error in n_references: arguments in ... must be passed by position, not name

[adugourd]

Hey Denes,

Since I updated my R packages to the latest versions, import_omnipath_enzsub isn't working anymore.

Here is the code i run to get the error

library(OmnipathR)

KSN <- import_omnipath_enzsub()

Here is the error:

Error in mutate():
ℹ In argument: n_references = ifelse(...).
Caused by error in map():
ℹ In index: 1.
Caused by error in .f():
! Arguments in ... must be passed by position, not name.
✖ Problematic argument:
• outsep = outsep

Here is my session infos:

R version 4.2.0 (2022-04-22)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] OmnipathR_3.7.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 pillar_1.8.1 compiler_4.2.0 cellranger_1.1.0 later_1.3.0 prettyunits_1.1.1 tools_4.2.0 progress_1.2.2
[9] bit_4.0.5 digest_0.6.31 evaluate_0.20 jsonlite_1.8.4 lifecycle_1.0.3 tibble_3.1.8 checkmate_2.1.0 pkgconfig_2.0.3
[17] rlang_1.0.6 igraph_1.3.5 cli_3.6.0 rstudioapi_0.14 yaml_2.3.7 curl_5.0.0 xfun_0.36 fastmap_1.1.0
[25] withr_2.5.0 stringr_1.5.0 xml2_1.3.3 knitr_1.42 dplyr_1.1.0 httr_1.4.4 generics_0.1.3 vctrs_0.5.2
[33] hms_1.1.2 rappdirs_0.3.3 bit64_4.0.5 tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.4 readxl_1.4.1
[41] vroom_1.6.1 rmarkdown_2.20 sessioninfo_1.2.2 tidyr_1.3.0 purrr_1.0.1 readr_2.1.3 tzdb_0.3.0 logger_0.2.2
[49] magrittr_2.0.3 htmltools_0.5.4 backports_1.4.1 ellipsis_0.3.2 rvest_1.0.3 utf8_1.2.2 stringi_1.7.12 crayon_1.5.2

Cheers,

Aurelien

[deeenes]

Hi Aurelien, Can you check if this is fixed in master now? Should be the same as #56

[adugourd]

It works now ! Thanks :)