`R_HOME` warning prevents reading macros after `devtools::load_all()`

[jakub-jedrusiak]

System details:

Positron and OS details:

Positron Version: 2025.07.0 build 74
Code - OSS Version: 1.100.0
Commit: fe621e8
Date: 2025-06-09T03:43:13.821Z
Electron: 34.5.1
Chromium: 132.0.6834.210
Node.js: 20.19.0
V8: 13.2.152.41-electron.0
OS: Linux x64 6.15.3-1-MANJARO

Interpreter details:

R 4.5.1

Describe the issue:

I'm working on my package in Positron. After I run devtools::load_all() it seems that a warning about the value of R_HOME is sucked into the file path of some macro:

Warning message:
In file(con, "r") :
  cannot open file 'WARNING: ignoring environment value of R_HOME
/usr/share/R//Rd/macros/system.Rd': No such file or directory

Note that the warning is inside the quotation marks. This warning appears from time to time while I'm writing code and it prevents me from accessing help files, e.g.:

> ?tidyr::unnest_wider
Warning message:
In file(con, "r") :
  cannot open file 'WARNING: ignoring environment value of R_HOME
/usr/share/R//Rd/macros/system.Rd': No such file or directory
Error in `file()`:
! cannot open the connection
Hide Traceback
     ▆
  1. └─`?`(tidyr::unnest_wider)
  2.   └─pkgload::dev_topic_find(topic, pkg)
  3.     └─pkgload:::dev_topic_path(topic$topic, path = ns_path(pkg_name))
  4.       └─pkgload::dev_topic_index(path)
  5.         └─pkgload:::build_topic_index(path)
  6.           └─pkgload:::load_rd_macros(path)
  7.             └─tools::loadPkgRdMacros(dir)
  8.               └─tools:::initialRdMacros(pkglist)
  9.                 └─tools::loadRdMacros(file = macros)
 10.                   └─tools::parse_Rd(file, fragment = TRUE, macros = macros, warningCalls = FALSE)
 11.                     └─base::readLines(file, warn = FALSE)
 12.                       └─base::file(con, "r")

Do note that I don't have a custom value of R_HOME set.

Steps to reproduce the issue:

1. Open a package as a workspace.
2. Run devtools::load_all().
3. Start writing code or try to access help file of any function.

Expected or desired behavior:

The error shouldn't appear, the warning message shouldn't be a part of the file path.

Were there any error messages in the UI, Output panel, or Developer Tools console?

No other errors were present.

[juliasilge]

I'm not able to reproduce this problem:

Do you observe this problem with all R packages, or just one specific one? Can you say more about how you have installed R (from CRAN, rig, etc)?

[jakub-jedrusiak]

It seems I get it for all packages. I have installed R from official Manjaro repository. It probably needs to be checked on Linux to be reproduced. Try it with this package:

https://github.com/jakub-jedrusiak/mtscr

[DavisVaughan]

What does R.home("share") return for you? Both inside Positron and in a standalone terminal with the same version of R running

[jakub-jedrusiak]

A standalone terminal returns:

[1] "/usr/share/R/"

The Positron console returns:

[1] "WARNING: ignoring environment value of R_HOME\n/usr/share/R/"

[DavisVaughan]

When you start up your standalone R console, do you see the WARNING echo'ed at the top? Like this

We have a decent idea of what is happening. We run an R process here and capture its stdout to capture

paste(R.home('share'), R.home('include'), R.home('doc'), sep=';')

But it seems that your R process is warning that R_HOME is set differently than the hardcoded R_HOME_DIR in your R's setup script, which would be weird. Unfortunately R emits that warning on stdout and we capture it by mistake as well and assume it is part of the R.home('share') output.

We really want to figure out why you get that WARNING at all though

[jakub-jedrusiak]

It doesn't appear on startup, niether in a standalone console, nor in Positron. It does appear if i manually export R_HOME=foo before running R. These are these commands one by one:

Standalone console:

> R.home('share')
[1] "/usr/share/R/"

> R.home('include')
[1] "/usr/include/R/"

> R.home('doc')
[1] "/usr/share/doc/R/"

Positron:

> R.home('share')
[1] "WARNING: ignoring environment value of R_HOME\n/usr/share/R/"

> R.home('include')
[1] "/usr/include/R/"

> R.home('doc')
[1] "/usr/share/doc/R/"