* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/frailtyMMpen.Rcheck’ * using R Under development (unstable) (2024-04-24 r86484) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 18.1.4 flang-new version 18.1.4 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘frailtyMMpen/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘frailtyMMpen’ version ‘1.2.1’ * package encoding: UTF-8 * 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 ‘frailtyMMpen’ can be installed ... [55s/49s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/frailtyMMpen-00install.html' for details. * used C++ compiler: ‘clang version 18.1.4’ * checking installed package size ... OK * checking package 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 ... 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [24s/30s] OK * checking Rd files ... NOTE checkRd: (-1) frailtyMM.Rd:71: Lost braces 71 | \if{latex}{\out{\begin{center}}{\figure{fig1.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:77: Lost braces 77 | \if{latex}{\out{\begin{center}}{\figure{fig4.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:82: Lost braces 82 | \if{latex}{\out{\begin{center}}{\figure{fig5.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:88: Lost braces 88 | \if{latex}{\out{\begin{center}}{\figure{fig6.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:93: Lost braces 93 | \if{latex}{\out{\begin{center}}{\figure{fig7.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:98: Lost braces 98 | \if{latex}{\out{\begin{center}}{\figure{fig8.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:103: Lost braces 103 | \if{latex}{\out{\begin{center}}{\figure{fig9.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:108: Lost braces 108 | \if{latex}{\out{\begin{center}}{\figure{fig10.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:113: Lost braces 113 | \if{latex}{\out{\begin{center}}{\figure{fig11.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:118: Lost braces 118 | \if{latex}{\out{\begin{center}}{\figure{fig12.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:123: Lost braces 123 | \if{latex}{\out{\begin{center}}{\figure{fig13.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:128: Lost braces 128 | \if{latex}{\out{\begin{center}}{\figure{fig14.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMM.Rd:136: Lost braces; missing escapes or markup? 136 | is fitted, please use {1,2...,K} to denote the event id from the input data. To run the recurrent event model, | ^ checkRd: (-1) frailtyMM.Rd:50: Lost braces; missing escapes or markup? 50 | \item{id}{id for individuals or clusters, {1,2...,a}. Note that, since the original id may not be the sequence starting from 1, this output | ^ checkRd: (-1) frailtyMMpen.Rd:84: Lost braces 84 | \if{latex}{\out{\begin{center}}{\figure{fig15.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMMpen.Rd:89: Lost braces 89 | \if{latex}{\out{\begin{center}}{\figure{fig16.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMMpen.Rd:94: Lost braces 94 | \if{latex}{\out{\begin{center}}{\figure{fig17.png}{options: width=5in}}\out{\end{center}}} | ^ checkRd: (-1) frailtyMMpen.Rd:65: Lost braces; missing escapes or markup? 65 | \item{id}{id for individuals or clusters, {1,2...,a}. Note that, since the original id may not be the sequence starting from 1, this output | ^ * 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 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 ... OK * checking examples ... OK * checking PDF version of manual ... [14s/19s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 NOTE