* using log directory ‘/srv/hornik/tmp/CRAN/RFlocalfdr.Rcheck’
* using R Under development (unstable) (2023-07-04 r84639)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (1)
    GNU Fortran (Debian 12.2.0-14) 12.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘RFlocalfdr/DESCRIPTION’ ... OK
* this is package ‘RFlocalfdr’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Robert Dunne <rob.dunne@csiro.au>’

New submission

Size of tarball: 15145704 bytes
* 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 ‘RFlocalfdr’ can be installed ... [21s/21s] 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
‘::’ or ‘:::’ imports not declared from:
  ‘randomForest’ ‘ranger’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [3s/3s] NOTE
significant.genes: no visible binding for global variable ‘x’
Undefined global functions or variables:
  x

Found if() conditions comparing class() to string:
File ‘RFlocalfdr/R/fit.to.data.set.R’: if (class(mm1.df) == "try-error" & try.counter == 0) ...
File ‘RFlocalfdr/R/fit.to.data.set.R’: if (class(mm1.df) == "try-error" & (try.counter < 2)) ...
File ‘RFlocalfdr/R/fit.to.data.set.R’: if (class(mm1.df) == "try-error" & try.counter == 3) ...
File ‘RFlocalfdr/R/fit.to.data.set.wrapper.R’: if (class(mm.df3) == "try-error") ...
File ‘RFlocalfdr/R/fit.to.data.set.wrapper.R’: if (class(mm.df1) == "try-error") ...
File ‘RFlocalfdr/R/fit.to.data.set.wrapper.R’: if (class(mm.df2) == "try-error") ...
File ‘RFlocalfdr/R/plotQ.R’: if (class(qq) == "numeric") ...
File ‘RFlocalfdr/R/plotQ.R’: if (class(final.estimates_cc) != "character") ...
File ‘RFlocalfdr/R/plotQ.R’: if (class(qq) == "numeric") ...
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 ... WARNING
Undocumented code objects:
  ‘dsn’ ‘psn’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
‘::’ or ‘:::’ imports not declared from:
  ‘ranger’ ‘vita’
‘library’ or ‘require’ calls not declared from:
  ‘ranger’ ‘vita’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [3s/3s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0s/0s] ERROR
Running examples in ‘RFlocalfdr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: count_variables
> ### Title: count the number of times each variable is used in the a ranger
> ###   forest
> ### Aliases: count_variables
> ### Keywords: counts
> 
> ### ** Examples
> 
> library(ranger)
Error in library(ranger) : there is no package called ‘ranger’
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/1s] OK
  Running ‘testthat.R’ [1s/1s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [2s/2s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 3 WARNINGs, 2 NOTEs