Question

Running FlowSOM in R problem

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Václav • 0

@vaclav-24085

Last seen 4.1 years ago

Hello, I have just installed R 4.0.3 and every time I try to load the flowsom package I get just this?

local({pkg <- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE)

if(nchar(pkg)) library(pkg, character.only=TRUE)}) Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

decompose, spectrum

The following object is masked from ‘package:base’:

union

Does anyone have an idea what it means and how to fix that?

Thank you.

FlowSOM • 2.0k views

ADD COMMENT • link updated 4.1 years ago by sofie.vangassen ▴ 10 • written 4.1 years ago by Václav • 0

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Hi, I have just tried on my Windows setup, with R 4.0.3 and Bioc 3.12, and get only the attaching and masking message. Could you report the package versions as below and your OS?

 > BiocManager::version()
[1] ‘3.12’
> packageVersion("igraph")
[1] ‘1.2.6’
> packageVersion("FlowSOM")
[1] ‘1.22.0’

Best.

ADD REPLY • link 4.1 years ago SamGG ▴ 360

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Hi, thanks for your reply. I should have added the info at the first time:

BiocManager::version() [1] ‘3.12’ packageVersion("igraph") [1] ‘1.2.6’ packageVersion("FlowSOM") [1] ‘1.22.0’

I am using the R 4.0.3, too.

Cheers.

ADD REPLY • link 4.1 years ago Václav • 0

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Fine. What is you OS: Windows, Mac, Linux?

The 'local...igraph' is just a message in my opinion. Others messages are OK. Try to run a FlowSOM analysis and report its achievement or not.

Best

ADD REPLY • link 4.1 years ago SamGG ▴ 360

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I have a silly question...do I have to load the Flowsom package first in order to use it ?

I use Windows 10 btw.

Best.

ADD REPLY • link 4.1 years ago Václav • 0

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do I have to load the Flowsom package first in order to use it ?

Mainly yes. Calling library(FlowSOM) is the recommended way to use a package, especially if you are going to use many of its functions. If you load a a lot of packages, the order is important, as some of functions are are overloaded by the latest packages you call with library().

I use Windows 10 btw.

Same as I do, so I don't understand the message 'local...igraph' you get. The others messages could be suppressed by suppressMessages(library(FlowSOM)).

HTH

ADD REPLY • link 4.1 years ago SamGG ▴ 360

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Hi Sam,

Thanks so much for your quick answers! I have also never encountered this "local(..." message myself, so I'm not sure where it could be coming from. If the rest of the functions behave as expected I guess it should not be an issue.

Instead of using the general suppressMessages(library(FlowSOM)), you could also use the suppressPackageStartupMessages(library(FlowSOM)) function, where the name states a bit more explicit that it is just the startup messages being supressed.

You could have an attempt at running the following code and see if the figure appears

suppressPackageStartupMessages(library(FlowSOM))

fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
fsom <- FlowSOM(fileName, compensate = TRUE, transform = TRUE,
                              scale = TRUE, colsToUse = c(9, 12, 14:18), nClus = 10)
PlotStars(fsom$FlowSOM)

ADD REPLY • link 4.1 years ago sofie.vangassen ▴ 10