when installing a R package, fatal error: R.h: No such file or directory, How to locate R.h?-CodePudding

when installing a R package from github

install_github("DataSlingers/ExclusiveLasso")

I get the error messages:

* installing *source* package 'ExclusiveLasso' ...
** using staged installation
** libs
g    -std=gnu  11 -I"/include" -DNDEBUG  -I'D:/R-4.2.2/library/Rcpp/include' -I'D:/R-4.2.2/library/RcppArmadillo/include'   -I"D:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ExclusiveLasso.cpp -o ExclusiveLasso.o
In file included from D:/R-4.2.2/library/Rcpp/include/RcppCommon.h:30,
                 from D:/R-4.2.2/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from D:/R-4.2.2/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from ExclusiveLasso.cpp:23:
D:/R-4.2.2/library/Rcpp/include/Rcpp/r/headers.h:66:10: fatal error: R.h: No such file or directory
   66 | #include <R.h>
      |          ^~~~~
compilation terminated.
make: *** [D:/R-4.2.2/etc/x64/Makeconf:260：ExclusiveLasso.o] 错误 1
ERROR: compilation failed for package 'ExclusiveLasso'
* removing 'D:/R-4.2.2/library/ExclusiveLasso'

I know where my R.h at, and I tried change

#include <R.h>

into

#include <D:/R-4.2.2/include>,

but there's too many files and errors like this

It seems that I should tell the g where to find D:/R-4.2.2/include, can someone guide me whether I should do that or what should I do.

I's using: R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Using vscode

CodePudding user response：

Works fine here on Ubuntu 22.10. Note in the log below how it uses -I"/usr/share/R/include" (which is something R itself adds) to point to R's headers. So to me it looks like your R installation is at fault because the src/Makevars.win in that repo is very standard and mostly likely correct.

edd@rob:~$ installGithub.r DataSlingers/ExclusiveLasso  # wrapper around install_github()
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo DataSlingers/ExclusiveLasso@HEAD

Skipping 1 packages ahead of CRAN: Rcpp
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/remotes2ac86f2646632b/DataSlingers-ExclusiveLasso-ed6b729/DESCRIPTION’ ...
─  preparing ‘ExclusiveLasso’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘ExclusiveLasso_0.0.tar.gz’
   
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘ExclusiveLasso’ ...
** using staged installation
** libs
ccache g    -std=gnu  11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O3 -Wall -pipe -pedantic -Wno-ignored-attributes  -c ExclusiveLasso.cpp -o ExclusiveLasso.o
ccache g    -std=gnu  11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O3 -Wall -pipe -pedantic -Wno-ignored-attributes  -c RcppExports.cpp -o RcppExports.o
ccache g   -std=gnu  11 -Wl,-S -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o ExclusiveLasso.so ExclusiveLasso.o RcppExports.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug *.o *.so; fi
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Darwin" ]] ; then /usr/bin/strip -S *.o *.so; fi
installing to /usr/local/lib/R/site-library/00LOCK-ExclusiveLasso/00new/ExclusiveLasso/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ExclusiveLasso)
edd@rob:~$

Looking at your installation attempt confirms that because you have

g    -std=gnu  11 -I"/include"

so R does not figure out where its installation is. Normally you should have

edd@rob:~$ R RHOME
/usr/lib/R
edd@rob:~$

but I suspect that too is borked at your end.