##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings metaseqR2_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/metaseqR2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaseqR2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaseqR2’ version ‘1.14.0’
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘metaseqR2’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... NOTE
getUcscUtr: no visible binding for global variable ‘customDir’
Undefined global functions or variables:
  customDir
* checking Rd files ... OK
* checking Rd metadata ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘metaseqR2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diagplotBoxplot
> ### Title: Boxplots wrapper for the metaseqR2 package
> ### Aliases: diagplotBoxplot
> 
> ### ** Examples
> 
> # Non-normalized boxplot
> require(DESeq2)
> dataMatrix <- metaseqR2:::exampleCountData(2000)
> sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
> diagplotBoxplot(dataMatrix,sampleList)
dev.new(): using pdf(file="Rplots1.pdf")
[1] "/home/biocbuild/bbs-3.18-bioc/meat/metaseqR2.Rcheck/boxplot_raw.x11"
> 
> # Normalized boxplot
> normArgs <- getDefaults("normalization","deseq2")
> object <- normalizeDeseq2(dataMatrix,sampleList,normArgs)
Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = " ")) instead.
converting counts to integer mode
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 1492216 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  downloaded 276 KB
  
  trying URL 'https://code.highcharts.com/highcharts-more.js'
  downloaded 94 KB
  
  trying URL 'https://code.highcharts.com/modules/exporting.js'
  downloaded 18 KB
  
  trying URL 'https://code.highcharts.com/modules/offline-exporting.js'
  downloaded 9688 bytes
  
  trying URL 'https://code.highcharts.com/modules/export-data.js'
  downloaded 11 KB
  
  trying URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/metaseqR2.Rcheck/00check.log’
for details.