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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings NormalyzerDE_1.23.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/NormalyzerDE.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘NormalyzerDE/DESCRIPTION’ ... OK
* this is package ‘NormalyzerDE’ version ‘1.23.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘NormalyzerDE’ can be installed ... OK
* 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 code 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 ... OK
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'calculateFeatureCV.Rd':
  ‘sampleReplicateGroups’

Documented arguments not in \usage in Rd file 'verifySummarizedExperiment.Rd':
  ‘fullMatrix’ ‘designMatrix’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘NormalyzerDE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generateStatsReport
> ### Title: Generate full output report plot document. Plots p-value
> ###   histograms for each contrast in the NormalyzerStatistics instance and
> ###   writes these to a PDF report.
> ### Aliases: generateStatsReport
> 
> ### ** Examples
> 
> data(example_stat_summarized_experiment)
> statObj <- NormalyzerStatistics(example_stat_summarized_experiment)
> statObj <- calculateContrasts(statObj, comparisons=c("1-2", "2-3"), 
+   condCol="group", type="limma")
> outputDir <- tempdir()
> generateStatsReport(statObj, "jobName", outputDir)
Error in grDevices::pdf(file = paste(jobDir, "/", suffix, "-", currentJob,  : 
  cannot open file '/tmp/RtmpGseqmi/Norm-stats-report-jobName.pdf'
Calls: generateStatsReport -> setupPlotting -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ...Error in file(con, "w") : cannot open the connection
Execution halted

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL NormalyzerDE
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘NormalyzerDE’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (NormalyzerDE)