* using log directory 'd:/RCompile/CRANincoming/R-devel/rsides.Rcheck' * using R Under development (unstable) (2024-05-16 r86559 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'rsides/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'rsides' version '0.1' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Alex Dmitrienko ' New submission * 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 'rsides' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 13.2.0' * checking installed package size ... OK * 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 ... 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [13s] OK * 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... NOTE File 'rsides/libs/x64/rsides.dll': Found 'rand', possibly from 'rand' (C) Object: 'rsides.o' Found 'srand', possibly from 'srand' (C) Object: 'rsides.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 ... ERROR Running examples in 'rsides-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Example1 > ### Title: Subgroup search in a clinical trial with a continuous endpoint > ### Aliases: Example1 > > ### ** Examples > > ############################################################################## > > # Primary endpoint parameters > > # Analysis strategy 1: Analysis of the continuous endpoint without > # accounting for any covariates > endpoint_parameters = list(outcome_variable = "outcome", + type = "continuous", + label = "Outcome", + analysis_method = "T-test", + direction = 1) > > # Analysis strategy 2: Analysis of the continuous endpoint using an ANCOVA > # model that accounts for two continuous covariates (cont1, cont2) and > # one class/categorical covariate (class1) > endpoint_parameters = list(outcome_variable = "outcome", + type = "continuous", + label = "Outcome", + analysis_method = "ANCOVA", + cont_covariates = "cont1, cont2", + class_covariates = "class1", + direction = 1) > > ############################################################################## > > # Data set parameters > > # Set of candidate biomarkers > biomarker_names = c("biomarker1", "biomarker2", + "biomarker3", "biomarker4", + "biomarker5") > > # Biomarker type > biomarker_types = c(rep("numeric", 4), "nominal") > > # Data set parameters > data_set_parameters = list(data_set = continuous, + treatment_variable_name = "treatment", + treatment_variable_control_value = "0", + biomarker_names = biomarker_names, + biomarker_types = biomarker_types) > > ############################################################################## > > # Algorithm parameters for the basic SIDES procedure > > # Algorithm > subgroup_search_algorithm = "SIDES procedure" > > # Number of permutations to compute multiplicity-adjusted treatment > # effect p-values within promising subgroups > n_perms_mult_adjust = 10 > > # Number of processor cores (use less or equal number of CPU cores on the current host) > ncores = 1 > > # Default values for the search depth (2), search width (2), > # maximum number of unique values for continuous biomarkers (20) > > # Algorithm parameters > algorithm_parameters = list( + n_perms_mult_adjust = n_perms_mult_adjust, + min_subgroup_size = 60, + subgroup_search_algorithm = subgroup_search_algorithm, + ncores = ncores, + random_seed = 3011) > > # Perform subgroup search > > # List of all parameters > parameters = list(endpoint_parameters = endpoint_parameters, + data_set_parameters = data_set_parameters, + algorithm_parameters = algorithm_parameters) > > results = SubgroupSearch(parameters) > > # Simple summary of subgroup search results > results *************************************** Subgroup search results *************************************** Subgroup Total size (Control, Treatment) Overall population 359 (182, 177) biomarker4<=-1: 145 (69, 76) biomarker2>0: 105 (59, 46) Estimate (SE) P-value (Adjusted p-value) 0 (0) 1 (NA) 504154718.2 (46321878836695.5) 0.5 (1) 541185003.88 (58771401983767.8) 0.5 (1) *************************************** Variable importance *************************************** Biomarker Variable importance score biomarker4 3.260 biomarker2 3.168 *************************************** Algorithm's parameters *************************************** Parameter Value Elapsed time (sec) 0.1 Type I error rate 0.3 > > # Generate a detailed Word-based report with a summary of subgroup search results > report_information = GenerateReport(results, + report_title = "Subgroup search report", + report_filename = tempfile( + "Continuous endpoint (SIDES).docx", + fileext=".docx" + ) + ) > > ############################################################################## > > # Algorithm parameters for the Fixed SIDEScreen procedure > > # Algorithm > subgroup_search_algorithm = "Fixed SIDEScreen procedure" > > # Number of permutations to compute multiplicity-adjusted treatment > # effect p-values within promising subgroups > n_perms_mult_adjust = 10 > > # Number of processor cores (use less or equal number of CPU cores on the current host) > ncores = 1 > > # Number of biomarkers selected for the second stage in the Fixed SIDEScreen algorithm > n_top_biomarkers = 3 > > # Default values for the search depth (2), search width (2), > # maximum number of unique values for continuous biomarkers (20) > > # Algorithm parameters > algorithm_parameters = list( + n_perms_mult_adjust = n_perms_mult_adjust, + min_subgroup_size = 60, + subgroup_search_algorithm = subgroup_search_algorithm, + ncores = ncores, + n_top_biomarkers = n_top_biomarkers, + random_seed = 3011) > > # Perform subgroup search > > # List of all parameters > parameters = list(endpoint_parameters = endpoint_parameters, + data_set_parameters = data_set_parameters, + algorithm_parameters = algorithm_parameters) > > results = SubgroupSearch(parameters) * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs