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Compilation failure #1996

Open
Vcald opened this issue Jun 23, 2019 · 7 comments · May be fixed by #2684
Open

Compilation failure #1996

Vcald opened this issue Jun 23, 2019 · 7 comments · May be fixed by #2684

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@Vcald
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Vcald commented Jun 23, 2019

Does someone have a clue for such compilation failure on fedora 30?

cmake .. -DRUN_SWIG=on -DPYTHON_BINDINGS=on -DBUILD_GUI=on

-- The C compiler identification is GNU 9.1.1
-- The CXX compiler identification is GNU 9.1.1
-- Check for working C compiler: /usr/lib64/ccache/cc
-- Check for working C compiler: /usr/lib64/ccache/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/lib64/ccache/c++
-- Check for working CXX compiler: /usr/lib64/ccache/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at CMakeLists.txt:12 (cmake_policy):
The OLD behavior for policy CMP0042 will be removed from a future version
of CMake.

The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.

-- Using included inchi library.
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.9")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Found wxWidgets: -pthread;;;-lwx_baseu-3.0;-lwx_gtk3u_core-3.0;-lwx_gtk3u_adv-3.0 (found version "3.0.4")
-- Looking for conio.h
-- Looking for conio.h - not found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for rpc/xdr.h
-- Looking for rpc/xdr.h - found
-- Looking for regex.h
-- Looking for regex.h - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for rint
-- Looking for rint - not found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for sranddev
-- Looking for sranddev - not found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of clock_t
-- Check size of clock_t - done
-- Performing Test SCANDIR_NEEDS_CONST
-- Performing Test SCANDIR_NEEDS_CONST - Failed
-- Performing Test HAVE_GCC_VISIBILITY
-- Performing Test HAVE_GCC_VISIBILITY - Success
-- Checking available shared pointer...
-- Performing Test HAVE_STD_SHARED_PTR
-- Performing Test HAVE_STD_SHARED_PTR - Success
-- Performing Test HAVE_STD_TR1_SHARED_PTR
-- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Success
-- Use std::shared_ptr in memory
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0")
-- Found PkgConfig: /usr/bin/pkg-config (found version "1.6.1")
-- Found RapidJSON: /usr/include (found suitable version "1.1.0", minimum required is "1.1.0")
-- JSON formats will be supported. Using RapidJSON 1.1.0 at /usr/include
-- Checking for module 'cairo'
-- Found cairo, version 1.16.0
-- Found Cairo: /usr/lib64/libcairo.so
-- Cairo found. PNG output will be supported.
-- Looking for getopt
-- Looking for getopt - found
-- Attempting to build the GUI
-- wxWidgets found => GUI will be built
-- Found PythonInterp: /usr/bin/python (found version "2.7.16")
-- Found SWIG: /usr/bin/swig (found version "3.0.12")
-- Found SWIG: /usr/bin/swig (found suitable version "3.0.12", minimum required is "2.0")
-- Found PythonLibs: /usr/lib64/libpython2.7.so (found version "2.7.16")
-- Python bindings will be compiled
-- Configuring done
-- Generating done
-- Build files have been written to: /mnt/usr/local/openbabel-2.4.1/build

make -j4

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In static member function ?static void OpenBabel::matrix3x3::jacobi(unsigned int, double*, double*, double*)?:
cc1plus: warning: iteration 2147483647 invokes undefined behavior [-Waggressive-loop-optimizations]
/mnt/usr/local/openbabel-2.4.1/src/math/matrix3x3.cpp:650:19: note: within this loop
650 | for (j = 0; j < static_cast(n)-1; j++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
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/mnt/usr/local/openbabel-2.4.1/src/stereo/perception.cpp: In function ?void OpenBabel::StereoRefToImplicit(OpenBabel::OBMol&, OpenBabel::OBStereo::Ref)?:
/mnt/usr/local/openbabel-2.4.1/src/stereo/perception.cpp:2880:16: warning: ?template class std::binder1st? is deprecated [-Wdeprecated-declarations]
2880 | const std::binder1st<std::equal_toOBStereo::Ref > equal_to_atomId = std::bind1st (equal_toOBStereo::Ref(), atomId);
| ^~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_function.h:1392,
from /usr/include/c++/9/bits/stl_tree.h:65,
from /usr/include/c++/9/map:60,
from /mnt/usr/local/openbabel-2.4.1/include/openbabel/base.h:26,
from /mnt/usr/local/openbabel-2.4.1/include/openbabel/stereo/stereo.h:27,
from /mnt/usr/local/openbabel-2.4.1/include/openbabel/stereo/tetranonplanar.h:27,
from /mnt/usr/local/openbabel-2.4.1/include/openbabel/stereo/tetrahedral.h:27,
from /mnt/usr/local/openbabel-2.4.1/src/stereo/perception.cpp:26:
/usr/include/c++/9/backward/binders.h:108:11: note: declared here
108 | class binder1st
| ^~~~~~~~~
/mnt/usr/local/openbabel-2.4.1/src/stereo/perception.cpp: In function ?void OpenBabel::ImplicitRefToStereo(OpenBabel::OBMol&, OpenBabel::OBStereo::Ref, OpenBabel::OBStereo::Ref)?:
/mnt/usr/local/openbabel-2.4.1/src/stereo/perception.cpp:2912:16: warning: ?template class std::binder1st? is deprecated [-Wdeprecated-declarations]
2912 | const std::binder1st<std::equal_toOBStereo::Ref > equal_to_implicitRef = std::bind1st (equal_toOBStereo::Ref(), (OBStereo::Ref) OBStereo::ImplicitRef);
| ^~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_function.h:1392,
from /usr/include/c++/9/bits/stl_tree.h:65,
from /usr/include/c++/9/map:60,
from /mnt/usr/local/openbabel-2.4.1/include/openbabel/base.h:26,
from /mnt/usr/local/openbabel-2.4.1/include/openbabel/stereo/stereo.h:27,
from /mnt/usr/local/openbabel-2.4.1/include/openbabel/stereo/tetranonplanar.h:27,
from /mnt/usr/local/openbabel-2.4.1/include/openbabel/stereo/tetrahedral.h:27,
from /mnt/usr/local/openbabel-2.4.1/src/stereo/perception.cpp:26:
/usr/include/c++/9/backward/binders.h:108:11: note: declared here
108 | class binder1st
| ^~~~~~~~~
[ 21%] Linking CXX shared library ../lib/libopenbabel.so
[ 21%] Built target openbabel
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[ 33%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o
[ 33%] Linking CXX shared module ../../lib/xyzformat.so
[ 33%] Built target xyzformat
Scanning dependencies of target xedformat
[ 33%] Building CXX object src/formats/CMakeFiles/xedformat.dir/xedformat.cpp.o
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Scanning dependencies of target unichemformat
[ 33%] Building CXX object src/formats/CMakeFiles/unichemformat.dir/unichemformat.cpp.o
[ 33%] Linking CXX shared module ../../lib/unichemformat.so
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Scanning dependencies of target thermoformat
[ 33%] Building CXX object src/formats/CMakeFiles/thermoformat.dir/thermoformat.cpp.o
[ 33%] Building CXX object src/formats/CMakeFiles/cmlformat.dir/xml/xml.cpp.o
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Scanning dependencies of target smileyformat
[ 33%] Building CXX object src/formats/CMakeFiles/smileyformat.dir/smileyformat.cpp.o
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Scanning dependencies of target shelxformat
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Scanning dependencies of target confabreport
[ 33%] Building CXX object src/formats/CMakeFiles/confabreport.dir/confabreport.cpp.o
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Scanning dependencies of target msiformat
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Scanning dependencies of target jaguarformat
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Scanning dependencies of target exyzformat
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Scanning dependencies of target gausscubeformat
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[ 37%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o
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Scanning dependencies of target gamessformat
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[ 37%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/xout.cpp.o
[ 37%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o
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[ 38%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o
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[ 39%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o
Scanning dependencies of target xmlformat
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Scanning dependencies of target nwchemformat
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[ 39%] Building CXX object src/formats/CMakeFiles/xmlformat.dir/xml/xml.cpp.o
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Scanning dependencies of target mdlformat
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[ 41%] Building CXX object src/formats/CMakeFiles/mdlformat.dir/mdlformat.cpp.o
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Scanning dependencies of target molreport
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Scanning dependencies of target pubchemjsonformat
[ 42%] Building CXX object src/formats/CMakeFiles/pubchemjsonformat.dir/json/pubchemjsonformat.cpp.o
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[ 42%] Building CXX object src/formats/CMakeFiles/cofformat.dir/cofformat.cpp.o
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[ 44%] Building CXX object src/formats/CMakeFiles/vaspformat.dir/vaspformat.cpp.o
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[ 44%] Linking CXX shared module ../../lib/mol2format.so
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[ 44%] Building CXX object src/formats/CMakeFiles/cssrformat.dir/cssrformat.cpp.o
[ 44%] Built target mol2format
Scanning dependencies of target pdbformat
[ 45%] Building CXX object src/formats/CMakeFiles/pdbformat.dir/pdbformat.cpp.o
/mnt/usr/local/openbabel-2.4.1/src/formats/CSRformat.cpp: In member function ?char* OpenBabel::CSRFormat::PadString(char*, int)?:
/mnt/usr/local/openbabel-2.4.1/src/formats/CSRformat.cpp:192:12: warning: ?char* strncpy(char*, const char*, size_t)? specified bound depends on the length of the source argument [-Wstringop-overflow=]
192 | strncpy(output, input, strlen(input));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 45%] Linking CXX shared module ../../lib/CSRformat.so
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[ 45%] Building CXX object src/formats/CMakeFiles/pwscfformat.dir/pwscfformat.cpp.o
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[ 47%] Building CXX object src/formats/CMakeFiles/fastaformat.dir/fastaformat.cpp.o
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[ 49%] Building CXX object src/formats/CMakeFiles/opendxformat.dir/opendxformat.cpp.o
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[ 52%] Building CXX object src/formats/CMakeFiles/bgfformat.dir/bgfformat.cpp.o
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[ 53%] Building CXX object src/formats/CMakeFiles/stlformat.dir/stlformat.cpp.o
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Scanning dependencies of target ghemicalformat
[ 53%] Building CXX object src/formats/CMakeFiles/ghemicalformat.dir/ghemicalformat.cpp.o
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[ 54%] Building CXX object src/formats/CMakeFiles/PQSformat.dir/PQSformat.cpp.o
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Scanning dependencies of target adfformat
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Scanning dependencies of target pngformat
[ 55%] Building CXX object src/formats/CMakeFiles/pngformat.dir/pngformat.cpp.o
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Scanning dependencies of target acesformat
[ 56%] Building CXX object src/formats/CMakeFiles/acesformat.dir/acesformat.cpp.o
[ 56%] Linking CXX shared module ../../lib/smilesformat.so
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[ 56%] Building CXX object src/formats/CMakeFiles/qchemformat.dir/qchemformat.cpp.o
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Scanning dependencies of target titleformat
[ 56%] Building CXX object src/formats/CMakeFiles/titleformat.dir/titleformat.cpp.o
[ 56%] Linking CXX shared module ../../lib/titleformat.so
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Scanning dependencies of target asciiformat
[ 56%] Building CXX object src/formats/CMakeFiles/cccformat.dir/cccformat.cpp.o
[ 56%] Building CXX object src/formats/CMakeFiles/asciiformat.dir/asciiformat.cpp.o
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Scanning dependencies of target cmlreactformat
[ 57%] Building CXX object src/formats/CMakeFiles/cmlreactformat.dir/xml/cmlreactformat.cpp.o
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Scanning dependencies of target castepformat
[ 58%] Building CXX object src/formats/CMakeFiles/castepformat.dir/castepformat.cpp.o
[ 58%] Linking CXX shared module ../../lib/qchemformat.so
[ 58%] Building CXX object src/formats/CMakeFiles/asciiformat.dir//depict/asciipainter.cpp.o
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Scanning dependencies of target APIInterface
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[ 59%] Building CXX object src/formats/CMakeFiles/cmlreactformat.dir/xml/xml.cpp.o
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[ 59%] Building CXX object src/formats/CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o
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Scanning dependencies of target alchemyformat
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[ 59%] Building CXX object src/formats/CMakeFiles/acrformat.dir/acrformat.cpp.o
[ 60%] Linking CXX shared module ../../lib/lpmdformat.so
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[ 60%] Building CXX object src/formats/CMakeFiles/inchiformat.dir/inchiformat.cpp.o
[ 60%] Building CXX object src/formats/CMakeFiles/balstformat.dir/balstformat.cpp.o
[ 60%] Linking CXX shared module ../../lib/balstformat.so
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Scanning dependencies of target outformat
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[ 61%] Built target acrformat
[ 61%] Building CXX object src/formats/CMakeFiles/inchiformat.dir/getinchi.cpp.o
[ 61%] Building CXX object src/formats/CMakeFiles/inchiformat.dir//ops/unique.cpp.o
[ 62%] Linking CXX shared module ../../lib/outformat.so
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Scanning dependencies of target boxformat
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Scanning dependencies of target gamessukformat
[ 63%] Building CXX object src/formats/CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o
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Scanning dependencies of target cacheformat
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Scanning dependencies of target carformat
[ 65%] Building CXX object src/formats/CMakeFiles/carformat.dir/carformat.cpp.o
[ 65%] Linking CXX shared module ../../lib/cacheformat.so
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Scanning dependencies of target chem3dformat
[ 65%] Building CXX object src/formats/CMakeFiles/chem3dformat.dir/chem3dformat.cpp.o
[ 66%] Linking CXX shared module ../../lib/MCDLformat.so
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Scanning dependencies of target chemtoolformat
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[ 66%] Building CXX object src/formats/CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o
[ 66%] Building CXX object src/formats/CMakeFiles/fhformat.dir/fhformat.cpp.o
[ 67%] Linking CXX shared module ../../lib/chem3dformat.so
[ 67%] Built target chem3dformat
Scanning dependencies of target xtcformat
[ 67%] Building CXX object src/formats/CMakeFiles/xtcformat.dir/xtcformat.cpp.o
[ 68%] Linking CXX shared module ../../lib/fhformat.so
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Scanning dependencies of target painterformat
[ 68%] Linking CXX shared module ../../lib/chemtoolformat.so
[ 68%] Building CXX object src/formats/CMakeFiles/painterformat.dir/painterformat.cpp.o
[ 68%] Built target chemtoolformat
Scanning dependencies of target cifformat
[ 69%] Building CXX object src/formats/CMakeFiles/cifformat.dir/cifformat.cpp.o
[ 69%] Linking CXX shared module ../../lib/gamessukformat.so
[ 69%] Building CXX object src/formats/CMakeFiles/painterformat.dir//depict/commandpainter.cpp.o
[ 69%] Linking CXX shared module ../../lib/xtcformat.so
[ 69%] Built target gamessukformat
Scanning dependencies of target crkformat
[ 69%] Building CXX object src/formats/CMakeFiles/crkformat.dir/crkformat.cpp.o
/usr/bin/ld: CMakeFiles/xtcformat.dir/xtcformat.cpp.o: in function OpenBabel::XTCFormat::xdropen(__rpc_xdr*, char const*, char const*)': xtcformat.cpp:(.text+0xd4): undefined reference to xdrstdio_create'
/usr/bin/ld: xtcformat.cpp:(.text+0x11a): undefined reference to xdrstdio_create' /usr/bin/ld: CMakeFiles/xtcformat.dir/xtcformat.cpp.o: in function OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*)':
xtcformat.cpp:(.text+0x856): undefined reference to xdr_int' /usr/bin/ld: xtcformat.cpp:(.text+0x8b2): undefined reference to xdr_float'
/usr/bin/ld: xtcformat.cpp:(.text+0x919): undefined reference to xdr_int' /usr/bin/ld: xtcformat.cpp:(.text+0x929): undefined reference to xdr_int'
/usr/bin/ld: xtcformat.cpp:(.text+0x939): undefined reference to xdr_int' /usr/bin/ld: xtcformat.cpp:(.text+0x949): undefined reference to xdr_int'
/usr/bin/ld: xtcformat.cpp:(.text+0x959): undefined reference to xdr_int' /usr/bin/ld: CMakeFiles/xtcformat.dir/xtcformat.cpp.o:xtcformat.cpp:(.text+0x969): more undefined references to xdr_int' follow
/usr/bin/ld: CMakeFiles/xtcformat.dir/xtcformat.cpp.o: in function OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*)': xtcformat.cpp:(.text+0xa77): undefined reference to xdr_opaque'
/usr/bin/ld: xtcformat.cpp:(.text+0xcf9): undefined reference to xdr_int' /usr/bin/ld: xtcformat.cpp:(.text+0xd14): undefined reference to xdr_float'
/usr/bin/ld: xtcformat.cpp:(.text+0xd27): undefined reference to xdr_vector' /usr/bin/ld: xtcformat.cpp:(.text+0xd33): undefined reference to xdr_float'
/usr/bin/ld: xtcformat.cpp:(.text+0xd46): undefined reference to xdr_vector' /usr/bin/ld: xtcformat.cpp:(.text+0xd5e): undefined reference to xdr_float'
/usr/bin/ld: xtcformat.cpp:(.text+0x10ab): undefined reference to xdr_int' /usr/bin/ld: xtcformat.cpp:(.text+0x10bb): undefined reference to xdr_int'
/usr/bin/ld: xtcformat.cpp:(.text+0x10cb): undefined reference to xdr_int' /usr/bin/ld: xtcformat.cpp:(.text+0x10db): undefined reference to xdr_int'
/usr/bin/ld: xtcformat.cpp:(.text+0x10eb): undefined reference to xdr_int' /usr/bin/ld: CMakeFiles/xtcformat.dir/xtcformat.cpp.o:xtcformat.cpp:(.text+0x10fb): more undefined references to xdr_int' follow
/usr/bin/ld: CMakeFiles/xtcformat.dir/xtcformat.cpp.o: in function OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*)': xtcformat.cpp:(.text+0x1aba): undefined reference to xdr_opaque'
/usr/bin/ld: CMakeFiles/xtcformat.dir/xtcformat.cpp.o: in function OpenBabel::XTCFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)': xtcformat.cpp:(.text+0x1d17): undefined reference to xdr_int'
/usr/bin/ld: xtcformat.cpp:(.text+0x1d30): undefined reference to xdr_int' /usr/bin/ld: xtcformat.cpp:(.text+0x1d54): undefined reference to xdr_int'
/usr/bin/ld: xtcformat.cpp:(.text+0x1d64): undefined reference to xdr_float' /usr/bin/ld: xtcformat.cpp:(.text+0x1d74): undefined reference to xdr_float'
/usr/bin/ld: xtcformat.cpp:(.text+0x1d84): undefined reference to xdr_float' /usr/bin/ld: xtcformat.cpp:(.text+0x1d94): undefined reference to xdr_float'
/usr/bin/ld: xtcformat.cpp:(.text+0x1da4): undefined reference to xdr_float' /usr/bin/ld: CMakeFiles/xtcformat.dir/xtcformat.cpp.o:xtcformat.cpp:(.text+0x1db4): more undefined references to xdr_float' follow
collect2: error: ld returned 1 exit status
make[2]: *** [src/formats/CMakeFiles/xtcformat.dir/build.make:92: lib/xtcformat.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:5102: src/formats/CMakeFiles/xtcformat.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 69%] Linking CXX shared module ../../lib/painterformat.so
[ 69%] Built target painterformat
[ 69%] Linking CXX shared module ../../lib/crkformat.so
[ 69%] Built target crkformat
[ 69%] Linking CXX shared module ../../lib/cifformat.so
[ 69%] Built target cifformat
make: *** [Makefile:141: all] Error 2
@baoilleach
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Are you using the development version? If not, it's not going to compile with the latest GCC.

@Vcald
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Vcald commented Jun 25, 2019

I have used the latest github version by git cloning https://github.com/openbabel/openbabel.git
Still I get this failure.
I tried on another pc with the same OS and I get no failure...after trying to track down the problem I realised that in the case of successful compilation I got not xtcformat directory under build/src/formats

@fredrikw
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It seems like a problem with a non-complete rpc/xdr.h. There is already an exception for Cygwin that is missing xdrstudio_create and it seems like your first install has the same problem. Maybe there should be a check for that symbol instead of just checking that the header exists? Something like changing line 215 in CmakeLists.txt from check_include_file(rpc/xdr.h HAVE_RPC_XDR_H) to check_symbol_exists(xdrstudio_create "rpc/xdr.h" HAVE_RPC_XDR_H) but I don't know CMake enough to be sure...

@Vcald
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Vcald commented Jun 26, 2019

Dear fredrikw,
that was the problem indeed...by applying the modification you suggested I can compile it fine.
The only thing I wonder is why this problem does not occur in all my machines which have the same OS and software installed.
Do you have any idea why on other fedora 30 boxes I could compile it fine without that modification?
Thanks

@fredrikw
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fredrikw commented Jul 1, 2019

My guess is that those boxes didn't have any trace of rpc/xdr and therefor skipped the entire xtcformat from building. It was already conditionally built only if rpc/xdr.h was present. The change instead looks for the symbol xdrstudio_create in xdr which is what is actually used.

@ghutchis ghutchis mentioned this issue May 7, 2020
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@meerfrau meerfrau mentioned this issue Jun 15, 2023
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@waarmond
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Error still present:

[ 76%] Building CXX object src/formats/CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o
[ 76%] Linking CXX shared module ../../lib/xtcformat.so
mold: error: undefined symbol: xdr_opaque
>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*))>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*))
mold: error: undefined symbol: xdr_int
>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*))>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*))>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*))>>> referenced 18 more times

mold: error: undefined symbol: xdr_vector
>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*))>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*))
mold: error: undefined symbol: xdrstdio_create
>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdropen(__rpc_xdr*, char const*, char const*))>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdropen(__rpc_xdr*, char const*, char const*))
mold: error: undefined symbol: xdr_float
>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*))>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*))>>> referenced by xtcformat.cpp
>>>               CMakeFiles/xtcformat.dir/xtcformat.cpp.o:(OpenBabel::XTCFormat::xdr3dfcoord(__rpc_xdr*, float*, int*, float*))>>> referenced 11 more times

fredrikw added a commit to fredrikw/openbabel that referenced this issue Mar 22, 2024
@fredrikw
Change check for rpc/xdr.h
765078d 
Change from checking if the file exists to if the symbol xdrstdio_create exists. Should fix openbabel#1996
@fredrikw fredrikw linked a pull request Mar 22, 2024 that will close this issue
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@fredrikw
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OK, so I created a PR for my proposed change above (with corrected spelling for xprstdio_create). It seems to work in my testing at least.

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Change check for rpc/xdr.h fredrikw/openbabel
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@baoilleach @fredrikw @Vcald @waarmond