Compilation of some R packages with R CMD build or install runs into a common clang error as follows;
clang-16: error: no such file or directory: 'Welcome'
clang-16: error: no such file or directory: 'at'
clang-16: error: no such file or directory: 'Thu'
clang-16: error: no such file or directory: 'Apr'
clang-16: error: no such file or directory: '20'
clang-16: error: no such file or directory: '19:30:11'
clang-16: error: no such file or directory: '2023'
A line, Welcome at Thu Apr 20 19:30:06 2023 appears at the very begging of R CMD build or install output as follows;
R CMD build dada2
Welcome at Thu Apr 20 19:30:06 2023
* checking for file ‘dada2/DESCRIPTION’ ... OK
* preparing ‘dada2’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
Welcome at Thu Apr 20 19:30:07 2023
* installing *source* package ‘dada2’ ...
** using staged installation
** libs
I am using M1 Mac with following;
sw_vers
ProductName: macOS
ProductVersion: 13.3.1
BuildVersion: 22E261
R.version
_
platform aarch64-apple-darwin20
arch aarch64
os darwin20
system aarch64, darwin20
status
major 4
minor 2.2
year 2022
month 10
day 31
svn rev 83211
language R
version.string R version 4.2.2 (2022-10-31)
nickname Innocent and Trusting
I am not sure this is a M1 Mac specific issue but happens occasionally with M1 Mac I'd really appreciate any pointers to address this issue.
I figured this one out. An issue was my .Rprofile;
>more .Rprofile
.First <- function(){
library(magrittr)
library(future)
Sys.setenv(R_HISTSIZE='100000')
options(future.globals.maxSize = 50 * 1024 ^ 3)
options(parallelly.fork.enable=T)
plan('multicore', workers=20)
#cat("\nWelcome at", date(), "\n")
}
The last line create a welcome note and this was causing the issue that I described. Once I commented out, everything just compiled fine but still a question remains as to why compilation of some packages got affected while a majority of others were fine.