* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/phytools.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (Debian 13.2.0-24) 13.2.0
    GNU Fortran (Debian 13.2.0-24) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘phytools/DESCRIPTION’ ... OK
* this is package ‘phytools’ version ‘2.1-1’
* 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 ‘phytools’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/phytools-00install.html' 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 ... [3s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
* checking whether the package can be unloaded cleanly ... [3s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
* checking loading without being on the library search path ... [3s/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 ... [167s/197s] OK
* checking Rd files ... [3s/4s] OK
* 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 ... [3s/4s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [58s/65s] OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
anc.Bayes 6.553  0.207   7.344
contMap   4.968  0.059   5.322
fitMk     4.633  0.044   5.053
ltt       4.479  0.042   6.050
genSeq    4.461  0.000   5.837
* checking PDF version of manual ... [18s/22s] OK
* checking HTML version of manual ... [13s/21s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: OK