* using log directory ‘/srv/hornik/tmp/CRAN/vsmi.Rcheck’ * using R Under development (unstable) (2024-04-24 r86484) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘vsmi/DESCRIPTION’ ... OK * this is package ‘vsmi’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [1s/1s] NOTE Maintainer: ‘Haoyu Yang ’ New submission Non-FOSS package license (`use_mit_license()`) The Title field should be in title case. Current version is: ‘Variable selection for multiple imputed data’ In title case that is: ‘Variable Selection for Multiple Imputed Data’ * 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 ‘vsmi’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: `use_mit_license()` Standardizable: FALSE * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] 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 ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING 'library' or 'require' calls not declared from: ‘MASS’ ‘Matrix’ 'library' or 'require' calls in package code: ‘MASS’ ‘Matrix’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [4s/4s] NOTE PEE : logit_QL_gl.alasso.estimate: no visible global function definition for ‘cor’ PEE : logit_QL_gl.alasso.estimate: no visible binding for global variable ‘rr’ PEE : Poisson_QL_gl.alasso.estimate: no visible global function definition for ‘cor’ PEE : Poisson_QL_gl.alasso.estimate: no visible binding for global variable ‘rr’ PEE: no visible global function definition for ‘head’ PEE: no visible binding for global variable ‘mi_data’ PEE: no visible binding for global variable ‘g1’ PEE: no visible global function definition for ‘qif’ PEE: no visible binding for global variable ‘binomial’ PEE: no visible binding for global variable ‘poisson’ PWLS : GEEsym.estimate: no visible global function definition for ‘cor’ PWLS : GEEsym.estimate: no visible binding for global variable ‘rr’ PWLS : GEEsym_gl.lasso.estimate: no visible global function definition for ‘cor’ PWLS : GEEsym_gl.lasso.estimate: no visible binding for global variable ‘rr’ PWLS : GEEsym_gl.alasso.estimate: no visible global function definition for ‘cor’ PWLS : GEEsym_gl.alasso.estimate: no visible binding for global variable ‘rr’ PWLS: no visible binding for global variable ‘mi_entire’ generate_pee_missing_data: no visible global function definition for ‘mvrnorm’ generate_pee_missing_data: no visible global function definition for ‘rbinom’ generate_pee_missing_data: no visible global function definition for ‘rpois’ generate_pwls_missing_data: no visible global function definition for ‘mvrnorm’ generate_pwls_missing_data: no visible global function definition for ‘rbinom’ generate_pwls_missing_data: no visible global function definition for ‘uniroot’ generate_pwls_missing_data: no visible binding for global variable ‘f1’ Undefined global functions or variables: binomial cor f1 g1 head mi_data mi_entire mvrnorm poisson qif rbinom rpois rr uniroot Consider adding importFrom("stats", "binomial", "cor", "poisson", "rbinom", "rpois", "uniroot") importFrom("utils", "head") 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 ... WARNING Undocumented arguments in Rd file 'PEE.Rd' ‘lamda.vec’ ‘Gamma’ Documented arguments not in \usage in Rd file 'PEE.Rd': ‘lamba.vec’ ‘gamma’ Undocumented arguments in Rd file 'PWLS.Rd' ‘lamda.vec’ ‘Gamma’ Documented arguments not in \usage in Rd file 'PWLS.Rd': ‘lamba.vec’ ‘gamma’ Documented arguments not in \usage in Rd file 'generate_pee_missing_data.Rd': ‘pt2’ 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 ... [284s/284s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed PWLS 202.306 0.156 202.471 PEE 80.854 0.439 81.297 * checking PDF version of manual ... [3s/2s] 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: 3 WARNINGs, 3 NOTEs