* using log directory 'd:/RCompile/CRANincoming/R-devel/MoCo.Rcheck' * using R Under development (unstable) (2025-02-15 r87726 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'MoCo/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MoCo' version '1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [52s] NOTE Maintainer: 'Jialu Ran ' New submission Possibly misspelled words in DESCRIPTION: MoCo (10:14) The Description field should not start with the package name, 'This package' or similar. * 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 ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'MoCo' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Authors@R field gives no person with maintainer role, valid email address and non-empty name. Author field differs from that derived from Authors@R Author: 'Jialu Ran [aut, cph], Benjamin Risk [aut, ths]' Authors@R: 'Jialu Ran [aut, cph, cre], Benjamin Risk [aut, ths]' Maintainer field differs from that derived from Authors@R Maintainer: 'Jialu Ran ' Authors@R: '' * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard file/directory found at top level: 'MoCo.Rproj' * 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 ... 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 ':::' imports not declared from: 'caret' 'hal9001' 'nloptr' 'quadprog' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [12s] NOTE fit_mechanism: no visible global function definition for 'binomial' fit_mechanism: no visible global function definition for 'gaussian' fit_mechanism: no visible global function definition for 'dnorm' fit_mechanism: no visible global function definition for 'sd' fit_mechanism: no visible binding for global variable 'mu_pseudo_A0_star_train' hypo_test: no visible global function definition for 'cor' hypo_test: no visible global function definition for 'quantile' one_step: no visible global function definition for 'binomial' one_step: no visible global function definition for 'gaussian' one_step: no visible global function definition for 'dnorm' one_step: no visible global function definition for 'sd' one_step: no visible global function definition for 'cov' one_step_cross: no visible global function definition for 'cov' plot_moco: no visible global function definition for 'ciftiTools.setOption' plot_moco: no visible global function definition for 'load_parc' plot_moco: no visible global function definition for 'read_xifti' plot_moco: no visible global function definition for 'move_from_mwall' plot_moco: no visible global function definition for 'select_xifti' plot_moco: no visible global function definition for 'newdata_xifti' Undefined global functions or variables: binomial ciftiTools.setOption cor cov dnorm gaussian load_parc move_from_mwall mu_pseudo_A0_star_train newdata_xifti quantile read_xifti sd select_xifti Consider adding importFrom("stats", "binomial", "cor", "cov", "dnorm", "gaussian", "quantile", "sd") to your NAMESPACE file. Found if() conditions comparing class() to string: File 'MoCo/R/utils.R': if (class(fit) != "error") ... File 'MoCo/R/utils.R': if (class(fit) != "error") ... File 'MoCo/R/utils.R': if (class(r) != "error") ... Use inherits() (or maybe is()) instead. * checking Rd files ... 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 ... WARNING Undocumented arguments in Rd file 'fit_mechanism.Rd' 'seed' '...' Documented arguments not in \usage in Rd file 'fit_mechanism.Rd': 'X' 'Z' 'A' 'M' 'Y' 'Delta_M' 'thresh' 'Delta_Y' 'cv_folds' Undocumented arguments in Rd file 'make_full_data_eif.Rd' 'Delta_Y' 'Delta_M' 'gDM' 'gDY_AXZ' 'pMXD' Documented arguments not in \usage in Rd file 'make_full_data_eif.Rd': 'Delta' 'gD' 'pMX' Undocumented arguments in Rd file 'moco.Rd' 'cv_folds' '...' Undocumented arguments in Rd file 'one_step.Rd' 'seed' '...' Undocumented arguments in Rd file 'one_step_cross.Rd' 'seed' '...' 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 ... OK * checking examples ... NONE * checking PDF version of manual ... [17s] OK * checking HTML version of manual ... OK * checking for code which exercises the package ... WARNING No examples, no tests, no vignettes * DONE Status: 3 WARNINGs, 4 NOTEs