* using log directory ‘/srv/hornik/tmp/CRAN_pretest/dtlcor.Rcheck’ * using R Under development (unstable) (2025-02-12 r87715) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.6 (1+b1) Debian flang-new version 19.1.6 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘dtlcor/DESCRIPTION’ ... OK * this is package ‘dtlcor’ version ‘0.0.0.9000’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [2s/2s] NOTE Maintainer: ‘Weibin Zhong ’ New submission Version contains large components (0.0.0.9000) Non-FOSS package license (See LICENSE.md) The Title field should be in title case. Current version is: ‘R Package of "Multiplicity Control in Oncology Clinical Trials with a Surrogate Endpoint-Based Drop-The-Losers Design"’ In title case that is: ‘R Package of "Multiplicity Control in Oncology Clinical Trials with a Surrogate Endpoint-Based Drop-the-Losers Design"’ * checking package namespace information ... OK * checking package dependencies ... INFO Depends: includes the non-default packages: 'MASS', 'gsDesign', 'survival', 'dplyr', 'tidyr', 'ggplot2', 'data.table', 'coin', 'ssanv', 'cubature', 'DT', 'shiny', 'shinythemes', 'plotly', 'stringr' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘dtlcor’ can be installed ... [6s/6s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: See LICENSE.md Standardizable: FALSE * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘LICENSE.md’ * 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 ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] 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 ... [2s/2s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘DT’ ‘MASS’ ‘coin’ ‘cubature’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘gsDesign’ ‘plotly’ ‘shiny’ ‘shinythemes’ ‘ssanv’ ‘stringr’ ‘survival’ ‘tidyr’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [2s/2s] NOTE dtl_app_get_alpha_t: no visible global function definition for ‘%>%’ dtl_app_get_alpha_t: no visible global function definition for ‘filter’ dtl_app_get_alpha_t: no visible binding for global variable ‘alpha_s’ dtl_app_get_alpha_t: no visible global function definition for ‘rename_with’ dtl_app_sim : dtl_app_ana: no visible global function definition for ‘if_else’ dtl_app_sim : dtl_app_ana: no visible global function definition for ‘case_when’ dtl_app_sim: no visible global function definition for ‘gsDesign’ dtl_app_sim: no visible global function definition for ‘%>%’ dtl_app_sim: no visible global function definition for ‘mutate’ dtl_app_sim: no visible binding for global variable ‘I_21’ dtl_app_sim: no visible binding for global variable ‘rej’ dtl_app_sim_single : get_S0 : solve_S0: no visible global function definition for ‘pexp’ dtl_app_sim_single : get_S0: no visible global function definition for ‘uniroot’ dtl_app_sim_single : get_f0: no visible global function definition for ‘dexp’ dtl_app_sim_single: no visible global function definition for ‘rexp’ dtl_app_sim_single: no visible global function definition for ‘dexp’ dtl_app_sim_single: no visible global function definition for ‘rbinom’ dtl_app_sim_single: no visible global function definition for ‘runif’ dtl_app_sim_single: no visible global function definition for ‘%>%’ dtl_app_sim_single: no visible global function definition for ‘tibble’ dtl_app_sim_single: no visible global function definition for ‘mutate’ dtl_app_sim_single: no visible global function definition for ‘case_when’ dtl_app_sim_single: no visible global function definition for ‘arrange’ dtl_app_sim_single: no visible binding for global variable ‘tt’ dtl_app_sim_single: no visible global function definition for ‘filter’ dtl_app_sim_single: no visible global function definition for ‘group_by’ dtl_app_sim_single: no visible global function definition for ‘slice’ dtl_app_sim_single: no visible global function definition for ‘summarise’ dtl_app_sim_single: no visible binding for global variable ‘censor’ dtl_app_sim_single: no visible global function definition for ‘if_else’ dtl_app_sim_single: no visible global function definition for ‘logrank_test’ dtl_cor_the_PH_upper_bound: no visible global function definition for ‘integrate’ dtl_get_alpha_s: no visible global function definition for ‘uniroot’ dtl_tier_the: no visible global function definition for ‘qnorm’ dtl_tier_the : int_prob: no visible global function definition for ‘pnorm’ dtl_tier_the : int_prob: no visible global function definition for ‘dnorm’ dtl_tier_the: no visible global function definition for ‘integrate’ dtl_tier_the: no visible global function definition for ‘gsDesign’ dtl_tier_the : int_prob: no visible global function definition for ‘dmvnorm’ Undefined global functions or variables: %>% I_21 alpha_s arrange case_when censor dexp dmvnorm dnorm filter group_by gsDesign if_else integrate logrank_test mutate pexp pnorm qnorm rbinom rej rename_with rexp runif slice summarise tibble tt uniroot Consider adding importFrom("stats", "dexp", "dnorm", "filter", "integrate", "pexp", "pnorm", "qnorm", "rbinom", "rexp", "runif", "uniroot") 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 examples ... NONE * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for code which exercises the package ... WARNING No examples, no tests, no vignettes * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 WARNINGs, 4 NOTEs