CRAN Package Check Results for Package MetabolomicsBasics

Last updated on 2021-04-15 09:50:05 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 16.70 161.28 177.98 OK
r-devel-linux-x86_64-debian-gcc 1.1 14.54 118.92 133.46 OK
r-devel-linux-x86_64-fedora-clang 1.1 231.63 ERROR
r-devel-linux-x86_64-fedora-gcc 1.1 220.22 ERROR
r-devel-windows-ix86+x86_64 1.1 52.00 198.00 250.00 OK
r-devel-windows-x86_64-gcc10-UCRT 1.1 OK
r-patched-linux-x86_64 1.1 16.80 146.87 163.67 OK
r-patched-solaris-x86 1.1 301.50 OK
r-release-linux-x86_64 1.1 17.82 148.26 166.08 OK
r-release-macos-x86_64 1.1 OK
r-release-windows-ix86+x86_64 1.1 42.00 210.00 252.00 OK
r-oldrel-macos-x86_64 1.1 OK
r-oldrel-windows-ix86+x86_64 1.1 24.00 128.00 152.00 OK

Check Details

Version: 1.1
Check: examples
Result: ERROR
    Running examples in ‘MetabolomicsBasics-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: ReplaceMissingValues
    > ### Title: ReplaceMissingValues.
    > ### Aliases: ReplaceMissingValues
    >
    > ### ** Examples
    >
    > # load raw data and sample description
    > utils::data(raw, package = "MetabolomicsBasics")
    > utils::data(sam, package = "MetabolomicsBasics")
    >
    > idx <- apply(raw, 2, CheckForOutliers, group=sam$GT, n_sd=5, method="logical")
    > sum(idx) # 215 values would be classified as outlier using a five-sigma band
    [1] 215
    > old_vals <- raw[idx] # keep outlier values for comparison
    > raw_filt <- raw
    > raw_filt[idx] <- NA
    > raw_means <- apply(raw, 2, function(x) {
    + sapply(split(x, sam$GT), mean, na.rm=TRUE)[as.numeric(sam$GT)]
    + })[idx]
    > raw_repl <- ReplaceMissingValues(x=raw_filt)
    
    ...replacing missing values in a data matrix of m x n = 120 x 112(=13440)Error in mixOmics::nipals(x, reconst = TRUE, ncomp = ncomp) :
     unused argument (reconst = TRUE)
    Calls: ReplaceMissingValues
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc