* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/rotl.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 ‘rotl/DESCRIPTION’ ... OK
* this is package ‘rotl’ version ‘3.1.0’
* 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 ‘rotl’ can be installed ... [11s/13s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/rotl-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 ... [17s/23s] OK
* checking Rd files ... NOTE
checkRd: (-1) get_study_meta.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_study_meta.Rd:57-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_study_meta.Rd:62-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_study_meta.Rd:66: Lost braces; missing escapes or markup?
    66 |   \item {get_study_year} { The year of publication of the study. }
       |         ^
checkRd: (-1) get_study_meta.Rd:66: Lost braces; missing escapes or markup?
    66 |   \item {get_study_year} { The year of publication of the study. }
       |                          ^
checkRd: (-1) rotl.Rd:27-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rotl.Rd:33-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) taxonomy_about.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_about.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_about.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_about.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_about.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_mrca.Rd:43-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_mrca.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_mrca.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_mrca.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_subtree.Rd:35-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_subtree.Rd:40-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_subtree.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy_subtree.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:46-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:64-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:75-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:82-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:88-89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:93-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_about.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:73-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:81-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:86-88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:91-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:100-101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:105-107: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:110-112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:115-116: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:118: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_mrca.Rd:120-121: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:59-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:66-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:79-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:92-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tol_node_info.Rd:98-100: 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [13s/16s] OK
  Running ‘test-all.R’ [13s/16s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [20s/25s] OK
* checking PDF version of manual ... [9s/15s] 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