Not detecting the R interpreter that is active in positron #2648
Description
System details
Publisher Version : 1.14.0
Connect Version : dev
Your OS : macOS 15.4.1
Content Type to Deploy : shiny app
Publisher Output and Logs
time=2025-05-16T07:32:51.529-05:00 level=DEBUG msg="Picking directory from request" directory=.
time=2025-05-16T07:32:51.530-05:00 level=DEBUG msg="Validating path to R executable found" path=/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R
time=2025-05-16T07:32:51.530-05:00 level=INFO msg="Getting R version" r=/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R
time=2025-05-16T07:32:51.530-05:00 level=DEBUG msg="Running command" cmd=/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R args=--version
time=2025-05-16T07:32:51.588-05:00 level=INFO msg="Parsing line for R version" l="R version 4.3.3 (2024-02-29) -- \"Angel Food Cake\""
time=2025-05-16T07:32:51.588-05:00 level=INFO msg="Detected R version" version=4.3.3
time=2025-05-16T07:32:51.588-05:00 level=DEBUG msg="Successful validation for R executable" rExecutable=/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R
time=2025-05-16T07:32:51.588-05:00 level=DEBUG msg="Successful validation for Python executable" pythonExecutable="" version=3.12.10
time=2025-05-16T07:32:51.627-05:00 level=DEBUG msg="applying defaults to Config.R section" before="&{Version: PackageFile: PackageManager: RequiresRVersion:}"
time=2025-05-16T07:32:51.627-05:00 level=INFO msg="Getting renv lockfile path from R executable" r=/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R
time=2025-05-16T07:32:51.627-05:00 level=DEBUG msg="Running command" cmd=/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R args="-s -e renv::paths$lockfile()"
time=2025-05-16T07:32:52.468-05:00 level=INFO msg="Parsing line for renv::path output" l="[1] \"/Users/jkeane/repos/connect-extensions/extensions/usage-metrics-dashboard/renv.lock\""
time=2025-05-16T07:32:52.468-05:00 level=INFO msg="renv::paths$lockfile returned lockfile path" path=/Users/jkeane/repos/connect-extensions/extensions/usage-metrics-dashboard/renv.lock
time=2025-05-16T07:32:52.468-05:00 level=DEBUG msg="renv lockfile found via R executable" renv_lock=/Users/jkeane/repos/connect-extensions/extensions/usage-metrics-dashboard/renv.lock
time=2025-05-16T07:32:52.470-05:00 level=DEBUG msg="after applying defaults to Config.R section" after="&{Version:4.3.3 PackageFile:renv.lock PackageManager:renv RequiresRVersion:~=4.3.0}"
time=2025-05-16T07:32:52.470-05:00 level=DEBUG msg="New account derived state created" account=dogfood config=usage-metrics-dashboard-E27U
time=2025-05-16T07:32:52.470-05:00 level=DEBUG msg="Looking for R on PATH" local_id=vlQU3DgDfTpWyU31 PATH=/Users/jkeane/.nvm/versions/node/v22.14.0/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/Apple/usr/bin:/Applications/quarto/bin
time=2025-05-16T07:32:52.470-05:00 level=DEBUG msg="Found R executable from PATH" local_id=vlQU3DgDfTpWyU31 path=/usr/local/bin/R
time=2025-05-16T07:32:52.470-05:00 level=DEBUG msg="Validating path to R executable found" local_id=vlQU3DgDfTpWyU31 path=/usr/local/bin/R
time=2025-05-16T07:32:52.470-05:00 level=INFO msg="Getting R version" local_id=vlQU3DgDfTpWyU31 r=/usr/local/bin/R
time=2025-05-16T07:32:52.470-05:00 level=DEBUG msg="Running command" local_id=vlQU3DgDfTpWyU31 cmd=/usr/local/bin/R args=--version
time=2025-05-16T07:32:52.494-05:00 level=INFO msg="Parsing line for R version" local_id=vlQU3DgDfTpWyU31 l="R version 4.5.0 (2025-04-11) -- \"How About a Twenty-Six\""
time=2025-05-16T07:32:52.494-05:00 level=INFO msg="Detected R version" local_id=vlQU3DgDfTpWyU31 version=4.5.0
time=2025-05-16T07:32:52.494-05:00 level=DEBUG msg="Successful validation for R executable" local_id=vlQU3DgDfTpWyU31 rExecutable=/usr/local/bin/R
time=2025-05-16T07:32:52.494-05:00 level=DEBUG msg="New publisher derived from state" local_id=vlQU3DgDfTpWyU31 account=dogfood config=usage-metrics-dashboard-E27U
time=2025-05-16T07:32:52.494-05:00 level=INFO msg="Access Log" method=POST url="/api/deployments/deployment-CJSO?dir=.&r=%2FLibrary%2FFrameworks%2FR.framework%2FVersions%2F4.3-arm64%2FResources%2Fbin%2FR&python=%2Fopt%2Fhomebrew%2Fbin%2Fpython3.12" elapsed_ms=965 status=202 req_size=91 resp_size=31 client_addr=127.0.0.1:54266 req.account=dogfood req.config=usage-metrics-dashboard-E27U req.secrets=map[] req.insecure=false
time=2025-05-16T07:32:52.494-05:00 level=INFO msg="Publishing from directory" local_id=vlQU3DgDfTpWyU31 event_op=agent path=/Users/jkeane/repos/connect-extensions/extensions/usage-metrics-dashboard localID=vlQU3DgDfTpWyU31
time=2025-05-16T07:32:52.495-05:00 level=INFO msg="Starting deployment to server" local_id=vlQU3DgDfTpWyU31 server=https://dogfood.team.pct.posit.it
time=2025-05-16T07:32:52.495-05:00 level=INFO msg="Updating deployment" local_id=vlQU3DgDfTpWyU31 content_id=ba28e7d7-f283-4bea-bbdb-51f46c82c339
time=2025-05-16T07:32:52.495-05:00 level=DEBUG msg="Built manifest from config" local_id=vlQU3DgDfTpWyU31 config=usage-metrics-dashboard-E27U
time=2025-05-16T07:32:52.495-05:00 level=INFO msg="Collecting R package descriptions" local_id=vlQU3DgDfTpWyU31 event_op=publish/getRPackageDescriptions
time=2025-05-16T07:32:52.495-05:00 level=DEBUG msg="Collecting manifest R packages" local_id=vlQU3DgDfTpWyU31 event_op=publish/getRPackageDescriptions lockfile=/Users/jkeane/repos/connect-extensions/extensions/usage-metrics-dashboard/renv.lock
time=2025-05-16T07:32:52.496-05:00 level=DEBUG msg="Running command" local_id=vlQU3DgDfTpWyU31 event_op=publish/getRPackageDescriptions cmd=/usr/local/bin/R args="-s -e cat(.libPaths(), sep=\"\\n\")"
time=2025-05-16T07:32:53.001-05:00 level=DEBUG msg="Running command" local_id=vlQU3DgDfTpWyU31 event_op=publish/getRPackageDescriptions cmd=/usr/local/bin/R args="-s -e (function() { pkgs <- available.packages( repos = setNames(c(\"https://cloud.r-project.org\"), c(\"CRAN\")), type = \"source\", filters = c(getOption(\"rsconnect.available_packages_filters\", default = c()), \"duplicates\"));info <- pkgs[,c(\"Package\", \"Version\", \"Repository\")];apply(info, 1, function(x) { cat(x, sep=\" \", collapse=\"\\n\") } );invisible()})()"
time=2025-05-16T07:32:54.027-05:00 level=DEBUG msg="Running command" local_id=vlQU3DgDfTpWyU31 event_op=publish/getRPackageDescriptions cmd=/usr/local/bin/R args="-s -e (function() { if (requireNamespace(\"BiocManager\", quietly = TRUE) || requireNamespace(\"BiocInstaller\", quietly = TRUE)) {repos <- getFromNamespace(\"renv_bioconductor_repos\", \"renv\")(\"/Users/jkeane/repos/connect-extensions/extensions/usage-metrics-dashboard\"); repos <- repos[setdiff(names(repos), \"CRAN\")]; cat(repos, labels=names(repos), fill=1); invisible()}})()"
Logs URL: https://dogfood.team.pct.posit.it/connect/#/apps/ba28e7d7-f283-4bea-bbdb-51f46c82c339/logs
time=2025-05-16T07:32:54.534-05:00 level=DEBUG msg="Attempting to update deployment record" local_id=vlQU3DgDfTpWyU31 path=/Users/jkeane/repos/connect-extensions/extensions/usage-metrics-dashboard/.posit/publish/deployments/deployment-CJSO.toml localIdIfDeploying=vlQU3DgDfTpWyU31
time=2025-05-16T07:32:54.537-05:00 level=DEBUG msg="Updating deployment record" local_id=vlQU3DgDfTpWyU31 path=/Users/jkeane/repos/connect-extensions/extensions/usage-metrics-dashboard/.posit/publish/deployments/deployment-CJSO.toml
time=2025-05-16T07:32:54.537-05:00 level=ERROR msg="Deployment failed" local_id=vlQU3DgDfTpWyU31 error="package MASS: versions in lockfile '7.3-60.0.1' and library '7.3-65' are out of sync. Use renv::restore() or renv::snapshot() to synchronize"
time=2025-05-16T07:32:54.678-05:00 level=DEBUG msg="Picking directory from request" directory=.
time=2025-05-16T07:32:54.678-05:00 level=DEBUG msg="Picking directory from request" directory=.
time=2025-05-16T07:32:54.687-05:00 level=DEBUG msg="excluding directory" path=/Users/jkeane/repos/connect-extensions/extensions/usage-metrics-dashboard/renv/library
time=2025-05-16T07:32:54.687-05:00 level=DEBUG msg="excluding directory" path=/Users/jkeane/repos/connect-extensions/extensions/usage-metrics-dashboard/renv/staging
time=2025-05-16T07:32:54.688-05:00 level=INFO msg="Access Log" method=GET url="/api/deployments?dir=.&recursive=true" elapsed_ms=9 status=200 req_size=0 resp_size=2034 client_addr=127.0.0.1:54286
time=2025-05-16T07:32:54.986-05:00 level=DEBUG msg="API request" method=GET path=/__api__/v1/content/ba28e7d7-f283-4bea-bbdb-51f46c82c339/environment body="" response=[] error=<nil>
time=2025-05-16T07:32:54.987-05:00 level=INFO msg="Access Log" method=GET url="/api/deployments/deployment-CJSO/environment?dir=." elapsed_ms=308 status=200 req_size=0 resp_size=3 client_addr=127.0.0.1:54285
Problem Statement
I have a project that I've configured to run in R 4.3.3 in positron (though 4.5.0 is on my path as the default). In some portions of the logs, we detect 4.3.3 correctly, but in others (and critically when we call renv::status() and then block deploying if that's not clean), we are detecting 4.5.0 and so getting the library(s) wrong and incorrectly saying that there's a package mismatch.
Steps to Reproduce
Use an interpreter in Positron that is different from the default path.
And as a note if anyone else is running into this: I ran rig default 4.3-arm64 to get make that 4.3.3 executable on my path, and that let the deploy go through just fine.