* using log directory ‘/srv/hornik/tmp/CRAN_pretest/phytoclass.Rcheck’
* using R Under development (unstable) (2024-11-12 r87323)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.1 (1)
    Debian flang-new version 19.1.1 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘phytoclass/DESCRIPTION’ ... OK
* this is package ‘phytoclass’ version ‘2.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] NOTE
Maintainer: ‘Alexander Hayward <phytoclass@outlook.com>’

Found the following (possibly) invalid URLs:
  URL: https://github.com/AndyMcKenzieFromNZ/phytoclass (moved to https://github.com/phytoclass/phytoclass)
    From: DESCRIPTION
    Status: 301
    Message: Moved Permanently
  URL: https://github.com/AndyMcKenzieFromNZ/phytoclass/issues (moved to https://github.com/phytoclass/phytoclass/issues)
    From: DESCRIPTION
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* 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 ‘phytoclass’ can be installed ... [2s/2s] 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 ... [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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘Bounded_weights’ ‘Condition_test’ ‘Default_min_max’ ‘Normalise_S’
  ‘SAALS’ ‘Weight_error’ ‘vectorise’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s/4s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'simulated_annealing.Rd':
  \examples lines wider than 100 characters:
     #Run the new file with your own set up (make sure all names between your data (S), F-marix, and min_max are correct)
       do_matrix_checks = TRUE, #You may want to change this to faults if your naming conventions are different.

These lines will be truncated in the PDF manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/0s] OK
  Running ‘testthat.R’ [0s/0s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [7s/7s] 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: 3 NOTEs