`importBugSigDB` function returns error

[npechl]

Context

Hi, I tried to import the complete collection of curated signatures from BugSigDB (importBugSigDB function) and I am getting the following error:

> library(bugsigdbr)
> 
> 
> bsdb <- importBugSigDB(cache = FALSE)
Error in `collect()`:
! Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
Run `rlang::last_trace()` to see where the error occurred.

After some googling I found that this might be relevant to Error: ! Failed to collect lazy table. Caused by error in db_collect() - using biomaRt package in R

Any suggestions? Is there anything wrong by my side? Thank you in advance!

R session information

> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.2 (2023-10-31 ucrt)
 os       Windows 11 x64 (build 22621)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       Europe/Athens
 date     2023-12-14
 rstudio  2023.06.1+524 Mountain Hydrangea (desktop)
 pandoc   NA

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 ! package       * version date (UTC) lib source
 V BiocFileCache   2.8.0   2023-12-14 [1] Github (Bioconductor/BiocFileCache@7b7c4d3) (on disk 2.11.1)
   BiocManager     1.30.22 2023-08-08 [1] CRAN (R 4.3.1)
   bit             4.0.5   2022-11-15 [1] CRAN (R 4.3.0)
   bit64           4.0.5   2020-08-30 [1] CRAN (R 4.3.0)
   blob            1.2.4   2023-03-17 [1] CRAN (R 4.3.0)
   bugsigdbr     * 1.6.6   2023-09-14 [1] Bioconductor
   cachem          1.0.8   2023-05-01 [1] CRAN (R 4.3.0)
   callr           3.7.3   2022-11-02 [1] CRAN (R 4.3.0)
   cli             3.6.2   2023-12-11 [1] CRAN (R 4.3.2)
   curl            5.2.0   2023-12-08 [1] CRAN (R 4.3.2)
   DBI             1.1.3   2022-06-18 [1] CRAN (R 4.3.0)
   dbplyr          2.4.0   2023-10-26 [1] CRAN (R 4.3.1)
   desc            1.4.3   2023-12-10 [1] CRAN (R 4.3.2)
   dplyr           1.1.4   2023-11-17 [1] CRAN (R 4.3.2)
   fansi           1.0.6   2023-12-08 [1] CRAN (R 4.3.2)
   fastmap         1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
   filelock        1.0.3   2023-12-11 [1] CRAN (R 4.3.2)
   generics        0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
   glue            1.6.2   2022-02-24 [1] CRAN (R 4.3.0)
   httr            1.4.7   2023-08-15 [1] CRAN (R 4.3.1)
   lifecycle       1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
   magrittr        2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
   memoise         2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
   pillar          1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
   pkgbuild        1.4.3   2023-12-10 [1] CRAN (R 4.3.2)
   pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
   processx        3.8.3   2023-12-10 [1] CRAN (R 4.3.2)
   ps              1.7.5   2023-04-18 [1] CRAN (R 4.3.0)
   purrr           1.0.2   2023-08-10 [1] CRAN (R 4.3.1)
   R6              2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
   remotes         2.4.2.1 2023-07-18 [1] CRAN (R 4.3.1)
   rlang           1.1.2   2023-11-04 [1] CRAN (R 4.3.2)
   RSQLite         2.3.4   2023-12-08 [1] CRAN (R 4.3.2)
   rstudioapi      0.15.0  2023-07-07 [1] CRAN (R 4.3.1)
   sessioninfo     1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
   tibble          3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
   tidyselect      1.2.0   2022-10-10 [1] CRAN (R 4.3.0)
   utf8            1.2.4   2023-10-22 [1] CRAN (R 4.3.1)
   vctrs           0.6.5   2023-12-01 [1] CRAN (R 4.3.2)

 V ── Loaded and on-disk version mismatch.

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

[lgeistlinger]

Can you upgrade to the latest version of bugsigdbr (1.8.1, you currently have 1.6.6) and try again?

https://bioconductor.org/packages/bugsigdbr

[npechl]

I tried re-installing bugsigdbr from Bioconductor but version 1.6.6 is installed (not 1.8.1). After installing the development version from the GitHub repo the functions seems to work properly:

> library(bugsigdbr)
> 
> 
> bsdb <- bugsigdbr::importBugSigDB()
  |================================================| 100%
Downloading: 500 kB   

Tnank you for your time! Should I close the issue?

[lgeistlinger]

Note that you can force a fresh installation from Bioconductor via:

BiocManager::install("bugsigdbr", force = TRUE)

Assuming you are working with Bioconductor 3.18 (check BiocManager::version()), this will bring in the latest release version of bugsigdbr (v1.8.1) from Bioconductor.