* using log directory ‘/srv/hornik/tmp/CRAN/surface.Rcheck’
* using R Under development (unstable) (2024-07-30 r86939)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (3)
    Debian flang-new version 18.1.8 (3)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘surface/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘surface’ version ‘0.6’
* checking CRAN incoming feasibility ... [4s/5s] NOTE
Maintainer: ‘Travis Ingram <travis.ingram@otago.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Travis",
                    family = "Ingram",
                    role = c("aut", "cre"),
                    email = "travis.ingram@otago.ac.nz")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.
* 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 ... [5s/5s] 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/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 ... [8s/8s] NOTE
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 ... [0s/0s] 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 ... [0s/0s] 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 ... [4s/4s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [41s/41s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs