* using log directory ‘/home/hornik/tmp/CRAN_special_noSuggests/MetabolomicsBasics.Rcheck’
* using R Under development (unstable) (2025-12-02 r89085)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-15 (Debian 15.2.0-4) 15.2.0
    GNU Fortran (Debian 15.2.0-4) 15.2.0
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘MetabolomicsBasics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetabolomicsBasics’ version ‘1.4.7’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/7s] NOTE
Maintainer: ‘Jan Lisec <jan.lisec@bam.de>’

Uses the non-portable package: ‘xcms’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘MetabolomicsBasics’ can be installed ... [11s/12s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [11s/11s] ERROR
Running examples in ‘MetabolomicsBasics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ReplaceMissingValues
> ### Title: ReplaceMissingValues.
> ### Aliases: ReplaceMissingValues
> 
> ### ** Examples
> 
> # load raw data and sample description
> raw <- MetabolomicsBasics::raw
> sam <- MetabolomicsBasics::sam
> 
> 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)
Warning in verify_suggested("mixOmics", default = x) :
  The use of this function requires package mixOmics. Please install.

...replacing missing values in a data matrix of m x n = 120 x 112(=13440)Error in loadNamespace(x) : there is no package called ‘mixOmics’
Calls: ReplaceMissingValues ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE