* using log directory '/home/kingaa/projects/Rpkg/ouch/revdep/surface.Rcheck'
* using R version 4.3.0 (2023-04-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'surface/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'surface' version '0.5'
* 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 serialization versions ... OK
* checking whether package 'surface' can be installed ... OK
* checking installed package size ... OK
* 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 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 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/19s] NOTE
surfaceBackward: local variable ‘n’ assigned but may not be used
surfaceBackward: local variable ‘nt’ assigned but may not be used
surfaceForward: local variable ‘n’ assigned but may not be used
surfaceForward: local variable ‘nt’ assigned but may not be used
surfaceSimulate : phytransform: no visible global function definition
  for ‘rescale’
surfaceTraitPlot: local variable ‘nnode’ assigned but may not be used
surfaceTreePlot: local variable ‘nnode’ assigned but may not be used
Undefined global functions or variables:
  rescale

Found if() conditions comparing class() to string:
File ‘surface/R/addRegime.R’: if (class(oldfit) != "list") ...
File ‘surface/R/addRegime.R’: if (class(te) == "try-error") ...
File ‘surface/R/collapseRegimes.R’: if (class(te) == "try-error") ...
File ‘surface/R/propRegMatch.R’: if (class(fit1) == "list") ...
File ‘surface/R/propRegMatch.R’: if (class(fit2) == "list") ...
File ‘surface/R/propRegMatch.R’: if (class(fit1) == "hansentree") ...
File ‘surface/R/propRegMatch.R’: if (class(fit2) == "hansentree") ...
File ‘surface/R/runSurface.R’: if (class(tree) != "phylo") ...
File ‘surface/R/surfaceSimulate.R’: if (class(hansenfit) == "hansentree") ...
File ‘surface/R/surfaceSimulate.R’: if (class(hansenfit[[1]]) == "hansentree") ...
File ‘surface/R/surfaceSimulate.R’: if (class(phy) == "phylo") ...
File ‘surface/R/surfaceSimulate.R’: if (class(phy) == "phylo") ...
File ‘surface/R/surfaceTraitPlot.R’: if (length(fit) > 1 | class(fit) == "list") ...
Use inherits() (or maybe is()) instead.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [43s/13s] OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
propRegMatch  2.975 12.143   2.325
startingModel 1.232  5.042   1.095
getAIC        1.172  4.470   0.873
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [1645s/170s] 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
