rPackages.ChemmineOB: fix compile error

[Kupac]

• Don't override openbabel
• fix pointer name in ChemmineOB src instead

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • sandbox = relaxed
  • sandbox = true
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 24.11 Release Notes (or backporting 23.11 and 24.05 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.

---

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[Kupac]

@ofborg build rPackages.ChemmineOB

[b-rodrigues]

Working on Linux, but failing on Darwin

m 31s
2s
2s
40s
2m 15s
2m 25s
/nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
^
In file included from ChemmineOB.cpp:1581:
/nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:58:15: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
  class OBAPI OBBond: public OBBase
              ^
/nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__memory/allocator.h:168:28: note: in implicit copy constructor for 'OpenBabel::OBBond' first required here
        ::new ((void*)__p) _Up(_VSTD::forward<_Args>(__args)...);
                           ^
/nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__memory/allocator_traits.h:296:13: note: in instantiation of function template specialization 'std::allocator<OpenBabel::OBBond>::construct<OpenBabel::OBBond, const OpenBabel::OBBond &>' requested here
        __a.construct(__p, _VSTD::forward<_Args>(__args)...);
            ^
/nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__memory/uninitialized_algorithms.h:553:31: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<OpenBabel::OBBond>>::construct<OpenBabel::OBBond, const OpenBabel::OBBond &, void>' requested here
    allocator_traits<_Alloc>::construct(__alloc, std::__to_address(__first2), *__first1);
                              ^
/nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/vector:1029:22: note: in instantiation of function template specialization 'std::__uninitialized_allocator_copy<std::allocator<OpenBabel::OBBond>, std::__wrap_iter<const OpenBabel::OBBond *>, std::__wrap_iter<const OpenBabel::OBBond *>, OpenBabel::OBBond *>' requested here
  __tx.__pos_ = std::__uninitialized_allocator_copy(__alloc(), __first, __last, __tx.__pos_);
                     ^
/nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/vector:1159:9: note: in instantiation of function template specialization 'std::vector<OpenBabel::OBBond>::__construct_at_end<std::__wrap_iter<const OpenBabel::OBBond *>, 0>' requested here
        __construct_at_end(__first, __last, __n);
        ^
ChemmineOB.cpp:2219:18: note: in instantiation of function template specialization 'std::vector<OpenBabel::OBBond>::vector<std::__wrap_iter<const OpenBabel::OBBond *>, 0>' requested here
      return new Sequence(vb, ve);
                 ^
ChemmineOB.cpp:3481:20: note: in instantiation of function template specialization 'swig::getslice<std::vector<OpenBabel::OBBond>, long>' requested here
      return swig::getslice(self, i, j);
                   ^
/nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
      OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
      ^
/nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
    #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
                                     ^
46 warnings and 7 errors generated.
make: *** [/nix/store/zaz1hm676fmxcr131i6g0jqm4c00f8sk-R-4.4.1/lib/R/etc/Makeconf:202: ChemmineOB.o] Error 1
ERROR: compilation failed for package ‘ChemmineOB’
* removing ‘/nix/store/58i28j92pz11a212vjmxbcqsxz7lkn48-r-ChemmineOB-1.42.0/library/ChemmineOB’
error: builder for '/nix/store/6kv1fx3b6ywwyhgd7la1vki1gc75hj70-r-ChemmineOB-1.42.0.drv' failed with exit code 1;
       last 25 log lines:
       > /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__memory/uninitialized_algorithms.h:553:31: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<OpenBabel::OBBond>>::construct<OpenBabel::OBBond, const OpenBabel::OBBond &, void>' requested here
       >     allocator_traits<_Alloc>::construct(__alloc, std::__to_address(__first2), *__first1);
       >                               ^
       > /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/vector:1029:22: note: in instantiation of function template specialization 'std::__uninitialized_allocator_copy<std::allocator<OpenBabel::OBBond>, std::__wrap_iter<const OpenBabel::OBBond *>, std::__wrap_iter<const OpenBabel::OBBond *>, OpenBabel::OBBond *>' requested here
       >   __tx.__pos_ = std::__uninitialized_allocator_copy(__alloc(), __first, __last, __tx.__pos_);
       >                      ^
       > /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/vector:1159:9: note: in instantiation of function template specialization 'std::vector<OpenBabel::OBBond>::__construct_at_end<std::__wrap_iter<const OpenBabel::OBBond *>, 0>' requested here
       >         __construct_at_end(__first, __last, __n);
       >         ^
       > ChemmineOB.cpp:2219:18: note: in instantiation of function template specialization 'std::vector<OpenBabel::OBBond>::vector<std::__wrap_iter<const OpenBabel::OBBond *>, 0>' requested here
       >       return new Sequence(vb, ve);
       >                  ^
       > ChemmineOB.cpp:3481:20: note: in instantiation of function template specialization 'swig::getslice<std::vector<OpenBabel::OBBond>, long>' requested here
       >       return swig::getslice(self, i, j);
       >                    ^
       > /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
       >       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
       >       ^
       > /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
       >     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
       >                                      ^
       > 46 warnings and 7 errors generated.
       > make: *** [/nix/store/zaz1hm676fmxcr131i6g0jqm4c00f8sk-R-4.4.1/lib/R/etc/Makeconf:202: ChemmineOB.o] Error 1
       > ERROR: compilation failed for package ‘ChemmineOB’
       > * removing ‘/nix/store/58i28j92pz11a212vjmxbcqsxz7lkn48-r-ChemmineOB-1.42.0/library/ChemmineOB’
       For full logs, run 'nix log /nix/store/6kv1fx3b6ywwyhgd7la1vki1gc75hj70-r-ChemmineOB-1.42.0.drv'.
error: 1 dependencies of derivation '/nix/store/xrbizm7m81wg4zwm7i6v92jd92m9lzp1-nix-shell.drv' failed to build 

[jbedo]

They all seem to be warnings, can you search the log for the error?

[b-rodrigues]

Click to expand

2024-10-27T21:11:30.4383110Z * installing *source* package ‘ChemmineOB’ ...
2024-10-27T21:11:30.4415880Z ** using staged installation
2024-10-27T21:11:31.3930320Z checking pkg-config is at least version 0.9.0... yes
2024-10-27T21:11:31.4217560Z checking for OPENBABEL... yes
2024-10-27T21:11:31.4218660Z checking for OPENBABEL... yes
2024-10-27T21:11:31.6308190Z checking for gcc... /nix/store/22a6p8311lg3z4ksrjbj018i7z3vgkva-clang-wrapper-16.0.6/bin/cc
2024-10-27T21:11:32.3454490Z checking whether the C compiler works... yes
2024-10-27T21:11:32.3455490Z checking for C compiler default output file name... a.out
2024-10-27T21:11:32.7099170Z checking for suffix of executables... 
2024-10-27T21:11:33.2477540Z checking whether we are cross compiling... no
2024-10-27T21:11:33.4010860Z checking for suffix of object files... o
2024-10-27T21:11:33.5067230Z checking whether we are using the GNU C compiler... yes
2024-10-27T21:11:33.6130650Z checking whether /nix/store/22a6p8311lg3z4ksrjbj018i7z3vgkva-clang-wrapper-16.0.6/bin/cc accepts -g... yes
2024-10-27T21:11:33.7976290Z checking for /nix/store/22a6p8311lg3z4ksrjbj018i7z3vgkva-clang-wrapper-16.0.6/bin/cc option to accept ISO C89... none needed
2024-10-27T21:11:34.0411690Z checking how to run the C preprocessor... /nix/store/22a6p8311lg3z4ksrjbj018i7z3vgkva-clang-wrapper-16.0.6/bin/cc -E
2024-10-27T21:11:34.2513630Z configure: creating ./config.status
2024-10-27T21:11:34.5159690Z config.status: creating src/Makevars
2024-10-27T21:11:34.6497590Z ** libs
2024-10-27T21:11:34.7540310Z using C++ compiler: ‘clang version 16.0.6’
2024-10-27T21:11:34.7774460Z /nix/store/22a6p8311lg3z4ksrjbj018i7z3vgkva-clang-wrapper-16.0.6/bin/c++ -std=gnu++17 -I"/nix/store/zaz1hm676fmxcr131i6g0jqm4c00f8sk-R-4.4.1/lib/R/include" -DNDEBUG -I/usr/include/openbabel3  -I/nix/store/2wjvn935djbywvvlxbd33qcxlwxapd6x-eigen-3.4.0/include/eigen3  -DUSE_BOOST -DHAVE_EIGEN  -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3  -I/nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3  -I'/nix/store/b7dpv827mnxpdhl0fc1m036cvx8g6h6k-r-BH-1.84.0-0/library/BH/include' -I'/nix/store/sasprr6322v661c2pyas82ksyqap03nw-r-Rcpp-1.0.13/library/Rcpp/include' -I'/nix/store/51fvm9m64zps6clkkqz260wga7w29krm-r-zlibbioc-1.50.0/library/zlibbioc/include' -isystem /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1    -fPIC  -g -O2   -c ChemmineOB.cpp -o ChemmineOB.o
2024-10-27T21:11:34.7818130Z /nix/store/22a6p8311lg3z4ksrjbj018i7z3vgkva-clang-wrapper-16.0.6/bin/c++ -std=gnu++17 -I"/nix/store/zaz1hm676fmxcr131i6g0jqm4c00f8sk-R-4.4.1/lib/R/include" -DNDEBUG -I/usr/include/openbabel3  -I/nix/store/2wjvn935djbywvvlxbd33qcxlwxapd6x-eigen-3.4.0/include/eigen3  -DUSE_BOOST -DHAVE_EIGEN  -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3  -I/nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3  -I'/nix/store/b7dpv827mnxpdhl0fc1m036cvx8g6h6k-r-BH-1.84.0-0/library/BH/include' -I'/nix/store/sasprr6322v661c2pyas82ksyqap03nw-r-Rcpp-1.0.13/library/Rcpp/include' -I'/nix/store/51fvm9m64zps6clkkqz260wga7w29krm-r-zlibbioc-1.50.0/library/zlibbioc/include' -isystem /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1    -fPIC  -g -O2   -c canonical.cpp -o canonical.o
2024-10-27T21:11:36.9602730Z In file included from ChemmineOB.cpp:1581:
2024-10-27T21:11:36.9635590Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:58:15: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
2024-10-27T21:11:36.9674840Z   class OBAPI OBBond: public OBBase
2024-10-27T21:11:36.9675400Z               ^
2024-10-27T21:11:36.9720440Z ChemmineOB.cpp:3496:31: note: in implicit copy assignment operator for 'OpenBabel::OBBond' first required here
2024-10-27T21:11:36.9721730Z       *(swig::getpos(self,i)) = x;
2024-10-27T21:11:36.9722180Z                               ^
2024-10-27T21:11:36.9723350Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
2024-10-27T21:11:36.9724740Z       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
2024-10-27T21:11:36.9725310Z       ^
2024-10-27T21:11:36.9726320Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:36.9727410Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:36.9727940Z                                      ^
2024-10-27T21:11:36.9728370Z In file included from ChemmineOB.cpp:1581:
2024-10-27T21:11:36.9731630Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:58:15: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
2024-10-27T21:11:36.9734750Z   class OBAPI OBBond: public OBBase
2024-10-27T21:11:36.9735820Z               ^
2024-10-27T21:11:36.9738610Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
2024-10-27T21:11:36.9741760Z       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
2024-10-27T21:11:36.9743250Z       ^
2024-10-27T21:11:36.9745770Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:36.9750060Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:36.9751470Z                                      ^
2024-10-27T21:11:37.1952420Z ChemmineOB.cpp:8829:43: warning: 'LookupBO' is deprecated: Easier to use the two-argument form [-Wdeprecated-declarations]
2024-10-27T21:11:37.1955540Z      arg2 = ptr; }  result = (int)(arg1)->LookupBO((std::string const &)*arg2); r_ans = Rf_ScalarInteger(result);
2024-10-27T21:11:37.1956120Z                                           ^
2024-10-27T21:11:37.1957100Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/data.h:256:7: note: 'LookupBO' has been explicitly marked deprecated here
2024-10-27T21:11:37.1958100Z       OB_DEPRECATED_MSG("Easier to use the two-argument form")
2024-10-27T21:11:37.1958490Z       ^
2024-10-27T21:11:37.1960340Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.1961370Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.1961720Z                                      ^
2024-10-27T21:11:37.2095190Z ChemmineOB.cpp:9577:105: warning: 'Get' is deprecated: use the constant operator() instead [-Wdeprecated-declarations]
2024-10-27T21:11:37.2098490Z   arg3 = static_cast< int >(INTEGER(column)[0]); result = (double)((OpenBabel::matrix3x3 const *)arg1)->Get(arg2,arg3);
2024-10-27T21:11:37.2099370Z                                                                                                         ^
2024-10-27T21:11:37.2100780Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/math/matrix3x3.h:171:7: note: 'Get' has been explicitly marked deprecated here
2024-10-27T21:11:37.2101890Z       OB_DEPRECATED_MSG("use the constant operator() instead")
2024-10-27T21:11:37.2102360Z       ^
2024-10-27T21:11:37.2103460Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.2104480Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.2105000Z                                      ^
2024-10-27T21:11:37.2105820Z ChemmineOB.cpp:9586:100: warning: 'Set' is deprecated: use the non-constant operator() instead [-Wdeprecated-declarations]
2024-10-27T21:11:37.2106950Z   arg3 = static_cast< int >(INTEGER(column)[0]); arg4 = static_cast< double >(REAL(v)[0]); (arg1)->Set(arg2,arg3,arg4);
2024-10-27T21:11:37.2107670Z                                                                                                    ^
2024-10-27T21:11:37.2108860Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/math/matrix3x3.h:188:7: note: 'Set' has been explicitly marked deprecated here
2024-10-27T21:11:37.2110130Z       OB_DEPRECATED_MSG("use the non-constant operator() instead")
2024-10-27T21:11:37.2110650Z       ^
2024-10-27T21:11:37.2111620Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.2112590Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.2113090Z                                      ^
2024-10-27T21:11:37.3439310Z ChemmineOB.cpp:13433:91: warning: 'GetOriginVector' is deprecated: Use GetOriginVector() instead [-Wdeprecated-declarations]
2024-10-27T21:11:37.3441870Z         arg2[_rswigi] = REAL(o)[_rswigi]; }  }  }  ((OpenBabel::OBGridData const *)arg1)->GetOriginVector(arg2);
2024-10-27T21:11:37.3443410Z                                                                                           ^
2024-10-27T21:11:37.3446680Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/griddata.h:88:5: note: 'GetOriginVector' has been explicitly marked deprecated here
2024-10-27T21:11:37.3449960Z     OB_DEPRECATED_MSG("Use GetOriginVector() instead")
2024-10-27T21:11:37.3450920Z     ^
2024-10-27T21:11:37.3453340Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.3455870Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.3456870Z                                      ^
2024-10-27T21:11:37.3458590Z ChemmineOB.cpp:13512:11: warning: 'SetLimits' is deprecated: Use vector version instead [-Wdeprecated-declarations]
2024-10-27T21:11:37.3460860Z   (arg1)->SetLimits((double const (*))arg2,(double const (*))arg3,(double const (*))arg4,(double const (*))arg5);
2024-10-27T21:11:37.3462260Z           ^
2024-10-27T21:11:37.3465310Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/griddata.h:111:5: note: 'SetLimits' has been explicitly marked deprecated here
2024-10-27T21:11:37.3466860Z     OB_DEPRECATED_MSG("Use vector version instead")
2024-10-27T21:11:37.3467260Z     ^
2024-10-27T21:11:37.3468230Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.3469190Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.3469590Z                                      ^
2024-10-27T21:11:37.3650900Z ChemmineOB.cpp:13728:45: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.3653460Z SWIGEXPORT SEXP R_swig_new_dummy ( ) { std::binary_function< char const *,char const *,bool > *result = 0 ;
2024-10-27T21:11:37.3655080Z                                        ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.3655950Z                                             __binary_function
2024-10-27T21:11:37.3658240Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.3660710Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.3661830Z ^
2024-10-27T21:11:37.3748530Z ChemmineOB.cpp:13730:18: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.3749670Z   result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
2024-10-27T21:11:37.3750300Z             ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.3750580Z                  __binary_function
2024-10-27T21:11:37.3751480Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.3752400Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.3753160Z ^
2024-10-27T21:11:37.3833720Z ChemmineOB.cpp:13730:79: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.3836160Z   result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
2024-10-27T21:11:37.3837860Z                                                                          ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.3838850Z                                                                               __binary_function
2024-10-27T21:11:37.3841140Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.3843550Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.3844670Z ^
2024-10-27T21:11:37.3923650Z ChemmineOB.cpp:13734:8: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.3927120Z   std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
2024-10-27T21:11:37.3928620Z   ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.3929210Z        __binary_function
2024-10-27T21:11:37.3931300Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.3934240Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.3935570Z ^
2024-10-27T21:11:37.4018070Z ChemmineOB.cpp:13734:72: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.4020500Z   std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
2024-10-27T21:11:37.4022230Z                                                                   ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.4023700Z                                                                        __binary_function
2024-10-27T21:11:37.4026140Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.4028490Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.4029610Z ^
2024-10-27T21:11:37.4105410Z ChemmineOB.cpp:13739:34: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.4107740Z    arg1 = reinterpret_cast< std::binary_function< char const *,char const *,bool > * >(argp1); delete arg1; r_ans = R_NilValue;
2024-10-27T21:11:37.4109400Z                             ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.4110220Z                                  __binary_function
2024-10-27T21:11:37.4112440Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.4115020Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.4116290Z ^
2024-10-27T21:11:37.5071830Z ChemmineOB.cpp:16952:26: warning: 'SetHybAndGeom' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.5077900Z   result = (bool)(arg1)->SetHybAndGeom(arg2); r_ans = Rf_ScalarLogical(result); vmaxset(r_vmax);
2024-10-27T21:11:37.5079340Z                          ^
2024-10-27T21:11:37.5081890Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/atom.h:399:7: note: 'SetHybAndGeom' has been explicitly marked deprecated here
2024-10-27T21:11:37.5084610Z       OB_DEPRECATED bool SetHybAndGeom(int);
2024-10-27T21:11:37.5085670Z       ^
2024-10-27T21:11:37.5088210Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.5089350Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.5089750Z                             ^
2024-10-27T21:11:37.5179620Z ChemmineOB.cpp:17323:21: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
2024-10-27T21:11:37.5182380Z   if (arg1) (arg1)->Visit = arg2; r_ans = R_NilValue; vmaxset(r_vmax); if(r_nprotect)  Rf_unprotect(r_nprotect); return r_ans; }
2024-10-27T21:11:37.5183960Z                     ^
2024-10-27T21:11:37.5186330Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
2024-10-27T21:11:37.5190640Z       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
2024-10-27T21:11:37.5191110Z       ^
2024-10-27T21:11:37.5192510Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.5196560Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.5196990Z                                      ^
2024-10-27T21:11:37.5197870Z ChemmineOB.cpp:17329:84: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
2024-10-27T21:11:37.5199210Z    arg1 = reinterpret_cast< OpenBabel::OBBond * >(argp1); result = (bool) ((arg1)->Visit); r_ans = Rf_ScalarLogical(result);
2024-10-27T21:11:37.5199900Z                                                                                    ^
2024-10-27T21:11:37.5200890Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
2024-10-27T21:11:37.5201910Z       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
2024-10-27T21:11:37.5202380Z       ^
2024-10-27T21:11:37.5203600Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.5204570Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.5204930Z                                      ^
2024-10-27T21:11:37.5368000Z ChemmineOB.cpp:18326:67: warning: 'GetFirstAtom' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.5369880Z   result = (OpenBabel::OBAtom *)((OpenBabel::OBMol const *)arg1)->GetFirstAtom();
2024-10-27T21:11:37.5371160Z                                                                   ^
2024-10-27T21:11:37.5373850Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/mol.h:287:5: note: 'GetFirstAtom' has been explicitly marked deprecated here
2024-10-27T21:11:37.5376220Z     OB_DEPRECATED
2024-10-27T21:11:37.5376930Z     ^
2024-10-27T21:11:37.5379130Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.5381480Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.5382330Z                             ^
2024-10-27T21:11:37.5694320Z ChemmineOB.cpp:20164:103: warning: 'PathSize' is deprecated: Use Size() instead [-Wdeprecated-declarations]
2024-10-27T21:11:37.5697190Z    arg1 = reinterpret_cast< OpenBabel::OBRing * >(argp1); result = ((OpenBabel::OBRing const *)arg1)->PathSize();
2024-10-27T21:11:37.5699050Z                                                                                                       ^
2024-10-27T21:11:37.5705260Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/ring.h:65:5: note: 'PathSize' has been explicitly marked deprecated here
2024-10-27T21:11:37.5707690Z     OB_DEPRECATED_MSG("Use Size() instead")
2024-10-27T21:11:37.5708490Z     ^
2024-10-27T21:11:37.5710900Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.5713460Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.5714390Z                                      ^
2024-10-27T21:11:37.6798670Z ChemmineOB.cpp:24550:110: warning: 'SetDelta' is deprecated: Has no effect. [-Wdeprecated-declarations]
2024-10-27T21:11:37.6801460Z    arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); arg2 = static_cast< double >(REAL(d)[0]); (arg1)->SetDelta(arg2);
2024-10-27T21:11:37.6803200Z                                                                                                              ^
2024-10-27T21:11:37.6810230Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:428:5: note: 'SetDelta' has been explicitly marked deprecated here
2024-10-27T21:11:37.6812730Z     OB_DEPRECATED_MSG("Has no effect.")
2024-10-27T21:11:37.6813550Z     ^
2024-10-27T21:11:37.6815960Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.6819560Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.6820480Z                                      ^
2024-10-27T21:11:37.6822110Z ChemmineOB.cpp:24557:85: warning: 'GetDelta' is deprecated: Has no effect. [-Wdeprecated-declarations]
2024-10-27T21:11:37.6824390Z    arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (double)(arg1)->GetDelta();
2024-10-27T21:11:37.6825780Z                                                                                     ^
2024-10-27T21:11:37.6828570Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:431:5: note: 'GetDelta' has been explicitly marked deprecated here
2024-10-27T21:11:37.6831010Z     OB_DEPRECATED_MSG("Has no effect.")
2024-10-27T21:11:37.6831880Z     ^
2024-10-27T21:11:37.6835630Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.6836820Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.6837320Z                                      ^
2024-10-27T21:11:37.6838140Z ChemmineOB.cpp:24565:102: warning: 'GetFixedAtoms' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.6839050Z    arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (OpenBabel::OBBitVec *) &(arg1)->GetFixedAtoms();
2024-10-27T21:11:37.6839660Z                                                                                                      ^
2024-10-27T21:11:37.6840770Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:434:5: note: 'GetFixedAtoms' has been explicitly marked deprecated here
2024-10-27T21:11:37.6841640Z     OB_DEPRECATED
2024-10-27T21:11:37.6841870Z     ^
2024-10-27T21:11:37.6842760Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.6843600Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.6843990Z                             ^
2024-10-27T21:11:37.6844570Z ChemmineOB.cpp:24578:69: warning: 'SetFixedAtoms' is deprecated: See SetFixedBonds [-Wdeprecated-declarations]
2024-10-27T21:11:37.6845560Z    arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetFixedAtoms(*arg2); r_ans = R_NilValue; vmaxset(r_vmax);
2024-10-27T21:11:37.6846190Z                                                                     ^
2024-10-27T21:11:37.6847170Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:437:5: note: 'SetFixedAtoms' has been explicitly marked deprecated here
2024-10-27T21:11:37.6848140Z     OB_DEPRECATED_MSG("See SetFixedBonds")
2024-10-27T21:11:37.6848490Z     ^
2024-10-27T21:11:37.6849720Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.6850640Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.6851000Z                                      ^
2024-10-27T21:11:37.6851970Z ChemmineOB.cpp:24585:102: warning: 'GetEvalAtoms' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.6852830Z    arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (OpenBabel::OBBitVec *) &(arg1)->GetEvalAtoms();
2024-10-27T21:11:37.6853520Z                                                                                                      ^
2024-10-27T21:11:37.6854560Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:440:5: note: 'GetEvalAtoms' has been explicitly marked deprecated here
2024-10-27T21:11:37.6855490Z     OB_DEPRECATED
2024-10-27T21:11:37.6855730Z     ^
2024-10-27T21:11:37.6857010Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.6859770Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.6860600Z                             ^
2024-10-27T21:11:37.6862100Z ChemmineOB.cpp:24598:69: warning: 'SetEvalAtoms' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.6862960Z    arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetEvalAtoms(*arg2); r_ans = R_NilValue; vmaxset(r_vmax);
2024-10-27T21:11:37.6863560Z                                                                     ^
2024-10-27T21:11:37.6864600Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:443:5: note: 'SetEvalAtoms' has been explicitly marked deprecated here
2024-10-27T21:11:37.6865440Z     OB_DEPRECATED
2024-10-27T21:11:37.6865730Z     ^
2024-10-27T21:11:37.6866880Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.6867770Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.6868080Z                             ^
2024-10-27T21:11:37.6868590Z ChemmineOB.cpp:24605:85: warning: 'GetRotAtoms' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.6869390Z    arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (void *)(arg1)->GetRotAtoms();
2024-10-27T21:11:37.6869940Z                                                                                     ^
2024-10-27T21:11:37.6870910Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:446:5: note: 'GetRotAtoms' has been explicitly marked deprecated here
2024-10-27T21:11:37.6871770Z     OB_DEPRECATED
2024-10-27T21:11:37.6871940Z     ^
2024-10-27T21:11:37.6872790Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.6873650Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.6873910Z                             ^
2024-10-27T21:11:37.6874560Z ChemmineOB.cpp:24614:72: warning: 'GetResolution' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations]
2024-10-27T21:11:37.6875470Z   result = (std::vector< double,std::allocator< double > > *) &(arg1)->GetResolution();
2024-10-27T21:11:37.6876090Z                                                                        ^
2024-10-27T21:11:37.6877110Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:449:5: note: 'GetResolution' has been explicitly marked deprecated here
2024-10-27T21:11:37.6878060Z     OB_DEPRECATED_MSG("See GetTorsionValues()")
2024-10-27T21:11:37.6878380Z     ^
2024-10-27T21:11:37.6881520Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.6883950Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.6884340Z                                      ^
2024-10-27T21:11:37.6884970Z ChemmineOB.cpp:24623:11: warning: 'SetNumCoords' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.6885780Z   (arg1)->SetNumCoords(arg2); r_ans = R_NilValue; vmaxset(r_vmax); if(r_nprotect)  Rf_unprotect(r_nprotect); return r_ans; }
2024-10-27T21:11:37.6886630Z           ^
2024-10-27T21:11:37.6887530Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:452:5: note: 'SetNumCoords' has been explicitly marked deprecated here
2024-10-27T21:11:37.6888450Z     OB_DEPRECATED
2024-10-27T21:11:37.6888730Z     ^
2024-10-27T21:11:37.6889590Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.6891140Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.6891900Z                             ^
2024-10-27T21:11:37.6892760Z ChemmineOB.cpp:24860:81: warning: 'IdentifyEvalAtoms' is deprecated: Not declared. Use Setup() for top-level functionality [-Wdeprecated-declarations]
2024-10-27T21:11:37.6893710Z    arg2 = reinterpret_cast< OpenBabel::OBMol * >(argp2); result = (bool)(arg1)->IdentifyEvalAtoms(*arg2);
2024-10-27T21:11:37.6894330Z                                                                                 ^
2024-10-27T21:11:37.6895350Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:627:5: note: 'IdentifyEvalAtoms' has been explicitly marked deprecated here
2024-10-27T21:11:37.6896560Z     OB_DEPRECATED_MSG("Not declared. Use Setup() for top-level functionality")
2024-10-27T21:11:37.6896920Z     ^
2024-10-27T21:11:37.6898890Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.6901010Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.6901330Z                                      ^
2024-10-27T21:11:37.6902160Z ChemmineOB.cpp:24872:69: warning: 'SetFixAtoms' is deprecated: See SetFixedBonds() [-Wdeprecated-declarations]
2024-10-27T21:11:37.6903080Z    arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetFixAtoms(*arg2); r_ans = R_NilValue; vmaxset(r_vmax);
2024-10-27T21:11:37.6904150Z                                                                     ^
2024-10-27T21:11:37.6907180Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:633:5: note: 'SetFixAtoms' has been explicitly marked deprecated here
2024-10-27T21:11:37.6919330Z     OB_DEPRECATED_MSG("See SetFixedBonds()")
2024-10-27T21:11:37.6920070Z     ^
2024-10-27T21:11:37.6922930Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.6923840Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.6924140Z                                      ^
2024-10-27T21:11:37.6924820Z ChemmineOB.cpp:24879:87: warning: 'HasFixedAtoms' is deprecated: See HasFixedBonds() [-Wdeprecated-declarations]
2024-10-27T21:11:37.6925650Z    arg1 = reinterpret_cast< OpenBabel::OBRotorList * >(argp1); result = (bool)(arg1)->HasFixedAtoms();
2024-10-27T21:11:37.6926170Z                                                                                       ^
2024-10-27T21:11:37.6927120Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:643:5: note: 'HasFixedAtoms' has been explicitly marked deprecated here
2024-10-27T21:11:37.6928010Z     OB_DEPRECATED_MSG("See HasFixedBonds()")
2024-10-27T21:11:37.6928480Z     ^
2024-10-27T21:11:37.6954720Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.6955610Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.6955920Z                                      ^
2024-10-27T21:11:37.6956560Z ChemmineOB.cpp:24886:72: warning: 'IgnoreSymmetryRemoval' is deprecated: Currently has no effect [-Wdeprecated-declarations]
2024-10-27T21:11:37.6957500Z    arg1 = reinterpret_cast< OpenBabel::OBRotorList * >(argp1); (arg1)->IgnoreSymmetryRemoval(); r_ans = R_NilValue;
2024-10-27T21:11:37.6958050Z                                                                        ^
2024-10-27T21:11:37.6959080Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/rotor.h:650:5: note: 'IgnoreSymmetryRemoval' has been explicitly marked deprecated here
2024-10-27T21:11:37.6960000Z     OB_DEPRECATED_MSG("Currently has no effect")
2024-10-27T21:11:37.6960910Z     ^
2024-10-27T21:11:37.6961710Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.6962550Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.6962860Z                                      ^
2024-10-27T21:11:37.7345530Z ChemmineOB.cpp:26780:81: warning: 'UpdateCoordinates' is deprecated: Use GetCooordinates instead. [-Wdeprecated-declarations]
2024-10-27T21:11:37.7346690Z    arg2 = reinterpret_cast< OpenBabel::OBMol * >(argp2); result = (bool)(arg1)->UpdateCoordinates(*arg2);
2024-10-27T21:11:37.7347240Z                                                                                 ^
2024-10-27T21:11:37.7348280Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/forcefield.h:713:5: note: 'UpdateCoordinates' has been explicitly marked deprecated here
2024-10-27T21:11:37.7349650Z     OB_DEPRECATED_MSG("Use GetCooordinates instead.")
2024-10-27T21:11:37.7349970Z     ^
2024-10-27T21:11:37.7350770Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.7351670Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.7351980Z                                      ^
2024-10-27T21:11:37.7361580Z ChemmineOB.cpp:26804:81: warning: 'UpdateConformers' is deprecated: Use GetConformers instead. [-Wdeprecated-declarations]
2024-10-27T21:11:37.7363910Z    arg2 = reinterpret_cast< OpenBabel::OBMol * >(argp2); result = (bool)(arg1)->UpdateConformers(*arg2);
2024-10-27T21:11:37.7365260Z                                                                                 ^
2024-10-27T21:11:37.7368010Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/forcefield.h:721:5: note: 'UpdateConformers' has been explicitly marked deprecated here
2024-10-27T21:11:37.7370560Z     OB_DEPRECATED_MSG("Use GetConformers instead.")
2024-10-27T21:11:37.7371330Z     ^
2024-10-27T21:11:37.7373470Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.7375830Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.7376630Z                                      ^
2024-10-27T21:11:37.7431920Z ChemmineOB.cpp:27253:73: warning: 'DistanceGeometry' is deprecated: Use OBDistanceGeometry class instead [-Wdeprecated-declarations]
2024-10-27T21:11:37.7435270Z    arg1 = reinterpret_cast< OpenBabel::OBForceField * >(argp1); (arg1)->DistanceGeometry(); r_ans = R_NilValue; vmaxset(r_vmax);
2024-10-27T21:11:37.7437150Z                                                                         ^
2024-10-27T21:11:37.7439930Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/forcefield.h:1049:5: note: 'DistanceGeometry' has been explicitly marked deprecated here
2024-10-27T21:11:37.7442590Z     OB_DEPRECATED_MSG("Use OBDistanceGeometry class instead")
2024-10-27T21:11:37.7443460Z     ^
2024-10-27T21:11:37.7445320Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.7446250Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.7446570Z                                      ^
2024-10-27T21:11:37.7479400Z ChemmineOB.cpp:27544:77: warning: 'LineSearch' is deprecated: Current code should use LineSearch(double *, double*) instead. [-Wdeprecated-declarations]
2024-10-27T21:11:37.7480660Z    arg3 = reinterpret_cast< OpenBabel::vector3 * >(argp3); result = (arg1)->LineSearch(arg2,*arg3);
2024-10-27T21:11:37.7481330Z                                                                             ^
2024-10-27T21:11:37.7483020Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/forcefield.h:1222:5: note: 'LineSearch' has been explicitly marked deprecated here
2024-10-27T21:11:37.7484140Z     OB_DEPRECATED_MSG("Current code should use LineSearch(double *, double*) instead.")
2024-10-27T21:11:37.7484630Z     ^
2024-10-27T21:11:37.7485500Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.7486420Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.7486820Z                                      ^
2024-10-27T21:11:37.7547900Z ChemmineOB.cpp:27933:45: warning: 'VectorLengthDerivative' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.7551460Z   result = (double)OpenBabel::OBForceField::VectorLengthDerivative(*arg1,*arg2);
2024-10-27T21:11:37.7552620Z                                             ^
2024-10-27T21:11:37.7557600Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/forcefield.h:1523:5: note: 'VectorLengthDerivative' has been explicitly marked deprecated here
2024-10-27T21:11:37.7560350Z     OB_DEPRECATED
2024-10-27T21:11:37.7561690Z     ^
2024-10-27T21:11:37.7563890Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.7566100Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.7566820Z                             ^
2024-10-27T21:11:37.7568160Z ChemmineOB.cpp:27974:45: warning: 'VectorAngleDerivative' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.7570070Z   result = (double)OpenBabel::OBForceField::VectorAngleDerivative(*arg1,*arg2,*arg3);
2024-10-27T21:11:37.7571260Z                                             ^
2024-10-27T21:11:37.7574100Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/forcefield.h:1539:5: note: 'VectorAngleDerivative' has been explicitly marked deprecated here
2024-10-27T21:11:37.7576620Z     OB_DEPRECATED
2024-10-27T21:11:37.7577090Z     ^
2024-10-27T21:11:37.7582590Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.7585980Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.7587310Z                             ^
2024-10-27T21:11:37.7588670Z ChemmineOB.cpp:28025:45: warning: 'VectorOOPDerivative' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.7590440Z   result = (double)OpenBabel::OBForceField::VectorOOPDerivative(*arg1,*arg2,*arg3,*arg4);
2024-10-27T21:11:37.7591620Z                                             ^
2024-10-27T21:11:37.7594300Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/forcefield.h:1556:5: note: 'VectorOOPDerivative' has been explicitly marked deprecated here
2024-10-27T21:11:37.7596750Z     OB_DEPRECATED
2024-10-27T21:11:37.7597230Z     ^
2024-10-27T21:11:37.7599380Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.7601650Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.7602390Z                             ^
2024-10-27T21:11:37.7603800Z ChemmineOB.cpp:28076:45: warning: 'VectorTorsionDerivative' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.7605700Z   result = (double)OpenBabel::OBForceField::VectorTorsionDerivative(*arg1,*arg2,*arg3,*arg4);
2024-10-27T21:11:37.7606920Z                                             ^
2024-10-27T21:11:37.7609640Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/forcefield.h:1572:5: note: 'VectorTorsionDerivative' has been explicitly marked deprecated here
2024-10-27T21:11:37.7613040Z     OB_DEPRECATED
2024-10-27T21:11:37.7613560Z     ^
2024-10-27T21:11:37.7615700Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.7617920Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.7618630Z                             ^
2024-10-27T21:11:37.7992730Z ChemmineOB.cpp:29725:27: warning: 'SetHybAndGeom' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.8004520Z   result = (bool)(*arg1)->SetHybAndGeom(arg2); r_ans = Rf_ScalarLogical(result); vmaxset(r_vmax);
2024-10-27T21:11:37.8009830Z                           ^
2024-10-27T21:11:37.8012270Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/atom.h:399:7: note: 'SetHybAndGeom' has been explicitly marked deprecated here
2024-10-27T21:11:37.8015270Z       OB_DEPRECATED bool SetHybAndGeom(int);
2024-10-27T21:11:37.8016860Z       ^
2024-10-27T21:11:37.8019310Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.8021540Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.8022250Z                             ^
2024-10-27T21:11:37.8250390Z ChemmineOB.cpp:31053:27: warning: 'SetHybAndGeom' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.8251470Z   result = (bool)(*arg1)->SetHybAndGeom(arg2); r_ans = Rf_ScalarLogical(result); vmaxset(r_vmax);
2024-10-27T21:11:37.8255380Z                           ^
2024-10-27T21:11:37.8256420Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/atom.h:399:7: note: 'SetHybAndGeom' has been explicitly marked deprecated here
2024-10-27T21:11:37.8257400Z       OB_DEPRECATED bool SetHybAndGeom(int);
2024-10-27T21:11:37.8257770Z       ^
2024-10-27T21:11:37.8258650Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.8259550Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.8259900Z                             ^
2024-10-27T21:11:37.8538430Z ChemmineOB.cpp:32387:27: warning: 'SetHybAndGeom' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.8540800Z   result = (bool)(*arg1)->SetHybAndGeom(arg2); r_ans = Rf_ScalarLogical(result); vmaxset(r_vmax);
2024-10-27T21:11:37.8542270Z                           ^
2024-10-27T21:11:37.8545000Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/atom.h:399:7: note: 'SetHybAndGeom' has been explicitly marked deprecated here
2024-10-27T21:11:37.8548400Z       OB_DEPRECATED bool SetHybAndGeom(int);
2024-10-27T21:11:37.8549370Z       ^
2024-10-27T21:11:37.8551810Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.8554280Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.8555210Z                             ^
2024-10-27T21:11:37.8639060Z ChemmineOB.cpp:33025:22: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
2024-10-27T21:11:37.8640030Z   if (arg1) (*arg1)->Visit = arg2; r_ans = R_NilValue; vmaxset(r_vmax); if(r_nprotect)  Rf_unprotect(r_nprotect); return r_ans; }
2024-10-27T21:11:37.8640540Z                      ^
2024-10-27T21:11:37.8641360Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
2024-10-27T21:11:37.8642320Z       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
2024-10-27T21:11:37.8642700Z       ^
2024-10-27T21:11:37.8643470Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.8645610Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.8645910Z                                      ^
2024-10-27T21:11:37.8646590Z ChemmineOB.cpp:33031:95: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
2024-10-27T21:11:37.8647470Z    arg1 = reinterpret_cast< OpenBabel::OBMolBondBFSIter * >(argp1); result = (bool) ((*arg1)->Visit);
2024-10-27T21:11:37.8647980Z                                                                                               ^
2024-10-27T21:11:37.8648900Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
2024-10-27T21:11:37.8649850Z       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
2024-10-27T21:11:37.8650220Z       ^
2024-10-27T21:11:37.8651130Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.8651970Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.8652270Z                                      ^
2024-10-27T21:11:37.8763020Z ChemmineOB.cpp:33739:22: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
2024-10-27T21:11:37.8766210Z   if (arg1) (*arg1)->Visit = arg2; r_ans = R_NilValue; vmaxset(r_vmax); if(r_nprotect)  Rf_unprotect(r_nprotect); return r_ans; }
2024-10-27T21:11:37.8777070Z                      ^
2024-10-27T21:11:37.8783240Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
2024-10-27T21:11:37.8787540Z       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
2024-10-27T21:11:37.8788630Z       ^
2024-10-27T21:11:37.8790790Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.8793120Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.8793940Z                                      ^
2024-10-27T21:11:37.8795730Z ChemmineOB.cpp:33745:92: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
2024-10-27T21:11:37.8798060Z    arg1 = reinterpret_cast< OpenBabel::OBMolBondIter * >(argp1); result = (bool) ((*arg1)->Visit);
2024-10-27T21:11:37.8799380Z                                                                                            ^
2024-10-27T21:11:37.8801890Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
2024-10-27T21:11:37.8804570Z       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
2024-10-27T21:11:37.8805820Z       ^
2024-10-27T21:11:37.8807980Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.8812820Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.8813160Z                                      ^
2024-10-27T21:11:37.8990740Z ChemmineOB.cpp:35115:27: warning: 'SetHybAndGeom' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.9050860Z   result = (bool)(*arg1)->SetHybAndGeom(arg2); r_ans = Rf_ScalarLogical(result); vmaxset(r_vmax);
2024-10-27T21:11:37.9059300Z                           ^
2024-10-27T21:11:37.9061230Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/atom.h:399:7: note: 'SetHybAndGeom' has been explicitly marked deprecated here
2024-10-27T21:11:37.9062290Z       OB_DEPRECATED bool SetHybAndGeom(int);
2024-10-27T21:11:37.9065850Z       ^
2024-10-27T21:11:37.9066760Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.9067670Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.9068050Z                             ^
2024-10-27T21:11:37.9143760Z ChemmineOB.cpp:35757:22: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
2024-10-27T21:11:37.9146480Z   if (arg1) (*arg1)->Visit = arg2; r_ans = R_NilValue; vmaxset(r_vmax); if(r_nprotect)  Rf_unprotect(r_nprotect); return r_ans; }
2024-10-27T21:11:37.9147930Z                      ^
2024-10-27T21:11:37.9150200Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
2024-10-27T21:11:37.9153540Z       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
2024-10-27T21:11:37.9154660Z       ^
2024-10-27T21:11:37.9156820Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.9159410Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.9160230Z                                      ^
2024-10-27T21:11:37.9162020Z ChemmineOB.cpp:35763:93: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
2024-10-27T21:11:37.9164370Z    arg1 = reinterpret_cast< OpenBabel::OBAtomBondIter * >(argp1); result = (bool) ((*arg1)->Visit);
2024-10-27T21:11:37.9165700Z                                                                                             ^
2024-10-27T21:11:37.9168210Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
2024-10-27T21:11:37.9170950Z       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
2024-10-27T21:11:37.9171980Z       ^
2024-10-27T21:11:37.9174040Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.9174970Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.9175290Z                                      ^
2024-10-27T21:11:37.9481240Z ChemmineOB.cpp:37794:27: warning: 'SetHybAndGeom' is deprecated [-Wdeprecated-declarations]
2024-10-27T21:11:37.9483230Z   result = (bool)(*arg1)->SetHybAndGeom(arg2); r_ans = Rf_ScalarLogical(result); vmaxset(r_vmax);
2024-10-27T21:11:37.9484460Z                           ^
2024-10-27T21:11:37.9487010Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/atom.h:399:7: note: 'SetHybAndGeom' has been explicitly marked deprecated here
2024-10-27T21:11:37.9489410Z       OB_DEPRECATED bool SetHybAndGeom(int);
2024-10-27T21:11:37.9490130Z       ^
2024-10-27T21:11:37.9492270Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
2024-10-27T21:11:37.9494650Z     #define OB_DEPRECATED [[deprecated]]
2024-10-27T21:11:37.9495360Z                             ^
2024-10-27T21:11:37.9631240Z ChemmineOB.cpp:38677:84: warning: 'PathSize' is deprecated: Use Size() instead [-Wdeprecated-declarations]
2024-10-27T21:11:37.9633370Z    arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); result = (*arg1)->PathSize();
2024-10-27T21:11:37.9634940Z                                                                                    ^
2024-10-27T21:11:37.9637750Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/ring.h:65:5: note: 'PathSize' has been explicitly marked deprecated here
2024-10-27T21:11:37.9641050Z     OB_DEPRECATED_MSG("Use Size() instead")
2024-10-27T21:11:37.9641990Z     ^
2024-10-27T21:11:37.9644500Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:37.9647160Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:37.9647990Z                                      ^
2024-10-27T21:11:37.9897720Z ChemmineOB.cpp:39656:27: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.9899930Z     return (void *)((std::binary_function< char const *,char const *,bool > *)  ((OpenBabel::CharPtrLess *) x));
2024-10-27T21:11:37.9901270Z                      ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.9902340Z                           __binary_function
2024-10-27T21:11:37.9907660Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.9908770Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.9909170Z ^
2024-10-27T21:11:38.6995780Z In file included from ChemmineOB.cpp:1581:
2024-10-27T21:11:38.7002140Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:58:15: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
2024-10-27T21:11:38.7006460Z   class OBAPI OBBond: public OBBase
2024-10-27T21:11:38.7006730Z               ^
2024-10-27T21:11:38.7007740Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__memory/allocator.h:168:28: note: in implicit copy constructor for 'OpenBabel::OBBond' first required here
2024-10-27T21:11:38.7008690Z         ::new ((void*)__p) _Up(_VSTD::forward<_Args>(__args)...);
2024-10-27T21:11:38.7009010Z                            ^
2024-10-27T21:11:38.7010270Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__memory/allocator_traits.h:296:13: note: in instantiation of function template specialization 'std::allocator<OpenBabel::OBBond>::construct<OpenBabel::OBBond, const OpenBabel::OBBond &>' requested here
2024-10-27T21:11:38.7011490Z         __a.construct(__p, _VSTD::forward<_Args>(__args)...);
2024-10-27T21:11:38.7011790Z             ^
2024-10-27T21:11:38.7013090Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__memory/uninitialized_algorithms.h:553:31: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<OpenBabel::OBBond>>::construct<OpenBabel::OBBond, const OpenBabel::OBBond &, void>' requested here
2024-10-27T21:11:38.7014430Z     allocator_traits<_Alloc>::construct(__alloc, std::__to_address(__first2), *__first1);
2024-10-27T21:11:38.7014890Z                               ^
2024-10-27T21:11:38.7016410Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/vector:1029:22: note: in instantiation of function template specialization 'std::__uninitialized_allocator_copy<std::allocator<OpenBabel::OBBond>, std::__wrap_iter<const OpenBabel::OBBond *>, std::__wrap_iter<const OpenBabel::OBBond *>, OpenBabel::OBBond *>' requested here
2024-10-27T21:11:38.7017900Z   __tx.__pos_ = std::__uninitialized_allocator_copy(__alloc(), __first, __last, __tx.__pos_);
2024-10-27T21:11:38.7018490Z                      ^
2024-10-27T21:11:38.7019710Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/vector:1159:9: note: in instantiation of function template specialization 'std::vector<OpenBabel::OBBond>::__construct_at_end<std::__wrap_iter<const OpenBabel::OBBond *>, 0>' requested here
2024-10-27T21:11:38.7020770Z         __construct_at_end(__first, __last, __n);
2024-10-27T21:11:38.7021040Z         ^
2024-10-27T21:11:38.7021840Z ChemmineOB.cpp:2219:18: note: in instantiation of function template specialization 'std::vector<OpenBabel::OBBond>::vector<std::__wrap_iter<const OpenBabel::OBBond *>, 0>' requested here
2024-10-27T21:11:38.7023180Z       return new Sequence(vb, ve);
2024-10-27T21:11:38.7023410Z                  ^
2024-10-27T21:11:38.7024100Z ChemmineOB.cpp:3481:20: note: in instantiation of function template specialization 'swig::getslice<std::vector<OpenBabel::OBBond>, long>' requested here
2024-10-27T21:11:38.7024750Z       return swig::getslice(self, i, j);
2024-10-27T21:11:38.7024990Z                    ^
2024-10-27T21:11:38.7025800Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
2024-10-27T21:11:38.7026790Z       OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
2024-10-27T21:11:38.7027160Z       ^
2024-10-27T21:11:38.7028200Z /nix/store/rcz5spinmx8j2cm3l4kc6qlbi7iijvla-openbabel-unstable-06-12-23/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
2024-10-27T21:11:38.7029100Z     #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
2024-10-27T21:11:38.7029420Z                                      ^
2024-10-27T21:11:39.0494870Z 46 warnings and 7 errors generated.

seems to be this:

2024-10-27T21:11:37.3650900Z ChemmineOB.cpp:13728:45: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.3653460Z SWIGEXPORT SEXP R_swig_new_dummy ( ) { std::binary_function< char const *,char const *,bool > *result = 0 ;
2024-10-27T21:11:37.3655080Z                                        ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.3655950Z                                             __binary_function
2024-10-27T21:11:37.3658240Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.3660710Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.3661830Z ^
2024-10-27T21:11:37.3748530Z ChemmineOB.cpp:13730:18: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.3749670Z   result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
2024-10-27T21:11:37.3750300Z             ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.3750580Z                  __binary_function
2024-10-27T21:11:37.3751480Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.3752400Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.3753160Z ^
2024-10-27T21:11:37.3833720Z ChemmineOB.cpp:13730:79: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.3836160Z   result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
2024-10-27T21:11:37.3837860Z                                                                          ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.3838850Z                                                                               __binary_function
2024-10-27T21:11:37.3841140Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.3843550Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.3844670Z ^
2024-10-27T21:11:37.3923650Z ChemmineOB.cpp:13734:8: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.3927120Z   std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
2024-10-27T21:11:37.3928620Z   ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.3929210Z        __binary_function
2024-10-27T21:11:37.3931300Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.3934240Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.3935570Z ^
2024-10-27T21:11:37.4018070Z ChemmineOB.cpp:13734:72: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.4020500Z   std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
2024-10-27T21:11:37.4022230Z                                                                   ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.4023700Z                                                                        __binary_function
2024-10-27T21:11:37.4026140Z /nix/store/z6r3bn5l51679pwkvh9nalp6c317z34m-libcxx-16.0.6-dev/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
2024-10-27T21:11:37.4028490Z using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
2024-10-27T21:11:37.4029610Z ^
2024-10-27T21:11:37.4105410Z ChemmineOB.cpp:13739:34: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
2024-10-27T21:11:37.4107740Z    arg1 = reinterpret_cast< std::binary_function< char const *,char const *,bool > * >(argp1); delete arg1; r_ans = R_NilValue;
2024-10-27T21:11:37.4109400Z                             ~~~~~^~~~~~~~~~~~~~~
2024-10-27T21:11:37.4110220Z                                  __binary_function

Googling for the error message shows that other software have the same issue when being compiled with clang: https://bugs.gentoo.org/869170

here's a comment that could help:

As a workaround, you can add -D_LIBCPP_ENABLE_CXX17_REMOVED_FEATURES or -stdlib=libstdc++ to CXXFLAGS while building clucene.

[Kupac]

Thanks for checking the Darwin issue, Watson. It looks like it's been Mr Swig all along. I've made sure he'll be behind bars until he behaves nicely.

@ofborg build rPackages.ChemmineOB

[Kupac]

Ah, forgot one more level of "or empty thing".
@ofborg build rPackages.ChemmineOB

[Kupac]

Looks like CXXFLAGS weren't passed to the compiler. I try with NIX_CFLAGS_COMPILE. But if you know how to pass this to clang, don't hold back pls. For now, I put this PR in draft.

[Kupac]

@ofborg build rPackages.ChemmineOB

[b-rodrigues]

your latest attempt works on aarch64-darwin 👍