* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/codyn.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 ‘codyn/DESCRIPTION’ ... OK
* this is package ‘codyn’ version ‘2.0.5’
* 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 ‘codyn’ can be installed ... [15s/20s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/codyn-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 ... [26s/33s] OK
* checking Rd files ... NOTE
checkRd: (-1) RAC_change.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_change.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_change.Rd:43-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_change.Rd:48-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_change.Rd:52-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_change.Rd:57-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_change.Rd:61-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_difference.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_difference.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_difference.Rd:54-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_difference.Rd:58-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_difference.Rd:62-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_difference.Rd:66-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_difference.Rd:70-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_difference.Rd:75-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_difference.Rd:79-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RAC_difference.Rd:85-88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_change.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_change.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_change.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_change.Rd:44-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_difference.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_difference.Rd:52-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_difference.Rd:57-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_difference.Rd:61-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_difference.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_difference.Rd:67-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_difference.Rd:71-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) abundance_difference.Rd:75-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) codyn-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) codyn-package.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) community_diversity.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) community_diversity.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) community_diversity.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) community_diversity.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) community_diversity.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) community_diversity.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) community_stability.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) community_stability.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) community_structure.Rd:29-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) community_structure.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) community_structure.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) community_structure.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) community_structure.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) community_structure.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) community_structure.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) community_structure.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) community_structure.Rd:46-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) confint.cyclic_shift.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) confint.cyclic_shift.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) confint.cyclic_shift.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) curve_change.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) curve_change.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) curve_change.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) curve_difference.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) curve_difference.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) curve_difference.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) curve_difference.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) curve_difference.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) curve_difference.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) curve_difference.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mean_rank_shift.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mean_rank_shift.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mean_rank_shift.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multivariate_change.Rd:43-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multivariate_change.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multivariate_change.Rd:49-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multivariate_change.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multivariate_difference.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multivariate_difference.Rd:46-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multivariate_difference.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multivariate_difference.Rd:50-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multivariate_difference.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multivariate_difference.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rank_shift.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rank_shift.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rank_shift.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rate_change.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rate_change.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rate_change_interval.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rate_change_interval.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rate_change_interval.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) synchrony.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) synchrony.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) synchrony.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) synchrony.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) turnover.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turnover.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turnover.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turnover.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) turnover.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) turnover.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) variance_ratio.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) variance_ratio.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) variance_ratio.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) variance_ratio.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) variance_ratio.Rd:49: 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 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 ... [14s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [98s/133s] OK
  Running ‘testthat.R’ [98s/132s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [55s/76s] OK
* checking PDF version of manual ... [9s/13s] 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