• using R Under development (unstable) (2026-10-10 r90659)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 23.1.3 (1)     Debian flang version 23.1.3 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-10-12 17:09:23 UTC
• checking for file ‘HaDeX2/DESCRIPTION’ ... OK
• this is package ‘HaDeX2’ version ‘1.0.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [3s/4s] OK
• 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 ‘HaDeX2’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [3s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/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 whether startup messages can be suppressed ... [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 ... [22s/27s] OK
• checking Rd files ... [1s/1s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [126s/124s] OK Examples with CPU (user + system) or elapsed time > 5s                                               user system elapsed plot_differential_uptake_curve 8.685 0.323 8.003 plot_coverage_heatmap 8.570 0.420 7.588 plot_differential_butterfly 8.079 0.339 8.558 plot_differential_chiclet 7.986 0.216 8.268 plot_manhattan 7.056 0.095 7.578 plot_volcano 6.992 0.111 7.649 calculate_aggregated_test_results 5.927 0.443 5.990 plot_uncertainty 4.833 0.079 6.041 create_p_diff_uptake_dataset 4.412 0.296 5.206 create_p_diff_uptake_dataset_with_confidence 4.441 0.073 6.566 calculate_aggregated_diff_uptake 3.260 0.098 5.045
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [139s/149s] OK   Running ‘spelling.R’ [0s/1s]   Running ‘testthat.R’ [139s/148s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [132s/168s] OK
• checking PDF version of manual ... [8s/10s] OK
• checking HTML version of manual ... [3s/4s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: OK