Does {startup} work with positron?

[baslat]

The startup package doesn't seem to work with position. I use {startup} with VSC all the time without issue, however it doesn't work in positron (not even if I trigger it manually with startup::startup()). I wonder if this could be related to ark?

[HenrikBengtsson]

I'm not a user of Positron. Does the ordinary ~/.Rprofile startup script work? Please verify that first; if that doesn't work, then report that to the Positron issue tracker. Without it, startup cannot work.

[baslat]

Yes, the ordinary ~/.Rprofile script works. If I set it to startup::startup(debug = TRUE) it seems as though it's not finding the ~/.Rprofile.d folder

# Positron
0.004s: startup::startup()-specific processing ...
0.004s: Found 'startup' directory '~/.Renviron.d'.
0.009s: - unloading the 'startup' package

# VSCode
0.005s: startup::startup()-specific processing ...
0.005s: Found 'startup' directory '~/.Renviron.d'.
0.007s: Found 'startup' directory '~/.Rprofile.d'.
0.013s: Processing 11 Rprofile files ...

[HenrikBengtsson]

That's all the output?

0.007s: Found 'startup' directory '~/.Rprofile.d'.
0.013s: Processing 11 Rprofile files ...

It clearly finds the folder and it identifies 11 files there-in.

[HenrikBengtsson]

You can also try to call

startup::startup(debug = TRUE

from the Positron prompt and see what you get. If you get an error, what does traceback() report?

[baslat]

The VSCode output is an example of {startup} working as expected, in contrast to the output from Positron which doesn't seem to find the ~/.Rprofile.d folder.

Manually running startup::startup(debug = TRUE) in Positron doesn't throw an error, but doesn't load the expected behaviour, as it doesn't find the ~/.Rprofile.d folder (same behaviour as when running on startup in Positron).

Here are the full logs from Positron

> startup::startup(debug = TRUE)
0.000s: System information:
0.001s: - R_HOME: '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources' (existing folder)
0.001s: - R call: ark --interactive --no-restore-data --quiet --no-site-file --no-init-file
0.001s: - Current directory: '/Users/bas'
0.001s: - User's home directory: '~' => '/Users/bas' (existing folder)
0.002s: - User's 'startup' config directory: '/Users/bas/Library/Preferences/org.R-project.R/R/startup' (non-existing directory)
0.002s: - Search path: '.GlobalEnv', 'tools:rstudio', 'tools:positron', 'package:stats', 'package:graphics', 'package:grDevices', 'package:utils', 'package:datasets', 'package:methods', 'Autoloads', 'package:base'
0.002s: - Loaded namespaces: 'compiler', 'startup', 'graphics', 'tools', 'utils', 'grDevices', 'stats', 'datasets', 'methods', 'base'
0.002s: The following has already been processed by R:
0.002s: - R_ENVIRON: ''
0.002s: - R_ENVIRON_USER: ''
0.003s: - '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/etc/Renviron' (23 lines; 1989 bytes) setting 23 environment variables ('R_PLATFORM', 'R_PAPERSIZE_USER', 'R_PAPERSIZE', 'R_PRINTCMD', 'R_RD4PDF', 'R_TEXI2DVICMD', 'R_GZIPCMD', 'R_UNZIPCMD', 'R_ZIPCMD', 'R_BZIPCMD', 'R_BROWSER', 'EDITOR', 'PAGER', 'R_PDFVIEWER', 'LN_S', 'MAKE', 'SED', 'TAR', 'R_STRIP_SHARED_LIB', 'R_STRIP_STATIC_LIB', 'R_LIBS_USER', 'R_LIBS_SITE', 'R_QPDF')
0.004s: - '.Renviron' (24 lines; 1344 bytes) setting 24 environment variables (**MY-ENV-VARS**)
0.004s: - tempdir(): '/var/folders/22/ln8pw35953b4hggsldkqb7mm0000gp/T//Rtmp5VqSue' (existing folder)
0.004s:   - TMPDIR: ‘/var/folders/22/ln8pw35953b4hggsldkqb7mm0000gp/T/’
0.004s:   - TMP: ‘’
0.004s:   - TEMP: ‘’
0.004s: - R_LIBS: ''
0.004s: - R_LIBS_SITE: '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/site-library'
0.004s: - R_LIBS_USER: '/Users/bas/Library/R/arm64/4.4/library'
0.004s: - R_SCRIPT_DEFAULT_PACKAGES (only if Rscript was used): ''
0.005s: - R_DEFAULT_PACKAGES: '' (= 'base,methods,datasets,utils,grDevices,graphics,stats')
0.005s: - '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/base/R/Rprofile' (160 code lines; 7953 bytes)
0.005s: - R_PROFILE: ''
0.005s: - R_PROFILE_USER: ''
0.005s: startup::startup()-specific processing ...
0.006s: Found 'startup' directory '~/.Renviron.d'.
0.010s: - unloading the 'startup' package
0.010s: - Search path: '.GlobalEnv', 'tools:rstudio', 'tools:positron', 'package:stats', 'package:graphics', 'package:grDevices', 'package:utils', 'package:datasets', 'package:methods', 'Autoloads', 'package:base'
0.010s: - Loaded namespaces: 'compiler', 'graphics', 'tools', 'utils', 'grDevices', 'stats', 'datasets', 'methods', 'base'
0.010s: startup::startup()-specific processing ... done
0.010s: The following will be processed next by R:
0.010s: - R_HISTFILE: ''
0.010s: - .First(): no such function on search()
0.011s: - Remaining packages per R_DEFAULT_PACKAGES to be attached by base::.First.sys() (in order): 
0.011s: - The R just-in-time (JIT) compiler:
0.011s:   - R_ENABLE_JIT: <not set>
0.011s:   - JIT compiler enabled by default
0.011s: The following will be processed when R terminates:
0.011s: - .Last(): no such function on search()
0.011s: - .Last.sys(): no such function on search()

[HenrikBengtsson]

I think I've identified the reason, and it has to do with Positron launching R using:

ark --interactive --no-restore-data --quiet --no-site-file --no-init-file

Specifically, startup::startup() sees --no-site-file and --no-init-file and interpret those as the Rprofile scripts should not be processed. I don't understand why they use those command-line options, but maybe there's a good reason. Until that is better understood, you can update your ~/.Rprofile script to use:

startup::startup(skip = FALSE)

That tells startup() to ignore any --no-site-file and --no-init-file options.

[baslat]

I'll try that out. I also updated to the dev version of {startup} asI saw you made some commits and get this error:

.Rprofile error: could not find function "is_ark"

[HenrikBengtsson]

.Rprofile error: could not find function "is_ark"

Oops - forgot to add some new files to repo.

[baslat]

Nice, things seem to be working now, thanks!