[R-pkg-devel] CRAN uses an old version of clang

[Serguei Sokol]

Not really responding the question, however another way could be to 
consider if your code is in Rcpp and calls to bessel and gamma function 
are not very frequent. These functions are available in base R and as 
such are callable via Function():

 > Rcpp::evalCpp('Function("besselK")(1., 0.2)')
[1] 0.42722
 > Rcpp::evalCpp('Function("gamma")(4)') # 3!
[1] 6

https://teuder.github.io/rcpp4everyone_en/230_R_function.html#function


Best,
Serguei.

Le 09/02/2024 à 15:59, Marcin Jurek a écrit :
> Dear community,
> 
> I recently submitted an update to my package. It previous version relied on
> Boost for Bessel and gamma functions but a colleague pointed out to me that
> they are included in the standard library beginning with the C++17
> standard.
> 
> I don't have access to a Mac so I tested my package on Rhub and on my local
> Linux and everything ran fine. However, it seems like CRAN is using an old
> version of Clang (14.03 vs 16 being the newest one) and it complained about
> these Bessel functions. I'm pasting the installation log below. I wonder if
> this is something I could hope to explain in cran-comments and have my
> package accepted as is?
> 
> I could also revert to using Boost although I only need it for these
> special functions and things are much cleaner without it. In addition, one
> of the main reasons for this update was related to some warnings Boost
> started throwing.
> 
> Really appreciate the help!
> 
> * installing *source* package ‘GPvecchia’ ...
> ** package ‘GPvecchia’ successfully unpacked and MD5 sums checked
> ** using staged installation
> ** libs
> using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
> using C++17
> using SDK: ‘MacOSX11.3.sdk’
> clang++ -arch x86_64 -std=gnu++17
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include'
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include'
> -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2
> -c Esqe.cpp -o Esqe.o
> clang++ -arch x86_64 -std=gnu++17
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include'
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include'
> -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2
> -c Matern.cpp -o Matern.o
> clang++ -arch x86_64 -std=gnu++17
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include'
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include'
> -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2
> -c MaxMin.cpp -o MaxMin.o
> clang++ -arch x86_64 -std=gnu++17
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include'
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include'
> -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2
> -c RcppExports.cpp -o RcppExports.o
> clang++ -arch x86_64 -std=gnu++17
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include'
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include'
> -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2
> -c U_NZentries.cpp -o U_NZentries.o
> clang++ -arch x86_64 -std=gnu++17
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include'
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include'
> -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2
> -c dist.cpp -o dist.o
> clang++ -arch x86_64 -std=gnu++17
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include'
> -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include'
> -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2
> -c fastTree.cpp -o fastTree.o
> Matern.cpp:80:68: error: no member named 'cyl_bessel_k' in namespace 'std'
>          covmat(j1,j2) = normcon*pow( scaledist, covparms(2)
> )*std::cyl_bessel_k(covparms(2),scaledist);
> //Rf_bessel_k(scaledist,covparms(2),1.0);
>                                                                ~~~~~^
> 1 error generated.
> make: *** [Matern.o] Error 1
> make: *** Waiting for unfinished jobs....
> ERROR: compilation failed for package ‘GPvecchia’
> * removing ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/GPvecchia.Rcheck/GPvecchia’
> 
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