* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/MetabolomicsBasics.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘MetabolomicsBasics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetabolomicsBasics’ version ‘1.4.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'ropls', 'xcms'
* 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 whether package ‘MetabolomicsBasics’ can be installed ... [31s/48s] OK
* checking package directory ... 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 ... [9s/12s] OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... [8s/11s] OK
* checking loading without being on the library search path ... [8s/11s] 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 ... [47s/60s] OK
* checking Rd files ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [28s/38s] 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
> 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)
Error in verify_suggested("mixOmics") : 
  The use of this function requires packagemixOmics. Please install.
Calls: ReplaceMissingValues -> verify_suggested
Execution halted
* checking PDF version of manual ... [9s/13s] OK
* checking HTML version of manual ... 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
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/MetabolomicsBasics.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:49.04, 243.60 + 23.77