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

[Marcin Jurek]

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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