* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/ccoptimalmatch.Rcheck’ * using R Under development (unstable) (2024-04-05 r86344) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘ccoptimalmatch/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ccoptimalmatch’ 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 whether package ‘ccoptimalmatch’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/ccoptimalmatch-00install.html' for details. * checking package directory ... 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 ... 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 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 ... OK * checking Rd files ... NOTE checkRd: (-1) being_processed.Rd:19: Lost braces; missing escapes or markup? 19 | \item {cluster_case}: {each case forms a cluster with all poosible controls to be matched} | ^ checkRd: (-1) being_processed.Rd:20: Lost braces; missing escapes or markup? 20 | \item {Patient_Id}: {Unique identifier for each patient} | ^ checkRd: (-1) being_processed.Rd:21: Lost braces; missing escapes or markup? 21 | \item {case_control}: {binary, if case==Colorectal Cancer, else control} | ^ checkRd: (-1) being_processed.Rd:22: Lost braces; missing escapes or markup? 22 | \item {case_ind}: {binary, if 1==case, else control} | ^ checkRd: (-1) being_processed.Rd:23: Lost braces; missing escapes or markup? 23 | \item {JCG}: {Year of Contact} | ^ checkRd: (-1) being_processed.Rd:24: Lost braces; missing escapes or markup? 24 | \item {entry_year}: {the year that the patient first entrered the database} | ^ checkRd: (-1) being_processed.Rd:25: Lost braces; missing escapes or markup? 25 | \item {CI}: {Comorbidity Index. Count of chronic diseases before index data} | ^ checkRd: (-1) being_processed.Rd:26: Lost braces; missing escapes or markup? 26 | \item {age_diff}: {difference of age between cases and controls} | ^ checkRd: (-1) being_processed.Rd:27: Lost braces; missing escapes or markup? 27 | \item {fup_diff}: {difference of follow-up between cases and controls} | ^ checkRd: (-1) being_processed.Rd:28: Lost braces; missing escapes or markup? 28 | \item {total_control_per_case}: {total controls that are available to be pooled per case} | ^ checkRd: (-1) being_processed.Rd:29: Lost braces; missing escapes or markup? 29 | \item {freq_of_controls}: {how many times the control is available to be matched for different cases} | ^ checkRd: (-1) not_processed.Rd:19: Lost braces; missing escapes or markup? 19 | \item {Patient_Id}: {Unique identifier for each patient} | ^ checkRd: (-1) not_processed.Rd:20: Lost braces; missing escapes or markup? 20 | \item {JCG}: {Year of Contact} | ^ checkRd: (-1) not_processed.Rd:21: Lost braces; missing escapes or markup? 21 | \item {Birth_Year}: {Patient's year of birth} | ^ checkRd: (-1) not_processed.Rd:22: Lost braces; missing escapes or markup? 22 | \item {Gender}: {Patient's Gender} | ^ checkRd: (-1) not_processed.Rd:23: Lost braces; missing escapes or markup? 23 | \item {Practice_Id}: {Patient's general practice} | ^ checkRd: (-1) not_processed.Rd:24: Lost braces; missing escapes or markup? 24 | \item {case_control}: {binary, if case==Colorectal Cancer, else control} | ^ checkRd: (-1) not_processed.Rd:25: Lost braces; missing escapes or markup? 25 | \item {entry_year}: {the year that the patient first entrered the database} | ^ checkRd: (-1) not_processed.Rd:26: Lost braces; missing escapes or markup? 26 | \item {fup_diff}: {difference of follow-up between cases and controls} | ^ checkRd: (-1) not_processed.Rd:27: Lost braces; missing escapes or markup? 27 | \item {CI}: {Comorbidity Index. Count of chronic diseases before index data} | ^ * 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 ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [42s/59s] OK * checking PDF version of manual ... [7s/12s] 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