* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/MetabolomicsBasics.Rcheck’ * using R Under development (unstable) (2024-08-23 r87043) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * 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 ... 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 whether package ‘MetabolomicsBasics’ can be installed ... [29s/35s] 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 ... [7s/11s] 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 ... OK * checking loading without being on the library search path ... [7s/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 ... [42s/53s] 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 ... [25s/35s] 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 ... [8s/12s] 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 See ‘/data/gannet/ripley/R/packages/tests-Suggests/MetabolomicsBasics.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 5:56.27, 232.47 + 26.06