* using log directory ‘/srv/hornik/tmp/CRAN_pretest/PTL.PRS.Rcheck’ * using R Under development (unstable) (2025-04-08 r88126) * 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 ‘PTL.PRS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PTL.PRS’ version ‘2.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Bokeum Cho ’ New submission Possibly misspelled words in DESCRIPTION: PRS (8:62) Polygenic (3:29) The Title field should be in title case. Current version is: ‘Transfer learning of Polygenic Risk Score with Pseudo-validation’ In title case that is: ‘Transfer Learning of Polygenic Risk Score with Pseudo-Validation’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... WARNING Subdirectory ‘src’ contains: MakeVars These are unlikely file names for src files. * 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 ‘PTL.PRS’ can be installed ... [11s/11s] OK * used C++ compiler: ‘Debian clang version 19.1.7 (3)’ * checking package directory ... OK * checking for future file timestamps ... 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 ... [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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [4s/4s] NOTE PRStr_calculation_pv_es: no visible binding for global variable ‘cor’ PRStr_calculation_pv_es : process_block: no visible global function definition for ‘cor’ PTL_PRS_test_pseudo: no visible global function definition for ‘median’ PTL_PRS_test_pseudo_list: no visible global function definition for ‘median’ PTL_PRS_train: no visible global function definition for ‘write.table’ PTL_PRS_train: no visible global function definition for ‘median’ PTL_PRS_train: no visible binding for global variable ‘sum_stats_target_train’ PTL_PRS_train: no visible binding for global variable ‘sum_stats_target_val’ download_read_LDblocks: no visible global function definition for ‘download.file’ linear_result_generator: no visible global function definition for ‘lm’ linear_result_generator: no visible global function definition for ‘confint’ logistic_result_generator: no visible global function definition for ‘glm’ nagelkerke: no visible global function definition for ‘update’ nagelkerke: no visible global function definition for ‘nobs’ nagelkerke: no visible global function definition for ‘logLik’ nagelkerke: no visible global function definition for ‘df.residual’ nagelkerke: no visible global function definition for ‘pchisq’ p2cor: no visible global function definition for ‘qt’ pseudo_split: no visible global function definition for ‘median’ pseudo_split: no visible binding for global variable ‘sd’ pseudo_split: no visible global function definition for ‘rnorm’ Undefined global functions or variables: confint cor df.residual download.file glm lm logLik median nobs pchisq qt rnorm sd sum_stats_target_train sum_stats_target_val update write.table Consider adding importFrom("stats", "confint", "cor", "df.residual", "glm", "lm", "logLik", "median", "nobs", "pchisq", "qt", "rnorm", "sd", "update") importFrom("utils", "download.file", "write.table") 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 'PTL_PRS_test.Rd' ‘outfile’ ‘Ytype’ ‘Covar_name’ ‘Y_name’ 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 line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... NOTE File ‘PTL.PRS/libs/PTL.PRS.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Object: ‘BedFileReader.o’ Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Object: ‘BedFileReader.o’ Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * 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: 3 WARNINGs, 3 NOTEs