Hello.. I am having trouble properly installing DESeq2. Currently have R version 4.0.2, trying to install with Bioconductor version 3.11. I tried troubleshooting with some info I found online with no luck. I have completely uninstalled R and reinstalled. I have tried commands for installing the package survival individually. The command library('DESeq2') results in an error message: Error in library("DESeq2"): there is no package called ‘DESeq2’. I would appreciate any help with this issue, preferably in non-technical terms when possible. I am unfamiliar with coding and this software. I'm attaching two screenshots of the issues I'm having. Thanks.
Are you using R Studio or just plain R? What happens when you enter:
If this gives you an error about needing the "survival" package, start a new R session and then try install.packages("survival") and then try the DESeq2 install.
I am using just plain R. When I enter what you provided above, I get the message: Installation path not writeable, unable to update packages: survival. I tried starting the new session, install.packages("survival") and repeated the install procedure. Afterward, I still received the same message. I'm posting the full output below (after trying to install survival).
I think you are all set
Yes, I just realized that everything is working. Thanks for the help.
I have the same problem, but even if I install the survival packages, it still doesn't work. At the end of the Deseq2 installation, it's writen for all the packages that it had non-zero exit status... What does it mean? And do you know what other alternatives I can do? Thank you!