Date: Fri, 10 Oct 2014 09:44:34 GMT From: pkg-fallout@FreeBSD.org To: jwbacon@tds.net Cc: pkg-fallout@FreeBSD.org Subject: [package - 10amd64-default][biology/plinkseq] Failed for plinkseq-0.08_3 in build Message-ID: <201410100944.s9A9iYc2008877@beefy2.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://beefy2.isc.freebsd.org/data/10amd64-default/2014-10-10_01h08m37s/logs/plinkseq-0.08_3.log Build URL: http://beefy2.isc.freebsd.org/build.html?mastername=10amd64-default&build=2014-10-10_01h08m37s Log: ====>> Building biology/plinkseq build started at Fri Oct 10 09:44:25 UTC 2014 port directory: /usr/ports/biology/plinkseq building for: FreeBSD 10amd64-default-job-05 10.0-RELEASE-p9 FreeBSD 10.0-RELEASE-p9 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: 1000510 ---Begin Environment--- OSVERSION=1000510 UNAME_v=FreeBSD 10.0-RELEASE-p9 UNAME_r=10.0-RELEASE-p9 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/10amd64-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=plinkseq-0.08_3 OLDPWD=/root PWD=/usr/local/poudriere/data/.m/10amd64-default/ref/.p/pool MASTERNAME=10amd64-default 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-- --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 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 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" MANPREFIX="/usr/local" 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=10.0 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 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 # clean-restricted ran via poudriere.conf NO_RESTRICTED #NO_RESTRICTED=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 [10amd64-default-job-05] 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 >============================ =========================================================================== =======================<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 [10amd64-default-job-05] 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-freebsd10.0 checking host system type... amd64-portbld-freebsd10.0 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 checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep 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... (cached) 262144 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking for /usr/bin/ld option to reload object files... -r checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from cc object... ok checking how to run the C preprocessor... cpp checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes 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 <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 -fno-strict-aliasing ' C++ Compiler: 'c++ -O2 -pipe -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 -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 -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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