* using log directory ‘/srv/hornik/tmp/CRAN/coxme.Rcheck’ * using R Under development (unstable) (2024-08-20 r87029) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘coxme/DESCRIPTION’ ... OK * this is package ‘coxme’ version ‘2.2-21’ * checking CRAN incoming feasibility ... [4s/4s] Note_to_CRAN_maintainers Maintainer: ‘Terry M. Therneau ’ * 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 serialization versions ... OK * checking whether package ‘coxme’ can be installed ... [8s/8s] OK * used C compiler: ‘Debian clang version 18.1.8 (9)’ * 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 ... [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 ... [9s/9s] OK * checking Rd files ... [0s/0s] 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 ... [0s/0s] 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 for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [3s/3s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [35s/35s] OK Running ‘brfit.R’ [2s/2s] Running ‘lmekin1.R’ [2s/2s] Comparing ‘lmekin1.Rout’ to ‘lmekin1.Rout.save’ ... OK Running ‘lmekin2.R’ [1s/1s] Comparing ‘lmekin2.Rout’ to ‘lmekin2.Rout.save’ ... OK Running ‘nest1.R’ [1s/1s] Comparing ‘nest1.Rout’ to ‘nest1.Rout.save’ ... OK Running ‘nest2.R’ [1s/1s] Comparing ‘nest2.Rout’ to ‘nest2.Rout.save’ ... OK Running ‘refine.R’ [1s/1s] Comparing ‘refine.Rout’ to ‘refine.Rout.save’ ... OK Running ‘refine1.R’ [1s/1s] Comparing ‘refine1.Rout’ to ‘refine1.Rout.save’ ... OK Running ‘refine2.R’ [1s/1s] Comparing ‘refine2.Rout’ to ‘refine2.Rout.save’ ... OK Running ‘refine3.R’ [1s/1s] Comparing ‘refine3.Rout’ to ‘refine3.Rout.save’ ... OK Running ‘shrink.R’ [1s/1s] Comparing ‘shrink.Rout’ to ‘shrink.Rout.save’ ... OK Running ‘slope1.R’ [5s/5s] Comparing ‘slope1.Rout’ to ‘slope1.Rout.save’ ... OK Running ‘slope2.R’ [2s/2s] Comparing ‘slope2.Rout’ to ‘slope2.Rout.save’ ... OK Running ‘slope3.R’ [2s/2s] Comparing ‘slope3.Rout’ to ‘slope3.Rout.save’ ... OK Running ‘slope4.R’ [4s/4s] Comparing ‘slope4.Rout’ to ‘slope4.Rout.save’ ... OK Running ‘strata1.R’ [1s/1s] Comparing ‘strata1.Rout’ to ‘strata1.Rout.save’ ... OK Running ‘test0.R’ [1s/1s] Comparing ‘test0.Rout’ to ‘test0.Rout.save’ ... OK Running ‘test1.R’ [1s/1s] Comparing ‘test1.Rout’ to ‘test1.Rout.save’ ... OK Running ‘test2.R’ [1s/1s] Comparing ‘test2.Rout’ to ‘test2.Rout.save’ ... OK Running ‘test3.R’ [1s/1s] Comparing ‘test3.Rout’ to ‘test3.Rout.save’ ... OK Running ‘test4.R’ [1s/1s] Comparing ‘test4.Rout’ to ‘test4.Rout.save’ ... OK Running ‘twoterm.R’ [1s/1s] Comparing ‘twoterm.Rout’ to ‘twoterm.Rout.save’ ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [22s/22s] OK * checking PDF version of manual ... [4s/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: OK