* using log directory ‘/srv/hornik/tmp/CRAN_pretest/confidenceSim.Rcheck’ * using R Under development (unstable) (2025-10-13 r88918) * 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 ‘confidenceSim/DESCRIPTION’ ... OK * this is package ‘confidenceSim’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Freda Werdiger ’ 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘confidenceSim’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... 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 ... [3s/3s] NOTE collectNodes: no visible binding for global variable ‘read.csv’ getAccrual: no visible global function definition for ‘rexp’ getBoundsFromConfidence: no visible global function definition for ‘qnorm’ getDataBin: no visible global function definition for ‘rbinom’ getDataCont: no visible global function definition for ‘rnorm’ getDataOrd: no visible global function definition for ‘rmultinom’ getGSDesign: no visible global function definition for ‘pastt0’ getSuffStats : : no visible global function definition for ‘sd’ getparlist: no visible global function definition for ‘pastt0’ runSingleTrial: no visible global function definition for ‘tail’ runSingleTrial: no visible global function definition for ‘read.csv’ runSingleTrial: no visible global function definition for ‘write.csv’ Undefined global functions or variables: pastt0 qnorm rbinom read.csv rexp rmultinom rnorm sd tail write.csv Consider adding importFrom("stats", "qnorm", "rbinom", "rexp", "rmultinom", "rnorm", "sd") importFrom("utils", "read.csv", "tail", "write.csv") to your NAMESPACE file. * checking Rd files ... [0s/0s] NOTE checkRd: (-1) getConfidenceFromBounds.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getConfidenceFromBounds.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getConfidenceFromBounds.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getConfidenceFromBounds.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getConfidenceFromBounds.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getCurrentData.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getCurrentData.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getCurrentData.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getCurrentData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getCurrentData.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runSingleTrial.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [0s/0s] ERROR Running examples in ‘confidenceSim-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: collectNodes > ### Title: Collect Nodes > ### Aliases: collectNodes > > ### ** Examples > > # load libraries for parallelization > library(parallel) > library(pbapply) > # load inputs from data > data(inputs) > # Example of input list to generate a two-arm-two-stage trial with binary outcome data > # Run 4 simulations with lapply without parallelization > num.sims <- 4 > conf <- lapply( + 1:num.sims, + runSingleTrial, + inputs=inputs, + save.plot=FALSE, + print=FALSE, + directory = '') Warning in gzfile(file, "wb") : cannot open compressed file '/865722/random_state_accrual.RData', probable reason 'No such file or directory' Error in gzfile(file, "wb") : cannot open the connection Calls: lapply -> FUN -> save -> gzfile Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [5s/4s] OK Running ‘testthat.R’ [4s/4s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] NOTE Found the following HTML validation problems: runSingleTrial.html:72:146 (runSingleTrial.Rd:34): Error: is not recognized! runSingleTrial.html:72:146 (runSingleTrial.Rd:34): Warning: discarding unexpected * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 4 NOTEs