Error arised while identifying ROIs in m/z dimensions....

[rogasan]

Ubuntu 24.04 + R 4.6.1 + MetaboAnalystR 4.30 + OptiLCMS 1.20：

mSet_ROI <- PerformROIExtraction(datapath = DataFiles, rt.idx = 0.9, rmConts = TRUE)
Step 0/6: Scanning ROIs for parameters optimization...
QC_01.mzML
QC_02.mzML
QC_03.mzML
QC_04.mzML
QC_05.mzML
Data Loading...
Raw file import begin...
Import data: QC_01.mzML finished!
Import data: QC_02.mzML finished!
Import data: QC_03.mzML finished!
Import data: QC_04.mzML finished!
Import data: QC_05.mzML finished!
Data Loaded !
Empty Scan detecting...
No Empty scan found !
Identifying regions of interest (ROI)...
Identifying regions of potential contaminants......Done!
51 potential contaminamts will not be used for parameters optimization !
Going to the next step...
MS data Preparing...
MS Data ready !
Identifying ROIs in m/z dimensions...
Error in x > good.bins.list[[4]][[1]] && x < good.bins.list[[4]][[2]] :
'length = 4' in coercion to 'logical(1)'

Gmini 3.1 Pro Says:

This error is caused by a strict rule change introduced in R version 4.3.0.

In older versions of R, using the scalar logical operator && on a vector (an object with a length greater than 1, like your x which has a length of 4) would only generate a warning. Starting with R 4.3.0, doing this triggers a hard error: 'length = 4' in coercion to 'logical(1)'.

This is a known bug in the source code of the OptiLCMS / MetaboAnalystR package where the developers accidentally used && instead of the vectorized & operator.

Here are the ways to fix this:

Option 1: Update the Packages (Recommended)
The Xia Lab (creators of MetaboAnalystR) frequently patches these R 4.3+ compatibility bugs on their GitHub repository. You should reinstall the latest versions of OptiLCMS and MetaboAnalystR directly from GitHub rather than CRAN.

Run this in your R console:

R

Install devtools if you haven't already

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

Force update OptiLCMS and MetaboAnalystR from GitHub

devtools::install_github("xia-lab/OptiLCMS", force = TRUE)
devtools::install_github("xia-lab/MetaboAnalystR", force = TRUE)
After updating, restart your R session and run your PerformROIExtraction code again.

Option 2: Downgrade R to version 4.2.3
If the developers haven't pushed a fix for this specific line of code yet, the easiest workaround is to temporarily downgrade your R installation to R 4.2.3.

In R 4.2.3, the expression x > good.bins.list[[4]][[1]] && x < good.bins.list[[4]][[2]] will only throw a silent warning and will successfully evaluate the first element, allowing your data pipeline to finish running without crashing.

Option 3: Clean your Global Environment
Occasionally, corrupted metadata in your current R environment can pass unexpectedly long vectors into the ROI function. If Option 1 doesn't work and you prefer not to downgrade R, try clearing your environment and recreating the DataFiles object:

R

Clear environment

rm(list = ls())

Re-initialize your path and run

DataFiles <- "path_to_your_data"
mSet_ROI <- PerformROIExtraction(datapath = DataFiles, rt.idx = 0.9, rmConts = TRUE)

Please fix it and refresh the OptiLCMS packages....