[MacPorts] #66208: hdf5 @1.12.2_0+cxx+gcc12+hl: Port hdf5 is still broken (cxx_stdlib mismatch) after rebuilding it more than 3 times.
MacPorts
noreply at macports.org
Tue Nov 29 10:50:40 UTC 2022
#66208: hdf5 @1.12.2_0+cxx+gcc12+hl: Port hdf5 is still broken (cxx_stdlib
mismatch) after rebuilding it more than 3 times.
------------------------+----------------------
Reporter: massonseb | Owner: eborisch
Type: defect | Status: assigned
Priority: Normal | Milestone:
Component: ports | Version: 2.8.0
Resolution: | Keywords:
Port: hdf5 |
------------------------+----------------------
Comment (by massonseb):
I also have an issue when trying to compile hdf5 with gcc12. \\
`sudo port install hdf5 +gcc12` or `sudo port install hdf5 +gcc12
+openmpi` are not working \\
whereas `sudo port install hdf5`, `sudo port install hdf5 +clan15`, `sudo
port install hdf5 +openmpi` are working. \\
with gcc12, the error message are listed bellow. I also attach the
main.log for details.
{{{
:info:build Undefined symbols for architecture arm64:
:info:build
"__ZNKSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE7compareEPKc",
referenced from:
:info:build __ZNK2H510AbstractDs12getTypeClassEv in H5AbstractDs.o
:info:build
"__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE10_M_disposeEv",
referenced from:
:info:build
__ZN2H59ExceptionC4ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_
in H5Exception.o
:info:build __ZN2H59ExceptionC4ERKS0_ in H5Exception.o
:info:build __ZNK2H59Exception14getMajorStringB5cxx11Ex in
H5Exception.o
:info:build __ZNK2H59Exception14getMinorStringB5cxx11Ex in
H5Exception.o
:info:build __ZN2H59Exception12setAutoPrintERPFixPvES1_ in
H5Exception.o
:info:build __ZN2H59Exception9dontPrintEv in H5Exception.o
:info:build __ZN2H59Exception12getAutoPrintERPFixPvEPS1_ in
H5Exception.o
:info:build ...
:info:build
"__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE10_M_replaceEmmPKcm",
referenced from:
:info:build __ZNK2H511IdComponent9inMemFuncB5cxx11EPKc in
H5IdComponent.o
:info:build __ZNK2H519DSetMemXferPropList16getDataTransformB5cxx11Ev
in H5DxferProp.o
:info:build __ZNK2H510H5Location10getCommentB5cxx11EPKcm in
H5Location.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEaSEPKc.isra.0 in
H5Attribute.o
:info:build __ZNK2H58H5Object10getObjNameB5cxx11Ev in H5Object.o
:info:build
__ZNK2H58H5Object10getObjNameERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm
in H5Object.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEaSEPKc.isra.0 in
H5AtomType.o
:info:build ...
:info:build
"__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE13_S_copy_charsEPcPKcS7_",
referenced from:
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5Exception.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5IdComponent.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5DataSpace.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5PropList.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5Library.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5FaccProp.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5FcreatProp.o
:info:build ...
:info:build
"__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE13_S_copy_charsEPcS5_S5_",
referenced from:
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4ERKS4_ in
H5Exception.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4ERKS4_ in
H5Object.o
:info:build
__ZNK2H55Group14throwExceptionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_
in H5Group.o
:info:build
__ZNK2H56H5File14throwExceptionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_
in H5File.o
:info:build
"__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE7_S_copyEPcPKcm",
referenced from:
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEaSEOS4_.isra.0 in
H5Location.o
:info:build
__ZNK2H59Attribute7getNameERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm
in H5Attribute.o
:info:build
__ZNK2H58H5Object10getObjNameERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm
in H5Object.o
:info:build
"__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_createERmm",
referenced from:
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4ERKS4_ in
H5Exception.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5Exception.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5IdComponent.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5DataSpace.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5PropList.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5Library.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5FaccProp.o
:info:build ...
:info:build "__ZNSt8ios_base4InitC1Ev", referenced from:
:info:build __GLOBAL__sub_I_H5DataSpace.cpp in H5DataSpace.o
:info:build __GLOBAL__sub_I_H5PropList.cpp in H5PropList.o
:info:build __GLOBAL__sub_I_H5FaccProp.cpp in H5FaccProp.o
:info:build __GLOBAL__sub_I_H5Location.cpp in H5Location.o
:info:build __GLOBAL__sub_I_H5Attribute.cpp in H5Attribute.o
:info:build __GLOBAL__sub_I_H5DataType.cpp in H5DataType.o
:info:build __GLOBAL__sub_I_H5DataSet.cpp in H5DataSet.o
:info:build ...
:info:build "__ZNSt8ios_base4InitD1Ev", referenced from:
:info:build __GLOBAL__sub_I_H5DataSpace.cpp in H5DataSpace.o
:info:build __GLOBAL__sub_I_H5PropList.cpp in H5PropList.o
:info:build __GLOBAL__sub_I_H5FaccProp.cpp in H5FaccProp.o
:info:build __GLOBAL__sub_I_H5Location.cpp in H5Location.o
:info:build __GLOBAL__sub_I_H5Attribute.cpp in H5Attribute.o
:info:build __GLOBAL__sub_I_H5DataType.cpp in H5DataType.o
:info:build __GLOBAL__sub_I_H5DataSet.cpp in H5DataSet.o
:info:build ...
:info:build "__ZSt19__throw_logic_errorPKc", referenced from:
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5Exception.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5IdComponent.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5DataSpace.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5PropList.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5Library.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5FaccProp.o
:info:build
__ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC4IS3_EEPKcRKS3_.constprop.0
in H5FcreatProp.o
:info:build ...
:info:build "__ZSt4cerr", referenced from:
:info:build __ZN2H59DataSpaceD4Ev in H5DataSpace.o
:info:build __ZN2H58PropListD4Ev in H5PropList.o
:info:build __ZN2H59AttributeD4Ev in H5Attribute.o
:info:build __ZN2H58DataTypeD4Ev in H5DataType.o
:info:build __ZN2H57DataSetD4Ev in H5DataSet.o
:info:build __ZN2H55GroupD4Ev in H5Group.o
:info:build __ZN2H56H5FileD4Ev in H5File.o
:info:build ...
:info:build
"__ZSt4endlIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_", referenced
from:
:info:build __ZN2H59DataSpaceD4Ev in H5DataSpace.o
:info:build __ZN2H58PropListD4Ev in H5PropList.o
:info:build __ZN2H59AttributeD4Ev in H5Attribute.o
:info:build __ZN2H58DataTypeD4Ev in H5DataType.o
:info:build __ZN2H57DataSetD4Ev in H5DataSet.o
:info:build __ZN2H55GroupD4Ev in H5Group.o
:info:build __ZN2H56H5FileD4Ev in H5File.o
:info:build ...
:info:build "__ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc",
referenced from:
:info:build __ZN2H59DataSpaceD4Ev in H5DataSpace.o
:info:build __ZN2H58PropListD4Ev in H5PropList.o
:info:build __ZN2H59AttributeD4Ev in H5Attribute.o
:info:build __ZN2H57DataSetD4Ev in H5DataSet.o
:info:build __ZN2H55GroupD4Ev in H5Group.o
:info:build __ZN2H56H5FileD4Ev in H5File.o
:info:build
"__ZStlsIcSt11char_traitsIcESaIcEERSt13basic_ostreamIT_T0_ES7_RKNSt7__cxx1112basic_stringIS4_S5_T1_EE",
referenced from:
:info:build __ZN2H59DataSpaceD4Ev in H5DataSpace.o
:info:build __ZN2H58PropListD4Ev in H5PropList.o
:info:build __ZN2H59AttributeD4Ev in H5Attribute.o
:info:build __ZN2H58DataTypeD4Ev in H5DataType.o
:info:build __ZN2H57DataSetD4Ev in H5DataSet.o
:info:build __ZN2H55GroupD4Ev in H5Group.o
:info:build __ZN2H56H5FileD4Ev in H5File.o
:info:build ...
:info:build ld: symbol(s) not found for architecture arm64
:info:build collect2: error: ld returned 1 exit status
:info:build make[2]: *** [libhdf5_cpp.la] Error 1
:info:build make[2]: Leaving directory
`/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.2/c++/src'
:info:build make[1]: *** [all-recursive] Error 1
:info:build make[1]: Leaving directory
`/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.2/c++'
:info:build make: *** [all-recursive] Error 1
:info:build make: Leaving directory
`/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.2'
:info:build Command failed: cd
"/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/work/hdf5-1.12.2"
&& /usr/bin/make -j10 -w all
:info:build Exit code: 2
:error:build Failed to build hdf5: command execution failed
:debug:build Error code: CHILDSTATUS 86150 2
:debug:build Backtrace: command execution failed
:debug:build while executing
:debug:build "system {*}$notty {*}$callback {*}$nice $fullcmdstring"
:debug:build invoked from within
:debug:build "command_exec -callback
portprogress::target_progress_callback build"
:debug:build (procedure "portbuild::build_main" line 8)
:debug:build invoked from within
:debug:build "$procedure $targetname"
:error:build See
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_hdf5/hdf5/main.log
for details.
}}}
--
Ticket URL: <https://trac.macports.org/ticket/66208#comment:6>
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