* using log directory 'd:/RCompile/CRANincoming/R-devel/BiostatsUHNplus.Rcheck' * using R Under development (unstable) (2023-11-21 r85583 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'BiostatsUHNplus/DESCRIPTION' ... OK * this is package 'BiostatsUHNplus' version '0.0.2' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Tyler Pittman ' New submission Possibly misspelled words in DESCRIPTION: AE (2:61) DSMB (2:42) * 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 hidden files and directories ... NOTE Found the following hidden files and directories: .nojekyll These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. CRAN-pack does not know about .nojekyll * checking for portable file names ... WARNING Found the following files with non-portable file names: dsmb_ccru_tables/ae_detail EXAMPLE_STUDY 30OCT2020.xlsx dsmb_ccru_tables/ae_detail EXAMPLE_STUDY Cohort A 30OCT2020.xlsx dsmb_ccru_tables/ae_detail EXAMPLE_STUDY Cohort B 30OCT2020.xlsx dsmb_ccru_tables/ae_detail EXAMPLE_STUDY Cohort C 30OCT2020.xlsx dsmb_ccru_tables/ae_detail EXAMPLE_STUDY Cohort D 30OCT2020.xlsx dsmb_ccru_tables/category ByEvent EXAMPLE_STUDY 30OCT2020.xlsx dsmb_ccru_tables/category ByEvent EXAMPLE_STUDY Cohort A 30OCT2020.xlsx dsmb_ccru_tables/category ByEvent EXAMPLE_STUDY Cohort B 30OCT2020.xlsx dsmb_ccru_tables/category ByEvent EXAMPLE_STUDY Cohort C 30OCT2020.xlsx dsmb_ccru_tables/category ByEvent EXAMPLE_STUDY Cohort D 30OCT2020.xlsx dsmb_ccru_tables/category BySubject EXAMPLE_STUDY 30OCT2020.xlsx dsmb_ccru_tables/category BySubject EXAMPLE_STUDY Cohort A 30OCT2020.xlsx dsmb_ccru_tables/category BySubject EXAMPLE_STUDY Cohort B 30OCT2020.xlsx dsmb_ccru_tables/category BySubject EXAMPLE_STUDY Cohort C 30OCT2020.xlsx dsmb_ccru_tables/category BySubject EXAMPLE_STUDY Cohort D 30OCT2020.xlsx These are not fully portable file names. See section 'Package structure' in the 'Writing R Extensions' manual. * checking whether package 'BiostatsUHNplus' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: 'README.Rmd' 'SettingUpSourceTree.txt' 'dev' 'docs' 'dsmb_ccru_tables' 'index.Rmd' * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: 'lifecycle' ':::' call which should be '::': 'purrr:::modify_if' See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: 'reportRmd:::covsum' 'reportRmd:::formatp' 'reportRmd:::replaceLbl' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [25s] NOTE ae_timeline_plot: no visible global function definition for 'na.fail' ae_timeline_plot: no visible binding for global variable 'ae' ae_timeline_plot: no visible binding for global variable 'Subject' ae_timeline_plot: no visible binding for global variable 'ae_detail' ae_timeline_plot: no visible binding for global variable 'ae_category' ae_timeline_plot: no visible binding for global variable 'AE_SEV_GD' ae_timeline_plot: no visible binding for global variable 'AE_ONSET_DT_INT' ae_timeline_plot: no visible binding for global variable 'drug1_ae' ae_timeline_plot: no visible global function definition for 'median' ae_timeline_plot: no visible global function definition for 'desc' ae_timeline_plot: no visible binding for global variable 'time_min' ae_timeline_plot: no visible binding for global variable 'time_max' ae_timeline_plot: no visible binding for global variable 'group' ae_timeline_plot: no visible binding for global variable 'time_median' ae_timeline_plot: no visible binding for global variable 'label' covsum_nested : covsIdData1: no visible global function definition for 'where' covsum_nested : covsIdData2: no visible global function definition for 'where' covsum_nested : maincovCovsIdData1: no visible global function definition for 'where' covsum_nested : maincovCovsIdData2: no visible global function definition for 'where' covsum_nested : : no visible global function definition for 'anova' covsum_nested : : no visible global function definition for 'as.formula' covsum_nested : : no visible binding for global variable 'binomial' covsum_nested : : no visible binding for global variable 'cl' dsmb_ccru: no visible binding for global variable 'Subject' dsmb_ccru: no visible binding for global variable 'gender_code' dsmb_ccru: no visible binding for global variable 'PT_ELIG_IND_3' dsmb_ccru: no visible binding for global variable 'PARTIC_ENROL_DT_INT' dsmb_ccru: no visible binding for global variable 'ae_grade_code_dyn_std' dsmb_ccru: no visible binding for global variable 'CTCAE5_LLT_NM' dsmb_ccru: no visible binding for global variable 'AE_VERBATIM_TRM_TXT' dsmb_ccru: no visible binding for global variable 'AE_ONSET_DT_INT' dsmb_ccru: no visible binding for global variable 'ae_detail' dsmb_ccru: no visible binding for global variable 'ae_category' dsmb_ccru: no visible binding for global variable 'ind' dsmb_ccru: no visible binding for global variable 'indH' dsmb_ccru: no visible binding for global variable 'indH_per' nice_mcmcglmm: no visible binding for global variable 'join' nice_mcmcglmm: no visible binding for global variable 'Variable' nice_mcmcglmm: no visible binding for global variable 'instance' nice_mcmcglmm: no visible binding for global variable 'OrigOrder' nice_mcmcglmm: no visible binding for global variable 'Ovar' rm_covsum_nested: no visible global function definition for 'stopCluster' rm_covsum_nested: no visible binding for global variable 'cl' Undefined global functions or variables: AE_ONSET_DT_INT AE_SEV_GD AE_VERBATIM_TRM_TXT CTCAE5_LLT_NM OrigOrder Ovar PARTIC_ENROL_DT_INT PT_ELIG_IND_3 Subject Variable ae ae_category ae_detail ae_grade_code_dyn_std anova as.formula binomial cl desc drug1_ae gender_code group ind indH indH_per instance join label median na.fail stopCluster time_max time_median time_min where Consider adding importFrom("stats", "anova", "as.formula", "binomial", "median", "na.fail") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: 'ae' 'demography' 'drug1_admin' 'drug2_admin' 'enrollment' 'ineligibility' Undocumented data sets: 'ae' 'demography' 'drug1_admin' 'drug2_admin' 'enrollment' 'ineligibility' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'ae_timeline_plot.Rd' '...' Undocumented arguments in Rd file 'as_numeric_parse.Rd' '...' Documented arguments not in \usage in Rd file 'covsum_nested.Rd': 'dropLevels' Undocumented arguments in Rd file 'dsmb_ccru.Rd' '...' Undocumented arguments in Rd file 'nice_mcmcglmm.Rd' 'dataset' Documented arguments not in \usage in Rd file 'nice_mcmcglmm.Rd': 'data' Undocumented arguments in Rd file 'rm_covsum_nested.Rd' 'markup' 'sanitize' '...' Documented arguments not in \usage in Rd file 'rm_covsum_nested.Rd': 'id' 'dropLevels' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... WARNING '::' or ':::' import not declared from: 'knitr' * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [18s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... OK Running 'testthat.R' * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... OK * DONE Status: 5 WARNINGs, 4 NOTEs