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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:pcaExplorer.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings pcaExplorer_2.27.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/pcaExplorer.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘pcaExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pcaExplorer’ version ‘2.27.1’
* 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 ‘pcaExplorer’ 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 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 startup messages can be suppressed ... 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
pcaExplorer: no visible binding for '<<-' assignment to
  ‘pcaexplorer_env’
pcaExplorer : <anonymous>: no visible binding for global variable
  ‘airway’
pcaExplorer : <anonymous>: no visible binding for global variable
  ‘pcaexplorer_env’
Undefined global functions or variables:
  airway pcaexplorer_env
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘pcaExplorer.Rmd’ using ‘UTF-8’... OK
  ‘upandrunning.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/pcaExplorer.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL pcaExplorer
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘pcaExplorer’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationForge’
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationForge’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationForge’
** testing if installed package keeps a record of temporary installation path
* DONE (pcaExplorer)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(pcaExplorer)

Welcome to pcaExplorer v2.27.1

If you use pcaExplorer in your work, please cite:

Federico Marini, Harald Binder
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
BMC Bioinformatics, 2019 - https://doi.org/10.1186/s12859-019-2879-1

Warning message:
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'AnnotationForge' 
> 
> test_check("pcaExplorer")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 17 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
 71.287   2.847  74.125