[package - 124amd64-default][science/jdftx] Failed for jdftx-1.7.0_3 in build
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Date: Tue, 10 Oct 2023 10:28:01 UTC
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
Log URL: https://pkg-status.freebsd.org/beefy6/data/124amd64-default/de9b672bc747/logs/jdftx-1.7.0_3.log
Build URL: https://pkg-status.freebsd.org/beefy6/build.html?mastername=124amd64-default&build=de9b672bc747
Log:
=>> Building science/jdftx
build started at Tue Oct 10 10:15:15 UTC 2023
port directory: /usr/ports/science/jdftx
package name: jdftx-1.7.0_3
building for: FreeBSD 124amd64-default-job-13 12.4-RELEASE-p6 FreeBSD 12.4-RELEASE-p6 amd64
maintained by: yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3+ accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> jdftx-1.7.0_3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.7.pkg
[124amd64-default-job-13] Installing pkg-1.20.7...
[124amd64-default-job-13] Extracting pkg-1.20.7: .......... done
===> jdftx-1.7.0_3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of jdftx-1.7.0_3
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3+ accepted by the user
===> Fetching all distfiles required by jdftx-1.7.0_3 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3+ accepted by the user
===> Fetching all distfiles required by jdftx-1.7.0_3 for building
=> SHA256 Checksum OK for shankar1729-jdftx-v1.7.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3+ accepted by the user
===> Fetching all distfiles required by jdftx-1.7.0_3 for building
===> Extracting for jdftx-1.7.0_3
=> SHA256 Checksum OK for shankar1729-jdftx-v1.7.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for jdftx-1.7.0_3
===> Applying FreeBSD patches for jdftx-1.7.0_3 from /usr/ports/science/jdftx/files
===========================================================================
=======================<phase: build-depends >============================
===> jdftx-1.7.0_3 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.2.15.pkg
[124amd64-default-job-13] Installing bash-5.2.15...
[124amd64-default-job-13] `-- Installing gettext-runtime-0.22_1...
[124amd64-default-job-13] | `-- Installing indexinfo-0.3.1...
[124amd64-default-job-13] | `-- Extracting indexinfo-0.3.1: .... done
[124amd64-default-job-13] `-- Extracting gettext-runtime-0.22_1: .......... done
[124amd64-default-job-13] `-- Installing readline-8.2.1...
<snip>
In file included from /wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/core/ScalarField.h:31:
In file included from /wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/core/scalar.h:25:
In file included from /usr/include/c++/v1/vector:275:
In file included from /usr/include/c++/v1/__bit_reference:15:
In file included from /usr/include/c++/v1/algorithm:653:
In file included from /usr/include/c++/v1/functional:500:
In file included from /usr/include/c++/v1/__functional/function.h:20:
/usr/include/c++/v1/__memory/shared_ptr.h:315:9: warning: destructor called on non-final 'FunctionalLDA' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
__get_elem()->~_Tp();
^
/usr/include/c++/v1/__memory/shared_ptr.h:290:14: note: in instantiation of member function 'std::__shared_ptr_emplace<FunctionalLDA, std::allocator<FunctionalLDA>>::__on_zero_shared' requested here
explicit __shared_ptr_emplace(_Alloc __a, _Args&& ...__args)
^
/usr/include/c++/v1/__memory/shared_ptr.h:1106:55: note: in instantiation of function template specialization 'std::__shared_ptr_emplace<FunctionalLDA, std::allocator<FunctionalLDA>>::__shared_ptr_emplace<LDA_Variant &, double &>' requested here
::new ((void*)_VSTD::addressof(*__guard.__get())) _ControlBlock(__a, _VSTD::forward<_Args>(__args)...);
^
/usr/include/c++/v1/__memory/shared_ptr.h:1115:19: note: in instantiation of function template specialization 'std::allocate_shared<FunctionalLDA, std::allocator<FunctionalLDA>, LDA_Variant &, double &, void>' requested here
return _VSTD::allocate_shared<_Tp>(allocator<_Tp>(), _VSTD::forward<_Args>(__args)...);
^
/wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/electronic/ExCorr.cpp:365:28: note: in instantiation of function template specialization 'std::make_shared<FunctionalLDA, LDA_Variant &, double &, void>' requested here
{ internal.push_back(std::make_shared<FunctionalLDA>(variant, scaleFac));
^
/usr/include/c++/v1/__memory/shared_ptr.h:315:24: note: qualify call to silence this warning
__get_elem()->~_Tp();
^
/usr/include/c++/v1/__memory/shared_ptr.h:315:9: warning: destructor called on non-final 'FunctionalGGA' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
__get_elem()->~_Tp();
^
/usr/include/c++/v1/__memory/shared_ptr.h:290:14: note: in instantiation of member function 'std::__shared_ptr_emplace<FunctionalGGA, std::allocator<FunctionalGGA>>::__on_zero_shared' requested here
explicit __shared_ptr_emplace(_Alloc __a, _Args&& ...__args)
^
/usr/include/c++/v1/__memory/shared_ptr.h:1106:55: note: in instantiation of function template specialization 'std::__shared_ptr_emplace<FunctionalGGA, std::allocator<FunctionalGGA>>::__shared_ptr_emplace<GGA_Variant &, double &>' requested here
::new ((void*)_VSTD::addressof(*__guard.__get())) _ControlBlock(__a, _VSTD::forward<_Args>(__args)...);
^
/usr/include/c++/v1/__memory/shared_ptr.h:1115:19: note: in instantiation of function template specialization 'std::allocate_shared<FunctionalGGA, std::allocator<FunctionalGGA>, GGA_Variant &, double &, void>' requested here
return _VSTD::allocate_shared<_Tp>(allocator<_Tp>(), _VSTD::forward<_Args>(__args)...);
^
/wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/electronic/ExCorr.cpp:368:28: note: in instantiation of function template specialization 'std::make_shared<FunctionalGGA, GGA_Variant &, double &, void>' requested here
{ internal.push_back(std::make_shared<FunctionalGGA>(variant, scaleFac));
^
/usr/include/c++/v1/__memory/shared_ptr.h:315:24: note: qualify call to silence this warning
__get_elem()->~_Tp();
^
/usr/include/c++/v1/__memory/shared_ptr.h:315:9: warning: destructor called on non-final 'FunctionalMGGA' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
__get_elem()->~_Tp();
^
/usr/include/c++/v1/__memory/shared_ptr.h:290:14: note: in instantiation of member function 'std::__shared_ptr_emplace<FunctionalMGGA, std::allocator<FunctionalMGGA>>::__on_zero_shared' requested here
explicit __shared_ptr_emplace(_Alloc __a, _Args&& ...__args)
^
/usr/include/c++/v1/__memory/shared_ptr.h:1106:55: note: in instantiation of function template specialization 'std::__shared_ptr_emplace<FunctionalMGGA, std::allocator<FunctionalMGGA>>::__shared_ptr_emplace<mGGA_Variant &, double &>' requested here
::new ((void*)_VSTD::addressof(*__guard.__get())) _ControlBlock(__a, _VSTD::forward<_Args>(__args)...);
^
/usr/include/c++/v1/__memory/shared_ptr.h:1115:19: note: in instantiation of function template specialization 'std::allocate_shared<FunctionalMGGA, std::allocator<FunctionalMGGA>, mGGA_Variant &, double &, void>' requested here
return _VSTD::allocate_shared<_Tp>(allocator<_Tp>(), _VSTD::forward<_Args>(__args)...);
^
/wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/electronic/ExCorr.cpp:371:28: note: in instantiation of function template specialization 'std::make_shared<FunctionalMGGA, mGGA_Variant &, double &, void>' requested here
{ internal.push_back(std::make_shared<FunctionalMGGA>(variant, scaleFac));
^
/usr/include/c++/v1/__memory/shared_ptr.h:315:24: note: qualify call to silence this warning
__get_elem()->~_Tp();
^
3 warnings generated.
[ 49%] Building CXX object CMakeFiles/jdftxlib.dir/electronic/ExCorr_OrbitalDep_GLLBsc.cpp.o
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[ 50%] Building CXX object CMakeFiles/jdftxlib.dir/electronic/ExactExchange.cpp.o
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[ 51%] Building CXX object CMakeFiles/jdftxlib.dir/electronic/IonInfo.cpp.o
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[ 51%] Building CXX object CMakeFiles/jdftxlib.dir/electronic/IonicDynamics.cpp.o
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[ 52%] Building CXX object CMakeFiles/jdftxlib.dir/electronic/IonicMinimizer.cpp.o
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/wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/electronic/IonicMinimizer.cpp:168:17: warning: loop variable 'sp' creates a copy from type 'const std::shared_ptr<SpeciesInfo>' [-Wrange-loop-construct]
for(const auto sp: e.iInfo.species)
^
/wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/electronic/IonicMinimizer.cpp:168:6: note: use reference type 'const std::shared_ptr<SpeciesInfo> &' to prevent copying
for(const auto sp: e.iInfo.species)
^~~~~~~~~~~~~~
&
1 warning generated.
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[ 56%] Building CXX object CMakeFiles/jdftxlib.dir/electronic/SpeciesInfo.cpp.o
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[ 56%] Building CXX object CMakeFiles/jdftxlib.dir/electronic/SpeciesInfo_atomic.cpp.o
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[ 57%] Building CXX object CMakeFiles/jdftxlib.dir/electronic/SpeciesInfo_augment.cpp.o
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[ 57%] Building CXX object CMakeFiles/jdftxlib.dir/electronic/SpeciesInfo_core.cpp.o
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[ 58%] Building CXX object CMakeFiles/jdftxlib.dir/electronic/SpeciesInfo_energy.cpp.o
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[ 62%] Building CXX object CMakeFiles/jdftxlib.dir/electronic/Symmetries.cpp.o
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[ 83%] Building CXX object CMakeFiles/jdftxlib.dir/fluid/SO3quad.cpp.o
/usr/bin/c++ -DLIBXC_ENABLED -DMPI_ENABLED -Djdftxlib_EXPORTS -I/wrkdirs/usr/ports/science/jdftx/work/.build -I/wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -O3 -Wno-unused-result -ftemplate-depth-512 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -fPIC -std=c++0x -MD -MT CMakeFiles/jdftxlib.dir/fluid/SO3quad.cpp.o -MF CMakeFiles/jdftxlib.dir/fluid/SO3quad.cpp.o.d -o CMakeFiles/jdftxlib.dir/fluid/SO3quad.cpp.o -c /wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/fluid/SO3quad.cpp
[ 83%] Building CXX object CMakeFiles/jdftxlib.dir/fluid/SaLSA.cpp.o
/usr/bin/c++ -DLIBXC_ENABLED -DMPI_ENABLED -Djdftxlib_EXPORTS -I/wrkdirs/usr/ports/science/jdftx/work/.build -I/wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -O3 -Wno-unused-result -ftemplate-depth-512 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -fPIC -std=c++0x -MD -MT CMakeFiles/jdftxlib.dir/fluid/SaLSA.cpp.o -MF CMakeFiles/jdftxlib.dir/fluid/SaLSA.cpp.o.d -o CMakeFiles/jdftxlib.dir/fluid/SaLSA.cpp.o -c /wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/fluid/SaLSA.cpp
/wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/fluid/SaLSA.cpp:344:22: warning: variable 'chiPol' set but not used [-Wunused-but-set-variable]
double chiRot = 0., chiPol = 0.;
^
1 warning generated.
[ 84%] Building CXX object CMakeFiles/jdftxlib.dir/fluid/TranslationOperator.cpp.o
/usr/bin/c++ -DLIBXC_ENABLED -DMPI_ENABLED -Djdftxlib_EXPORTS -I/wrkdirs/usr/ports/science/jdftx/work/.build -I/wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -O3 -Wno-unused-result -ftemplate-depth-512 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -fPIC -std=c++0x -MD -MT CMakeFiles/jdftxlib.dir/fluid/TranslationOperator.cpp.o -MF CMakeFiles/jdftxlib.dir/fluid/TranslationOperator.cpp.o.d -o CMakeFiles/jdftxlib.dir/fluid/TranslationOperator.cpp.o -c /wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/fluid/TranslationOperator.cpp
In file included from /wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/fluid/TranslationOperator.cpp:20:
In file included from /wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/fluid/TranslationOperator.h:28:
In file included from /wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/core/ScalarField.h:33:
In file included from /wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/core/ManagedMemory.h:25:
/wrkdirs/usr/ports/science/jdftx/work/jdftx-1.7.0/jdftx/core/BlasExtra.h:30:10: fatal error: 'gsl/gsl_cblas.h' file not found
#include <gsl/gsl_cblas.h>
^~~~~~~~~~~~~~~~~
1 error generated.
*** Error code 1
Stop.
make[3]: stopped in /wrkdirs/usr/ports/science/jdftx/work/.build
*** Error code 1
Stop.
make[2]: stopped in /wrkdirs/usr/ports/science/jdftx/work/.build
*** Error code 1
Stop.
make[1]: stopped in /wrkdirs/usr/ports/science/jdftx/work/.build
*** Error code 1
Stop.
make: stopped in /usr/ports/science/jdftx