* using log directory ‘/srv/hornik/tmp/CRAN/RCPA.Rcheck’
* using R Under development (unstable) (2023-11-15 r85536)
* 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 ‘RCPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCPA’ version ‘0.1.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Ha Nguyen <hvn0006@auburn.edu>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Efron (16:5)
  Gu (17:5)
  Korotkevich (15:5)
  Ritchie (12:5)
  al (12:16, 13:13, 14:17, 15:20, 16:14)
  et (12:13, 13:10, 14:14, 15:17, 16:11)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2023-11-12 for policy violation.

  On Internet access.
* 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 ‘RCPA’ can be installed ... [22s/22s] 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [30s/30s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'getGeneSets.Rd':
  \examples lines wider than 100 characters:
     GOterms <- getGeneSets("GO", taxid = 9606, namespace = "biological_process", minSize = 10, maxSize = 1000)

Rd file 'plotMA.Rd':
  \examples lines wider than 100 characters:
     plotObj <- RCPA::plotMA(rowData(RNASeqDEExperiment), logFCThreshold = 0.5) + ggtitle("RNASeq - GSE153873")

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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [24s/31s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
getCommonDEGenes 4.201  0.229   8.832
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [1s/1s] 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