gabora
commented
2 years ago Dear Emanuele,
thanks for contacting. Based on your error report, R could not launch the CBC solver: note the 4th line from the bottom:
sh: cbc/cbc: Permission denied
if CBC was launched, then no results were generated, which led to the final error.
honestly, I haven't seen this issue before, but it might be easily solved by changing the file permissions, e.g. following this link: https://www.educative.io/answers/how-to-resolve-the-permission-denied-error-in-linux
best, Attila
I'm using the runInverseCarnival function on my RNAseq data using the output of dorothea as measurements (217 TFs, tried also with 50), the output of progeny as weights and the omnipath interactome (sif, processed as suggested in the tutorial). I've set the Carnival options as follows:
carnivalOptions <- defaultCbcSolveCarnivalOptions() carnivalOptions$solverPath <- "cbc/cbc" carnivalOptions$threads <- 15 carnivalOptions$timelimit <- 3600*0.5 carnivalOptions$keepLPFiles <- FALSE checkOptionsValidity(solver = "cbc")
dir.create("CBC_Carnival", showWarnings = FALSE) carnivalOptions$outputFolder <- "CBC_Carnival"
and am calling the function like so: resultCarnival <- runInverseCarnival( measurements = measurements, priorKnowledgeNetwork = sif, weights = weights, carnivalOptions = carnivalOptions )
I'm getting the following error, and I'm not sure if it's an issue with something I'm doing or with accessing cbc
--- Start of the CARNIVAL pipeline --- 10:27:35 11.07.2022 Carnival flavour: inverse Perturbations are not provided, all parents nodes are added as potential perturbations. Warning in checkMeasurements(measurements, nodesPriorKnowledgeNetwork) : These measurement nodes are not in prior knowledge network and will be ignored: TFAP2C | ZNF263 | PRDM14 | ZNF384 | ZBTB7A | PBX2 | ZFX | CTCFL | SNAI2 | ZKSCAN1 | FOXP1 Warning in checkWeights(weights, nodesPriorKnowledgeNetwork) : These nodes are not in prior knowledge network and will be ignored: P53 10:27:35 11.07.2022 Generating variables for lp problem 10:27:35 11.07.2022 Done: generating variables for lp problem Saving preprocessed data. Done: saving parsed data: CBC_Carnival//parsedData_t10_27_35d11_07_2022n93.RData 10:27:35 11.07.2022 Generating formulation for LP problem 10:27:47 11.07.2022 Done: generating formulation for LP problem. Saving LP file Done: Saving LP file: CBC_Carnival//lpFile_t10_27_35d11_07_2022n93.lp 10:28:01 11.07.2022 Solving LP problem sh: cbc/cbc: Permission denied Warning in file(file, "rt") : cannot open file 'CBC_Carnival//result_t10_27_35d11_07_2022n93.csv': No such file or directory Error in file(file, "rt") : cannot open the connection
Can you please help?
Thanks,
Emanuele