Package check result: ERROR Check: CRAN incoming feasibility, Result: NOTE Maintainer: ‘Alexandre Godmer ’ Possibly misspelled words in DESCRIPTION: Desorption (11:199) MALDI (11:257, 11:623) Spectrometry (11:243) TOF (11:263, 11:629) spectrometry (11:787) Check: examples, Result: ERROR Running examples in ‘MSclassifR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: PredictLogReg > ### Title: Prediction of the category to which a mass spectrum belongs > ### Aliases: PredictLogReg > > ### ** Examples > > ## No test: > library(MSclassifR) > library(MALDIquant) > > ## 1) Preprocess and detect peaks > data("CitrobacterRKIspectra", "CitrobacterRKImetadata", package = "MSclassifR") > spectra <- SignalProcessing(CitrobacterRKIspectra) [SignalProcessingUltra] N=14; workers=1; align=lowess; OS=unix 1) Transform: sqrt 2) Smooth: Wavelet 3) Baseline: SNIP 4) Calibrate: TIC 5) Building reference peaks (minFrequency=0.5, method=strict) 6) Align: lowess > peaks <- MSclassifR::PeakDetection(x = spectra, averageMassSpec = FALSE) Detecting peaks (method=MAD, SNR=3) [serial] Aligning peaks in discrete bins > > ## 2) Build X and Y (sample-by-peak intensities + labels) > ## Option A: if you prefer the helper and a sparse return: > Y <- factor(CitrobacterRKImetadata$Species) > xy <- build_XY_from_peaks(peaks, labels = Y, normalize = "max", sparse = FALSE) > X <- xy$X > Y <- xy$Y > > ## Option B: via MALDIquant::intensityMatrix (as in the original examples) > ##IntMat <- MALDIquant::intensityMatrix(peaks) > ##rownames(IntMat) <- paste(CitrobacterRKImetadata$Strain_name_spot) > ##IntMat[is.na(IntMat)] <- 0 > ##IntMat <- t(apply(IntMat, 1, function(x) x / max(x))) # per-spectrum max norm > ##X <- t(IntMat) # features in columns > ##Y <- factor(CitrobacterRKImetadata$Species) > > ## 3) Select discriminant m/z with "cvp" method > a <- MSclassifR::SelectionVar( + X, Y, + MethodSelection = "cvp", + MethodValidation = "cv", + PreProcessing = c("center","scale","nzv","corr"), + NumberCV = 2, + Metric = "Kappa" + ) No sampling method selected Selection variables with cvp method > sel_moz <- a$sel_moz > > ## 4) Train several models on the shortlisted m/z > model_lm <- MSclassifR::LogReg(X = X, moz = sel_moz, Y = Y, number = 2, + repeats = 2, Metric = "Kappa", kind = "linear") LogReg function according to the following parameters: No sampling method selected Error in .check_ncores(length(names)) : 31 simultaneous processes spawned Calls: -> -> makePSOCKcluster -> .check_ncores Execution halted