* using log directory ‘/srv/hornik/tmp/CRAN_pretest/gPIPE.Rcheck’ * using R Under development (unstable) (2025-03-10 r87922) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘gPIPE/DESCRIPTION’ ... OK * this is package ‘gPIPE’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Xiaoran Lai ’ New submission Possibly misspelled words in DESCRIPTION: Cheung (12:59) Mander (10:83) Sweeting (11:5) al (12:69) et (12:66) Found the following (possibly) invalid DOIs: DOI: 10.1214/21-aoas1603 From: DESCRIPTION Status: 404 Message: Not Found * 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 ‘gPIPE’ 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 ... [0s/0s] 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 calculate_cumulative_dlt: no visible global function definition for ‘%>%’ calculate_cumulative_dlt: no visible binding for global variable ‘cohort’ calculate_cumulative_dlt: no visible binding for global variable ‘doseCombination’ calculate_cumulative_dlt: no visible binding for global variable ‘outcome’ calculate_cumulative_dlt: no visible binding for global variable ‘cumulative_DLT’ calculate_cumulative_dlt: no visible binding for global variable ‘cumulative_count’ calculate_cumulative_dlt: no visible binding for global variable ‘Drug1’ calculate_cumulative_dlt: no visible binding for global variable ‘Drug2’ calibrate_epsilon : calculate_metrics: no visible global function definition for ‘tail’ calibrate_epsilon: no visible global function definition for ‘setNames’ create_summary_table: no visible global function definition for ‘%>%’ create_summary_table: no visible binding for global variable ‘doseCombination’ create_summary_table: no visible binding for global variable ‘DLT_prob’ find_beta_parameters : : no visible global function definition for ‘uniroot’ generate_gamma_config: no visible global function definition for ‘%>%’ generate_gamma_config: no visible binding for global variable ‘.’ generate_gamma_config: no visible global function definition for ‘slice’ objective_function: no visible global function definition for ‘qbeta’ plot_dlt_proportion: no visible binding for global variable ‘Drug1’ plot_dlt_proportion: no visible binding for global variable ‘Drug2’ plot_dlt_proportion: no visible binding for global variable ‘cumulative_DLT_proportion’ plot_dlt_proportion: no visible binding for global variable ‘x’ plot_dlt_proportion: no visible binding for global variable ‘y’ plot_dlt_proportion: no visible global function definition for ‘%>%’ plot_dlt_proportion: no visible binding for global variable ‘cumulative_count’ plot_dlt_proportion: no visible binding for global variable ‘cumulative_DLT’ runTrialSimulation: no visible binding for global variable ‘current_dose_level’ runTrialSimulation: no visible global function definition for ‘%>%’ runTrialSimulation: no visible global function definition for ‘pull’ runTrialSimulation: no visible binding for global variable ‘doseCombination’ Undefined global functions or variables: %>% . DLT_prob Drug1 Drug2 cohort cumulative_DLT cumulative_DLT_proportion cumulative_count current_dose_level doseCombination outcome pull qbeta setNames slice tail uniroot x y Consider adding importFrom("stats", "qbeta", "setNames", "uniroot") importFrom("utils", "tail") to your NAMESPACE file. * 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 ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [1s/1s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [2s/2s] OK * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 NOTEs