- using R Under development (unstable) (2024-06-26 r86840)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 18.1.8 (1)
Debian flang-new version 18.1.8 (1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘paleotree/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘paleotree’ version ‘3.4.5’
- 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 ‘paleotree’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... 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 ... [4s/5s] OK
- checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
- checking whether the package can be unloaded cleanly ... [4s/5s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
- checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
- checking loading without being on the library search path ... [4s/4s] 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 ... [76s/89s] OK
- checking Rd files ... [2s/2s] NOTE
checkRd: (-1) branchClasses.Rd:15: Lost braces; missing escapes or markup?
15 | \item{whichExtant}{A logical vector with length equal to number of tips in the tree. A {TRUE} value indicates
| ^
checkRd: (-1) minCharChange.Rd:134: Lost braces; missing escapes or markup?
134 | an identical name in function \code{phyDat} in package {phangorn}.
| ^
checkRd: (-1) resolveTreeChar.Rd:98: Lost braces; missing escapes or markup?
98 | an identical name in function \code{phyDat} in package {phangorn}.
| ^
checkRd: (-1) simFossilRecord.Rd:44: Lost braces
44 | since its origination time is code{D},
| ^
- 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/1s] OK
- checking data for ASCII and uncompressed saves ... OK
- checking examples ... [101s/117s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
termTaxa 9.233 0.020 11.376
taxa2phylo 8.444 0.007 10.860
sampleRanges 7.965 0.025 10.284
compareTimescaling 6.737 0.195 7.660
DiversityCurves 6.792 0.101 8.252
occData2timeList 6.800 0.030 7.368
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [165s/184s] OK
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [164s/184s]
- checking PDF version of manual ... [16s/19s] OK
- checking HTML version of manual ... [10s/16s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 NOTE