plot function in flowType under R4.0.0
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Entering edit mode
lifengt • 0
@lifengt-23536
Last seen 4.4 years ago

This is my first post, so please forgive and correct me if I am wrong. Basically, I installed the FlowType under R4.0.0 and try to use it for my flow data analysis. Below is my code chunk and ERROR output from my console.

### copy from here

R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

[Workspace loaded from ~/.RData]

> if (!requireNamespace("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")
> 
> BiocManager::install("flowType")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'flowType'
trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.0/flowType_2.25.0.zip'
Content type 'application/zip' length 1804990 bytes (1.7 MB)
downloaded 1.7 MB

package ‘flowType’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\tianl\AppData\Local\Temp\RtmpGuezKX\downloaded_packages
Old packages: 'RcppArmadillo', 'S4Vectors'
Update all/some/none? [a/s/n]: 
n
> library(flowType)
Loading required package: Rcpp
Loading required package: BH
Warning message:
multiple methods tables found for ‘plot’ 
> data(DLBCLExample)
> #These markers will be analyzed
> PropMarkers <- 3:5
> MFIMarkers <- PropMarkers
> MarkerNames <- c('FS', 'SS','CD3','CD5','CD19')
> #Run flowType
> Res <- flowType(DLBCLExample, PropMarkers, MFIMarkers, 'kmeans', MarkerNames);
> plot(Res, DLBCLExample)
Error in as.double(x) : 
  cannot coerce type 'S4' to vector of type 'double'
> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

software error • 388 views
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Entering edit mode

The function still works on R 3.6.3:

library(flowType)
data(DLBCLExample)
PropMarkers <- 3:5
MFIMarkers <- PropMarkers
MarkerNames <- c('FS', 'SS','CD3','CD5','CD19')
Res <- flowType(DLBCLExample, PropMarkers, MFIMarkers, 'kmeans', MarkerNames)
plot(Res, DLBCLExample)

g

However, the package is failing on the internal build system: https://www.bioconductor.org/packages/release/bioc/html/flowType.html

I will ask.

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