* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/phylopomp.Rcheck'
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'phylopomp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phylopomp' version '0.10.3.0'
* 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 'phylopomp' can be installed ... [52s/63s] OK
* used C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0'
* used C++ compiler: 'g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0'
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
* 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 R 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 startup messages can be suppressed ... 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 ... [21s/13s] OK
* checking Rd files ... 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 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 installed files from 'inst/doc' ... OK
* checking examples ... [16s/16s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
3a4,33
> Registered S3 methods overwritten by 'treeio':
>   method              from    
>   MRCA.phylo          tidytree
>   MRCA.treedata       tidytree
>   Nnode.treedata      tidytree
>   Ntip.treedata       tidytree
>   ancestor.phylo      tidytree
>   ancestor.treedata   tidytree
>   child.phylo         tidytree
>   child.treedata      tidytree
>   full_join.phylo     tidytree
>   full_join.treedata  tidytree
>   groupClade.phylo    tidytree
>   groupClade.treedata tidytree
>   groupOTU.phylo      tidytree
>   groupOTU.treedata   tidytree
>   inner_join.phylo    tidytree
>   inner_join.treedata tidytree
>   is.rooted.treedata  tidytree
>   nodeid.phylo        tidytree
>   nodeid.treedata     tidytree
>   nodelab.phylo       tidytree
>   nodelab.treedata    tidytree
>   offspring.phylo     tidytree
>   offspring.treedata  tidytree
>   parent.phylo        tidytree
>   parent.treedata     tidytree
>   root.treedata       tidytree
>   rootnode.phylo      tidytree
>   sibling.phylo       tidytree
5a6,35
> Registered S3 methods overwritten by 'treeio':
>   method              from    
>   MRCA.phylo          tidytree
>   MRCA.treedata       tidytree
>   Nnode.treedata      tidytree
>   Ntip.treedata       tidytree
>   ancestor.phylo      tidytree
>   ancestor.treedata   tidytree
>   child.phylo         tidytree
>   child.treedata      tidytree
>   full_join.phylo     tidytree
>   full_join.treedata  tidytree
>   groupClade.phylo    tidytree
>   groupClade.treedata tidytree
>   groupOTU.phylo      tidytree
>   groupOTU.treedata   tidytree
>   inner_join.phylo    tidytree
>   inner_join.treedata tidytree
>   is.rooted.treedata  tidytree
>   nodeid.phylo        tidytree
>   nodeid.treedata     tidytree
>   nodelab.phylo       tidytree
>   nodelab.treedata    tidytree
>   offspring.phylo     tidytree
>   offspring.treedata  tidytree
>   parent.phylo        tidytree
>   parent.treedata     tidytree
>   root.treedata       tidytree
>   rootnode.phylo      tidytree
>   sibling.phylo       tidytree
3a4,33
> Registered S3 methods overwritten by 'treeio':
>   method              from    
>   MRCA.phylo          tidytree
>   MRCA.treedata       tidytree
>   Nnode.treedata      tidytree
>   Ntip.treedata       tidytree
>   ancestor.phylo      tidytree
>   ancestor.treedata   tidytree
>   child.phylo         tidytree
>   child.treedata      tidytree
>   full_join.phylo     tidytree
>   full_join.treedata  tidytree
>   groupClade.phylo    tidytree
>   groupClade.treedata tidytree
>   groupOTU.phylo      tidytree
>   groupOTU.treedata   tidytree
>   inner_join.phylo    tidytree
>   inner_join.treedata tidytree
>   is.rooted.treedata  tidytree
>   nodeid.phylo        tidytree
>   nodeid.treedata     tidytree
>   nodelab.phylo       tidytree
>   nodelab.treedata    tidytree
>   offspring.phylo     tidytree
>   offspring.treedata  tidytree
>   parent.phylo        tidytree
>   parent.treedata     tidytree
>   root.treedata       tidytree
>   rootnode.phylo      tidytree
>   sibling.phylo       tidytree
 [117s/90s] OK
* checking PDF version of manual ... 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
