R installed via conda cannot start (Windows 11)

Possibly related to #3791 and #1397

System details:

Processor 11th Gen Intel(R) Core(TM) i7-11850H @ 2.50GHz (2.50 GHz)
Installed RAM 32.0 GB (31.2 GB usable)
System type 64-bit operating system, x64-based processor

Edition Windows 11 Enterprise
Version 24H2
Installed on ‎19-‎Aug-‎25
OS build 26100.4946
Experience Windows Feature Experience Pack 1000.26100.197.0

Positron and OS details:

Positron Version: 2025.10.0 (user setup) build 14
Code - OSS Version: 1.103.0
Commit: c3ee3a3a9d01ff2046879b5481b9b4ee5baa9dec
Date: 2025-09-01T07:31:16.992Z
Electron: 37.2.3
Chromium: 138.0.7204.100
Node.js: 22.17.0
V8: 13.8.500258-electron.0
OS: Windows_NT x64 10.0.26100

Session details:

R 4.4.3

Describe the issue:

R installation (R > 4.2) from a conda environment is not recognised by Positron, while the Python from the same conda environment is found.

Steps to reproduce the issue:

1. Install miniforge3
2. Create environment from config.yml via conda env create -f config.yml:

name: viz
channels:
    - conda-forge
dependencies:
    - r-base=4.4.3

3. Activate environment and check R in cmd:

conda env activate -n viz
where R
#> C:\scoop\apps\mambaforge\current\envs\viz\Scripts\R.exe
R -e "R.home()"
#> [1] "C:/scoop/apps/mambaforge/current/envs/viz/lib/R"

4. Open Positron
5. Check interpreters. Mind that python from viz env has been discovered, but not R. R Language Pack output hasn't discovered it:

6. Go to settings.json and explicitly specify R path:

    "positron.r.customBinaries": [
        "C:/scoop/apps/mambaforge/current/envs/viz/Scripts/R.exe"
    ]

7. Restart Positron
8. See no difference in interpreters dropdown menu, but now R Language Pack output has warning "[warning] Some discovered R installations are unusable by Positron." See full log below:

2025-08-31 13:57:23.432 [info] Log level: Info
2025-08-31 13:57:23.432 [info] Refreshing testthat status
2025-08-31 13:57:23.432 [info] Not working in an R package
2025-08-31 13:57:23.432 [info] Context key 'testthatIsConfigured' is 'false'
2025-08-31 13:57:23.432 [info] Context key 'testthatHasTests' is 'false'
2025-08-31 13:57:24.149 [info] Registry key HKEY_LOCAL_MACHINE\SOFTWARE\R-core\R64\InstallPath reports the current R installation is at C:\Program Files\R\R-4.5.1patched
2025-08-31 13:57:24.149 [info] Identified the current R binary: C:\Program Files\R\R-4.5.1patched\bin\x64\R.exe
2025-08-31 13:57:24.325 [info] Possibly found R on PATH: C:\Program Files\R\bin\R.BAT.
2025-08-31 13:57:24.326 [info] Unsupported extension: .bat.
2025-08-31 13:57:24.326 [info] Ignoring R headquarters directory C:\Users\TsyplenkovA\AppData\Local\Programs\R because it does not exist.
2025-08-31 13:57:24.350 [info] Registry key HKEY_LOCAL_MACHINE\SOFTWARE\R-core\R64\4.4.1\InstallPath reports an R installation at C:\Program Files\R\R-4.4.1
2025-08-31 13:57:24.350 [info] Registry key HKEY_LOCAL_MACHINE\SOFTWARE\R-core\R64\4.4.3\InstallPath reports an R installation at C:\Program Files\R\R-4.4.3
2025-08-31 13:57:24.350 [info] Registry key HKEY_LOCAL_MACHINE\SOFTWARE\R-core\R64\4.5.0\InstallPath reports an R installation at C:\Program Files\R\R-4.5.0
2025-08-31 13:57:24.351 [info] Ignoring ad hoc R binary /usr/bin/R because it does not exist.
2025-08-31 13:57:24.351 [info] Ignoring ad hoc R binary /usr/local/bin/R because it does not exist.
2025-08-31 13:57:24.351 [info] Ignoring ad hoc R binary /opt/local/bin/R because it does not exist.
2025-08-31 13:57:24.351 [info] Ignoring ad hoc R binary /opt/homebrew/bin/R because it does not exist.
2025-08-31 13:57:24.351 [info] R binaries from 'positron.r.customBinaries' to discover:
[
  "C:/scoop/apps/mambaforge/current/envs/viz/Scripts/R.exe"
]
2025-08-31 13:57:24.394 [info] Candidate R binary at C:\Program Files\R\R-4.5.1patched\bin\x64\R.exe
2025-08-31 13:57:24.394 [info] R installation discovered: {
  "usable": true,
  "supported": true,
  "reasonDiscovered": [
    "Found in Windows registry",
    "Found in the primary location for R versions on this operating system"
  ],
  "reasonRejected": null,
  "binpath": "C:\\Program Files\\R\\R-4.5.1patched\\bin\\x64\\R.exe",
  "homepath": "C:\\Program Files\\R\\R-4.5.1patched",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.5.1",
    "major": 4,
    "minor": 5,
    "patch": 1,
    "prerelease": [],
    "build": [],
    "version": "4.5.1"
  },
  "version": "4.5.1",
  "arch": "x86_64",
  "current": true,
  "orthogonal": true,
  "default": false
}
2025-08-31 13:57:24.394 [info] Candidate R binary at C:\Program Files\R\R-4.4.1\bin\x64\R.exe
2025-08-31 13:57:24.394 [info] R installation discovered: {
  "usable": true,
  "supported": true,
  "reasonDiscovered": [
    "Found in the primary location for R versions on this operating system",
    "Found in Windows registry"
  ],
  "reasonRejected": null,
  "binpath": "C:\\Program Files\\R\\R-4.4.1\\bin\\x64\\R.exe",
  "homepath": "C:\\Program Files\\R\\R-4.4.1",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.4.1",
    "major": 4,
    "minor": 4,
    "patch": 1,
    "prerelease": [],
    "build": [],
    "version": "4.4.1"
  },
  "version": "4.4.1",
  "arch": "x86_64",
  "current": false,
  "orthogonal": true,
  "default": false
}
2025-08-31 13:57:24.394 [info] Candidate R binary at C:\Program Files\R\R-4.4.3\bin\x64\R.exe
2025-08-31 13:57:24.394 [info] R installation discovered: {
  "usable": true,
  "supported": true,
  "reasonDiscovered": [
    "Found in the primary location for R versions on this operating system",
    "Found in Windows registry"
  ],
  "reasonRejected": null,
  "binpath": "C:\\Program Files\\R\\R-4.4.3\\bin\\x64\\R.exe",
  "homepath": "C:\\Program Files\\R\\R-4.4.3",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.4.3",
    "major": 4,
    "minor": 4,
    "patch": 3,
    "prerelease": [],
    "build": [],
    "version": "4.4.3"
  },
  "version": "4.4.3",
  "arch": "x86_64",
  "current": false,
  "orthogonal": true,
  "default": false
}
2025-08-31 13:57:24.394 [info] Candidate R binary at C:\Program Files\R\R-4.5.0\bin\x64\R.exe
2025-08-31 13:57:24.394 [info] R installation discovered: {
  "usable": true,
  "supported": true,
  "reasonDiscovered": [
    "Found in the primary location for R versions on this operating system",
    "Found in Windows registry"
  ],
  "reasonRejected": null,
  "binpath": "C:\\Program Files\\R\\R-4.5.0\\bin\\x64\\R.exe",
  "homepath": "C:\\Program Files\\R\\R-4.5.0",
  "semVersion": {
    "options": {},
    "loose": false,
    "includePrerelease": false,
    "raw": "4.5.0",
    "major": 4,
    "minor": 5,
    "patch": 0,
    "prerelease": [],
    "build": [],
    "version": "4.5.0"
  },
  "version": "4.5.0",
  "arch": "x86_64",
  "current": false,
  "orthogonal": true,
  "default": false
}
2025-08-31 13:57:24.395 [info] Candidate R binary at C:\scoop\persist\mambaforge\envs\viz\Scripts\R.exe
2025-08-31 13:57:24.395 [info] Can't determine R_HOME_DIR from the path to the R binary: C:\scoop\persist\mambaforge\envs\viz\Scripts\R.exe
2025-08-31 13:57:24.395 [info] Filtering out C:\scoop\persist\mambaforge\envs\viz\Scripts\R.exe, reason: Invalid installation.
2025-08-31 13:57:24.395 [warning] Some discovered R installations are unusable by Positron.
2025-08-31 13:57:24.395 [warning] Learn more about R discovery at https://positron.posit.co/r-installations

Start with the R Language Pack discovery output and the handling of the positron.r.customBinaries setting, then reproduce the conda environment using the supplied config.yml and Windows paths. Trace why the Scripts/R.exe candidate cannot determine R_HOME_DIR; done means the conda-installed R appears as a usable interpreter in Positron.