no package 'macos' was found

[abduazizR]

I keep getting this warning message in R console and I am not sure if there is an R package called macos that I need to install

Warning messages:
1: In utils::packageDescription(package, fields = "Version") :
  no package 'macos' was found
2: In utils::packageDescription(package, fields = "Version") :
  no package 'macos' was found

Session Info

─ Session info ─────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       macOS Sonoma 14.5
 system   aarch64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Chicago
 date     2024-07-01
 pandoc   NA

─ Packages ─────────────────────────────────────────────────────────
 ! package            * version date (UTC) lib source
   abind                1.4-5   2016-07-21 [1] RSPM (R 4.4.0)
 P arrow              * 16.1.0  2024-05-25 [?] RSPM
 P assertthat           0.2.1   2019-03-21 [?] RSPM
 P backports            1.5.0   2024-05-23 [?] RSPM
 P base64enc            0.1-3   2015-07-28 [?] RSPM
   binman               0.1.3   2022-09-01 [1] RSPM (R 4.4.0)
 P BiocManager          1.30.23 2024-05-04 [?] RSPM
 P bit                  4.0.5   2022-11-15 [?] RSPM
 P bit64                4.0.5   2020-08-30 [?] RSPM
 P bitops               1.0-7   2021-04-24 [?] RSPM
 P broom                1.0.6   2024-05-17 [?] RSPM
 P broom.helpers        1.15.0  2024-04-05 [?] RSPM
   car                  3.1-2   2023-03-30 [1] RSPM (R 4.4.0)
   carData              3.0-5   2022-01-06 [1] RSPM (R 4.4.0)
   caTools              1.18.2  2021-03-28 [1] RSPM (R 4.4.0)
 P cellranger           1.1.0   2016-07-27 [?] RSPM
   cli                  3.6.2   2023-12-11 [1] RSPM (R 4.4.0)
 P clipr                0.8.0   2022-02-22 [?] RSPM
   colorspace           2.1-0   2023-01-23 [1] RSPM (R 4.4.0)
   countrycode          1.6.0   2024-03-22 [1] RSPM (R 4.4.0)
   ctrdata            * 1.19.0  2024-06-30 [1] RSPM (R 4.4.0)
   curl                 5.2.1   2024-03-01 [1] RSPM (R 4.4.0)
 P data.table           1.15.4  2024-03-30 [?] RSPM
 P DBI                * 1.2.3   2024-06-02 [?] RSPM
 P digest               0.6.35  2024-03-11 [?] RSPM
   dplyr              * 1.1.4   2023-11-17 [1] RSPM (R 4.4.0)
 P duckdb             * 1.0.0   2024-06-13 [?] RSPM
 P evaluate             0.24.0  2024-06-10 [?] RSPM
   fansi                1.0.6   2023-12-08 [1] RSPM (R 4.4.0)
   fastDummies        * 1.7.3   2023-07-06 [1] RSPM (R 4.4.0)
 P fastmap              1.2.0   2024-05-15 [?] RSPM
 P forcats            * 1.0.0   2023-01-29 [?] RSPM
   generics             0.1.3   2022-07-05 [1] RSPM (R 4.4.0)
   ggplot2            * 3.5.1   2024-04-23 [1] RSPM (R 4.4.0)
   glue               * 1.7.0   2024-01-09 [1] RSPM (R 4.4.0)
 P gt                   0.10.1  2024-01-17 [?] RSPM
   gtable               0.3.5   2024-04-22 [1] RSPM (R 4.4.0)
 P gtsummary          * 1.7.2   2023-07-15 [?] RSPM
 P here               * 1.0.1   2020-12-13 [?] RSPM
 P highr                0.11    2024-05-26 [?] RSPM
 P hms                  1.1.3   2023-03-21 [?] RSPM
 P htmltools            0.5.8.1 2024-04-04 [?] RSPM
 P httr                 1.4.7   2023-08-15 [?] RSPM
 P httr2              * 1.0.1   2024-04-01 [?] RSPM
 P janitor            * 2.2.0   2023-02-02 [?] RSPM
   jqr                  1.3.3   2023-12-04 [1] RSPM (R 4.4.0)
 P jsonlite             1.8.8   2023-12-04 [?] RSPM
 P knitr                1.47    2024-05-29 [?] RSPM
 P lattice              0.22-6  2024-03-20 [?] CRAN (R 4.4.1)
 P lazyeval             0.2.2   2019-03-15 [?] RSPM
   lifecycle            1.0.4   2023-11-07 [1] RSPM (R 4.4.0)
   lubridate          * 1.9.3   2023-09-27 [1] RSPM (R 4.4.0)
   magrittr             2.0.3   2022-03-30 [1] RSPM (R 4.4.0)
   munsell              0.5.1   2024-04-01 [1] RSPM (R 4.4.0)
   netstat            * 0.1.2   2022-08-28 [1] RSPM (R 4.4.0)
 P nlme                 3.1-164 2023-11-27 [?] CRAN (R 4.4.1)
   nodbi              * 0.10.5  2024-06-30 [1] RSPM (R 4.4.0)
 P pacman               0.5.1   2019-03-11 [?] RSPM
   pillar               1.9.0   2023-03-22 [1] RSPM (R 4.4.0)
   pkgconfig            2.0.3   2019-09-22 [1] RSPM (R 4.4.0)
 P processx             3.8.4   2024-03-16 [?] RSPM
 P ps                   1.7.6   2024-01-18 [?] RSPM
   purrr              * 1.0.2   2023-08-10 [1] RSPM (R 4.4.0)
   R.methodsS3          1.8.2   2022-06-13 [1] RSPM (R 4.4.0)
   R.oo                 1.26.0  2024-01-24 [1] RSPM (R 4.4.0)
   R.utils              2.12.3  2023-11-18 [1] RSPM (R 4.4.0)
   R6                   2.5.1   2021-08-19 [1] RSPM (R 4.4.0)
 P rappdirs             0.3.3   2021-01-31 [?] RSPM
   Rcpp                 1.0.12  2024-01-09 [1] RSPM (R 4.4.0)
 P readr              * 2.1.5   2024-01-10 [?] RSPM
 P readxl               1.4.3   2023-07-06 [?] RSPM
   renv                 1.0.7   2024-04-11 [1] RSPM (R 4.4.0)
   repr                 1.1.7   2024-03-22 [1] RSPM (R 4.4.0)
   rlang                1.1.4   2024-06-04 [1] RSPM (R 4.4.0)
 P RPostgreSQL        * 0.7-6   2024-01-11 [?] RSPM
 P rprojroot            2.0.4   2023-11-05 [?] RSPM
   RSelenium          * 1.7.9   2022-09-02 [1] RSPM (R 4.4.0)
   rstatix            * 0.7.2   2023-02-01 [1] RSPM (R 4.4.0)
 P RVerbalExpressions * 0.1.1   2024-03-20 [?] RSPM
 P rvest              * 1.0.4   2024-02-12 [?] RSPM
   scales               1.3.0   2023-11-28 [1] RSPM (R 4.4.0)
 P selectr              0.4-2   2019-11-20 [?] RSPM
   semver               0.2.0   2017-01-06 [1] RSPM (R 4.4.0)
 P sessioninfo          1.2.2   2021-12-06 [?] RSPM
   skimr              * 2.1.5   2022-12-23 [1] RSPM (R 4.4.0)
 P snakecase            0.11.1  2023-08-27 [?] RSPM
   stringi              1.8.4   2024-05-06 [1] RSPM (R 4.4.0)
   stringr            * 1.5.1   2023-11-14 [1] RSPM (R 4.4.0)
   tibble             * 3.2.1   2023-03-20 [1] RSPM (R 4.4.0)
   tidyr              * 1.3.1   2024-01-24 [1] RSPM (R 4.4.0)
   tidyselect           1.2.1   2024-03-11 [1] RSPM (R 4.4.0)
 P tidyverse          * 2.0.0   2023-02-22 [?] RSPM
   timechange           0.3.0   2024-01-18 [1] RSPM (R 4.4.0)
 P tzdb                 0.4.0   2023-05-12 [?] RSPM
   utf8                 1.2.4   2023-10-22 [1] RSPM (R 4.4.0)
 P V8                   4.4.2   2024-02-15 [?] RSPM
   vctrs                0.6.5   2023-12-01 [1] RSPM (R 4.4.0)
 P waldo              * 0.5.2   2023-11-02 [?] RSPM
   wdman              * 0.2.6   2022-09-01 [1] RSPM (R 4.4.0)
   withr                3.0.0   2024-01-16 [1] RSPM (R 4.4.0)
   xfun                 0.45    2024-06-16 [1] RSPM (R 4.4.0)
   xml2                 1.3.6   2023-12-04 [1] RSPM (R 4.4.0)
 P yaml                 2.3.8   2023-12-11 [?] RSPM
 P zip                  2.3.1   2024-01-27 [?] RSPM

 [1] /Users/abdullah/Dissertation/dissertation_work/renv/library/macos/R-4.4/aarch64-apple-darwin20
 [2] /Users/abdullah/Library/Caches/org.R-project.R/R/renv/sandbox/macos/R-4.4/aarch64-apple-darwin20/f7156815

 P ── Loaded and on-disk path mismatch.

────────────────────────────────────────────────────────────────────

[jennybc]

I've never seen this. Do you have any "interesting" startup files? Meaning: site or user-level or project-specific .Rprofile or similar.

[jennybc]

Oh, yeah, I see this is an renv project. Can you reproduce this warning outside of Positron?

[DavisVaughan]

This renv vignette on "renv in packages"
https://github.com/rstudio/renv/blob/1f99d7d8ce7829fa67f3295f5a447e3df09c7a38/vignettes/packages.Rmd#L75

has this

For package projects using renv, a library path outside of the project
directory will be used instead. As an example, on macOS, this might look like:

```
> .libPaths()
[1] "/Users/kevin/Library/Caches/org.R-project.R/R/renv/library/example-552f6e80/R-4.3/aarch64-apple-darwin20"
[2] "/Users/kevin/Library/Caches/org.R-project.R/R/renv/sandbox/R-4.3/aarch64-apple-darwin20/ac5c2659"
```

Note the example-552f6e80 in the place where macos is above in the session info output

 [1] /Users/abdullah/Dissertation/dissertation_work/renv/library/macos/R-4.4/aarch64-apple-darwin20
 [2] /Users/abdullah/Library/Caches/org.R-project.R/R/renv/sandbox/macos/R-4.4/aarch64-apple-darwin20/f7156815

that certainly seems like a place to start. Possibly this issue only comes up when using renv in an R package

[DavisVaughan]

It seems like the addition of the macos/ bit is relatively new, from here:
rstudio/renv@a65b13f

[jennybc]

I wonder @kevinushey will immediately spot the problem.

[DavisVaughan]

@abduazizR if there is anything else you can provide (like a video) of what you were doing when this warning popped up, that would be helpful.

I've got R 4.5.0 along with the latest renv in an renv project and don't see these warnings

> .libPaths()
[1] "/Users/davis/Desktop/posit-user-training/renv/library/macos/R-4.5-r86792/aarch64-apple-darwin20"              
[2] "/Users/davis/Library/Caches/org.R-project.R/R/renv/sandbox/macos/R-4.5-r86792/aarch64-apple-darwin20/4cd76b74"

[abduazizR]

I tried working the last couple of days running different things to get the message but I don't get it anymore for some reason! I will post it if I see it gain

[jennybc]

I'm going to optimistically chalk this up to some unhappy renv state that you have successfully worked through 🤞

[baslat]

I'm getting this warning too. Also on a renv project, but not a package. R 4.4.1. Typically use VSCode, but trying out positron. Haven't seen the warning before in VSC. Seems to happen fairly regularly when I run tar_load() (but not always). I'll keep playing around.

[juliasilge]

@baslat If you are able to come up with a clear example where this happens for you, we would be super appreciative!

[baslat]

No luck getting it reproducible yet, but I can confirm that the {rlang} functions below don't capture the warning.

rlang::global_entrace()
options(rlang_backtrace_on_warning_report = "full")

# do something to make the warning appear

rlang::last_warnings() # shows nothing
last.warning # shows the 'macos' warning

[VLucet]

I'm getting something similar, while using renv and targets in conjunction with positron (latest build as of writing). It seems to happen when using tab completion... I am not able to isolate this either.

In utils::packageDescription(package, fields = "Version") :
  no package 'linux-pop-jammy' was found

[DavisVaughan]

If you can get it to reliably reproduce, then you could try:

• Setting options(warn = 2) at the beginning of your R session
• Triggering the issue, which should error now
• Run traceback() and report everything you see

It is possible that could help us

[VLucet]

@DavisVaughan I have been trying to set options(warn = 2) to catch that error. I must have tried a dozen time, either setting the option when I start my session, or half-way through it when I see the warning pop up. It feels like whenever I change the option, the behavior also disappears. I know that sounds odd but it is really what it seems.

[kevinushey]

I wonder if this would help identify the issue:

trace(utils::packageDescription, quote({
   if (identical(pkg, "macos")) {
      print(rlang::trace_back())
   }
}))

(replace "macos" with "linux-pop-jammy" as appropriate)

[kevinushey]

Sorry, I should clarify. After running that code, you need to then try to trigger the unexpected warning messages again; if the warning occurs, you should also hopefully get an R backtrace printed to the console.

[VLucet]

Here is an example of what gets printed:

Tracing utils::packageDescription(package, fields = "Version") on entry 
    ▆
 1. └─.ps.help.getHtmlHelpContents(topic = "mutate")
 2.   └─getHtmlHelpContentsInstalled(helpFiles, package)
 3.     └─tools::Rd2HTML(rd, out = htmlFile, package = package)
 4.       └─utils::packageDescription(package, fields = "Version")
Warning in utils::packageDescription(package, fields = "Version") :
  no package 'linux-pop-jammy' was found

[DavisVaughan]

Oh that's super helpful @VLucet thanks!

It looks like we are somehow extracting the wrong package here
https://github.com/posit-dev/ark/blob/70552b8664708b682df52f29116d61decc745775/crates/ark/src/modules/positron/help.R#L142-L149

Note that we are looking for a pattern like "/library/([^/]+)/" and renv does seem to create a libpath like that

> .libPaths()
[1] "/Users/davis/Desktop/posit-user-training/renv/library/macos/R-4.5-r86792/aarch64-apple-darwin20"

And the match there would indeed be macos

---

So it looks like we need to reinvestigate how .ps.help.getHtmlHelpContents(topic = "mutate") can get triggered (probably help on hover or something) and then refresh ourselves with what the helpFile path looks like to see if there is a more robust way to get at the package name.

Maybe we can follow the same heuristics as utils:::.getHelpFile()? We call it in getHtmlHelpContentsInstalled() with helpFile and it does this, which locates the package name and presumably works?

> utils:::.getHelpFile
function (file) 
{
    path <- dirname(file)
    dirpath <- dirname(path)
    if (!file.exists(dirpath)) 
        stop(gettextf("invalid %s argument", sQuote("file")), 
            domain = NA)
    pkgname <- basename(dirpath)
    RdDB <- file.path(path, pkgname)
    if (!file.exists(paste0(RdDB, ".rdx"))) 
        stop(gettextf("package %s exists but was not installed under R >= 2.10.0 so help cannot be accessed", 
            sQuote(pkgname)), domain = NA)
    tools:::fetchRdDB(RdDB, basename(file))
}

[blairj09]

FWIW I'm also seeing this (the macos flavor)

[whipson]

I'm seeing this too in an renv project on R 4.4.1:

Warning message:
In utils::packageDescription(package, fields = "Version") :
  no package 'macos' was found

[DavisVaughan]

QA - See this note about a reliable way to reproduce the original issue posit-dev/ark#537 (comment)

[jonvanausdeln]

Verified Fixed

Positron Version(s) : 2024.09.0-95
OS Version(s) : MacOS 14

Test scenario(s)

Using repro steps provided, works as expected.

Link(s) to TestRail test cases run or created: