Date: Sat, 1 Jul 2017 01:35:37 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][biology/plinkseq] Failed for plinkseq-0.10_1 in build Message-ID: <201707010135.v611ZbQ6007818@beefy8.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: bacon4000@gmail.com Last committer: linimon@FreeBSD.org Ident: $FreeBSD: head/biology/plinkseq/Makefile 440746 2017-05-13 03:35:51Z linimon $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p444810_s320521/logs/plinkseq-0.10_1.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p444810_s320521 Log: ====>> Building biology/plinkseq build started at Sat Jul 1 01:28:03 UTC 2017 port directory: /usr/ports/biology/plinkseq qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 551 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 551 (calling anyway) qemu: unsupported syscall: 551 (calling anyway) qemu: unsupported syscall: 551 (calling anyway) building for: FreeBSD head-armv6-default-job-19 12.0-CURRENT FreeBSD 12.0-CURRENT 1200036 arm maintained by: bacon4000@gmail.com Makefile ident: $FreeBSD: head/biology/plinkseq/Makefile 440746 2017-05-13 03:35:51Z linimon $ Poudriere version: 3.1.19-40-ga434dff0 Host OSVERSION: 1200033 Jail OSVERSION: 1200036 Job Id: 19 !!! Jail is newer than host. (Jail: 1200036, Host: 1200033) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200036 UNAME_v=FreeBSD 12.0-CURRENT 1200036 UNAME_r=12.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref QEMU_EMULATING=1 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=plinkseq-0.10_1 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.19-40-ga434dff0 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=12.0 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--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes MACHINE=arm MACHINE_ARCH=armv6 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### ARCH=armv6 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=12.0 OSVERSION=1200036 PYTHONBASE=/usr/local UID=0 _JAVA_OS_LIST_REGEXP=native\|linux _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ _OSRELEASE=12.0-CURRENT #### Misc Poudriere #### GID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> plinkseq-0.10_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz qemu: unsupported syscall: 551 (calling anyway) qemu: unsupported syscall: 551 (calling anyway) qemu: unsupported syscall: 556 (calling anyway) qemu: unsupported syscall: 554 (calling anyway) qemu: unsupported syscall: 554 (calling anyway) qemu: unsupported syscall: 551 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 555 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 551 (calling anyway) qemu: unsupported syscall: 551 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 551 (calling anyway) <snip> 8 warnings generated. qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) /nxb-bin/usr/bin/c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/netfunc.cpp -o build/lib/netfunc.o qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) /nxb-bin/usr/bin/c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/statistics.cpp -o build/lib/statistics.o sources/lib/statistics.cpp:31:17: warning: implicit conversion from 'double' to 'int' changes value from 1.0E-6 to 0 [-Wliteral-conversion] const int EPS = 1.0e-6; ~~~ ^~~~~~ sources/lib/statistics.cpp:53:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ sources/lib/statistics.cpp:60:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ sources/lib/statistics.cpp:1911:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 4 warnings generated. qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) /nxb-bin/usr/bin/c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/r8lib.cpp -o build/lib/r8lib.o sources/lib/r8lib.cpp:16365:49: warning: for loop has empty body [-Wempty-body] for ( jlo = 1; jlo <= jmax; jlo = jlo + nn ); ^ sources/lib/r8lib.cpp:16365:49: note: put the semicolon on a separate line to silence this warning 1 warning generated. qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) /nxb-bin/usr/bin/c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/reffuncs.cpp -o build/lib/reffuncs.o In file included from sources/lib/reffuncs.cpp:2: In file included from ./sources/include/plinkseq/gstore.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/reffuncs.cpp:2: In file included from ./sources/include/plinkseq/gstore.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/reffuncs.cpp:2: In file included from ./sources/include/plinkseq/gstore.h:15: 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/reffuncs.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. qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) /nxb-bin/usr/bin/c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/genotype.cpp -o build/lib/genotype.o In file included from sources/lib/genotype.cpp:2: 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/genotype.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; ~ ^ ~ sources/lib/genotype.cpp:127:12: warning: enumeration value 'GENOTYPE_MODEL_UNSPEC' not handled in switch [-Wswitch] switch ( model ) ^ sources/lib/genotype.cpp:295:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ In file included from sources/lib/genotype.cpp:2: 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 ) ^ ./sources/include/plinkseq/meta.h:656:2: warning: control may reach end of non-void function [-Wreturn-type] } ^ sources/lib/genotype.cpp:410:10: note: in instantiation of member function 'MetaInformation<GenMeta>::set' requested here meta.set( tok , &formats ); ^ 9 warnings generated. qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) /nxb-bin/usr/bin/c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/seqdb.cpp -o build/lib/seqdb.o In file included from sources/lib/seqdb.cpp:2: In file included from ./sources/include/plinkseq/seqdb.h:8: In file included from ./sources/include/plinkseq/regions.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/seqdb.cpp:2: In file included from ./sources/include/plinkseq/seqdb.h:8: 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/seqdb.cpp:4: In file included from ./sources/include/plinkseq/gstore.h:15: 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/seqdb.cpp:4: 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; } ^ sources/lib/seqdb.cpp:93:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ sources/lib/seqdb.cpp:120:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ sources/lib/seqdb.cpp:175:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ sources/lib/seqdb.cpp:184:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 10 warnings generated. qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) /nxb-bin/usr/bin/c++ -c -O2 -pipe -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/network.cpp -o build/lib/network.o In file included from sources/lib/network.cpp:1: In file included from ./sources/include/plinkseq/network.h:14: In file included from ./sources/include/plinkseq/regions.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/network.cpp:1: In file included from ./sources/include/plinkseq/network.h:14: 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; ~ ^ ~ 4 warnings generated. qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) /nxb-bin/usr/bin/cc -c -O2 -pipe -fno-strict-aliasing -DSQLITE_OMIT_LOAD_EXTENSION -I./sources/include -I../ext/sources/include/ sources/lib/sqlite3.c -o build/lib/sqlite3.o qemu: unsupported syscall: 552 (calling anyway) ar rv build/lib/libplinkseq.a build/lib/bgzf.o build/lib/bcf.o build/lib/sqlwrap.o build/lib/defs.o build/lib/meta.o build/lib/refdb.o build/lib/fisher.o build/lib/token.o build/lib/regions.o build/lib/mask.o build/lib/gstore.o build/lib/matrix_exponential.o build/lib/protdb.o build/lib/vcfz.o build/lib/vgroup.o build/lib/vardb.o build/lib/output.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/netdb.o build/lib/zfstream.o build/lib/vcfiterate.o build/lib/bed.o build/lib/em.o build/lib/crandom.o build/lib/iterate.o build/lib/annot.o build/lib/individual.o build/lib/indmap.o build/lib/varfunc.o build/lib/variant.o build/lib/dose.o build/lib/c8lib.o build/lib/segments.o build/lib/matdb.o build/lib/matrix.pb.o build/lib/eval.o build/lib/inddb.o build/lib/dcdflib.o build/lib/globals.o build/lib/varmeta.o build/lib/vcf.o build/lib/locdb.o build/lib/allele.o build/lib/matrix.o build/lib/filemap.o b uild/lib/netfunc.o build/lib/statistics.o build/lib/r8lib.o build/lib/reffuncs.o build/lib/genotype.o build/lib/seqdb.o build/lib/network.o build/lib/sqlite3.o qemu: unsupported syscall: 552 (calling anyway) qemu: uncaught target signal 11 (Segmentation fault) - core dumped qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) qemu: unsupported syscall: 552 (calling anyway) gmake[3]: *** [../../config_rules.Makefile:24: build/lib/libplinkseq.a] Segmentation fault qemu: unsupported syscall: 552 (calling anyway) 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
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