CODEWITHSUNDEEP
rnamespaceslazy-loading
Berna de Vries
Berna de Vries

Reputation: 11

Unable to install package Sleuth in R

I've been trying to install the Sleuth package in R all morning and it keeps giving me errors. This is how I tried to install it:

if(!requireNamespace("BiocManager", quietly = TRUE))  
install.packages("BiocManager")
BiocManager::install("DESeq2") 

BiocManager::install ("rhdf5")
install.packages("devtools") 
devtools:: install_github("pachterlab/sleuth")

I did use the library() command.

I get the following error messages: Error: object 'h5write.default' is not exported by 'namespace:rhdf5' Execution halted ERROR: lazy loading failed for package 'sleuth'

Upvotes: 1

Views: 1040

Answers (1)

Thomaz Guadagnini
Thomaz Guadagnini

Reputation: 11

I was having the same issue and found that there's current an open issue on Github discussing this problem.

Currently there is a workaround which was shared in the same issue on Github:

  • Run git clone https://github.com/pachterlab/sleuth
  • Remove the last line in ./sleuth/NAMESPACE which is the h5write.default that raises the error during installation - ignore the warning in the first line
  • Then in R: devtools::install('./sleuth/')

It worked for me while using Linux - ZorinOS and R 4.1.2 but it should work on Windows as well.

Someone also opened a PR to fix the whole issue but it seems they are not updating the package anymore (unfortunately).

Upvotes: 1

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