- using R version 4.4.1 Patched (2024-08-05 r86980)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (Debian 14.2.0-3) 14.2.0
GNU Fortran (Debian 14.2.0-3) 14.2.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘divDyn/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘divDyn’ version ‘0.8.2’
- 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 ‘divDyn’ can be installed ... OK
See the install log for details.
- used C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’
- used C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
- 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/1s] OK
- checking whether the package can be unloaded cleanly ... [0s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
- checking loading without being on the library search path ... [0s/1s] OK
- checking whether startup messages can be suppressed ... [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 ... [19s/24s] OK
- checking Rd files ... [1s/1s] NOTE
checkRd: (-1) fadlad.Rd:30: Lost braces
30 | \item{diffbin}{\code{(logical)}: Difference-based duration for discreet time (only applicabble to cases when \code{bin} is provided). If set to \code{TRUE}, single-interval taxa will \code{0} durations. Setting this argument to \code{FALSE} will add code{1} to the durations of all taxa.}
| ^
checkRd: (-1) slice.Rd:27: Lost braces
27 | Due to stratigraphic constraints, we can only process deep time data, when it is sliced to discrete bins. It is suggested that you do this separately for most of your analyses. This function is also used by the code{\link{divDyn}} function when \code{age} entries are provided.
| ^
checkRd: (-1) tabinate.Rd:31: Lost braces
31 | Setting both \code{bin} If \code{bin=NULL} and code{tax=NULL}, will run \code{FUN} on the entire dataset (no effect). Providing either \code{bin} or \code{tax} and keeping the other \code{NULL} will iterate \code{FUN} for every \code{bin} or \code{tax} entry (whichever is presented).
| ^
- 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 ... [1s/1s] OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... 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 ... [23s/28s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tabinate 4.983 0.046 6.407
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [167s/220s] OK
- checking PDF version of manual ... [6s/8s] OK
- checking HTML version of manual ... [2s/3s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 NOTE