CRAN Package Check Results for Package tidycwl

Last updated on 2020-02-27 18:50:15 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.4 5.46 42.55 48.01 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.4 4.51 36.19 40.70 OK
r-devel-linux-x86_64-fedora-clang 1.0.4 66.31 OK
r-devel-linux-x86_64-fedora-gcc 1.0.4 60.10 OK
r-devel-windows-ix86+x86_64 1.0.4 13.00 65.00 78.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.0.4 14.00 65.00 79.00 OK
r-patched-linux-x86_64 1.0.4 4.67 40.85 45.52 OK
r-patched-solaris-x86 1.0.4 81.80 OK
r-release-linux-x86_64 1.0.4 4.59 43.05 47.64 OK
r-release-windows-ix86+x86_64 1.0.4 10.00 65.00 75.00 OK
r-release-osx-x86_64 1.0.4 OK
r-oldrel-windows-ix86+x86_64 1.0.4 8.00 82.00 90.00 OK
r-oldrel-osx-x86_64 1.0.4 OK

Check Details

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