Date: Fri, 13 Jan 2017 15:19:24 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110mips-quarterly][biology/plinkseq] Failed for plinkseq-0.10 in build Message-ID: <201701131519.v0DFJOwx007901@beefy14.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: branches/2017Q1/biology/plinkseq/Makefile 425879 2016-11-11 09:31:02Z linimon $ Log URL: http://beefy14.nyi.freebsd.org/data/110mips-quarterly/431207/logs/plinkseq-0.10.log Build URL: http://beefy14.nyi.freebsd.org/build.html?mastername=110mips-quarterly&build=431207 Log: ====>> Building biology/plinkseq build started at Fri Jan 13 15:02:03 UTC 2017 port directory: /usr/ports/biology/plinkseq building for: FreeBSD 110mips-quarterly-job-02 11.0-RELEASE-p7 FreeBSD 11.0-RELEASE-p7 r311916 mips maintained by: bacon4000@gmail.com Makefile ident: $FreeBSD: branches/2017Q1/biology/plinkseq/Makefile 425879 2016-11-11 09:31:02Z linimon $ Poudriere version: 3.1.14 Host OSVERSION: 1200017 Jail OSVERSION: 1100122 Job Id: 02 ---Begin Environment--- SHELL=/bin/csh UNAME_p=mips UNAME_m=mips ABI_FILE=/usr/lib/crt1.o UNAME_v=FreeBSD 11.0-RELEASE-p7 r311916 UNAME_r=11.0-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=mips SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110mips-quarterly/ref QEMU_EMULATING=1 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-p7 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=28 PWD=/usr/local/poudriere/data/.m/110mips-quarterly/ref/.p/pool MASTERNAME=110mips-quarterly 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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -G0 -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -G0 -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--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MACHINE=mips MACHINE_ARCH=mips 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 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--- =======================<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-1.9.4_1.txz [110mips-quarterly-job-02] Installing pkg-1.9.4_1... [110mips-quarterly-job-02] Extracting pkg-1.9.4_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 /nxb-bin/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 /nxb-bin/usr/bin/sed -i.bak -e 's|g++|/nxb-bin/usr/bin/c++|g' -e 's|gcc|/nxb-bin/usr/bin/cc|g' -e 's|CXXFLAGS = -O3|CXXFLAGS = -O2 -pipe -G0 -fno-strict-aliasing |g' -e 's|ALL_CFLAGS =-O3|ALL_CFLAGS = -O2 -pipe -G0 -fno-strict-aliasing|g' /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/config_defs.Makefile /nxb-bin/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 [110mips-quarterly-job-02] Installing gmake-4.2.1_1... [110mips-quarterly-job-02] `-- Installing indexinfo-0.2.6... [110mips-quarterly-job-02] `-- Extracting indexinfo-0.2.6: .... done [110mips-quarterly-job-02] `-- Installing gettext-runtime-0.19.8.1_1... [110mips-quarterly-job-02] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [110mips-quarterly-job-02] 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 /usr/local/bin/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' /usr/local/bin/gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/plinkseq gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/plinkseq' mkdir -p build/lib making depend sources/lib/sqlite3.c making depend sources/lib/network.cpp making depend sources/lib/seqdb.cpp making depend sources/lib/genotype.cpp making depend sources/lib/reffuncs.cpp making depend sources/lib/r8lib.cpp making depend sources/lib/statistics.cpp making depend sources/lib/netfunc.cpp making depend sources/lib/filemap.cpp making depend sources/lib/matrix.cpp making depend sources/lib/allele.cpp making depend sources/lib/locdb.cpp making depend sources/lib/vcf.cpp making depend sources/lib/varmeta.cpp making depend sources/lib/globals.cpp making depend sources/lib/dcdflib.cpp making depend sources/lib/inddb.cpp making depend sources/lib/eval.cpp making depend sources/lib/matrix.pb.cpp In file included from ../ext/sources/include/google/protobuf/stubs/atomicops.h:59, from ../ext/sources/include/google/protobuf/stubs/once.h:81, from sources/lib/matrix.pb.cpp:10: ./ext/sources/include/google/protobuf/stubs/platform_macros.h:61:2: error: #error Host architecture was not detected as supported by protobuf making depend sources/lib/matdb.cpp making depend sources/lib/segments.cpp making depend sources/lib/c8lib.cpp making depend sources/lib/dose.cpp making depend sources/lib/variant.cpp making depend sources/lib/varfunc.cpp making depend sources/lib/indmap.cpp making depend sources/lib/individual.cpp making depend sources/lib/annot.cpp making depend sources/lib/iterate.cpp making depend sources/lib/crandom.cpp making depend sources/lib/em.cpp making depend sources/lib/bed.cpp making depend sources/lib/vcfiterate.cpp making depend sources/lib/zfstream.cpp making depend sources/lib/netdb.cpp making depend sources/lib/permute.cpp making depend sources/lib/helper.cpp making depend sources/lib/glm.cpp making depend sources/lib/prob.cpp making depend sources/lib/phmap.cpp making depend sources/lib/variant.pb.cpp In file included from ../ext/sources/include/google/protobuf/stubs/atomicops.h:59, from ../ext/sources/include/google/protobuf/stubs/once.h:81, from sources/lib/variant.pb.cpp:10: ./ext/sources/include/google/protobuf/stubs/platform_macros.h:61:2: error: #error Host architecture was not detected as supported by protobuf making depend sources/lib/svar.cpp making depend sources/lib/output.cpp making depend sources/lib/vardb.cpp making depend sources/lib/vgroup.cpp making depend sources/lib/vcfz.cpp making depend sources/lib/protdb.cpp making depend sources/lib/matrix_exponential.cpp making depend sources/lib/gstore.cpp making depend sources/lib/mask.cpp making depend sources/lib/regions.cpp making depend sources/lib/token.cpp making depend sources/lib/fisher.cpp making depend sources/lib/refdb.cpp making depend sources/lib/meta.cpp making depend sources/lib/defs.cpp making depend sources/lib/sqlwrap.cpp making depend sources/lib/bcf.cpp making depend sources/lib/bgzf.cpp /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/bgzf.cpp -o build/lib/bgzf.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/bcf.cpp -o build/lib/bcf.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/sqlwrap.cpp -o build/lib/sqlwrap.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/defs.cpp -o build/lib/defs.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/meta.cpp -o build/lib/meta.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/refdb.cpp -o build/lib/refdb.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/fisher.cpp -o build/lib/fisher.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/token.cpp -o build/lib/token.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/regions.cpp -o build/lib/regions.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/mask.cpp -o build/lib/mask.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/gstore.cpp -o build/lib/gstore.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/matrix_exponential.cpp -o build/lib/matrix_exponential.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/protdb.cpp -o build/lib/protdb.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vcfz.cpp -o build/lib/vcfz.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vgroup.cpp -o build/lib/vgroup.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/vardb.cpp -o build/lib/vardb.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/output.cpp -o build/lib/output.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/svar.cpp -o build/lib/svar.o /nxb-bin/usr/bin/c++ -c -O2 -pipe -G0 -fno-strict-aliasing -I./sources/include -I../ext/sources/include/ sources/lib/variant.pb.cpp -o build/lib/variant.pb.o In file included from ../ext/sources/include/google/protobuf/stubs/atomicops.h:59, from ../ext/sources/include/google/protobuf/stubs/once.h:81, from sources/lib/variant.pb.cpp:10: ./ext/sources/include/google/protobuf/stubs/platform_macros.h:61:2: error: #error Host architecture was not detected as supported by protobuf In file included from ../ext/sources/include/google/protobuf/stubs/once.h:81, from sources/lib/variant.pb.cpp:10: ./ext/sources/include/google/protobuf/stubs/atomicops.h:188: error: stray '#' in program ./ext/sources/include/google/protobuf/stubs/atomicops.h:188: error: expected constructor, destructor, or type conversion before string constant gmake[3]: *** [../../config_rules.Makefile:16: build/lib/variant.pb.o] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/plinkseq' gmake[2]: *** [Makefile:170: sources/plinkseq] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10' gmake[1]: *** [Makefile:165: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10' *** Error code 1 Stop. make: stopped in /usr/ports/biology/plinkseq
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