* using log directory 'd:/RCompile/CRANincoming/R-devel/PCMBase.Rcheck' * using R Under development (unstable) (2024-03-08 r86072 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'PCMBase/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PCMBase' version '1.2.14' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [10s] NOTE Maintainer: 'Venelin Mitov ' Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Found the following (possibly) invalid URLs: URL: https://codecov.io/github/venelin/PCMBase?branch=master (moved to https://app.codecov.io/github/venelin/PCMBase?branch=master) From: README.md Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * 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 'PCMBase' can be installed ... OK * checking installed package size ... 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 R 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 whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: 'BiocManager' 'abind' 'covr' 'cowplot' 'ggtree' 'knitr' 'mvSLOUCH' 'rmarkdown' 'testthat' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [30s] OK * checking Rd files ... NOTE checkRd: (-1) PCM.Rd:67-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) PCM.Rd:69-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) PCM.Rd:71-72: Lost braces in \itemize; meant \describe ? checkRd: (-1) PCMGenerateModelTypes.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) PCMGenerateModelTypes.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) PCMOptions.Rd:13-15: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:16-18: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:19: Lost braces 19 | \item{\item{PCMBase.Raise.Lik.Errors} }{Should numerical and other sort of | ^ checkRd: (-1) PCMOptions.Rd:19-23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:24-26: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:27-32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:33-38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:39-43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:44-50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:62-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:69-73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMOptions.Rd:74-81: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMPExpxMeanExp.Rd:5: Lost braces; missing escapes or markup? 5 | \title{Create a function of time that calculates (1-exp(-lambda_{ij}*time))/lambda_{ij} | ^ checkRd: (-1) PCMPExpxMeanExp.Rd:5: Lost braces; missing escapes or markup? 5 | \title{Create a function of time that calculates (1-exp(-lambda_{ij}*time))/lambda_{ij} | ^ checkRd: (-1) PCMPExpxMeanExp.Rd:6: Lost braces; missing escapes or markup? 6 | for every element lambda_{ij} of the input matrix Lambda_ij.} | ^ checkRd: (-1) PCMPExpxMeanExp.Rd:31: Lost braces; missing escapes or markup? 31 | Create a function of time that calculates (1-exp(-lambda_{ij}*time))/lambda_{ij} | ^ checkRd: (-1) PCMPExpxMeanExp.Rd:31: Lost braces; missing escapes or markup? 31 | Create a function of time that calculates (1-exp(-lambda_{ij}*time))/lambda_{ij} | ^ checkRd: (-1) PCMPExpxMeanExp.Rd:32: Lost braces; missing escapes or markup? 32 | for every element lambda_{ij} of the input matrix Lambda_ij. | ^ checkRd: (-1) PCMPExpxMeanExp.Rd:35: Lost braces; missing escapes or markup? 35 | the function (1-exp(-lambda_{ij}*time))/lambda_{ij} corresponds to the product | ^ checkRd: (-1) PCMPExpxMeanExp.Rd:35: Lost braces; missing escapes or markup? 35 | the function (1-exp(-lambda_{ij}*time))/lambda_{ij} corresponds to the product | ^ checkRd: (-1) PCMPExpxMeanExp.Rd:36: Lost braces; missing escapes or markup? 36 | of the CDF of an exponential distribution with rate Lambda_{ij} multiplied by its mean value (mean waiting time). | ^ checkRd: (-1) PCMPExpxMeanExp.Rd:28: Lost braces; missing escapes or markup? 28 | above function or the limit, time, if |Lambda_{ij}|<=trehshold0. | ^ checkRd: (-1) PCMTrajectory.Rd:59-61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTrajectory.Rd:62-64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeDropClade.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeDropClade.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeDtNodes.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeDtNodes.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeDtNodes.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeDtNodes.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeDtNodes.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeDtNodes.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeDtNodes.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeDtNodes.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeExtractClade.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeExtractClade.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeSplitAtNode.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeSplitAtNode.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeSplitAtNode.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) PCMTreeSplitAtNode.Rd:31: 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 ... 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 ... [11s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... OK Running 'testthat.R' * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [13s] OK * checking PDF version of manual ... [20s] OK * checking HTML version of manual ... [18s] OK * DONE Status: 3 NOTEs