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Maintainer: bacon4...@gmail.com Last committer: swi...@freebsd.org Ident: $FreeBSD: head/biology/plinkseq/Makefile 413746 2016-04-21 16:43:14Z swills $ Log URL: http://thunderx1.nyi.freebsd.org/data/110arm64-default/424442/logs/plinkseq-0.10.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=110arm64-default&build=424442 Log: ====>> Building biology/plinkseq build started at Sun Oct 23 02:28:42 UTC 2016 port directory: /usr/ports/biology/plinkseq building for: FreeBSD 110arm64-default-job-06 11.0-RELEASE-p1 FreeBSD 11.0-RELEASE-p1 r306420 arm64 maintained by: bacon4...@gmail.com Makefile ident: $FreeBSD: head/biology/plinkseq/Makefile 413746 2016-04-21 16:43:14Z swills $ Poudriere version: 3.1.14 Host OSVERSION: 1100121 Jail OSVERSION: 1100122 !!! Jail is newer than host. (Jail: 1100122, Host: 1100121) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_v=FreeBSD 11.0-RELEASE-p1 r306420 UNAME_r=11.0-RELEASE-p1 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=aarch64 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110arm64-default/ref UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=plinkseq-0.10 OSREL=11.0 _OSRELEASE=11.0-RELEASE-p1 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=48 PWD=/usr/local/poudriere/data/.m/110arm64-default/ref/.p/pool MASTERNAME=110arm64-default SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=1100122 ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/plinkseq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/plinkseq/work HOME=/wrkdirs/usr/ports/biology/plinkseq/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/plinkseq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/plinkseq/work HOME=/wrkdirs/usr/ports/biology/plinkseq/work TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 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=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/plinkseq" EXAMPLESDIR="share/examples/plinkseq" DATADIR="share/plinkseq" WWWDIR="www/plinkseq" ETCDIR="etc/plinkseq" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/plinkseq DOCSDIR=/usr/local/share/doc/plinkseq EXAMPLESDIR=/usr/local/share/examples/plinkseq WWWDIR=/usr/local/www/plinkseq ETCDIR=/usr/local/etc/plinkseq --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> plinkseq-0.10 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.1.txz [110arm64-default-job-06] Installing pkg-1.9.1... [110arm64-default-job-06] Extracting pkg-1.9.1: .......... done ===> plinkseq-0.10 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of plinkseq-0.10 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.10 for building =========================================================================== =======================<phase: checksum >============================ ===> 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. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> 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. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for plinkseq-0.10 /usr/bin/sed -i.bak -e 's|PF_INET|AF_INET|g' /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/mongoose/sources/lib/mongoose.c /usr/bin/sed -i.bak -e 's|g++|c++|g' -e 's|gcc|cc|g' -e 's|CXXFLAGS = -O3|CXXFLAGS = -O2 -pipe -fno-strict-aliasing |g' -e 's|ALL_CFLAGS =-O3|ALL_CFLAGS = -O2 -pipe -fno-strict-aliasing|g' /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/config_defs.Makefile /usr/bin/sed -i.bak -e 's| -ldl||g' -e 's| $(STATIC_FLAG)||g' /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/Makefile =========================================================================== =======================<phase: build-depends >============================ ===> plinkseq-0.10 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz [110arm64-default-job-06] Installing gmake-4.2.1_1... [110arm64-default-job-06] `-- Installing indexinfo-0.2.5... [110arm64-default-job-06] `-- Extracting indexinfo-0.2.5: .... done [110arm64-default-job-06] `-- Installing gettext-runtime-0.19.8.1... [110arm64-default-job-06] `-- Extracting gettext-runtime-0.19.8.1: .......... done [110arm64-default-job-06] Extracting gmake-4.2.1_1: .......... done ===> plinkseq-0.10 depends on executable: gmake - found ===> Returning to build of plinkseq-0.10 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for plinkseq-0.10 =========================================================================== =======================<phase: build >============================ ===> Building for plinkseq-0.10 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10' mkdir -p build/lib mkdir -p build/execs making depend sources/execs/pseq.cpp making depend sources/execs/gcol.cpp making depend sources/execs/browser.cpp making depend sources/execs/behead.cpp making depend sources/execs/mm.cpp making depend sources/execs/smp.cpp making depend sources/execs/tab2vcf.cpp making depend sources/execs/mongoose.cpp making depend sources/execs/pdas.cpp gmake ./sources/plinkseq ./sources/pseq ./sources/util ./sources/mongoose ./sources/browser ./sources/pdas ./sources/ext gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10' gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/plinkseq gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/plinkseq' mkdir -p build/lib making depend sources/lib/sqlite3.c c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated making depend sources/lib/network.cpp making depend sources/lib/seqdb.cpp making depend sources/lib/genotype.cpp making depend sources/lib/reffuncs.cpp making depend sources/lib/r8lib.cpp making depend sources/lib/statistics.cpp making depend sources/lib/netfunc.cpp making depend sources/lib/filemap.cpp making depend sources/lib/matrix.cpp making depend sources/lib/allele.cpp making depend sources/lib/locdb.cpp <snip> if ( tok( 8 ) != "" && tok( 8 ) != "." ) ^ ~~ sources/lib/protdb.cpp:267:39: warning: result of comparison against a string literal is unspecified (use strncmp instead) [-Wstring-compare] if ( tok( 8 ) != "" && tok( 8 ) != "." ) ^ ~~~ 6 warnings generated. c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vcfz.cpp -o build/lib/vcfz.o In file included from sources/lib/vcfz.cpp:2: In file included from ./sources/include/plinkseq/vcfz.h:6: ./sources/include/plinkseq/meta.h:580:15: warning: enumeration values 'META_UNDEFINED' and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ ./sources/include/plinkseq/meta.h:617:15: warning: enumeration values 'META_FLAG', 'META_UNDEFINED', and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ In file included from sources/lib/vcfz.cpp:3: In file included from ./sources/include/plinkseq/variant.h:19: In file included from ./sources/include/plinkseq/filemap.h:33: ./sources/include/plinkseq/bcf.h:45:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if ( p < 0 || p >= num2string.size() ) return false; ~ ^ ~ ./sources/include/plinkseq/bcf.h:82:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if ( p < 0 || p >= contig_num2string.size() ) return false; ~ ^ ~ In file included from sources/lib/vcfz.cpp:4: In file included from ./sources/include/plinkseq/vardb.h:8: ./sources/include/plinkseq/mask.h:2151:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from sources/lib/vcfz.cpp:4: ./sources/include/plinkseq/vardb.h:329:59: warning: control reaches end of non-void function [-Wreturn-type] bool compression( const bool b ) { using_compression=b; } ^ 6 warnings generated. c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vgroup.cpp -o build/lib/vgroup.o In file included from sources/lib/vgroup.cpp:1: In file included from ./sources/include/plinkseq/vgroup.h:4: In file included from ./sources/include/plinkseq/variant.h:14: In file included from ./sources/include/plinkseq/genotype.h:11: In file included from ./sources/include/plinkseq/individual.h:8: ./sources/include/plinkseq/meta.h:580:15: warning: enumeration values 'META_UNDEFINED' and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ ./sources/include/plinkseq/meta.h:617:15: warning: enumeration values 'META_FLAG', 'META_UNDEFINED', and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ In file included from sources/lib/vgroup.cpp:1: In file included from ./sources/include/plinkseq/vgroup.h:4: In file included from ./sources/include/plinkseq/variant.h:19: In file included from ./sources/include/plinkseq/filemap.h:33: ./sources/include/plinkseq/bcf.h:45:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if ( p < 0 || p >= num2string.size() ) return false; ~ ^ ~ ./sources/include/plinkseq/bcf.h:82:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if ( p < 0 || p >= contig_num2string.size() ) return false; ~ ^ ~ In file included from sources/lib/vgroup.cpp:1: In file included from ./sources/include/plinkseq/vgroup.h:6: ./sources/include/plinkseq/mask.h:2151:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from sources/lib/vgroup.cpp:2: In file included from ./sources/include/plinkseq/gstore.h:15: ./sources/include/plinkseq/vardb.h:329:59: warning: control reaches end of non-void function [-Wreturn-type] bool compression( const bool b ) { using_compression=b; } ^ 6 warnings generated. c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vardb.cpp -o build/lib/vardb.o In file included from sources/lib/vardb.cpp:2: In file included from ./sources/include/plinkseq/vardb.h:6: In file included from ./sources/include/plinkseq/variant.h:14: In file included from ./sources/include/plinkseq/genotype.h:11: In file included from ./sources/include/plinkseq/individual.h:8: ./sources/include/plinkseq/meta.h:580:15: warning: enumeration values 'META_UNDEFINED' and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ ./sources/include/plinkseq/meta.h:617:15: warning: enumeration values 'META_FLAG', 'META_UNDEFINED', and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ In file included from sources/lib/vardb.cpp:2: In file included from ./sources/include/plinkseq/vardb.h:6: In file included from ./sources/include/plinkseq/variant.h:19: In file included from ./sources/include/plinkseq/filemap.h:33: ./sources/include/plinkseq/bcf.h:45:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if ( p < 0 || p >= num2string.size() ) return false; ~ ^ ~ ./sources/include/plinkseq/bcf.h:82:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if ( p < 0 || p >= contig_num2string.size() ) return false; ~ ^ ~ In file included from sources/lib/vardb.cpp:2: In file included from ./sources/include/plinkseq/vardb.h:8: ./sources/include/plinkseq/mask.h:2151:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from sources/lib/vardb.cpp:2: ./sources/include/plinkseq/vardb.h:329:59: warning: control reaches end of non-void function [-Wreturn-type] bool compression( const bool b ) { using_compression=b; } ^ sources/lib/vardb.cpp:826:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ sources/lib/vardb.cpp:841:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ sources/lib/vardb.cpp:849:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ sources/lib/vardb.cpp:857:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 10 warnings generated. c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/output.cpp -o build/lib/output.o In file included from sources/lib/output.cpp:1: In file included from ./sources/include/plinkseq/output.h:4: In file included from ./sources/include/plinkseq/filemap.h:31: ./sources/include/plinkseq/meta.h:580:15: warning: enumeration values 'META_UNDEFINED' and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ ./sources/include/plinkseq/meta.h:617:15: warning: enumeration values 'META_FLAG', 'META_UNDEFINED', and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ In file included from sources/lib/output.cpp:1: In file included from ./sources/include/plinkseq/output.h:4: In file included from ./sources/include/plinkseq/filemap.h:33: ./sources/include/plinkseq/bcf.h:45:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if ( p < 0 || p >= num2string.size() ) return false; ~ ^ ~ ./sources/include/plinkseq/bcf.h:82:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if ( p < 0 || p >= contig_num2string.size() ) return false; ~ ^ ~ 4 warnings generated. c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/svar.cpp -o build/lib/svar.o In file included from sources/lib/svar.cpp:2: In file included from ./sources/include/plinkseq/svar.h:5: ./sources/include/plinkseq/meta.h:580:15: warning: enumeration values 'META_UNDEFINED' and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ ./sources/include/plinkseq/meta.h:617:15: warning: enumeration values 'META_FLAG', 'META_UNDEFINED', and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ In file included from sources/lib/svar.cpp:3: In file included from ./sources/include/plinkseq/mask.h:6: In file included from ./sources/include/plinkseq/regions.h:10: In file included from ./sources/include/plinkseq/variant.h:19: In file included from ./sources/include/plinkseq/filemap.h:33: ./sources/include/plinkseq/bcf.h:45:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if ( p < 0 || p >= num2string.size() ) return false; ~ ^ ~ ./sources/include/plinkseq/bcf.h:82:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if ( p < 0 || p >= contig_num2string.size() ) return false; ~ ^ ~ In file included from sources/lib/svar.cpp:3: ./sources/include/plinkseq/mask.h:2151:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from sources/lib/svar.cpp:5: ./sources/include/plinkseq/vardb.h:329:59: warning: control reaches end of non-void function [-Wreturn-type] bool compression( const bool b ) { using_compression=b; } ^ 6 warnings generated. c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/variant.pb.cpp -o build/lib/variant.pb.o In file included from sources/lib/variant.pb.cpp:10: In file included from ../ext/sources/include/google/protobuf/stubs/once.h:81: In file included from ../ext/sources/include/google/protobuf/stubs/atomicops.h:59: ./ext/sources/include/google/protobuf/stubs/platform_macros.h:61:2: error: Host architecture was not detected as supported by protobuf #error Host architecture was not detected as supported by protobuf ^ In file included from sources/lib/variant.pb.cpp:10: In file included from ../ext/sources/include/google/protobuf/stubs/once.h:81: ./ext/sources/include/google/protobuf/stubs/atomicops.h:188:1: error: expected unqualified-id GOOGLE_PROTOBUF_ATOMICOPS_ERROR ^ ./ext/sources/include/google/protobuf/stubs/atomicops.h:160:41: note: expanded from macro 'GOOGLE_PROTOBUF_ATOMICOPS_ERROR' #define GOOGLE_PROTOBUF_ATOMICOPS_ERROR \ ^ In file included from sources/lib/variant.pb.cpp:10: ./ext/sources/include/google/protobuf/stubs/once.h:125:30: error: cannot initialize a parameter of type 'const volatile Atomic32 *' (aka 'const volatile int *') with an lvalue of type 'ProtobufOnceType *' (aka 'long *') if (internal::Acquire_Load(once) != ONCE_STATE_DONE) { ^~~~ ./ext/sources/include/google/protobuf/stubs/atomicops.h:129:48: note: passing argument to parameter 'ptr' here Atomic32 Acquire_Load(volatile const Atomic32* ptr); ^ In file included from sources/lib/variant.pb.cpp:10: ./ext/sources/include/google/protobuf/stubs/once.h:134:30: error: cannot initialize a parameter of type 'const volatile Atomic32 *' (aka 'const volatile int *') with an lvalue of type 'ProtobufOnceType *' (aka 'long *') if (internal::Acquire_Load(once) != ONCE_STATE_DONE) { ^~~~ ./ext/sources/include/google/protobuf/stubs/atomicops.h:129:48: note: passing argument to parameter 'ptr' here Atomic32 Acquire_Load(volatile const Atomic32* ptr); ^ 4 errors generated. gmake[3]: *** [../../config_rules.Makefile:16: build/lib/variant.pb.o] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/plinkseq' gmake[2]: *** [Makefile:170: sources/plinkseq] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10' gmake[1]: *** [Makefile:165: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10' *** Error code 1 Stop. make: stopped in /usr/ports/biology/plinkseq _______________________________________________ freebsd-pkg-fallout@freebsd.org mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "freebsd-pkg-fallout-unsubscr...@freebsd.org"
