* using log directory ‘/home/hornik/tmp/CRAN_special_donttest/RCPA.Rcheck’
* using R Under development (unstable) (2024-10-14 r87233)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-1) 14.2.0
    GNU Fortran (Debian 14.2.0-1) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* using option ‘--run-donttest’
* checking for file ‘RCPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCPA’ version ‘0.2.4’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/4s] NOTE
Maintainer: ‘Ha Nguyen <hvn0006@auburn.edu>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Efron (10:478)
  Gu (10:544)
  Korotkevich (10:428)
  Ritchie (10:268)
  al (10:179, 10:279, 10:324, 10:380, 10:443, 10:487)
  et (10:176, 10:276, 10:321, 10:377, 10:440, 10:484)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2024-10-10 for policy violation.

  On Internet access.

Found the following (possibly) invalid DOIs:
  DOI: https://doi.org/10.1002/cpz1.1036
    From: inst/CITATION
    Status: 404
    Message: Not Found
* 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 ... [25s/25s] 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [35s/35s] OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [85s/559s] ERROR
Running examples in ‘RCPA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: processAgilent
> ### Title: Process and normalize agilent-based dataset
> ### Aliases: processAgilent
> 
> ### ** Examples
> 
> ## No test: 
> library(RCPA)
> geoId <- "GSE28522"
> 
> downloadPath <- file.path(tempdir(), geoId)
> fileList <- RCPA::downloadGEO(GEOID = geoId, protocol = "agilent",
+                               platform ="GPL4133", destDir = downloadPath)
The destination directory does not exist. It will be created.
Found 1 file(s)
GSE28522_series_matrix.txt.gz
Error in max(getOption("timeout"), 120) : 
  invalid 'type' (list) of argument
Calls: <Anonymous> ... .downloadGEOObject -> getGEO -> getAndParseGSEMatrices -> downloadFile
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [2s/2s] OK
* checking PDF version of manual ... [4s/4s] 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 ... NOTE
Found the following files/directories:
  ‘calibre_7.19.0_tmp_nwihofdr’ ‘calibre_7.19.0_tmp_qy9q84yw’
* DONE
Status: 1 ERROR, 2 NOTEs