Unable to install package Sleuth in R

Question

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'

• removing 'C:/Users/31625/OneDrive/Documents/R/win-library/4.1/sleuth'

Answer 1

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).