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This is my first question on stack ! Hope I follow correctly the guidelines...

Device

  • Thinkpad series
  • Manjaro KDE (kernel 5.13)
  • Fresh R install (4.2)
  • Fresh Rstudio install
  • Several packages installed yesterday evening, following approximately this roadmap (it includes rstan, which has specific installation requirements)

Problem

So, installing several packages of R (4.2) in rstudio, I encountered the same error with several dependencies (but not all). Eg here for mvtnorm or nleqslv (both while installing brms). (see error at the bottom of this message).

It seems that the problem concerns the line 82 of the Eigen/Core header, located in Rcppeigen directory. The #include <new> isn't correctly understood by the compiler.

What I've already done

  • Trying to reinstall Rcppeigen (but it didn't work)
  • Online queries around this include new problem : I found a little amount of similar errors, but only with quite surprising devices (like an Arduino here)...

As I'm on a Thinkpad laptop, this shouldn't appear. Should I use another compiler ?

Thanks for your help !

Log

* installing *source* package ‘mvtnorm’ ...
** package ‘mvtnorm’ correctement décompressé et sommes MD5 vérifiées
** using staged installation
** libs
gcc -I"/usr/include/R/" -DNDEBUG   -I"/home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include/"  -I"/home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/RcppEigen/include/"  -I"/home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/RcppEigen/include/unsupported"  -I"/home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/BH/include" -I"/home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/include/src/"  -I"/home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/include/"  -I"/home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/RcppParallel/include/"  -I"/home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DBOOST_NO_AUTO_PTR  -include '/home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto=auto -ffat-lto-objects  -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
Dans le fichier inclus depuis /home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/RcppEigen/include/Eigen/Dense:1,
                 depuis /home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 depuis <ligne-de-commande>:
/home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/RcppEigen/include/Eigen/Core:82:12: erreur fatale: new : Aucun fichier ou dossier de ce type
   82 |   #include <new>
      |            ^~~~~
compilation terminée.
make: *** [/usr/lib64/R/etc/Makeconf:169 : C_FORTRAN_interface.o] Erreur 1
ERROR: compilation failed for package ‘mvtnorm’
* removing ‘/home/jpapir/R/x86_64-pc-linux-gnu-library/4.2/mvtnorm’
Warning in install.packages :
  l'installation du package ‘mvtnorm’ a eu un statut de sortie non nul
marc_s
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user21048379
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  • It's probably not your hardware, but rather your OS. I've never heard of Manjaro, but it would appear to be an arch linux based distribution. My guess is that you're missing some key system libraries that prevent you from compiling some programs. Since I'm not familiar with Arch/Manjaro, somebody else will have to chip in. Sorry. – Roman Luštrik Jan 20 '23 at 08:54

1 Answers1

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Well, finally I solved it myself after some hours stacking with it.

So. In order to install Rstan, I followed these instructions. In order to revert it, I deleted the content of the file .R/Makevars and I restarted R. I don't know why it was creating this error. But the issue seems now to be solved.

user21048379
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