rstan and RStudio on linux with an R installation using subarchitectures

[BATurlach]

Summary:

As indicated when raising issue #504, on my linux machine (Ubuntu 14.04.4 LTS), I compile R from source, and install both a 32 bit version and a 64 bit version; both as subarchitectures. To my surprise, I noticed that I cannot run stan() from the rstan package on my machine when I use RStudio.

Description:

The work-around to issue #504 that I am currently using is to create a symbolic link in R_HOME library/StanHeaders/libs/64/libStanHeaders.a to library/StanHeaders/libs/libStanHeaders.a. stan() works if R is started from the console, but not if it is started from RStudio. The error message I get is:

Error in get_makefile_txt() : 
  file /opt/R/R-3.4.3/lib/R/etc//Makeconf does not exist

Problem:

The error seems to be produced by lines 28-34 in the function get_makefile_txt() in rstan/R/makefile_op.R:

  WINDOWS <- .Platform$OS.type == "windows"
  rarch <- Sys.getenv("R_ARCH") # unix only
  if (WINDOWS && nzchar(.Platform$r_arch))
    rarch <- paste0("/", .Platform$r_arch)
  site <- file.path(R.home("etc"), rarch, "Makevars.site")

  sys_makeconf <- file.path(R.home("etc"), rarch, "Makeconf")

On my Linux machine, if I start R from the console, I get the following result:

> Sys.getenv("R_ARCH")
[1] "/64"

When I start R via RStudio, I get:

> Sys.getenv("R_ARCH")
[1] ""

By way of contrast, on a Windows machine, whether I start R directly or via RStudio, I always get:

> Sys.getenv("R_ARCH")
[1] "/x64"

Proposed Solution:

Looking at makeconf_path() in rstan/R/misc.R (lines 1377-1388), a solution might be to replace the above lines with:

  WINDOWS <- .Platform$OS.type == "windows"
  rarch <- .Platform$r_arch
  if (rarch = ''){
    site <- file.path(R.home("etc"), "Makevars.site")
    sys_makeconf <- file.path(R.home("etc"), "Makeconf")
  }else{
    site <- file.path(R.home("etc"), rarch, "Makevars.site")
    sys_makeconf <- file.path(R.home("etc"), rarch, "Makeconf")
  }

Not sure if the if() construct is needed as R does not seem to have problems with paths created by file.path() that contain // (in my limited experience).

I am not sure whether the logic of last_makefile() in rstan/R/makefile_op.R (lines 99-114) also needs revisiting.

RStan Version:

2.17.3

R Version:

R version 3.4.3 (2017-11-30)

> RStudio.Version()$version
[1] ‘1.1.423’

Operating System:

$ uname -a
Linux ECM-DTC-716 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 16.04.4 LTS
Release:	16.04
Codename:	xenial

[bgoodri]

Does this function work on your machine(s)?

get_makefile_txt <- function() {
  out <- system2(file.path(Sys.getenv("R_HOME"), "bin", "R"),
                 args = "CMD SHLIB --dry-run", stdout = TRUE)[2]
  makefiles <- strsplit(sub("SHLIB.*$", "", out), split = "-f ")[[1]][-1]
  makefiles <- gsub("'", "", makefiles)
  makefiles <- gsub("[[:space:]]*$", "", makefiles)
  makefiles <- makefiles[file.exists(makefiles)]
  do.call(c, lapply(makefiles, function(f) readLines(f, warn = FALSE))) 
}

[BATurlach]

G'day Ben (?), apologies if you receive this twice, on my first attempt I hit the reply-all button. Perhaps I am supposed to hit reply only (my usual default)?

On Wed, 13 Jun 2018 14:33:21 -0700 bgoodri ***@***.***> wrote: Does this function work on your machine(s)?

It seems it does, when I start rstudio on my machine:

R> rstan:::get_makefile_txt() Error in rstan:::get_makefile_txt() : file /opt/R/R-3.5.0/lib/R/etc//Makeconf does not exist R> get_makefile_txt <- function() { + out <- system2(file.path(Sys.getenv("R_HOME"), "bin", "R"), + args = "CMD SHLIB --dry-run", stdout = TRUE)[2] + makefiles <- strsplit(sub("SHLIB.*$", "", out), split = "-f ")[[1]][-1] + makefiles <- gsub("'", "", makefiles) + makefiles <- gsub("[[:space:]]*$", "", makefiles) + makefiles <- makefiles[file.exists(makefiles)] + do.call(c, lapply(makefiles, function(f) readLines(f, warn = FALSE))) + } R> get_makefile_txt() [1] "# etc/Makeconf. Generated from Makeconf.in by configure." [2] "#" [3] "# ${R_HOME}/etc/Makeconf"

Well, the output seems to be one long line, and reads 210 lines from Makesfiles altogether. Thank you for your help. Cheers, Berwin