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Date:      Sat, 12 Oct 2019 01:36:38 GMT
From:      pkg-fallout@FreeBSD.org
To:        jwb@FreeBSD.org
Cc:        pkg-fallout@FreeBSD.org
Subject:   [package - head-amd64-default][biology/plinkseq] Failed for plinkseq-0.10_1 in build
Message-ID:  <201910120136.x9C1acid063564@beefy18.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:     jwb@FreeBSD.org
Last committer: jwb@FreeBSD.org
Ident:          $FreeBSD: head/biology/plinkseq/Makefile 460452 2018-01-31 01:07:07Z jwb $
Log URL:        http://beefy18.nyi.freebsd.org/data/head-amd64-default/p514309_s353449/logs/plinkseq-0.10_1.log
Build URL:      http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p514309_s353449
Log:

=>> Building biology/plinkseq
build started at Sat Oct 12 01:27:13 UTC 2019
port directory: /usr/ports/biology/plinkseq
package name: plinkseq-0.10_1
building for: FreeBSD head-amd64-default-job-17 13.0-CURRENT FreeBSD 13.0-CURRENT 1300050 amd64
maintained by: jwb@FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/plinkseq/Makefile 460452 2018-01-31 01:07:07Z jwb $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300040
Jail OSVERSION: 1300050
Job Id: 17




!!! Jail is newer than host. (Jail: 1300050, Host: 1300040) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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jwb@FreeBSD.org
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--CONFIGURE_ENV--
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=======================<phase: check-sanity   >============================
===>  License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   plinkseq-0.10_1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.12.0.txz
[head-amd64-default-job-17] Installing pkg-1.12.0...
[head-amd64-default-job-17] Extracting pkg-1.12.0: .......... done
===>   plinkseq-0.10_1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of plinkseq-0.10_1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by plinkseq-0.10_1 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by plinkseq-0.10_1 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_1 for building
===>  Extracting for plinkseq-0.10_1
=> SHA256 Checksum OK for plinkseq-src-0.10.tgz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for plinkseq-0.10_1
===>  Applying FreeBSD patches for plinkseq-0.10_1
/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
/usr/bin/sed -i.bak  -e 's|g++|c++|g'  -e 's|gcc|cc|g'  -e 's|CXXFLAGS = -O3|CXXFLAGS = -O2 -pipe -fstack-protector-strong -fno-strict-aliasing  |g'  -e 's|ALL_CFLAGS =-O3|ALL_CFLAGS = -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing |g'  /wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/config_defs.Makefile
/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_1 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_3.txz
[head-amd64-default-job-17] Installing gmake-4.2.1_3...
[head-amd64-default-job-17] `-- Installing gettext-runtime-0.20.1...
[head-amd64-default-job-17] |   `-- Installing indexinfo-0.3.1...
[head-amd64-default-job-17] |   `-- Extracting indexinfo-0.3.1: .... done
[head-amd64-default-job-17] `-- Extracting gettext-runtime-0.20.1: .......... done
<snip>
a - build/lib/kbac.o
a - build/lib/clusters.o
a - build/lib/cnv.o
a - build/lib/summaries.o
a - build/lib/stepup.o
a - build/lib/netassoc.o
a - build/lib/compare.o
a - build/lib/loaders.o
a - build/lib/func.o
a - build/lib/assoc.o
a - build/lib/sockets.o
a - build/lib/varfunc.o
a - build/lib/genic.o
a - build/lib/webcheck.o
a - build/lib/prot.o
a - build/lib/extra.o
a - build/lib/chet.o
a - build/lib/matdb.o
a - build/lib/ibd.o
a - build/lib/glm-tests.o
a - build/lib/util.o
ranlib build/lib/libpseq.a
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/pseq'
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing    -I./sources/include -I../ext/sources/include/  sources/lib/c8lib.cpp -o build/lib/c8lib.o
In file included from sources/lib/dose.cpp:3:
In file included from ./sources/include/plinkseq/gstore.h:15:
In file included from ./sources/include/plinkseq/vardb.h:8:
./sources/include/plinkseq/mask.h:2151:5: warning: control reaches end of non-void function [-Wreturn-type]
    }
    ^
In file included from sources/lib/dose.cpp:3:
In file included from ./sources/include/plinkseq/gstore.h:15:
./sources/include/plinkseq/vardb.h:329:59: warning: control reaches end of non-void function [-Wreturn-type]
  bool compression( const bool b ) { using_compression=b; }
                                                          ^
sources/lib/dose.cpp:328:35: warning: result of comparison against a string literal is unspecified (use strncmp instead) [-Wstring-compare]
              if ( toks[ 1 + id_offset ] == "." || toks[ 2 + id_offset ] == "." ) continue;
                                         ^  ~~~
sources/lib/dose.cpp:328:67: warning: result of comparison against a string literal is unspecified (use strncmp instead) [-Wstring-compare]
              if ( toks[ 1 + id_offset ] == "." || toks[ 2 + id_offset ] == "." ) continue;
                                                                         ^  ~~~
sources/lib/dose.cpp:337:31: warning: result of comparison against a string literal is unspecified (use strncmp instead) [-Wstring-compare]
          if ( toks[ 1 + id_offset ] == "." || toks[ 2 + id_offset ] == "." ) continue;
                                     ^  ~~~
sources/lib/dose.cpp:337:63: warning: result of comparison against a string literal is unspecified (use strncmp instead) [-Wstring-compare]
          if ( toks[ 1 + id_offset ] == "." || toks[ 2 + id_offset ] == "." ) continue;
                                                                     ^  ~~~
sources/lib/c8lib.cpp:1236:31: warning: expression result unused [-Wunused-value]
  r = pow ( x - xc, 2 ) + ( y - yc, 2 );
                            ~ ^ ~~
sources/lib/c8lib.cpp:1245:31: warning: expression result unused [-Wunused-value]
  r = pow ( x - xc, 2 ) + ( y - yc, 2 );
                            ~ ^ ~~
sources/lib/c8lib.cpp:1257:31: warning: expression result unused [-Wunused-value]
  r = pow ( x - xc, 2 ) + ( y - yc, 2 );
                            ~ ^ ~~
sources/lib/c8lib.cpp:1269:31: warning: expression result unused [-Wunused-value]
  r = pow ( x - xc, 2 ) + ( y - yc, 2 );
                            ~ ^ ~~
4 warnings generated.
gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/util
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/util'
mkdir -p build/lib
making depend sources/lib/char_tok.cpp
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing    -I./sources/include  sources/lib/char_tok.cpp -o build/lib/char_tok.o
ar rv build/lib/libutil.a build/lib/char_tok.o
ar: warning: creating build/lib/libutil.a
a - build/lib/char_tok.o
ranlib build/lib/libutil.a
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/util'
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing    -I./sources/include -I../ext/sources/include/  sources/lib/segments.cpp -o build/lib/segments.o
In file included from sources/lib/segments.cpp:2:
In file included from ./sources/include/plinkseq/segments.h:5:
In file included from ./sources/include/plinkseq/gstore.h:6:
In file included from ./sources/include/plinkseq/variant.h:14:
In file included from ./sources/include/plinkseq/genotype.h:11:
In file included from ./sources/include/plinkseq/individual.h:8:
./sources/include/plinkseq/meta.h:580:15: warning: enumeration values 'META_UNDEFINED' and 'META_CHAR' not handled in switch [-Wswitch]
                    switch( m->mt ) 
                            ^
./sources/include/plinkseq/meta.h:617:15: warning: enumeration values 'META_FLAG', 'META_UNDEFINED', and 'META_CHAR' not handled in switch [-Wswitch]
                    switch( m->mt )
                            ^
In file included from sources/lib/segments.cpp:2:
In file included from ./sources/include/plinkseq/segments.h:5:
In file included from ./sources/include/plinkseq/gstore.h:15:
In file included from ./sources/include/plinkseq/vardb.h:8:
./sources/include/plinkseq/mask.h:2151:5: warning: control reaches end of non-void function [-Wreturn-type]
    }
    ^
In file included from sources/lib/segments.cpp:2:
In file included from ./sources/include/plinkseq/segments.h:5:
In file included from ./sources/include/plinkseq/gstore.h:15:
./sources/include/plinkseq/vardb.h:329:59: warning: control reaches end of non-void function [-Wreturn-type]
  bool compression( const bool b ) { using_compression=b; }
                                                          ^
8 warnings generated.
gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/mongoose
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/mongoose'
mkdir -p build/lib
making depend sources/lib/mongoose.c
clang-cpp: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
cc -c -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -DSQLITE_OMIT_LOAD_EXTENSION -I./sources/include   sources/lib/mongoose.c -o build/lib/mongoose.o
ar rv build/lib/libmongoose.a build/lib/mongoose.o
ar: warning: creating build/lib/libmongoose.a
a - build/lib/mongoose.o
ranlib build/lib/libmongoose.a
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/mongoose'
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing    -I./sources/include -I../ext/sources/include/  sources/lib/matdb.cpp -o build/lib/matdb.o
4 warnings generated.
gmake DBGCXXFLAGS="" USE_DEBUG="" -C sources/browser
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/browser'
mkdir -p build/lib
making depend sources/lib/lines.cpp
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing    -I./sources/include -I../plinkseq/sources/include/ -I../ext/sources/include/  sources/lib/lines.cpp -o build/lib/lines.o
In file included from sources/lib/matdb.cpp:4:
./sources/include/plinkseq/matrix.pb.h:35:7: error: definition of type 'double_t' conflicts with typedef of the same name
class double_t;
      ^
/usr/include/math.h:136:20: note: 'double_t' declared here
typedef __double_t      double_t;
                        ^
In file included from sources/lib/matdb.cpp:4:
./sources/include/plinkseq/matrix.pb.h:81:7: error: definition of type 'double_t' conflicts with typedef of the same name
class double_t : public ::google::protobuf::Message {
      ^
/usr/include/math.h:136:20: note: 'double_t' declared here
typedef __double_t      double_t;
                        ^
In file included from sources/lib/matdb.cpp:4:
./sources/include/plinkseq/matrix.pb.h:560:12: error: 'double_t' (aka 'double') is not a class, namespace, or enumeration
inline int double_t::data_size() const {
           ^
./sources/include/plinkseq/matrix.pb.h:563:13: error: 'double_t' (aka 'double') is not a class, namespace, or enumeration
inline void double_t::clear_data() {
            ^
./sources/include/plinkseq/matrix.pb.h:566:15: error: 'double_t' (aka 'double') is not a class, namespace, or enumeration
inline double double_t::data(int index) const {
              ^
./sources/include/plinkseq/matrix.pb.h:569:13: error: 'double_t' (aka 'double') is not a class, namespace, or enumeration
inline void double_t::set_data(int index, double value) {
            ^
./sources/include/plinkseq/matrix.pb.h:572:13: error: 'double_t' (aka 'double') is not a class, namespace, or enumeration
inline void double_t::add_data(double value) {
            ^
./sources/include/plinkseq/matrix.pb.h:576:1: error: 'double_t' (aka 'double') is not a class, namespace, or enumeration
double_t::data() const {
^
./sources/include/plinkseq/matrix.pb.h:580:1: error: 'double_t' (aka 'double') is not a class, namespace, or enumeration
double_t::mutable_data() {
^
sources/lib/matdb.cpp:139:10: error: member reference base type 'double_t' (aka 'double') is not a structure or union
    pbCol.add_data( x[r] ); 
    ~~~~~^~~~~~~~~
sources/lib/matdb.cpp:142:8: error: member reference base type 'double_t' (aka 'double') is not a structure or union
  pbCol.SerializeToString(&s);
  ~~~~~^~~~~~~~~~~~~~~~~~
sources/lib/matdb.cpp:153:8: error: member reference base type 'double_t' (aka 'double') is not a structure or union
  pbCol.ParseFromString( b.get_string() );
  ~~~~~^~~~~~~~~~~~~~~~
sources/lib/matdb.cpp:155:32: error: member reference base type 'double_t' (aka 'double') is not a structure or union
  const int nrow_stored = pbCol.data_size();      
                          ~~~~~^~~~~~~~~~
sources/lib/matdb.cpp:160:17: error: member reference base type 'double_t' (aka 'double') is not a structure or union
    x[r] = pbCol.data(r);
           ~~~~~^~~~~
In file included from sources/lib/matdb.cpp:4:
In file included from ./sources/include/plinkseq/matrix.pb.h:24:
./ext/sources/include/google/protobuf/repeated_field.h:337:48: error: member reference base type 'double' is not a structure or union
  static void Clear(GenericType* value) { value->Clear(); }
                                          ~~~~~^ ~~~~~
./ext/sources/include/google/protobuf/repeated_field.h:857:18: note: in instantiation of member function 'google::protobuf::internal::GenericTypeHandler<double>::Clear' requested here
    TypeHandler::Clear(cast<TypeHandler>(elements_[i]));
                 ^
./ext/sources/include/google/protobuf/repeated_field.h:1085:25: note: in instantiation of function template specialization 'google::protobuf::internal::RepeatedPtrFieldBase::Clear<google::protobuf::RepeatedPtrField<double>::TypeHandler>' requested here
  RepeatedPtrFieldBase::Clear<TypeHandler>();
                        ^
./sources/include/plinkseq/matrix.pb.h:811:13: note: in instantiation of member function 'google::protobuf::RepeatedPtrField<double>::Clear' requested here
  d_double_.Clear();
            ^
15 errors generated.
gmake[3]: *** [../../config_rules.Makefile:16: build/lib/matdb.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]: *** Waiting for unfinished jobs....
ar rv build/lib/libbrowser.a build/lib/lines.o
ar: warning: creating build/lib/libbrowser.a
a - build/lib/lines.o
ranlib build/lib/libbrowser.a
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/plinkseq/work/plinkseq-0.10/sources/browser'
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'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/plinkseq



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