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SlavovLab / SCP_recommendations

Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments. The code is distributed under an MIT license.
MIT License
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Required packages #3

Open richardcoca opened 1 year ago

richardcoca commented 1 year ago

Hi there,

I'm struggling with loading the necessary packages for this. I have installed these packages, but they seem to not be loading, which leads to some error messages down the line. Are these all the packages required/what syntax was used to the install the packages (if that has an effect)?

library("destiny") library("ggplot2") library("patchwork") library("plotly") library("scater") Error: package or namespace load failed for ‘scater’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘irlba’ In addition: Warning message: package ‘scater’ was built under R version 4.0.4

cvanderaa commented 1 year ago

Hello @richardcoca,

You need to install irlba in order to load scater. I don't know what command you used to install your packages, but I like to use the Bioconductor utilities because it takes care of all dependencies for me (I'm lazy and I don't like struggling with dependencies :wink:) Using this command works on my side:

install.packages("BiocManager")
BiocManager::install("scater")

Another thing is that I see you have a warning package ‘scater’ was built under R version 4.0.4. What version of R are you using? If the the trick above did not work, you may want to update your R (https://www.r-project.org) to at least that version (I'd recommend using the latest version).