* using log directory ‘/srv/hornik/tmp/CRAN_pretest/HaDeX.Rcheck’ * using R Under development (unstable) (2025-06-25 r88360) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux 13 (trixie) * using session charset: UTF-8 * checking for file ‘HaDeX/DESCRIPTION’ ... OK * this is package ‘HaDeX’ version ‘1.2.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/15s] NOTE Maintainer: ‘Weronika Puchala ’ New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: HDX (18:45, 19:77) Spectrometry (3:9, 18:19) eXchange (17:89) CRAN repository db overrides: X-CRAN-Comment: Archived on 2025-06-13 as issues were not corrected despite reminders. Found the following (possibly) invalid URLs: URL: http://mslab-ibb.pl/shiny/HaDeX/ (moved to https://mslab-ibb.pl/shiny/HaDeX/) From: inst/doc/HaDeX.html Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * 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 serialization versions ... OK * checking whether package ‘HaDeX’ can be installed ... [4s/4s] OK * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] NOTE absolute_comparison_plot: no visible binding for global variable ‘Start’ absolute_comparison_plot: no visible binding for global variable ‘abs_avg_theo_in_time_1’ absolute_comparison_plot: no visible binding for global variable ‘End’ absolute_comparison_plot: no visible binding for global variable ‘abs_avg_theo_in_time_2’ absolute_comparison_plot: no visible binding for global variable ‘Med_Sequence’ absolute_comparison_plot: no visible binding for global variable ‘err_abs_avg_theo_in_time_1’ absolute_comparison_plot: no visible binding for global variable ‘err_abs_avg_theo_in_time_2’ absolute_comparison_plot: no visible binding for global variable ‘abs_frac_exch_state_1’ absolute_comparison_plot: no visible binding for global variable ‘abs_frac_exch_state_2’ absolute_comparison_plot: no visible binding for global variable ‘err_abs_frac_exch_state_1’ absolute_comparison_plot: no visible binding for global variable ‘err_abs_frac_exch_state_2’ absolute_woods_plot: no visible binding for global variable ‘Start’ absolute_woods_plot: no visible binding for global variable ‘abs_diff_theo_frac_exch’ absolute_woods_plot: no visible binding for global variable ‘End’ absolute_woods_plot: no visible binding for global variable ‘colour’ absolute_woods_plot: no visible binding for global variable ‘Med_Sequence’ absolute_woods_plot: no visible binding for global variable ‘err_abs_diff_theo_frac_exch’ absolute_woods_plot: no visible binding for global variable ‘abs_diff_frac_exch’ absolute_woods_plot: no visible binding for global variable ‘err_abs_diff_frac_exch’ calculate_kinetics: no visible binding for global variable ‘Protein’ calculate_kinetics: no visible binding for global variable ‘Sequence’ calculate_kinetics: no visible binding for global variable ‘State’ calculate_kinetics: no visible binding for global variable ‘Start’ calculate_kinetics: no visible binding for global variable ‘End’ calculate_kinetics: no visible binding for global variable ‘time_chosen’ calculate_state_deuteration: no visible binding for global variable ‘Center’ calculate_state_deuteration: no visible binding for global variable ‘z’ calculate_state_deuteration: no visible binding for global variable ‘Modification’ calculate_state_deuteration: no visible binding for global variable ‘Fragment’ calculate_state_deuteration: no visible binding for global variable ‘Sequence’ calculate_state_deuteration: no visible binding for global variable ‘Start’ calculate_state_deuteration: no visible binding for global variable ‘End’ calculate_state_deuteration: no visible binding for global variable ‘MHP’ calculate_state_deuteration: no visible binding for global variable ‘MaxUptake’ calculate_state_deuteration: no visible binding for global variable ‘State’ calculate_state_deuteration: no visible binding for global variable ‘Exposure’ calculate_state_deuteration: no visible binding for global variable ‘Protein’ calculate_state_deuteration: no visible binding for global variable ‘File’ calculate_state_deuteration: no visible binding for global variable ‘exp_mass’ calculate_state_deuteration: no visible binding for global variable ‘Inten’ calculate_state_deuteration: no visible binding for global variable ‘.’ calculate_state_deuteration: no visible binding for global variable ‘avg_exp_mass’ calculate_state_deuteration: no visible binding for global variable ‘time_chosen_mean’ calculate_state_deuteration: no visible binding for global variable ‘time_in_mean’ calculate_state_deuteration: no visible binding for global variable ‘time_out_mean’ calculate_state_deuteration: no visible binding for global variable ‘err_time_chosen_mean’ calculate_state_deuteration: no visible binding for global variable ‘err_time_in_mean’ calculate_state_deuteration: no visible binding for global variable ‘err_time_out_mean’ calculate_state_deuteration: no visible binding for global variable ‘frac_exch_state’ calculate_state_deuteration: no visible binding for global variable ‘err_frac_exch_state’ calculate_state_deuteration: no visible binding for global variable ‘abs_frac_exch_state’ calculate_state_deuteration: no visible binding for global variable ‘err_abs_frac_exch_state’ calculate_state_deuteration: no visible binding for global variable ‘avg_theo_in_time’ calculate_state_deuteration: no visible binding for global variable ‘err_avg_theo_in_time’ calculate_state_deuteration: no visible binding for global variable ‘abs_avg_theo_in_time’ calculate_state_deuteration: no visible binding for global variable ‘err_abs_avg_theo_in_time’ calculate_state_deuteration: no visible binding for global variable ‘Med_Sequence’ plot_coverage: no visible binding for global variable ‘Protein’ plot_coverage: no visible binding for global variable ‘Start’ plot_coverage: no visible binding for global variable ‘End’ plot_coverage: no visible binding for global variable ‘State’ plot_coverage: no visible binding for global variable ‘.’ plot_coverage: no visible binding for global variable ‘value’ plot_coverage: no visible binding for global variable ‘ID’ plot_kinetics: no visible binding for global variable ‘Sequence’ plot_kinetics: no visible binding for global variable ‘State’ plot_kinetics: no visible binding for global variable ‘time_chosen’ plot_kinetics: no visible binding for global variable ‘avg_theo_in_time’ plot_kinetics: no visible binding for global variable ‘prop’ plot_kinetics: no visible binding for global variable ‘err_avg_theo_in_time’ plot_kinetics: no visible binding for global variable ‘abs_avg_theo_in_time’ plot_kinetics: no visible binding for global variable ‘err_abs_avg_theo_in_time’ plot_kinetics: no visible binding for global variable ‘frac_exch_state’ plot_kinetics: no visible binding for global variable ‘err_frac_exch_state’ plot_kinetics: no visible binding for global variable ‘abs_frac_exch_state’ plot_kinetics: no visible binding for global variable ‘err_abs_frac_exch_state’ plot_position_frequency: no visible binding for global variable ‘Protein’ plot_position_frequency: no visible binding for global variable ‘Start’ plot_position_frequency: no visible binding for global variable ‘End’ plot_position_frequency: no visible binding for global variable ‘State’ plot_position_frequency: no visible binding for global variable ‘.’ plot_position_frequency: no visible binding for global variable ‘x’ plot_position_frequency: no visible binding for global variable ‘coverage’ prepare_dataset: no visible binding for global variable ‘Center’ prepare_dataset: no visible binding for global variable ‘z’ prepare_dataset: no visible binding for global variable ‘Protein’ prepare_dataset: no visible binding for global variable ‘Sequence’ prepare_dataset: no visible binding for global variable ‘Start’ prepare_dataset: no visible binding for global variable ‘End’ prepare_dataset: no visible binding for global variable ‘MHP’ prepare_dataset: no visible binding for global variable ‘MaxUptake’ prepare_dataset: no visible binding for global variable ‘State’ prepare_dataset: no visible binding for global variable ‘Exposure’ prepare_dataset: no visible binding for global variable ‘File’ prepare_dataset: no visible binding for global variable ‘exp_mass’ prepare_dataset: no visible binding for global variable ‘Inten’ prepare_dataset: no visible binding for global variable ‘State_Exposure’ prepare_dataset: no visible binding for global variable ‘avg_exp_mass’ prepare_dataset: no visible binding for global variable ‘chosen_time_mean_1’ prepare_dataset: no visible binding for global variable ‘in_time_mean_1’ prepare_dataset: no visible binding for global variable ‘out_time_mean_1’ prepare_dataset: no visible binding for global variable ‘err_chosen_time_mean_1’ prepare_dataset: no visible binding for global variable ‘err_in_time_mean_1’ prepare_dataset: no visible binding for global variable ‘err_out_time_mean_1’ prepare_dataset: no visible binding for global variable ‘chosen_time_mean_2’ prepare_dataset: no visible binding for global variable ‘in_time_mean_2’ prepare_dataset: no visible binding for global variable ‘out_time_mean_2’ prepare_dataset: no visible binding for global variable ‘err_chosen_time_mean_2’ prepare_dataset: no visible binding for global variable ‘err_in_time_mean_2’ prepare_dataset: no visible binding for global variable ‘err_out_time_mean_2’ prepare_dataset: no visible binding for global variable ‘frac_exch_state_1’ prepare_dataset: no visible binding for global variable ‘frac_exch_state_2’ prepare_dataset: no visible binding for global variable ‘err_frac_exch_state_1’ prepare_dataset: no visible binding for global variable ‘err_frac_exch_state_2’ prepare_dataset: no visible binding for global variable ‘abs_frac_exch_state_1’ prepare_dataset: no visible binding for global variable ‘abs_frac_exch_state_2’ prepare_dataset: no visible binding for global variable ‘err_abs_frac_exch_state_1’ prepare_dataset: no visible binding for global variable ‘err_abs_frac_exch_state_2’ prepare_dataset: no visible binding for global variable ‘avg_theo_in_time_1’ prepare_dataset: no visible binding for global variable ‘avg_theo_in_time_2’ prepare_dataset: no visible binding for global variable ‘err_avg_theo_in_time_1’ prepare_dataset: no visible binding for global variable ‘err_avg_theo_in_time_2’ prepare_dataset: no visible binding for global variable ‘abs_avg_theo_in_time_1’ prepare_dataset: no visible binding for global variable ‘abs_avg_theo_in_time_2’ prepare_dataset: no visible binding for global variable ‘err_abs_avg_theo_in_time_1’ prepare_dataset: no visible binding for global variable ‘err_abs_avg_theo_in_time_2’ prepare_dataset: no visible binding for global variable ‘.’ prepare_dataset: no visible binding for global variable ‘Med_Sequence’ prepare_dataset: no visible binding for global variable ‘diff_frac_exch’ prepare_dataset: no visible binding for global variable ‘err_frac_exch’ prepare_dataset: no visible binding for global variable ‘abs_diff_frac_exch’ prepare_dataset: no visible binding for global variable ‘err_abs_diff_frac_exch’ prepare_dataset: no visible binding for global variable ‘diff_theo_frac_exch’ prepare_dataset: no visible binding for global variable ‘err_diff_theo_frac_exch’ prepare_dataset: no visible binding for global variable ‘abs_diff_theo_frac_exch’ prepare_dataset: no visible binding for global variable ‘err_abs_diff_theo_frac_exch’ read_hdx: no visible binding for global variable ‘Protein’ read_hdx: no visible binding for global variable ‘Start’ read_hdx: no visible binding for global variable ‘End’ read_hdx: no visible binding for global variable ‘Sequence’ read_hdx: no visible binding for global variable ‘Modification’ read_hdx: no visible binding for global variable ‘State’ read_hdx: no visible binding for global variable ‘Exposure’ read_hdx: no visible binding for global variable ‘File’ read_hdx: no visible binding for global variable ‘.’ read_hdx: no visible binding for global variable ‘n_rep’ reconstruct_sequence: no visible binding for global variable ‘Protein’ reconstruct_sequence: no visible binding for global variable ‘Start’ reconstruct_sequence: no visible binding for global variable ‘End’ reconstruct_sequence: no visible binding for global variable ‘Sequence’ reconstruct_sequence: no visible binding for global variable ‘.’ relative_comparison_plot: no visible binding for global variable ‘Start’ relative_comparison_plot: no visible binding for global variable ‘avg_theo_in_time_1’ relative_comparison_plot: no visible binding for global variable ‘End’ relative_comparison_plot: no visible binding for global variable ‘avg_theo_in_time_2’ relative_comparison_plot: no visible binding for global variable ‘Med_Sequence’ relative_comparison_plot: no visible binding for global variable ‘err_avg_theo_in_time_1’ relative_comparison_plot: no visible binding for global variable ‘err_avg_theo_in_time_2’ relative_comparison_plot: no visible binding for global variable ‘frac_exch_state_1’ relative_comparison_plot: no visible binding for global variable ‘frac_exch_state_2’ relative_comparison_plot: no visible binding for global variable ‘err_frac_exch_state_1’ relative_comparison_plot: no visible binding for global variable ‘err_frac_exch_state_2’ relative_woods_plot: no visible binding for global variable ‘Start’ relative_woods_plot: no visible binding for global variable ‘diff_theo_frac_exch’ relative_woods_plot: no visible binding for global variable ‘End’ relative_woods_plot: no visible binding for global variable ‘colour’ relative_woods_plot: no visible binding for global variable ‘Med_Sequence’ relative_woods_plot: no visible binding for global variable ‘err_diff_theo_frac_exch’ relative_woods_plot: no visible binding for global variable ‘diff_frac_exch’ relative_woods_plot: no visible binding for global variable ‘err_frac_exch’ Undefined global functions or variables: . Center End Exposure File Fragment ID Inten MHP MaxUptake Med_Sequence Modification Protein Sequence Start State State_Exposure abs_avg_theo_in_time abs_avg_theo_in_time_1 abs_avg_theo_in_time_2 abs_diff_frac_exch abs_diff_theo_frac_exch abs_frac_exch_state abs_frac_exch_state_1 abs_frac_exch_state_2 avg_exp_mass avg_theo_in_time avg_theo_in_time_1 avg_theo_in_time_2 chosen_time_mean_1 chosen_time_mean_2 colour coverage diff_frac_exch diff_theo_frac_exch err_abs_avg_theo_in_time err_abs_avg_theo_in_time_1 err_abs_avg_theo_in_time_2 err_abs_diff_frac_exch err_abs_diff_theo_frac_exch err_abs_frac_exch_state err_abs_frac_exch_state_1 err_abs_frac_exch_state_2 err_avg_theo_in_time err_avg_theo_in_time_1 err_avg_theo_in_time_2 err_chosen_time_mean_1 err_chosen_time_mean_2 err_diff_theo_frac_exch err_frac_exch err_frac_exch_state err_frac_exch_state_1 err_frac_exch_state_2 err_in_time_mean_1 err_in_time_mean_2 err_out_time_mean_1 err_out_time_mean_2 err_time_chosen_mean err_time_in_mean err_time_out_mean exp_mass frac_exch_state frac_exch_state_1 frac_exch_state_2 in_time_mean_1 in_time_mean_2 n_rep out_time_mean_1 out_time_mean_2 prop time_chosen time_chosen_mean time_in_mean time_out_mean value x z * checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [6s/6s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [4s/5s] OK Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [4s/4s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [32s/32s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 NOTEs