Received this error message from Perseus after trying to use imputeLMCD using a script from the PerseusR package. I'm not sure if it possible download a different version of Rcpp (1.1.0) and/or how I might go about doing that. Thank you in advance for help.

My sincere apologies that my colleagues had ignored your question.

The error you encountered arises because the installed binary version of the mzR package was built against a different version of Rcpp than the one currently on your system. This mismatch can occur after updates to Rcpp, particularly on Windows systems where packages are often installed as binaries rather than compiled from source.

To resolve this, do not downgrade Rcpp. Instead, reinstall mzR from source using BiocManager. This will compile mzR against your current Rcpp version. Ensure that RTools is properly configured in your system's PATH environment variable, as it provides the necessary compilers.

First, install BiocManager if it is not already present:

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

Then, reinstall mzR from source:

BiocManager::install("mzR", type = "source")

After reinstalling, restart your R session and attempt to load mzR again:

library(mzR)

If the warning persists, update your entire Bioconductor installation:

BiocManager::install()

This should address the compatibility issue and allow the imputeLCMD function from PerseusR to execute without errors related to mzR.

Kevin

There are two issues here.

First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different Rcpp version than you have installed. This used to be a problem in the early days of Rcpp. We could probably safely remove the warning nowadays.

Kevin's installation instructions are correct, but probably not necessary. Just note that installing mzR from source has system dependencies, that you might need to install.

Second, there's an error in the read.perseus() function, when it calls read.table() - the error says that there are more columns that names. There's either because your input data has a problem, or there's a bug in their function or the expected outputs have changed.

This second problem isn't related to Bioconductor, and you should enquirer with the authors of the PerseusR package.