* using log directory ‘/srv/hornik/tmp/CRAN/ClueR.Rcheck’
* using R Under development (unstable) (2023-11-12 r85514)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.4 (1)
    Debian flang-new version 17.0.4 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘ClueR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClueR’ version ‘1.4.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Pengyi Yang <yangpy7@gmail.com>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  CLUster (8:14)
  ClueR (11:77)
  README (12:19)
  al (13:25)
  cmeans (10:15)
  et (13:22)
  kinases (10:73)
  kmeans (10:25)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2023-08-14 as issues were not corrected
    in time.

Found the following (possibly) invalid URLs:
  URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004403 (moved to https://journals.plos.org:443/ploscompbiol/article?id=10.1371/journal.pcbi.1004403)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: http://www.phosphosite.org (moved to https://www.phosphosite.org:443/)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://github.com/PengyiYang/ClueR (moved to https://github.com/PYangLab/ClueR)
    From: DESCRIPTION
    Status: 301
    Message: Moved Permanently
  URL: https://github.com/PengyiYang/ClueR/releases (moved to https://github.com/PYangLab/ClueR/releases)
    From: README.md
    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 Date field is over a month old.
* 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 ‘ClueR’ can be installed ... [1s/1s] 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/2s] NOTE
clustEnrichment: no visible global function definition for ‘pchisq’
clustOptimal: no visible global function definition for ‘kmeans’
clustOptimal: no visible global function definition for ‘cor’
enrichmentTest: no visible global function definition for ‘fisher.test’
fuzzPlot: no visible global function definition for ‘dev.new’
fuzzPlot: no visible global function definition for ‘par’
fuzzPlot: no visible global function definition for ‘lines’
runClue: no visible binding for global variable ‘sd’
runClue: no visible binding for global variable ‘median’
temporalSimu: no visible global function definition for ‘rnorm’
temporalSimu: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor dev.new fisher.test kmeans lines median par pchisq rnorm sd
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cor", "fisher.test", "kmeans", "median", "pchisq",
             "rnorm", "sd")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'runClue.Rd':
  \examples lines wider than 100 characters:
     cl <- runClue(Tc=simuData, annotation=kinaseAnno, rep=3, kRange=2:8, standardise = TRUE, universe = NULL)
     cl <- runClue(Tc=hES, annotation=PhosphoSite.human, rep=5, kRange=2:15, standardise = TRUE, universe = NULL)
     cl <- runClue(Tc=adipocyte.selected, annotation=Pathways.KEGG, rep=3, kRange=10:20, standardise = TRUE, universe = NULL)

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 data for ASCII and uncompressed saves ... OK
* checking examples ... [4s/3s] 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: 3 NOTEs