Unable to load data "pasillaGenes" in R because DESeq is not installed?
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kanhasunny • 0
Last seen 6 days ago


I am unable to load data "pasillaGenes" in R. Please see below

> data("pasillaGenes") 
Warning: namespace ‘DESeq’ is not available and has been replaced
by .GlobalEnv when processing object ‘pasillaGenes’
Loading required package: DESeq
Error in .requirePackage(package) : 
  unable to find required package ‘DESeq’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘DESeq’

I then proceeded to install DESeq but then the below returned.

> BiocManager::install("DESeq")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'DESeq'
Warning message:
package ‘DESeq’ is not available for this version of R

FYI, I already had DESeq2 installed. Please also kindly see my session info below.

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DESeq2_1.30.0               SummarizedExperiment_1.20.0 Biobase_2.50.0             
 [4] MatrixGenerics_1.2.0        matrixStats_0.57.0          GenomicRanges_1.42.0       
 [7] GenomeInfoDb_1.26.2         IRanges_2.24.1              S4Vectors_0.28.1           
[10] BiocGenerics_0.36.0         pasilla_1.18.0

Thank you so much in advance for any help!

DESeq2 pasillaGenes • 120 views
Entering edit mode

If it is only about accessing the data in the RData then you can still manually compile the DESeq package, so download the source via git clone https://git.bioconductor.org/packages/DESeq, then via command line cd into the directory that contains the DESeq folder and then run R CMD INSTALL DESeq. On Mac this probably compiles without error and without too much trouble, might complain a bit about deprecation etc... but you should be able to load the RData afterwards. At least this is what I did a while back when I was in a similar situation.

Entering edit mode
Last seen 2 days ago
United States

It looks like pasilla may need an update so that pasillaGenes can be loaded without the DESeq package which is deprecated.


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