A Question About Installing sleuth (in R) of kallisto-sleuth

Question

[ianlee96]

Looking for help

First of all, I use this code:

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

and then

BiocManager::install("rhdf5")
install.packages("devtools")
library(rhdf5)
library(Rhdf5lib)
library(rhdf5filter)
library(devtools)
devtools::install_github("pachterlab/sleuth")

the codes were typed line by line, when the last code finished, what R returned are as follows:

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)
Installing github package(s) 'pachterlab/sleuth'
Downloading GitHub repo pachterlab/sleuth@HEAD
√  checking for file 'C:\Users\IanLe\AppData\Local\Temp\Rtmpi6kZSF\remotesc043c9f2fcc\pachterlab-sleuth-e5ac761/DESCRIPTION' ...
-  preparing 'sleuth':
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
   Omitted 'LazyData' from DESCRIPTION
-  building 'sleuth_0.30.0.tar.gz'

* installing *source* package 'sleuth' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
错误: 'namespace:rhdf5'没有出口'h5write.default'这个对象
停止执行
ERROR: lazy loading failed for package 'sleuth'
* removing 'C:/SCIProgram/R/R-4.1.3/library/sleuth'
Old packages: 'cluster', 'gert', 'MASS', 'Matrix', 'mgcv', 'nlme',
  'survival', 'testthat'
Update all/some/none? [a/s/n]: 

I returned this:

n

and then R showed this

Warning message:
In i.p(...) :
  installation of package ‘C:/Users/IanLe/AppData/Local/Temp/Rtmpi6kZSF/filec0456a37560/sleuth_0.30.0.tar.gz’ had non-zero exit status

What can I do to finish sleuth installing? Looking for help. Thank you.

Answer 1

[dsull]

See the solution here: https://github.com/pachterlab/sleuth/issues/259

sleuth has been on hold for around 2 years, but I can confirm that the developers will get back to maintaining it soon. In the meantime, use the solution presented in the link above.

[ianlee96]

Thank you！ It helps!