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symbioticMe / proBatch

Tools for Batch Effects Diagnostics and Correction
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Not able to load proBatch package #5

Closed Marievlm closed 3 years ago

Marievlm commented 3 years ago

Hi,

First, thank you so much for the release of your new package proBatch. It seems to be very helpful for the batch correction.

After loading the necessary packages and execute conscientiously the Rcode from the documentation, I am not able to load the library proBatch. In Fact, 

> library(proBatch)
Erreur : package or namespace load failed for ‘proBatch’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 aucun package nommé ‘GO.db’ n'est trouvé

I try to download from different sources the package "GO.db" -> without success.

Can you bring me some tips in the way to use your package.

Thank you so much !

ppedrioli commented 3 years ago

Hi Marie,

Sorry for probably confirming the obvious, but did you already try:

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

BiocManager::install("GO.db")

Also, could you please have a look at the repository for building the docker version of proBatch. Specifically at the Dockerfile and install_probatch.R and see if any of the dependencies installed there will help you. Note that that image is built on top of rocker/r-base:4.0.0 and I did not test with other R versions.

Finally, if that does not solve it and you just want to give proBatch a try, you could use the docker image available on dockerhub.

Marievlm commented 3 years ago

Hi Patrick,

Thank you for your very precise answer and your reactivity.

Now, it works perfectly !!!