* using log directory ‘/srv/hornik/tmp/CRAN_pretest/NonLinearRC.Rcheck’ * using R Under development (unstable) (2025-10-19 r88945) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (7) Debian flang-new version 19.1.7 (7) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘NonLinearRC/DESCRIPTION’ ... OK * this is package ‘NonLinearRC’ version ‘0.0.0.9000’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [2s/2s] NOTE Maintainer: ‘Trevor Thomson ’ New submission Version contains large components (0.0.0.9000) Non-FOSS package license (`use_mit_license()`) * checking package namespace information ... OK * checking package dependencies ... INFO Package in Depends/Imports which should probably only be in LinkingTo: ‘RcppArmadillo’ * 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 ‘NonLinearRC’ can be installed ... [6s/6s] OK * used C++ compiler: ‘Debian clang version 19.1.7 (7)’ * 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 '::' or ':::' import not declared from: ‘numDeriv’ Missing or unexported object: ‘splines2::deriv’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [3s/3s] NOTE Baseline_Hazard_GRC_func: no visible global function definition for ‘ave’ H_partialH_func: no visible global function definition for ‘rnorm’ NL_RC: no visible global function definition for ‘lm’ NL_RC: no visible global function definition for ‘predict’ NL_RC: no visible global function definition for ‘var’ NL_RC : : no visible global function definition for ‘quantile’ NL_RC : : no visible global function definition for ‘var’ True_SF_func: no visible global function definition for ‘predict’ Undefined global functions or variables: ave lm predict quantile rnorm var Consider adding importFrom("stats", "ave", "lm", "predict", "quantile", "rnorm", "var") 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... 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 ... OK * checking examples ... [0s/0s] ERROR Running examples in ‘NonLinearRC-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: NL_RC > ### Title: Nonlinear Regression Calibration Under a Cox Regression Model > ### Aliases: NL_RC > > ### ** Examples > > data(df_Analysis) > data(df_Biomarker) > data(df_Replicate) > > # ---------------------------------------------------------------------- > # LINEAR REGRESSION CALIBRATION > # ---------------------------------------------------------------------- > > Results_Polynomial_LRC = NL_RC(df1 = df_Analysis, + df2 = df_Biomarker, + df3 = df_Replicate, + df1_ID_index = 1, + df1_U_index = 3, + df1_delta_index = 4, + df1_Q_index = 7, + df1_X_index = 5, + df2_ID_index = 1, + df2_Response_index = 2, + df2_Covariates_index = c(3,5), + df3_ID_index = 1, + Function_Type = "Polynomial", + DF = 1, + Method = "Linear", + EstimateNuisance_Logi = T, + mu_vec = NULL, + Variance_vec = NULL, + t_grid = seq(0,20, length.out = 101), + z_grid = seq(-3, 3, length.out = 11), + C = 1000, + seed = 235346, + x = 0, + Spline_Z_vec = NULL, + Boundary.knots = NULL, + Estimate_CI_Surv = F) # True beta: -0.2, True gamma: 0.1 Error in NL_RC(df1 = df_Analysis, df2 = df_Biomarker, df3 = df_Replicate, : T used instead of TRUE Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [0s/0s] * checking PDF version of manual ... [3s/3s] 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: 1 ERROR, 2 WARNINGs, 2 NOTEs