* using log directory 'd:/RCompile/CRANincoming/R-devel/ciu.Rcheck'
* using R Under development (unstable) (2025-06-04 r88278 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'ciu/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ciu' version '0.8'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [10s] NOTE
Maintainer: 'Kary Främling <Kary.Framling@umu.se>'

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Kary",
                    family = "Främling",
                    role = c("aut", "cre"),
                    email = "kary.framling@umu.se")
as necessary.

Found the following (possibly) invalid URLs:
  URL: https://tel.archives-ouvertes.fr/tel-00825854/document (moved to https://theses.hal.science/tel-00825854/document)
    From: man/ciu-package.Rd
          man/ciu.new.Rd
    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.

The Description field contains
  Främling (2020) <arXiv:2009.13996>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
* 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 hidden files and directories ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.

CRAN-pack does not know about
  .github
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'ciu' can be installed ... OK
* checking installed package size ... OK
* 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 code 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 ... [12s] NOTE
ciu.ggplot.col: no visible binding for global variable 'feature.labels'
ciu.ggplot.col: no visible binding for global variable 'phi'
ciu.ggplot.col: no visible binding for global variable 'Positive.Phi'
ciu.ggplot.contrastive: no visible binding for global variable
  'feature.name'
Undefined global functions or variables:
  Positive.Phi feature.labels feature.name phi
* 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 examples ... [181s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
                              user system elapsed
ciu.plots.beeswarm          113.29   1.36  114.70
ciu.explain.long.data.frame  57.52   0.97   58.53
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... OK
* DONE
Status: 4 NOTEs