Resolving very slow

[courtiol]

I am not sure why, but I cannot use pkgdepends or pak since the resolve ~never~ finishes only after a very long time on one of my computers (not on the others).

E.g.

pd <- new_pkg_deps("tibble")
pd$solve()

displays "Found 1 deps for 0/1 pkgs [⠏] Resolving standard (CRAN/BioC) packages" and get stuck there for many minutes. I did check my internet connection and I don't seem to have any issue with it. I do have my packages up to date (although not the latest R on this computer).

I am happy to run tests to clarify the situation if instructed.

sessioninfo::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.2 Patched (2022-11-10 r83330)
 os       Ubuntu 22.04.3 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Berlin
 date     2023-10-15
 rstudio  2023.09.0+463 Desert Sunflower (desktop)
 pandoc   NA

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version    date (UTC) lib source
 callr         3.7.3      2022-11-02 [1] CRAN (R 4.2.1)
 cli           3.6.1      2023-03-23 [1] CRAN (R 4.2.2)
 crayon        1.5.2      2022-09-29 [1] CRAN (R 4.2.1)
 curl          5.1.0      2023-10-02 [1] CRAN (R 4.2.2)
 desc          1.4.2      2022-09-08 [1] CRAN (R 4.2.1)
 fansi         1.0.5      2023-10-08 [1] CRAN (R 4.2.2)
 filelock      1.0.2      2018-10-05 [1] CRAN (R 4.2.2)
 glue          1.6.2      2022-02-24 [1] CRAN (R 4.2.0)
 jsonlite      1.8.7      2023-06-29 [1] CRAN (R 4.2.2)
 lifecycle     1.0.3      2022-10-07 [1] CRAN (R 4.2.1)
 lpSolve       5.6.19     2023-09-13 [1] CRAN (R 4.2.2)
 pillar        1.9.0      2023-03-22 [1] CRAN (R 4.2.2)
 pkgbuild      1.4.2      2023-06-26 [1] CRAN (R 4.2.2)
 pkgcache      2.2.0.1    2023-07-18 [1] CRAN (R 4.2.2)
 pkgdepends  * 0.6.0.9000 2023-10-15 [1] Github (r-lib/pkgdepends@9718c02)
 prettyunits   1.2.0      2023-09-24 [1] CRAN (R 4.2.2)
 processx      3.8.2      2023-06-30 [1] CRAN (R 4.2.2)
 ps            1.7.5      2023-04-18 [1] CRAN (R 4.2.2)
 R6            2.5.1      2021-08-19 [1] CRAN (R 4.2.0)
 rappdirs      0.3.3      2021-01-31 [1] CRAN (R 4.2.0)
 rlang         1.1.1      2023-04-28 [1] CRAN (R 4.2.2)
 rprojroot     2.0.3      2022-04-02 [1] CRAN (R 4.2.0)
 rstudioapi    0.15.0     2023-07-07 [1] CRAN (R 4.2.2)
 sessioninfo   1.2.2      2021-12-06 [1] CRAN (R 4.2.0)
 utf8          1.2.3      2023-01-31 [1] CRAN (R 4.2.2)
 vctrs         0.6.4      2023-10-12 [1] CRAN (R 4.2.2)
 zip           2.3.0      2023-04-17 [1] CRAN (R 4.2.2)

 [1] /home/courtiol/R/x86_64-pc-linux-gnu-library/4.2
 [2] /usr/local/lib/R/site-library
 [3] /usr/lib/R/site-library
 [4] /usr/lib/R/library

[gaborcsardi]

What is getOption("repos")?

[courtiol]

> getOption("repos")
                         CRAN 
"https://cloud.r-project.org" 

[courtiol]

OK, I did let it run for longer, and it does work but it takes many minutes, while on the other computers it is very fast.

[courtiol]

It is faster now, so perhaps it was a glitch of the network after all. I close and will reopen the issue only if it resurfaces. Sorry for the bother...

[courtiol]

FYI: I have problems with R CMD check too that may be related to the problem:

* checking CRAN incoming feasibility ...Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES'

This seems to be caused by me using R 4.2 which looks for bioconductor old addresses that no longer seem up and running.