Missing arugument in PXDatatset

[KoppGergely]

I'm new to MS analysis, and was trying to follow the Bioconductor Vignette for your package. But I got an error quite at the beginning:

library(rpx)
id <- "PXD000001"
px <- PXDataset(id)

resulted in:

Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'bfcquery': 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?`

Do you have a suggestion on how to avoid this issue? Thank you!

Session info:

R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
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
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: Europe/Budapest
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rpx_2.8.0

loaded via a namespace (and not attached):
 [1] utf8_1.2.4          generics_0.1.3      tidyr_1.3.0         bitops_1.0-7        rstatix_0.7.2       xml2_1.3.5         
 [7] RSQLite_2.3.3       magrittr_2.0.3      grid_4.3.1          fastmap_1.1.1       blob_1.2.4          jsonlite_1.8.7     
[13] backports_1.4.1     DBI_1.1.3           BiocManager_1.30.22 httr_1.4.7          purrr_1.0.2         fansi_1.0.5        
[19] scales_1.3.0        abind_1.4-5         cli_3.6.1           rlang_1.1.2         dbplyr_2.4.0        bit64_4.0.5        
[25] munsell_0.5.0       cachem_1.0.8        tools_4.3.1         memoise_2.0.1       ggsignif_0.6.4      dplyr_1.1.4        
[31] colorspace_2.1-0    ggplot2_3.4.4       ggpubr_0.6.0        filelock_1.0.2      broom_1.0.5         curl_5.1.0         
[37] vctrs_0.6.4         R6_2.5.1            lifecycle_1.0.4     BiocFileCache_2.8.0 car_3.1-2           bit_4.0.5          
[43] pkgconfig_2.0.3     pillar_1.9.0        gtable_0.3.4        glue_1.6.2          tibble_3.2.1        tidyselect_1.2.0   
[49] rstudioapi_0.15.0   carData_3.0-5       compiler_4.3.1      RCurl_1.98-1.13  

[lgatto]

You have an old version - current is 2.10.0, but I don't necessarily think that is the reason.

I know that there were issues with an indirect dependency. My suggestion would be to update Bioconductor with BiocManager::install(version = "3.18") (I think your R version should support it) and try again. If it still doesn't work, I would suggest to post your issue on https://support.bioconductor.org/, where other users/developers might know what is happening under the hood (and feel free to tag the rols package as part of your question, so that I get a notification and can participate).

[KoppGergely]

Thank you, issue solved, I can reproduce th results in the vignette. All I needed was to update for Bioconductor 3.18.