Package: src:openbabel
Version: 3.1.1+dfsg-11
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with=python3 --builddirectory=/<<PKGBUILDDIR>>/builddir
dh_auto_clean -O--builddirectory=/<<BUILDDIR>>/openbabel-3.1.1\+dfsg/builddir
dh_autoreconf_clean
-O--builddirectory=/<<BUILDDIR>>/openbabel-3.1.1\+dfsg/builddir
dh_clean -O--builddirectory=/<<BUILDDIR>>/openbabel-3.1.1\+dfsg/builddir
debian/rules binary
dh binary --with=python3 --builddirectory=/<<PKGBUILDDIR>>/builddir
dh_update_autotools_config
-O--builddirectory=/<<BUILDDIR>>/openbabel-3.1.1\+dfsg/builddir
dh_autoreconf -O--builddirectory=/<<BUILDDIR>>/openbabel-3.1.1\+dfsg/builddir
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -DCMAKE_BUILD_TYPE=None -DLIB_SUFFIX=/x86_64-linux-gnu
-DPYTHON_BINDINGS=ON -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPERL_BINDINGS=ON
-DOBPERL_INSTALLDIRS=vendor -DRUN_SWIG=ON -DCMAKE_SKIP_RPATH=ON -DBUILD_GUI=ON
-DENABLE_OPENMP=ON -DBUILD_DOCS=ON -DOPENBABEL_USE_SYSTEM_INCHI=ON
cd builddir && DEB_PYTHON_INSTALL_LAYOUT=deb
PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr
-DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc
-DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON
-DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON
-DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run
-DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles"
-DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu
-DCMAKE_BUILD_TYPE=None -DLIB_SUFFIX=/x86_64-linux-gnu -DPYTHON_BINDINGS=ON
-DPYTHON_EXECUTABLE=/usr/bin/python3 -DPERL_BINDINGS=ON
-DOBPERL_INSTALLDIRS=vendor -DRUN_SWIG=ON -DCMAKE_SKIP_RPATH=ON -DBUILD_GUI=ON
-DENABLE_OPENMP=ON -DBUILD_DOCS=ON -DOPENBABEL_USE_SYSTEM_INCHI=ON ..
CMake Deprecation Warning at CMakeLists.txt:3 (cmake_minimum_required):
[... snipped ...]
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/include/openbabel/obmolecformat.h:36,
from /<<PKGBUILDDIR>>/src/formats/xedformat.cpp:17:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 68%] Linking CXX shared module ../../lib/x86_64-linux-gnu/xedformat.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script
CMakeFiles/xedformat.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-Wl,--dependency-file=CMakeFiles/xedformat.dir/link.d -Wl,--enable-new-dtags
-Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro
-shared -o ../../lib/x86_64-linux-gnu/xedformat.so
CMakeFiles/xedformat.dir/xedformat.cpp.o -lmaeparser -lcoordgen -lm -ldl -lz
-lcairo -linchi -lm ../../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 68%] Built target xedformat
make -f src/formats/CMakeFiles/xyzformat.dir/build.make
src/formats/CMakeFiles/xyzformat.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
cd /<<PKGBUILDDIR>>/builddir && /usr/bin/cmake -E cmake_depends "Unix
Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/formats
/<<PKGBUILDDIR>>/builddir /<<PKGBUILDDIR>>/builddir/src/formats
/<<PKGBUILDDIR>>/builddir/src/formats/CMakeFiles/xyzformat.dir/DependInfo.cmake
"--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make -f src/formats/CMakeFiles/xyzformat.dir/build.make
src/formats/CMakeFiles/xyzformat.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
[ 69%] Building CXX object src/formats/CMakeFiles/xyzformat.dir/xyzformat.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Dxyzformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/xyzformat.dir/xyzformat.cpp.o
-MF CMakeFiles/xyzformat.dir/xyzformat.cpp.o.d -o
CMakeFiles/xyzformat.dir/xyzformat.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/xyzformat.cpp
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/include/openbabel/obmolecformat.h:36,
from /<<PKGBUILDDIR>>/src/formats/xyzformat.cpp:17:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 69%] Linking CXX shared module ../../lib/x86_64-linux-gnu/wlnformat.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script
CMakeFiles/wlnformat.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
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CMakeFiles/wlnformat.dir/wlnformat.cpp.o
"CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o" -lmaeparser -lcoordgen -lm -ldl
-lz -lcairo -linchi -lm ../../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 69%] Built target wlnformat
make -f src/formats/CMakeFiles/yasaraformat.dir/build.make
src/formats/CMakeFiles/yasaraformat.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
cd /<<PKGBUILDDIR>>/builddir && /usr/bin/cmake -E cmake_depends "Unix
Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/formats
/<<PKGBUILDDIR>>/builddir /<<PKGBUILDDIR>>/builddir/src/formats
/<<PKGBUILDDIR>>/builddir/src/formats/CMakeFiles/yasaraformat.dir/DependInfo.cmake
"--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make -f src/formats/CMakeFiles/yasaraformat.dir/build.make
src/formats/CMakeFiles/yasaraformat.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
[ 69%] Building CXX object
src/formats/CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Dyasaraformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT
src/formats/CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o -MF
CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o.d -o
CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/yasaraformat.cpp
[ 69%] Linking CXX shared module ../../lib/x86_64-linux-gnu/xyzformat.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script
CMakeFiles/xyzformat.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
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-Wl,--dependency-file=CMakeFiles/xyzformat.dir/link.d -Wl,--enable-new-dtags
-Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro
-shared -o ../../lib/x86_64-linux-gnu/xyzformat.so
CMakeFiles/xyzformat.dir/xyzformat.cpp.o -lmaeparser -lcoordgen -lm -ldl -lz
-lcairo -linchi -lm ../../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 69%] Built target xyzformat
make -f src/formats/CMakeFiles/rxnformat.dir/build.make
src/formats/CMakeFiles/rxnformat.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
cd /<<PKGBUILDDIR>>/builddir && /usr/bin/cmake -E cmake_depends "Unix
Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/formats
/<<PKGBUILDDIR>>/builddir /<<PKGBUILDDIR>>/builddir/src/formats
/<<PKGBUILDDIR>>/builddir/src/formats/CMakeFiles/rxnformat.dir/DependInfo.cmake
"--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make -f src/formats/CMakeFiles/rxnformat.dir/build.make
src/formats/CMakeFiles/rxnformat.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
[ 70%] Building CXX object src/formats/CMakeFiles/rxnformat.dir/rxnformat.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Drxnformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/rxnformat.dir/rxnformat.cpp.o
-MF CMakeFiles/rxnformat.dir/rxnformat.cpp.o.d -o
CMakeFiles/rxnformat.dir/rxnformat.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/rxnformat.cpp
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/include/openbabel/obmolecformat.h:36,
from /<<PKGBUILDDIR>>/src/formats/yasaraformat.cpp:34:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/src/formats/rxnformat.cpp:26:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /<<PKGBUILDDIR>>/src/formats/rxnformat.cpp:18:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/formats/yasaraformat.cpp: In member function âvirtual
bool OpenBabel::YOBFormat::WriteMolecule(OpenBabel::OBBase*,
OpenBabel::OBConversion*)â:
/<<PKGBUILDDIR>>/src/formats/yasaraformat.cpp:572:36: warning:
â__builtin___snprintf_chkâ output truncated before the last format
character [-Wformat-truncation=]
572 | snprintf(&buffer[12], 4, "%4d",res->GetNum()); }
| ^
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54:
In function âint snprintf(char*, size_t, const char*, ...)â,
inlined from âvirtual bool
OpenBabel::YOBFormat::WriteMolecule(OpenBabel::OBBase*,
OpenBabel::OBConversion*)â at
/<<PKGBUILDDIR>>/src/formats/yasaraformat.cpp:572:15:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note:
â__builtin___snprintf_chkâ output between 5 and 12 bytes into a destination
of size 4
68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 70%] Linking CXX shared module ../../lib/x86_64-linux-gnu/yasaraformat.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script
CMakeFiles/yasaraformat.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
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CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o -lmaeparser -lcoordgen -lm -ldl
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make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 70%] Built target yasaraformat
make -f src/formats/CMakeFiles/chemdrawcdx.dir/build.make
src/formats/CMakeFiles/chemdrawcdx.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
cd /<<PKGBUILDDIR>>/builddir && /usr/bin/cmake -E cmake_depends "Unix
Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/formats
/<<PKGBUILDDIR>>/builddir /<<PKGBUILDDIR>>/builddir/src/formats
/<<PKGBUILDDIR>>/builddir/src/formats/CMakeFiles/chemdrawcdx.dir/DependInfo.cmake
"--color="
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make -f src/formats/CMakeFiles/chemdrawcdx.dir/build.make
src/formats/CMakeFiles/chemdrawcdx.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
[ 70%] Building CXX object
src/formats/CMakeFiles/chemdrawcdx.dir/chemdrawcdx.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Dchemdrawcdx_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
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-std=gnu++11 -fPIC -MD -MT
src/formats/CMakeFiles/chemdrawcdx.dir/chemdrawcdx.cpp.o -MF
CMakeFiles/chemdrawcdx.dir/chemdrawcdx.cpp.o.d -o
CMakeFiles/chemdrawcdx.dir/chemdrawcdx.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/chemdrawcdx.cpp
[ 70%] Linking CXX shared module ../../lib/x86_64-linux-gnu/rxnformat.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script
CMakeFiles/rxnformat.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
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make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/include/openbabel/obmolecformat.h:36,
from /<<PKGBUILDDIR>>/src/formats/chemdrawcdx.cpp:17:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 70%] Built target rxnformat
make -f src/formats/CMakeFiles/chemkinformat.dir/build.make
src/formats/CMakeFiles/chemkinformat.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
cd /<<PKGBUILDDIR>>/builddir && /usr/bin/cmake -E cmake_depends "Unix
Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/formats
/<<PKGBUILDDIR>>/builddir /<<PKGBUILDDIR>>/builddir/src/formats
/<<PKGBUILDDIR>>/builddir/src/formats/CMakeFiles/chemkinformat.dir/DependInfo.cmake
"--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make -f src/formats/CMakeFiles/chemkinformat.dir/build.make
src/formats/CMakeFiles/chemkinformat.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
[ 70%] Building CXX object
src/formats/CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Dchemkinformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT
src/formats/CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o -MF
CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o.d -o
CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/chemkinformat.cpp
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/src/formats/chemkinformat.cpp:31:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /<<PKGBUILDDIR>>/src/formats/chemkinformat.cpp:18:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 70%] Linking CXX shared module ../../lib/x86_64-linux-gnu/chemdrawcdx.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script
CMakeFiles/chemdrawcdx.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-Wl,--dependency-file=CMakeFiles/chemdrawcdx.dir/link.d -Wl,--enable-new-dtags
-Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro
-shared -o ../../lib/x86_64-linux-gnu/chemdrawcdx.so
CMakeFiles/chemdrawcdx.dir/chemdrawcdx.cpp.o -lmaeparser -lcoordgen -lm -ldl
-lz -lcairo -linchi -lm ../../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 70%] Built target chemdrawcdx
make -f src/formats/CMakeFiles/rinchiformat.dir/build.make
src/formats/CMakeFiles/rinchiformat.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
cd /<<PKGBUILDDIR>>/builddir && /usr/bin/cmake -E cmake_depends "Unix
Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/formats
/<<PKGBUILDDIR>>/builddir /<<PKGBUILDDIR>>/builddir/src/formats
/<<PKGBUILDDIR>>/builddir/src/formats/CMakeFiles/rinchiformat.dir/DependInfo.cmake
"--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make -f src/formats/CMakeFiles/rinchiformat.dir/build.make
src/formats/CMakeFiles/rinchiformat.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
[ 70%] Building CXX object
src/formats/CMakeFiles/rinchiformat.dir/rinchiformat.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Drinchiformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT
src/formats/CMakeFiles/rinchiformat.dir/rinchiformat.cpp.o -MF
CMakeFiles/rinchiformat.dir/rinchiformat.cpp.o.d -o
CMakeFiles/rinchiformat.dir/rinchiformat.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/rinchiformat.cpp
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/src/formats/rinchiformat.cpp:23:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /<<PKGBUILDDIR>>/src/formats/rinchiformat.cpp:17:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 71%] Linking CXX shared module ../../lib/x86_64-linux-gnu/rinchiformat.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script
CMakeFiles/rinchiformat.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-Wl,--dependency-file=CMakeFiles/rinchiformat.dir/link.d -Wl,--enable-new-dtags
-Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro
-shared -o ../../lib/x86_64-linux-gnu/rinchiformat.so
CMakeFiles/rinchiformat.dir/rinchiformat.cpp.o -lmaeparser -lcoordgen -lm -ldl
-lz -lcairo -linchi -lm ../../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 71%] Linking CXX shared module ../../lib/x86_64-linux-gnu/chemkinformat.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script
CMakeFiles/chemkinformat.dir/link.txt --verbose=1
[ 71%] Built target rinchiformat
make -f src/formats/CMakeFiles/rsmiformat.dir/build.make
src/formats/CMakeFiles/rsmiformat.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
cd /<<PKGBUILDDIR>>/builddir && /usr/bin/cmake -E cmake_depends "Unix
Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/formats
/<<PKGBUILDDIR>>/builddir /<<PKGBUILDDIR>>/builddir/src/formats
/<<PKGBUILDDIR>>/builddir/src/formats/CMakeFiles/rsmiformat.dir/DependInfo.cmake
"--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make -f src/formats/CMakeFiles/rsmiformat.dir/build.make
src/formats/CMakeFiles/rsmiformat.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
[ 71%] Building CXX object
src/formats/CMakeFiles/rsmiformat.dir/rsmiformat.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Drsmiformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT
src/formats/CMakeFiles/rsmiformat.dir/rsmiformat.cpp.o -MF
CMakeFiles/rsmiformat.dir/rsmiformat.cpp.o.d -o
CMakeFiles/rsmiformat.dir/rsmiformat.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/rsmiformat.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-Wl,--dependency-file=CMakeFiles/chemkinformat.dir/link.d
-Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings
-Wl,--no-undefined -lc -Wl,-z,relro -shared -o
../../lib/x86_64-linux-gnu/chemkinformat.so
CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o -lmaeparser -lcoordgen -lm
-ldl -lz -lcairo -linchi -lm ../../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 71%] Built target chemkinformat
make -f src/formats/CMakeFiles/png2format.dir/build.make
src/formats/CMakeFiles/png2format.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
cd /<<PKGBUILDDIR>>/builddir && /usr/bin/cmake -E cmake_depends "Unix
Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/formats
/<<PKGBUILDDIR>>/builddir /<<PKGBUILDDIR>>/builddir/src/formats
/<<PKGBUILDDIR>>/builddir/src/formats/CMakeFiles/png2format.dir/DependInfo.cmake
"--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make -f src/formats/CMakeFiles/png2format.dir/build.make
src/formats/CMakeFiles/png2format.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
[ 72%] Building CXX object
src/formats/CMakeFiles/png2format.dir/png2format.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Dpng2format_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT
src/formats/CMakeFiles/png2format.dir/png2format.cpp.o -MF
CMakeFiles/png2format.dir/png2format.cpp.o.d -o
CMakeFiles/png2format.dir/png2format.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/png2format.cpp
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/src/formats/rsmiformat.cpp:23:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /<<PKGBUILDDIR>>/src/formats/rsmiformat.cpp:17:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/include/openbabel/obmolecformat.h:36,
from /<<PKGBUILDDIR>>/src/formats/png2format.cpp:15:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 72%] Linking CXX shared module ../../lib/x86_64-linux-gnu/rsmiformat.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script
CMakeFiles/rsmiformat.dir/link.txt --verbose=1
[ 72%] Building CXX object
src/formats/CMakeFiles/png2format.dir/__/depict/cairopainter.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Dpng2format_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT
src/formats/CMakeFiles/png2format.dir/__/depict/cairopainter.cpp.o -MF
CMakeFiles/png2format.dir/__/depict/cairopainter.cpp.o.d -o
CMakeFiles/png2format.dir/__/depict/cairopainter.cpp.o -c
/<<PKGBUILDDIR>>/src/depict/cairopain
ter.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-Wl,--dependency-file=CMakeFiles/rsmiformat.dir/link.d -Wl,--enable-new-dtags
-Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro
-shared -o ../../lib/x86_64-linux-gnu/rsmiformat.so
CMakeFiles/rsmiformat.dir/rsmiformat.cpp.o -lmaeparser -lcoordgen -lm -ldl -lz
-lcairo -linchi -lm ../../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 72%] Built target rsmiformat
make -f src/formats/CMakeFiles/cdxmlformat.dir/build.make
src/formats/CMakeFiles/cdxmlformat.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
cd /<<PKGBUILDDIR>>/builddir && /usr/bin/cmake -E cmake_depends "Unix
Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/formats
/<<PKGBUILDDIR>>/builddir /<<PKGBUILDDIR>>/builddir/src/formats
/<<PKGBUILDDIR>>/builddir/src/formats/CMakeFiles/cdxmlformat.dir/DependInfo.cmake
"--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make -f src/formats/CMakeFiles/cdxmlformat.dir/build.make
src/formats/CMakeFiles/cdxmlformat.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
[ 73%] Building CXX object
src/formats/CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Dcdxmlformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT
src/formats/CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o -MF
CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o.d -o
CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/xml/cdxmlformat.cpp
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/include/openbabel/xml.h:21,
from /<<PKGBUILDDIR>>/src/formats/xml/cdxmlformat.cpp:20:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 73%] Linking CXX shared module ../../lib/x86_64-linux-gnu/png2format.so
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/cmake -E cmake_link_script
CMakeFiles/png2format.dir/link.txt --verbose=1
In file included from /usr/include/unicode/uenum.h:25,
from /usr/include/unicode/ucnv.h:52,
from /usr/include/libxml2/libxml/encoding.h:31,
from /usr/include/libxml2/libxml/parser.h:812,
from /usr/include/libxml2/libxml/globals.h:18,
from /usr/include/libxml2/libxml/threads.h:35,
from /usr/include/libxml2/libxml/xmlmemory.h:218,
from /usr/include/libxml2/libxml/tree.h:1307,
from /usr/include/libxml2/libxml/xmlreader.h:14,
from /<<PKGBUILDDIR>>/include/openbabel/xml.h:25:
/usr/include/unicode/localpointer.h:561:26: error: parameter declared âautoâ
561 | template <typename Type, auto closeFunction>
| ^~~~
/usr/include/unicode/localpointer.h:573:76: error: template argument 2 is
invalid
573 | explicit LocalOpenPointer(std::unique_ptr<Type,
decltype(closeFunction)> &&p)
|
^
/usr/include/unicode/localpointer.h:583:78: error: template argument 2 is
invalid
583 | LocalOpenPointer &operator=(std::unique_ptr<Type,
decltype(closeFunction)> &&p) {
|
^
/usr/include/unicode/localpointer.h:599:59: error: template argument 2 is
invalid
599 | operator std::unique_ptr<Type, decltype(closeFunction)> () && {
| ^
/usr/include/unicode/uenum.h:69:1: note: invalid template non-type parameter
69 | U_DEFINE_LOCAL_OPEN_POINTER(LocalUEnumerationPointer, UEnumeration,
uenum_close);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/unicode/ucnv.h:597:1: note: invalid template non-type parameter
597 | U_DEFINE_LOCAL_OPEN_POINTER(LocalUConverterPointer, UConverter,
ucnv_close);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-Wl,--dependency-file=CMakeFiles/png2format.dir/link.d -Wl,--enable-new-dtags
-Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro
-shared -o ../../lib/x86_64-linux-gnu/png2format.so
CMakeFiles/png2format.dir/png2format.cpp.o
CMakeFiles/png2format.dir/__/depict/cairopainter.cpp.o -lmaeparser -lcoordgen
-lm -ldl -lz -lcairo -linchi -lm
../../lib/x86_64-linux-gnu/libopenbabel.so.7.0.0
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
[ 73%] Built target png2format
[ 73%] Building CXX object src/formats/CMakeFiles/cdxmlformat.dir/xml/xml.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Dcdxmlformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cdxmlformat.dir/xml/xml.cpp.o
-MF CMakeFiles/cdxmlformat.dir/xml/xml.cpp.o.d -o
CMakeFiles/cdxmlformat.dir/xml/xml.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/xml/xml.cpp
make[4]: *** [src/formats/CMakeFiles/cdxmlformat.dir/build.make:82:
src/formats/CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make -f src/formats/CMakeFiles/cmlformat.dir/build.make
src/formats/CMakeFiles/cmlformat.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
cd /<<PKGBUILDDIR>>/builddir && /usr/bin/cmake -E cmake_depends "Unix
Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/formats
/<<PKGBUILDDIR>>/builddir /<<PKGBUILDDIR>>/builddir/src/formats
/<<PKGBUILDDIR>>/builddir/src/formats/CMakeFiles/cmlformat.dir/DependInfo.cmake
"--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make -f src/formats/CMakeFiles/cmlformat.dir/build.make
src/formats/CMakeFiles/cmlformat.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/builddir'
[ 73%] Building CXX object
src/formats/CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Dcmlformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT
src/formats/CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o -MF
CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o.d -o
CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/xml/cmlformat.cpp
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/include/openbabel/xml.h:21,
from /<<PKGBUILDDIR>>/src/formats/xml/xml.cpp:15:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/unicode/uenum.h:25,
from /usr/include/unicode/ucnv.h:52,
from /usr/include/libxml2/libxml/encoding.h:31,
from /usr/include/libxml2/libxml/parser.h:812,
from /usr/include/libxml2/libxml/globals.h:18,
from /usr/include/libxml2/libxml/threads.h:35,
from /usr/include/libxml2/libxml/xmlmemory.h:218,
from /usr/include/libxml2/libxml/tree.h:1307,
from /usr/include/libxml2/libxml/xmlreader.h:14,
from /<<PKGBUILDDIR>>/include/openbabel/xml.h:25:
/usr/include/unicode/localpointer.h:561:26: error: parameter declared âautoâ
561 | template <typename Type, auto closeFunction>
| ^~~~
/usr/include/unicode/localpointer.h:573:76: error: template argument 2 is
invalid
573 | explicit LocalOpenPointer(std::unique_ptr<Type,
decltype(closeFunction)> &&p)
|
^
/usr/include/unicode/localpointer.h:583:78: error: template argument 2 is
invalid
583 | LocalOpenPointer &operator=(std::unique_ptr<Type,
decltype(closeFunction)> &&p) {
|
^
/usr/include/unicode/localpointer.h:599:59: error: template argument 2 is
invalid
599 | operator std::unique_ptr<Type, decltype(closeFunction)> () && {
| ^
/usr/include/unicode/uenum.h:69:1: note: invalid template non-type parameter
69 | U_DEFINE_LOCAL_OPEN_POINTER(LocalUEnumerationPointer, UEnumeration,
uenum_close);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/unicode/ucnv.h:597:1: note: invalid template non-type parameter
597 | U_DEFINE_LOCAL_OPEN_POINTER(LocalUConverterPointer, UConverter,
ucnv_close);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: *** [src/formats/CMakeFiles/cdxmlformat.dir/build.make:96:
src/formats/CMakeFiles/cdxmlformat.dir/xml/xml.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make[3]: *** [CMakeFiles/Makefile2:5594:
src/formats/CMakeFiles/cdxmlformat.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
[ 73%] Building CXX object src/formats/CMakeFiles/cmlformat.dir/xml/xml.cpp.o
cd /<<PKGBUILDDIR>>/builddir/src/formats && /usr/bin/c++ -DBUILD_LINK_AS_DLL
-DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER
-DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64
-D__WXGTK__ -Dcmlformat_EXPORTS -I/<<PKGBUILDDIR>>/builddir/include
-I/<<PKGBUILDDIR>>/data -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3
-I/usr/include/cairo -I/usr/include/libxml2 -isystem
/usr/lib/x86_64-linux-gnu/wx/include/gtk3-unicode-3.2 -isystem
/usr/include/wx-3.2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=gnu++98 -Wdate-time
-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp
-std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cmlformat.dir/xml/xml.cpp.o
-MF CMakeFiles/cmlformat.dir/xml/xml.cpp.o.d -o
CMakeFiles/cmlformat.dir/xml/xml.cpp.o -c
/<<PKGBUILDDIR>>/src/formats/xml/xml.cpp
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/include/openbabel/xml.h:21,
from /<<PKGBUILDDIR>>/src/formats/xml/cmlformat.cpp:29:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /<<PKGBUILDDIR>>/include/openbabel/math/matrix3x3.h:24,
from /<<PKGBUILDDIR>>/src/formats/xml/cmlformat.cpp:19:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/unicode/uenum.h:25,
from /usr/include/unicode/ucnv.h:52,
from /usr/include/libxml2/libxml/encoding.h:31,
from /usr/include/libxml2/libxml/parser.h:812,
from /usr/include/libxml2/libxml/globals.h:18,
from /usr/include/libxml2/libxml/threads.h:35,
from /usr/include/libxml2/libxml/xmlmemory.h:218,
from /usr/include/libxml2/libxml/tree.h:1307,
from /usr/include/libxml2/libxml/xmlreader.h:14,
from /<<PKGBUILDDIR>>/include/openbabel/xml.h:25:
/usr/include/unicode/localpointer.h:561:26: error: parameter declared âautoâ
561 | template <typename Type, auto closeFunction>
| ^~~~
/usr/include/unicode/localpointer.h:573:76: error: template argument 2 is
invalid
573 | explicit LocalOpenPointer(std::unique_ptr<Type,
decltype(closeFunction)> &&p)
|
^
/usr/include/unicode/localpointer.h:583:78: error: template argument 2 is
invalid
583 | LocalOpenPointer &operator=(std::unique_ptr<Type,
decltype(closeFunction)> &&p) {
|
^
/usr/include/unicode/localpointer.h:599:59: error: template argument 2 is
invalid
599 | operator std::unique_ptr<Type, decltype(closeFunction)> () && {
| ^
/usr/include/unicode/uenum.h:69:1: note: invalid template non-type parameter
69 | U_DEFINE_LOCAL_OPEN_POINTER(LocalUEnumerationPointer, UEnumeration,
uenum_close);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/unicode/ucnv.h:597:1: note: invalid template non-type parameter
597 | U_DEFINE_LOCAL_OPEN_POINTER(LocalUConverterPointer, UConverter,
ucnv_close);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/openbabel/format.h:22,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:37,
from /<<PKGBUILDDIR>>/include/openbabel/xml.h:21,
from /<<PKGBUILDDIR>>/src/formats/xml/xml.cpp:15:
/<<PKGBUILDDIR>>/include/openbabel/plugin.h:41:42: warning: âtemplate<class
_Arg1, class _Arg2, class _Result> struct std::binary_functionâ is deprecated
[-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const
char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /<<PKGBUILDDIR>>/include/openbabel/obconversion.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/unicode/uenum.h:25,
from /usr/include/unicode/ucnv.h:52,
from /usr/include/libxml2/libxml/encoding.h:31,
from /usr/include/libxml2/libxml/parser.h:812,
from /usr/include/libxml2/libxml/globals.h:18,
from /usr/include/libxml2/libxml/threads.h:35,
from /usr/include/libxml2/libxml/xmlmemory.h:218,
from /usr/include/libxml2/libxml/tree.h:1307,
from /usr/include/libxml2/libxml/xmlreader.h:14,
from /<<PKGBUILDDIR>>/include/openbabel/xml.h:25:
/usr/include/unicode/localpointer.h:561:26: error: parameter declared âautoâ
561 | template <typename Type, auto closeFunction>
| ^~~~
/usr/include/unicode/localpointer.h:573:76: error: template argument 2 is
invalid
573 | explicit LocalOpenPointer(std::unique_ptr<Type,
decltype(closeFunction)> &&p)
|
^
/usr/include/unicode/localpointer.h:583:78: error: template argument 2 is
invalid
583 | LocalOpenPointer &operator=(std::unique_ptr<Type,
decltype(closeFunction)> &&p) {
|
^
/usr/include/unicode/localpointer.h:599:59: error: template argument 2 is
invalid
599 | operator std::unique_ptr<Type, decltype(closeFunction)> () && {
| ^
/usr/include/unicode/uenum.h:69:1: note: invalid template non-type parameter
69 | U_DEFINE_LOCAL_OPEN_POINTER(LocalUEnumerationPointer, UEnumeration,
uenum_close);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/unicode/ucnv.h:597:1: note: invalid template non-type parameter
597 | U_DEFINE_LOCAL_OPEN_POINTER(LocalUConverterPointer, UConverter,
ucnv_close);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: *** [src/formats/CMakeFiles/cmlformat.dir/build.make:96:
src/formats/CMakeFiles/cmlformat.dir/xml/xml.cpp.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: *** [src/formats/CMakeFiles/cmlformat.dir/build.make:82:
src/formats/CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make[3]: *** [CMakeFiles/Makefile2:5626:
src/formats/CMakeFiles/cmlformat.dir/all] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make[2]: *** [Makefile:149: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
dh_auto_build: error: cd builddir && make -j2 "INSTALL=install
--strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:34: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:28: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202503/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:openbabel, so that this is still
visible in the BTS web page for this package.
Thanks.
