Re: [R-pkg-devel] CRAN uses an old version of clang
Just to include the necessary details: macOS CRAN build uses Apple clang-14, so
you cannot assume anything higher. Also the target is macOS 11 SDK.
That said, LLVM does not support the special math functions at all according to
the status report (see Mathematical Special Functions for C++17 at
https://libcxx.llvm.org/Status/Cxx17.html) so Boost is your best bet.
BTW: this is not a Mac thing - you can replicate it on any other system, eg. in
Linux:
$ clang++-17 -std=c++17 -stdlib=libc++ bes.cc
bes.cc:11:49: error: no member named 'cyl_bessel_k' in namespace 'std'
11 | std::cout << "K_.5(" << x << ") = " << std::cyl_bessel_k(.5, x) <<
'\n'
|~^
bes.cc:13:35: error: no member named 'cyl_bessel_i' in namespace 'std'
13 | << (pi / 2) * (std::cyl_bessel_i(-.5, x)
| ~^
bes.cc:14:25: error: no member named 'cyl_bessel_i' in namespace 'std'
14 | - std::cyl_bessel_i(.5, x)) / std::sin(.5 * pi) <<
'\n';
|~^
3 errors generated.
Cheers,
Simon
> On 10/02/2024, at 8:04 AM, Marcin Jurek wrote:
>
> All this makes sense, thanks for your tips, everyone!
>
> Marcin
>
> On Fri, Feb 9, 2024 at 9:44 AM Dirk Eddelbuettel wrote:
>
>>
>> On 9 February 2024 at 08:59, Marcin Jurek wrote:
>> | 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.
>>
>> There is an often overlooked bit of 'fine print': _compiler support_ for a
>> C++ standard is not the same as the _compiler shipping a complete library_
>> for that same standard. This can be frustrating. See the release notes for
>> gcc/g++ and clang/clang++, IIRC they usually have a separate entry for C++
>> library support.
>>
>> In this case, can probably rely on LinkingTo: BH which has been helping
>> with
>> Boost headers for over a decade.
>>
>> Writing R Extensions is also generally careful in reminding us that such
>> language standard support is always dependent on the compiler at hand. So
>> package authors ought to check, just like R does via its extensive
>> configure
>> script when it builds.
>>
>> Dirk
>>
>> --
>> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>>
>
> [[alternative HTML version deleted]]
>
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Re: [R-pkg-devel] CRAN uses an old version of clang
All this makes sense, thanks for your tips, everyone! Marcin On Fri, Feb 9, 2024 at 9:44 AM Dirk Eddelbuettel wrote: > > On 9 February 2024 at 08:59, Marcin Jurek wrote: > | 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. > > There is an often overlooked bit of 'fine print': _compiler support_ for a > C++ standard is not the same as the _compiler shipping a complete library_ > for that same standard. This can be frustrating. See the release notes for > gcc/g++ and clang/clang++, IIRC they usually have a separate entry for C++ > library support. > > In this case, can probably rely on LinkingTo: BH which has been helping > with > Boost headers for over a decade. > > Writing R Extensions is also generally careful in reminding us that such > language standard support is always dependent on the compiler at hand. So > package authors ought to check, just like R does via its extensive > configure > script when it builds. > > Dirk > > -- > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN uses an old version of clang
On 9 February 2024 at 08:59, Marcin Jurek wrote: | 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. There is an often overlooked bit of 'fine print': _compiler support_ for a C++ standard is not the same as the _compiler shipping a complete library_ for that same standard. This can be frustrating. See the release notes for gcc/g++ and clang/clang++, IIRC they usually have a separate entry for C++ library support. In this case, can probably rely on LinkingTo: BH which has been helping with Boost headers for over a decade. Writing R Extensions is also generally careful in reminding us that such language standard support is always dependent on the compiler at hand. So package authors ought to check, just like R does via its extensive configure script when it builds. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN uses an old version of clang
Your users may also use old versions of clang. Hence please correct it. CRAN is also checking with the clang18 release candidate. Best, Uwe Ligges On 09.02.2024 15:59, Marcin Jurek wrote: 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’ [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN uses an old version of clang
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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[R-pkg-devel] CRAN uses an old version of clang
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’ [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
