Unable to load data "pasillaGenes" in R because DESeq is not installed?
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kanhasunny • 0
@4f07e997
Last seen 6 days ago

Hello,

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Warning: namespace ‘DESeq’ is not available and has been replaced
by .GlobalEnv when processing object ‘pasillaGenes’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

locale:
[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
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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.

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@mikelove
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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