• using R version 4.5.1 (2025-06-13)
  • using platform: x86_64-apple-darwin20
  • R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
  • running under: macOS Ventura 13.3.1
  • using session charset: UTF-8
  • checking for file ‘readyomics/DESCRIPTION’ ... OK
  • checking extension type ... Package
  • this is package ‘readyomics’ version ‘0.1.0’
  • package encoding: UTF-8
  • checking package namespace information ... OK
  • checking package dependencies ... INFO Packages suggested but not available for checking: 'IHW', 'ropls'
  • 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 ‘readyomics’ can be installed ... [3s/3s] OK See the install log for details.
  • checking installed package size ... OK
  • checking package directory ... OK
  • checking ‘build’ 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 ... [0s/0s] OK
  • checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
  • checking whether the package can be unloaded cleanly ... [0s/0s] OK
  • checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
  • checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
  • checking loading without being on the library search path ... [0s/0s] 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 ... [3s/4s] OK
  • checking Rd files ... [0s/0s] OK
  • checking Rd metadata ... OK
  • checking Rd cross-references ... INFO Packages unavailable to check Rd xrefs: ‘IHW’, ‘ropls’
  • 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 installed files from ‘inst/doc’ ... OK
  • checking files in ‘vignettes’ ... OK
  • checking examples ... [10s/16s] ERROR Running examples in ‘readyomics-Ex.R’ failed The error most likely occurred in: > ### Name: mva > ### Title: Multivariate analysis (PCA, PLS, OPLS) > ### Aliases: mva > > ### ** Examples > > # PCA > set.seed(123) > mock_X <- matrix(rnorm(40), + nrow = 10, + dimnames = list(paste0("sample", 1:10), + paste0("feat", 1:4)) + ) > > sample_data <- data.frame( + sample_id = rownames(mock_X), + group = factor(rep(c("A", "B"), each = 5)), + batch = factor(rep(1:2, times = 5)), + row.names = rownames(mock_X), + stringsAsFactors = FALSE + ) > > result <- mva( + X = mock_X, + sample_data = sample_data, + group_colour = "group", + group_shape = "batch", + plot_title = "Test PCA Plot", + predI = 2, # PCA: set components + verbose = FALSE + ) Error in loadNamespace(x) : there is no package called ‘ropls’ Calls: mva ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted
  • checking for unstated dependencies in ‘tests’ ... OK
  • checking tests ... [12s/18s] OK   Running ‘testthat.R’ [11s/18s]
  • checking for unstated dependencies in vignettes ... OK
  • checking package vignettes ... OK
  • checking re-building of vignette outputs ... [35s/57s] ERROR Error(s) in re-building vignettes: --- re-building ‘readyomics.Rmd’ using rmarkdown Quitting from readyomics.Rmd:176-185 [unnamed-chunk-12] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `loadNamespace()`: ! there is no package called 'ropls' --- Backtrace:     ▆  1. ├─readyomics::mva(...)  2. └─base::loadNamespace(x)  3. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)  4. └─base (local) withOneRestart(expr, restarts[[1L]])  5. └─base (local) doWithOneRestart(return(expr), restart) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'readyomics.Rmd' failed with diagnostics: there is no package called 'ropls' --- failed re-building ‘readyomics.Rmd’ SUMMARY: processing the following file failed:   ‘readyomics.Rmd’ Error: Vignette re-building failed. Execution halted
  • checking PDF version of manual ... [6s/8s] OK
  • DONE Status: 2 ERRORs
  • using check arguments '--no-clean-on-error '