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Date:      Sat, 11 Oct 2014 20:52:06 GMT
From:      pkg-fallout@FreeBSD.org
To:        jwbacon@tds.net
Cc:        pkg-fallout@FreeBSD.org
Subject:   [package - head-amd64-default][biology/plinkseq] Failed for plinkseq-0.08_3 in build
Message-ID:  <201410112052.s9BKq6DQ074609@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/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---
=======================<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
[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
===========================================================================
=======================<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
[head-amd64-default-job-06] 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
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
<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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