How use the option -std=c99 for installing R packages - r

Question

I have problem in installing plyr R package, and got the following error:
Installing package into '/home/mousavian/R/x86_64-pc-linux-gnu-library/3.2'
(as 'lib' is unspecified)
* installing *source* package 'plyr' ...
** package 'plyr' successfully unpacked and MD5 sums checked
** libs
g++ -I/share/apps/R/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/mousavian/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
gcc -I/share/apps/R/lib64/R/include -DNDEBUG -I/usr/local/include -I"/home/mousavian/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -fpic -g -O2 -c loop_apply.c -o loop_apply.o
loop_apply.c: In function 'loop_apply':
loop_apply.c:15:3: error: 'for' loop initial declarations are only allowed in C99 or C11 mode
for(int i = 0; i < n1; i++) {
^
loop_apply.c:15:3: note: use option -std=c99, -std=gnu99, -std=c11 or -std=gnu11 to compile your code
make: *** [loop_apply.o] Error 1
ERROR: compilation failed for package 'plyr'
* removing '/home/mousavian/R/x86_64-pc-linux-gnu-library/3.2/plyr'
Warning message:
In install.packages("R packages/plyr_1.8.3.tar.gz", repos = NULL) :
installation of package 'R packages/plyr_1.8.3.tar.gz' had non-zero exit status
How can I use -std=c99 option when try to install R packages from the source by install.packages command?
Thanks

Answer 1

Try C11 First
The compiler error tells you to choose either C99 or C11. So unless you're knowingly compiling legacy code, try C11 first. You can always then try the legacy C99 if that doesn't work.
Use withr::with_makevars
Editing individual package Makevars or coordinating global changes to your include/lib directories for every package that doesn't directly compile from source is not a happy strategy for the future. Don't do that! A great alternative to editing your R's make configuration is to use withr::with_makevars to manipulate the Makevars only for the installation command:
library(withr)
with_makevars(c(PKG_CFLAGS = "-std=c11"),
install.packages("plyr", repos = NULL, type = "source"),
assignment = "+=")
Plus, you likely already have withr installed since it's a devtools dependency.

Answer 2

If not already existing, create a directory in your $HOME (/home/mousavian/.R in your case). Inside, create a Makevars file (no extension). Edit this file with your favorite editor and write:
CC = gcc -std=c99
Then, save it and after starting R, simply run
install.packages("plyr", dependencies = TRUE)
It should compile with gcc -std=c99.

Answer 3

The default /etc/R/Makeconf includes CC = gcc -std=gnu99 (R 3.3.2 and probably most or all other recent versions, although I think the in-progress development version jumps up into the 21st century)
The accepted answer may well work, but is not the R default. Setting CC=gcc with no other options would drop this default, and this another reason for getting this error. Best to leave defaults alone unless you know what you're doing.

Answer 4

As an addendum, to possibly save someone a few minutes: I ran into a similar issue after an R update to 3.3.2 on an Rstudio server (that I have no control over), but with g++. Compiler options for g++ may be added to Makevars like this:
CXX1XSTD = -std=gnu++11
(the package I needed to compile required gnu++11)