* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ImputeLongiCovs.Rcheck’ * using R Under development (unstable) (2024-04-27 r86487) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.4 (1) Debian flang-new version 18.1.4 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘ImputeLongiCovs/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ImputeLongiCovs’ version ‘0.1.0’ * 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 serialization versions ... OK * checking whether package ‘ImputeLongiCovs’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/ImputeLongiCovs-00install.html' for details. * 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/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 ... [7s/8s] OK * checking Rd files ... [0s/1s] NOTE checkRd: (-1) analyses_data.Rd:19: Lost braces; missing escapes or markup? 19 | \item {patient_id}: {Unique identifier for each patient} | ^ checkRd: (-1) analyses_data.Rd:20: Lost braces; missing escapes or markup? 20 | \item {tran_Year}: {numeric, starting from 1 up to the number of transitions} | ^ checkRd: (-1) analyses_data.Rd:21: Lost braces; missing escapes or markup? 21 | \item {transition_year}: {text explanation of the transition} | ^ checkRd: (-1) analyses_data.Rd:22: Lost braces; missing escapes or markup? 22 | \item {state_from}: {the state at the beginning of a transition} | ^ checkRd: (-1) analyses_data.Rd:23: Lost braces; missing escapes or markup? 23 | \item {state_to}: {the state at the end of a transition} | ^ checkRd: (-1) analyses_data.Rd:24: Lost braces; missing escapes or markup? 24 | \item {prob_matrix}: {the probability matrix that was generated by the initial data} | ^ checkRd: (-1) analyses_data.Rd:25: Lost braces; missing escapes or markup? 25 | \item {cardio_state_from}: {cardiovascular disease at the beginning of the transition, binary, if 1 == Yes, else No} | ^ checkRd: (-1) analyses_data.Rd:26: Lost braces; missing escapes or markup? 26 | \item {cardio_state_to}: {cardiovascular disease at the end of the transition, binary, if 1 == Yes, else No} | ^ checkRd: (-1) analyses_data.Rd:27: Lost braces; missing escapes or markup? 27 | \item {flu_vaccination_state_from}: {flu vaccination at the end of the transition, binary, if 1 == Yes, else No} | ^ checkRd: (-1) analyses_data.Rd:28: Lost braces; missing escapes or markup? 28 | \item {flu_vaccination_state_to}: {flu vaccination disease at the end of the transition, binary, if 1 == Yes, else No} | ^ checkRd: (-1) initial_data.Rd:19: Lost braces; missing escapes or markup? 19 | \item {patient_id}: {Unique identifier for each patient} | ^ checkRd: (-1) initial_data.Rd:20: Lost braces; missing escapes or markup? 20 | \item {tran_Year}: {numeric, starting from 1 up to the number of transitions} | ^ checkRd: (-1) initial_data.Rd:21: Lost braces; missing escapes or markup? 21 | \item {transition_year}: {text explanation of the transition} | ^ checkRd: (-1) initial_data.Rd:22: Lost braces; missing escapes or markup? 22 | \item {state_from}: {the state at the beginning of a transition} | ^ checkRd: (-1) initial_data.Rd:23: Lost braces; missing escapes or markup? 23 | \item {state_to}: {the state at the end of a transition} | ^ checkRd: (-1) initial_data.Rd:24: Lost braces; missing escapes or markup? 24 | \item {cardio_state_from}: {cardiovascular disease at the beginning of the transition, binary, if 1 == Yes, else No} | ^ checkRd: (-1) initial_data.Rd:25: Lost braces; missing escapes or markup? 25 | \item {cardio_state_to}: {cardiovascular disease at the end of the transition, binary, if 1 == Yes, else No} | ^ checkRd: (-1) initial_data.Rd:26: Lost braces; missing escapes or markup? 26 | \item {flu_vaccination_state_from}: {flu vaccination at the end of the transition, binary, if 1 == Yes, else No} | ^ checkRd: (-1) initial_data.Rd:27: Lost braces; missing escapes or markup? 27 | \item {flu_vaccination_state_to}: {flu vaccination disease at the end of the transition, binary, if 1 == Yes, else No} | ^ * 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 ... [17s/20s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed impute_categorical_covariates 12.494 0.135 15.224 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [12s/14s] OK * checking PDF version of manual ... [5s/7s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 NOTE