero_copy_stream_impl.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT zero_copy_stream_impl.lo -MD -MP -MF .deps/zero_copy_stream_impl.Tpo -c google/protobuf/io/zero_copy_stream_impl.cc -fPIC -DPIC -o .libs/zero_copy_stream_impl.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT zero_copy_stream_impl.lo -MD -MP -MF .deps/zero_copy_stream_impl.Tpo -c google/protobuf/io/zero_copy_stream_impl.cc -o zero_copy_stream_impl.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT tokenizer.lo -MD -MP -MF .deps/tokenizer.Tpo -c google/protobuf/io/tokenizer.cc -o tokenizer.o >/dev/null 2>&1 mv -f .deps/zero_copy_stream_impl.Tpo .deps/zero_copy_stream_impl.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vcf.cpp -o build/lib/vcf.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT importer.lo -MD -MP -MF .deps/importer.Tpo -c -o importer.lo `test -f 'google/protobuf/compiler/importer.cc' || echo './'`google/protobuf/compiler/importer.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT importer.lo -MD -MP -MF .deps/importer.Tpo -c google/protobuf/compiler/importer.cc -fPIC -DPIC -o .libs/importer.o mv -f .deps/tokenizer.Tpo .deps/tokenizer.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/bed.cpp -o build/lib/bed.o In file included from ./google/protobuf/descriptor.h:59:0, from ./google/protobuf/compiler/importer.h:44, from google/protobuf/compiler/importer.cc:47: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c -o parser.lo `test -f 'google/protobuf/compiler/parser.cc' || echo './'`google/protobuf/compiler/parser.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c google/protobuf/compiler/parser.cc -fPIC -DPIC -o .libs/parser.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT importer.lo -MD -MP -MF .deps/importer.Tpo -c google/protobuf/compiler/importer.cc -o importer.o >/dev/null 2>&1 In file included from ./google/protobuf/stubs/hash.h:39:0, from google/protobuf/compiler/parser.cc:38: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/assoc.cpp -o build/lib/assoc.o mv -f .deps/importer.Tpo .deps/importer.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/iterate.cpp -o build/lib/iterate.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c google/protobuf/compiler/parser.cc -o parser.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT code_generator.lo -MD -MP -MF .deps/code_generator.Tpo -c -o code_generator.lo `test -f 'google/protobuf/compiler/code_generator.cc' || echo './'`google/protobuf/compiler/code_generator.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT code_generator.lo -MD -MP -MF .deps/code_generator.Tpo -c google/protobuf/compiler/code_generator.cc -fPIC -DPIC -o .libs/code_generator.o In file included from ./google/protobuf/compiler/code_generator.h:41:0, from google/protobuf/compiler/code_generator.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT code_generator.lo -MD -MP -MF .deps/code_generator.Tpo -c google/protobuf/compiler/code_generator.cc -o code_generator.o >/dev/null 2>&1 mv -f .deps/code_generator.Tpo .deps/code_generator.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/inddb.cpp -o build/lib/inddb.o mv -f .deps/parser.Tpo .deps/parser.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT command_line_interface.lo -MD -MP -MF .deps/command_line_interface.Tpo -c -o command_line_interface.lo `test -f 'google/protobuf/compiler/command_line_interface.cc' || echo './'`google/protobuf/compiler/command_line_interface.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT command_line_interface.lo -MD -MP -MF .deps/command_line_interface.Tpo -c google/protobuf/compiler/command_line_interface.cc -fPIC -DPIC -o .libs/command_line_interface.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT plugin.lo -MD -MP -MF .deps/plugin.Tpo -c -o plugin.lo `test -f 'google/protobuf/compiler/plugin.cc' || echo './'`google/protobuf/compiler/plugin.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT plugin.lo -MD -MP -MF .deps/plugin.Tpo -c google/protobuf/compiler/plugin.cc -fPIC -DPIC -o .libs/plugin.o In file included from ./google/protobuf/compiler/command_line_interface.h:41:0, from google/protobuf/compiler/command_line_interface.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT plugin.lo -MD -MP -MF .deps/plugin.Tpo -c google/protobuf/compiler/plugin.cc -o plugin.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT plugin.pb.lo -MD -MP -MF .deps/plugin.pb.Tpo -c -o plugin.pb.lo `test -f 'google/protobuf/compiler/plugin.pb.cc' || echo './'`google/protobuf/compiler/plugin.pb.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT plugin.pb.lo -MD -MP -MF .deps/plugin.pb.Tpo -c google/protobuf/compiler/plugin.pb.cc -fPIC -DPIC -o .libs/plugin.pb.o mv -f .deps/plugin.Tpo .deps/plugin.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/phmap.cpp -o build/lib/phmap.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT subprocess.lo -MD -MP -MF .deps/subprocess.Tpo -c -o subprocess.lo `test -f 'google/protobuf/compiler/subprocess.cc' || echo './'`google/protobuf/compiler/subprocess.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT subprocess.lo -MD -MP -MF .deps/subprocess.Tpo -c google/protobuf/compiler/subprocess.cc -fPIC -DPIC -o .libs/subprocess.o In file included from ./google/protobuf/compiler/subprocess.h:43:0, from google/protobuf/compiler/subprocess.cc:33: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT subprocess.lo -MD -MP -MF .deps/subprocess.Tpo -c google/protobuf/compiler/subprocess.cc -o subprocess.o >/dev/null 2>&1 mv -f .deps/subprocess.Tpo .deps/subprocess.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/output.cpp -o build/lib/output.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT command_line_interface.lo -MD -MP -MF .deps/command_line_interface.Tpo -c google/protobuf/compiler/command_line_interface.cc -o command_line_interface.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT plugin.pb.lo -MD -MP -MF .deps/plugin.pb.Tpo -c google/protobuf/compiler/plugin.pb.cc -o plugin.pb.o >/dev/null 2>&1 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/varfunc.cpp -o build/lib/varfunc.o mv -f .deps/plugin.pb.Tpo .deps/plugin.pb.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/varfunc.cpp -o build/lib/varfunc.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT zip_writer.lo -MD -MP -MF .deps/zip_writer.Tpo -c -o zip_writer.lo `test -f 'google/protobuf/compiler/zip_writer.cc' || echo './'`google/protobuf/compiler/zip_writer.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT zip_writer.lo -MD -MP -MF .deps/zip_writer.Tpo -c google/protobuf/compiler/zip_writer.cc -fPIC -DPIC -o .libs/zip_writer.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT zip_writer.lo -MD -MP -MF .deps/zip_writer.Tpo -c google/protobuf/compiler/zip_writer.cc -o zip_writer.o >/dev/null 2>&1 mv -f .deps/zip_writer.Tpo .deps/zip_writer.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/zfstream.cpp -o build/lib/zfstream.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_enum.lo -MD -MP -MF .deps/cpp_enum.Tpo -c -o cpp_enum.lo `test -f 'google/protobuf/compiler/cpp/cpp_enum.cc' || echo './'`google/protobuf/compiler/cpp/cpp_enum.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_enum.lo -MD -MP -MF .deps/cpp_enum.Tpo -c google/protobuf/compiler/cpp/cpp_enum.cc -fPIC -DPIC -o .libs/cpp_enum.o In file included from ./google/protobuf/compiler/cpp/cpp_options.h:38:0, from ./google/protobuf/compiler/cpp/cpp_enum.h:39, from google/protobuf/compiler/cpp/cpp_enum.cc:38: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_enum_field.lo -MD -MP -MF .deps/cpp_enum_field.Tpo -c -o cpp_enum_field.lo `test -f 'google/protobuf/compiler/cpp/cpp_enum_field.cc' || echo './'`google/protobuf/compiler/cpp/cpp_enum_field.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_enum_field.lo -MD -MP -MF .deps/cpp_enum_field.Tpo -c google/protobuf/compiler/cpp/cpp_enum_field.cc -fPIC -DPIC -o .libs/cpp_enum_field.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/variant.cpp -o build/lib/variant.o In file included from ./google/protobuf/compiler/cpp/cpp_field.h:41:0, from ./google/protobuf/compiler/cpp/cpp_enum_field.h:40, from google/protobuf/compiler/cpp/cpp_enum_field.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ mv -f .deps/command_line_interface.Tpo .deps/command_line_interface.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/meta.cpp -o build/lib/meta.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_enum_field.lo -MD -MP -MF .deps/cpp_enum_field.Tpo -c google/protobuf/compiler/cpp/cpp_enum_field.cc -o cpp_enum_field.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_enum.lo -MD -MP -MF .deps/cpp_enum.Tpo -c google/protobuf/compiler/cpp/cpp_enum.cc -o cpp_enum.o >/dev/null 2>&1 mv -f .deps/cpp_enum_field.Tpo .deps/cpp_enum_field.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/c8lib.cpp -o build/lib/c8lib.o mv -f .deps/cpp_enum.Tpo .deps/cpp_enum.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_extension.lo -MD -MP -MF .deps/cpp_extension.Tpo -c -o cpp_extension.lo `test -f 'google/protobuf/compiler/cpp/cpp_extension.cc' || echo './'`google/protobuf/compiler/cpp/cpp_extension.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_extension.lo -MD -MP -MF .deps/cpp_extension.Tpo -c google/protobuf/compiler/cpp/cpp_extension.cc -fPIC -DPIC -o .libs/cpp_extension.o In file included from ./google/protobuf/compiler/cpp/cpp_extension.h:39:0, from google/protobuf/compiler/cpp/cpp_extension.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_field.lo -MD -MP -MF .deps/cpp_field.Tpo -c -o cpp_field.lo `test -f 'google/protobuf/compiler/cpp/cpp_field.cc' || echo './'`google/protobuf/compiler/cpp/cpp_field.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_field.lo -MD -MP -MF .deps/cpp_field.Tpo -c google/protobuf/compiler/cpp/cpp_field.cc -fPIC -DPIC -o .libs/cpp_field.o In file included from ./google/protobuf/compiler/cpp/cpp_field.h:41:0, from google/protobuf/compiler/cpp/cpp_field.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_field.lo -MD -MP -MF .deps/cpp_field.Tpo -c google/protobuf/compiler/cpp/cpp_field.cc -o cpp_field.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_file.lo -MD -MP -MF .deps/cpp_file.Tpo -c -o cpp_file.lo `test -f 'google/protobuf/compiler/cpp/cpp_file.cc' || echo './'`google/protobuf/compiler/cpp/cpp_file.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_file.lo -MD -MP -MF .deps/cpp_file.Tpo -c google/protobuf/compiler/cpp/cpp_file.cc -fPIC -DPIC -o .libs/cpp_file.o In file included from ./google/protobuf/compiler/cpp/cpp_file.h:40:0, from google/protobuf/compiler/cpp/cpp_file.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_file.lo -MD -MP -MF .deps/cpp_file.Tpo -c google/protobuf/compiler/cpp/cpp_file.cc -o cpp_file.o >/dev/null 2>&1 mv -f .deps/cpp_field.Tpo .deps/cpp_field.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/em.cpp -o build/lib/em.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_extension.lo -MD -MP -MF .deps/cpp_extension.Tpo -c google/protobuf/compiler/cpp/cpp_extension.cc -o cpp_extension.o >/dev/null 2>&1 mv -f .deps/cpp_file.Tpo .deps/cpp_file.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/matrix.pb.cpp -o build/lib/matrix.pb.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_generator.lo -MD -MP -MF .deps/cpp_generator.Tpo -c -o cpp_generator.lo `test -f 'google/protobuf/compiler/cpp/cpp_generator.cc' || echo './'`google/protobuf/compiler/cpp/cpp_generator.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_generator.lo -MD -MP -MF .deps/cpp_generator.Tpo -c google/protobuf/compiler/cpp/cpp_generator.cc -fPIC -DPIC -o .libs/cpp_generator.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_generator.lo -MD -MP -MF .deps/cpp_generator.Tpo -c google/protobuf/compiler/cpp/cpp_generator.cc -o cpp_generator.o >/dev/null 2>&1 mv -f .deps/cpp_extension.Tpo .deps/cpp_extension.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vcfz.cpp -o build/lib/vcfz.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_helpers.lo -MD -MP -MF .deps/cpp_helpers.Tpo -c -o cpp_helpers.lo `test -f 'google/protobuf/compiler/cpp/cpp_helpers.cc' || echo './'`google/protobuf/compiler/cpp/cpp_helpers.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_helpers.lo -MD -MP -MF .deps/cpp_helpers.Tpo -c google/protobuf/compiler/cpp/cpp_helpers.cc -fPIC -DPIC -o .libs/cpp_helpers.o mv -f .deps/cpp_generator.Tpo .deps/cpp_generator.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/eval.cpp -o build/lib/eval.o In file included from ./google/protobuf/stubs/hash.h:39:0, from google/protobuf/compiler/cpp/cpp_helpers.cc:38: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ google/protobuf/compiler/cpp/cpp_helpers.cc: In function 'std::__cxx11::string google::protobuf::compiler::cpp::DefaultValue(const google::protobuf::FieldDescriptor*)': google/protobuf/compiler/cpp/cpp_helpers.cc:265:57: warning: typedef 'kint32min_value_error' locally defined but not used [-Wunused-local-typedefs] GOOGLE_COMPILE_ASSERT(kint32min == -0x80000000, kint32min_value_error); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ google/protobuf/compiler/cpp/cpp_helpers.cc:276:24: warning: typedef 'kint64min_value_error' locally defined but not used [-Wunused-local-typedefs] kint64min_value_error); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/svar.cpp -o build/lib/svar.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_helpers.lo -MD -MP -MF .deps/cpp_helpers.Tpo -c google/protobuf/compiler/cpp/cpp_helpers.cc -o cpp_helpers.o >/dev/null 2>&1 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/genic.cpp -o build/lib/genic.o mv -f .deps/cpp_helpers.Tpo .deps/cpp_helpers.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_message.lo -MD -MP -MF .deps/cpp_message.Tpo -c -o cpp_message.lo `test -f 'google/protobuf/compiler/cpp/cpp_message.cc' || echo './'`google/protobuf/compiler/cpp/cpp_message.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_message.lo -MD -MP -MF .deps/cpp_message.Tpo -c google/protobuf/compiler/cpp/cpp_message.cc -fPIC -DPIC -o .libs/cpp_message.o In file included from ./google/protobuf/stubs/hash.h:39:0, from google/protobuf/compiler/cpp/cpp_message.cc:36: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_message_field.lo -MD -MP -MF .deps/cpp_message_field.Tpo -c -o cpp_message_field.lo `test -f 'google/protobuf/compiler/cpp/cpp_message_field.cc' || echo './'`google/protobuf/compiler/cpp/cpp_message_field.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_message_field.lo -MD -MP -MF .deps/cpp_message_field.Tpo -c google/protobuf/compiler/cpp/cpp_message_field.cc -fPIC -DPIC -o .libs/cpp_message_field.o In file included from ./google/protobuf/compiler/cpp/cpp_field.h:41:0, from ./google/protobuf/compiler/cpp/cpp_message_field.h:40, from google/protobuf/compiler/cpp/cpp_message_field.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_message_field.lo -MD -MP -MF .deps/cpp_message_field.Tpo -c google/protobuf/compiler/cpp/cpp_message_field.cc -o cpp_message_field.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_primitive_field.lo -MD -MP -MF .deps/cpp_primitive_field.Tpo -c -o cpp_primitive_field.lo `test -f 'google/protobuf/compiler/cpp/cpp_primitive_field.cc' || echo './'`google/protobuf/compiler/cpp/cpp_primitive_field.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_primitive_field.lo -MD -MP -MF .deps/cpp_primitive_field.Tpo -c google/protobuf/compiler/cpp/cpp_primitive_field.cc -fPIC -DPIC -o .libs/cpp_primitive_field.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_message.lo -MD -MP -MF .deps/cpp_message.Tpo -c google/protobuf/compiler/cpp/cpp_message.cc -o cpp_message.o >/dev/null 2>&1 In file included from ./google/protobuf/compiler/cpp/cpp_field.h:41:0, from ./google/protobuf/compiler/cpp/cpp_primitive_field.h:40, from google/protobuf/compiler/cpp/cpp_primitive_field.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ mv -f .deps/cpp_message_field.Tpo .deps/cpp_message_field.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/protdb.cpp -o build/lib/protdb.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_primitive_field.lo -MD -MP -MF .deps/cpp_primitive_field.Tpo -c google/protobuf/compiler/cpp/cpp_primitive_field.cc -o cpp_primitive_field.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_service.lo -MD -MP -MF .deps/cpp_service.Tpo -c -o cpp_service.lo `test -f 'google/protobuf/compiler/cpp/cpp_service.cc' || echo './'`google/protobuf/compiler/cpp/cpp_service.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_service.lo -MD -MP -MF .deps/cpp_service.Tpo -c google/protobuf/compiler/cpp/cpp_service.cc -fPIC -DPIC -o .libs/cpp_service.o mv -f .deps/cpp_primitive_field.Tpo .deps/cpp_primitive_field.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/annot.cpp -o build/lib/annot.o In file included from ./google/protobuf/compiler/cpp/cpp_service.h:40:0, from google/protobuf/compiler/cpp/cpp_service.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_service.lo -MD -MP -MF .deps/cpp_service.Tpo -c google/protobuf/compiler/cpp/cpp_service.cc -o cpp_service.o >/dev/null 2>&1 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/webcheck.cpp -o build/lib/webcheck.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_string_field.lo -MD -MP -MF .deps/cpp_string_field.Tpo -c -o cpp_string_field.lo `test -f 'google/protobuf/compiler/cpp/cpp_string_field.cc' || echo './'`google/protobuf/compiler/cpp/cpp_string_field.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_string_field.lo -MD -MP -MF .deps/cpp_string_field.Tpo -c google/protobuf/compiler/cpp/cpp_string_field.cc -fPIC -DPIC -o .libs/cpp_string_field.o In file included from ./google/protobuf/compiler/cpp/cpp_field.h:41:0, from ./google/protobuf/compiler/cpp/cpp_string_field.h:40, from google/protobuf/compiler/cpp/cpp_string_field.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ mv -f .deps/cpp_service.Tpo .deps/cpp_service.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/locdb.cpp -o build/lib/locdb.o mv -f .deps/cpp_message.Tpo .deps/cpp_message.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/allele.cpp -o build/lib/allele.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT cpp_string_field.lo -MD -MP -MF .deps/cpp_string_field.Tpo -c google/protobuf/compiler/cpp/cpp_string_field.cc -o cpp_string_field.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_enum.lo -MD -MP -MF .deps/java_enum.Tpo -c -o java_enum.lo `test -f 'google/protobuf/compiler/java/java_enum.cc' || echo './'`google/protobuf/compiler/java/java_enum.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_enum.lo -MD -MP -MF .deps/java_enum.Tpo -c google/protobuf/compiler/java/java_enum.cc -fPIC -DPIC -o .libs/java_enum.o mv -f .deps/cpp_string_field.Tpo .deps/cpp_string_field.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/matdb.cpp -o build/lib/matdb.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/func.cpp -o build/lib/func.o In file included from ./google/protobuf/descriptor.h:59:0, from ./google/protobuf/compiler/java/java_enum.h:40, from google/protobuf/compiler/java/java_enum.cc:38: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_enum.lo -MD -MP -MF .deps/java_enum.Tpo -c google/protobuf/compiler/java/java_enum.cc -o java_enum.o >/dev/null 2>&1 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/filemap.cpp -o build/lib/filemap.o mv -f .deps/java_enum.Tpo .deps/java_enum.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_enum_field.lo -MD -MP -MF .deps/java_enum_field.Tpo -c -o java_enum_field.lo `test -f 'google/protobuf/compiler/java/java_enum_field.cc' || echo './'`google/protobuf/compiler/java/java_enum_field.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_enum_field.lo -MD -MP -MF .deps/java_enum_field.Tpo -c google/protobuf/compiler/java/java_enum_field.cc -fPIC -DPIC -o .libs/java_enum_field.o In file included from ./google/protobuf/compiler/java/java_field.h:39:0, from ./google/protobuf/compiler/java/java_enum_field.h:40, from google/protobuf/compiler/java/java_enum_field.cc:38: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_enum_field.lo -MD -MP -MF .deps/java_enum_field.Tpo -c google/protobuf/compiler/java/java_enum_field.cc -o java_enum_field.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_extension.lo -MD -MP -MF .deps/java_extension.Tpo -c -o java_extension.lo `test -f 'google/protobuf/compiler/java/java_extension.cc' || echo './'`google/protobuf/compiler/java/java_extension.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_extension.lo -MD -MP -MF .deps/java_extension.Tpo -c google/protobuf/compiler/java/java_extension.cc -fPIC -DPIC -o .libs/java_extension.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_field.lo -MD -MP -MF .deps/java_field.Tpo -c -o java_field.lo `test -f 'google/protobuf/compiler/java/java_field.cc' || echo './'`google/protobuf/compiler/java/java_field.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_field.lo -MD -MP -MF .deps/java_field.Tpo -c google/protobuf/compiler/java/java_field.cc -fPIC -DPIC -o .libs/java_field.o In file included from ./google/protobuf/compiler/java/java_extension.h:40:0, from google/protobuf/compiler/java/java_extension.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_field.lo -MD -MP -MF .deps/java_field.Tpo -c google/protobuf/compiler/java/java_field.cc -o java_field.o >/dev/null 2>&1 mv -f .deps/java_enum_field.Tpo .deps/java_enum_field.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/netfunc.cpp -o build/lib/netfunc.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_file.lo -MD -MP -MF .deps/java_file.Tpo -c -o java_file.lo `test -f 'google/protobuf/compiler/java/java_file.cc' || echo './'`google/protobuf/compiler/java/java_file.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_file.lo -MD -MP -MF .deps/java_file.Tpo -c google/protobuf/compiler/java/java_file.cc -fPIC -DPIC -o .libs/java_file.o mv -f .deps/java_field.Tpo .deps/java_field.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/reffuncs.cpp -o build/lib/reffuncs.o In file included from ./google/protobuf/compiler/java/java_file.h:40:0, from google/protobuf/compiler/java/java_file.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_generator.lo -MD -MP -MF .deps/java_generator.Tpo -c -o java_generator.lo `test -f 'google/protobuf/compiler/java/java_generator.cc' || echo './'`google/protobuf/compiler/java/java_generator.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_generator.lo -MD -MP -MF .deps/java_generator.Tpo -c google/protobuf/compiler/java/java_generator.cc -fPIC -DPIC -o .libs/java_generator.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_file.lo -MD -MP -MF .deps/java_file.Tpo -c google/protobuf/compiler/java/java_file.cc -o java_file.o >/dev/null 2>&1 In file included from ./google/protobuf/compiler/code_generator.h:41:0, from ./google/protobuf/compiler/java/java_generator.h:41, from google/protobuf/compiler/java/java_generator.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_extension.lo -MD -MP -MF .deps/java_extension.Tpo -c google/protobuf/compiler/java/java_extension.cc -o java_extension.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_generator.lo -MD -MP -MF .deps/java_generator.Tpo -c google/protobuf/compiler/java/java_generator.cc -o java_generator.o >/dev/null 2>&1 mv -f .deps/java_file.Tpo .deps/java_file.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/r8lib.cpp -o build/lib/r8lib.o mv -f .deps/java_generator.Tpo .deps/java_generator.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/varmeta.cpp -o build/lib/varmeta.o mv -f .deps/java_extension.Tpo .deps/java_extension.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_helpers.lo -MD -MP -MF .deps/java_helpers.Tpo -c -o java_helpers.lo `test -f 'google/protobuf/compiler/java/java_helpers.cc' || echo './'`google/protobuf/compiler/java/java_helpers.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_helpers.lo -MD -MP -MF .deps/java_helpers.Tpo -c google/protobuf/compiler/java/java_helpers.cc -fPIC -DPIC -o .libs/java_helpers.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/ibs.cpp -o build/lib/ibs.o In file included from ./google/protobuf/descriptor.pb.h:9:0, from ./google/protobuf/compiler/java/java_helpers.h:39, from google/protobuf/compiler/java/java_helpers.cc:38: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_message.lo -MD -MP -MF .deps/java_message.Tpo -c -o java_message.lo `test -f 'google/protobuf/compiler/java/java_message.cc' || echo './'`google/protobuf/compiler/java/java_message.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_message.lo -MD -MP -MF .deps/java_message.Tpo -c google/protobuf/compiler/java/java_message.cc -fPIC -DPIC -o .libs/java_message.o In file included from ./google/protobuf/compiler/java/java_message.h:39:0, from google/protobuf/compiler/java/java_message.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_helpers.lo -MD -MP -MF .deps/java_helpers.Tpo -c google/protobuf/compiler/java/java_helpers.cc -o java_helpers.o >/dev/null 2>&1 mv -f .deps/java_helpers.Tpo .deps/java_helpers.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/genotype.cpp -o build/lib/genotype.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/seqdb.cpp -o build/lib/seqdb.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/matdb.cpp -o build/lib/matdb.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_message.lo -MD -MP -MF .deps/java_message.Tpo -c google/protobuf/compiler/java/java_message.cc -o java_message.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_message_field.lo -MD -MP -MF .deps/java_message_field.Tpo -c -o java_message_field.lo `test -f 'google/protobuf/compiler/java/java_message_field.cc' || echo './'`google/protobuf/compiler/java/java_message_field.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_message_field.lo -MD -MP -MF .deps/java_message_field.Tpo -c google/protobuf/compiler/java/java_message_field.cc -fPIC -DPIC -o .libs/java_message_field.o In file included from ./google/protobuf/compiler/java/java_field.h:39:0, from ./google/protobuf/compiler/java/java_message_field.h:40, from google/protobuf/compiler/java/java_message_field.cc:38: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_message_field.lo -MD -MP -MF .deps/java_message_field.Tpo -c google/protobuf/compiler/java/java_message_field.cc -o java_message_field.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_primitive_field.lo -MD -MP -MF .deps/java_primitive_field.Tpo -c -o java_primitive_field.lo `test -f 'google/protobuf/compiler/java/java_primitive_field.cc' || echo './'`google/protobuf/compiler/java/java_primitive_field.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_primitive_field.lo -MD -MP -MF .deps/java_primitive_field.Tpo -c google/protobuf/compiler/java/java_primitive_field.cc -fPIC -DPIC -o .libs/java_primitive_field.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/extra.cpp -o build/lib/extra.o In file included from ./google/protobuf/compiler/java/java_field.h:39:0, from ./google/protobuf/compiler/java/java_primitive_field.h:40, from google/protobuf/compiler/java/java_primitive_field.cc:38: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_primitive_field.lo -MD -MP -MF .deps/java_primitive_field.Tpo -c google/protobuf/compiler/java/java_primitive_field.cc -o java_primitive_field.o >/dev/null 2>&1 mv -f .deps/java_message.Tpo .deps/java_message.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/network.cpp -o build/lib/network.o /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_service.lo -MD -MP -MF .deps/java_service.Tpo -c -o java_service.lo `test -f 'google/protobuf/compiler/java/java_service.cc' || echo './'`google/protobuf/compiler/java/java_service.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_service.lo -MD -MP -MF .deps/java_service.Tpo -c google/protobuf/compiler/java/java_service.cc -fPIC -DPIC -o .libs/java_service.o mv -f .deps/java_message_field.Tpo .deps/java_message_field.Plo cc -c -pipe -O2 -fno-strict-aliasing -DSQLITE_OMIT_LOAD_EXTENSION -I./sources/include -I../ext/sources/include/ sources/lib/sqlite3.c -o build/lib/sqlite3.o In file included from ./google/protobuf/descriptor.h:59:0, from ./google/protobuf/compiler/java/java_service.h:39, from google/protobuf/compiler/java/java_service.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ mv -f .deps/java_primitive_field.Tpo .deps/java_primitive_field.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_string_field.lo -MD -MP -MF .deps/java_string_field.Tpo -c -o java_string_field.lo `test -f 'google/protobuf/compiler/java/java_string_field.cc' || echo './'`google/protobuf/compiler/java/java_string_field.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_string_field.lo -MD -MP -MF .deps/java_string_field.Tpo -c google/protobuf/compiler/java/java_string_field.cc -fPIC -DPIC -o .libs/java_string_field.o In file included from ./google/protobuf/compiler/java/java_field.h:39:0, from ./google/protobuf/compiler/java/java_string_field.h:41, from google/protobuf/compiler/java/java_string_field.cc:39: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/ibd.cpp -o build/lib/ibd.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_string_field.lo -MD -MP -MF .deps/java_string_field.Tpo -c google/protobuf/compiler/java/java_string_field.cc -o java_string_field.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_service.lo -MD -MP -MF .deps/java_service.Tpo -c google/protobuf/compiler/java/java_service.cc -o java_service.o >/dev/null 2>&1 mv -f .deps/java_string_field.Tpo .deps/java_string_field.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_doc_comment.lo -MD -MP -MF .deps/java_doc_comment.Tpo -c -o java_doc_comment.lo `test -f 'google/protobuf/compiler/java/java_doc_comment.cc' || echo './'`google/protobuf/compiler/java/java_doc_comment.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_doc_comment.lo -MD -MP -MF .deps/java_doc_comment.Tpo -c google/protobuf/compiler/java/java_doc_comment.cc -fPIC -DPIC -o .libs/java_doc_comment.o mv -f .deps/java_service.Tpo .deps/java_service.Plo /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT python_generator.lo -MD -MP -MF .deps/python_generator.Tpo -c -o python_generator.lo `test -f 'google/protobuf/compiler/python/python_generator.cc' || echo './'`google/protobuf/compiler/python/python_generator.cc libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT python_generator.lo -MD -MP -MF .deps/python_generator.Tpo -c google/protobuf/compiler/python/python_generator.cc -fPIC -DPIC -o .libs/python_generator.o In file included from ./google/protobuf/descriptor.h:59:0, from ./google/protobuf/compiler/java/java_doc_comment.h:38, from google/protobuf/compiler/java/java_doc_comment.cc:35: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT java_doc_comment.lo -MD -MP -MF .deps/java_doc_comment.Tpo -c google/protobuf/compiler/java/java_doc_comment.cc -o java_doc_comment.o >/dev/null 2>&1 In file included from ./google/protobuf/compiler/code_generator.h:41:0, from ./google/protobuf/compiler/python/python_generator.h:40, from google/protobuf/compiler/python/python_generator.cc:51: ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:319:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_int64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ ./google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)': ./google/protobuf/stubs/strutil.h:325:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs] sizeof_uint64_is_not_sizeof_long_long); ^ ./google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT' msg[bool(expr) ? 1 : -1] ^ mv -f .deps/java_doc_comment.Tpo .deps/java_doc_comment.Plo /bin/sh ../libtool --tag=CXX --mode=link c++ -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -version-info 8:0:0 -export-dynamic -no-undefined -o libprotobuf.la -rpath /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib atomicops_internals_x86_gcc.lo atomicops_internals_x86_msvc.lo common.lo once.lo stringprintf.lo extension_set.lo generated_message_util.lo message_lite.lo repeated_field.lo wire_format_lite.lo coded_stream.lo zero_copy_stream.lo zero_copy_stream_impl_lite.lo strutil.lo substitute.lo structurally_valid.lo descriptor.lo descriptor.pb.lo descriptor_database.lo dynamic_message.lo extension_set_heavy.lo generated_message_reflection.lo message.lo reflection_ops.lo service.lo text_format.lo unknown_field_set.lo wire_format.lo gzip_stream.lo printer.lo tokenizer.lo zero_copy_stream_impl.lo importer.lo parser.lo -lpthread -lz libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc50/crtbeginS.o .libs/atomicops_internals_x86_gcc.o .libs/atomicops_internals_x86_msvc.o .libs/common.o .libs/once.o .libs/stringprintf.o .libs/extension_set.o .libs/generated_message_util.o .libs/message_lite.o .libs/repeated_field.o .libs/wire_format_lite.o .libs/coded_stream.o .libs/zero_copy_stream.o .libs/zero_copy_stream_impl_lite.o .libs/strutil.o .libs/substitute.o .libs/structurally_valid.o .libs/descriptor.o .libs/descriptor.pb.o .libs/descriptor_database.o .libs/dynamic_message.o .libs/extension_set_heavy.o .libs/generated_message_reflection.o .libs/message.o .libs/reflection_ops.o .libs/service.o .libs/text_format.o .libs/unknown_field_set.o .libs/wire_format.o .libs/gzip_stream.o .libs/printer.o .libs/tokenizer.o .libs/zero_copy_stream_impl.o .libs/importer.o .libs/parser.o -lpthread -lz -L/usr/lib/gcc50 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc50/crtendS.o /usr/lib/crtn.o -pthread -O2 -pthread -Wl,-soname -Wl,libprotobuf.so.8 -o .libs/libprotobuf.so.8.0.0 libtool: link: (cd ".libs" && rm -f "libprotobuf.so.8" && ln -s "libprotobuf.so.8.0.0" "libprotobuf.so.8") libtool: link: (cd ".libs" && rm -f "libprotobuf.so" && ln -s "libprotobuf.so.8.0.0" "libprotobuf.so") libtool: link: ar cru .libs/libprotobuf.a atomicops_internals_x86_gcc.o atomicops_internals_x86_msvc.o common.o once.o stringprintf.o extension_set.o generated_message_util.o message_lite.o repeated_field.o wire_format_lite.o coded_stream.o zero_copy_stream.o zero_copy_stream_impl_lite.o strutil.o substitute.o structurally_valid.o descriptor.o descriptor.pb.o descriptor_database.o dynamic_message.o extension_set_heavy.o generated_message_reflection.o message.o reflection_ops.o service.o text_format.o unknown_field_set.o wire_format.o gzip_stream.o printer.o tokenizer.o zero_copy_stream_impl.o importer.o parser.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libprotobuf.a libtool: link: ( cd ".libs" && rm -f "libprotobuf.la" && ln -s "../libprotobuf.la" "libprotobuf.la" ) c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/sockets.cpp -o build/lib/sockets.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/util.cpp -o build/lib/util.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -MT python_generator.lo -MD -MP -MF .deps/python_generator.Tpo -c google/protobuf/compiler/python/python_generator.cc -o python_generator.o >/dev/null 2>&1 mv -f .deps/python_generator.Tpo .deps/python_generator.Plo /bin/sh ../libtool --tag=CXX --mode=link c++ -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -version-info 8:0:0 -export-dynamic -no-undefined -o libprotoc.la -rpath /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib code_generator.lo command_line_interface.lo plugin.lo plugin.pb.lo subprocess.lo zip_writer.lo cpp_enum.lo cpp_enum_field.lo cpp_extension.lo cpp_field.lo cpp_file.lo cpp_generator.lo cpp_helpers.lo cpp_message.lo cpp_message_field.lo cpp_primitive_field.lo cpp_service.lo cpp_string_field.lo java_enum.lo java_enum_field.lo java_extension.lo java_field.lo java_file.lo java_generator.lo java_helpers.lo java_message.lo java_message_field.lo java_primitive_field.lo java_service.lo java_string_field.lo java_doc_comment.lo python_generator.lo -lpthread libprotobuf.la -lz libtool: link: c++ -fPIC -DPIC -shared -nostdlib 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-lc -lgcc -lgcc_pic /usr/lib/gcc50/crtendS.o /usr/lib/crtn.o -pthread -O2 -pthread -Wl,-soname -Wl,libprotoc.so.8 -o .libs/libprotoc.so.8.0.0 libtool: link: (cd ".libs" && rm -f "libprotoc.so.8" && ln -s "libprotoc.so.8.0.0" "libprotoc.so.8") libtool: link: (cd ".libs" && rm -f "libprotoc.so" && ln -s "libprotoc.so.8.0.0" "libprotoc.so") libtool: link: ar cru .libs/libprotoc.a code_generator.o command_line_interface.o plugin.o plugin.pb.o subprocess.o zip_writer.o cpp_enum.o cpp_enum_field.o cpp_extension.o cpp_field.o cpp_file.o cpp_generator.o cpp_helpers.o cpp_message.o cpp_message_field.o cpp_primitive_field.o cpp_service.o cpp_string_field.o java_enum.o java_enum_field.o java_extension.o java_field.o java_file.o java_generator.o java_helpers.o java_message.o java_message_field.o java_primitive_field.o java_service.o java_string_field.o java_doc_comment.o python_generator.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libprotoc.a libtool: link: ( cd ".libs" && rm -f "libprotoc.la" && ln -s "../libprotoc.la" "libprotoc.la" ) /bin/sh ../libtool --tag=CXX --mode=link c++ -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -pthread -o protoc main.o -lpthread libprotobuf.la libprotoc.la -lz libtool: link: c++ -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -pthread -o .libs/protoc main.o -lpthread ./.libs/libprotobuf.so ./.libs/libprotoc.so -lz -pthread -Wl,-rpath -Wl,/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib oldpwd=`pwd` && ( cd . && $oldpwd/protoc -I. --cpp_out=$oldpwd google/protobuf/unittest.proto google/protobuf/unittest_empty.proto google/protobuf/unittest_import.proto google/protobuf/unittest_import_public.proto google/protobuf/unittest_mset.proto google/protobuf/unittest_optimize_for.proto google/protobuf/unittest_embed_optimize_for.proto google/protobuf/unittest_custom_options.proto google/protobuf/unittest_lite.proto google/protobuf/unittest_import_lite.proto google/protobuf/unittest_import_public_lite.proto google/protobuf/unittest_lite_imports_nonlite.proto google/protobuf/unittest_no_generic_services.proto google/protobuf/compiler/cpp/cpp_test_bad_identifiers.proto ) touch unittest_proto_middleman gmake all-am gmake[7]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' /bin/sh ../libtool --tag=CXX --mode=link c++ -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -version-info 8:0:0 -export-dynamic -no-undefined -o libprotobuf-lite.la -rpath /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib atomicops_internals_x86_gcc.lo atomicops_internals_x86_msvc.lo common.lo once.lo stringprintf.lo extension_set.lo generated_message_util.lo message_lite.lo repeated_field.lo wire_format_lite.lo coded_stream.lo zero_copy_stream.lo zero_copy_stream_impl_lite.lo -lpthread -lz libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc50/crtbeginS.o .libs/atomicops_internals_x86_gcc.o .libs/atomicops_internals_x86_msvc.o .libs/common.o .libs/once.o .libs/stringprintf.o .libs/extension_set.o .libs/generated_message_util.o .libs/message_lite.o .libs/repeated_field.o .libs/wire_format_lite.o .libs/coded_stream.o .libs/zero_copy_stream.o .libs/zero_copy_stream_impl_lite.o -lpthread -lz -L/usr/lib/gcc50 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc50/crtendS.o /usr/lib/crtn.o -pthread -O2 -pthread -Wl,-soname -Wl,libprotobuf-lite.so.8 -o .libs/libprotobuf-lite.so.8.0.0 libtool: link: (cd ".libs" && rm -f "libprotobuf-lite.so.8" && ln -s "libprotobuf-lite.so.8.0.0" "libprotobuf-lite.so.8") libtool: link: (cd ".libs" && rm -f "libprotobuf-lite.so" && ln -s "libprotobuf-lite.so.8.0.0" "libprotobuf-lite.so") libtool: link: ar cru .libs/libprotobuf-lite.a atomicops_internals_x86_gcc.o atomicops_internals_x86_msvc.o common.o once.o stringprintf.o extension_set.o generated_message_util.o message_lite.o repeated_field.o wire_format_lite.o coded_stream.o zero_copy_stream.o zero_copy_stream_impl_lite.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libprotobuf-lite.a libtool: link: ( cd ".libs" && rm -f "libprotobuf-lite.la" && ln -s "../libprotobuf-lite.la" "libprotobuf-lite.la" ) gmake[7]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[6]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[5]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[4]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[4]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' Making install in . gmake[5]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[6]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[6]: Nothing to be done for 'install-exec-am'. test -z "/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/pkgconfig" || ./install-sh -c -d "/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/pkgconfig" /usr/bin/install -c -m 644 protobuf.pc protobuf-lite.pc '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/pkgconfig' gmake[6]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[5]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' Making install in src gmake[5]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake install-am gmake[6]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[7]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' test -z "/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib" || .././install-sh -c -d "/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib" test -z "/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include" || .././install-sh -c -d "/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include" test -z "/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include" || .././install-sh -c -d "/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include" /bin/sh ../libtool --mode=install /usr/bin/install -c libprotobuf-lite.la libprotobuf.la libprotoc.la '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib' .././install-sh -c -d '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf' libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.so.8.0.0 /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf-lite.so.8.0.0 libtool: install: (cd /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib && { ln -s -f libprotobuf-lite.so.8.0.0 libprotobuf-lite.so.8 || { rm -f libprotobuf-lite.so.8 && ln -s libprotobuf-lite.so.8.0.0 libprotobuf-lite.so.8; }; }) libtool: install: (cd /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib && { ln -s -f libprotobuf-lite.so.8.0.0 libprotobuf-lite.so || { rm -f libprotobuf-lite.so && ln -s libprotobuf-lite.so.8.0.0 libprotobuf-lite.so; }; }) libtool: 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install: (cd /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/src; /bin/sh /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/libtool --tag CXX --mode=relink c++ -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -version-info 8:0:0 -export-dynamic -no-undefined -o libprotoc.la -rpath /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib code_generator.lo command_line_interface.lo plugin.lo plugin.pb.lo subprocess.lo zip_writer.lo cpp_enum.lo cpp_enum_field.lo cpp_extension.lo cpp_field.lo cpp_file.lo cpp_generator.lo cpp_helpers.lo cpp_message.lo cpp_message_field.lo cpp_primitive_field.lo cpp_service.lo cpp_string_field.lo java_enum.lo java_enum_field.lo java_extension.lo java_field.lo java_file.lo java_generator.lo java_helpers.lo java_message.lo java_message_field.lo java_primitive_field.lo java_service.lo java_string_field.lo java_doc_comment.lo python_generator.lo -lpthread libprotobuf.la -lz ) .././install-sh -c -d '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler/python' /usr/bin/install -c -m 644 google/protobuf/compiler/python/python_generator.h '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler/python' .././install-sh -c -d '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler/cpp' /usr/bin/install -c -m 644 google/protobuf/compiler/cpp/cpp_generator.h '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler/cpp' .././install-sh -c -d '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/stubs' /usr/bin/install -c -m 644 google/protobuf/stubs/atomicops.h google/protobuf/stubs/atomicops_internals_arm_gcc.h google/protobuf/stubs/atomicops_internals_arm_qnx.h google/protobuf/stubs/atomicops_internals_atomicword_compat.h google/protobuf/stubs/atomicops_internals_macosx.h google/protobuf/stubs/atomicops_internals_mips_gcc.h google/protobuf/stubs/atomicops_internals_pnacl.h google/protobuf/stubs/atomicops_internals_x86_gcc.h google/protobuf/stubs/atomicops_internals_x86_msvc.h google/protobuf/stubs/common.h google/protobuf/stubs/platform_macros.h google/protobuf/stubs/once.h google/protobuf/stubs/template_util.h google/protobuf/stubs/type_traits.h '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/stubs' .././install-sh -c -d '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/io' /usr/bin/install -c -m 644 google/protobuf/io/coded_stream.h google/protobuf/io/gzip_stream.h google/protobuf/io/printer.h google/protobuf/io/tokenizer.h google/protobuf/io/zero_copy_stream.h google/protobuf/io/zero_copy_stream_impl.h google/protobuf/io/zero_copy_stream_impl_lite.h '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/io' .././install-sh -c -d '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf' /usr/bin/install -c -m 644 google/protobuf/descriptor.h google/protobuf/descriptor.pb.h google/protobuf/descriptor_database.h google/protobuf/dynamic_message.h google/protobuf/extension_set.h google/protobuf/generated_enum_reflection.h google/protobuf/generated_message_util.h google/protobuf/generated_message_reflection.h google/protobuf/message.h google/protobuf/message_lite.h google/protobuf/reflection_ops.h google/protobuf/repeated_field.h google/protobuf/service.h google/protobuf/text_format.h google/protobuf/unknown_field_set.h google/protobuf/wire_format.h google/protobuf/wire_format_lite.h google/protobuf/wire_format_lite_inl.h '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf' .././install-sh -c -d '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler/java' /usr/bin/install -c -m 644 google/protobuf/compiler/java/java_generator.h '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler/java' .././install-sh -c -d '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler' /usr/bin/install -c -m 644 google/protobuf/compiler/code_generator.h google/protobuf/compiler/command_line_interface.h google/protobuf/compiler/importer.h google/protobuf/compiler/parser.h google/protobuf/compiler/plugin.h google/protobuf/compiler/plugin.pb.h '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler' /usr/bin/install -c -m 644 google/protobuf/descriptor.proto '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf' .././install-sh -c -d '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler' /usr/bin/install -c -m 644 google/protobuf/compiler/plugin.proto '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler' libtool: relink: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc50/crtbeginS.o .libs/code_generator.o .libs/command_line_interface.o .libs/plugin.o .libs/plugin.pb.o .libs/subprocess.o .libs/zip_writer.o .libs/cpp_enum.o .libs/cpp_enum_field.o .libs/cpp_extension.o .libs/cpp_field.o .libs/cpp_file.o .libs/cpp_generator.o .libs/cpp_helpers.o .libs/cpp_message.o .libs/cpp_message_field.o .libs/cpp_primitive_field.o .libs/cpp_service.o .libs/cpp_string_field.o .libs/java_enum.o .libs/java_enum_field.o .libs/java_extension.o .libs/java_field.o .libs/java_file.o .libs/java_generator.o .libs/java_helpers.o .libs/java_message.o .libs/java_message_field.o .libs/java_primitive_field.o .libs/java_service.o .libs/java_string_field.o .libs/java_doc_comment.o .libs/python_generator.o -Wl,-rpath -Wl,/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib -lpthread ./.libs/libprotobuf.so -lz -L/usr/lib/gcc50 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc50/crtendS.o /usr/lib/crtn.o -pthread -O2 -pthread -Wl,-soname -Wl,libprotoc.so.8 -o .libs/libprotoc.so.8.0.0 libtool: install: /usr/bin/install -c .libs/libprotoc.so.8.0.0T /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotoc.so.8.0.0 libtool: install: (cd /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib && { ln -s -f libprotoc.so.8.0.0 libprotoc.so.8 || { rm -f libprotoc.so.8 && ln -s libprotoc.so.8.0.0 libprotoc.so.8; }; }) libtool: install: (cd /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib && { ln -s -f libprotoc.so.8.0.0 libprotoc.so || { rm -f libprotoc.so && ln -s libprotoc.so.8.0.0 libprotoc.so; }; }) libtool: install: /usr/bin/install -c .libs/libprotoc.lai /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotoc.la libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.a /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf-lite.a libtool: install: chmod 644 /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf-lite.a libtool: install: ranlib /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf-lite.a libtool: install: /usr/bin/install -c .libs/libprotobuf.a /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf.a libtool: install: chmod 644 /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf.a libtool: install: ranlib /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf.a libtool: install: /usr/bin/install -c .libs/libprotoc.a /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotoc.a libtool: install: chmod 644 /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotoc.a libtool: install: ranlib /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotoc.a test -z "/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/bin" || .././install-sh -c -d "/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/bin" /bin/sh ../libtool --mode=install /usr/bin/install -c protoc '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/bin' libtool: install: /usr/bin/install -c .libs/protoc /construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/bin/protoc gmake[7]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[6]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[5]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[4]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[3]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/ext' ar rv build/lib/libpseq.a build/lib/chet.o build/lib/nets.o build/lib/views.o build/lib/glm-tests.o build/lib/gseq.o build/lib/skat.o build/lib/pops.o build/lib/kbac.o build/lib/clusters.o build/lib/davies.o build/lib/cnv.o build/lib/summaries.o build/lib/stepup.o build/lib/netassoc.o build/lib/compare.o build/lib/loaders.o build/lib/prot.o build/lib/assoc.o build/lib/varfunc.o build/lib/genic.o build/lib/webcheck.o build/lib/func.o build/lib/ibs.o build/lib/matdb.o build/lib/extra.o build/lib/ibd.o build/lib/sockets.o build/lib/util.o /usr/libexec/binutils227/elf/ar: creating build/lib/libpseq.a a - build/lib/chet.o a - build/lib/nets.o a - build/lib/views.o a - build/lib/glm-tests.o a - build/lib/gseq.o a - build/lib/skat.o a - build/lib/pops.o a - build/lib/kbac.o a - build/lib/clusters.o a - build/lib/davies.o a - build/lib/cnv.o a - build/lib/summaries.o a - build/lib/stepup.o a - build/lib/netassoc.o a - build/lib/compare.o a - build/lib/loaders.o a - build/lib/prot.o a - build/lib/assoc.o a - build/lib/varfunc.o a - build/lib/genic.o a - build/lib/webcheck.o a - build/lib/func.o a - build/lib/ibs.o a - build/lib/matdb.o a - build/lib/extra.o a - build/lib/ibd.o a - build/lib/sockets.o a - build/lib/util.o ranlib build/lib/libpseq.a gmake[3]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/pseq' ar rv build/lib/libplinkseq.a build/lib/bgzf.o build/lib/bcf.o build/lib/defs.o build/lib/indmap.o build/lib/dose.o build/lib/fisher.o build/lib/segments.o build/lib/netdb.o build/lib/regions.o build/lib/mask.o build/lib/glm.o build/lib/gstore.o build/lib/matrix_exponential.o build/lib/individual.o build/lib/refdb.o build/lib/vgroup.o build/lib/vardb.o build/lib/dcdflib.o build/lib/matrix.o build/lib/token.o build/lib/crandom.o build/lib/prob.o build/lib/statistics.o build/lib/helper.o build/lib/permute.o build/lib/globals.o build/lib/sqlwrap.o build/lib/vcfiterate.o build/lib/variant.pb.o build/lib/vcf.o build/lib/bed.o build/lib/iterate.o build/lib/inddb.o build/lib/phmap.o build/lib/output.o build/lib/varfunc.o build/lib/zfstream.o build/lib/variant.o build/lib/meta.o build/lib/c8lib.o build/lib/em.o build/lib/matrix.pb.o build/lib/vcfz.o build/lib/eval.o build/lib/svar.o build/lib/protdb.o build/lib/annot.o build/lib/locdb.o build/lib/allele.o build/lib/matdb.o build/lib/filemap.o build/lib/netfunc.o build/lib/reffuncs.o build/lib/r8lib.o build/lib/varmeta.o build/lib/genotype.o build/lib/seqdb.o build/lib/network.o build/lib/sqlite3.o /usr/libexec/binutils227/elf/ar: creating build/lib/libplinkseq.a a - build/lib/bgzf.o a - build/lib/bcf.o a - build/lib/defs.o a - build/lib/indmap.o a - build/lib/dose.o a - build/lib/fisher.o a - build/lib/segments.o a - build/lib/netdb.o a - build/lib/regions.o a - build/lib/mask.o a - build/lib/glm.o a - build/lib/gstore.o a - build/lib/matrix_exponential.o a - build/lib/individual.o a - build/lib/refdb.o a - build/lib/vgroup.o a - build/lib/vardb.o a - build/lib/dcdflib.o a - build/lib/matrix.o a - build/lib/token.o a - build/lib/crandom.o a - build/lib/prob.o a - build/lib/statistics.o a - build/lib/helper.o a - build/lib/permute.o a - build/lib/globals.o a - build/lib/sqlwrap.o a - build/lib/vcfiterate.o a - build/lib/variant.pb.o a - build/lib/vcf.o a - build/lib/bed.o a - build/lib/iterate.o a - build/lib/inddb.o a - build/lib/phmap.o a - build/lib/output.o a - build/lib/varfunc.o a - build/lib/zfstream.o a - build/lib/variant.o a - build/lib/meta.o a - build/lib/c8lib.o a - build/lib/em.o a - build/lib/matrix.pb.o a - build/lib/vcfz.o a - build/lib/eval.o a - build/lib/svar.o a - build/lib/protdb.o a - build/lib/annot.o a - build/lib/locdb.o a - build/lib/allele.o a - build/lib/matdb.o a - build/lib/filemap.o a - build/lib/netfunc.o a - build/lib/reffuncs.o a - build/lib/r8lib.o a - build/lib/varmeta.o a - build/lib/genotype.o a - build/lib/seqdb.o a - build/lib/network.o a - build/lib/sqlite3.o ranlib build/lib/libplinkseq.a gmake[3]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10/sources/plinkseq' gmake[2]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10' gmake ./pdas ./mongoose ./tab2vcf ./smp ./mm ./behead ./browser ./gcol ./pseq gmake[2]: Entering directory '/construction/biology/plinkseq/plinkseq-0.10' c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I./sources/plinkseq/./sources/include/ -I./sources/pseq/./sources/include/ -I./sources/util/./sources/include/ -I./sources/mongoose/./sources/include/ -I./sources/browser/./sources/include/ -I./sources/pdas/./sources/include/ -I./sources/ext/./sources/include/ sources/execs/pdas.cpp -o build/execs/pdas.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I./sources/plinkseq/./sources/include/ -I./sources/pseq/./sources/include/ -I./sources/util/./sources/include/ -I./sources/mongoose/./sources/include/ -I./sources/browser/./sources/include/ -I./sources/pdas/./sources/include/ -I./sources/ext/./sources/include/ sources/execs/mongoose.cpp -o build/execs/mongoose.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I./sources/plinkseq/./sources/include/ -I./sources/pseq/./sources/include/ -I./sources/util/./sources/include/ -I./sources/mongoose/./sources/include/ -I./sources/browser/./sources/include/ -I./sources/pdas/./sources/include/ -I./sources/ext/./sources/include/ sources/execs/tab2vcf.cpp -o build/execs/tab2vcf.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I./sources/plinkseq/./sources/include/ -I./sources/pseq/./sources/include/ -I./sources/util/./sources/include/ -I./sources/mongoose/./sources/include/ -I./sources/browser/./sources/include/ -I./sources/pdas/./sources/include/ -I./sources/ext/./sources/include/ sources/execs/smp.cpp -o build/execs/smp.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I./sources/plinkseq/./sources/include/ -I./sources/pseq/./sources/include/ -I./sources/util/./sources/include/ -I./sources/mongoose/./sources/include/ -I./sources/browser/./sources/include/ -I./sources/pdas/./sources/include/ -I./sources/ext/./sources/include/ sources/execs/mm.cpp -o build/execs/mm.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I./sources/plinkseq/./sources/include/ -I./sources/pseq/./sources/include/ -I./sources/util/./sources/include/ -I./sources/mongoose/./sources/include/ -I./sources/browser/./sources/include/ -I./sources/pdas/./sources/include/ -I./sources/ext/./sources/include/ sources/execs/behead.cpp -o build/execs/behead.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I./sources/plinkseq/./sources/include/ -I./sources/pseq/./sources/include/ -I./sources/util/./sources/include/ -I./sources/mongoose/./sources/include/ -I./sources/browser/./sources/include/ -I./sources/pdas/./sources/include/ -I./sources/ext/./sources/include/ sources/execs/browser.cpp -o build/execs/browser.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I./sources/plinkseq/./sources/include/ -I./sources/pseq/./sources/include/ -I./sources/util/./sources/include/ -I./sources/mongoose/./sources/include/ -I./sources/browser/./sources/include/ -I./sources/pdas/./sources/include/ -I./sources/ext/./sources/include/ sources/execs/gcol.cpp -o build/execs/gcol.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I./sources/plinkseq/./sources/include/ -I./sources/pseq/./sources/include/ -I./sources/util/./sources/include/ -I./sources/mongoose/./sources/include/ -I./sources/browser/./sources/include/ -I./sources/pdas/./sources/include/ -I./sources/ext/./sources/include/ sources/execs/pseq.cpp -o build/execs/pseq.o c++ -pipe -O2 -fno-strict-aliasing -L./sources/plinkseq/./build/lib/ -L./sources/pseq/./build/lib/ -L./sources/util/./build/lib/ -L./sources/mongoose/./build/lib/ -L./sources/browser/./build/lib/ -L./sources/pdas/./build/lib/ -L./sources/ext/./build/lib/ build/execs/mongoose.o sources/mongoose/./build/lib/libmongoose.a -lpthread -o build/execs/mongoose c++ -pipe -O2 -fno-strict-aliasing -L./sources/plinkseq/./build/lib/ -L./sources/pseq/./build/lib/ -L./sources/util/./build/lib/ -L./sources/mongoose/./build/lib/ -L./sources/browser/./build/lib/ -L./sources/pdas/./build/lib/ -L./sources/ext/./build/lib/ build/execs/tab2vcf.o sources/util/./build/lib/libutil.a -o build/execs/tab2vcf c++ -pipe -O2 -fno-strict-aliasing -L./sources/plinkseq/./build/lib/ -L./sources/pseq/./build/lib/ -L./sources/util/./build/lib/ -L./sources/mongoose/./build/lib/ -L./sources/browser/./build/lib/ -L./sources/pdas/./build/lib/ -L./sources/ext/./build/lib/ build/execs/mm.o sources/util/./build/lib/libutil.a -o build/execs/mm c++ -pipe -O2 -fno-strict-aliasing -L./sources/plinkseq/./build/lib/ -L./sources/pseq/./build/lib/ -L./sources/util/./build/lib/ -L./sources/mongoose/./build/lib/ -L./sources/browser/./build/lib/ -L./sources/pdas/./build/lib/ -L./sources/ext/./build/lib/ build/execs/behead.o -o build/execs/behead c++ -pipe -O2 -fno-strict-aliasing -L./sources/plinkseq/./build/lib/ -L./sources/pseq/./build/lib/ -L./sources/util/./build/lib/ -L./sources/mongoose/./build/lib/ -L./sources/browser/./build/lib/ -L./sources/pdas/./build/lib/ -L./sources/ext/./build/lib/ build/execs/gcol.o -o build/execs/gcol ln -fs build/execs/mongoose mongoose ln -fs build/execs/tab2vcf tab2vcf ln -fs build/execs/mm mm ln -fs build/execs/behead behead ln -fs build/execs/gcol gcol c++ -pipe -O2 -fno-strict-aliasing -L./sources/plinkseq/./build/lib/ -L./sources/pseq/./build/lib/ -L./sources/util/./build/lib/ -L./sources/mongoose/./build/lib/ -L./sources/browser/./build/lib/ -L./sources/pdas/./build/lib/ -L./sources/ext/./build/lib/ build/execs/pdas.o sources/pdas/./build/lib/libpdas.a sources/plinkseq/./build/lib/libplinkseq.a sources/ext/./build/lib/libprotobuf.a -lz -lpthread -o build/execs/pdas ln -fs build/execs/pdas pdas c++ -pipe -O2 -fno-strict-aliasing -L./sources/plinkseq/./build/lib/ -L./sources/pseq/./build/lib/ -L./sources/util/./build/lib/ -L./sources/mongoose/./build/lib/ -L./sources/browser/./build/lib/ -L./sources/pdas/./build/lib/ -L./sources/ext/./build/lib/ build/execs/smp.o sources/util/./build/lib/libutil.a sources/plinkseq/./build/lib/libplinkseq.a sources/ext/./build/lib/libprotobuf.a -lz -lpthread -o build/execs/smp ln -fs build/execs/smp smp c++ -pipe -O2 -fno-strict-aliasing -L./sources/plinkseq/./build/lib/ -L./sources/pseq/./build/lib/ -L./sources/util/./build/lib/ -L./sources/mongoose/./build/lib/ -L./sources/browser/./build/lib/ -L./sources/pdas/./build/lib/ -L./sources/ext/./build/lib/ build/execs/pseq.o sources/pseq/./build/lib/libpseq.a sources/plinkseq/./build/lib/libplinkseq.a sources/ext/./build/lib/libprotobuf.a -lpthread -lz -o build/execs/pseq ln -fs build/execs/pseq pseq c++ -pipe -O2 -fno-strict-aliasing -L./sources/plinkseq/./build/lib/ -L./sources/pseq/./build/lib/ -L./sources/util/./build/lib/ -L./sources/mongoose/./build/lib/ -L./sources/browser/./build/lib/ -L./sources/pdas/./build/lib/ -L./sources/ext/./build/lib/ build/execs/browser.o sources/browser/./build/lib/libbrowser.a sources/plinkseq/./build/lib/libplinkseq.a sources/ext/./build/lib/libprotobuf.a -lz -lpthread -o build/execs/browser ln -fs build/execs/browser browser gmake[2]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10' gmake[1]: Leaving directory '/construction/biology/plinkseq/plinkseq-0.10' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for plinkseq-0.10_1 ===> Generating temporary packing list install -s -m 555 /construction/biology/plinkseq/plinkseq-0.10/build/execs/behead /construction/biology/plinkseq/stage/usr/local/bin install -s -m 555 /construction/biology/plinkseq/plinkseq-0.10/build/execs/browser /construction/biology/plinkseq/stage/usr/local/bin install -s -m 555 /construction/biology/plinkseq/plinkseq-0.10/build/execs/gcol /construction/biology/plinkseq/stage/usr/local/bin install -s -m 555 /construction/biology/plinkseq/plinkseq-0.10/build/execs/mm /construction/biology/plinkseq/stage/usr/local/bin install -s -m 555 /construction/biology/plinkseq/plinkseq-0.10/build/execs/mongoose /construction/biology/plinkseq/stage/usr/local/bin install -s -m 555 /construction/biology/plinkseq/plinkseq-0.10/build/execs/pdas /construction/biology/plinkseq/stage/usr/local/bin install -s -m 555 /construction/biology/plinkseq/plinkseq-0.10/build/execs/pseq /construction/biology/plinkseq/stage/usr/local/bin install -s -m 555 /construction/biology/plinkseq/plinkseq-0.10/build/execs/smp /construction/biology/plinkseq/stage/usr/local/bin install -s -m 555 /construction/biology/plinkseq/plinkseq-0.10/build/execs/tab2vcf /construction/biology/plinkseq/stage/usr/local/bin install -m 0644 /construction/biology/plinkseq/plinkseq-0.10/sources/plinkseq/build/lib/libplinkseq.a /construction/biology/plinkseq/stage/usr/local/lib ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for plinkseq-0.10_1 file sizes/checksums [13]: . done packing files [13]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 11 APR 2018 at 02:46:13 UTC Duration: 00:05:36