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no package 'macos' was found
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.
────────────────────────────────────────────────────────────────────
I've never seen this. Do you have any "interesting" startup files? Meaning: site or user-level or project-specific .Rprofile or similar.
Oh, yeah, I see this is an renv project. Can you reproduce this warning outside of Positron?
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
It seems like the addition of the macos/ bit is relatively new, from here:
https://github.com/rstudio/renv/commit/a65b13f558fc38e24e8309a935f577d946e488d9
@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"
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
I'm going to optimistically chalk this up to some unhappy renv state that you have successfully worked through 🤞
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.
@baslat If you are able to come up with a clear example where this happens for you, we would be super appreciative!
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
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
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
@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.
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)
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.
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
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))
}
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
QA - See this note about a reliable way to reproduce the original issue https://github.com/posit-dev/ark/pull/537#issuecomment-2359247039
Verified Fixed
Positron Version(s) : 2024.09.0-95 OS Version(s) : MacOS 14
Test scenario(s)
Using repro steps provided, works as expected.
