problem installing sleuth

pachterlab / sleuth

Differential analysis of RNA-Seq

http://pachterlab.github.io/sleuth

GNU General Public License v3.0

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problem installing sleuth #241

Closed Kappy2 closed 3 years ago

Kappy2 commented 4 years ago

I finally got bioconductor to install. Now I have this error message when trying to install sleuth.

BiocManager::install("pachterlab/sleuth")

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12) Installing github package(s) 'pachterlab/sleuth' Error: Failed to install 'unknown package' from GitHub: Problem with the SSL CA cert (path? access rights?)

Someone please help me, I have been at this for the past week, first installing newest R, then trying to get bioconductor to work. I am so close... (Had to start everything from scratch because previous version of R was not up to date...can you sense the despair?) THANK YOU

clydeandforth commented 4 years ago

Hi Kappy2,

I think you have to install devtools and rhdf5 first then install Sleuth via devtools as described here:

https://pachterlab.github.io/sleuth/download

racng commented 4 years ago

The line source("http://bioconductor.org/biocLite.R") from the sleuth manual is not working for R version >3.5 because it now requires BiocManager to install Bioconductor packages. Here are updated instructions for installing sleuth (only changing the first step): 1) Install rhdf5:

BiocManager::install("rhdf5")

2) Install devtools:

install.packages("devtools")

3) Install sleuth:

devtools::install_github("pachterlab/sleuth")