=> Building biology/plinkseq build started at Tue Oct 4 17:46:04 PDT 2016 port directory: /usr/ports/biology/plinkseq building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: bacon4000@gmail.com ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../04//usr/ports/biology/plinkseq/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=plinkseq-0.10 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/biology/plinkseq XDG_CONFIG_HOME=/wrkdirs/biology/plinkseq HOME=/wrkdirs/biology/plinkseq TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/plinkseq XDG_CONFIG_HOME=/wrkdirs/biology/plinkseq HOME=/wrkdirs/biology/plinkseq TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" 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 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/plinkseq" EXAMPLESDIR="share/examples/plinkseq" DATADIR="share/plinkseq" WWWDIR="www/plinkseq" ETCDIR="etc/plinkseq" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/plinkseq DOCSDIR=/usr/local/share/doc/plinkseq EXAMPLESDIR=/usr/local/share/examples/plinkseq WWWDIR=/usr/local/www/plinkseq ETCDIR=/usr/local/etc/plinkseq --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===> plinkseq-0.10 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> plinkseq-0.10 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of plinkseq-0.10 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.10 for building =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.10 for building => SHA256 Checksum OK for plinkseq-src-0.10.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.10 for building ===> Extracting for plinkseq-0.10 => SHA256 Checksum OK for plinkseq-src-0.10.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for plinkseq-0.10 /usr/bin/sed -i.bak -e 's|PF_INET|AF_INET|g' /wrkdirs/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' /wrkdirs/biology/plinkseq/plinkseq-0.10/config_defs.Makefile /usr/bin/sed -i.bak -e 's| -ldl||g' -e 's| $(STATIC_FLAG)||g' /wrkdirs/biology/plinkseq/plinkseq-0.10/Makefile =========================================================================== =================================================== ===> plinkseq-0.10 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... `-- Installing indexinfo-0.2.5... `-- Extracting indexinfo-0.2.5: .... done `-- Installing gettext-runtime-0.19.8.1... `-- Extracting gettext-runtime-0.19.8.1: .......... done Extracting gmake-4.2.1_1: .......... done ===> plinkseq-0.10 depends on executable: gmake - found ===> Returning to build of plinkseq-0.10 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for plinkseq-0.10 =========================================================================== =================================================== ===> Building for plinkseq-0.10 gmake[1]: Entering directory '/wrkdirs/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/tab2vcf.cpp making depend sources/execs/mongoose.cpp making depend sources/execs/pdas.cpp gmake ./sources/plinkseq ./sources/pseq ./sources/util ./sources/mongoose ./sources/browser ./sources/pdas ./sources/ext gmake[2]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10' gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/plinkseq gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/pseq gmake[3]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/plinkseq' 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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/util' gmake[3]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/mongoose' gmake[3]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/pseq' mkdir -p build/lib making depend sources/lib/sqlite3.c mkdir -p build/lib gmake[3]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/browser' making depend sources/lib/util.cpp mkdir -p build/lib making depend sources/lib/lines.cpp mkdir -p build/lib making depend sources/lib/mongoose.c mkdir -p build/lib making depend sources/lib/char_tok.cpp cc -c -pipe -O2 -fno-strict-aliasing -DSQLITE_OMIT_LOAD_EXTENSION -I./sources/include sources/lib/mongoose.c -o build/lib/mongoose.o 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/network.cpp 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/glm-tests.cpp making depend sources/lib/seqdb.cpp making depend sources/lib/genotype.cpp making depend sources/lib/ibd.cpp making depend sources/lib/extra.cpp making depend sources/lib/varmeta.cpp ar rv build/lib/libutil.a build/lib/char_tok.o /usr/libexec/binutils225/elf/ar: creating build/lib/libutil.a a - build/lib/char_tok.o ranlib build/lib/libutil.a gmake[3]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/util' making depend sources/lib/matdb.cpp gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/pdas making depend sources/lib/vardb.cpp gmake[3]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/pdas' mkdir -p build/lib making depend sources/lib/socks.cpp making depend sources/lib/chet.cpp making depend sources/lib/statistics.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/ibs.cpp making depend sources/lib/output.cpp making depend sources/lib/func.cpp making depend sources/lib/token.cpp making depend sources/lib/webcheck.cpp making depend sources/lib/netfunc.cpp making depend sources/lib/filemap.cpp making depend sources/lib/genic.cpp making depend sources/lib/matdb.cpp making depend sources/lib/segments.cpp making depend sources/lib/varfunc.cpp making depend sources/lib/locdb.cpp making depend sources/lib/sockets.cpp making depend sources/lib/c8lib.cpp making depend sources/lib/annot.cpp making depend sources/lib/assoc.cpp making depend sources/lib/reffuncs.cpp making depend sources/lib/prot.cpp making depend sources/lib/protdb.cpp making depend sources/lib/loaders.cpp making depend sources/lib/inddb.cpp making depend sources/lib/eval.cpp making depend sources/lib/compare.cpp making depend sources/lib/vcfz.cpp making depend sources/lib/netassoc.cpp making depend sources/lib/matrix.pb.cpp making depend sources/lib/stepup.cpp making depend sources/lib/allele.cpp making depend sources/lib/r8lib.cpp making depend sources/lib/summaries.cpp making depend sources/lib/meta.cpp ar rv build/lib/libpdas.a build/lib/socks.o /usr/libexec/binutils225/elf/ar: creating build/lib/libpdas.a a - build/lib/socks.o ranlib build/lib/libpdas.a gmake[3]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/pdas' making depend sources/lib/cnv.cpp making depend sources/lib/variant.cpp gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/ext gmake[3]: Entering directory '/wrkdirs/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/clusters.cpp making depend sources/lib/kbac.cpp checking whether to enable maintainer-specific portions of Makefiles... yes checking build system type... making depend sources/lib/pops.cpp x86_64-unknown-dragonfly4.7 checking host system type... x86_64-unknown-dragonfly4.7 checking target system type... x86_64-unknown-dragonfly4.7 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... making depend sources/lib/skat.cpp ar rv build/lib/libbrowser.a build/lib/lines.o /usr/libexec/binutils225/elf/ar: creating build/lib/libbrowser.a a - build/lib/lines.o ranlib build/lib/libbrowser.a gmake[3]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/browser' making depend sources/lib/varfunc.cpp making depend sources/lib/gseq.cpp making depend sources/lib/refdb.cpp making depend sources/lib/views.cpp making depend sources/lib/indmap.cpp making depend sources/lib/individual.cpp making depend sources/lib/nets.cpp making depend sources/lib/iterate.cpp making depend sources/lib/davies.cpp making depend sources/lib/em.cpp c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ -I../plinkseq/sources/include/ sources/lib/davies.cpp -o build/lib/davies.o 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/bed.cpp making depend sources/lib/vcfiterate.cpp making depend sources/lib/zfstream.cpp making depend sources/lib/permute.cpp making depend sources/lib/helper.cpp making depend sources/lib/glm.cpp making depend sources/lib/prob.cpp 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/phmap.cpp checking whether the C compiler works... making depend sources/lib/variant.pb.cpp yes checking for C compiler default output file name... a.out checking for suffix of executables... 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/svar.cpp checking whether we are cross compiling... no checking for suffix of object files... making depend sources/lib/matrix.cpp o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... making depend sources/lib/dcdflib.cpp 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... making depend sources/lib/netdb.cpp gcc3 making depend sources/lib/vgroup.cpp checking whether we are using the GNU C++ compiler... making depend sources/lib/defs.cpp yes checking whether c++ accepts -g... making depend sources/lib/matrix_exponential.cpp yes checking dependency style of c++... making depend sources/lib/gstore.cpp gcc3 checking how to run the C++ preprocessor... making depend sources/lib/mask.cpp 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... making depend sources/lib/regions.cpp making depend sources/lib/globals.cpp yes checking for sys/types.h... making depend sources/lib/fisher.cpp yes checking for sys/stat.h... making depend sources/lib/vcf.cpp yes checking for stdlib.h... yes checking for string.h... making depend sources/lib/dose.cpp yes checking for memory.h... making depend sources/lib/bcf.cpp yes checking for strings.h... yes checking for inttypes.h... making depend sources/lib/sqlwrap.cpp yes checking for stdint.h... making depend sources/lib/crandom.cpp yes checking for unistd.h... making depend sources/lib/bgzf.cpp yes checking minix/config.h usability... c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/bgzf.cpp -o build/lib/bgzf.o 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... c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/crandom.cpp -o build/lib/crandom.o 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... c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/sqlwrap.cpp -o build/lib/sqlwrap.o 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-dragonfly4.7 file names to x86_64-unknown-dragonfly4.7 format... func_convert_file_noop checking how to convert x86_64-unknown-dragonfly4.7 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 ar rv build/lib/libmongoose.a build/lib/mongoose.o /usr/libexec/binutils225/elf/ar: creating build/lib/libmongoose.a a - build/lib/mongoose.o ranlib build/lib/libmongoose.a gmake[3]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/mongoose' c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/bcf.cpp -o build/lib/bcf.o 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... dragonfly4.7 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... dragonfly4.7 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... 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 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 config.status: executing libtool commands === configuring in gtest (/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/gtest) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY' '--exec-prefix=/wrkdirs/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=. 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... 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-dragonfly4.7 checking host system type... x86_64-unknown-dragonfly4.7 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... /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-dragonfly4.7 file names to x86_64-unknown-dragonfly4.7 format... func_convert_file_noop checking how to convert x86_64-unknown-dragonfly4.7 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... dragonfly4.7 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... dragonfly4.7 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/ sources/lib/dose.cpp -o build/lib/dose.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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake all-recursive gmake[5]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' Making all in . gmake[6]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[6]: Leaving directory 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'./'`google/protobuf/stubs/strutil.cc 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 -fPIC -DPIC -o .libs/strutil.o In file included from ./google/protobuf/stubs/strutil.h:38:0, from google/protobuf/stubs/strutil.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] ^ /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 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] ^ 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 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/gstore.cpp -o build/lib/gstore.o 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 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 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 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 mv -f .deps/structurally_valid.Tpo .deps/structurally_valid.Plo 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 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 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/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 descriptor.lo -MD -MP -MF .deps/descriptor.Tpo -c google/protobuf/descriptor.cc -o descriptor.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.pb.lo -MD -MP -MF .deps/descriptor.pb.Tpo -c google/protobuf/descriptor.pb.cc -o descriptor.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/compare.cpp -o build/lib/compare.o 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 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_exponential.cpp -o build/lib/matrix_exponential.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 /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 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 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 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 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/ -I../plinkseq/sources/include/ sources/lib/assoc.cpp -o build/lib/assoc.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_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/defs.cpp -o build/lib/defs.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 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 mv -f .deps/descriptor_database.Tpo .deps/descriptor_database.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 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 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 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/vgroup.cpp -o build/lib/vgroup.o 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 /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] ^ 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 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 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/netdb.cpp -o build/lib/netdb.o mv -f .deps/message.Tpo .deps/message.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 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/reflection_ops.Tpo .deps/reflection_ops.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/dcdflib.cpp -o build/lib/dcdflib.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 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 /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 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] ^ 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 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/ -I../plinkseq/sources/include/ sources/lib/genic.cpp -o build/lib/genic.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 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 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/wire_format.Tpo .deps/wire_format.Plo 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 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/svar.cpp -o build/lib/svar.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 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/text_format.Tpo .deps/text_format.Plo 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 /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] ^ mv -f .deps/printer.Tpo .deps/printer.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 tokenizer.lo -MD -MP -MF .deps/tokenizer.Tpo -c google/protobuf/io/tokenizer.cc -o tokenizer.o >/dev/null 2>&1 mv -f .deps/tokenizer.Tpo .deps/tokenizer.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 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 mv -f .deps/zero_copy_stream_impl.Tpo .deps/zero_copy_stream_impl.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 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 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] ^ mv -f .deps/importer.Tpo .deps/importer.Plo 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 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/phmap.cpp -o build/lib/phmap.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 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/prob.cpp -o build/lib/prob.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 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 /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 mv -f .deps/parser.Tpo .deps/parser.Plo 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 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] ^ c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/glm.cpp -o build/lib/glm.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 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 /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 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 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/helper.cpp -o build/lib/helper.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 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/permute.cpp -o build/lib/permute.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.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 /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/ -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 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/ sources/lib/zfstream.cpp -o build/lib/zfstream.o 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 /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/vcfiterate.cpp -o build/lib/vcfiterate.o mv -f .deps/plugin.pb.Tpo .deps/plugin.pb.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_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] ^ 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 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 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_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/bed.cpp -o build/lib/bed.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] ^ 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 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/em.cpp -o build/lib/em.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_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 mv -f .deps/cpp_enum_field.Tpo .deps/cpp_enum_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 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_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] ^ 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 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_field.Tpo .deps/cpp_field.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/iterate.cpp -o build/lib/iterate.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_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 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/individual.cpp -o build/lib/individual.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 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_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 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_generator.Tpo .deps/cpp_generator.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/indmap.cpp -o build/lib/indmap.o mv -f .deps/cpp_extension.Tpo .deps/cpp_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 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 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] ^ 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/refdb.cpp -o build/lib/refdb.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 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 ar rv build/lib/libpseq.a build/lib/davies.o build/lib/nets.o build/lib/views.o build/lib/gseq.o build/lib/skat.o build/lib/pops.o build/lib/kbac.o build/lib/clusters.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/sockets.o build/lib/varfunc.o build/lib/genic.o build/lib/webcheck.o build/lib/func.o build/lib/ibs.o build/lib/chet.o build/lib/matdb.o build/lib/extra.o build/lib/ibd.o build/lib/glm-tests.o build/lib/util.o /usr/libexec/binutils225/elf/ar: creating build/lib/libpseq.a a - build/lib/davies.o a - build/lib/nets.o a - build/lib/views.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/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/sockets.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/chet.o a - build/lib/matdb.o a - build/lib/extra.o a - build/lib/ibd.o a - build/lib/glm-tests.o a - build/lib/util.o ranlib build/lib/libpseq.a gmake[3]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/pseq' c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/varfunc.cpp -o build/lib/varfunc.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/variant.cpp -o build/lib/variant.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_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 mv -f .deps/cpp_message_field.Tpo .deps/cpp_message_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 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 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] ^ 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_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 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 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/meta.cpp -o build/lib/meta.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] ^ 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 mv -f .deps/cpp_service.Tpo .deps/cpp_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 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_message.Tpo .deps/cpp_message.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/r8lib.cpp -o build/lib/r8lib.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] ^ 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/allele.cpp -o build/lib/allele.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_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 /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 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 /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_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] ^ 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.Tpo .deps/java_enum.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 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_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_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 mv -f .deps/java_field.Tpo .deps/java_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_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_file.lo -MD -MP -MF .deps/java_file.Tpo -c google/protobuf/compiler/java/java_file.cc -fPIC -DPIC -o .libs/java_file.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_generator.lo -MD -MP -MF .deps/java_generator.Tpo -c google/protobuf/compiler/java/java_generator.cc -fPIC -DPIC -o .libs/java_generator.o 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] ^ mv -f .deps/java_extension.Tpo .deps/java_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 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 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] ^ mv -f .deps/java_enum_field.Tpo .deps/java_enum_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_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 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] ^ 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 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/eval.cpp -o build/lib/eval.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_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_file.Tpo .deps/java_file.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_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] ^ 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/inddb.cpp -o build/lib/inddb.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 /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 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] ^ 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] ^ 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/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 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_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 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] ^ 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 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_message_field.Tpo .deps/java_message_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 /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 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_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 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] ^ 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] ^ 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 mv -f .deps/java_doc_comment.Tpo .deps/java_doc_comment.Plo c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/annot.cpp -o build/lib/annot.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/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] ^ 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 mv -f .deps/java_string_field.Tpo .deps/java_string_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 c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/locdb.cpp -o build/lib/locdb.o /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 /wrkdirs/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 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/ sources/lib/segments.cpp -o build/lib/segments.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 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/ sources/lib/filemap.cpp -o build/lib/filemap.o 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 /wrkdirs/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 /usr/lib/crti.o /usr/lib/gcc50/crtbeginS.o .libs/code_generator.o 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-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 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,/wrkdirs/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 '/wrkdirs/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 /wrkdirs/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 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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[6]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[5]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[4]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[4]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' Making install in . gmake[5]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[6]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[6]: Nothing to be done for 'install-exec-am'. test -z "/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/pkgconfig" || ./install-sh -c -d "/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/pkgconfig" /usr/bin/install -c -m 644 protobuf.pc protobuf-lite.pc '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/pkgconfig' gmake[6]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[5]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' Making install in src gmake[5]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake install-am gmake[6]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[7]: Entering directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' test -z "/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib" || .././install-sh -c -d "/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib" /bin/sh ../libtool --mode=install /usr/bin/install -c libprotobuf-lite.la libprotobuf.la libprotoc.la '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib' libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.so.8.0.0 /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf-lite.so.8.0.0 libtool: install: (cd /wrkdirs/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 /wrkdirs/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: install: /usr/bin/install -c .libs/libprotobuf-lite.lai /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf-lite.la libtool: install: /usr/bin/install -c .libs/libprotobuf.so.8.0.0 /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf.so.8.0.0 libtool: install: (cd /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib && { ln -s -f libprotobuf.so.8.0.0 libprotobuf.so.8 || { rm -f libprotobuf.so.8 && ln -s libprotobuf.so.8.0.0 libprotobuf.so.8; }; }) libtool: install: (cd /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib && { ln -s -f libprotobuf.so.8.0.0 libprotobuf.so || { rm -f libprotobuf.so && ln -s libprotobuf.so.8.0.0 libprotobuf.so; }; }) libtool: install: /usr/bin/install -c .libs/libprotobuf.lai /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf.la libtool: install: warning: relinking `libprotoc.la' libtool: install: (cd /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/src; /bin/sh /wrkdirs/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 /wrkdirs/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: 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,/wrkdirs/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 /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotoc.so.8.0.0 libtool: install: (cd /wrkdirs/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 /wrkdirs/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 /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotoc.la libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.a /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf-lite.a libtool: install: chmod 644 /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf-lite.a libtool: install: ranlib /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf-lite.a libtool: install: /usr/bin/install -c .libs/libprotobuf.a /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf.a libtool: install: chmod 644 /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf.a libtool: install: ranlib /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotobuf.a libtool: install: /usr/bin/install -c .libs/libprotoc.a /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotoc.a libtool: install: chmod 644 /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotoc.a libtool: install: ranlib /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/lib/libprotoc.a test -z "/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include" || .././install-sh -c -d "/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include" .././install-sh -c -d '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf' /usr/bin/install -c -m 644 google/protobuf/descriptor.proto '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf' .././install-sh -c -d '/wrkdirs/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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler' test -z "/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include" || .././install-sh -c -d "/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include" .././install-sh -c -d '/wrkdirs/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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler/python' .././install-sh -c -d '/wrkdirs/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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler/cpp' .././install-sh -c -d '/wrkdirs/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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/stubs' .././install-sh -c -d '/wrkdirs/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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/io' .././install-sh -c -d '/wrkdirs/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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf' .././install-sh -c -d '/wrkdirs/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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler/java' .././install-sh -c -d '/wrkdirs/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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../sources/include/DUMMY/include/google/protobuf/compiler' test -z "/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/bin" || .././install-sh -c -d "/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/bin" /bin/sh ../libtool --mode=install /usr/bin/install -c protoc '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/bin' libtool: install: /usr/bin/install -c .libs/protoc /wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf/../build/bin/protoc gmake[7]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[6]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[5]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0/src' gmake[4]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext/protobuf-2.5.0' gmake[3]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/ext' c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/netfunc.cpp -o build/lib/netfunc.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/token.cpp -o build/lib/token.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/output.cpp -o build/lib/output.o 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/ sources/lib/vardb.cpp -o build/lib/vardb.o c++ -c -pipe -O2 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/varmeta.cpp -o build/lib/varmeta.o 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/ sources/lib/network.cpp -o build/lib/network.o 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 ar rv build/lib/libplinkseq.a build/lib/bgzf.o build/lib/crandom.o build/lib/sqlwrap.o build/lib/bcf.o build/lib/dose.o build/lib/vcf.o build/lib/fisher.o build/lib/globals.o build/lib/regions.o build/lib/mask.o build/lib/gstore.o build/lib/matrix_exponential.o build/lib/defs.o build/lib/vgroup.o build/lib/netdb.o build/lib/dcdflib.o build/lib/matrix.o build/lib/svar.o build/lib/variant.pb.o build/lib/phmap.o build/lib/prob.o build/lib/glm.o build/lib/helper.o build/lib/permute.o build/lib/zfstream.o build/lib/vcfiterate.o build/lib/bed.o build/lib/em.o build/lib/iterate.o build/lib/individual.o build/lib/indmap.o build/lib/refdb.o build/lib/varfunc.o build/lib/variant.o build/lib/meta.o build/lib/r8lib.o build/lib/allele.o build/lib/matrix.pb.o build/lib/vcfz.o build/lib/eval.o build/lib/inddb.o build/lib/protdb.o build/lib/reffuncs.o build/lib/annot.o build/lib/c8lib.o build/lib/locdb.o build/lib/segments.o build/lib/matdb.o build/lib/filemap.o build/lib/netfunc.o build/lib/token.o build/lib/output.o build/lib/statistics.o build/lib/vardb.o build/lib/varmeta.o build/lib/genotype.o build/lib/seqdb.o build/lib/network.o build/lib/sqlite3.o /usr/libexec/binutils225/elf/ar: creating build/lib/libplinkseq.a a - build/lib/bgzf.o a - build/lib/crandom.o a - build/lib/sqlwrap.o a - build/lib/bcf.o a - build/lib/dose.o a - build/lib/vcf.o a - build/lib/fisher.o a - build/lib/globals.o a - build/lib/regions.o a - build/lib/mask.o a - build/lib/gstore.o a - build/lib/matrix_exponential.o a - build/lib/defs.o a - build/lib/vgroup.o a - build/lib/netdb.o a - build/lib/dcdflib.o a - build/lib/matrix.o a - build/lib/svar.o a - build/lib/variant.pb.o a - build/lib/phmap.o a - build/lib/prob.o a - build/lib/glm.o a - build/lib/helper.o a - build/lib/permute.o a - build/lib/zfstream.o a - build/lib/vcfiterate.o a - build/lib/bed.o a - build/lib/em.o a - build/lib/iterate.o a - build/lib/individual.o a - build/lib/indmap.o a - build/lib/refdb.o a - build/lib/varfunc.o a - build/lib/variant.o a - build/lib/meta.o a - build/lib/r8lib.o a - build/lib/allele.o a - build/lib/matrix.pb.o a - build/lib/vcfz.o a - build/lib/eval.o a - build/lib/inddb.o a - build/lib/protdb.o a - build/lib/reffuncs.o a - build/lib/annot.o a - build/lib/c8lib.o a - build/lib/locdb.o a - build/lib/segments.o a - build/lib/matdb.o a - build/lib/filemap.o a - build/lib/netfunc.o a - build/lib/token.o a - build/lib/output.o a - build/lib/statistics.o a - build/lib/vardb.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 '/wrkdirs/biology/plinkseq/plinkseq-0.10/sources/plinkseq' gmake[2]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10' gmake ./pdas ./mongoose ./tab2vcf ./smp ./mm ./behead ./browser ./gcol ./pseq gmake[2]: Entering directory '/wrkdirs/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/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 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 gmake[2]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10' gmake[1]: Leaving directory '/wrkdirs/biology/plinkseq/plinkseq-0.10' =========================================================================== =================================================== =========================================================================== =================================================== ===> Staging for plinkseq-0.10 ===> Generating temporary packing list install -s -m 555 /wrkdirs/biology/plinkseq/plinkseq-0.10/build/execs/behead /wrkdirs/biology/plinkseq/stage/usr/local/bin install -s -m 555 /wrkdirs/biology/plinkseq/plinkseq-0.10/build/execs/browser 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/wrkdirs/biology/plinkseq/stage/usr/local/lib ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for plinkseq-0.10 file sizes/checksums [13]: . done packing files [13]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for plinkseq-0.10 build of biology/plinkseq ended at Tue Oct 4 17:54:39 PDT 2016 build time: 00:08:35