Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-11-26 11:05:59 -0500 (Sat, 26 Nov 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences" 4462
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-10-11 r83083 ucrt) -- "Unsuffered Consequences" 4201
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences" 4231
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for pcaExplorer on nebbiolo1


To the developers/maintainers of the pcaExplorer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pcaExplorer.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1433/2154HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcaExplorer 2.25.0  (landing page)
Federico Marini
Snapshot Date: 2022-11-25 14:00:12 -0500 (Fri, 25 Nov 2022)
git_url: https://git.bioconductor.org/packages/pcaExplorer
git_branch: master
git_last_commit: 7d019e7
git_last_commit_date: 2022-11-01 11:13:31 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is not available

Summary

Package: pcaExplorer
Version: 2.25.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pcaExplorer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings pcaExplorer_2.25.0.tar.gz
StartedAt: 2022-11-25 22:28:16 -0500 (Fri, 25 Nov 2022)
EndedAt: 2022-11-25 22:40:33 -0500 (Fri, 25 Nov 2022)
EllapsedTime: 736.8 seconds
RetCode: 0
Status:   OK  
CheckDir: pcaExplorer.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pcaExplorer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings pcaExplorer_2.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pcaExplorer.Rcheck’
* using R Under development (unstable) (2022-10-25 r83175)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘pcaExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pcaExplorer’ version ‘2.25.0’
* 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 ‘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
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
get_annotation_orgdb 8.446  0.348  13.079
get_annotation       5.745  0.404   9.257
pcaplot              5.942  0.164   8.228
pcaplot3d            2.883  0.040   5.101
* 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-3.17-bioc/meat/pcaExplorer.Rcheck/00check.log’
for details.



Installation output

pcaExplorer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL pcaExplorer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences"
Copyright (C) 2022 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 v2.25.0

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")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 17 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
 82.495   3.230  97.660 

Example timings

pcaExplorer.Rcheck/pcaExplorer-Ex.timings

nameusersystemelapsed
correlatePCs3.2710.1043.376
distro_expr2.0280.1642.192
geneprofiler1.5830.0321.615
genespca2.2550.0322.287
get_annotation5.7450.4049.257
get_annotation_orgdb 8.446 0.34813.079
hi_loadings1.5790.0041.584
limmaquickpca2go1.9560.1602.190
makeExampleDESeqDataSet_multifac0.4590.0080.467
pair_corr1.9620.0642.027
pca2go1.9770.0782.054
pcaExplorer2.3670.0362.403
pcaplot5.9420.1648.228
pcaplot3d2.8830.0405.101
pcascree3.2950.2483.543
plotPCcorrs2.9230.1843.107
topGOtable2.1280.1602.288