Question

FlowSOM error system.file()

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agus_rizzo • 0

@8d63a973

Last seen 11 months ago

Argentina

Hi, i m having trouble with the system.file() function. It gives me the following error.

Error in system.file("extdata", "Bue018 cfu normal 00000337 431", package = "FlowSOM", : no file found

I can´t understand why since i have set de directory correctly with setwd() function. Would someone help me please?

fileName <- system.file("extdata", "Bue018 cfu normal 00000337 431.LMD", package="FlowSOM", mustWork = TRUE)

FlowSOM • 589 views

ADD COMMENT • link updated 11 months ago by SamGG ▴ 350 • written 11 months ago by agus_rizzo • 0

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What is your sessionInfo()

The FlowSOM maintainers might have a better answer but currently those files are not included in the FlowSOM package extdata. setwd() wouldn't have any affect on a system.file call unless you generated these files and wrote them to that directory (which really isn't good practice). You also have spaces in the system.file call which I think would cause issues.

ADD REPLY • link 11 months ago shepherl 4.1k

score 0 · Answer 1 · 2023-11-22

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SamGG ▴ 350

@samgg-6428

Last seen 6 days ago

France/Marseille/Inserm

Your data file is in the working directory you specified. You don't need anything else.

fileName <- "Bue018 cfu normal 00000337 431.LMD"

The extra code you copied from the vignette (I guess) aims to locate a demo file that resides in the FlowSOM package, which is not your case.

Best.

ADD COMMENT • link 11 months ago SamGG ▴ 350