* using log directory ‘/srv/hornik/tmp/CRAN_pretest/iclogcondist.Rcheck’ * using R Under development (unstable) (2024-11-27 r87386) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.1 (1) Debian flang-new version 19.1.1 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘iclogcondist/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘iclogcondist’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Chaoyu Yuan ’ New submission No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = c("Chi", "Wing"), family = "Chu", role = "aut"), person(given = c("Hok", "Kan"), family = "Ling", role = "aut"), person(given = "Chaoyu", family = "Yuan", role = c("aut", "cre"), email = "chaoyu.yuan@columbia.edu")) as necessary. The Title field should be in title case. Current version is: ‘Nonparametric Estimation for a Log-concave Distribution Function with Interval-censored Data’ In title case that is: ‘Nonparametric Estimation for a Log-Concave Distribution Function with Interval-Censored Data’ * 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 ... WARNING Subdirectory ‘iclogcondist/src’ contains apparent object files/libraries icconcLF.dll icenF.dll Object files/libraries should not be included in a source package. Subdirectory ‘src’ contains: icconcLF.dll icenF.dll These are unlikely file names for src files. * checking if there is a namespace ... OK * checking for executable files ... WARNING Found the following executable files: src/icconcLF.dll src/icenF.dll Source packages should not contain undeclared executable files. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘iclogcondist’ can be installed ... [13s/13s] OK * used C++ compiler: ‘Debian clang version 19.1.3 (2)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘iclogcondist_Example.Rmd’ ‘iclogcondist_Example.pdf’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [8s/8s] NOTE ic_UMLE: no visible global function definition for ‘tail’ iclogcondist_visualization: no visible binding for global variable ‘true_values_log’ iclogcondist_visualization: no visible binding for global variable ‘log_F_est’ iclogcondist_visualization: no visible binding for global variable ‘true_values’ iclogcondist_visualization: no visible binding for global variable ‘F_est’ neg_log_like: no visible global function definition for ‘eta_to_phi_cpp’ plot.iclogcondist : prepare_plot_data: no visible binding for global variable ‘tau’ plot.iclogcondist : prepare_plot_data: no visible binding for global variable ‘tau_lead’ plot.iclogcondist : prepare_plot_data: no visible binding for global variable ‘.’ plot.iclogcondist: no visible binding for global variable ‘tau’ ptlnorm: no visible global function definition for ‘plnorm’ ptweibull: no visible global function definition for ‘pweibull’ qtllogis : : no visible global function definition for ‘uniroot’ qtlnorm: no visible global function definition for ‘qlnorm’ qtlnorm: no visible global function definition for ‘plnorm’ qtlnorm : : no visible global function definition for ‘uniroot’ qtlnorm : : : no visible global function definition for ‘plnorm’ qtweibull: no visible global function definition for ‘qweibull’ qtweibull: no visible global function definition for ‘pweibull’ qtweibull : : no visible global function definition for ‘uniroot’ qtweibull : : : no visible global function definition for ‘pweibull’ rtlnorm: no visible global function definition for ‘rlnorm’ rtweibull: no visible global function definition for ‘rweibull’ rtweibull: no visible global function definition for ‘runif’ simulate_ic_data: no visible global function definition for ‘runif’ Undefined global functions or variables: . F_est eta_to_phi_cpp log_F_est plnorm pweibull qlnorm qweibull rlnorm runif rweibull tail tau tau_lead true_values true_values_log uniroot Consider adding importFrom("stats", "plnorm", "pweibull", "qlnorm", "qweibull", "rlnorm", "runif", "rweibull", "uniroot") importFrom("utils", "tail") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'iclogcondist_visualization.Rd': \examples lines wider than 100 characters: iclogcondist_visualization(X = lgnm, range = c(0, 10), fit_list = list("UMLE" = fit_UMLE,"LCMLE" = fit_LCMLE)) These lines will be truncated in the PDF manual. * 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 ... ERROR Warning: parse error in file 'lines': 8: unexpected '[' 22: case_II_X(event_times, survey_times) 23: [ ^ ** will not attempt to run examples * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] 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 ... SKIPPED * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] 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, 4 NOTEs