Compilation failed during installation: `cc1plus: some warnings being treated as errors`.

[iago-lito]

Hello, installation failed today on my machine with the following logs :(

$ R -e "options(repos = structure(c(CRAN = 'http://cran.rstudio.com/'))); install.packages('ape', Ncpus=$(nproc))"
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> options(repos = structure(c(CRAN = 'http://cran.rstudio.com/'))); install.packages('ape', Ncpus=20)
Installing package into ‘/home/iago-lito/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/ape_5.8.tar.gz'
Content type 'application/x-gzip' length 1579438 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 14.1.1 20240522’
using C++ compiler: ‘g++ (GCC) 14.1.1 20240522’
gcc -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/Rcpp/include' -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection         -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c BIONJ.c -o BIONJ.o
gcc -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/Rcpp/include' -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection         -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c NNI.c -o NNI.o
g++ -std=gnu++17 -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/Rcpp/include' -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection         -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects   -c RcppExports.cpp -o RcppExports.o
In file included from /usr/lib/R/library/Rcpp/include/Rcpp/routines.h:26,
                 from /usr/lib/R/library/Rcpp/include/RcppCommon.h:128,
                 from /usr/lib/R/library/Rcpp/include/Rcpp.h:27,
                 from RcppExports.cpp:4:
/usr/lib/R/library/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function ‘std::streamsize Rcpp::Rstreambuf<OUTPUT>::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]’:
/usr/lib/R/library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
   53 |         Rprintf("%.*s", num, s);
      |                  ~~^~   ~~~
      |                    |    |
      |                    int  std::streamsize {aka long int}
/usr/lib/R/library/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function ‘std::streamsize Rcpp::Rstreambuf<OUTPUT>::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]’:
/usr/lib/R/library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
   57 |         REprintf("%.*s", num, s);
      |                   ~~^~   ~~~
      |                     |    |
      |                     int  std::streamsize {aka long int}
In file included from /usr/lib/R/library/Rcpp/include/RcppCommon.h:181:
/usr/lib/R/library/Rcpp/include/Rcpp/print.h: In function ‘void Rcpp::warningcall(SEXP, const std::string&)’:
/usr/lib/R/library/Rcpp/include/Rcpp/print.h:30:19: error: format not a string literal and no format arguments [-Werror=format-security]
   30 |     Rf_warningcall(call, s.c_str());
      |     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
cc1plus: some warnings being treated as errors
make: *** [/usr/lib64/R/etc/Makeconf:204: RcppExports.o] Error 1
ERROR: compilation failed for package ‘ape’
* removing ‘/home/iago-lito/R/x86_64-pc-linux-gnu-library/4.4/ape’

The downloaded source packages are in
    ‘/tmp/RtmpMfxcZJ/downloaded_packages’
Warning message:
In install.packages("ape", Ncpus = 20) :
  installation of package ‘ape’ had non-zero exit status

Should I attempt to have the compiler ignore the warnings? Or should they rather be fixed in ape sources?

[iago-lito]

Possible relevant discussion about the issue: https://github.com/RcppCore/Rcpp/issues/1287.

[iago-lito]

Okay, the problem seems to be that my /usr/lib/R/library/Rcpp was a somewhat lingering old version of Rcpp. The problem is solved with a fresh Rcpp install ;)