I am trying to run some alternative splicing analysis for two biological triplicates using IsoformSwitchAnalyzeR (with a pipeline that worked before for me). But in the ImportRdata step the program keep returning this error in the import GTF step. I've searched in many forums but apparently nobody reported this error.

    <error/rlib_error_dots_nonempty>
Error in `dplyr::full_join()`:
! `...` must be empty.
✖ Problematic argument:
• all = TRUE
Run `rlang::last_trace()` to see where the error occurred.

and then 'rlang tracing' gives me this:

Backtrace:
     ▆
  1. └─IsoformSwitchAnalyzeR::importRdata(...)
  2.   ├─base::suppressWarnings(...)
  3.   │ └─base::withCallingHandlers(...)
  4.   └─IsoformSwitchAnalyzeR::importGTF(...)
  5.     ├─dplyr::full_join(...)
  6.     └─dplyr:::full_join.data.frame(...)
  7.       └─rlang::check_dots_empty0(...)
  8.         └─rlang::check_dots_empty(call = call)
  9.           └─rlang:::action_dots(...)
 10.             ├─base (local) try_dots(...)
 11.             └─rlang (local) action(...)

That is the commands I've used so far (the error stops in the importRdata part)

quants.df <- importIsoformExpression(parentDir=quants.dir, addIsofomIdAsColumn=TRUE)
design.df <- data.frame(sampleID=c("SRR1953775", "SRR1953776", "SRR1953777", "SRR1953778", "SRR1953779", "SRR19537710"), condition=c("Blood", "Blood", "Blood", "Lung", "Lung", "Lung"))

aSwitchlist <- importRdata(isoformCountMatrix=quants.df$counts, isoformRepExpression=quants.df$abundance, designMatrix=design.df, isoformExonAnnoation="/home/ramon/Documentos/PIBIC/eonSPE_altsplicing/coordinates_files/pteVam1.109.gtf", isoformNtFasta="/home/ramon/Documentos/PIBIC/eonSPE_altsplicing/coordinates_files/pteVam1.cdna.all.fa", fixStringTieAnnotationProblem=TRUE, showProgress=FALSE)

I was able to fix this issue by updating IsoformSwitchAnalyzeR to the latest version on Github (v. 2.01.13)