error: 'isfinite' was not declared in this scope; did you mean 'std::isfinite'?

[barracuda156]

cum_median.cpp: In function 'int cum_median(int, double*, double*, double*)':
cum_median.cpp:10:9: error: 'isfinite' was not declared in this scope; did you mean 'std::isfinite'?
   10 |     if(!isfinite(data_value)){
      |         ^~~~~~~~
      |         std::isfinite
In file included from /opt/local/include/LegacySupport/cmath:54,
                 from PiecewiseFunction.h:16,
                 from cum_median.cpp:3:
/opt/local/include/gcc12/c++/cmath:578:5: note: 'std::isfinite' declared here
  578 |     isfinite(_Tp __x)
      |     ^~~~~~~~
make: *** [cum_median.o] Error 1

[tdhock]

hi @barracuda156 thanks for the report, but can you please include the g++ command line that was used to get this warning? I tried compiling using gcc12 on ubuntu but I did not observe that warning, see below.

(base) tdhock@tdhock-MacBook:~/R/binsegRcpp(master)$ R CMD INSTALL .
Le chargement a nécessité le package : grDevices
* installing to library ‘/home/tdhock/lib/R/library’
* installing *source* package ‘binsegRcpp’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 12.3.0’
g++ -std=gnu++17 -I"/home/tdhock/lib/R/include" -DNDEBUG  -I'/home/tdhock/lib/R/library/Rcpp/include' -march=core2 -I/home/tdhock/include    -fpic  -g -O2  -c PiecewiseFunction.cpp -o PiecewiseFunction.o
g++ -std=gnu++17 -I"/home/tdhock/lib/R/include" -DNDEBUG  -I'/home/tdhock/lib/R/library/Rcpp/include' -march=core2 -I/home/tdhock/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/tdhock/lib/R/include" -DNDEBUG  -I'/home/tdhock/lib/R/library/Rcpp/include' -march=core2 -I/home/tdhock/include    -fpic  -g -O2  -c binseg.cpp -o binseg.o
g++ -std=gnu++17 -I"/home/tdhock/lib/R/include" -DNDEBUG  -I'/home/tdhock/lib/R/library/Rcpp/include' -march=core2 -I/home/tdhock/include    -fpic  -g -O2  -c cum_median.cpp -o cum_median.o
g++ -std=gnu++17 -I"/home/tdhock/lib/R/include" -DNDEBUG  -I'/home/tdhock/lib/R/library/Rcpp/include' -march=core2 -I/home/tdhock/include    -fpic  -g -O2  -c depth_first.cpp -o depth_first.o
g++ -std=gnu++17 -I"/home/tdhock/lib/R/include" -DNDEBUG  -I'/home/tdhock/lib/R/library/Rcpp/include' -march=core2 -I/home/tdhock/include    -fpic  -g -O2  -c interface.cpp -o interface.o
g++ -std=gnu++17 -shared -L/home/tdhock/lib/R/lib -L/home/tdhock/lib -Wl,-rpath=/home/tdhock/lib -o binsegRcpp.so PiecewiseFunction.o RcppExports.o binseg.o cum_median.o depth_first.o interface.o -L/home/tdhock/lib/R/lib -lR
installing to /home/tdhock/lib/R/library/00LOCK-binsegRcpp/00new/binsegRcpp/libs
** R
** byte-compile and prepare package for lazy loading
Le chargement a nécessité le package : grDevices
** help
*** installing help indices
** building package indices
Le chargement a nécessité le package : grDevices
** installing vignettes
** testing if installed package can be loaded from temporary location
Le chargement a nécessité le package : grDevices
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Le chargement a nécessité le package : grDevices
** testing if installed package keeps a record of temporary installation path
* DONE (binsegRcpp)

[barracuda156]

@tdhock I think the problem is that when you use isfinite, you rely on system headers, which may or may not have it defined; at the same time, std::isfinite uses headers provided by the compiler, so it works regardless.
(UPD. And when defined in system headers, it may require additional OS-specific macros.)

I will re-run the build without the patch and copy the output here.

[barracuda156]

** using staged installation
** libs
using C++ compiler: ‘g++-mp-12 (MacPorts gcc12 12.2.0_0) 12.2.0’
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-12 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c PiecewiseFunction.cpp -o PiecewiseFunction.o
/opt/local/bin/g++-mp-12 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c RcppExports.cpp -o RcppExports.o
/opt/local/bin/g++-mp-12 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c binseg.cpp -o binseg.o
/opt/local/bin/g++-mp-12 -std=gnu++17 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c cum_median.cpp -o cum_median.o
cum_median.cpp: In function 'int cum_median(int, double*, double*, double*)':
cum_median.cpp:10:9: error: 'isfinite' was not declared in this scope; did you mean 'std::isfinite'?
   10 |     if(!isfinite(data_value)){
      |         ^~~~~~~~
      |         std::isfinite
In file included from /opt/local/include/LegacySupport/cmath:54,
                 from PiecewiseFunction.h:16,
                 from cum_median.cpp:3:
/opt/local/include/gcc12/c++/cmath:578:5: note: 'std::isfinite' declared here
  578 |     isfinite(_Tp __x)
      |     ^~~~~~~~
make: *** [cum_median.o] Error 1
ERROR: compilation failed for package ‘binsegRcpp’

P. S. I do not recall what exactly was the reason for this kind of errors (we had then with a few other ports besides binsegRcpp and openexr), it is header-related, but conclusion was that switching to std:: fixes everything.

[tdhock]

flags unique to your g++ command:
-I"/opt/local/Library/Frameworks/R.framework/Resources/include"
-I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include'
-isystem/opt/local/include/LegacySupport
-I/opt/local/include
-pipe
-Os
-arch ppc

flags unique to my g++ command:
-I"/home/tdhock/lib/R/include"
-I'/home/tdhock/lib/R/library/Rcpp/include'
-march=core2
-I/home/tdhock/include
-g
-O2

[tdhock]

https://cplusplus.com/reference/cmath/isfinite/ says that #include <math.h> should define isfinite (without having to use std::) so this may actually be a bug in your includes?

[tdhock]

to verify if your math.h is the source of the issue, can you check if your C pre-processor output has the following? (remove -o flag from your g++ command line, then add -E |grep isfinite)

(base) tdhock@tdhock-MacBook:~/R/binsegRcpp/src(master)$ g++ -std=gnu++17 -I"/home/tdhock/lib/R/include" -DNDEBUG  -I'/home/tdhock/lib/R/library/Rcpp/include' -march=core2 -I/home/tdhock/include    -fpic  -g -O2  -c cum_median.cpp -E |grep isfinite
  isfinite(float __x)
  { return __builtin_isfinite(__x); }
  isfinite(double __x)
  { return __builtin_isfinite(__x); }
  isfinite(long double __x)
  { return __builtin_isfinite(__x); }
    isfinite(_Tp __x)
using std::isfinite;
    if(!isfinite(data_value)){

[tdhock]

I downloaded source code for both gcc-12.2 and gcc-12.3, and checked to see if isfinite is defined in both versions of the math.h file, and they both seem to have that defined, so I suspect there may be some incomplete installation of gcc-12.2 on your system.

(base) tdhock@tdhock-MacBook:~/src$ grep isfinite gcc-12.2.0/libstdc++-v3/include/c_compatibility/math.h 
using std::isfinite;
(base) tdhock@tdhock-MacBook:~/src$ grep isfinite gcc-12.3.0/libstdc++-v3/include/c_compatibility/math.h 
using std::isfinite;

[barracuda156]

https://cplusplus.com/reference/cmath/isfinite/ says that #include <math.h> should define isfinite (without having to use std::) so this may actually be a bug in your includes?

I think it is a conflict between some includes. Obviously Apple headers from 2008 have no idea about modern GCC, and something does not work together. The error points to GCC’s cmath header. Then we got math.h in the OS, math.h in GCC itself and math.h in Macports legacy-support library. I will need to dig into that to figure out what exactly causes the issue, but as long as using std:: is fine, the fix is trivial and consistent.