ChemmineOB not compiling from Bioconductor in Mac 13.5.2

[deb-m]

When I try to install ChemmineOB from Bioconductor using this command

if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager") 
BiocManager::install("ChemmineOB", force = TRUE)"

I am getting the following output. I know it did not find openbabel, though the problem seems to be related to compilation issue with respect to using "std::binary_function" instead of "std::__binary_function" in the ChemmineOB.cpp source code.

getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29)
Installing package(s) 'ChemmineOB'
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/ChemmineOB_1.40.0.tar.gz'
Content type 'application/x-gzip' length 1366043 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘ChemmineOB’ ...
** using staged installation
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENBABEL... no
checking for OPENBABEL... no
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX14.0.sdk’
clang++ -std=gnu++17 -I"/usr/local/Cellar/r/4.3.3/lib/R/include" -DNDEBUG -I/usr/include/openbabel3  -I/usr/include/eigen3  -DUSE_BOOST -DHAVE_EIGEN  -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3    -I'/usr/local/lib/R/4.3/site-library/BH/include' -I'/usr/local/lib/R/4.3/site-library/Rcpp/include' -I'/usr/local/lib/R/4.3/site-library/zlibbioc/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include    -fPIC  -g -O2  -c ChemmineOB.cpp -o ChemmineOB.o
In file included from ChemmineOB.cpp:1587:
In file included from /usr/local/include/openbabel3/openbabel/obconversion.h:37:
In file included from /usr/local/include/openbabel3/openbabel/format.h:22:
/usr/local/include/openbabel3/openbabel/plugin.h:41:42: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
                                    ~~~~~^~~~~~~~~~~~~~~
                                         __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:13728:45: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
SWIGEXPORT SEXP R_swig_new_dummy ( ) { std::binary_function< char const *,char const *,bool > *result = 0 ;
                                       ~~~~~^~~~~~~~~~~~~~~
                                            __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:13730:18: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
  result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
            ~~~~~^~~~~~~~~~~~~~~
                 __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:13730:79: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
  result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
                                                                         ~~~~~^~~~~~~~~~~~~~~
                                                                              __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:13734:8: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
  std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
  ~~~~~^~~~~~~~~~~~~~~
       __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:13734:72: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
  std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
                                                                  ~~~~~^~~~~~~~~~~~~~~
                                                                       __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:13739:34: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
   arg1 = reinterpret_cast< std::binary_function< char const *,char const *,bool > * >(argp1); delete arg1; r_ans = R_NilValue;
                            ~~~~~^~~~~~~~~~~~~~~
                                 __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:39656:27: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
    return (void *)((std::binary_function< char const *,char const *,bool > *)  ((OpenBabel::CharPtrLess *) x));
                     ~~~~~^~~~~~~~~~~~~~~
                          __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
8 errors generated.
make: *** [ChemmineOB.o] Error 1
ERROR: compilation failed for package ‘ChemmineOB’
* removing ‘/usr/local/lib/R/4.3/site-library/ChemmineOB’

The downloaded source packages are in
	‘/private/var/folders/zq/177206l93831d3zm33nvmc4w0000gn/T/Rtmp1Qy5L3/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘ChemmineOB’ had non-zero exit status

Any help regarding this issue will be much appreciated.
Thanks
Deb

[khoran]

Sorry you're having trouble. The underscores are likely a result of name mangling rather than actual function names. The code compiles fine for me with the same function names. Can you tell me what version of OpenBabel you have installed? Also, it would be important for the configure script to find openbabel, as it will then set various options differently which could affect the compilation. I'm not too familiar with macs or how to get it to detect the OpenBabel package, unfortunately, nor do I have a mac handy to test things on.

Ideally, the line that currently says:

checking for OPENBABEL... no

should say "yes".

[Aariq]

I'm also having issues building ChemmineOB from source on macOS both on my macbook and on a GitHub runner.

Output from BiocManager::install

> BiocManager::install("ChemmineOB", force = TRUE, type = "source")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing package(s) 'ChemmineOB'
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/ChemmineOB_1.40.0.tar.gz'
Content type 'application/x-gzip' length 1366043 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘ChemmineOB’ ...
** using staged installation
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENBABEL... no
checking for OPENBABEL... no
checking for gcc... clang -arch x86_64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch x86_64 -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using SDK: ‘MacOSX14.4.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/include" -DNDEBUG -I/usr/include/openbabel3  -I/usr/include/eigen3  -DUSE_BOOST -DHAVE_EIGEN  -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3    -I'/Users/ericscott/Library/R/x86_64/4.3/library/BH/include' -I'/Users/ericscott/Library/R/x86_64/4.3/library/Rcpp/include' -I'/Users/ericscott/Library/R/x86_64/4.3/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ChemmineOB.cpp -o ChemmineOB.o
In file included from ChemmineOB.cpp:1576:
/usr/local/include/openbabel3/openbabel/griddata.h:74:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual]
    double GetValue(int i, int j, int k) const;
           ^
/usr/local/include/openbabel3/openbabel/base.h:228:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 3)
    virtual const std::string &GetValue()  const
                               ^
In file included from ChemmineOB.cpp:1576:
/usr/local/include/openbabel3/openbabel/griddata.h:76:12: warning: 'OpenBabel::OBGridData::GetValue' hides overloaded virtual function [-Woverloaded-virtual]
    double GetValue (vector3 pos) const;
           ^
/usr/local/include/openbabel3/openbabel/base.h:228:32: note: hidden overloaded virtual function 'OpenBabel::OBGenericData::GetValue' declared here: different number of parameters (0 vs 1)
    virtual const std::string &GetValue()  const
                               ^
In file included from ChemmineOB.cpp:1582:
/usr/local/include/openbabel3/openbabel/reaction.h:99:15: warning: 'OpenBabel::OBReaction::GetTitle' hides overloaded virtual function [-Woverloaded-virtual]
  std::string GetTitle()        const { return _title; }
              ^
/usr/local/include/openbabel3/openbabel/base.h:286:28: note: hidden overloaded virtual function 'OpenBabel::OBBase::GetTitle' declared here: different number of parameters (1 vs 0)
      virtual const char  *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";}
                           ^
In file included from ChemmineOB.cpp:1582:
/usr/local/include/openbabel3/openbabel/reaction.h:101:8: warning: 'OpenBabel::OBReaction::SetTitle' hides overloaded virtual function [-Woverloaded-virtual]
  void SetTitle(const std::string& title) { _title=title; }
       ^
/usr/local/include/openbabel3/openbabel/base.h:287:21: note: hidden overloaded virtual function 'OpenBabel::OBBase::SetTitle' declared here: type mismatch at 1st parameter ('const char *' vs 'const std::string &' (aka 'const basic_string<char> &'))
      virtual void  SetTitle(const char *) {}
                    ^
In file included from ChemmineOB.cpp:1587:
In file included from /usr/local/include/openbabel3/openbabel/obconversion.h:37:
In file included from /usr/local/include/openbabel3/openbabel/format.h:22:
/usr/local/include/openbabel3/openbabel/plugin.h:41:42: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
                                    ~~~~~^~~~~~~~~~~~~~~
                                         __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:4160:7: warning: unused variable 'ecode' [-Wunused-variable]
  int ecode = 0; arg1 = (std::ios_base::event) swigarg_arg1; arg2 = (std::ios_base *) &swigarg_arg2; arg3 = (int) swigarg_arg3;
      ^
ChemmineOB.cpp:13728:45: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
SWIGEXPORT SEXP R_swig_new_dummy ( ) { std::binary_function< char const *,char const *,bool > *result = 0 ;
                                       ~~~~~^~~~~~~~~~~~~~~
                                            __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:13730:18: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
  result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
            ~~~~~^~~~~~~~~~~~~~~
                 __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:13730:79: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
  result = (std::binary_function< char const *,char const *,bool > *)new std::binary_function< char const *,char const *,bool >();
                                                                         ~~~~~^~~~~~~~~~~~~~~
                                                                              __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:13734:8: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
  std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
  ~~~~~^~~~~~~~~~~~~~~
       __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:13734:72: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
  std::binary_function< char const *,char const *,bool > *arg1 = (std::binary_function< char const *,char const *,bool > *) 0 ;
                                                                  ~~~~~^~~~~~~~~~~~~~~
                                                                       __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:13739:34: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
   arg1 = reinterpret_cast< std::binary_function< char const *,char const *,bool > * >(argp1); delete arg1; r_ans = R_NilValue;
                            ~~~~~^~~~~~~~~~~~~~~
                                 __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
ChemmineOB.cpp:39656:27: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
    return (void *)((std::binary_function< char const *,char const *,bool > *)  ((OpenBabel::CharPtrLess *) x));
                     ~~~~~^~~~~~~~~~~~~~~
                          __binary_function
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/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>;
^
5 warnings and 8 errors generated.
make: *** [ChemmineOB.o] Error 1
ERROR: compilation failed for package ‘ChemmineOB’
* removing ‘/Users/ericscott/Library/R/x86_64/4.3/library/ChemmineOB’
* restoring previous ‘/Users/ericscott/Library/R/x86_64/4.3/library/ChemmineOB’

I have OpenBabel 3.1.0 installed. which obabel returns /usr/local/bin/obabel

[barracuda156]

This is related to Clang, apparently, since it builds normally with GCC.

UPD. Wait, maybe I know the reason. Could be a local issue, though not sure, since the earlier version built fine.

[barracuda156]

@khoran

Ideally, the line that currently says:

checking for OPENBABEL... no

should say "yes".

Configure is pretty broken and searches some rather random paths.

[barracuda156]

By the way, while GCC compiles it, it still complains:

--->  Configuring R-ChemmineOB
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-ChemmineOB/R-ChemmineOB/work/ChemmineOB" && /opt/local/bin/R CMD build . --no-manual --no-build-vignettes --keep-empty-dirs 
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘ChemmineOB’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* checking vignette meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘ChemmineOB_1.42.0.tar.gz’

--->  Building R-ChemmineOB
xinstall: mkdir /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-ChemmineOB/R-ChemmineOB/work/build
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-ChemmineOB/R-ChemmineOB/work/ChemmineOB" && /opt/local/bin/R CMD INSTALL . --library=/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-ChemmineOB/R-ChemmineOB/work/build --install-tests 
* installing *source* package ‘ChemmineOB’ ...
** using staged installation
checking for pkg-config... /opt/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENBABEL... no
checking for OPENBABEL... no
checking for gcc... /opt/local/bin/gcc-mp-13
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /opt/local/bin/gcc-mp-13 accepts -g... yes
checking for /opt/local/bin/gcc-mp-13 option to accept ISO C89... none needed
checking how to run the C preprocessor... /opt/local/bin/gcc-mp-13 -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++-mp-13 (MacPorts gcc13 13.2.0_4+stdlib_flag) 13.2.0’
Warning in system2("xcrun", "--show-sdk-path", TRUE, TRUE) :
  running command ''xcrun' --show-sdk-path 2>&1' had status 64
using SDK: ‘NA’‘NA’‘NA’‘NA’‘NA’‘NA’
/opt/local/bin/g++-mp-13 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_GLIBCXX_USE_CXX11_ABI=0 -DUSE_BOOST -DHAVE_EIGEN -I/opt/local/include/openbabel3 -I/opt/local/include/eigen3 -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/BH/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/Rcpp/include' -I'/opt/local/Library/Frameworks/R.framework/Versions/4.4/Resources/library/zlibbioc/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc   -c ChemmineOB.cpp -o ChemmineOB.o
In file included from /opt/local/include/openbabel3/openbabel/format.h:22,
                 from /opt/local/include/openbabel3/openbabel/obconversion.h:37,
                 from ChemmineOB.cpp:1587:
/opt/local/include/openbabel3/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 /opt/local/include/gcc13/c++/string:49,
                 from /opt/local/include/gcc13/c++/stdexcept:39,
                 from ChemmineOB.cpp:1559:
/opt/local/include/gcc13/c++/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
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 ;
      |                                             ^~~~~~~~~~~~~~~
/opt/local/include/gcc13/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 >();
      |                  ^~~~~~~~~~~~~~~
/opt/local/include/gcc13/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 >();
      |                                                                               ^~~~~~~~~~~~~~~
/opt/local/include/gcc13/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 ;
      |        ^~~~~~~~~~~~~~~
/opt/local/include/gcc13/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 ;
      |                                                                        ^~~~~~~~~~~~~~~
/opt/local/include/gcc13/c++/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
. . .

[barracuda156]

It can likely be fixed by adding -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION when building against libc++ (no need to add it with libstdc++).

[khoran]

It can likely be fixed by adding -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION when building against libc++ (no need to add it with libstdc++).

If someone can confirm if that suggestion helps I'd be happy to add it. I can't test it myself as I don't have a mac build machine handy.

[barracuda156]

@khoran As you can see, we have it fixed for every macOS version: https://ports.macports.org/port/R-ChemmineOB/details

Flags are chosen depending on stdlib being used in this chunk: https://github.com/macports/macports-ports/blob/5cf0c73dd96a13ab007b4290a7c5cc895aca1b5a/R/R-ChemmineOB/Portfile#L29-L40

[Aariq]

@khoran As you can see, we have it fixed for every macOS version: https://ports.macports.org/port/R-ChemmineOB/details

ChemmineOB v1.42.0 still fails to build on GitHub actions macOS runner

[barracuda156]

@khoran As you can see, we have it fixed for every macOS version: https://ports.macports.org/port/R-ChemmineOB/details

ChemmineOB v1.42.0 still fails to build on GitHub actions macOS runner

As far as I can see, everything builds on buildbots: https://ports.macports.org/port/R-ChemmineOB/details
That should imply CI gonna pass as well, unless something got broken from dependencies.