New R, Newest BioC versions of XCMS and MSnbase, same error. I will update everything and let you know what happens. Loaded via a namespace (and not attached): parallel stats graphics grDevices utils datasets methods base LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 Running under: Windows 7 圆4 (build 7601) Service Pack 1 If it helps I can post a couple of files. This is my first go at this, but this seems like an abnormal amount of time to read in the data. I am running this from a solid state local drive, so I can rule out network issues. The time consuming part is in the for loop (for (f in files) ). I tried using the mzR process in isolation (msdata <- mzR::openMSfile(f, backend = "netCDF")), and this was as fast as previously experienced. This process took 7.3 hours (I had misformatted my pheno dataframe so it errored at that point, but I assume the 7.3 hours is a representative minimum. Raw_data <- readMSData(files = filedata$files, msLevel. Waters Databridge spits data out in this format. XCMS user here, finally trying to adapt an older workflow to new XCMS/MSnbase.
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