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CHECK report for pcaExplorer on malbec2

This page was generated on 2020-10-17 11:55:21 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE pcaExplorer PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1280/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcaExplorer 2.14.2
Federico Marini
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/pcaExplorer
Branch: RELEASE_3_11
Last Commit: 5953c87
Last Changed Date: 2020-06-05 18:08:15 -0400 (Fri, 05 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pcaExplorer
Version: 2.14.2
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:pcaExplorer.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings pcaExplorer_2.14.2.tar.gz
StartedAt: 2020-10-17 03:57:42 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:05:22 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 459.8 seconds
RetCode: 0
Status:  OK 
CheckDir: pcaExplorer.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:pcaExplorer.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings pcaExplorer_2.14.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/pcaExplorer.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pcaExplorer’ version ‘2.14.2’
* 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/pcaExplorer.Rcheck/00check.log’
for details.



Installation output

pcaExplorer.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL pcaExplorer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘pcaExplorer’ ...
** using staged installation
** R
** 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 (pcaExplorer)

Tests output

pcaExplorer.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 v2.14.2

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

> 
> test_check("pcaExplorer")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 17 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 76.691   0.885  81.052 

Example timings

pcaExplorer.Rcheck/pcaExplorer-Ex.timings

nameusersystemelapsed
correlatePCs3.2940.0803.382
distro_expr2.4300.0162.446
geneprofiler1.5610.0001.562
genespca3.2030.0043.206
get_annotation3.4680.0493.516
get_annotation_orgdb2.5920.0362.628
hi_loadings2.2060.0042.210
limmaquickpca2go3.0630.0363.099
makeExampleDESeqDataSet_multifac0.3120.0000.312
pair_corr2.1250.0282.205
pca2go2.1440.0162.161
pcaExplorer2.0090.0282.044
pcaplot3.8930.0083.903
pcaplot3d2.0400.0162.097
pcascree2.8750.0082.884
plotPCcorrs2.1910.0042.197
topGOtable2.2150.0802.427