From owner-freebsd-pkg-fallout@FreeBSD.ORG Sat Oct 11 20:52:07 2014 Return-Path: Delivered-To: pkg-fallout@FreeBSD.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 4A5AC9D5 for ; Sat, 11 Oct 2014 20:52:07 +0000 (UTC) Received: from beefy2.isc.freebsd.org (beefy2.isc.freebsd.org [IPv6:2001:4f8:3:ffe0:4072:0:16:39]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 29D7380E; Sat, 11 Oct 2014 20:52:07 +0000 (UTC) Received: from beefy2.isc.freebsd.org (localhost [127.0.0.1]) by beefy2.isc.freebsd.org (8.14.9/8.14.9) with ESMTP id s9BKq7kd075220; Sat, 11 Oct 2014 20:52:07 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy2.isc.freebsd.org (8.14.9/8.14.9/Submit) id s9BKq6DQ074609; Sat, 11 Oct 2014 20:52:06 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 11 Oct 2014 20:52:06 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201410112052.s9BKq6DQ074609@beefy2.isc.freebsd.org> To: jwbacon@tds.net Subject: [package - head-amd64-default][biology/plinkseq] Failed for plinkseq-0.08_3 in build Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.18-1 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 11 Oct 2014 20:52:07 -0000 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/head-amd64-default/2014-10-11_09h41m49s/logs/plinkseq-0.08_3.log Build URL: http://beefy2.isc.freebsd.org/build.html?mastername=head-amd64-default&build=2014-10-11_09h41m49s Log: ====>> Building biology/plinkseq build started at Sat Oct 11 20:51:55 UTC 2014 port directory: /usr/ports/biology/plinkseq building for: FreeBSD head-amd64-default-job-06 11.0-CURRENT FreeBSD 11.0-CURRENT r272340 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: 1100036 !!! Jail is newer than host. (Jail: 1100036, Host: 1100027) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- OSVERSION=1100036 UNAME_v=FreeBSD 11.0-CURRENT r272340 UNAME_r=11.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-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/head-amd64-default/ref/.p/pool MASTERNAME=head-amd64-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=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 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--- =================================================== ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===> 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 [head-amd64-default-job-06] 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 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by plinkseq-0.08_3 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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 =========================================================================== =================================================== =========================================================================== =================================================== ===> 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 [head-amd64-default-job-06] Installing protobuf-2.6.0... done ===> Returning to build of plinkseq-0.08_3 =========================================================================== =================================================== ===> 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 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 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 []' where the optional is: all - build all binaries install - install everything -------------------------------------------------- =========================================================================== =================================================== ===> 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, allocator > *') 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, allocator > *') 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, allocator > *') 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, allocator > *') 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, allocator > *') 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, allocator > *') 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, allocator > *') 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, allocator > *') 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