• using R Under development (unstable) (2025-12-04 r89100)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-9) 15.2.0     GNU Fortran (Debian 15.2.0-9) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘SpoMAG/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘SpoMAG’ version ‘0.1.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/1s] OK
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘caret’
• 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 ‘SpoMAG’ can be installed ... OK See the install log for details.
• 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 ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
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• checking for unstated dependencies in examples ... OK
• checking examples ... [4s/4s] ERROR Running examples in ‘SpoMAG-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: predict_sporulation > ### Title: Predict Sporulation Potential > ### Aliases: predict_sporulation > > ### ** Examples > > # Load package > library(SpoMAG) > > # Load example annotation tables > file_spor <- system.file("extdata", "one_sporulating.csv.gz", package = "SpoMAG") > file_aspo <- system.file("extdata", "one_asporogenic.csv.gz", package = "SpoMAG") > > # Read files > df_spor <- readr::read_csv(file_spor, show_col_types = FALSE) > df_aspo <- readr::read_csv(file_aspo, show_col_types = FALSE) > > # Step 1: Extract sporulation-related genes > genes_spor <- sporulation_gene_name(df_spor) Looking for genes related to Sporulation Onset and Checkpoints Looking for genes related to Spo0A Regulon Looking for genes related to Engulfment Looking for genes related to SigF Regulon Looking for genes related to SigG Regulon Looking for genes related to SigE Regulon Looking for genes related to SigK Regulon Looking for genes related to Spore Cortex Looking for genes related to Spore Coat Looking for genes related to Germination > genes_aspo <- sporulation_gene_name(df_aspo) Looking for genes related to Sporulation Onset and Checkpoints Looking for genes related to Spo0A Regulon Looking for genes related to Engulfment Looking for genes related to SigF Regulon Looking for genes related to SigG Regulon Looking for genes related to SigE Regulon Looking for genes related to SigK Regulon Looking for genes related to Spore Cortex Looking for genes related to Spore Coat Looking for genes related to Germination > > # Step 2: Convert to binary matrix > bin_spor <- build_binary_matrix(genes_spor) > bin_aspo <- build_binary_matrix(genes_aspo) > > # Step 3: Predict using ensemble model (preloaded in package) > > result_spor <- predict_sporulation(bin_spor) Warning: namespace ‘caret’ is not available and has been replaced by .GlobalEnv when processing object ‘rf_model’ Error in predict_sporulation(bin_spor) : Package caret is required Execution halted
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• checking tests ... [1s/1s] OK   Running ‘testthat.R’ [1s/1s]
• checking PDF version of manual ... [3s/3s] OK
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• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR