Last updated on 2020-08-07 01:50:28 CEST.
| Package | ERROR | OK |
|---|---|---|
| biocompute | 12 | |
| tidycwl | 1 | 11 |
Current CRAN status: OK: 12
Current CRAN status: ERROR: 1, OK: 11
Version: 1.0.4
Check: examples
Result: ERROR
Running examples in 'tidycwl-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_edges
> ### Title: Get edges in a CWL workflow into a data frame
> ### Aliases: get_edges
>
> ### ** Examples
>
> # edges represented by a dictionary
> flow <- system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>% read_cwl_json()
> get_edges(
+ flow %>% parse_outputs(),
+ flow %>% parse_steps()
+ ) %>% str()
'data.frame': 62 obs. of 5 variables:
$ from : chr "Salmon_Quant___Reads" "Salmon_Quant___Reads" "reads" "max_number_of_parallel_jobs" ...
$ to : chr "SBG_Create_Expression_Matrix___Transcripts" "SBG_Create_Expression_Matrix___Genes" "SBG_Pair_FASTQs_by_Metadata_1" "SBG_Pair_FASTQs_by_Metadata_1" ...
$ port_from: chr "quant_sf" "quant_genes_sf" NA NA ...
$ port_to : chr NA NA NA NA ...
$ type : chr "step_to_step" "step_to_step" "input_to_step" "input_to_step" ...
>
> # edges represented by a list
> flow <- system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>% read_cwl_yaml()
Warning in readLines(file) :
invalid input found on input connection '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/tidycwl/cwl/sbg/workflow/rnaseq-salmon.cwl'
Warning in readLines(file) :
incomplete final line found on '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/tidycwl/cwl/sbg/workflow/rnaseq-salmon.cwl'
> get_edges(
+ flow %>% parse_outputs(),
+ flow %>% parse_steps()
+ ) %>% str()
Error in obj[sapply(obj, is.null)] <- NA : invalid subscript type 'list'
Calls: %>% ... get_el_from_list -> sapply -> lapply -> get_el_from_list
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang