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. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300054 UNAME_v=FreeBSD 13.0-CURRENT 1300054 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---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-- --datarootdir=/usr/local/share/bagel --with-libxc --with-mpi=openmpi --enable-scalapack --enable-smith --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran9" FC="gfortran9" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc9" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc9" MAKE=gmake PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/wrkdirs/usr/ports/science/bagel/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/bagel/work HOME=/wrkdirs/usr/ports/science/bagel/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/bagel/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran9" FC="gfortran9" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc9" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc9" XDG_DATA_HOME=/wrkdirs/usr/ports/science/bagel/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/bagel/work HOME=/wrkdirs/usr/ports/science/bagel/work TMPDIR="/tmp" 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USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. 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[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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