CARNIVAL not running with demo datasets?

[anikaliu]

Hi FUNKI Team:)
I've just tried to run CARNIVAL with the contrast demo data and lpSolve, but it didn't generate any output. Do you have an idea what the problem could be?

Much thanks in advance!

Best,
Anika

Delimiter: ","
dbl (7): ID, logFC, AveExpr, t, P.Value, adj.P.Val, B

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
'select()' returned 1:1 mapping between keys and columns
[1] "153 identifiers could not be mapped to gene symbole."
[1] "0 genes have ambiguous maping to gene symbole and were removed."
 
--- Start of the CARNIVAL pipeline ---
12:20:31 10.03.2023 Carnival flavour: inverse
Perturbations are not provided, all parents nodes are added as potential perturbations.
12:20:31 10.03.2023 Generating variables for lp problem
12:20:31 10.03.2023 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: /home/liuanika/ShinyFUNKI/FUNKI//parsedData_t12_20_31d10_03_2023n94.RData
12:20:31 10.03.2023 Generating formulation for LP problem
12:20:31 10.03.2023 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: /home/liuanika/ShinyFUNKI/FUNKI//lpFile_t12_20_31d10_03_2023n94.lp
12:20:31 10.03.2023 Solving LP problem
Parsing .lp file for lpSolve
Rows: 388 Columns: 1                                                                                                                          
── Column specification ───────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (1): X1

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Done: parsing .lp file for lpSolve
12:20:31 10.03.2023 Done: solving LP problem.
12:20:31 10.03.2023 Getting the solution matrix
12:20:31 10.03.2023 Done: getting the solution matrix.
12:20:31 10.03.2023 Exporting solution matrix
12:20:31 10.03.2023 Done: exporting solution matrix.
Cleaning intermediate files
Done: cleaning
12:20:31 10.03.2023 All tasks finished.

--- End of the CARNIVAL pipeline --- 

Warning: Error in dplyr::mutate: ℹ In argument: `shape = dplyr::case_when(...)`.
Caused by error in `dplyr::case_when()`:
! Failed to evaluate the left-hand side of formula 1.
Caused by error:
! object 'NodeType' not found
  157: <Anonymous>
  156: signalCondition
  155: signal_abort
  154: abort
  153: <Anonymous>
  152: signalCondition
  151: signal_abort
  150: abort
  149: handlers[[1L]]
  148: h
  147: .handleSimpleError
  146: eval_tidy
  138: case_formula_evaluate
  137: dplyr::case_when
  136: eval
  135: mask$eval_all_mutate
  134: mutate_col
  132: mutate_cols
  131: mutate.data.frame
  130: dplyr::mutate
  129: dplyr::mutate
  128: dplyr::mutate
  127: dplyr::mutate
  126: dplyr::mutate
  125: dplyr::mutate
  124: dplyr::mutate
  104: %in%
  103: visNetwork::visIgraphLayout
  102: %in%
  101: visNetwork::visEdges
  100: %in%
   99: visNetwork::visLegend
   97: shinyRenderWidget [sub/06_server_carnival.R#317]
   96: func
   83: renderFunc
   82: output$network
    1: runApp
Input to asJSON(keep_vec_names=TRUE) is a named vector. In a future version of jsonlite, this option will not be supported, and named vectors will be translated into arrays instead of objects. If you want JSON object output, please use a named list instead. See ?toJSON.
Warning: Error in dplyr::mutate: ℹ In argument: `shape = dplyr::case_when(...)`.
Caused by error in `dplyr::case_when()`:
! Failed to evaluate the left-hand side of formula 1.
Caused by error:
! object 'NodeType' not found
  1: runApp
Warning: Error in dplyr::mutate: ℹ In argument: `shape = dplyr::case_when(...)`.
Caused by error in `dplyr::case_when()`:
! Failed to evaluate the left-hand side of formula 1.
Caused by error:
! object 'NodeType' not found
  1: runApp