* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ciu.Rcheck’
* using R Under development (unstable) (2025-06-04 r88278)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3)
    Debian flang-new version 19.1.7 (3)
* running under: Debian GNU/Linux 13 (trixie)
* 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 ... [4s/5s] 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 executable files ... 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 for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘ciu’ can be installed ... [3s/3s] 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 ... [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 ... [6s/6s] 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 ... [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 examples ... [92s/92s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
ciu.plots.beeswarm          57.399  0.156  57.587
ciu.explain.long.data.frame 29.588  0.448  30.152
* 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: 4 NOTEs