Hello,

I'm currently analyzing metabolomics data, and I've encountered an issue while attempting to plot the Total Ion Chromatogram (TIC) for all of my samples. Strangely, I was able to accomplish this task effortlessly in the past, but for some reason, I'm now facing difficulties in replicating the process. I'm uncertain whether this issue stems from a connectivity problem or if there's another underlying cause. Your assistance in resolving this matter would be greatly appreciated.

The error is :
Error: BiocParallel errors 1 remote errors, element index: 2 14 unevaluated and other errors first remote error: cannot open the connection In addition: Warning message: stop worker failed: wrong args for environment subassignment

library(plotly)
library(xcms)
library(msdata)
library(enviPat)
library(tidyverse)
library(enviPat)
library(plotly)
library(RColorBrewer)
library(DT)
library(stats)
library(BiocParallel)
library(stats)

path.mzML <- "C://Users//mvaldez//OneDrive - IRTA//Documentos//master omicas//Proteomics//MUESTRAS//MUESTRAS"
mzML.files <- list.files(path.mzML, pattern= ".mzXML",  recursive=T, full.names = T)
pheno <- phenoDataFromPaths(mzML.files)
raw_data <- readMSData(files = mzML.files,
                       pdata = new("NAnnotatedDataFrame", pheno),
                       mode = "onDisk")

TICs <- chromatogram(raw_data, aggregationFun = "sum")

Error: BiocParallel errors
  1 remote errors, element index: 2
  14 unevaluated and other errors
  first remote error: cannot open the connection
In addition: Warning message:
stop worker failed:
  wrong args for environment subassignment  


sessionInfo( )

The error cannot open the connection is what you get when trying to open a file that doesn't exist, or that you don't have read privileges for.

## non-existant
> read.table("thisfiledoesntexist")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'thisfiledoesntexist': No such file or directory
## no privileges
> cat("words", file = "thisfiledoesexist")
> system("chmod 333 thisfiledoesexist")
> scan("thisfiledoesexist","c")
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
  cannot open file 'thisfiledoesexist': Permission denied

You don't show where the error arises (showing unevaluated code and then the error rather than console output is suboptimal), but my guess is that either the file doesn't exist, or you don't have read privileges.

The problem only happened using windows. I changed to Linux I dindt have any proble. I solve it.