r-lib
error with bioconductor URL
Hi,
I get the following error when I try to use pak::pak(). It occured after I upgraded to R 4.4 and its for package that I try to download
I'm not trying to use bioconductor as my repo and not sure why it is looking for it
! error in pak subprocess
Caused by error in `download.file(url, tmp, quiet = TRUE)`:
! cannot open URL 'http://bioconductor.org/config.yaml'
session info below
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C LC_TIME=English_United States.utf8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] marquee_0.1.0 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] gtable_0.3.5 compiler_4.4.0 tidyselect_1.2.1 systemfonts_1.1.0 scales_1.3.0 textshaping_0.4.0 R6_2.5.1 pak_0.7.2 labeling_0.4.3 generics_0.1.3 munsell_0.5.1 pillar_1.9.0
[13] tzdb_0.4.0 rlang_1.1.4 utf8_1.2.4 stringi_1.8.4 timechange_0.3.0 cli_3.6.2 withr_3.0.0 magrittr_2.0.3 grid_4.4.0 rstudioapi_0.16.0 hms_1.1.3 lifecycle_1.0.4
[25] vctrs_0.6.5 glue_1.7.0 farver_2.1.2 fansi_1.0.6 colorspace_2.1-0 tools_4.4.0 pkgconfig_2.0.3
Can you access that URL from R?
Sorry for delay.
When I use the httr package I get the below screen shot results
I'm facing the same issue.
While there may be more to this, I think the issue might be that:
- the bioconductor URL in pak uses
httpinstead ofhttps. - some (enterprise) networks may filter out requests to URLs that use
http
In any case, I notice that pak fails when corporate VPN is enabled and succeeds when VPN is disabled.
#> r$> pak::pak("gt")
Error:
! error in pak subprocess
Caused by error in `download.file(url, tmp, quiet = TRUE)`:
! cannot open URL 'http://bioconductor.org/config.yaml'
Type .Last.error to see the more details.
#> r$> .Last.error
<callr_error/rlib_error_3_0/rlib_error/error>
Error:
! error in pak subprocess
Caused by error in `download.file(url, tmp, quiet = TRUE)`:
! cannot open URL 'http://bioconductor.org/config.yaml'
---
Backtrace:
1. pak::pak("gt")
2. pak::pkg_install(pkg, ...)
3. pak:::remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...), ..4. err$throw(res$error)
---
Subprocess backtrace:
1. base::withCallingHandlers(cli_message = function(msg) { ...
2. get("pkg_install_make_plan", asNamespace("pak"))(...)
3. pkgdepends::new_pkg_installation_proposal(pkg, config = list(library = lib, ...
4. pkg_installation_proposal$new(refs, config = config, ...)
5. local initialize(...)
6. pkg_plan$new(refs, config = config, library = config$library, ...
7. local initialize(...)
8. pkgdepends:::pkgplan_init(self, private, refs, config, library, remote_types, ...
9. pkgcache::cranlike_metadata_cache$new(replica_path = private$config$get("metada...
10. local initialize(...)
11. pkgcache:::cmc_init(self, private, primary_path, replica_path, platforms, ...
12. pkgcache:::cmc__get_repos(repos, bioc, cran_mirror, r_version)
13. bioconductor$get_repos()
14. local get_bioc_version(getRversion(), forget)
15. local get_matching_bioc_version(r_version, forget = forget)
16. local get_version_map(forget = forget)
17. local get_yaml_config(forget)
18. base::stop(new)
19. global (function (e) ...
#> r$> # disabling VPN, which filters out requests to sites with http
#> r$> pak::pak("gt")
✔ Updated metadata database: 1.42 MB in 2 files.
✔ Updating metadata database ... done
When I try the bioconductor URL in the web browser (even while VPN is enabled)--that is, copy-paste the bioconductor URL from the pak error message--I seem to get redirected to the bioconductor URL that uses https. I'm guessing that the request sent through pak doesn't follow redirects.
I am also getting this error with pak::local_install(), when building a package.
It seems to be random, and usually works when I build the package again a few seconds later.
Could it be the bioconductor server that is unstable?
I have no dependencies from bioconductor.
Why does pak::local_install() even try to access the bioconductor server?
pak::local_install(upgrade = FALSE)
Error:
! error in pak subprocess
Caused by error in `download.file(url, tmp, quiet = TRUE)`:
! cannot open URL 'http://bioconductor.org/config.yaml'
---
Backtrace:
1. pak::local_install(upgrade = FALSE)
2. pak:::remote(function(...) get("local_install_make_plan", asNamespace("pak"))(...…
3. err$throw(res$error)
---
Subprocess backtrace:
1. base::withCallingHandlers(cli_message = function(msg) { …
2. get("local_install_make_plan", asNamespace("pak"))(...)
3. pak:::pkg_install_make_plan(pkg, lib, upgrade, ask, start, dependencies, …
4. pkgdepends::new_pkg_installation_proposal(pkg, config = list(library = lib,…
5. pkg_installation_proposal$new(refs, config = config, ...)
6. local initialize(...)
7. pkg_plan$new(refs, config = config, library = config$library, …
8. local initialize(...)
9. pkgdepends:::pkgplan_init(self, private, refs, config, library, remote_types, …
10. pkgcache::cranlike_metadata_cache$new(replica_path = private$config$get("me…
11. local initialize(...)
12. pkgcache:::cmc_init(self, private, primary_path, replica_path, platforms, …
13. pkgcache:::cmc__get_repos(repos, bioc, cran_mirror, r_version, auth = FALSE)
14. bioconductor$get_repos()
15. local get_bioc_version(getRversion(), forget)
16. local get_matching_bioc_version(r_version, forget = forget)
17. local get_version_map(forget = forget)
18. local get_yaml_config(forget)
19. base::stop(new)
20. global (function (e) …
Execution halted
