[package - 121amd64-default][science/bagel] Failed for bagel-1.2.2_6 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Fri Sep 11 08:06:38 UTC 2020
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 at FreeBSD.org
Last committer: thierry at FreeBSD.org
Ident: $FreeBSD: head/science/bagel/Makefile 538716 2020-06-14 09:14:03Z thierry $
Log URL: http://beefy6.nyi.freebsd.org/data/121amd64-default/548176/logs/bagel-1.2.2_6.log
Build URL: http://beefy6.nyi.freebsd.org/build.html?mastername=121amd64-default&build=548176
Log:
=>> Building science/bagel
build started at Fri Sep 11 06:55:34 UTC 2020
port directory: /usr/ports/science/bagel
package name: bagel-1.2.2_6
building for: FreeBSD 121amd64-default-job-02 12.1-RELEASE-p9 FreeBSD 12.1-RELEASE-p9 amd64
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/science/bagel/Makefile 538716 2020-06-14 09:14:03Z thierry $
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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---
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> bagel-1.2.2_6 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.15.4.txz
[121amd64-default-job-02] Installing pkg-1.15.4...
[121amd64-default-job-02] Extracting pkg-1.15.4: .......... done
===> bagel-1.2.2_6 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bagel-1.2.2_6
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bagel-1.2.2_6 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bagel-1.2.2_6 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_6 for building
===> Extracting for bagel-1.2.2_6
=> SHA256 Checksum OK for nubakery-bagel-v1.2.2_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for bagel-1.2.2_6
===> Applying FreeBSD patches for bagel-1.2.2_6 from /usr/ports/science/bagel/files
===========================================================================
=======================<phase: build-depends >============================
===> bagel-1.2.2_6 depends on executable: gfortran9 - not found
===> Installing existing package /packages/All/gcc9-9.3.0_1.txz
[121amd64-default-job-02] Installing gcc9-9.3.0_1...
[121amd64-default-job-02] `-- Installing binutils-2.33.1_3,1...
[121amd64-default-job-02] | `-- Installing gettext-runtime-0.21...
[121amd64-default-job-02] | | `-- Installing indexinfo-0.3.1...
[121amd64-default-job-02] | | `-- Extracting indexinfo-0.3.1: .... done
[121amd64-default-job-02] | `-- Extracting gettext-runtime-0.21: .......... done
[121amd64-default-job-02] `-- Extracting binutils-2.33.1_3,1: .......... done
[121amd64-default-job-02] `-- Installing gmp-6.2.0...
[121amd64-default-job-02] `-- Extracting gmp-6.2.0: .......... done
[121amd64-default-job-02] `-- Installing mpc-1.1.0_2...
[121amd64-default-job-02] | `-- Installing mpfr-4.1.0...
<snip>
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 nevpt2/nevpt2.cc:28:
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 nevpt2/nevpt2.cc:28:
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;
^
In file included from nevpt2/nevpt2.cc:29:
In file included from ../../src/multi/casscf/cassecond.h:29:
In file included from ../../src/multi/casscf/casscf.h:35:
In file included from ../../src/ci/fci/distfci.h:30:
./../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 nevpt2/nevpt2.cc:29:
In file included from ../../src/multi/casscf/cassecond.h:29:
In file included from ../../src/multi/casscf/casscf.h:36:
In file included from ../../src/ci/fci/knowles.h:32:
./../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;
^
9 warnings generated.
depbase=`echo dmp2/dmp2.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 dmp2/dmp2.lo -MD -MP -MF $depbase.Tpo -c -o dmp2/dmp2.lo dmp2/dmp2.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 dmp2/dmp2.lo -MD -MP -MF dmp2/.deps/dmp2.Tpo -c dmp2/dmp2.cc -fPIC -DPIC -o dmp2/.libs/dmp2.o
In file included from dmp2/dmp2.cc:31:
In file included from ../../src/df/reldffull.h:28:
In file included from ../../src/df/reldf.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:
In file included from ../../src/integral/rys/rysintegral.h:32:
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 dmp2/dmp2.cc:31:
In file included from ../../src/df/reldffull.h:28:
In file included from ../../src/df/reldf.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 dmp2/dmp2.cc:31:
In file included from ../../src/df/reldffull.h:28:
In file included from ../../src/df/reldf.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;
^
3 warnings generated.
/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 -lscalapack -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc9 -L/usr/local/lib/gcc9 -B/usr/local/bin -fstack-protector-strong -o libbagel_pt2.la mp2/mp2.lo mp2/mp2grad.lo mp2/mp2cache.lo nevpt2/nevpt2.lo dmp2/dmp2.lo -lxc -lboost_regex -lboost_unit_test_framework -lboost_serialization -lscalapack -L/usr/local/lib
libtool: link: /usr/local/bin/ar cru .libs/libbagel_pt2.a mp2/.libs/mp2.o mp2/.libs/mp2grad.o mp2/.libs/mp2cache.o nevpt2/.libs/nevpt2.o dmp2/.libs/dmp2.o
/usr/local/bin/ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: /usr/local/bin/ranlib .libs/libbagel_pt2.a
libtool: link: ( cd ".libs" && rm -f "libbagel_pt2.la" && ln -s "../libbagel_pt2.la" "libbagel_pt2.la" )
gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2/src/pt2'
Making all in wfn
gmake[4]: Entering directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2/src/wfn'
/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 reference.lo -MD -MP -MF .deps/reference.Tpo -c -o reference.lo reference.cc
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 reference.lo -MD -MP -MF .deps/reference.Tpo -c reference.cc -fPIC -DPIC -o .libs/reference.o
In file included from reference.cc:25:
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 reference.cc:25:
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 reference.cc:25:
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;
^
In file included from reference.cc:29:
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 reference.cc:29:
./../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;
^
c++: error: unable to execute command: Killed
c++: error: clang frontend command failed due to signal (use -v to see invocation)
FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1)
Target: x86_64-unknown-freebsd12.1
Thread model: posix
InstalledDir: /usr/bin
c++: 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.
c++: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
c++: note: diagnostic msg: /tmp/reference-c97b24.cpp
c++: note: diagnostic msg: /tmp/reference-c97b24.sh
c++: note: diagnostic msg:
********************
gmake[4]: *** [Makefile:418: reference.lo] Error 1
gmake[4]: Leaving directory '/wrkdirs/usr/ports/science/bagel/work/bagel-1.2.2/src/wfn'
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'
*** Error code 1
Stop.
make: stopped in /usr/ports/science/bagel
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