* using log directory ‘/home/hornik/tmp/CRAN_special_donttest/RCPA.Rcheck’
* using R Under development (unstable) (2024-10-04 r87206)
* 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 ... [5s/5s] NOTE
Maintainer: ‘Ha Nguyen <hvn0006@auburn.edu>’

Suggests or Enhances not in mainstream repositories:
  org.Hs.eg.db, pd.hg.u133.plus.2

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 ... INFO
Package suggested but not available for checking: ‘pd.hg.u133.plus.2’
* 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 ... [7s/7s] 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 ... [108s/169s] 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
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
processAffymetrix       25.044  1.613  30.245
getCePaPathwayCatalogue 16.440  0.256  19.566
getSPIAKEGGNetwork      15.599  0.112  17.316
getCommonDEGenes         7.116  0.060  12.792
plotKEGGMap              4.894  0.296  12.581
plotDEGeneHeatmap        3.209  0.083   6.798
downloadGEO              2.720  0.276  20.074
* 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_p6m7hknd’ ‘calibre_7.19.0_tmp_pa_szyol’
* DONE
Status: 1 ERROR, 2 NOTEs