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###
### Running command:
###
### chmod a+r ChemmineOB -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ChemmineOB
###
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* checking for file 'ChemmineOB/DESCRIPTION' ... OK
* preparing 'ChemmineOB':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package 'ChemmineOB' ...
** this is package 'ChemmineOB' version '1.47.1'
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -Ic:/openbabel3/src/x64/include -IC:/openbabel3/deps/eigen-3.4.0 -DHAVE_EIGEN -DHAVE_ISFINITE -Wno-misleading-indentation -fPIC -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ChemmineOB.cpp -o ChemmineOB.o
In file included from c:/openbabel3/src/x64/include/openbabel/generic.h:31,
from ChemmineOB.cpp:1575:
c:/openbabel3/src/x64/include/openbabel/base.h:228:32: warning: 'virtual const std::string& OpenBabel::OBGenericData::GetValue() const' was hidden [-Woverloaded-virtual=]
228 | virtual const std::string &GetValue() const
| ^~~~~~~~
In file included from ChemmineOB.cpp:1576:
c:/openbabel3/src/x64/include/openbabel/griddata.h:76:12: note: by 'OpenBabel::OBGridData::GetValue'
76 | double GetValue (vector3 pos) const;
| ^~~~~~~~
c:/openbabel3/src/x64/include/openbabel/base.h:287:21: warning: 'virtual void OpenBabel::OBBase::SetTitle(const char*)' was hidden [-Woverloaded-virtual=]
287 | virtual void SetTitle(const char *) {}
| ^~~~~~~~
In file included from ChemmineOB.cpp:1582:
c:/openbabel3/src/x64/include/openbabel/reaction.h:101:8: note: by 'void OpenBabel::OBReaction::SetTitle(const std::string&)'
101 | void SetTitle(const std::string& title) { _title=title; }
| ^~~~~~~~
c:/openbabel3/src/x64/include/openbabel/base.h:286:28: warning: 'virtual const char* OpenBabel::OBBase::GetTitle(bool) const' was hidden [-Woverloaded-virtual=]
286 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";}
| ^~~~~~~~
c:/openbabel3/src/x64/include/openbabel/reaction.h:99:15: note: by 'std::string OpenBabel::OBReaction::GetTitle() const'
99 | std::string GetTitle() const { return _title; }
| ^~~~~~~~
In file included from c:/openbabel3/src/x64/include/openbabel/format.h:22,
from c:/openbabel3/src/x64/include/openbabel/obconversion.h:37,
from ChemmineOB.cpp:1587:
c:/openbabel3/src/x64/include/openbabel/plugin.h:41:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/string:49,
from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/stdexcept:39,
from ChemmineOB.cpp:1559:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp: In function 'void _p_f_enum_std__ios_base__event_r_std__ios_base_int__void(std::ios_base::event, std::ios_base&, int)':
ChemmineOB.cpp:4160:7: warning: unused variable 'ecode' [-Wunused-variable]
4160 | int ecode = 0; arg1 = (std::ios_base::event) swigarg_arg1; arg2 = (std::ios_base *) &swigarg_arg2; arg3 = (int) swigarg_arg3;
| ^~~~~
ChemmineOB.cpp: In function 'SEXPREC* R_swig_new_dummy()':
ChemmineOB.cpp:13728:45: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13728 | SWIGEXPORT SEXP R_swig_new_dummy ( ) { std::binary_function< char const *,char const *,bool > *result = 0 ;
| ^~~~~~~~~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13730:18: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13730 | result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
| ^~~~~~~~~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13730:79: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13730 | result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
| ^~~~~~~~~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp: In function 'SEXPREC* R_swig_delete_dummy(SEXP)':
ChemmineOB.cpp:13734:8: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13734 | std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
| ^~~~~~~~~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13734:72: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13734 | std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
| ^~~~~~~~~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp:13739:34: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
13739 | arg1 = reinterpret_cast< std::binary_function< char const *,char const *,bool > * >(argp1); delete arg1; r_ans = R_NilValue;
| ^~~~~~~~~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
ChemmineOB.cpp: In function 'void* _p_OpenBabel__CharPtrLessTo_p_std__binary_functionT_char_const_p_char_const_p_bool_t(void*, int*)':
ChemmineOB.cpp:39656:27: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
39656 | return (void *)((std::binary_function< char const *,char const *,bool > *) ((OpenBabel::CharPtrLess *) x));
| ^~~~~~~~~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -Ic:/openbabel3/src/x64/include -IC:/openbabel3/deps/eigen-3.4.0 -DHAVE_EIGEN -DHAVE_ISFINITE -Wno-misleading-indentation -fPIC -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c canonical.cpp -o canonical.o
In file included from c:/openbabel3/src/x64/include/openbabel/op.h:25,
from canonical.cpp:3:
c:/openbabel3/src/x64/include/openbabel/plugin.h:41:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
| ^~~~~~~~~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/string:49,
from c:/openbabel3/src/x64/include/openbabel/op.h:23:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o ChemmineOB.dll tmp.def ChemmineOB.o canonical.o -Lc:/openbabel3/bin/x64/bin -lopenbabel -lz -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text+0x60bc): undefined reference to `bioc_inflateInit2_'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text+0x644a): undefined reference to `bioc_inflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text+0x7406): undefined reference to `bioc_deflateInit2_'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text+0x76e9): undefined reference to `bioc_deflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEED1Ev[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEED1Ev]+0x17): undefined reference to `bioc_inflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE8overflowEi[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE8overflowEi]+0x58): undefined reference to `bioc_crc32'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE8overflowEi[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE8overflowEi]+0x79): undefined reference to `bioc_deflate'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZThn232_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev[_ZThn232_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev]+0x3b): undefined reference to `bioc_inflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev[_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev]+0x3d): undefined reference to `bioc_inflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev[_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev]+0x3c): undefined reference to `bioc_inflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZThn232_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev[_ZThn232_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev]+0x41): undefined reference to `bioc_inflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZTv0_n24_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev[_ZTv0_n24_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev]+0x42): undefined reference to `bioc_inflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZTv0_n24_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev[_ZTv0_n24_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev]+0x48): more undefined references to `bioc_inflateEnd' follow
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekposESt4fposI9_MbstatetESt13_Ios_Openmode[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekposESt4fposI9_MbstatetESt13_Ios_Openmode]+0x9a): undefined reference to `bioc_inflateInit2_'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode]+0x85): undefined reference to `bioc_inflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode]+0xfa): undefined reference to `bioc_inflateInit2_'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv]+0xa1): undefined reference to `bioc_inflate'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv]+0x10f): undefined reference to `bioc_crc32'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv]+0x1ca): undefined reference to `bioc_inflateReset'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE5flushEv[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE5flushEv]+0x21): undefined reference to `bioc_crc32'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE5flushEv[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE5flushEv]+0x34): undefined reference to `bioc_deflate'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEED1Ev[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEED1Ev]+0x1c): undefined reference to `bioc_deflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEED0Ev[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEED0Ev]+0x1e): undefined reference to `bioc_deflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcEED1Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcEED1Ev]+0x72): undefined reference to `bioc_deflateEnd'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(pngformat.cpp.obj):pngformat.cpp:(.text+0x73e): undefined reference to `bioc_crc32'
C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(pngformat.cpp.obj):pngformat.cpp:(.text+0x82f): undefined reference to `bioc_crc32'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'ChemmineOB'
* removing 'F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp6ZniDQ/Rinst71986a3b6e8d/ChemmineOB'
-----------------------------------
ERROR: package installation failed