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ODonoghueLab / Minardo-Model

R package for ordering events identified from time series biomolecular data sets
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Installing Minardo Model Package in R Studio #14

Open AQPH222 opened 3 years ago

AQPH222 commented 3 years ago

Hi,

Thank you for writing the extensive and helpful readme file. However, I cannot find the command for installing the Minardo Model in R. I have tried the following:

BiocManager::install("MinardoModel") BiocManager::install("Minardo-Model") BiocManager::install("Minardo Model") devtools::install_github("ODonoghueLab/Minardo-Model")

The BiocManager commands return that the package is not available for R version 4.0.2, while the install_github command returns that nem cannot be installed (I can provide the exact error code if needed). The readme states to use biocLite to install the mfuzz package, which has been replaced by BiocManager (and I successfully installed mfuzz using BiocManager).

Is there a command I should be using instead to install Minardo Model?

Thank you for your time, Andrew

crystalsand10 commented 3 years ago

Hi Andrew,

Thanks for bringing this up. We haven't submitted the package to Bioconductor, hence it is to be installed directly from github. As you pointed out, we realised that the package 'nem' is no longer maintained for R > 4. But it can still be installed from source first, then installing MinardoModel works fine.

To install nem from source: Download 'nem.tar.gz' from https://www.bioconductor.org/packages/3.10/bioc/html/nem.html (see Package Archives section at the bottom of page).

Then in that folder run: 

install.packages('devtools') 
install.packages(‘BiocManager’)
library('BiocManager') 

install.packages('e1071') 
BiocManager::install('graph')
BiocManager::install('RBGL') 
install.packages('RColorBrewer')
BiocManager::install('Rgraphviz') 
install.packages('statmod') 
install.packages('plotrix') 
install.packages('boot')
BiocManager::install('limma') 
install.packages('nem_2.60.0.tar.gz', repos=NULL, type='source') # if running R from the same folder, prepend pathname to the .tar.gz file 

library(devtools) 
install_github('https://github.com/ODonoghueLab/Minardo-Model')

We will set up an installation page (and update installation instructions for Mfuzz) - thank you very much for your comments! Please let us know if you have any further issues and we will try to get back to you ASAP.