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Date:      Thu, 24 Oct 2019 07:48:05 GMT
From:      pkg-fallout@FreeBSD.org
To:        yuri@FreeBSD.org
Cc:        pkg-fallout@FreeBSD.org
Subject:   [package - head-amd64-default][science/bagel] Failed for bagel-1.2.2_4 in build
Message-ID:  <201910240748.x9O7m57f029518@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:     yuri@FreeBSD.org
Last committer: jbeich@FreeBSD.org
Ident:          $FreeBSD: head/science/bagel/Makefile 509290 2019-08-19 15:35:27Z jbeich $
Log URL:        http://beefy18.nyi.freebsd.org/data/head-amd64-default/p515319_s353967/logs/bagel-1.2.2_4.log
Build URL:      http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p515319_s353967
Log:

=>> Building science/bagel
build started at Thu Oct 24 06:57:13 UTC 2019
port directory: /usr/ports/science/bagel
package name: bagel-1.2.2_4
building for: FreeBSD head-amd64-default-job-21 13.0-CURRENT FreeBSD 13.0-CURRENT 1300054 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:      $FreeBSD: head/science/bagel/Makefile 509290 2019-08-19 15:35:27Z jbeich $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300047
Jail OSVERSION: 1300054
Job Id: 21




!!! Jail is newer than host. (Jail: 1300054, Host: 1300047) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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---Begin OPTIONS List---
===> The following configuration options are available for bagel-1.2.2_4:
     LIBXC=on: Build DFT with libxc
     MPI=on: MPI (Message Passing Interface) support
     SCALAPACK=on: Use ScaLapack library for parallelized linear algebra
     SMITH=on: Compile SMITH generated code
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--
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--End CONFIGURE_ARGS--

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=======================<phase: check-sanity   >============================
===>  License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   bagel-1.2.2_4 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.12.0.txz
[head-amd64-default-job-21] Installing pkg-1.12.0...
[head-amd64-default-job-21] Extracting pkg-1.12.0: .......... done
===>   bagel-1.2.2_4 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of bagel-1.2.2_4
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by bagel-1.2.2_4 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by bagel-1.2.2_4 for building
=> SHA256 Checksum OK for nubakery-bagel-v1.2.2_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by bagel-1.2.2_4 for building
===>  Extracting for bagel-1.2.2_4
=> SHA256 Checksum OK for nubakery-bagel-v1.2.2_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for bagel-1.2.2_4
===>  Applying FreeBSD patches for bagel-1.2.2_4
===========================================================================
=======================<phase: build-depends  >============================
===>   bagel-1.2.2_4 depends on executable: gfortran9 - not found
===>   Installing existing package /packages/All/gcc9-9.2.0.txz
[head-amd64-default-job-21] Installing gcc9-9.2.0...
[head-amd64-default-job-21] `-- Installing binutils-2.32_1,1...
<snip>
                 ^
./../../src/integral/rys/eribatch_base.h:96:30: note: in instantiation of template class 'bagel::ERIBatch_Base<std::__1::complex<double>, bagel::Int_t::London>' requested here
extern template class bagel::ERIBatch_Base<std::complex<double>,bagel::Int_t::London>;
                             ^
./../../src/integral/rys/rysintegral.h:92:18: note: overridden virtual function is here
    virtual void root_weight(const int ps) = 0;
                 ^
In file included from zcasnoopt.cc:29:
In file included from ../../../src/mat1e/rel/relhcore.h:32:
In file included from ../../../src/mat1e/rel/small1e.h:31:
In file included from ../../../src/integral/rys/naibatch.h:28:
In file included from ../../../src/integral/rys/coulombbatch_energy.h:28:
./../../src/integral/rys/coulombbatch_base.h:50:18: warning: 'root_weight' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
    virtual void root_weight(const int ps) = 0;
                 ^
./../../src/integral/rys/coulombbatch_base.h:99:30: note: in instantiation of template class 'bagel::CoulombBatch_Base<double, bagel::Int_t::Standard>' requested here
extern template class bagel::CoulombBatch_Base<double>;
                             ^
./../../src/integral/rys/rysintegral.h:92:18: note: overridden virtual function is here
    virtual void root_weight(const int ps) = 0;
                 ^
In file included from zcasnoopt.cc:29:
In file included from ../../../src/mat1e/rel/relhcore.h:32:
In file included from ../../../src/mat1e/rel/small1e.h:31:
In file included from ../../../src/integral/rys/naibatch.h:28:
In file included from ../../../src/integral/rys/coulombbatch_energy.h:28:
./../../src/integral/rys/coulombbatch_base.h:50:18: warning: 'root_weight' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
    virtual void root_weight(const int ps) = 0;
                 ^
./../../src/integral/rys/coulombbatch_base.h:100:30: note: in instantiation of template class 'bagel::CoulombBatch_Base<std::__1::complex<double>, bagel::Int_t::London>' requested here
extern template class bagel::CoulombBatch_Base<std::complex<double>,bagel::Int_t::London>;
                             ^
./../../src/integral/rys/rysintegral.h:92:18: note: overridden virtual function is here
    virtual void root_weight(const int ps) = 0;
                 ^
7 warnings generated.
mv -f .deps/zcasnoopt.Tpo .deps/zcasnoopt.Plo
/bin/sh ../../../libtool  --tag=CXX   --mode=link mpicxx -I../../.. -O2 -pipe  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing   -isystem /usr/local/include -std=c++11   -L/usr/local/lib  -lcblas -lscalapack -Wl,-rpath=/usr/local/lib/gcc9  -L/usr/local/lib/gcc9 -B/usr/local/bin -fstack-protector-strong  -o libbagel_zcasscf.la  zcasscf.lo zcassecond.lo zcassecond_compute.lo zqvec.lo zcasnoopt.lo  -lxc -lboost_regex -lboost_unit_test_framework -lboost_serialization -lscalapack  -L/usr/local/lib
libtool: link: /usr/local/bin/ar cru .libs/libbagel_zcasscf.a .libs/zcasscf.o .libs/zcassecond.o .libs/zcassecond_compute.o .libs/zqvec.o .libs/zcasnoopt.o 
/usr/local/bin/ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: /usr/local/bin/ranlib .libs/libbagel_zcasscf.a
libtool: link: ( cd ".libs" && rm -f "libbagel_zcasscf.la" && ln -s "../libbagel_zcasscf.la" "libbagel_zcasscf.la" )
gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2/src/multi/zcasscf'
gmake[5]: Entering directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2/src/multi'
gmake[5]: Nothing to be done for 'all-am'.
gmake[5]: Leaving directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2/src/multi'
gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2/src/multi'
Making all in smith
gmake[4]: Entering directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2/src/smith'
depbase=`echo smith_info.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../../libtool  --tag=CXX   --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I../..   -isystem /usr/local/include -I/usr/local/include -I../.. -O2 -pipe  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing   -isystem /usr/local/include -std=c++11  -MT smith_info.lo -MD -MP -MF $depbase.Tpo -c -o smith_info.lo smith_info.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo indexrange.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../../libtool  --tag=CXX   --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I../..   -isystem /usr/local/include -I/usr/local/include -I../.. -O2 -pipe  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing   -isystem /usr/local/include -std=c++11  -MT indexrange.lo -MD -MP -MF $depbase.Tpo -c -o indexrange.lo indexrange.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  mpicxx -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -I/usr/local/include -I../.. -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -MT smith_info.lo -MD -MP -MF .deps/smith_info.Tpo -c smith_info.cc  -fPIC -DPIC -o .libs/smith_info.o
libtool: compile:  mpicxx -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -I/usr/local/include -I../.. -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -MT indexrange.lo -MD -MP -MF .deps/indexrange.Tpo -c indexrange.cc  -fPIC -DPIC -o .libs/indexrange.o
In file included from smith_info.cc:28:
In file included from ../../src/smith/smith_info.h:28:
In file included from ../../src/wfn/relreference.h:28:
In file included from ../../src/wfn/reference.h:30:
In file included from ../../src/mat1e/hcore.h:29:
In file included from ../../src/wfn/hcoreinfo.h:29:
In file included from ../../src/molecule/molecule.h:29:
In file included from ../../src/molecule/atom.h:29:
In file included from ../../src/molecule/shell.h:29:
./../src/util/math/zmatrix.h:73:18: warning: 'diagonalize' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
    virtual void diagonalize(VecView vec);
                 ^
./../src/util/math/matrix_base.h:123:18: note: overridden virtual function is here
    virtual void diagonalize(VecView vec) = 0;
                 ^
In file included from smith_info.cc:28:
In file included from ../../src/smith/smith_info.h:28:
In file included from ../../src/wfn/relreference.h:28:
In file included from ../../src/wfn/reference.h:32:
In file included from ../../src/wfn/geometry.h:29:
In file included from ../../src/df/df.h:28:
In file included from ../../src/df/paralleldf.h:29:
In file included from ../../src/df/dfinttask_old.h:28:
./../src/integral/rys/rysintegral.h:153:18: warning: 'compute' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
    virtual void compute() = 0;
                 ^
./../src/integral/rys/rysintegral.h:173:30: note: in instantiation of template class 'bagel::RysIntegral<double, bagel::Int_t::Standard>' requested here
extern template class bagel::RysIntegral<double,bagel::Int_t::Standard>;
                             ^
./../src/integral/integral.h:42:18: note: overridden virtual function is here
    virtual void compute() = 0;
                 ^
In file included from smith_info.cc:28:
In file included from ../../src/smith/smith_info.h:28:
In file included from ../../src/wfn/relreference.h:28:
In file included from ../../src/wfn/reference.h:32:
In file included from ../../src/wfn/geometry.h:29:
In file included from ../../src/df/df.h:28:
In file included from ../../src/df/paralleldf.h:29:
In file included from ../../src/df/dfinttask_old.h:28:
./../src/integral/rys/rysintegral.h:153:18: warning: 'compute' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
    virtual void compute() = 0;
                 ^
./../src/integral/rys/rysintegral.h:174:30: note: in instantiation of template class 'bagel::RysIntegral<std::__1::complex<double>, bagel::Int_t::London>' requested here
extern template class bagel::RysIntegral<std::complex<double>,bagel::Int_t::London>;
                             ^
./../src/integral/integral.h:42:18: note: overridden virtual function is here
    virtual void compute() = 0;
                 ^
depbase=`echo storage.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../../libtool  --tag=CXX   --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I../..   -isystem /usr/local/include -I/usr/local/include -I../.. -O2 -pipe  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing   -isystem /usr/local/include -std=c++11  -MT storage.lo -MD -MP -MF $depbase.Tpo -c -o storage.lo storage.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  mpicxx -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -I/usr/local/include -I../.. -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -MT storage.lo -MD -MP -MF .deps/storage.Tpo -c storage.cc  -fPIC -DPIC -o .libs/storage.o
In file included from smith_info.cc:30:
In file included from ../../src/ci/fci/fci.h:29:
./../src/ci/fci/fci_base.h:154:46: warning: 'conv_to_ref' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
    virtual std::shared_ptr<const Reference> conv_to_ref() const = 0;
                                             ^
./../src/wfn/method.h:57:46: note: overridden virtual function is here
    virtual std::shared_ptr<const Reference> conv_to_ref() const = 0;
                                             ^
In file included from smith_info.cc:30:
./../src/ci/fci/fci.h:95:18: warning: 'update' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
    virtual void update(std::shared_ptr<const Matrix>) = 0;
                 ^
./../src/ci/fci/fci_base.h:104:18: note: overridden virtual function is here
    virtual void update(std::shared_ptr<const Matrix>) = 0;
                 ^
depbase=`echo storagekramers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../../libtool  --tag=CXX   --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I../..   -isystem /usr/local/include -I/usr/local/include -I../.. -O2 -pipe  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing   -isystem /usr/local/include -std=c++11  -MT storagekramers.lo -MD -MP -MF $depbase.Tpo -c -o storagekramers.lo storagekramers.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  mpicxx -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -I/usr/local/include -I../.. -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -MT storagekramers.lo -MD -MP -MF .deps/storagekramers.Tpo -c storagekramers.cc  -fPIC -DPIC -o .libs/storagekramers.o
In file included from storagekramers.cc:28:
./../src/smith/storagekramers.h:182:10: warning: 'put_block' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
    void put_block(const std::unique_ptr<DataType[]>& dat, const std::vector<Index> indices);
         ^
./../src/smith/storagekramers.h:203:23: note: in instantiation of template class 'bagel::SMITH::StorageKramers<double>' requested here
extern template class StorageKramers<double>;
                      ^
./../src/smith/storage.h:217:18: note: overridden virtual function is here
    virtual void put_block(const std::unique_ptr<DataType[]>& dat, const std::vector<Index> i);
                 ^
In file included from storagekramers.cc:28:
./../src/smith/storagekramers.h:182:10: warning: 'put_block' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
    void put_block(const std::unique_ptr<DataType[]>& dat, const std::vector<Index> indices);
         ^
./../src/smith/storagekramers.h:204:23: note: in instantiation of template class 'bagel::SMITH::StorageKramers<std::__1::complex<double> >' requested here
extern template class StorageKramers<std::complex<double>>;
                      ^
./../src/smith/storage.h:217:18: note: overridden virtual function is here
    virtual void put_block(const std::unique_ptr<DataType[]>& dat, const std::vector<Index> i);
                 ^
clang-cpp: error: unable to execute command: Killed
clang-cpp: error: clang frontend command failed due to signal (use -v to see invocation)
FreeBSD clang version 9.0.0 (tags/RELEASE_900/final 372316) (based on LLVM 9.0.0)
Target: x86_64-unknown-freebsd13.0
Thread model: posix
InstalledDir: /usr/bin
clang-cpp: note: diagnostic msg: PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script.
clang-cpp: error: unable to execute command: Killed
clang-cpp: error: clang frontend command failed due to signal (use -v to see invocation)
FreeBSD clang version 9.0.0 (tags/RELEASE_900/final 372316) (based on LLVM 9.0.0)
Target: x86_64-unknown-freebsd13.0
Thread model: posix
InstalledDir: /usr/bin
clang-cpp: note: diagnostic msg: PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script.
clang-cpp: note: diagnostic msg: 
********************

PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang-cpp: note: diagnostic msg: /tmp/storagekramers-5c3015.cpp
clang-cpp: note: diagnostic msg: /tmp/storagekramers-5c3015.sh
clang-cpp: note: diagnostic msg: 

********************
gmake[4]: *** [Makefile:1558: storagekramers.lo] Error 1
gmake[4]: *** Waiting for unfinished jobs....
clang-cpp: note: diagnostic msg: 
********************

PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang-cpp: note: diagnostic msg: /tmp/smith_info-ca6eaf.cpp
clang-cpp: note: diagnostic msg: /tmp/smith_info-ca6eaf.sh
clang-cpp: note: diagnostic msg: 

********************
gmake[4]: *** [Makefile:1558: smith_info.lo] Error 1
gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2/src/smith'
gmake[3]: *** [Makefile:640: all-recursive] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2/src'
gmake[2]: *** [Makefile:421: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2'
gmake[1]: *** [Makefile:353: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2'
===> 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/science/bagel



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