loading gdscdata

[smartinezzz]

Hello!

I am having trouble loading the gdscdata. Could you please assist me with this? Below is the error I receive.

Thank you!

Siera

devtools::install_github("cancerrxgene/gdscdata", build_vignettes=TRUE)
Using GitHub PAT from the git credential store.
Downloading GitHub repo cancerrxgene/gdscdata@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\g23706642\AppData\Local\Temp\1\RtmpQHWSMR\remotesb882c8b799\CancerRxGene-gdscdata-61dd771/DESCRIPTION' (542ms)
─ preparing 'gdscdata':
✔ checking DESCRIPTION meta-information ...
─ installing the package to build vignettes
E creating vignettes (1m 12.3s)
--- re-building 'gdsc_v17.Rmd' using rmarkdown
trying URL 'ftp://ftp.sanger.ac.uk/pub/project/cancerrxgene/releases/release-6.0/v17_fitted_dose_response.xlsx'
Content type 'unknown' length 11123758 bytes (10.6 MB)
==================================================

Quitting from gdsc_v17.Rmd:134-169 [compare results]

<error/dplyr:::mutate_error>
Error in `distinct()`:
ℹ In argument: `COSMIC_ID = CL`.
Caused by error:
! object 'CL' not found
---
Backtrace:
     ▆
  1. ├─... %>% nrow()
  2. ├─base::nrow(.)
  3. ├─generics::setdiff(...)
  4. ├─dplyr:::setdiff.data.frame(...)
  5. │ └─dplyr:::check_compatible(x, y)
  6. │   └─dplyr:::is_compatible(...)
  7. │     └─base::is.data.frame(y)
  8. ├─new_ic50s %>% distinct(COSMIC_ID = CL)
  9. ├─dplyr::distinct(., COSMIC_ID = CL)
 10. └─dplyr:::distinct.data.frame(., COSMIC_ID = CL)
 11.   └─dplyr::distinct_prepare(...)
 12.     └─dplyr:::add_computed_columns(.data, vars, error_call = error_call)
 13.       └─dplyr:::mutate_cols(...)
 14.         ├─base::withCallingHandlers(...)
 15.         └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 16.           └─mask$eval_all_mutate(quo)
 17.             └─dplyr (local) eval()

Error: processing vignette 'gdsc_v17.Rmd' failed with diagnostics:
ℹ In argument: COSMIC_ID = CL.
Caused by error:
! object 'CL' not found
--- failed re-building 'gdsc_v17.Rmd'

SUMMARY: processing the following file failed:
'gdsc_v17.Rmd'

Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'gdscdata' from GitHub:
! System command 'Rcmd.exe' failed