[package - head-amd64-default][science/bagel] Failed for bagel-1.2.2_4 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue Oct 29 11:12:06 UTC 2019
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: jbeich at 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/p515946_s354143/logs/bagel-1.2.2_4.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p515946_s354143
Log:
=>> Building science/bagel
build started at Tue Oct 29 09:52:18 UTC 2019
port directory: /usr/ports/science/bagel
package name: bagel-1.2.2_4
building for: FreeBSD head-amd64-default-job-09 13.0-CURRENT FreeBSD 13.0-CURRENT 1300054 amd64
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/science/bagel/Makefile 509290 2019-08-19 15:35:27Z jbeich $
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===> 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---
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yuri at FreeBSD.org
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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-09] Installing pkg-1.12.0...
[head-amd64-default-job-09] 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-09] Installing gcc9-9.2.0...
[head-amd64-default-job-09] `-- Installing binutils-2.32_1,1...
<snip>
./../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;
^
1 warning generated.
depbase=`echo multitensor.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 multitensor.lo -MD -MP -MF $depbase.Tpo -c -o multitensor.lo multitensor.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: mpicxx -DHAVE_CONFIG_H -I. -I../.. -isystem /usr/local/include -I/usr/local/include -I../.. -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -MT multitensor.lo -MD -MP -MF .deps/multitensor.Tpo -c multitensor.cc -fPIC -DPIC -o .libs/multitensor.o
In file included from multitensor.cc:28:
In file included from ../../src/smith/multitensor.h:29:
In file included from ../../src/smith/tensor.h:35:
In file included from ../../src/util/math/matop.h:30:
./../src/util/math/zmatrix.h:73:18: warning: 'diagonalize' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
virtual void diagonalize(VecView vec);
^
./../src/util/math/matrix_base.h:123:18: note: overridden virtual function is here
virtual void diagonalize(VecView vec) = 0;
^
1 warning generated.
depbase=`echo spinfreebase.lo | sed 's|[^/]*$|.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 spinfreebase.lo -MD -MP -MF $depbase.Tpo -c -o spinfreebase.lo spinfreebase.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 spinfreebase.lo -MD -MP -MF .deps/spinfreebase.Tpo -c spinfreebase.cc -fPIC -DPIC -o .libs/spinfreebase.o
In file included from spinfreebase.cc:29:
In file included from ../../src/smith/moint.h:36:
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 spinfreebase.cc:29:
In file included from ../../src/smith/moint.h:36:
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 spinfreebase.cc:29:
In file included from ../../src/smith/moint.h:36:
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;
^
In file included from spinfreebase.cc:29:
In file included from ../../src/smith/moint.h:38:
In file included from ../../src/scf/hf/fock.h:31:
In file included from ../../src/integral/rys/eribatch.h:28:
./../src/integral/rys/eribatch_base.h:41:18: 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/eribatch_base.h:95:30: note: in instantiation of template class 'bagel::ERIBatch_Base<double, bagel::Int_t::Standard>' requested here
extern template class bagel::ERIBatch_Base<double,bagel::Int_t::Standard>;
^
./../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 spinfreebase.cc:29:
In file included from ../../src/smith/moint.h:38:
In file included from ../../src/scf/hf/fock.h:31:
In file included from ../../src/integral/rys/eribatch.h:28:
./../src/integral/rys/eribatch_base.h:41:18: 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/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 spinfreebase.cc:30:
In file included from ../../src/smith/spinfreebase.h:35:
./../src/smith/denom.h:94:20: warning: 'shalf' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
const ViewType shalf(const std::string tag, const int ist) const { return *(shalf_.at(tag)[ist]); }
^
/usr/include/c++/v1/type_traits:1451:66: note: in instantiation of template class 'bagel::SMITH::Denom_SSSR<double>' requested here
: public integral_constant<bool, __is_convertible_to(_T1, _T2) &&
^
/usr/include/c++/v1/memory:3646:39: note: in instantiation of template class 'std::__1::is_convertible<bagel::SMITH::Denom_SSSR<double> *, bagel::SMITH::Denom<double> *>' requested here
typename enable_if<is_convertible<_Yp*, element_type*>::value, __nat>::type = __nat())
^
spinfreebase.cc:287:13: note: while substituting deduced template arguments into function template 'shared_ptr' [with _Yp = bagel::SMITH::Denom_SSSR<double>]
denom = make_shared<Denom_SSSR<double>>(fockact_, nstates, info_->thresh_overlap());
^
./../src/smith/denom.h:62:28: note: overridden virtual function is here
virtual const ViewType shalf(const std::string, const int) const = 0;
^
./../src/smith/denom.h:126:20: warning: 'shalf' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
const ViewType shalf(const std::string tag, const int ist) const {
^
/usr/include/c++/v1/type_traits:1451:66: note: in instantiation of template class 'bagel::SMITH::Denom_MSMR<double>' requested here
: public integral_constant<bool, __is_convertible_to(_T1, _T2) &&
^
/usr/include/c++/v1/memory:3646:39: note: in instantiation of template class 'std::__1::is_convertible<bagel::SMITH::Denom_MSMR<double> *, bagel::SMITH::Denom<double> *>' requested here
typename enable_if<is_convertible<_Yp*, element_type*>::value, __nat>::type = __nat())
^
spinfreebase.cc:289:13: note: while substituting deduced template arguments into function template 'shared_ptr' [with _Yp = bagel::SMITH::Denom_MSMR<double>]
denom = make_shared<Denom_MSMR<double>>(fockact_, nstates, info_->thresh_overlap());
^
./../src/smith/denom.h:62:28: note: overridden virtual function is here
virtual const ViewType shalf(const std::string, const int) const = 0;
^
./../src/smith/denom.h:94:20: warning: 'shalf' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
const ViewType shalf(const std::string tag, const int ist) const { return *(shalf_.at(tag)[ist]); }
^
/usr/include/c++/v1/type_traits:1451:66: note: in instantiation of template class 'bagel::SMITH::Denom_SSSR<std::__1::complex<double> >' requested here
: public integral_constant<bool, __is_convertible_to(_T1, _T2) &&
^
/usr/include/c++/v1/memory:3646:39: note: in instantiation of template class 'std::__1::is_convertible<bagel::SMITH::Denom_SSSR<std::__1::complex<double> > *, bagel::SMITH::Denom<std::complex<double> > *>' requested here
typename enable_if<is_convertible<_Yp*, element_type*>::value, __nat>::type = __nat())
^
spinfreebase.cc:363:13: note: while substituting deduced template arguments into function template 'shared_ptr' [with _Yp = bagel::SMITH::Denom_SSSR<std::__1::complex<double> >]
denom = make_shared<Denom_SSSR<complex<double>>>(fockact_, nstates, info_->thresh_overlap());
^
./../src/smith/denom.h:62:28: note: overridden virtual function is here
virtual const ViewType shalf(const std::string, const int) const = 0;
^
./../src/smith/denom.h:126:20: warning: 'shalf' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
const ViewType shalf(const std::string tag, const int ist) const {
^
/usr/include/c++/v1/type_traits:1451:66: note: in instantiation of template class 'bagel::SMITH::Denom_MSMR<std::__1::complex<double> >' requested here
: public integral_constant<bool, __is_convertible_to(_T1, _T2) &&
^
/usr/include/c++/v1/memory:3646:39: note: in instantiation of template class 'std::__1::is_convertible<bagel::SMITH::Denom_MSMR<std::__1::complex<double> > *, bagel::SMITH::Denom<std::complex<double> > *>' requested here
typename enable_if<is_convertible<_Yp*, element_type*>::value, __nat>::type = __nat())
^
spinfreebase.cc:365:13: note: while substituting deduced template arguments into function template 'shared_ptr' [with _Yp = bagel::SMITH::Denom_MSMR<std::__1::complex<double> >]
denom = make_shared<Denom_MSMR<complex<double>>>(fockact_, nstates, info_->thresh_overlap());
^
./../src/smith/denom.h:62:28: note: overridden virtual function is here
virtual const ViewType shalf(const std::string, const int) const = 0;
^
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-a0b00b.cpp
clang-cpp: note: diagnostic msg: /tmp/storagekramers-a0b00b.sh
clang-cpp: note: diagnostic msg:
********************
gmake[4]: *** [Makefile:1558: storagekramers.lo] Error 1
gmake[4]: *** Waiting for unfinished jobs....
9 warnings generated.
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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