pak install fails when Bioconductor is inaccessible even if CRAN is

[Moohan]

Our corporate network is restrictive; for some reason, http://bioconductor.org/config.yaml seems inaccessible from RStudio. Unfortunately, this prevents pak from installing packages from CRAN, even if I specifically ask it to. This seems like a bug.

pak::pak()
#> Error: ! error in pak subprocess
#> Caused by error in `find_package_root(path = root)`:
#> ! Could not find R package in `.` or its parent directories.

pak::pak("testthat")
#> Error: ! error in pak subprocess
#> Caused by error in `download.file(url, tmp, quiet = TRUE)`:
#> ! cannot open URL 'http://bioconductor.org/config.yaml'

pak::pak("cran::testthat")
#> Error: ! error in pak subprocess
#> Caused by error in `download.file(url, tmp, quiet = TRUE)`:
#> ! cannot open URL 'http://bioconductor.org/config.yaml'

install.packages("testthat")
#> Installing package into 'C:/Users/USER/AppData/Local/R/win-library/4.4'
#> (as 'lib' is unspecified)
#> also installing the dependencies 'pkgbuild', 'diffobj', 'brio', 'pkgload', 'praise', 'waldo'
#> 
#>   There is a binary version available but the source version is later:
#>           binary source needs_compilation
#> testthat 3.2.1.1  3.2.2              TRUE
#> 
#> package 'pkgbuild' successfully unpacked and MD5 sums checked
#> package 'diffobj' successfully unpacked and MD5 sums checked
#> package 'brio' successfully unpacked and MD5 sums checked
#> package 'pkgload' successfully unpacked and MD5 sums checked
#> package 'praise' successfully unpacked and MD5 sums checked
#> package 'waldo' successfully unpacked and MD5 sums checked
#> 
#> The downloaded binary packages are in
#>  C:\Users\USER\AppData\Local\Temp\RtmpkRdhAE\downloaded_packages
#> installing the source package 'testthat'

^{Created on 2024-12-17 with reprex v2.1.1}

The expected behaviour would maybe be a warning / message about the unavailability of Bioconductor, and no message at all if a package is specified as cran::package.

[gaborcsardi]

Did you try to turn off the Bioc support in pak?

[Moohan]

I did a Google to try and do that, but didn't find it obviously.

[gaborcsardi]

See https://pak.r-lib.org/reference/pak-config.html

[Moohan]

If I do options(pkg.use_bioconductor = FALSE) I get the same error when trying pak::pak. Weirdly if I try a reprex it gives a different error though...

options(pkg.use_bioconductor = FALSE)
pak::pak()
#> Error: ! error in pak subprocess
#> Caused by error in `find_package_root(path = root)`:
#> ! Could not find R package in `.` or its parent directories.

^{Created on 2024-12-17 with reprex v2.1.1}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.1 (2024-06-14 ucrt)
#>  os       Windows 10 x64 (build 19045)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  English_United Kingdom.utf8
#>  ctype    English_United Kingdom.utf8
#>  tz       Europe/London
#>  date     2024-12-17
#>  pandoc   3.1.11 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  cli           3.6.3   2024-06-21 [1] CRAN (R 4.4.2)
#>  digest        0.6.37  2024-08-19 [1] CRAN (R 4.4.2)
#>  evaluate      1.0.1   2024-10-10 [1] CRAN (R 4.4.2)
#>  fastmap       1.2.0   2024-05-15 [1] CRAN (R 4.4.2)
#>  fs            1.6.5   2024-10-30 [1] CRAN (R 4.4.2)
#>  glue          1.8.0   2024-09-30 [1] CRAN (R 4.4.2)
#>  htmltools     0.5.8.1 2024-04-04 [1] CRAN (R 4.4.2)
#>  knitr         1.49    2024-11-08 [1] CRAN (R 4.4.2)
#>  lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.4.2)
#>  pak           0.8.0   2024-08-26 [1] CRAN (R 4.4.2)
#>  reprex        2.1.1   2024-07-06 [1] RSPM (R 4.4.0)
#>  rlang         1.1.4   2024-06-04 [1] CRAN (R 4.4.2)
#>  rmarkdown     2.29    2024-11-04 [1] CRAN (R 4.4.2)
#>  rstudioapi    0.17.1  2024-10-22 [1] CRAN (R 4.4.2)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.4.2)
#>  withr         3.0.2   2024-10-28 [1] CRAN (R 4.4.2)
#>  xfun          0.49    2024-10-31 [1] CRAN (R 4.4.2)
#>  yaml          2.3.10  2024-07-26 [1] CRAN (R 4.4.1)
#> 
#>  [1] C:/Users/USER/AppData/Local/R/win-library/4.4
#>  [2] C:/Program Files/R/R-4.4.1/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

and

options(pkg.use_bioconductor = FALSE)
pak::pak("testthat")
#> Error: ! error in pak subprocess
#> Caused by error in `download.file(url, tmp, quiet = TRUE)`:
#> ! cannot open URL 'http://bioconductor.org/config.yaml'

^{Created on 2024-12-17 with reprex v2.1.1}

[gaborcsardi]

Here is a workaround: #295 (comment)

[gaborcsardi]

With #696 use_bioconductor should work better, so that a good step towards fixing this.

[gaborcsardi]

Sorry for dropping the ball on this. Do you still have this issue?

[Moohan]

Our organisation has now allowed connections to bioconductor, so it's no longer an issue for us! I'm not sure how to 'mock' blocking a connection to test if it's still an issue in general though.

[janxkoci]

I'm not sure how to 'mock' blocking a connection

Just FYI that's a job for a firewall, you can install one on your machine and start blocking connections, ports, etc...