Date: Thu, 9 Oct 2014 07:55:59 GMT From: pkg-fallout@FreeBSD.org To: jwbacon@tds.net Cc: pkg-fallout@FreeBSD.org Subject: [package - head-amd64-default-ssp][biology/plinkseq] Failed for plinkseq-0.08_3 in build Message-ID: <201410090755.s997txdf024126@beefy4.isc.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: jwbacon@tds.net Last committer: sunpoet@FreeBSD.org Ident: $FreeBSD: head/biology/plinkseq/Makefile 369969 2014-10-04 15:12:44Z sunpoet $ Log URL: http://beefy4.isc.freebsd.org/data/head-amd64-default-ssp/2014-10-08_15h00m31s/logs/plinkseq-0.08_3.log Build URL: http://beefy4.isc.freebsd.org/build.html?mastername=head-amd64-default-ssp&build=2014-10-08_15h00m31s Log: ====>> Building biology/plinkseq build started at Thu Oct 9 07:55:46 UTC 2014 port directory: /usr/ports/biology/plinkseq building for: FreeBSD pkg.FreeBSD.org 11.0-CURRENT FreeBSD 11.0-CURRENT r272720 amd64 maintained by: jwbacon@tds.net Makefile ident: $FreeBSD: head/biology/plinkseq/Makefile 369969 2014-10-04 15:12:44Z sunpoet $ Poudriere version: 3.1-pre Host OSVERSION: 1100027 Jail OSVERSION: 1100037 !!! Jail is newer than host. (Jail: 1100037, Host: 1100027) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- OSVERSION=1100037 UNAME_v=FreeBSD 11.0-CURRENT r272720 UNAME_r=11.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default-ssp/ref PKG_EXT=txz FORCE_PACKAGE=yes PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNG=1 PKGNAME=plinkseq-0.08_3 PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f PKG_ADD=/usr/local/sbin/pkg-static add OLDPWD=/root PWD=/usr/local/poudriere/data/.m/head-amd64-default-ssp/ref/.p/pool MASTERNAME=head-amd64-default-ssp USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes PKG_VERSION=/.p/pkg-static version PKG_BIN=/usr/local/sbin/pkg-static ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --with-protobuf=/usr/local --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_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" SHELL=/bin/sh CONFIG_SHELL=/bin/sh PATH=/usr/local/libexec/ccache:/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin CCACHE_DIR="/root/.ccache" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --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 SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing " MANPREFIX="/usr/local" PATH=/usr/local/libexec/ccache:/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin CCACHE_DIR="/root/.ccache" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 0644" BSD_INSTALL_MAN="install -o root -g wheel -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 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### WITH_PKGNG=yes #WITH_PKGNG=devel #### /usr/local/etc/poudriere.d/ssp-make.conf #### WITH_SSP_PORTS=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> plinkseq-0.08_3 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.3.8_3.txz [pkg.FreeBSD.org] Installing pkg-1.3.8_3... done Message for pkg-1.3.8_3: If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of plinkseq-0.08_3 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.08_3 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.08_3 for building => SHA256 Checksum OK for plinkseq-0.08.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.08_3 for building ===> Extracting for plinkseq-0.08_3 => SHA256 Checksum OK for plinkseq-0.08.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for plinkseq-0.08_3 ===> Converting DOS text files to UNIX text files ===> Applying FreeBSD patches for plinkseq-0.08_3 /usr/bin/sed -i.bak -e 's|PF_INET|AF_INET|g' /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.08/browser/mongoose.c /usr/bin/sed -i.bak -e 's|-ldl||g' /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.08/browser/Makefile.in /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.08/client/Makefile.in /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.08/index/Makefile.in =========================================================================== =======================<phase: build-depends >============================ ===> plinkseq-0.08_3 depends on file: /usr/local/bin/ccache - not found ===> Verifying install for /usr/local/bin/ccache in /usr/ports/devel/ccache ===> Installing existing package /packages/All/ccache-3.1.9_8.txz [pkg.FreeBSD.org] Installing ccache-3.1.9_8... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) Message for ccache-3.1.9_8: NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> Returning to build of plinkseq-0.08_3 =========================================================================== =======================<phase: lib-depends >============================ ===> plinkseq-0.08_3 depends on shared library: libprotobuf.so - not found ===> Verifying for libprotobuf.so in /usr/ports/devel/protobuf ===> Installing existing package /packages/All/protobuf-2.6.0.txz [pkg.FreeBSD.org] Installing protobuf-2.6.0... done ===> Returning to build of plinkseq-0.08_3 =========================================================================== =======================<phase: configure >============================ ===> Configuring for plinkseq-0.08_3 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.08/m4/libtool.m4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.08/aclocal.m4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.08/configure configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c -o root -g wheel checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking build system type... amd64-portbld-freebsd11.0 checking host system type... amd64-portbld-freebsd11.0 checking for style of include used by make... GNU checking for gcc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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 dependency style of cc... gcc3 <snip> config.status: creating index/index config.status: creating util/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands ------------------------------------------------- PLINK/SEQ Version 0.08 Prefix: '/usr/local'. C Compiler: 'cc -O2 -pipe -fstack-protector -fno-strict-aliasing ' C++ Compiler: 'c++ -O2 -pipe -fstack-protector -fno-strict-aliasing ' Now type 'make [<target>]' where the optional <target> is: all - build all binaries install - install everything -------------------------------------------------- =========================================================================== =======================<phase: build >============================ ===> Building for plinkseq-0.08_3 /usr/bin/make all-recursive Making all in lib /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I /usr/local/include -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libplinkseq_la-eval.lo -MD -MP -MF .deps/libplinkseq_la-eval.Tpo -c -o libplinkseq_la-eval.lo `test -f 'eval.cpp' || echo './'`eval.cpp libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I /usr/local/include -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libplinkseq_la-eval.lo -MD -MP -MF .deps/libplinkseq_la-eval.Tpo -c eval.cpp -fPIC -DPIC -o .libs/libplinkseq_la-eval.o In file included from eval.cpp:8: In file included from ./eval.h:4: In file included from ./token.h:4: In file included from ./variant.h:14: In file included from ./genotype.h:11: In file included from ./individual.h:8: In file included from ./meta.h:13: ./helper.h:730:3: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from eval.cpp:8: In file included from ./eval.h:4: In file included from ./token.h:4: In file included from ./variant.h:14: In file included from ./genotype.h:11: In file included from ./individual.h:8: ./meta.h:554:15: warning: enumeration values 'META_UNDEFINED' and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ ./meta.h:589:11: warning: enumeration values 'META_FLAG', 'META_UNDEFINED', and 'META_CHAR' not handled in switch [-Wswitch] switch( m->mt ) ^ In file included from eval.cpp:8: In file included from ./eval.h:4: In file included from ./token.h:4: In file included from ./variant.h:22: In file included from ./svar.h:6: ./variant.pb.h:17:2: error: This file was generated by an older version of protoc which is #error This file was generated by an older version of protoc which is ^ ./variant.pb.h:18:2: error: incompatible with your Protocol Buffer headers. Please #error incompatible with your Protocol Buffer headers. Please ^ ./variant.pb.h:19:2: error: regenerate this file with a newer version of protoc. #error regenerate this file with a newer version of protoc. ^ ./variant.pb.h:930:47: error: no member named 'kEmptyString' in namespace 'google::protobuf::internal'; did you mean 'GetEmptyString'? if (name_ != &::google::protobuf::internal::kEmptyString) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ GetEmptyString /usr/local/include/google/protobuf/generated_message_util.h:83:48: note: 'GetEmptyString' declared here LIBPROTOBUF_EXPORT inline const ::std::string& GetEmptyString() { ^ In file included from eval.cpp:8: In file included from ./eval.h:4: In file included from ./token.h:4: In file included from ./variant.h:22: In file included from ./svar.h:6: ./variant.pb.h:930:13: error: comparison of distinct pointer types ('::std::string *' (aka 'basic_string<char, char_traits<char>, allocator<char> > *') and 'const ::std::string &(*)()') if (name_ != &::google::protobuf::internal::kEmptyString) { ~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./variant.pb.h:940:47: error: no member named 'kEmptyString' in namespace 'google::protobuf::internal'; did you mean 'GetEmptyString'? if (name_ == &::google::protobuf::internal::kEmptyString) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ GetEmptyString /usr/local/include/google/protobuf/generated_message_util.h:83:48: note: 'GetEmptyString' declared here LIBPROTOBUF_EXPORT inline const ::std::string& GetEmptyString() { ^ In file included from eval.cpp:8: In file included from ./eval.h:4: In file included from ./token.h:4: In file included from ./variant.h:22: In file included from ./svar.h:6: ./variant.pb.h:940:13: error: comparison of distinct pointer types ('::std::string *' (aka 'basic_string<char, char_traits<char>, allocator<char> > *') and 'const ::std::string &(*)()') if (name_ == &::google::protobuf::internal::kEmptyString) { ~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./variant.pb.h:947:47: error: no member named 'kEmptyString' in namespace 'google::protobuf::internal'; did you mean 'GetEmptyString'? if (name_ == &::google::protobuf::internal::kEmptyString) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ GetEmptyString /usr/local/include/google/protobuf/generated_message_util.h:83:48: note: 'GetEmptyString' declared here LIBPROTOBUF_EXPORT inline const ::std::string& GetEmptyString() { ^ In file included from eval.cpp:8: In file included from ./eval.h:4: In file included from ./token.h:4: In file included from ./variant.h:22: In file included from ./svar.h:6: ./variant.pb.h:947:13: error: comparison of distinct pointer types ('::std::string *' (aka 'basic_string<char, char_traits<char>, allocator<char> > *') and 'const ::std::string &(*)()') if (name_ == &::google::protobuf::internal::kEmptyString) { ~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./variant.pb.h:954:47: error: no member named 'kEmptyString' in namespace 'google::protobuf::internal'; did you mean 'GetEmptyString'? if (name_ == &::google::protobuf::internal::kEmptyString) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ GetEmptyString /usr/local/include/google/protobuf/generated_message_util.h:83:48: note: 'GetEmptyString' declared here LIBPROTOBUF_EXPORT inline const ::std::string& GetEmptyString() { ^ In file included from eval.cpp:8: In file included from ./eval.h:4: In file included from ./token.h:4: In file included from ./variant.h:22: In file included from ./svar.h:6: ./variant.pb.h:954:13: error: comparison of distinct pointer types ('::std::string *' (aka 'basic_string<char, char_traits<char>, allocator<char> > *') and 'const ::std::string &(*)()') if (name_ == &::google::protobuf::internal::kEmptyString) { ~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./variant.pb.h:961:47: error: no member named 'kEmptyString' in namespace 'google::protobuf::internal'; did you mean 'GetEmptyString'? if (name_ == &::google::protobuf::internal::kEmptyString) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ GetEmptyString /usr/local/include/google/protobuf/generated_message_util.h:83:48: note: 'GetEmptyString' declared here LIBPROTOBUF_EXPORT inline const ::std::string& GetEmptyString() { ^ In file included from eval.cpp:8: In file included from ./eval.h:4: In file included from ./token.h:4: In file included from ./variant.h:22: In file included from ./svar.h:6: ./variant.pb.h:961:13: error: comparison of distinct pointer types ('::std::string *' (aka 'basic_string<char, char_traits<char>, allocator<char> > *') and 'const ::std::string &(*)()') if (name_ == &::google::protobuf::internal::kEmptyString) { ~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./variant.pb.h:968:47: error: no member named 'kEmptyString' in namespace 'google::protobuf::internal'; did you mean 'GetEmptyString'? if (name_ == &::google::protobuf::internal::kEmptyString) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ GetEmptyString /usr/local/include/google/protobuf/generated_message_util.h:83:48: note: 'GetEmptyString' declared here LIBPROTOBUF_EXPORT inline const ::std::string& GetEmptyString() { ^ In file included from eval.cpp:8: In file included from ./eval.h:4: In file included from ./token.h:4: In file included from ./variant.h:22: In file included from ./svar.h:6: ./variant.pb.h:968:13: error: comparison of distinct pointer types ('::std::string *' (aka 'basic_string<char, char_traits<char>, allocator<char> > *') and 'const ::std::string &(*)()') if (name_ == &::google::protobuf::internal::kEmptyString) { ~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./variant.pb.h:972:72: error: no member named 'kEmptyString' in namespace 'google::protobuf::internal'; did you mean 'GetEmptyString'? name_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ GetEmptyString /usr/local/include/google/protobuf/generated_message_util.h:83:48: note: 'GetEmptyString' declared here LIBPROTOBUF_EXPORT inline const ::std::string& GetEmptyString() { ^ In file included from eval.cpp:8: In file included from ./eval.h:4: In file included from ./token.h:4: In file included from ./variant.h:22: In file included from ./svar.h:6: ./variant.pb.h:972:13: error: const_cast from 'const ::std::string &(*)()' to '::std::string *' (aka 'basic_string<char, char_traits<char>, allocator<char> > *') is not allowed name_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./variant.pb.h:1134:47: error: no member named 'kEmptyString' in namespace 'google::protobuf::internal'; did you mean 'GetEmptyString'? if (name_ != &::google::protobuf::internal::kEmptyString) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ GetEmptyString /usr/local/include/google/protobuf/generated_message_util.h:83:48: note: 'GetEmptyString' declared here LIBPROTOBUF_EXPORT inline const ::std::string& GetEmptyString() { ^ In file included from eval.cpp:8: In file included from ./eval.h:4: In file included from ./token.h:4: In file included from ./variant.h:22: In file included from ./svar.h:6: ./variant.pb.h:1134:13: error: comparison of distinct pointer types ('::std::string *' (aka 'basic_string<char, char_traits<char>, allocator<char> > *') and 'const ::std::string &(*)()') if (name_ != &::google::protobuf::internal::kEmptyString) { ~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fatal error: too many errors emitted, stopping now [-ferror-limit=] 3 warnings and 20 errors generated. *** Error code 1 Stop. make[3]: stopped in /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.08/lib *** Error code 1 Stop. make[2]: stopped in /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.08 *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.08 *** Error code 1 Stop. make: stopped in /usr/ports/biology/plinkseq
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